diff --git a/.gitattributes b/.gitattributes index 02b13c8ee5..660c85d619 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,3 +1,5 @@ .gitattributes export-ignore .gitignore export-ignore .github export-ignore +.lgtm.yml export-ignore +SECURITY.md export-ignore diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 8457af3af9..56fcf548e6 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -13,29 +13,38 @@ lib/kim/* @ellio167 lib/mesont/* @iafoss # whole packages -src/COMPRESS/* @akohlmey +src/COMPRESS/* @rbberger src/GPU/* @ndtrung81 src/KOKKOS/* @stanmoore1 src/KIM/* @ellio167 src/LATTE/* @cnegre src/MESSAGE/* @sjplimp +src/MLIAP/* @athomps +src/SNAP/* @athomps src/SPIN/* @julient31 +src/USER-BROWNIAN/* @samueljmcameron src/USER-CGDNA/* @ohenrich src/USER-CGSDK/* @akohlmey src/USER-COLVARS/* @giacomofiorin +src/USER-DIELECTRIC/* @ndtrung81 +src/USER-FEP/* @agiliopadua +src/USER-HDNNP/* @singraber src/USER-INTEL/* @wmbrownintel src/USER-MANIFOLD/* @Pakketeretet2 +src/USER-MDI/* @taylor-a-barnes src/USER-MEAMC/* @martok src/USER-MESONT/* @iafoss src/USER-MOFFF/* @hheenen src/USER-MOLFILE/* @akohlmey src/USER-NETCDF/* @pastewka +src/USER-PACE/* @yury-lysogorskiy src/USER-PLUMED/* @gtribello src/USER-PHONON/* @lingtikong src/USER-PTM/* @pmla src/USER-OMP/* @akohlmey src/USER-QMMM/* @akohlmey src/USER-REAXC/* @hasanmetin +src/USER-REACTION/* @jrgissing src/USER-SCAFACOS/* @rhalver src/USER-TALLY/* @akohlmey src/USER-UEF/* @danicholson @@ -47,7 +56,6 @@ src/GPU/pair_vashishta_gpu.* @andeplane src/KOKKOS/pair_vashishta_kokkos.* @andeplane src/MANYBODY/pair_vashishta_table.* @andeplane src/MANYBODY/pair_atm.* @sergeylishchuk -src/USER-REACTION/fix_bond_react.* @jrgissing src/USER-MISC/*_grem.* @dstelter92 src/USER-MISC/compute_stress_mop*.* @RomainVermorel @@ -122,6 +130,8 @@ tools/emacs/* @HaoZeke tools/singularity/* @akohlmey @rbberger tools/code_standard/* @rbberger tools/valgrind/* @akohlmey +tools/swig/* @akohlmey +tools/offline/* @rbberger # tests unittest/* @akohlmey @rbberger @@ -130,7 +140,7 @@ unittest/* @akohlmey @rbberger cmake/* @junghans @rbberger cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167 -cmake/presets/*.cmake @junghans @rbberger @akohlmey +cmake/presets/*.cmake @akohlmey # python python/* @rbberger @@ -142,6 +152,7 @@ fortran/* @akohlmey doc/utils/*/* @rbberger doc/Makefile @rbberger doc/README @rbberger +examples/plugin/* @akohlmey # for releases src/version.h @sjplimp diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 62e7186360..31b9becc0c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -26,11 +26,11 @@ __ ## I don't want to read this whole thing I just have a question! -> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. +> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category. ## How Can I Contribute? -There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code +There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers. ### Discussing How To Use LAMMPS @@ -42,6 +42,8 @@ Anyone can browse/search previous questions/answers in the archives. You do not If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive. +The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list. + ### Reporting Bugs While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version. diff --git a/.github/codeql/cpp.yml b/.github/codeql/cpp.yml new file mode 100644 index 0000000000..6244ba707d --- /dev/null +++ b/.github/codeql/cpp.yml @@ -0,0 +1,4 @@ +paths: + - src + - lib + - tools diff --git a/.github/codeql/python.yml b/.github/codeql/python.yml new file mode 100644 index 0000000000..c02a54e3ea --- /dev/null +++ b/.github/codeql/python.yml @@ -0,0 +1,5 @@ +paths: + - python/lammps + +queries: + - uses: security-and-quality diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml index 827306c9aa..064ba6c652 100644 --- a/.github/workflows/codeql-analysis.yml +++ b/.github/workflows/codeql-analysis.yml @@ -31,16 +31,18 @@ jobs: uses: github/codeql-action/init@v1 with: languages: ${{ matrix.language }} + config-file: ./.github/codeql/${{ matrix.language }}.yml - name: Create Build Environment - run: cmake -E make_directory ${{github.workspace}}/build + if: ${{ matrix.language == 'cpp' }} + run: mkdir build - name: Building LAMMPS via CMake if: ${{ matrix.language == 'cpp' }} shell: bash - working-directory: ${{github.workspace}}/build + working-directory: build run: | - cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake + cmake -C ../cmake/presets/most.cmake ../cmake cmake --build . --parallel 2 - name: Perform CodeQL Analysis diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml index a65db7636b..88e28513e8 100644 --- a/.github/workflows/unittest-macos.yml +++ b/.github/workflows/unittest-macos.yml @@ -10,6 +10,8 @@ jobs: name: MacOS Unit Test if: ${{ github.repository == 'lammps/lammps' }} runs-on: macos-latest + env: + CCACHE_DIR: ${{ github.workspace }}/.ccache steps: - name: Checkout repository @@ -17,18 +19,36 @@ jobs: with: fetch-depth: 2 + - name: Install ccache + run: brew install ccache + - name: Create Build Environment - run: cmake -E make_directory ${{github.workspace}}/build + run: mkdir build + + - name: Set up ccache + uses: actions/cache@v2 + with: + path: ${{ env.CCACHE_DIR }} + key: macos-ccache-${{ github.sha }} + restore-keys: macos-ccache- - name: Building LAMMPS via CMake shell: bash - working-directory: ${{github.workspace}}/build + working-directory: build run: | - cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \ - -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON + ccache -z + cmake -C ../cmake/presets/clang.cmake \ + -C ../cmake/presets/most.cmake \ + -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -D CMAKE_C_COMPILER_LAUNCHER=ccache \ + -D ENABLE_TESTING=on \ + -D BUILD_SHARED_LIBS=on \ + -D LAMMPS_EXCEPTIONS=on \ + ../cmake cmake --build . --parallel 2 + ccache -s - name: Run Tests - working-directory: ${{github.workspace}}/build + working-directory: build shell: bash run: ctest -V diff --git a/.lgtm.yml b/.lgtm.yml new file mode 100644 index 0000000000..e5a62fd04b --- /dev/null +++ b/.lgtm.yml @@ -0,0 +1,14 @@ +extraction: + cpp: + configure: + command: + - "mkdir build" + - "cd build" + - "cmake -G Ninja -C ../cmake/presets/most.cmake ../cmake" + index: + build_command: + - "cd build" + - "ninja" + python: + python_setup: + version: 3 diff --git a/README b/README index 5b832790f3..bb0f335848 100644 --- a/README +++ b/README @@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). +under the terms of the GNU Public License (GPL) version 2. The primary author of the code is Steve Plimpton, who can be emailed -at sjplimp@sandia.gov. The LAMMPS WWW Site at lammps.sandia.gov has +at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has more information about the code and its uses. The LAMMPS distribution includes the following files and directories: @@ -37,14 +37,14 @@ tools pre- and post-processing tools Point your browser at any of these files to get started: -https://lammps.sandia.gov/doc/Manual.html LAMMPS manual -https://lammps.sandia.gov/doc/Intro.html hi-level introduction -https://lammps.sandia.gov/doc/Build.html how to build LAMMPS -https://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS -https://lammps.sandia.gov/doc/Commands_all.html Table of available commands -https://lammps.sandia.gov/doc/Library.html LAMMPS library interfaces -https://lammps.sandia.gov/doc/Modify.html how to modify and extend LAMMPS -https://lammps.sandia.gov/doc/Developer.html LAMMPS developer info +https://docs.lammps.org/Manual.html LAMMPS manual +https://docs.lammps.org/Intro.html hi-level introduction +https://docs.lammps.org/Build.html how to build LAMMPS +https://docs.lammps.org/Run_head.html how to run LAMMPS +https://docs.lammps.org/Commands_all.html Table of available commands +https://docs.lammps.org/Library.html LAMMPS library interfaces +https://docs.lammps.org/Modify.html how to modify and extend LAMMPS +https://docs.lammps.org/Developer.html LAMMPS developer info You can also create these doc pages locally: diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 0000000000..9f65e2f88e --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,35 @@ +# Security Policy + +LAMMPS is designed as a user-level application to conduct computer +simulations for research using classical mechanics. As such LAMMPS +depends to some degrees on users providing correctly formatted input and +LAMMPS needs to read and write files based on uncontrolled user input. +As a parallel application for use in high-performance computing +environments, performance critical steps are also done without checking +data. + +LAMMPS also is interfaced to a number of external libraries, including +libraries with experimental research software, that are not validated +and tested by the LAMMPS developers, so it is easy to import bad +behavior from calling functions in one of those libraries. + +Thus is is quite easy to crash LAMMPS through malicious input and do all +kinds of filesystem manipulations. And because of that LAMMPS should +**NEVER** be compiled or **run** as superuser, either from a "root" or +"administrator" account directly or indirectly via "sudo" or "su". + +Therefore what could be seen as a security vulnerability is usually +either a user mistake or a bug in the code. Bugs can be reported in +the LAMMPS project +[issue tracker on GitHub](https://github.com/lammps/lammps/issues). + + +# Version Updates + +LAMMPS follows continuous release development model. We aim to keep all +release versions (stable or patch) fully functional and employ a variety +of automatic testing procedures to detect failures of existing +functionality from adding new features before releases are made. Thus +bugfixes and updates are only integrated into the current development +branch and thus the next (patch) release and users are recommended to +update regularly. diff --git a/bench/POTENTIALS/README b/bench/POTENTIALS/README index d42726c184..a9e319a6c4 100644 --- a/bench/POTENTIALS/README +++ b/bench/POTENTIALS/README @@ -1,7 +1,7 @@ These are input scripts used to run benchmark tests for many of the interatomic potentials in LAMMPS. The results of running these scripts on different machines are shown on the Potentials section of -the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench). +the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html). Examples are shown below of how to run these scripts. Log files for running them on 1 and 4 processors of a Linux box are included in the diff --git a/bench/README b/bench/README index 0806fcded6..7d5aced119 100644 --- a/bench/README +++ b/bench/README @@ -2,7 +2,7 @@ LAMMPS benchmark problems This directory contains 5 benchmark problems which are discussed in the Benchmark section of the LAMMPS documentation, and on the -Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench). +Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html). This directory also has several sub-directories: @@ -11,7 +11,7 @@ KEPLER benchmark scripts for GPU cluster with Kepler GPUs POTENTIALS benchmarks scripts for various potentials in LAMMPS The results for all of these benchmarks are displayed and discussed on -the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench. +the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html The remainder of this file refers to the 5 problems in the top-level of this directory and how to run them on CPUs, either in serial or diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 06600d02c4..ab1fd6bba6 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10) if(POLICY CMP0074) cmake_policy(SET CMP0074 NEW) endif() +# set policy to silence warnings about missing executable permissions in +# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW +if(POLICY CMP0109) + cmake_policy(SET CMP0109 OLD) +endif() ######################################## project(lammps CXX) @@ -22,6 +27,11 @@ set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools) set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python) set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials) +set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads") +set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials") +set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty") +mark_as_advanced(LAMMPS_DOWNLOADS_URL) + find_package(Git) # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed @@ -31,7 +41,7 @@ endif() # If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF) -if (LAMMPS_INSTALL_RPATH) +if(LAMMPS_INSTALL_RPATH) set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR}) set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON) endif() @@ -67,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR}) include(CheckIncludeFileCXX) # set required compiler flags and compiler/CPU arch specific optimizations -if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") +if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512") @@ -81,6 +91,11 @@ set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions") +# export all symbols when building a .dll file on windows +if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS) + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON) +endif() + ######################################################################## # User input options # ######################################################################## @@ -99,11 +114,23 @@ endif() option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF) option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF) +# allow enabling clang-tidy for C++ files +set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling") +if(ENABLE_CLANG_TIDY) + set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "") +endif() + include(GNUInstallDirs) file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES}) add_library(lammps ${ALL_SOURCES}) + +# tell CMake to export all symbols to a .dll on Windows with MinGW cross-compilers +if(BUILD_SHARED_LIBS AND (CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) + set_target_properties(lammps PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols") +endif() + add_executable(lmp ${MAIN_SOURCES}) target_link_libraries(lmp PRIVATE lammps) set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) @@ -113,13 +140,13 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS - QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI + PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF - USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF) + USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP + USER-H5MD USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT + USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN) set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) @@ -146,12 +173,13 @@ if(NOT CMAKE_CROSSCOMPILING) find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) else() + set(MPI_CXX_SKIP_MPICXX TRUE) option(BUILD_MPI "Build MPI version" OFF) endif() if(BUILD_MPI) # We use a non-standard procedure to cross-compile with MPI on Windows - if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING) + if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) include(MPI4WIN) target_link_libraries(lammps PUBLIC MPI::MPI_CXX) else() @@ -185,7 +213,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES}) # posix_memalign is not available on Windows -if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") +if(CMAKE_SYSTEM_NAME STREQUAL "Windows") set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE) else() set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable") @@ -207,6 +235,7 @@ pkg_depends(USER-ATC MANYBODY) pkg_depends(USER-LB MPI) pkg_depends(USER-PHONON KSPACE) pkg_depends(USER-SCAFACOS MPI) +pkg_depends(USER-DIELECTRIC KSPACE) # detect if we may enable OpenMP support by default set(BUILD_OMP_DEFAULT OFF) @@ -227,8 +256,10 @@ if(BUILD_OMP) message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") endif() - if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR - (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR + if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR + (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR + (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. @@ -240,68 +271,6 @@ if(BUILD_OMP) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) endif() -# Compiler specific features for testing -if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") - option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) - mark_as_advanced(ENABLE_COVERAGE) - if(ENABLE_COVERAGE) - if(CMAKE_VERSION VERSION_LESS 3.13) - if(CMAKE_CXX_FLAGS) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") - else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage") - endif() - else() - target_compile_options(lammps PUBLIC --coverage) - target_link_options(lammps PUBLIC --coverage) - endif() - endif() -endif() - -####################################### -# add custom target for IWYU analysis -####################################### -set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") -mark_as_advanced(ENABLE_IWYU) -if(ENABLE_IWYU) - find_program(IWYU_EXE NAMES include-what-you-use iwyu) - find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) - if (IWYU_EXE AND IWYU_TOOL) - add_custom_target( - iwyu - ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp - COMMENT "Running IWYU") - add_dependencies(iwyu lammps) - else() - message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" - "and the iwyu-tool/iwyu_tool script installed in your PATH") - endif() -endif() - -set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") -mark_as_advanced(ENABLE_SANITIZER) -set(ENABLE_SANITIZER_VALUES none address leak thread undefined) -set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES}) -validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES) -string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER) -if(NOT ENABLE_SANITIZER STREQUAL "none") - if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) - if(CMAKE_VERSION VERSION_LESS 3.13) - if(CMAKE_CXX_FLAGS) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}") - else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}") - endif() - else() - target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) - target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) - endif() - else() - message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.") - set(ENABLE_SANITIZER "none") - endif() -endif() - if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) enable_language(C) find_package(LAPACK) @@ -353,7 +322,7 @@ find_program(GZIP_EXECUTABLE gzip) find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE) option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND}) if(WITH_GZIP) - if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) + if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)) target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP) else() message(FATAL_ERROR "gzip executable not found") @@ -364,7 +333,7 @@ find_program(FFMPEG_EXECUTABLE ffmpeg) find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE) option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND}) if(WITH_FFMPEG) - if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) + if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)) target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG) else() message(FATAL_ERROR "ffmpeg executable not found") @@ -381,8 +350,8 @@ else() set(CUDA_REQUEST_PIC) endif() -foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM - USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS) +foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF + USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() @@ -479,7 +448,7 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) - if(PKG_LIB STREQUAL mesont) + if(PKG_LIB STREQUAL "mesont") enable_language(Fortran) file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90) @@ -491,9 +460,9 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES}) set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE}) target_link_libraries(lammps PRIVATE ${PKG_LIB}) - if(PKG_LIB STREQUAL awpmd) + if(PKG_LIB STREQUAL "awpmd") target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include) - elseif(PKG_LIB STREQUAL h5md) + elseif(PKG_LIB STREQUAL "h5md") target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS}) else() target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}) @@ -506,7 +475,7 @@ if(PKG_USER-AWPMD) endif() if(PKG_USER-ATC) - if(LAMMPS_SIZES STREQUAL BIGBIG) + if(LAMMPS_SIZES STREQUAL "BIGBIG") message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG") endif() target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES}) @@ -533,12 +502,24 @@ foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU endif() endforeach() +if(PKG_PLUGIN) + if(BUILD_SHARED_LIBS) + target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN) + else() + message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled") + endif() + # link with -ldl or equivalent for plugin loading; except on Windows + if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS}) + endif() +endif() + ###################################################################### # the windows version of LAMMPS requires a couple extra libraries # and the MPI library - if use - has to be linked right before those # and after everything else that is compiled locally ###################################################################### -if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") +if(CMAKE_SYSTEM_NAME STREQUAL "Windows") target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi) endif() @@ -587,8 +568,8 @@ add_dependencies(lammps gitversion) # Actually add executable and lib to build ############################################ get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) -list (FIND LANGUAGES "Fortran" _index) -if(${_index} GREATER -1) +list(FIND LANGUAGES "Fortran" _index) +if(_index GREATER -1) target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) endif() set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h @@ -666,7 +647,7 @@ if(BUILD_SHARED_LIBS) else() find_package(Python COMPONENTS Interpreter) endif() - if (Python_EXECUTABLE) + if(Python_EXECUTABLE) add_custom_target( install-python ${CMAKE_COMMAND} -E remove_directory build COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h @@ -699,7 +680,7 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON) else() find_package(Python COMPONENTS Interpreter) endif() - if (Python_EXECUTABLE) + if(Python_EXECUTABLE) file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python) install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})") endif() @@ -713,7 +694,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS) include(FeatureSummary) feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND) message(STATUS "<<< Build configuration >>> - Operating System: ${CMAKE_SYSTEM_NAME} + Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION} Build type: ${CMAKE_BUILD_TYPE} Install path: ${CMAKE_INSTALL_PREFIX} Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}") @@ -744,15 +725,15 @@ if(OPTIONS) message(" Options: ${OPTIONS}") endif() get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) -list (FIND LANGUAGES "Fortran" _index) -if(${_index} GREATER -1) +list(FIND LANGUAGES "Fortran" _index) +if(_index GREATER -1) message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER} Type: ${CMAKE_Fortran_COMPILER_ID} Version: ${CMAKE_Fortran_COMPILER_VERSION} Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}") endif() -list (FIND LANGUAGES "C" _index) -if(${_index} GREATER -1) +list(FIND LANGUAGES "C" _index) +if(_index GREATER -1) message(STATUS "C compiler: ${CMAKE_C_COMPILER} Type: ${CMAKE_C_COMPILER_ID} Version: ${CMAKE_C_COMPILER_VERSION} @@ -782,9 +763,12 @@ if(BUILD_MPI) endif() if(PKG_GPU) message(STATUS "<<< GPU package settings >>> --- GPU API: ${GPU_API}") +-- GPU API: ${GPU_API}") if(GPU_API STREQUAL "CUDA") + message(STATUS "CUDA Compiler: ${CUDA_NVCC_EXECUTABLE}") message(STATUS "GPU default architecture: ${GPU_ARCH}") + message(STATUS "GPU binning with CUDPP: ${CUDPP_OPT}") + message(STATUS "CUDA MPS support: ${CUDA_MPS_SUPPORT}") elseif(GPU_API STREQUAL "HIP") message(STATUS "HIP platform: ${HIP_PLATFORM}") message(STATUS "HIP architecture: ${HIP_ARCH}") @@ -794,7 +778,7 @@ if(PKG_GPU) message(STATUS "HIP GPU sorting: off") endif() endif() - message(STATUS "GPU precision: ${GPU_PREC}") + message(STATUS "GPU precision: ${GPU_PREC}") endif() if(PKG_KOKKOS) message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") @@ -814,7 +798,7 @@ if(PKG_KSPACE) endif() if(PKG_KOKKOS) if(Kokkos_ENABLE_CUDA) - if (${FFT} STREQUAL "KISS") + if(FFT STREQUAL "KISS") message(STATUS "Kokkos FFT: KISS") else() message(STATUS "Kokkos FFT: cuFFT") diff --git a/cmake/Modules/CodingStandard.cmake b/cmake/Modules/CodingStandard.cmake index 646bdcdd4a..6bb607be12 100644 --- a/cmake/Modules/CodingStandard.cmake +++ b/cmake/Modules/CodingStandard.cmake @@ -15,6 +15,11 @@ if(Python3_EXECUTABLE) ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py . WORKING_DIRECTORY ${LAMMPS_DIR} COMMENT "Check for whitespace errors") + add_custom_target( + check-homepage + ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py . + WORKING_DIRECTORY ${LAMMPS_DIR} + COMMENT "Check for homepage URL errors") add_custom_target( check-permissions ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py . @@ -25,6 +30,11 @@ if(Python3_EXECUTABLE) ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f . WORKING_DIRECTORY ${LAMMPS_DIR} COMMENT "Fix whitespace errors") + add_custom_target( + fix-homepage + ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f . + WORKING_DIRECTORY ${LAMMPS_DIR} + COMMENT "Fix homepage URL errors") add_custom_target( fix-permissions ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f . diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake index 5a42244b9e..16dd5dd4fa 100644 --- a/cmake/Modules/Documentation.cmake +++ b/cmake/Modules/Documentation.cmake @@ -55,11 +55,15 @@ if(BUILD_DOC) COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade ) + set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball") + set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball") + mark_as_advanced(MATHJAX_URL) + # download mathjax distribution and unpack to folder "mathjax" if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5) - file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" + file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" - EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53) + EXPECTED_MD5 ${MATHJAX_MD5}) execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*) execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake new file mode 100644 index 0000000000..8a97b7dd81 --- /dev/null +++ b/cmake/Modules/FindN2P2.cmake @@ -0,0 +1,61 @@ +include(FindPackageHandleStandardArgs) + +# Check if N2P2_DIR is set manually. +if (DEFINED ENV{N2P2_DIR}) + set(N2P2_DIR "${N2P2_DIR}") +# If not, try if directory "lib/hdnnp/n2p2" exists. +else() + get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/hdnnp/n2p2" REALPATH) + if (EXISTS ${_fullpath}) + set(N2P2_DIR "${_fullpath}") + endif() +endif() + +# Set path to include directory. +find_path(N2P2_INCLUDE_DIR InterfaceLammps.h HINTS "${N2P2_DIR}/include") +# Two libraries need to be linked: libnnp and libnnpif. +find_library(N2P2_LIBNNP NAMES nnp HINTS "${N2P2_DIR}/lib") +find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib") +# Users could compile n2p2 with extra flags which are then also required for +# pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2 +# writes a file with cmake commands, e.g. +# +# target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS) +# +# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake. +find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib") + +find_package_handle_standard_args(N2P2 DEFAULT_MSG + N2P2_DIR + N2P2_INCLUDE_DIR + N2P2_LIBNNP + N2P2_LIBNNPIF + N2P2_CMAKE_EXTRA) + +if(N2P2_FOUND) + if (NOT TARGET N2P2::N2P2) + # n2p2 core library "libnnp" + add_library(N2P2::LIBNNP UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNP PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNP}) + # n2p2 interface library "libnnpif" + add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNPIF PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNPIF}) + # Put libnnp, libnnpif and include directory together. + add_library(N2P2::N2P2 INTERFACE IMPORTED) + set_property(TARGET N2P2::N2P2 PROPERTY + INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP) + set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA}) + endif() +endif() + +mark_as_advanced( + N2P2_DIR + N2P2_INCLUDE_DIR + N2P2_LIBNNP + N2P2_LIBNNPIF + N2P2_CMAKE_EXTRA +) diff --git a/cmake/Modules/GTest.cmake b/cmake/Modules/GTest.cmake index 0c62291d5e..211b506d2f 100644 --- a/cmake/Modules/GTest.cmake +++ b/cmake/Modules/GTest.cmake @@ -1,6 +1,6 @@ message(STATUS "Downloading and building Google Test library") -if(CMAKE_BUILD_TYPE STREQUAL Debug) +if(CMAKE_BUILD_TYPE STREQUAL "Debug") set(GTEST_LIB_POSTFIX d) else() set(GTEST_LIB_POSTFIX) @@ -8,10 +8,12 @@ endif() include(ExternalProject) set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball") +set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball") mark_as_advanced(GTEST_URL) +mark_as_advanced(GTEST_MD5) ExternalProject_Add(googletest - URL ${GTEST_URL} - URL_MD5 ecd1fa65e7de707cd5c00bdac56022cd + URL ${GTEST_URL} + URL_MD5 ${GTEST_MD5} SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src" BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build" CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS} diff --git a/cmake/Modules/GenerateOpenCLHeader.cmake b/cmake/Modules/GenerateOpenCLHeader.cmake new file mode 100644 index 0000000000..18dfac1604 --- /dev/null +++ b/cmake/Modules/GenerateOpenCLHeader.cmake @@ -0,0 +1,3 @@ +# utility script to call WriteOpenCLHeader function +include(${SOURCE_DIR}/Modules/OpenCLUtils.cmake) +WriteOpenCLHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES}) diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 37275843fa..6cb23db12a 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader) # fetch missing potential files function(FetchPotentials pkgfolder potfolder) if (EXISTS "${pkgfolder}/potentials.txt") - set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials") file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].") foreach(line ${linelist}) string(FIND ${line} " " blank) @@ -105,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder) endforeach() endif() endfunction(FetchPotentials) + +# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux +if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release)) + file(STRINGS /etc/os-release distro REGEX "^NAME=") + string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}") + file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=") + string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}") + set(CMAKE_LINUX_DISTRO ${distro}) + set(CMAKE_DISTRO_VERSION ${disversion}) +endif() diff --git a/cmake/Modules/MPI4WIN.cmake b/cmake/Modules/MPI4WIN.cmake index 529cefeab0..aa0c9e1833 100644 --- a/cmake/Modules/MPI4WIN.cmake +++ b/cmake/Modules/MPI4WIN.cmake @@ -1,16 +1,25 @@ # Download and configure custom MPICH files for Windows message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") +set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball") +set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball") +set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball") +set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball") +mark_as_advanced(MPICH2_WIN64_DEVEL_URL) +mark_as_advanced(MPICH2_WIN32_DEVEL_URL) +mark_as_advanced(MPICH2_WIN64_DEVEL_MD5) +mark_as_advanced(MPICH2_WIN32_DEVEL_MD5) + include(ExternalProject) if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") ExternalProject_Add(mpi4win_build - URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz - URL_MD5 4939fdb59d13182fd5dd65211e469f14 + URL ${MPICH2_WIN64_DEVEL_URL} + URL_MD5 ${MPICH2_WIN64_DEVEL_MD5} CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" BUILD_BYPRODUCTS /lib/libmpi.a) else() ExternalProject_Add(mpi4win_build - URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz - URL_MD5 a61d153500dce44e21b755ee7257e031 + URL ${MPICH2_WIN32_DEVEL_URL} + URL_MD5 ${MPICH2_WIN32_DEVEL_MD5} CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" BUILD_BYPRODUCTS /lib/libmpi.a) endif() diff --git a/cmake/Modules/OpenCLLoader.cmake b/cmake/Modules/OpenCLLoader.cmake index 5ab121f841..ea83f8e447 100644 --- a/cmake/Modules/OpenCLLoader.cmake +++ b/cmake/Modules/OpenCLLoader.cmake @@ -1,11 +1,13 @@ message(STATUS "Downloading and building OpenCL loader library") +set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball") +set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball") +mark_as_advanced(OPENCL_LOADER_URL) +mark_as_advanced(OPENCL_LOADER_MD5) include(ExternalProject) -set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball") -mark_as_advanced(OPENCL_LOADER_URL) ExternalProject_Add(opencl_loader - URL ${OPENCL_LOADER_URL} - URL_MD5 011cdcbd41030be94f3fced6d763a52a + URL ${OPENCL_LOADER_URL} + URL_MD5 ${OPENCL_LOADER_MD5} SOURCE_DIR "${CMAKE_BINARY_DIR}/opencl_loader-src" BINARY_DIR "${CMAKE_BINARY_DIR}/opencl_loader-build" CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS} diff --git a/cmake/Modules/OpenCLUtils.cmake b/cmake/Modules/OpenCLUtils.cmake index a9441ce518..eb17da0b3d 100644 --- a/cmake/Modules/OpenCLUtils.cmake +++ b/cmake/Modules/OpenCLUtils.cmake @@ -1,10 +1,8 @@ -function(GenerateOpenCLHeader varname outfile files) - message("Creating ${outfile}...") +function(WriteOpenCLHeader varname outfile files) file(WRITE ${outfile} "const char * ${varname} = \n") - math(EXPR ARG_END "${ARGC}-1") + separate_arguments(files) - foreach(IDX RANGE 2 ${ARG_END}) - list(GET ARGV ${IDX} filename) + foreach(filename ${files}) file(READ ${filename} content) string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}") string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}") @@ -15,4 +13,16 @@ function(GenerateOpenCLHeader varname outfile files) endforeach() file(APPEND ${outfile} ";\n") +endfunction(WriteOpenCLHeader) + +function(GenerateOpenCLHeader varname outfile files) + list(REMOVE_AT ARGV 0 1) + add_custom_command(OUTPUT ${outfile} + COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} + -D VARNAME=${varname} + -D HEADER_FILE=${outfile} + -D SOURCE_FILES="${ARGV}" + -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateOpenCLHeader.cmake + DEPENDS ${ARGV} + COMMENT "Generating ${outfile}...") endfunction(GenerateOpenCLHeader) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 9aa917144b..2b6977005d 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -48,7 +48,7 @@ if(GPU_API STREQUAL "CUDA") # ensure that no *cubin.h files exist from a compile in the lib/gpu folder file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h) - if (GPU_LIB_OLD_CUBIN_HEADERS) + if(GPU_LIB_OLD_CUBIN_HEADERS) message(FATAL_ERROR "########################################################################\n" "Found file(s) generated by the make-based build system in lib/gpu\n" "Please run\n" @@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA") endif() cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC} - -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) + -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES}) cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC} - -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) + -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES}) foreach(CU_OBJ ${GPU_GEN_OBJS}) get_filename_component(CU_NAME ${CU_OBJ} NAME_WE) @@ -131,7 +131,7 @@ if(GPU_API STREQUAL "CUDA") add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS}) target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY}) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS}) - target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS}) + target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS}) if(CUDPP_OPT) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) target_compile_definitions(gpu PRIVATE -DUSE_CUDPP) @@ -145,9 +145,16 @@ if(GPU_API STREQUAL "CUDA") target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS}) elseif(GPU_API STREQUAL "OPENCL") - option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON) + # the static OpenCL loader doesn't seem to work on macOS. use the system provided + # version by default instead (for as long as it will be available) + if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin") + set(_opencl_static_default OFF) + else() + set(_opencl_static_default ON) + endif() + option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default}) mark_as_advanced(USE_STATIC_OPENCL_LOADER) - if (USE_STATIC_OPENCL_LOADER) + if(USE_STATIC_OPENCL_LOADER) include(OpenCLLoader) else() find_package(OpenCL REQUIRED) @@ -218,7 +225,7 @@ elseif(GPU_API STREQUAL "HIP") if(NOT DEFINED HIP_PLATFORM) if(NOT DEFINED ENV{HIP_PLATFORM}) - set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation") + set(HIP_PLATFORM "amd" CACHE PATH "HIP Platform to be used during compilation") else() set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation") endif() @@ -226,7 +233,7 @@ elseif(GPU_API STREQUAL "HIP") set(ENV{HIP_PLATFORM} ${HIP_PLATFORM}) - if(HIP_PLATFORM STREQUAL "hcc") + if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture") elseif(HIP_PLATFORM STREQUAL "nvcc") find_package(CUDA REQUIRED) @@ -284,23 +291,23 @@ elseif(GPU_API STREQUAL "HIP") set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin") set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h") - if(HIP_PLATFORM STREQUAL "hcc") + if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) if(HIP_COMPILER STREQUAL "clang") add_custom_command(OUTPUT ${CUBIN_FILE} - VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} DEPENDS ${CU_CPP_FILE} COMMENT "Generating ${CU_NAME}.cubin") else() add_custom_command(OUTPUT ${CUBIN_FILE} - VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE} DEPENDS ${CU_CPP_FILE} COMMENT "Generating ${CU_NAME}.cubin") endif() elseif(HIP_PLATFORM STREQUAL "nvcc") add_custom_command(OUTPUT ${CUBIN_FILE} - VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE} DEPENDS ${CU_FILE} COMMENT "Generating ${CU_NAME}.cubin") endif() @@ -338,11 +345,16 @@ elseif(GPU_API STREQUAL "HIP") if(DOWNLOAD_CUB) message(STATUS "CUB download requested") + set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball") + set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball") + mark_as_advanced(CUB_URL) + mark_as_advanced(CUB_MD5) + include(ExternalProject) ExternalProject_Add(CUB - GIT_REPOSITORY https://github.com/NVlabs/cub - TIMEOUT 5 + URL ${CUB_URL} + URL_MD5 ${CUB_MD5} PREFIX "${CMAKE_CURRENT_BINARY_DIR}" CONFIGURE_COMMAND "" BUILD_COMMAND "" @@ -354,7 +366,7 @@ elseif(GPU_API STREQUAL "HIP") else() find_package(CUB) if(NOT CUB_FOUND) - message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it") + message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_CUB=ON to download it") endif() endif() @@ -381,6 +393,12 @@ elseif(GPU_API STREQUAL "HIP") target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__) target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include) + elseif(HIP_PLATFORM STREQUAL "amd") + target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__) + target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include) + + target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__) + target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include) endif() target_link_libraries(lammps PRIVATE gpu) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 5482d3071c..2a2a1cde78 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -35,9 +35,13 @@ if(DOWNLOAD_KIM) include(ExternalProject) enable_language(C) enable_language(Fortran) + set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball") + set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball") + mark_as_advanced(KIM_URL) + mark_as_advanced(KIM_MD5) ExternalProject_Add(kim_build - URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz - URL_MD5 ae1ddda2ef7017ea07934e519d023dca + URL ${KIM_URL} + URL_MD5 ${KIM_MD5} BINARY_DIR build CMAKE_ARGS ${CMAKE_REQUEST_PIC} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 1dfb0bf389..234c1f140d 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS) list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}") list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}") include(ExternalProject) + set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball") + set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball") + mark_as_advanced(KOKKOS_URL) + mark_as_advanced(KOKKOS_MD5) ExternalProject_Add(kokkos_build - URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz - URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a + URL ${KOKKOS_URL} + URL_MD5 ${KOKKOS_MD5} CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS} BUILD_BYPRODUCTS /lib/libkokkoscore.a ) @@ -54,7 +58,7 @@ if(DOWNLOAD_KOKKOS) target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS) add_dependencies(LAMMPS::KOKKOS kokkos_build) elseif(EXTERNAL_KOKKOS) - find_package(Kokkos 3.3.01 REQUIRED CONFIG) + find_package(Kokkos 3.4.01 REQUIRED CONFIG) target_link_libraries(lammps PRIVATE Kokkos::kokkos) target_link_libraries(lmp PRIVATE Kokkos::kokkos) else() @@ -95,7 +99,7 @@ if(PKG_KSPACE) ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp) if(Kokkos_ENABLE_CUDA) - if(NOT ${FFT} STREQUAL "KISS") + if(NOT (FFT STREQUAL "KISS")) target_compile_definitions(lammps PRIVATE -DFFT_CUFFT) target_link_libraries(lammps PRIVATE cufft) endif() diff --git a/cmake/Modules/Packages/LATTE.cmake b/cmake/Modules/Packages/LATTE.cmake index e66f83fa43..ddf31a68ed 100644 --- a/cmake/Modules/Packages/LATTE.cmake +++ b/cmake/Modules/Packages/LATTE.cmake @@ -15,10 +15,14 @@ endif() option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT}) if(DOWNLOAD_LATTE) message(STATUS "LATTE download requested - we will build our own") + set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball") + set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball") + mark_as_advanced(LATTE_URL) + mark_as_advanced(LATTE_MD5) include(ExternalProject) ExternalProject_Add(latte_build - URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz - URL_MD5 820e73a457ced178c08c71389a385de7 + URL ${LATTE_URL} + URL_MD5 ${LATTE_MD5} SOURCE_SUBDIR cmake CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES} diff --git a/cmake/Modules/Packages/MESSAGE.cmake b/cmake/Modules/Packages/MESSAGE.cmake index 6ff4e322aa..b5a61a1607 100644 --- a/cmake/Modules/Packages/MESSAGE.cmake +++ b/cmake/Modules/Packages/MESSAGE.cmake @@ -1,4 +1,4 @@ -if(LAMMPS_SIZES STREQUAL BIGBIG) +if(LAMMPS_SIZES STREQUAL "BIGBIG") message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG") endif() option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) diff --git a/cmake/Modules/Packages/MSCG.cmake b/cmake/Modules/Packages/MSCG.cmake index 6cb389fb13..6ac62cb012 100644 --- a/cmake/Modules/Packages/MSCG.cmake +++ b/cmake/Modules/Packages/MSCG.cmake @@ -7,10 +7,15 @@ else() endif() option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT}) if(DOWNLOAD_MSCG) + set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball") + set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball") + mark_as_advanced(MSCG_URL) + mark_as_advanced(MSCG_MD5) + include(ExternalProject) ExternalProject_Add(mscg_build - URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz - URL_MD5 8c45e269ee13f60b303edd7823866a91 + URL ${MSCG_URL} + URL_MD5 ${MSCG_MD5} SOURCE_SUBDIR src/CMake CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} diff --git a/cmake/Modules/Packages/QEQ.cmake b/cmake/Modules/Packages/QEQ.cmake index 1bdaa02f43..041d34cf9d 100644 --- a/cmake/Modules/Packages/QEQ.cmake +++ b/cmake/Modules/Packages/QEQ.cmake @@ -1,18 +1,13 @@ # Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ) -file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h) -file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp) +get_property(hlist GLOBAL PROPERTY FIX) if(NOT PKG_MANYBODY) - list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h) - list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp) + list(REMOVE_ITEM hlist ${QEQ_SOURCES_DIR}/fix_qeq_fire.h) + get_target_property(LAMMPS_SOURCES lammps SOURCES) + list(REMOVE_ITEM LAMMPS_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp) + set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES}) endif() -set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}") +set_property(GLOBAL PROPERTY FIX "${hlist}") -foreach(MY_HEADER ${QEQ_HEADERS}) - AddStyleHeader(${MY_HEADER} FIX) -endforeach() - -get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES) -target_sources(lammps PRIVATE ${QEQ_SOURCES}) target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/USER-HDNNP.cmake b/cmake/Modules/Packages/USER-HDNNP.cmake new file mode 100644 index 0000000000..44873b9929 --- /dev/null +++ b/cmake/Modules/Packages/USER-HDNNP.cmake @@ -0,0 +1,127 @@ +find_package(N2P2 QUIET) +if(N2P2_FOUND) + set(DOWNLOAD_N2P2_DEFAULT OFF) +else() + set(DOWNLOAD_N2P2_DEFAULT ON) +endif() +option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT}) +if(DOWNLOAD_N2P2) + set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball") + set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball") + mark_as_advanced(N2P2_URL) + mark_as_advanced(N2P2_MD5) + + # adjust settings from detected compiler to compiler platform in n2p2 library + # set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7) + if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")) + set(N2P2_COMP llvm) + set(N2P2_CXX_STD "-std=c++11") + elseif((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")) + set(N2P2_COMP intel) + set(N2P2_CXX_STD "-std=c++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") + set(N2P2_COMP gnu) + set(N2P2_CXX_STD "-std=gnu++11") + elseif((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC")) + set(N2P2_COMP gnu) + set(N2P2_CXX_STD "--c++11") + else() # default + set(N2P2_COMP "") + endif() + + # pass on archive creator command. prefer compiler specific version, if set. + # important when using cross compiler. + if(CMAKE_CXX_COMPILER_AR) + set(N2P2_AR ${CMAKE_CXX_COMPILER_AR}) + else() + set(N2P2_AR ${CMAKE_AR}) + endif() + + # adjust compilation of n2p2 library to whether MPI is requested in LAMMPS or not + # need special care for compiling for MPICH2 with Linux-to-Windows cross compiler. + if(NOT BUILD_MPI) + set(N2P2_PROJECT_OPTIONS "-DN2P2_NO_MPI") + else() + # get path to MPI include directory when cross-compiling to windows + if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING) + get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES) + set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1") + set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER}) + endif() + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES) + set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1") + set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER}) + endif() + endif() + + # prefer GNU make, if available. N2P2 lib seems to need it. + find_program(N2P2_MAKE NAMES gmake make) + + # override compiler (optimization) flags in n2p2 library to flags used for LAMMPS + # specifically -march=native can result in problems when compiling on HPC clusters or with a cross compiler + # this convoluted way gets correct quoting/escaping when configuring the external project + string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) + set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}") + set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG=" + "PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}" + "PROJECT_AR=${N2P2_AR}") + # echo final flag for debugging + message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}") + + # download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling) + include(ExternalProject) + ExternalProject_Add(n2p2_build + URL ${N2P2_URL} + URL_MD5 ${N2P2_MD5} + UPDATE_COMMAND "" + CONFIGURE_COMMAND "" + PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp + BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS} + BUILD_ALWAYS YES + INSTALL_COMMAND "" + BUILD_IN_SOURCE 1 + LOG_BUILD ON + SOURCE_SUBDIR src/ + BUILD_BYPRODUCTS /lib/libnnp.a /lib/libnnpif.a + ) + + # create imported target LAMMPS::N2P2 from two libraries nnp and nnpif + ExternalProject_get_property(n2p2_build SOURCE_DIR) + # n2p2 core library "libnnp" + add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED) + set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnp.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include") + # n2p2 interface library "libnnpif" + add_library(LAMMPS::N2P2::LIBNNPIF UNKNOWN IMPORTED) + set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnpif.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include") + # nnpif library has MPI calls if MPI is enabled, so we must link with MPI libs + if(BUILD_MPI) + set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES + INTERFACE_LINK_LIBRARIES MPI::MPI_CXX) + if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING) + add_dependencies(LAMMPS::N2P2::LIBNNPIF MPI::MPI_CXX) + endif() + endif() + + # final step to define imported target + add_library(LAMMPS::N2P2 INTERFACE IMPORTED) + set_property(TARGET LAMMPS::N2P2 PROPERTY + INTERFACE_LINK_LIBRARIES LAMMPS::N2P2::LIBNNPIF LAMMPS::N2P2::LIBNNP) + target_link_libraries(lammps PRIVATE LAMMPS::N2P2) + + add_dependencies(LAMMPS::N2P2 n2p2_build) + # work around issues with older CMake versions + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + file(MAKE_DIRECTORY "${SOURCE_DIR}/lib") +else() + find_package(N2P2) + if(NOT N2P2_FOUND) + message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it") + endif() + target_link_libraries(lammps PRIVATE N2P2::N2P2) + include(${N2P2_CMAKE_EXTRAS}) +endif() diff --git a/cmake/Modules/Packages/USER-INTEL.cmake b/cmake/Modules/Packages/USER-INTEL.cmake index 90ab6167a3..ecad135b70 100644 --- a/cmake/Modules/Packages/USER-INTEL.cmake +++ b/cmake/Modules/Packages/USER-INTEL.cmake @@ -79,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL") else() if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") include(CheckCXXCompilerFlag) - foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict) - check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG}) - if(COMPILER_SUPPORTS${_FLAG}) + foreach(_FLAG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict) + string(REGEX REPLACE "[ =\"]" "" _FLAGX ${_FLAG}) + check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX}) + if(COMPILER_SUPPORTS${_FLAGX}) + separate_arguments(_FLAG UNIX_COMMAND "${_FLAG}") target_compile_options(lammps PRIVATE ${_FLAG}) endif() endforeach() diff --git a/cmake/Modules/Packages/USER-MDI.cmake b/cmake/Modules/Packages/USER-MDI.cmake new file mode 100644 index 0000000000..a75160a6d6 --- /dev/null +++ b/cmake/Modules/Packages/USER-MDI.cmake @@ -0,0 +1,118 @@ +find_package(mdi QUIET) +if(${mdi_FOUND}) + set(DOWNLOAD_MDI_DEFAULT OFF) +else() + set(DOWNLOAD_MDI_DEFAULT ON) +endif() +option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT}) + +if(DOWNLOAD_MDI) + message(STATUS "MDI download requested - we will build our own") + set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball") + set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball") + mark_as_advanced(MDI_URL) + mark_as_advanced(MDI_MD5) + enable_language(C) + + # only ON/OFF are allowed for "mpi" flag when building MDI library + # so translate boolean value of BUILD_MPI + # always disable MPI when cross-compiling to Windows. + if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)) + set(MDI_USE_MPI ON) + else() + set(MDI_USE_MPI OFF) + endif() + + # detect if we have python development support and thus can enable python plugins + set(MDI_USE_PYTHON_PLUGINS OFF) + if(CMAKE_VERSION VERSION_LESS 3.12) + find_package(PythonLibs QUIET) # Deprecated since version 3.12 + if(PYTHONLIBS_FOUND) + set(MDI_USE_PYTHON_PLUGINS ON) + endif() + else() + find_package(Python QUIET COMPONENTS Development) + if(Python_Development_FOUND) + set(MDI_USE_PYTHON_PLUGINS ON) + endif() + endif() + + # download/ build MDI library + # always build static library with -fpic + # support cross-compilation and ninja-build + include(ExternalProject) + ExternalProject_Add(mdi_build + URL ${MDI_URL} + URL_MD5 ${MDI_MD5} + CMAKE_ARGS ${CMAKE_REQUEST_PIC} + -DCMAKE_INSTALL_PREFIX= + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} + -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} + -Dlanguage=C + -Dlibtype=STATIC + -Dmpi=${MDI_USE_MPI} + -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS} + UPDATE_COMMAND "" + INSTALL_COMMAND "" + BUILD_BYPRODUCTS "/MDI_Library/libmdi.a" + ) + + # where is the compiled library? + ExternalProject_get_property(mdi_build BINARY_DIR) + set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library") + # workaround for older CMake versions + file(MAKE_DIRECTORY ${MDI_BINARY_DIR}) + + # create imported target for the MDI library + add_library(LAMMPS::MDI UNKNOWN IMPORTED) + add_dependencies(LAMMPS::MDI mdi_build) + set_target_properties(LAMMPS::MDI PROPERTIES + IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a" + INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR} + ) + + set(MDI_DEP_LIBS "") + # if compiling with python plugins we need + # to add python libraries as dependency. + if(MDI_USE_PYTHON_PLUGINS) + if(CMAKE_VERSION VERSION_LESS 3.12) + list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES}) + else() + list(APPEND MDI_DEP_LIBS Python::Python) + endif() + + endif() + # need to add support for dlopen/dlsym, except when compiling for Windows. + if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows")) + list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}") + endif() + if(MDI_DEP_LIBS) + set_target_properties(LAMMPS::MDI PROPERTIES + IMPORTED_LINK_INTERFACE_LIBRARIES "${MDI_DEP_LIBS}") + endif() + + target_link_libraries(lammps PRIVATE LAMMPS::MDI) + target_link_libraries(lmp PRIVATE LAMMPS::MDI) + +else() + + find_package(mdi) + if(NOT mdi_FOUND) + message(FATAL_ERROR "MDI library not found. Help CMake to find it " + "by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON " + "to download and compile it") + endif() + + # Link the lammps library against MDI + target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR}) + target_link_libraries(lammps PRIVATE ${mdi_LIBRARY}) + + # Link the lammps executable against MDI + target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR}) + target_link_libraries(lmp PRIVATE ${mdi_LIBRARY}) +endif() + +target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI) +target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI) diff --git a/cmake/Modules/Packages/USER-MOLFILE.cmake b/cmake/Modules/Packages/USER-MOLFILE.cmake index 4d414acead..427f0ed6fa 100644 --- a/cmake/Modules/Packages/USER-MOLFILE.cmake +++ b/cmake/Modules/Packages/USER-MOLFILE.cmake @@ -2,8 +2,4 @@ set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}") add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS}) -# no need to link with -ldl on windows -if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") - target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) -endif() target_link_libraries(lammps PRIVATE molfile) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake new file mode 100644 index 0000000000..ccc7423355 --- /dev/null +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -0,0 +1,25 @@ + +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +mark_as_advanced(PACELIB_URL) +mark_as_advanced(PACELIB_MD5) + +# download library sources to build folder +file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) + +# uncompress downloaded sources +execute_process( + COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace* + COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} +) + +file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE) +file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp) +list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) + +add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) +set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) +target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) +target_link_libraries(lammps PRIVATE pace) + diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 53abf5771a..e9eba779f5 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -53,10 +53,17 @@ if(DOWNLOAD_PLUMED) elseif(PLUMED_MODE STREQUAL "RUNTIME") set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumedWrapper.a") endif() + + set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball") + set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball") + + mark_as_advanced(PLUMED_URL) + mark_as_advanced(PLUMED_MD5) + include(ExternalProject) ExternalProject_Add(plumed_build - URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz - URL_MD5 95f29dd0c067577f11972ff90dfc7d12 + URL ${PLUMED_URL} + URL_MD5 ${PLUMED_MD5} BUILD_IN_SOURCE 1 CONFIGURE_COMMAND /configure --prefix= ${CONFIGURE_REQUEST_PIC} @@ -65,6 +72,7 @@ if(DOWNLOAD_PLUMED) ${PLUMED_CONFIG_OMP} CXX=${PLUMED_CONFIG_CXX} CC=${PLUMED_CONFIG_CC} + PATCH_COMMAND sed -i "/^#include /a #include " /src/lepton/Operation.h BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS} ) ExternalProject_get_property(plumed_build INSTALL_DIR) diff --git a/cmake/Modules/Packages/USER-SCAFACOS.cmake b/cmake/Modules/Packages/USER-SCAFACOS.cmake index dc5c400c36..fd355420c3 100644 --- a/cmake/Modules/Packages/USER-SCAFACOS.cmake +++ b/cmake/Modules/Packages/USER-SCAFACOS.cmake @@ -14,15 +14,19 @@ endif() option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT}) if(DOWNLOAD_SCAFACOS) message(STATUS "ScaFaCoS download requested - we will build our own") + set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball") + set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball") + mark_as_advanced(SCAFACOS_URL) + mark_as_advanced(SCAFACOS_MD5) # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later. - file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff + file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032) include(ExternalProject) ExternalProject_Add(scafacos_build - URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz - URL_MD5 bd46d74e3296bd8a444d731bb10c1738 + URL ${SCAFACOS_URL} + URL_MD5 ${SCAFACOS_MD5} PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff CONFIGURE_COMMAND /configure --prefix= --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m diff --git a/cmake/Modules/Packages/USER-SMD.cmake b/cmake/Modules/Packages/USER-SMD.cmake index 67f4aae99d..6d941f9798 100644 --- a/cmake/Modules/Packages/USER-SMD.cmake +++ b/cmake/Modules/Packages/USER-SMD.cmake @@ -7,10 +7,14 @@ endif() option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT}) if(DOWNLOAD_EIGEN3) message(STATUS "Eigen3 download requested - we will build our own") + set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball") + set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball") + mark_as_advanced(EIGEN3_URL) + mark_as_advanced(EIGEN3_MD5) include(ExternalProject) ExternalProject_Add(Eigen3_build - URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz - URL_MD5 9e30f67e8531477de4117506fe44669b + URL ${EIGEN3_URL} + URL_MD5 ${EIGEN3_MD5} CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" ) ExternalProject_get_property(Eigen3_build SOURCE_DIR) diff --git a/cmake/Modules/Packages/VORONOI.cmake b/cmake/Modules/Packages/VORONOI.cmake index 1d6893a978..7feea4c52e 100644 --- a/cmake/Modules/Packages/VORONOI.cmake +++ b/cmake/Modules/Packages/VORONOI.cmake @@ -7,6 +7,11 @@ endif() option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT}) if(DOWNLOAD_VORO) message(STATUS "Voro++ download requested - we will build our own") + set(VORO_URL "${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" CACHE STRING "URL for Voro++ tarball") + set(VORO_MD5 "2338b824c3b7b25590e18e8df5d68af9" CACHE STRING "MD5 checksum for Voro++ tarball") + mark_as_advanced(VORO_URL) + mark_as_advanced(VORO_MD5) + include(ExternalProject) if(BUILD_SHARED_LIBS) @@ -22,8 +27,8 @@ if(DOWNLOAD_VORO) endif() ExternalProject_Add(voro_build - URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz - URL_MD5 2338b824c3b7b25590e18e8df5d68af9 + URL ${VORO_URL} + URL_MD5 ${VORO_MD5} PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} diff --git a/cmake/Modules/PreventInSourceBuilds.cmake b/cmake/Modules/PreventInSourceBuilds.cmake index 31f2376aa1..f9b8fc3368 100644 --- a/cmake/Modules/PreventInSourceBuilds.cmake +++ b/cmake/Modules/PreventInSourceBuilds.cmake @@ -9,7 +9,7 @@ function(prevent_in_source_builds) get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH) # disallow in-source builds - if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}") + if(("${srcdir}" STREQUAL "${bindir}") OR ("${srcdir2}" STREQUAL "${bindir}") OR ("${srcdir3}" STREQUAL "${bindir}")) message(FATAL_ERROR "\ CMake must not to be run in the source directory. \ diff --git a/cmake/Modules/Testing.cmake b/cmake/Modules/Testing.cmake index 6d2f39b0f3..2bb9c4757b 100644 --- a/cmake/Modules/Testing.cmake +++ b/cmake/Modules/Testing.cmake @@ -16,11 +16,14 @@ if(ENABLE_TESTING) set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command") set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options") - # check if a faster linker is available. - # only verified with GNU and Clang compilers and new CMake - if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) - if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") - OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) + # we need to build and link a LOT of tester executables, so it is worth checking if + # a faster linker is available. requires GNU or Clang compiler, newer CMake. + # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails) + if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) + AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") + OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))) + if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04)) + OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30))) include(CheckCXXCompilerFlag) set(CMAKE_CUSTOM_LINKER_DEFAULT default) check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG) @@ -53,3 +56,76 @@ if(ENABLE_TESTING) get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE) add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN}) endif() + +# Compiler specific features for testing +if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") + option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) + mark_as_advanced(ENABLE_COVERAGE) + if(ENABLE_COVERAGE) + if(CMAKE_VERSION VERSION_LESS 3.13) + if(CMAKE_CXX_FLAGS) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage") + endif() + else() + target_compile_options(lammps PUBLIC --coverage) + target_link_options(lammps PUBLIC --coverage) + endif() + endif() +endif() + +####################################### +# add custom target for IWYU analysis +####################################### +set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") +mark_as_advanced(ENABLE_IWYU) +if(ENABLE_IWYU) + # enforce these settings + set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE) + if(NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU"))) + message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers") + endif() + # detect the "native" header folder so we can include them first + execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS) + string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS}) + find_program(IWYU_EXE NAMES include-what-you-use iwyu) + find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) + if(IWYU_EXE AND IWYU_TOOL) + add_custom_target( + iwyu + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp + COMMENT "Running IWYU") + add_dependencies(iwyu lammps) + else() + message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" + "and the iwyu-tool/iwyu_tool script installed in your PATH") + endif() +endif() + +####################################### +# select code sanitizer options +####################################### +set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") +mark_as_advanced(ENABLE_SANITIZER) +set(ENABLE_SANITIZER_VALUES none address leak thread undefined) +set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES}) +validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES) +string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER) +if(NOT ENABLE_SANITIZER STREQUAL "none") + if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) + if(CMAKE_VERSION VERSION_LESS 3.13) + if(CMAKE_CXX_FLAGS) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}") + else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}") + endif() + else() + target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) + target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) + endif() + else() + message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.") + set(ENABLE_SANITIZER "none") + endif() +endif() diff --git a/cmake/Modules/Tools.cmake b/cmake/Modules/Tools.cmake index 078b4ebcf4..29b21dc390 100644 --- a/cmake/Modules/Tools.cmake +++ b/cmake/Modules/Tools.cmake @@ -45,7 +45,7 @@ if(BUILD_LAMMPS_SHELL) target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell) # workaround for broken readline pkg-config file on FreeBSD - if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD) + if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD") target_include_directories(lammps-shell PRIVATE /usr/local/include) endif() target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE) diff --git a/cmake/Modules/YAML.cmake b/cmake/Modules/YAML.cmake index f2ba34e1b6..77ee804111 100644 --- a/cmake/Modules/YAML.cmake +++ b/cmake/Modules/YAML.cmake @@ -2,16 +2,31 @@ message(STATUS "Downloading and building YAML library") include(ExternalProject) set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball") +set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball") mark_as_advanced(YAML_URL) +mark_as_advanced(YAML_MD5) + +# support cross-compilation to windows +if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows")) + if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86") + set(YAML_CROSS_HOST --host=i686-mingw64) + elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") + set(YAML_CROSS_HOST --host=x86_64-mingw64) + else() + message(FATAL_ERROR "Unsupported cross-compilation " + " for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}" + " on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}") + endif() +endif() + ExternalProject_Add(libyaml URL ${YAML_URL} - URL_MD5 bb15429d8fb787e7d3f1c83ae129a999 + URL_MD5 ${YAML_MD5} SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src" BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build" CONFIGURE_COMMAND /configure ${CONFIGURE_REQUEST_PIC} - CXX=${CMAKE_CXX_COMPILER} - CC=${CMAKE_C_COMPILER} - --prefix= --disable-shared + CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER} + --prefix= --disable-shared ${YAML_CROSS_HOST} BUILD_BYPRODUCTS /lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX} TEST_COMMAND "") diff --git a/cmake/Modules/generate_lmpgitversion.cmake b/cmake/Modules/generate_lmpgitversion.cmake index 4ff01c7501..b19716d74b 100644 --- a/cmake/Modules/generate_lmpgitversion.cmake +++ b/cmake/Modules/generate_lmpgitversion.cmake @@ -17,7 +17,7 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git) ERROR_QUIET WORKING_DIRECTORY ${LAMMPS_DIR} OUTPUT_STRIP_TRAILING_WHITESPACE) - execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified + execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always OUTPUT_VARIABLE temp_git_describe ERROR_QUIET WORKING_DIRECTORY ${LAMMPS_DIR} diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in index ca2c6191b7..42c8fddadd 100644 --- a/cmake/pkgconfig/liblammps.pc.in +++ b/cmake/pkgconfig/liblammps.pc.in @@ -24,7 +24,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@ Name: liblammps@LAMMPS_MACHINE@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library -URL: http://lammps.sandia.gov +URL: https://www.lammps.org Version: @PROJECT_VERSION@ Requires: Libs: -L${libdir} -llammps@LAMMPS_MACHINE@ diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index bd94b9dbe5..457750c690 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -2,16 +2,16 @@ # an existing package selection without losing any other settings set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP - MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK - SNAP SPIN SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ - USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE + MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD + USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP + USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN + USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 438c119c4c..ae40bb0809 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -4,16 +4,16 @@ # with just a working C++ compiler and an MPI library. set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP - MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK - SNAP SPIN SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ - USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE + MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD + USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP + USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN + USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/clang.cmake b/cmake/presets/clang.cmake index 47df6dcc6f..073bcec3f2 100644 --- a/cmake/presets/clang.cmake +++ b/cmake/presets/clang.cmake @@ -1,13 +1,26 @@ # preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes) +# prefer flang over gfortran, if available +find_program(CLANG_FORTRAN NAMES flang gfortran f95) +set(ENV{OMPI_FC} ${CLANG_FORTRAN}) + set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE) set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE) +set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f95" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f95" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f95" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) + set(MPI_CXX "clang++" CACHE STRING "" FORCE) set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) -unset(HAVE_OMP_H_INCLUDE CACHE) +unset(HAVE_OMP_H_INCLUDE CACHE) set(OpenMP_C "clang" CACHE STRING "" FORCE) set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE) set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE) diff --git a/cmake/presets/download.cmake b/cmake/presets/download.cmake index 84629ce785..ebab6ab658 100644 --- a/cmake/presets/download.cmake +++ b/cmake/presets/download.cmake @@ -1,7 +1,7 @@ -# preset that turns on packages with automatic downloads of sources of potentials -# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time. +# Preset that turns on packages with automatic downloads of sources or potentials. +# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time. -set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT) +set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) @@ -9,9 +9,11 @@ endforeach() set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE) set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE) +set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE) set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE) set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE) +set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE) set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE) set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/gcc.cmake b/cmake/presets/gcc.cmake index 51003c75fb..7942b2a4ce 100644 --- a/cmake/presets/gcc.cmake +++ b/cmake/presets/gcc.cmake @@ -2,10 +2,22 @@ set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE) set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE) -set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) -set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) set(MPI_CXX "g++" CACHE STRING "" FORCE) set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) +set(MPI_C "gcc" CACHE STRING "" FORCE) +set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) +set(MPI_Fortran "gfortran" CACHE STRING "" FORCE) +set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) unset(HAVE_OMP_H_INCLUDE CACHE) set(OpenMP_C "gcc" CACHE STRING "" FORCE) diff --git a/cmake/presets/intel.cmake b/cmake/presets/intel.cmake index d101a0f699..9baf873608 100644 --- a/cmake/presets/intel.cmake +++ b/cmake/presets/intel.cmake @@ -3,10 +3,20 @@ set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE) set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE) set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) + set(MPI_CXX "icpc" CACHE STRING "" FORCE) set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) -unset(HAVE_OMP_H_INCLUDE CACHE) +unset(HAVE_OMP_H_INCLUDE CACHE) set(OpenMP_C "icc" CACHE STRING "" FORCE) set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE) set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 32b17d43c2..e1a6c5cf79 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -1,13 +1,13 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI - USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF - USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD + USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP + USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF - USER-YAFF) + USER-YAFF USER-DIELECTRIC) foreach(PKG ${WIN_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index bddefc077b..e124b25d2b 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -4,11 +4,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI - POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI - USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION - USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD - USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION - USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF) + PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI + USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC + USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION + USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF USER-DIELECTRIC) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 0245b58cc7..08a3a531a1 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -1,10 +1,11 @@ # preset that turns off all packages that require some form of external # library or special compiler (fortran or cuda) or equivalent. -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON - VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB - USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP - USER-SCAFACOS USER-SMD USER-VTK) +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG + PYTHON VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE + USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP + USER-SCAFACOS USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/oneapi.cmake b/cmake/presets/oneapi.cmake index ef04167305..403494c409 100644 --- a/cmake/presets/oneapi.cmake +++ b/cmake/presets/oneapi.cmake @@ -1,12 +1,22 @@ -# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes) +# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes) set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE) set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE) set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) + set(MPI_CXX "icpx" CACHE STRING "" FORCE) set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) -unset(HAVE_OMP_H_INCLUDE CACHE) +unset(HAVE_OMP_H_INCLUDE CACHE) set(OpenMP_C "icx" CACHE STRING "" FORCE) set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE) set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE) diff --git a/cmake/presets/pedantic.cmake b/cmake/presets/pedantic.cmake new file mode 100644 index 0000000000..11c74dbaa4 --- /dev/null +++ b/cmake/presets/pedantic.cmake @@ -0,0 +1,26 @@ +# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes) + +set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE) +set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE) +set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE) +set(MPI_CXX "g++" CACHE STRING "" FORCE) +set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) +set(MPI_C "gcc" CACHE STRING "" FORCE) +set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE) +set(CMAKE_C_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE) +set(MPI_Fortran "gfortran" CACHE STRING "" FORCE) +set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE) +unset(HAVE_OMP_H_INCLUDE CACHE) + +set(OpenMP_C "gcc" CACHE STRING "" FORCE) +set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE) +set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE) +set(OpenMP_CXX "g++" CACHE STRING "" FORCE) +set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE) +set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE) +set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE) diff --git a/doc/Makefile b/doc/Makefile index 7deaaf2a2e..d61f844a1b 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -10,7 +10,6 @@ endif BUILDDIR = ${CURDIR} RSTDIR = $(BUILDDIR)/src VENV = $(BUILDDIR)/docenv -TXT2RST = $(VENV)/bin/txt2rst ANCHORCHECK = $(VENV)/bin/rst_anchor_check SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config MATHJAX = $(SPHINXCONFIG)/_static/mathjax @@ -59,7 +58,7 @@ SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiproc # we only want to use explicitly listed files. DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') -.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check xmlgen +.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen # ------------------------------------------ @@ -68,7 +67,6 @@ help: @echo "Please use \`make ' where is one of" @echo " html create HTML pages in html dir" @echo " pdf create Manual.pdf in this dir" - @echo " fetch fetch HTML and PDF files from LAMMPS web site" @echo " epub create ePUB format manual for e-book readers" @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)" @echo " (requires ebook-convert tool from calibre)" @@ -185,13 +183,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) @rm -rf latex/PDF/.[sg]* @echo "Build finished. Manual.pdf is in this directory." -fetch: - @rm -rf html_www Manual_www.pdf - @curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf - @curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz - @tar xzf lammps-doc.tar.gz - @rm -f lammps-doc.tar.gz - anchor_check : $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ @@ -213,6 +204,9 @@ package_check : $(VENV) deactivate ;\ ) +char_check : + @( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : ) + xmlgen : doxygen/xml/index.xml doxygen/Doxyfile: doxygen/Doxyfile.in @@ -236,9 +230,9 @@ $(VENV): ) $(MATHJAX): - @git clone --depth 1 git://github.com/mathjax/MathJax.git $@ + @git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@ -$(TXT2RST) $(ANCHORCHECK): $(VENV) +$(ANCHORCHECK): $(VENV) @( \ . $(VENV)/bin/activate; \ (cd utils/converters;\ diff --git a/doc/README b/doc/README index 8af4021a60..fed2e515b3 100644 --- a/doc/README +++ b/doc/README @@ -25,16 +25,11 @@ github-development-workflow.md notes on the LAMMPS development workflow include-file-conventions.md notes on LAMMPS' include file conventions documentation_conventions.md notes on writing documentation for LAMMPS -If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html +If you downloaded a LAMMPS tarball from www.lammps.org, then the html folder and the PDF manual should be included. If you downloaded LAMMPS -from GitHub then you either need to download them or build them. +from GitHub then you either need to build them. -(a) You can "fetch" the current HTML and PDF files from the LAMMPS web -site. Just type "make fetch". This should create a html_www directory -and Manual_www.pdf file. These will always represent the latest published -patch/development version of LAMMPS. - -(b) You can build the HTML and PDF files yourself, by typing "make html" +You can build the HTML and PDF files yourself, by typing "make html" or by "make pdf", respectively. This requires various tools and files. Some of them have to be installed (more on that below). For the rest the build process will attempt to download and install into a python virtual @@ -78,4 +73,4 @@ the tool 'ebook-convert' from the 'calibre' e-book management software ---------------- More details this can be found in the manual itself. The online -version is at: https://lammps.sandia.gov/doc/Manual_build.html +version is at: https://docs.lammps.org/Build_manual.html diff --git a/doc/graphviz/lammps-classes.dot b/doc/graphviz/lammps-classes.dot index 3c2d2f418d..390dd2cc4b 100644 --- a/doc/graphviz/lammps-classes.dot +++ b/doc/graphviz/lammps-classes.dot @@ -18,8 +18,8 @@ digraph lammps { Up [shape=box label="Update" color=blue] Un [shape=box label="Universe" color=blue] Ti [shape=box label="Timer" color=blue] - Lt [label="Lattice"] Rg [label="Region" color=red] + Lt [label="Lattice"] Rb [shape=box label="RegionBlock"] Rs [shape=box label="RegionSphere"] Av [label="AtomVec" color=red] @@ -34,6 +34,7 @@ digraph lammps { Du [label="Dump" color=red] Fi [label="Fix" color=red] Cp [label="Compute" color=red] + Cm [label="Command" color=red] Th [label="Thermo"] Va [label="Variable"] Ew [shape=box label="Ewald"] @@ -71,16 +72,19 @@ digraph lammps { Dg [shape=box label="DumpCFG"] Ve [shape=box label="Verlet"] Rr [shape=box label="Respa"] + Ru [shape=box label="Run"] + Se [shape=box label="Set"] Pt [shape=box label="PPPMTIP4P"] Vs [shape=box label="VerletSplit"] Ro [shape=box label="RespaOMP"] Mc [shape=box label="MinCG"] Mf [shape=box label="MinFire"] La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2] - Do -> {Lt Rg} [penwidth=2] + Do -> {Rg Lt} [penwidth=2] Rg -> {Rb Rs} [style=dashed penwidth=2] Co -> {Cb Ct} [style=dashed penwidth=2] - In -> Va [penwidth=2] + In -> {Va Cm} [penwidth=2] + Cm -> {Ru Se} [style=dashed penwidth=2] Mo -> {Fi Cp} [penwidth=2] Fo -> {Pa Bo An Di Im Ks} [penwidth=2] Ks -> {Ew Pp} [style=dashed penwidth=2] diff --git a/doc/lammps.1 b/doc/lammps.1 index 6ce463bfba..f18a9a118d 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "10 March 2021" "2021-03-10" +.TH LAMMPS "27 May 2021" "2021-05-27" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. @@ -34,7 +34,7 @@ semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. -See https://lammps.sandia.gov/ for more information and documentation. +See https://www.lammps.org/ for more information and documentation. .SH EXECUTABLE NAME The diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index 7789ae6e7b..a4a1076831 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -1129,6 +1129,9 @@ Bibliography **(Sutmann)** Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013) +**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems. + In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014. + **(Swinburne)** Swinburne and Marinica, Physical Review Letters, 120, 1 (2018) @@ -1285,9 +1288,6 @@ Bibliography **(Wennberg)** Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013). -**(Who)** - Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012). - **(Wicaksono1)** Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016). diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index af6120630d..30e668a283 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -1,7 +1,7 @@ Basic build options =================== -The following topics are covered on this page, for building both with +The following topics are covered on this page, for building with both CMake and make: * :ref:`Serial vs parallel build ` diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index 9c5f5ea61e..ea5c969056 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -28,6 +28,28 @@ variable VERBOSE set to 1: ---------- +.. _clang-tidy: + +Enable static code analysis with clang-tidy +------------------------------------------- + +The `clang-tidy tool `_ is a +static code analysis tool to diagnose (and potentially fix) typical +programming errors or coding style violations. It has a modular framework +of tests that can be adjusted to help identifying problems before they +become bugs and also assist in modernizing large code bases (like LAMMPS). +It can be enabled for all C++ code with the following CMake flag + +.. code-block:: bash + + -D ENABLE_CLANG_TIDY=value # value = no (default) or yes + +With this flag enabled all source files will be processed twice, first to +be compiled and then to be analyzed. Please note that the analysis can be +significantly more time consuming than the compilation itself. + +---------- + .. _iwyu_processing: Report missing and unneeded '#include' statements @@ -447,12 +469,24 @@ The following options are available. .. code-block:: bash - make check-whitespace # generate coverage report in HTML format - make fix-whitespace # generate coverage report in XML format - make check-permissions # delete folder with HTML format coverage report - make fix-permissions # delete all collected coverage data and HTML output + make check-whitespace # search for files with whitespace issues + make fix-whitespace # correct whitespace issues in files + make check-homepage # search for files with old LAMMPS homepage URLs + make fix-homepage # correct LAMMPS homepage URLs in files + make check-permissions # search for files with permissions issues + make fix-permissions # correct permissions issues in files -For the code in the ``unittest`` tree we are using the `clang-format` -tool (Clang version 8.0 or later is required). If available, the source -code files in the ``unittest`` tree can be updated to conform to the -formatting settings using ``make format-tests``. +For the code in the ``unittest`` and ``src`` trees we are transitioning +to use the `clang-format` tool to assist with having a consistent source +code style. The `clang-format` command bundled with Clang version 8.0 +or later is required. The configuration is in files ``.clang-format`` +in the respective folders. Since the modifications from `clang-format` +can be significant and - especially for "legacy style code" - also is +not always improving readability, a large number of files currently have +a ``// clang-format off`` at the top, which will disable the processing. +Over time, files will be refactored and updated to that `clang-format` +may be applied to them (at least in part). + +If `clang-format` is available, the source code files in the ``unittest`` +tree can be updated to conform to the formatting settings using +``make format-tests`` and the files in ``src`` with ``make format-src``. diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 2081dc4bcd..423897fd7a 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -48,10 +48,13 @@ This is the list of packages that may require additional steps. * :ref:`USER-AWPMD ` * :ref:`USER-COLVARS ` * :ref:`USER-H5MD ` + * :ref:`USER-HDNNP ` * :ref:`USER-INTEL ` + * :ref:`USER-MDI ` * :ref:`USER-MESONT ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` + * :ref:`USER-PACE ` * :ref:`USER-PLUMED ` * :ref:`USER-OMP ` * :ref:`USER-QMMM ` @@ -125,7 +128,7 @@ CMake build # default is sm_50 -D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip # value depends on selected HIP_PLATFORM - # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc + # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc -D HIP_USE_DEVICE_SORT=value # enables GPU sorting # value = yes (default) or no -D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs) @@ -169,17 +172,24 @@ desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`. If you are compiling with HIP, note that before running CMake you will have to set appropriate environment variables. Some variables such as -:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc` +:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc` and the linker to work correctly. .. code:: bash - # AMDGPU target + # AMDGPU target (ROCm <= 4.0) export HIP_PLATFORM=hcc export HCC_AMDGPU_TARGET=gfx906 cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc .. make -j 4 +.. code:: bash + + # AMDGPU target (ROCm >= 4.1) + export HIP_PLATFORM=amd + cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc .. + make -j 4 + .. code:: bash # CUDA target (not recommended, use GPU_ARCH=cuda) @@ -447,6 +457,9 @@ They must be specified in uppercase. * - ZEN2 - HOST - AMD Zen2 class CPU (AVX 2) + * - ZEN3 + - HOST + - AMD Zen3 class CPU (AVX 2) * - ARMV80 - HOST - ARMv8.0 Compatible CPU @@ -459,6 +472,9 @@ They must be specified in uppercase. * - ARMV8_THUNDERX2 - HOST - ARMv8 Cavium ThunderX2 CPU + * - A64FX + - HOST + - ARMv8.2 with SVE Support * - WSM - HOST - Intel Westmere CPU (SSE 4.2) @@ -531,6 +547,9 @@ They must be specified in uppercase. * - AMPERE80 - GPU - NVIDIA Ampere generation CC 8.0 GPU + * - AMPERE86 + - GPU + - NVIDIA Ampere generation CC 8.6 GPU * - VEGA900 - GPU - AMD GPU MI25 GFX900 @@ -539,12 +558,12 @@ They must be specified in uppercase. - AMD GPU MI50/MI60 GFX906 * - VEGA908 - GPU - - AMD GPU GFX908 + - AMD GPU MI100 GFX908 * - INTEL_GEN - GPU - Intel GPUs Gen9+ -This list was last updated for version 3.3 of the Kokkos library. +This list was last updated for version 3.4.1 of the Kokkos library. .. tabs:: @@ -1240,6 +1259,46 @@ be built for the most part with all major versions of the C++ language. ---------- +.. _user-pace: + +USER-PACE package +----------------------------- + +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, which must be done before building +LAMMPS with this package. The code for the library can be found +at: `https://github.com/ICAMS/lammps-user-pace/ `_ + +.. tabs:: + + .. tab:: CMake build + + By default the library will be downloaded from the git repository + and built automatically when the USER-PACE package is enabled with + ``-D PKG_USER-PACE=yes``. The location for the sources may be + customized by setting the variable ``PACELIB_URL`` when + configuring with CMake (e.g. to use a local archive on machines + without internet access). Since CMake checks the validity of the + archive with ``md5sum`` you may also need to set ``PACELIB_MD5`` + if you provide a different library version than what is downloaded + automatically. + + + .. tab:: Traditional make + + You can download and build the USER-PACE library + in one step from the ``lammps/src`` dir, using these commands, + which invoke the ``lib/pace/Install.py`` script. + + .. code-block:: bash + + $ make lib-pace # print help message + $ make lib-pace args="-b" # download and build the default version in lib/pace + + You should not need to edit the ``lib/pace/Makefile.lammps`` file. + +---------- + .. _user-plumed: USER-PLUMED package @@ -1415,6 +1474,60 @@ the HDF5 library. ---------- +.. _user-hdnnp: + +USER-HDNNP package +--------------------------------- + +To build with the USER-HDNNP package it is required to download and build the +external `n2p2 `__ library ``v2.1.4`` +(or higher). The LAMMPS build process offers an automatic download and +compilation of *n2p2* or allows you to choose the installation directory of +*n2p2* manually. Please see the boxes below for the CMake and traditional build +system for detailed information. + +In case of a manual installation of *n2p2* you only need to build the *n2p2* core +library ``libnnp`` and interface library ``libnnpif``. When using GCC it should +suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more +details please see ``lib/hdnnp/README`` and the `n2p2 build documentation +`__. + +.. tabs:: + + .. tab:: CMake build + + .. code-block:: bash + + -D DOWNLOAD_N2P2=value # download n2p2 for build, value = no (default) or yes + -D N2P2_DIR=path # n2p2 base directory (only needed if a custom location) + + If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and + built inside the CMake build directory. If the *n2p2* library is already + on your system (in a location CMake cannot find it), set the ``N2P2_DIR`` + to path where *n2p2* is located. If *n2p2* is located directly in + ``lib/hdnnp/n2p2`` it will be automatically found by CMake. + + .. tab:: Traditional make + + You can download and build the *n2p2* library manually if you prefer; + follow the instructions in ``lib/hdnnp/README``\ . You can also do it in + one step from the ``lammps/src`` dir, using a command like these, which + simply invoke the ``lib/hdnnp/Install.py`` script with the specified args: + + .. code-block:: bash + + $ make lib-hdnnp # print help message + $ make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-... + $ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version + $ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2 + + Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and + ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to + ``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``, + respectively. When LAMMPS is built in ``src`` it will use these links. + +---------- + .. _user-intel: USER-INTEL package @@ -1485,6 +1598,35 @@ TBB and MKL. ---------- +.. _user-mdi: + +USER-MDI package +----------------------------- + +.. tabs:: + + .. tab:: CMake build + + .. code-block:: bash + + -D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes + + .. tab:: Traditional make + + Before building LAMMPS, you must build the MDI Library in + ``lib/mdi``\ . You can do this by executing a command like one + of the following from the ``lib/mdi`` directory: + + .. code-block:: bash + + $ python Install.py -m gcc # build using gcc compiler + $ python Install.py -m icc # build using icc compiler + + The build should produce two files: ``lib/mdi/includelink/mdi.h`` + and ``lib/mdi/liblink/libmdi.so``\ . + +---------- + .. _user-mesont: USER-MESONT package diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index 3bf0337b31..e379153e6f 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -28,29 +28,18 @@ If you downloaded LAMMPS as a tarball from `the LAMMPS website `_, the html folder and the PDF files should be included. If you downloaded LAMMPS from the public git repository, then the HTML -and PDF files are not included. Instead you need to create them, in one -of two ways: - -a. You can "fetch" the current HTML and PDF files from the LAMMPS web - site. Just type ``make fetch``. This should download a ``html_www`` - directory and a ``Manual_www.pdf`` file. Note that if new LAMMPS features - have been added more recently than the date of your LAMMPS version, the - fetched documentation will include those changes (but your source code - will not, unless you update your local repository). - -b. You can build the HTML or PDF files yourself, by typing ``make html`` - or ``make pdf`` in the ``doc`` folder. This requires various tools - and files. Some of them have to be installed (see below). For the - rest the build process will attempt to download and install them into - a python virtual environment and local folders. +and PDF files are not included. You can build the HTML or PDF files yourself, +by typing ``make html`` or ``make pdf`` in the ``doc`` folder. This requires +various tools and files. Some of them have to be installed (see below). For +the rest the build process will attempt to download and install them into +a python virtual environment and local folders. A current version of the manual (latest patch release, aka unstable branch) is is available online at: -`https://lammps.sandia.gov/doc/Manual.html -`_ A version of the manual -corresponding to the ongoing development (aka master branch) is -available online at: `https://docs.lammps.org/ -`_ +`https://docs.lammps.org/Manual.html `_. +A version of the manual corresponding to the ongoing development (aka master branch) +is available online at: `https://docs.lammps.org/latest/ +`_ Build using GNU make -------------------- @@ -257,4 +246,4 @@ the file ``lammps/doc/utils/sphinx-config/false_positives.txt``. .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index f9fc52f8db..2b2993de50 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras ` page. These links take you to the extra instructions for those select packages: -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-NETCDF ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-HDNNP ` | :ref:`USER-INTEL ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ The mechanism for including packages is simple but different for CMake versus make. diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index 132425948e..c708228be7 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands. * :doc:`lattice ` * :doc:`log ` * :doc:`mass ` + * :doc:`mdi/engine ` * :doc:`message ` * :doc:`minimize ` * :doc:`min_modify ` @@ -86,6 +87,7 @@ An alphabetic list of all general LAMMPS commands. * :doc:`pair_style ` * :doc:`pair_write ` * :doc:`partition ` + * :doc:`plugin ` * :doc:`prd ` * :doc:`print ` * :doc:`processors ` diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index a826228219..70a021849d 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -126,7 +126,7 @@ OPT. * :doc:`quadratic (o) ` * :doc:`spherical ` * :doc:`table (o) ` - * :doc:`table/cut ` + * :doc:`table/cut ` .. _improper: diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 6841485f8f..72cc305bb3 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -47,11 +47,13 @@ KOKKOS, o = USER-OMP, t = OPT. * :doc:`dihedral ` * :doc:`dihedral/local ` * :doc:`dilatation/atom ` + * :doc:`dipole ` * :doc:`dipole/chunk ` * :doc:`displace/atom ` * :doc:`dpd ` * :doc:`dpd/atom ` * :doc:`edpd/temp/atom ` + * :doc:`efield/atom ` * :doc:`entropy/atom ` * :doc:`erotate/asphere ` * :doc:`erotate/rigid ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 4793568288..c9c55277b2 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -39,6 +39,9 @@ OPT. * :doc:`ave/time ` * :doc:`aveforce ` * :doc:`balance ` + * :doc:`brownian ` + * :doc:`brownian/asphere ` + * :doc:`brownian/sphere ` * :doc:`bocs ` * :doc:`bond/break ` * :doc:`bond/create ` @@ -46,6 +49,7 @@ OPT. * :doc:`bond/react ` * :doc:`bond/swap ` * :doc:`box/relax ` + * :doc:`charge/regulation ` * :doc:`client/md ` * :doc:`cmap ` * :doc:`colvars ` @@ -97,6 +101,7 @@ OPT. * :doc:`lb/viscous ` * :doc:`lineforce ` * :doc:`manifoldforce ` + * :doc:`mdi/engine ` * :doc:`meso/move ` * :doc:`momentum (k) ` * :doc:`momentum/chunk ` @@ -157,6 +162,9 @@ OPT. * :doc:`planeforce ` * :doc:`plumed ` * :doc:`poems ` + * :doc:`polarize/bem/gmres ` + * :doc:`polarize/bem/icc ` + * :doc:`polarize/functional ` * :doc:`pour ` * :doc:`precession/spin ` * :doc:`press/berendsen ` diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index 18fa5b5442..2f7cd35f15 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -28,6 +28,7 @@ OPT. * :doc:`ewald/dipole/spin ` * :doc:`msm (o) ` * :doc:`msm/cg (o) ` + * :doc:`msm/dielectric ` * :doc:`pppm (giko) ` * :doc:`pppm/cg (o) ` * :doc:`pppm/dipole ` @@ -36,4 +37,5 @@ OPT. * :doc:`pppm/disp/tip4p (o) ` * :doc:`pppm/stagger ` * :doc:`pppm/tip4p (o) ` + * :doc:`pppm/dielectric ` * :doc:`scafacos ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index da403aa87e..192c40b27a 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -26,6 +26,7 @@ OPT. * :doc:`zero ` * :doc:`hybrid (k) ` * :doc:`hybrid/overlay (k) ` + * :doc:`hybrid/scaled ` * :doc:`kim ` * :doc:`list ` * @@ -33,7 +34,6 @@ OPT. * * * - * * :doc:`adp (o) ` * :doc:`agni (o) ` * :doc:`airebo (io) ` @@ -69,12 +69,15 @@ OPT. * :doc:`comb3 ` * :doc:`cosine/squared ` * :doc:`coul/cut (gko) ` + * :doc:`coul/cut/dielectric ` + * :doc:`coul/cut/global (o) ` * :doc:`coul/cut/soft (o) ` * :doc:`coul/debye (gko) ` * :doc:`coul/diel (o) ` * :doc:`coul/dsf (gko) ` * :doc:`coul/long (gko) ` * :doc:`coul/long/cs (g) ` + * :doc:`coul/long/dielectric ` * :doc:`coul/long/soft (o) ` * :doc:`coul/msm (o) ` * :doc:`coul/slater/cut ` @@ -86,6 +89,8 @@ OPT. * :doc:`coul/wolf/cs ` * :doc:`dpd (gio) ` * :doc:`dpd/fdt ` + * :doc:`dpd/ext ` + * :doc:`dpd/ext/tstat ` * :doc:`dpd/fdt/energy (k) ` * :doc:`dpd/tstat (go) ` * :doc:`dsmc ` @@ -115,6 +120,7 @@ OPT. * :doc:`gw/zbl ` * :doc:`hbond/dreiding/lj (o) ` * :doc:`hbond/dreiding/morse (o) ` + * :doc:`hdnnp ` * :doc:`ilp/graphene/hbn ` * :doc:`kolmogorov/crespi/full ` * :doc:`kolmogorov/crespi/z ` @@ -139,13 +145,17 @@ OPT. * :doc:`lj/cubic (go) ` * :doc:`lj/cut (gikot) ` * :doc:`lj/cut/coul/cut (gko) ` + * :doc:`lj/cut/coul/cut/dielectric (o) ` * :doc:`lj/cut/coul/cut/soft (o) ` * :doc:`lj/cut/coul/debye (gko) ` + * :doc:`lj/cut/coul/debye/dielectric ` * :doc:`lj/cut/coul/dsf (gko) ` * :doc:`lj/cut/coul/long (gikot) ` * :doc:`lj/cut/coul/long/cs ` + * :doc:`lj/cut/coul/long/dielectric (o) ` * :doc:`lj/cut/coul/long/soft (o) ` * :doc:`lj/cut/coul/msm (go) ` + * :doc:`lj/cut/coul/msm/dielectric ` * :doc:`lj/cut/coul/wolf (o) ` * :doc:`lj/cut/dipole/cut (go) ` * :doc:`lj/cut/dipole/long (g) ` @@ -160,6 +170,7 @@ OPT. * :doc:`lj/gromacs (gko) ` * :doc:`lj/gromacs/coul/gromacs (ko) ` * :doc:`lj/long/coul/long (iot) ` + * :doc:`lj/long/coul/long/dielectric ` * :doc:`lj/long/dipole/long ` * :doc:`lj/long/tip4p/long (o) ` * :doc:`lj/mdf ` @@ -168,7 +179,7 @@ OPT. * :doc:`lj/sdk/coul/long (go) ` * :doc:`lj/sdk/coul/msm (o) ` * :doc:`lj/sf/dipole/sf (go) ` - * :doc:`lj/smooth (o) ` + * :doc:`lj/smooth (go) ` * :doc:`lj/smooth/linear (o) ` * :doc:`lj/switch3/coulgauss/long ` * :doc:`lj96/cut (go) ` @@ -187,7 +198,7 @@ OPT. * :doc:`mgpt ` * :doc:`mie/cut (g) ` * :doc:`mliap ` - * :doc:`mm3/switch3/coulgauss/long ` + * :doc:`mm3/switch3/coulgauss/long ` * :doc:`momb ` * :doc:`morse (gkot) ` * :doc:`morse/smooth/linear (o) ` @@ -215,6 +226,7 @@ OPT. * :doc:`oxrna2/stk ` * :doc:`oxrna2/xstk ` * :doc:`oxrna2/coaxstk ` + * :doc:`pace ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` @@ -222,6 +234,7 @@ OPT. * :doc:`polymorphic ` * :doc:`python ` * :doc:`quip ` + * :doc:`rann ` * :doc:`reax/c (ko) ` * :doc:`rebo (io) ` * :doc:`resquared (go) ` diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst index 64d5100715..563b18a4c2 100644 --- a/doc/src/Commands_parse.rst +++ b/doc/src/Commands_parse.rst @@ -164,7 +164,7 @@ LAMMPS: allowed, but that should be sufficient for most use cases. .. admonition:: ASCII versus UTF-8 - :class: note + :class: note LAMMPS expects and processes 7-bit ASCII format text internally. Many modern environments use UTF-8 encoding, which is a superset diff --git a/doc/src/Developer.rst b/doc/src/Developer.rst index 3a0c03b7ea..f54bc4152f 100644 --- a/doc/src/Developer.rst +++ b/doc/src/Developer.rst @@ -14,6 +14,7 @@ of time and requests from the LAMMPS user community. Developer_flow Developer_write Developer_notes + Developer_plugins Developer_unittest Classes Developer_utils diff --git a/doc/src/Developer_org.rst b/doc/src/Developer_org.rst index 6ecccf084d..133d567cb3 100644 --- a/doc/src/Developer_org.rst +++ b/doc/src/Developer_org.rst @@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries which may have different conventions, all C and C++ header files have a ``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a ``.c`` extension. A small number of C++ classes and utility functions -are implemented with only a ``.h`` file. Examples are the Pointer class -or the MathVec functions. +are implemented with only a ``.h`` file. Examples are the Pointers and +Commands classes or the MathVec functions. Class topology -------------- @@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in between runs. For these an instance of the class is created, its command() method called and then, after completion, the class instance deleted. Examples for this are the create_box, create_atoms, minimize, -run, or velocity command styles. +run, set, or velocity command styles. For all those ``styles`` certain naming conventions are employed: for the fix nve command the class is called FixNVE and the source files are @@ -175,11 +175,11 @@ follows: - The Input class reads and processes input input strings and files, stores variables, and invokes :doc:`commands `. -- As discussed above, command style classes are directly derived from - the Pointers class. They provide input script commands that perform - one-time operations before/after/between simulations or which invoke a - simulation. They are instantiated from within the Input class, - invoked, then immediately destructed. +- Command style classes are derived from the Command class. They provide + input script commands that perform one-time operations + before/after/between simulations or which invoke a simulation. They + are usually instantiated from within the Input class, its ``command`` + method invoked, and then immediately destructed. - The Finish class is instantiated to print statistics to the screen after a simulation is performed, by commands like run and minimize. diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst new file mode 100644 index 0000000000..1beedcf213 --- /dev/null +++ b/doc/src/Developer_plugins.rst @@ -0,0 +1,251 @@ +Writing plugins +--------------- + +Plugins provide a mechanism to add functionality to a LAMMPS executable +without recompiling LAMMPS. The functionality for this and the +:doc:`plugin command ` are implemented in the +:ref:`PLUGIN package ` which must be installed to use plugins. + +Plugins use the operating system's capability to load dynamic shared +object (DSO) files in a way similar shared libraries and then reference +specific functions in those DSOs. Any DSO file with plugins has to include +an initialization function with a specific name, "lammpsplugin_init", that +has to follow specific rules described below. When loading the DSO with +the "plugin" command, this function is looked up and called and will then +register the contained plugin(s) with LAMMPS. + +From the programmer perspective this can work because of the object +oriented design of LAMMPS where all pair style commands are derived from +the class Pair, all fix style commands from the class Fix and so on and +usually only functions present in those base classes are called +directly. When a :doc:`pair_style` command or :doc:`fix` command is +issued a new instance of such a derived class is created. This is done +by a so-called factory function which is mapped to the style name. Thus +when, for example, the LAMMPS processes the command ``pair_style lj/cut +2.5``, LAMMPS will look up the factory function for creating the +``PairLJCut`` class and then execute it. The return value of that +function is a ``Pair *`` pointer and the pointer will be assigned to the +location for the currently active pair style. + +A DSO file with a plugin thus has to implement such a factory function +and register it with LAMMPS so that it gets added to the map of available +styles of the given category. To register a plugin with LAMMPS an +initialization function has to be present in the DSO file called +``lammpsplugin_init`` which is called with three ``void *`` arguments: +a pointer to the current LAMMPS instance, a pointer to the opened DSO +handle, and a pointer to the registration function. The registration +function takes two arguments: a pointer to a ``lammpsplugin_t`` struct +with information about the plugin and a pointer to the current LAMMPS +instance. Please see below for an example of how the registration is +done. + +Members of ``lammpsplugin_t`` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Member + - Description + * - version + - LAMMPS Version string the plugin was compiled for + * - style + - Style of the plugin (pair, bond, fix, command, etc.) + * - name + - Name of the plugin style + * - info + - String with information about the plugin + * - author + - String with the name and email of the author + * - creator.v1 + - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles + * - creator.v2 + - Pointer to factory function for compute, fix, or region styles + * - handle + - Pointer to the open DSO file handle + +Only one of the three alternate creator entries can be used at a time +and which of those is determined by the style of plugin. The +"creator.v1" element is for factory functions of supported styles +computing forces (i.e. command, pair, bond, angle, dihedral, or +improper styles) and the function takes as single argument the pointer +to the LAMMPS instance. The factory function is cast to the +``lammpsplugin_factory1`` type before assignment. The "creator.v2" +element is for factory functions creating an instance of a fix, compute, +or region style and takes three arguments: a pointer to the LAMMPS +instance, an integer with the length of the argument list and a ``char +**`` pointer to the list of arguments. The factory function pointer +needs to be cast to the ``lammpsplugin_factory2`` type before +assignment. + +Pair style example +^^^^^^^^^^^^^^^^^^ + +As an example, a hypothetical pair style plugin "morse2" implemented in +a class ``PairMorse2`` in the files ``pair_morse2.h`` and +``pair_morse2.cpp`` with the factory function and initialization +function would look like this: + +.. code-block:: C++ + + #include "lammpsplugin.h" + #include "version.h" + #include "pair_morse2.h" + + using namespace LAMMPS_NS; + + static Pair *morse2creator(LAMMPS *lmp) + { + return new PairMorse2(lmp); + } + + extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) + { + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + lammpsplugin_t plugin; + + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "morse2"; + plugin.info = "Morse2 variant pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); + } + +The factory function in this example is called ``morse2creator()``. It +receives a pointer to the LAMMPS class as only argument and thus has to +be assigned to the *creator.v1* member of the plugin struct and cast to +the ``lammpsplugin_factory1`` function pointer type. It returns a +pointer to the allocated class instance derived from the ``Pair`` class. +This function may be declared static to avoid clashes with other +plugins. The name of the derived class, ``PairMorse2``, however must be +unique inside the entire LAMMPS executable. + +Fix style example +^^^^^^^^^^^^^^^^^ + +If the factory function would be for a fix or compute, which take three +arguments (a pointer to the LAMMPS class, the number of arguments and the +list of argument strings), then the pointer type is ``lammpsplugin_factory2`` +and it must be assigned to the *creator.v2* member of the plugin struct. +Below is an example for that: + +.. code-block:: C++ + + #include "lammpsplugin.h" + #include "version.h" + #include "fix_nve2.h" + + using namespace LAMMPS_NS; + + static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv) + { + return new FixNVE2(lmp,argc,argv); + } + + extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) + { + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + lammpsplugin_t plugin; + + plugin.version = LAMMPS_VERSION; + plugin.style = "fix"; + plugin.name = "nve2"; + plugin.info = "NVE2 variant fix style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); + } + +Command style example +^^^^^^^^^^^^^^^^^^^^^ +Command styles also use the first variant of factory function as +demonstrated in the following example, which also shows that the +implementation of the plugin class may be within the same source +file as the plugin interface code: + +.. code-block:: C++ + + #include "lammpsplugin.h" + + #include "comm.h" + #include "error.h" + #include "command.h" + #include "version.h" + + #include + + namespace LAMMPS_NS { + class Hello : public Command { + public: + Hello(class LAMMPS *lmp) : Command(lmp) {}; + void command(int, char **); + }; + } + + using namespace LAMMPS_NS; + + void Hello::command(int argc, char **argv) + { + if (argc != 1) error->all(FLERR,"Illegal hello command"); + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0])); + } + + static void hellocreator(LAMMPS *lmp) + { + return new Hello(lmp); + } + + extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) + { + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + plugin.version = LAMMPS_VERSION; + plugin.style = "command"; + plugin.name = "hello"; + plugin.info = "Hello world command v1.1"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); + } + +Additional Details +^^^^^^^^^^^^^^^^^^ + +The initialization function **must** be called ``lammpsplugin_init``, it +**must** have C bindings and it takes three void pointers as arguments. +The first is a pointer to the LAMMPS class that calls it and it needs to +be passed to the registration function. The second argument is a +pointer to the internal handle of the DSO file, this needs to be added +to the plugin info struct, so that the DSO can be closed and unloaded +when all its contained plugins are unloaded. The third argument is a +function pointer to the registration function and needs to be stored +in a variable of ``lammpsplugin_regfunc`` type and then called with a +pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS +instance as arguments to register a single plugin. There may be multiple +calls to multiple plugins in the same initialization function. + +To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled +with relevant info: current LAMMPS version string, kind of style, name of +style, info string, author string, pointer to factory function, and the +DSO handle. The registration function is called with a pointer to the address +of this struct and the pointer of the LAMMPS class. The registration function +will then add the factory function of the plugin style to the respective +style map under the provided name. It will also make a copy of the struct +in a list of all loaded plugins and update the reference counter for loaded +plugins from this specific DSO file. + +The pair style itself (i.e. the PairMorse2 class in this example) can be +written just like any other pair style that is included in LAMMPS. For +a plugin, the use of the ``PairStyle`` macro in the section encapsulated +by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class +name to the style name is done by the plugin registration function with +the information from the ``lammpsplugin_t`` struct. It may be included +in case the new code is intended to be later included in LAMMPS directly. diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index 4487dff11c..52753ee1b4 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -4,10 +4,10 @@ Adding tests for unit testing This section discusses adding or expanding tests for the unit test infrastructure included into the LAMMPS source code distribution. Unlike example inputs, unit tests focus on testing the "local" behavior -of individual features, tend to run very fast, and should be set up to -cover as much of the added code as possible. When contributing code to -the distribution, the LAMMPS developers will appreciate if additions -to the integrated unit test facility are included. +of individual features, tend to run fast, and should be set up to cover +as much of the added code as possible. When contributing code to the +distribution, the LAMMPS developers will appreciate if additions to the +integrated unit test facility are included. Given the complex nature of MD simulations where many operations can only be performed when suitable "real" simulation environment has been @@ -50,6 +50,9 @@ available: * - File name: - Test name: - Description: + * - ``test_argutils.cpp`` + - ArgInfo + - Tests for ``ArgInfo`` class used by LAMMPS * - ``test_fmtlib.cpp`` - FmtLib - Tests for ``fmtlib::`` functions used by LAMMPS @@ -155,23 +158,27 @@ have the desired effect: { ASSERT_EQ(lmp->update->ntimestep, 0); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_timestep 10"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + BEGIN_HIDE_OUTPUT(); + command("reset_timestep 10"); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->ntimestep, 10); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_timestep 0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + BEGIN_HIDE_OUTPUT(); + command("reset_timestep 0"); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->ntimestep, 0); + + TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10");); + TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep");); + TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10");); + TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx");); } -Please note the use of the (global) verbose variable to control whether -the LAMMPS command will be silent by capturing the output or not. In -the default case, verbose == false, the test output will be compact and -not mixed with LAMMPS output. However setting the verbose flag (via -setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be -helpful to understand why tests fail unexpectedly. +Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT`` +functions that will capture output from running LAMMPS. This is normally +discarded but by setting the verbose flag (via setting the ``TEST_ARGS`` +environment variable, ``TEST_ARGS=-v``) it can be printed and used to +understand why tests fail unexpectedly. Another complexity of these tests stems from the need to capture situations where LAMMPS will stop with an error, i.e. handle so-called @@ -210,6 +217,12 @@ The following test programs are currently available: * - ``test_lattice_region.cpp`` - LatticeRegion - Tests to validate the :doc:`lattice ` and :doc:`region ` commands + * - ``test_groups.cpp`` + - GroupTest + - Tests to validate the :doc:`group ` command + * - ``test_variables.cpp`` + - VariableTest + - Tests to validate the :doc:`variable ` command * - ``test_kim_commands.cpp`` - KimCommands - Tests for several commands from the :ref:`KIM package ` diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 992df6ba63..44210218c0 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -9,14 +9,29 @@ reading or writing to files with error checking or translation of strings into specific types of numbers with checking for validity. This reduces redundant implementations and encourages consistent behavior. -I/O with status check -^^^^^^^^^^^^^^^^^^^^^ +I/O with status check and similar functions +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -These are wrappers around the corresponding C library calls like -``fgets()`` or ``fread()``. They will check if there were errors -on reading or an unexpected end-of-file state was reached. In that -case, the functions will stop the calculation with an error message, -indicating the name of the problematic file, if possible. +The the first two functions are wrappers around the corresponding C +library calls ``fgets()`` or ``fread()``. They will check if there +were errors on reading or an unexpected end-of-file state was reached. +In that case, the functions will stop with an error message, indicating +the name of the problematic file, if possible unless the *error* argument +is a NULL pointer. + +The :cpp:func:`fgets_trunc` function will work similar for ``fgets()`` +but it will read in a whole line (i.e. until the end of line or end +of file), but store only as many characters as will fit into the buffer +including a final newline character and the terminating NULL byte. +If the line in the file is longer it will thus be truncated in the buffer. +This function is used by :cpp:func:`read_lines_from_file` to read individual +lines but make certain they follow the size constraints. + +The :cpp:func:`read_lines_from_file` function will read the requested +number of lines of a maximum length into a buffer and will return 0 +if successful or 1 if not. It also guarantees that all lines are +terminated with a newline character and the entire buffer with a +NULL character. ---------- @@ -26,6 +41,12 @@ indicating the name of the problematic file, if possible. .. doxygenfunction:: sfread :project: progguide +.. doxygenfunction:: fgets_trunc + :project: progguide + +.. doxygenfunction:: read_lines_from_file + :project: progguide + ---------- String to number conversions with validity check @@ -101,6 +122,9 @@ and parsing files or arguments. .. doxygenfunction:: split_words :project: progguide +.. doxygenfunction:: split_lines + :project: progguide + .. doxygenfunction:: strmatch :project: progguide @@ -161,7 +185,10 @@ Argument processing Convenience functions ^^^^^^^^^^^^^^^^^^^^^ -.. doxygenfunction:: logmesg +.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args) + :project: progguide + +.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg) :project: progguide .. doxygenfunction:: getsyserror diff --git a/doc/src/Developer_write.rst b/doc/src/Developer_write.rst index 5e0f9d12bb..37ac9ca126 100644 --- a/doc/src/Developer_write.rst +++ b/doc/src/Developer_write.rst @@ -59,7 +59,7 @@ of each timestep. First of all, implement a constructor: } In the constructor you should parse your fix arguments which are -specified in the script. All fixes have pretty the same syntax: +specified in the script. All fixes have pretty much the same syntax: ``fix ``. The first 3 parameters are parsed by Fix base class constructor, while ```` should be parsed by you. In our case, we need to diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst index d2714c86b1..1ea368a5a3 100644 --- a/doc/src/Errors_bugs.rst +++ b/doc/src/Errors_bugs.rst @@ -5,8 +5,8 @@ If you are confident that you have found a bug in LAMMPS, please follow the steps outlined below: * Check the `New features and bug fixes - `_ section of the `LAMMPS WWW site - `_ or the + `_ section of the `LAMMPS WWW site + `_ or the `GitHub Releases page `_ to see if the bug has already been addressed in a patch release. * Check that your issue can be reproduced with the latest development @@ -17,7 +17,7 @@ the steps outlined below: if your issue has already been reported and if it is still open. * Check the `GitHub Pull Requests page `_ to see if there is already a fix for your bug pending. - * Check the `mailing list archives `_ + * Check the `mailing list archives `_ to see if the issue has been discussed before. If none of these steps yields any useful information, please file a new diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 4d4483efec..11e517f513 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -39,7 +39,7 @@ figure out your physics or numerical mistakes, like choosing too big a timestep, specifying erroneous force field coefficients, or putting 2 atoms on top of each other! If you run into errors that LAMMPS does not catch that you think it should flag, please send an email to -the `developers `_. +the `developers `_. If you get an error message about an invalid command in your input script, you can determine what command is causing the problem by diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index aa38b3c0ba..d532ce7a31 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -3871,7 +3871,7 @@ Doc page with :doc:`WARNING messages ` *Fix orient/fcc found self twice* The neighbor lists used by fix orient/fcc are messed up. If this error occurs, it is likely a bug, so send an email to the - `developers `_. + `developers `_. *Fix peri neigh does not exist* Somehow a fix that the pair style defines has been deleted. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 8a76dca66e..3eb25d5b30 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -18,7 +18,7 @@ files and image files. If you uncomment the :doc:`dump ` command in the input script, a text dump file will be produced, which can be animated by various -`visualization programs `_. +`visualization programs `_. If you uncomment the :doc:`dump image ` command in the input script, and assuming you have built LAMMPS with a JPG library, JPG @@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the :doc:`dump image ` doc page. Animations of many of the examples can be viewed on the Movies section -of the `LAMMPS web site `_. +of the `LAMMPS web site `_. There are two kinds of sub-directories in the examples folder. Lower case named directories contain one or a few simple, quick-to-run @@ -108,6 +108,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | msst | MSST shock dynamics | +-------------+------------------------------------------------------------------+ +| multi | multi neighboring for systems with large interaction disparities | ++-------------+------------------------------------------------------------------+ | nb3b | use of non-bonded 3-body harmonic pair style | +-------------+------------------------------------------------------------------+ | neb | nudged elastic band (NEB) calculation for barrier finding | @@ -164,7 +166,7 @@ Here is how you can run and visualize one of the sample problems: Running the simulation produces the files *dump.indent* and *log.lammps*\ . You can visualize the dump file of snapshots with a variety of third-party tools highlighted on the -`Visualization `_ page of the LAMMPS +`Visualization `_ page of the LAMMPS web site. If you uncomment the :doc:`dump image ` line(s) in the input diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index ff75b751b1..8d8b7fb059 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -3,7 +3,7 @@ Howto discussions These doc pages describe how to perform various tasks with LAMMPS, both for users and developers. The -`glossary `_ website page also lists MD +`glossary `_ website page also lists MD terminology with links to corresponding LAMMPS manual pages. The example input scripts included in the examples directory of the LAMMPS distribution and highlighted on the :doc:`Examples ` doc page @@ -23,6 +23,7 @@ General howto Howto_library Howto_couple Howto_client_server + Howto_mdi Settings howto ============== diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index bac1b566e1..9bffe5d4c9 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -91,6 +91,7 @@ documentation for the formula it computes. * :doc:`bond_style ` harmonic * :doc:`bond_style ` morse +* :doc:`angle_style ` cosine/squared * :doc:`angle_style ` harmonic * :doc:`angle_style ` cosine * :doc:`angle_style ` cosine/periodic diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index d95f5c02aa..24c21f27b1 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts have to be modified to include the Drude dipoles and how to handle them. +Example input scripts available: examples/USER/drude + ---------- **Overview of Drude induced dipoles** diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst index c696d44249..70c2b2fbb7 100644 --- a/doc/src/Howto_granular.rst +++ b/doc/src/Howto_granular.rst @@ -18,12 +18,13 @@ This compute calculates rotational kinetic energy which can be :doc:`output with thermodynamic info `. -Use one of these 3 pair potentials, which compute forces and torques +Use one of these 4 pair potentials, which compute forces and torques between interacting pairs of particles: -* :doc:`pair_style ` gran/history -* :doc:`pair_style ` gran/no_history -* :doc:`pair_style ` gran/hertzian +* :doc:`pair_style gran/history ` +* :doc:`pair_style gran/no_history ` +* :doc:`pair_style gran/hertzian ` +* :doc:`pair_style granular ` These commands implement fix options specific to granular systems: @@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems: * :doc:`fix pour ` * :doc:`fix viscous ` * :doc:`fix wall/gran ` +* :doc:`fix wall/gran/region ` The fix style *freeze* zeroes both the force and torque of frozen atoms, and should be used for granular system instead of the fix style diff --git a/doc/src/Howto_mdi.rst b/doc/src/Howto_mdi.rst new file mode 100644 index 0000000000..7cfcd01a50 --- /dev/null +++ b/doc/src/Howto_mdi.rst @@ -0,0 +1,132 @@ +Using LAMMPS with the MDI library for code coupling +=================================================== + +.. note:: + + This Howto doc page will eventually replace the + :doc:`Howto client/server ` doc page. + +Client/server coupling of two codes is where one code is the "client" +and sends request messages (data) to a "server" code. The server +responds to each request with a reply message. This enables the two +codes to work in tandem to perform a simulation. LAMMPS can act as +either a client or server code; it does this by using the `MolSSI +Driver Interface (MDI) library +`_, +developed by the `Molecular Sciences Software Institute (MolSSI) +`_. + +Alternate methods for code coupling with LAMMPS are described on the +:doc:`Howto couple ` doc page. + +Some advantages of client/server coupling are that the two codes can run +as stand-alone executables; they need not be linked together. Thus +neither code needs to have a library interface. This also makes it easy +to run the two codes on different numbers of processors. If a message +protocol (format and content) is defined for a particular kind of +simulation, then in principle any code which implements the client-side +protocol can be used in tandem with any code which implements the +server-side protocol. Neither code needs to know what specific other +code it is working with. + +In MDI nomenclature, a client code is the "driver", and a server code is +an "engine". One driver code can communicate with one or more instances +of one or more engine codes. Driver and engine codes can be written in +any language: C, C++, Fortran, Python, etc. + +In addition to allowing driver and engine(s) running to run as +stand-alone executables, MDI also enables a server code to be a +"plugin" to the client code. In this scenario, server code(s) are +compiled as shared libraries, and one (or more) instances of the +server are instantiated by the driver code. If the driver code runs +in parallel, it can split its MPI communicator into multiple +sub-communicators, and launch each plugin engine instance on a +sub-communicator. Driver processors in that sub-communicator exchange +messages with that engine instance, and can also send MPI messages to +other processors in the driver. The driver code can also destroy +engine instances and re-instantiate them. + +The way that a driver communicates with an engine is by making +MDI_Send() and MDI_Recv() calls, which are conceptually similar to +MPI_Send() and MPI_Recv() calls. Each send or receive has a string +which identifies the command name, and optionally some data, which can +be a single value or vector of values of any data type. Inside the +MDI library, data is exchanged between the driver and engine via MPI +calls or sockets. This a run-time choice by the user. + +------------- + +As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a +suite of quantum DFT codes), can work together via the MDI library to +perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD +simulation and sends a message each timestep to ``pw.x`` asking it to +compute quantum forces on the current configuration of atoms. Here is +how the 2 codes are launched to communicate by MPI: + +.. code-block:: bash + + % mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \ + -in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI" + +In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16 +processors. + +Here is how the 2 codes are launched to communicate by sockets: + +.. code-block:: bash + + % mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd + % mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost" + +These commands could be issued in different windows on a desktop +machine. Or in the same window, if the first command is ended with +"&" so as to run in the background. If "localhost" is replaced by an +IP address, ``pw.x`` could be run on another machine on the same network, or +even on another machine across the country. + +After both codes initialize themselves to model the same system, this is +what occurs each timestep: + +* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords +* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms +* LAMMPS send a "` command. This will put LAMMPS into +"engine mode" where it waits for messages and data from the driver. +When the driver sends an "EXIT" command, LAMMPS will exit engine mode +and the input script will continue. + +If LAMMPS is used as a plugin engine it operates the same way, except +that the driver will pass LAMMPS an input script to initialize itself. +Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the +input script will continue. After finishing execution of the input +script, the instance of LAMMPS will be destroyed. + +LAMMPS supports the full set of MD-appropriate engine commands defined +by the MDI library. See the :doc:`mdi/engine ` doc page for +a list of these. + +If those commands are not sufficient for a user-developed driver to use +LAMMPS as an engine, then new commands can be easily added. See these +two files which implement the definition of MDI commands and the logic +for responding to them: + +* src/MDI/mdi_engine.cpp +* src/MDI/fix_mdi_engine.cpp diff --git a/doc/src/Howto_spins.rst b/doc/src/Howto_spins.rst index 0afcc12c91..87e30a5f6f 100644 --- a/doc/src/Howto_spins.rst +++ b/doc/src/Howto_spins.rst @@ -21,8 +21,8 @@ orientations and their associated inter-atomic distances. The command :doc:`fix precession/spin ` allows to apply a constant magnetic torque on all the spins in the system. This -torque can be an external magnetic field (Zeeman interaction), or an -uniaxial magnetic anisotropy. +torque can be an external magnetic field (Zeeman interaction), and an +uniaxial or cubic magnetic anisotropy. A Langevin thermostat can be applied to those magnetic spins using :doc:`fix langevin/spin `. Typically, this thermostat diff --git a/doc/src/Howto_wsl.rst b/doc/src/Howto_wsl.rst index 874be46c37..28251ba5ee 100644 --- a/doc/src/Howto_wsl.rst +++ b/doc/src/Howto_wsl.rst @@ -201,7 +201,7 @@ build configuration and any binaries generated during compilation. There are countless ways to compile LAMMPS. It is beyond the scope of this tutorial. If you want to find out more about what can be enabled, please -consult the extensive `documentation `_. +consult the extensive `documentation `_. To compile a minimal version of LAMMPS, we're going to use a preset. Presets are a way to specify a collection of CMake options using a file. diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index a84f31a80d..1a07b7f917 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -78,7 +78,7 @@ this is as follows. $ git checkout tagID Stable versions and what tagID to use for a particular stable version -are discussed on `this page `_. +are discussed on `this page `_. Note that this command will print some warnings, because in order to get back to the latest revision and to be able to update with ``git pull`` again, you will need to do ``git checkout unstable`` (or @@ -86,33 +86,59 @@ check out any other desired branch) first. Once you have updated your local files with a ``git pull`` (or ``git checkout``), you still need to re-build LAMMPS if any source files have -changed. To do this, you should cd to the src directory and type: +changed. How to do this depends on the build system you are using. -.. code-block:: bash +.. tabs:: - $ make purge # remove any deprecated src files - $ make package-update # sync package files with src files - $ make foo # re-build for your machine (mpi, serial, etc) + .. tab:: CMake build -just as described on the :doc:`Apply patch ` page, -after a patch has been installed. + Change to your build folder and type: -.. warning:: + .. code-block:: bash - If you wish to edit/change a src file that is from a - package, you should edit the version of the file inside the package - sub-directory with src, then re-install the package. The version in - the source directory is merely a copy and will be wiped out if you type "make - package-update". + cmake . --build -.. warning:: + CMake should auto-detect whether it needs to re-run the CMake + configuration step and otherwise redo the build for all files + that have been changed or files that depend on changed files. + In case some build options have been changed or renamed, you + may have to update those by running: - The GitHub servers support both the "git://" and - "https://" access protocols for anonymous read-only access. If you - have a correspondingly configured GitHub account, you may also use - SSH access with the URL "git@github.com:lammps/lammps.git". + .. code-block:: bash -The LAMMPS GitHub project is managed by Christoph Junghans (LANL, -junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at -gmail.com) and Richard Berger (Temple U, richard.berger at -temple.edu). + cmake . + + and then rebuild. + + .. tab:: Traditional make + + Switch to the src directory and type: + + .. code-block:: bash + + $ make purge # remove any deprecated src files + $ make package-update # sync package files with src files + $ make foo # re-build for your machine (mpi, serial, etc) + + Just as described on the :doc:`Apply patch ` page, + after a patch has been installed. + + .. warning:: + + If you wish to edit/change a src file that is from a package, + you should edit the version of the file inside the package + sub-directory with src, then re-install the package. The + version in the source directory is merely a copy and will be + wiped out if you type "make package-update". + +.. admonition:: Git protocols + :class: note + + The servers at github.com support the "git://" and "https://" access + protocols for anonymous, read-only access. If you have a suitably + configured GitHub account, you may also use SSH protocol with the + URL "git@github.com:lammps/lammps.git". + +The LAMMPS GitHub project is currently managed by Axel Kohlmeyer +(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U, +richard.berger at temple.edu). diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst index 39e007bb67..f1f37f86c2 100644 --- a/doc/src/Install_patch.rst +++ b/doc/src/Install_patch.rst @@ -10,7 +10,7 @@ If you prefer to download a tarball, as described on the :doc:`tarball download ` page, you can stay current by downloading "patch files" when new patch releases are made. A link to a patch file is posted on the -`bug fixes and new feature page `_ +`bug fixes and new feature page `_ of the LAMMPS website, along with a list of changed files and details about what is in the new patch release. This page explains how to apply the patch file to your local @@ -43,24 +43,54 @@ up to date. * A list of updated files print out to the screen. The -b switch creates backup files of your originals (e.g. src/force.cpp.orig), so you can manually undo the patch if something goes wrong. -* Type the following from the src directory, to enforce consistency - between the src and package directories. This is OK to do even if you - don't use one or more packages. If you are applying several patches - successively, you only need to type this once at the end. The purge - command removes deprecated src files if any were removed by the patch - from package sub-directories. - .. code-block:: bash +* Once you have updated your local files you need to re-build LAMMPS. + If you are applying several patches successively, you only need to + do the rebuild once at the end. How to do it depends on the build + system you are using. - $ make purge - $ make package-update + .. tabs:: -* Re-build LAMMPS via the "make" command. + .. tab:: CMake build -.. warning:: + Change to your build folder and type: - If you wish to edit/change a source file that is part of a package, - you should edit the version of the file inside the package folder in - src, and then re-install or update the package. The version in the - src directory is merely a copy and will be wiped out when you type - "make package-update". + .. code-block:: bash + + cmake . --build + + CMake should auto-detect whether it needs to re-run the CMake + configuration step and otherwise redo the build for all files + that have been changed or files that depend on changed files. + In case some build options have been changed or renamed, you + may have to update those by running: + + .. code-block:: bash + + cmake . + + and then rebuild. + + .. tab:: Traditional make + + Switch to the src directory and type: + + .. code-block:: bash + + $ make purge # remove any deprecated src files + $ make package-update # sync package files with src files + $ make foo # re-build for your machine (mpi, serial, etc) + + to enforce consistency of the source between the src folder + and package directories. This is OK to do even if you don't + use any packages. The "make purge" command removes any deprecated + src files if they were removed by the patch from a package + sub-directory. + + .. warning:: + + If you wish to edit/change a src file that is from a package, + you should edit the version of the file inside the package + sub-directory with src, then re-install the package. The + version in the source directory is merely a copy and will be + wiped out if you type "make package-update". diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index 6f87df8a21..921ce8785a 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -4,10 +4,10 @@ Download source and documentation as a tarball You can download a current LAMMPS tarball from the `download page `_ of the `LAMMPS website `_. -.. _download: https://lammps.sandia.gov/download.html -.. _bug: https://lammps.sandia.gov/bug.html -.. _older: https://lammps.sandia.gov/tars -.. _lws: https://lammps.sandia.gov +.. _download: https://www.lammps.org/download.html +.. _bug: https://www.lammps.org/bug.html +.. _older: https://www.lammps.org/tars +.. _lws: https://www.lammps.org You have two choices of tarballs, either the most recent stable release or the most current patch release. Stable releases occur a diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 56ca84f3ff..1df7ae7f3f 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -14,7 +14,7 @@ current and older versions of LAMMPS are available. 32-bit and 64-bit installers are available, and each installer contains both a serial and parallel executable. The installer web site also explains how to install the Windows MPI package (MPICH2 from Argonne National Labs), -needed to run in parallel. +needed to run in parallel with MPI. The LAMMPS binaries contain *all* :doc:`optional packages ` included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON, diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index 6d2b4b7ef2..6af3996d1e 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -11,14 +11,14 @@ University: * Richard Berger, richard.berger at temple.edu .. _sjp: http://www.cs.sandia.gov/~sjplimp -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org Past developers include Paul Crozier and Mark Stevens, both at Sandia, and Ray Shan, now at Materials Design. ---------- -The `Authors page `_ of the +The `Authors page `_ of the `LAMMPS website `_ has a comprehensive list of all the individuals who have contributed code for a new feature or command or tool to LAMMPS. @@ -46,7 +46,7 @@ general-purpose as it is without their expertise and efforts. ---------- -As discussed on the `History page `_ of the website, LAMMPS +As discussed on the `History page `_ of the website, LAMMPS originated as a cooperative project between DOE labs and industrial partners. Folks involved in the design and testing of the original version of LAMMPS were the following: diff --git a/doc/src/Intro_citing.rst b/doc/src/Intro_citing.rst index e758992e2b..978def9f15 100644 --- a/doc/src/Intro_citing.rst +++ b/doc/src/Intro_citing.rst @@ -38,8 +38,8 @@ In addition there are DOIs for individual stable releases. Currently there are: Home page ^^^^^^^^^ -The LAMMPS website at `https://lammps.sandia.gov/ -`_ is the canonical location for information +The LAMMPS website at `https://www.lammps.org/ +`_ is the canonical location for information about LAMMPS and its features. Citing contributions diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index 767f8e1f61..d034ccb443 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks: linear bead-spring polymer chains. The moltemplate program is a true molecular builder that will generate complex molecular models. See the :doc:`Tools ` doc page for details on tools packaged with - LAMMPS. The `Pre/post processing page `_ of the LAMMPS website + LAMMPS. The `Pre/post processing page `_ of the LAMMPS website describes a variety of third party tools for this task. Furthermore, some LAMMPS internal commands allow to reconstruct, or selectively add topology information, as well as provide the option to insert molecule @@ -67,7 +67,7 @@ Here are suggestions on how to perform these tasks: them to an external program, `FFmpeg `_ to generate movies from them. For high-quality, interactive visualization there are many excellent and free tools available. See the - `Visualization Tools `_ page of the + `Visualization Tools `_ page of the LAMMPS website for visualization packages that can process LAMMPS output data. * **Plotting:** See the next bullet about Pizza.py as well as the diff --git a/doc/src/Intro_opensource.rst b/doc/src/Intro_opensource.rst index f9fe99e252..635982fd18 100644 --- a/doc/src/Intro_opensource.rst +++ b/doc/src/Intro_opensource.rst @@ -2,18 +2,20 @@ LAMMPS open-source license -------------------------- LAMMPS is a freely-available open-source code, distributed under the -terms of the `GNU Public License `_, which means you can use or -modify the code however you wish. +terms of the `GNU Public License Version 2 `_, which means you can +use or modify the code however you wish for your own purposes, but have +to adhere to certain rules when redistributing it or software derived +from it or that includes parts of it. LAMMPS comes with no warranty of any kind. As each source file states in its header, it is a copyrighted code that is distributed free-of- -charge, under the terms of the `GNU Public License `_ (GPL). This -is often referred to as open-source distribution - see -`www.gnu.org `_ or `www.opensource.org `_. The legal -text of the GPL is in the LICENSE file included in the LAMMPS +charge, under the terms of the `GNU Public License Version 2 `_ +(GPLv2). This is often referred to as open-source distribution - see +`www.gnu.org `_ or `www.opensource.org `_. The +legal text of the GPL is in the LICENSE file included in the LAMMPS distribution. -.. _gnu: http://www.gnu.org/copyleft/gpl.html +.. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE .. _gnuorg: http://www.gnu.org @@ -24,14 +26,14 @@ Here is a summary of what the GPL means for LAMMPS users: (1) Anyone is free to use, modify, or extend LAMMPS in any way they choose, including for commercial purposes. -(2) If you distribute a modified version of LAMMPS, it must remain -open-source, meaning you distribute it under the terms of the GPL. -You should clearly annotate such a code as a derivative version of -LAMMPS. +(2) If you **distribute** a modified version of LAMMPS, it must remain +open-source, meaning you distribute **all** of it under the terms of +the GPL. You should clearly annotate such a code as a derivative version +of LAMMPS. -(3) If you release any code that includes LAMMPS source code, then it -must also be open-sourced, meaning you distribute it under the terms -of the GPL. +(3) If you release any code that includes or uses LAMMPS source code, +then it must also be open-sourced, meaning you distribute it under +the terms of the GPL. (4) If you give LAMMPS files to someone else, the GPL LICENSE file and source file headers (including the copyright and GPL notices) should diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index efaff8a914..8ab85a0d99 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -16,10 +16,10 @@ shared-memory boxes and distributed-memory clusters and supercomputers. .. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org LAMMPS is written in C++. Earlier versions were written in F77 and -F90. See the `History page `_ of +F90. See the `History page `_ of the website for details. All versions can be downloaded from the `LAMMPS website `_. diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst index 201020a4f8..3fccaf4dca 100644 --- a/doc/src/Intro_website.rst +++ b/doc/src/Intro_website.rst @@ -5,31 +5,31 @@ The `LAMMPS website `_ has a variety of additional info about LAMMPS, beyond what is in this manual. Some other useful resources available online are listed below. -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org * `Brief intro and recently added significant features `_ -* `List of features `_ -* `List of non-features `_ -* `Recent bug fixes and new features `_ +* `List of features `_ +* `List of non-features `_ +* `Recent bug fixes and new features `_ -* `Download info `_ +* `Download info `_ * `GitHub site `_ * `SourceForge site `_ -* `LAMMPS open-source license `_ +* `LAMMPS open-source license `_ -* `Glossary of terms relevant to LAMMPS `_ -* `LAMMPS highlights with images `_ -* `LAMMPS highlights with movies `_ -* `Mail list `_ -* `Workshops `_ -* `Tutorials `_ +* `Glossary of terms relevant to LAMMPS `_ +* `LAMMPS highlights with images `_ +* `LAMMPS highlights with movies `_ +* `Mail list `_ +* `Workshops `_ +* `Tutorials `_ -* `Pre- and post-processing tools for LAMMPS `_ -* `Other software usable with LAMMPS `_ -* `Viz tools usable with LAMMPS `_ +* `Pre- and post-processing tools for LAMMPS `_ +* `Other software usable with LAMMPS `_ +* `Viz tools usable with LAMMPS `_ -* `Benchmark performance `_ -* `Publications that have cited LAMMPS `_ -* `Authors of LAMMPS `_ -* `History of LAMMPS development `_ -* `Funding for LAMMPS `_ +* `Benchmark performance `_ +* `Publications that have cited LAMMPS `_ +* `Authors of LAMMPS `_ +* `History of LAMMPS development `_ +* `Funding for LAMMPS `_ diff --git a/doc/src/JPG/lammps-classes.png b/doc/src/JPG/lammps-classes.png index e401328783..71b5af9ccc 100644 Binary files a/doc/src/JPG/lammps-classes.png and b/doc/src/JPG/lammps-classes.png differ diff --git a/doc/src/Library_config.rst b/doc/src/Library_config.rst index a5b87e23a7..04b12f35de 100644 --- a/doc/src/Library_config.rst +++ b/doc/src/Library_config.rst @@ -15,6 +15,8 @@ This section documents the following functions: - :cpp:func:`lammps_config_package_count` - :cpp:func:`lammps_config_package_name` - :cpp:func:`lammps_config_accelerator` +- :cpp:func:`lammps_has_gpu_device` +- :cpp:func:`lammps_gpu_device_info` - :cpp:func:`lammps_has_style` - :cpp:func:`lammps_style_count` - :cpp:func:`lammps_style_name` @@ -132,6 +134,16 @@ approach. ----------------------- +.. doxygenfunction:: lammps_has_gpu_device + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_get_gpu_device_info + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_has_style :project: progguide diff --git a/doc/src/Library_scatter.rst b/doc/src/Library_scatter.rst index 40a79c2d9b..b45f45f6fb 100644 --- a/doc/src/Library_scatter.rst +++ b/doc/src/Library_scatter.rst @@ -76,7 +76,7 @@ It documents the following functions: ----------------------- -.. doxygenfunction:: lammps_create_atoms(void *handle, int n, int *id, int *type, double *x, double *v, int *image, int bexpand) +.. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand) :project: progguide diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 9198f545bc..2bbf2d95be 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -1,6 +1,6 @@ -###################################### -LAMMPS version |version| Documentation -###################################### +######################################## +LAMMPS Documentation (|version| version) +######################################## LAMMPS stands for **L**\ arge-scale **A**\ tomic/**M**\ olecular **M**\ assively **P**\ arallel **S**\ imulator. @@ -11,11 +11,12 @@ computers. It was developed originally at Sandia National Laboratories, a US Department of Energy facility. The majority of funding for LAMMPS has come from the US Department of Energy (DOE). LAMMPS is an open-source code, distributed freely under the terms of -the GNU Public License (GPL). +the GNU Public License Version 2 (GPLv2). The `LAMMPS website `_ has a variety of information about the code. It includes links to an on-line version of this manual, a -`mailing list `_ where users can +`mailing list `_ and +`online forum `_ where users can post questions, and a `GitHub site `_ where all LAMMPS development is coordinated. @@ -30,11 +31,13 @@ please :ref:`see this note `. ----------- -The manual is organized in two parts: +The manual is organized in three parts: 1) the :ref:`User Guide ` for how to install -and use LAMMPS and 2) the :ref:`Programmer Guide ` +and use LAMMPS, 2) the :ref:`Programmer Guide ` for how to write programs using the LAMMPS library from different -programming languages and how to modify and extend LAMMPS. +programming languages and how to modify and extend LAMMPS, and 3) the +:ref:`Command Reference ` which includes detailed +descriptions of all commands included in the LAMMPS code. .. only:: html @@ -42,7 +45,7 @@ programming languages and how to modify and extend LAMMPS. :doc:`this page ` since it gives quick access the documentation for all LAMMPS commands. -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org ---------- @@ -89,10 +92,15 @@ Programmer Guide Modify Developer +***************** +Command Reference +***************** + +.. _command_reference: .. toctree:: - :caption: Index - :name: index - :hidden: + :name: reference + :maxdepth: 1 + :caption: Command Reference commands_list fixes @@ -116,12 +124,13 @@ Indices and tables .. _webbrowser: .. admonition:: Web Browser Compatibility + :class: note The HTML version of the manual makes use of advanced features present - int "modern" web browsers. This can lead to incompatibilities with older + in "modern" web browsers. This can lead to incompatibilities with older web browsers (released more than 4 years ago) and specific vendor browsers (e.g. Internet Explorer on Windows; Microsoft Edge works well though) where parts of the pages are not rendered as expected (e.g. the layout is broken or mathematical expressions not typeset). In that case we recommend to install/use a different/newer web browser or use - the `PDF version of the manual `_. + the `PDF version of the manual `_. diff --git a/doc/src/Manual_version.rst b/doc/src/Manual_version.rst index 5ad816b3ed..a57c8512a6 100644 --- a/doc/src/Manual_version.rst +++ b/doc/src/Manual_version.rst @@ -5,7 +5,7 @@ The LAMMPS "version" is the date when it was released, such as 1 May 2014. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it in the next *patch* release, which are typically made every couple of weeks. Info on patch releases are on -`this website page `_. Every few +`this website page `_. Every few months, the latest patch release is subjected to more thorough testing and labeled as a *stable* version. diff --git a/doc/src/Modify_command.rst b/doc/src/Modify_command.rst index 2d0a1d99d9..e0e3ecbb8d 100644 --- a/doc/src/Modify_command.rst +++ b/doc/src/Modify_command.rst @@ -1,14 +1,15 @@ Input script command style ========================== -New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. +New commands can be added to LAMMPS input scripts by adding new classes +that are derived from the Command class and thus must have a "command" +method. For example, the create_atoms, read_data, velocity, and run +commands are all implemented in this fashion. When such a command is +encountered in the LAMMPS input script, LAMMPS simply creates a class +instance with the corresponding name, invokes the "command" method of +the class, and passes it the arguments from the input script. The +command method can perform whatever operations it wishes on LAMMPS data +structures. The single method your new class must define is as follows: diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 4998712a3d..4382753c42 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -2,7 +2,7 @@ Submitting new features for inclusion in LAMMPS =============================================== We encourage users to submit new features or modifications for LAMMPS to -`the core developers `_ so they +`the core developers `_ so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is via the LAMMPS project on `GitHub `_. Please see the :doc:`GitHub @@ -10,15 +10,15 @@ Tutorial ` for a demonstration on how to do that. An alternative is to contact the LAMMPS developers or the indicated developer of a package or feature directly and send in your contribution via e-mail, but that can add a significant delay on getting your -contribution included, depending on how busy the developer is you -contact, how complex a task it would be to integrate that code, and how +contribution included, depending on how busy the respective developer +is, how complex a task it would be to integrate that code, and how many - if any - changes are required before the code can be included. For any larger modifications or programming project, you are encouraged -to contact the LAMMPS developers ahead of time, in order to discuss -implementation strategies and coding guidelines, that will make it -easier to integrate your contribution and result in less work for -everybody involved. You are also encouraged to search through the list +to contact the LAMMPS developers ahead of time in order to discuss +implementation strategies and coding guidelines. That will make it +easier to integrate your contribution and results in less work for +everybody involved. You are also encouraged to search through the list of `open issues on GitHub `_ and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work @@ -31,21 +31,22 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS you are working on. Only discussions related to LAMMPS development are tolerated, so this is **NOT** for people that look for help with compiling, installing, or using LAMMPS. Please contact the `lammps-users mailing -list `_ for those purposes instead. +list `_ for those purposes instead. How quickly your contribution will be integrated depends largely on how -much effort it will cause to integrate and test it, how much it requires -changes to the core codebase, and of how much interest it is to the -larger LAMMPS community. Please see below for a checklist of typical -requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub -Tutorial ` page for instructions on -how to submit your changes or new files through a GitHub pull -request. If you prefer to submit patches or full files, you should first -make certain, that your code works correctly with the latest patch-level -version of LAMMPS and contains all bug fixes from it. Then create a -gzipped tar file of all changed or added files or a corresponding patch -file using 'diff -u' or 'diff -c' and compress it with gzip. Please only -use gzip compression, as this works well on all platforms. +much effort it will cause to integrate and test it, how many and what +kind of changes it requires to the core codebase, and of how much +interest it is to the larger LAMMPS community. Please see below for a +checklist of typical requirements. Once you have prepared everything, +see the :doc:`LAMMPS GitHub Tutorial ` page for +instructions on how to submit your changes or new files through a GitHub +pull request. If you prefer to submit patches or full files, you should +first make certain, that your code works correctly with the latest +patch-level version of LAMMPS and contains all bug fixes from it. Then +create a gzipped tar file of all changed or added files or a +corresponding patch file using 'diff -u' or 'diff -c' and compress it +with gzip. Please only use gzip compression, as this works well and is +available on all platforms. If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a :doc:`standard package `. Else we will add them as a @@ -57,13 +58,16 @@ added to the LAMMPS distribution. All the standard and user packages are listed and described on the :doc:`Packages details ` doc page. Note that by providing us files to release, you are agreeing to make -them open-source, i.e. we can release them under the terms of the GPL, -used as a license for the rest of LAMMPS. See the :doc:`LAMMPS license -` doc page for details. +them open-source, i.e. we can release them under the terms of the GPL +(version 2), used as a license for the rest of LAMMPS. And as part of +a LGPL (version 2.1) distribution that we make available to developers +on request only and with files that are authorized for that kind of +distribution removed (e.g. interface to FFTW). See the +:doc:`LAMMPS license ` doc page for details. With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source -code and on the `Authors page `_ +code and on the `Authors page `_ of the `LAMMPS WWW site `_), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make @@ -77,13 +81,13 @@ unusual event). If you prefer to actively develop and support your add-on feature yourself, then you may wish to make it available for download from your own website, as a user package that LAMMPS users can add to - their copy of LAMMPS. See the `Offsite LAMMPS packages and tools `_ page of the LAMMPS web + their copy of LAMMPS. See the `Offsite LAMMPS packages and tools `_ page of the LAMMPS web site for examples of groups that do this. We are happy to advertise your package and web site from that page. Simply email the - `developers `_ with info about + `developers `_ with info about your package and we will post it there. -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org The previous sections of this doc page describe how to add new "style" files of various kinds to LAMMPS. Packages are simply collections of @@ -92,7 +96,7 @@ LAMMPS input script. If designed correctly, these additions typically do not require changes to the main core of LAMMPS; they are simply add-on files. If you think your new feature requires non-trivial changes in core LAMMPS files, you should `communicate with the -developers `_, since we may or +developers `_, since we may or may not want to include those changes for some reason. An example of a trivial change is making a parent-class method "virtual" when you derive a new child class from it. @@ -112,7 +116,7 @@ packages in the src directory for examples. If you are uncertain, please ask. your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per - level, **no tabs**\ , no lines over 80 characters. I/O is done via + level, **no tabs**\ , no lines over 100 characters. I/O is done via the C-style stdio library (mixing of stdio and iostreams is generally discouraged), class header files should not import any system headers outside of , STL containers should be avoided in headers, @@ -131,6 +135,31 @@ packages in the src directory for examples. If you are uncertain, please ask. LAMMPS source files, including the use of the error class for error and warning messages. +* To simplify reformatting contributed code in a way that is compatible + with the LAMMPS formatting styles, you can use clang-format (version 8 + or later). The LAMMPS distribution includes a suitable ``.clang-format`` + file which will be applied if you run ``clang-format -i some_file.cpp`` + on your files inside the LAMMPS src tree. Please only reformat files + that you have contributed. For header files containing a + ``SomeStyle(keyword, ClassName)`` macros it is required to have this + macro embedded with a pair of ``// clang-format off``, ``// clang-format on`` + commends and the line must be terminated with a semi-colon (;). + Example: + + .. code-block:: c++ + + #ifdef COMMAND_CLASS + // clang-format off + CommandStyle(run,Run); + // clang-format on + #else + + #ifndef LMP_RUN_H + [...] + + You may also use ``// clang-format on/off`` throughout your file + to protect sections of the file from being reformatted. + * If you want your contribution to be added as a user-contributed feature, and it's a single file (actually a \*.cpp and \*.h file) it can rapidly be added to the USER-MISC directory. Send us the one-line diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index e858593c4c..478bc2c282 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -50,6 +50,7 @@ page gives those details. * :ref:`MSCG ` * :ref:`OPT ` * :ref:`PERI ` + * :ref:`PLUGIN ` * :ref:`POEMS ` * :ref:`PYTHON ` * :ref:`QEQ ` @@ -68,18 +69,22 @@ page gives those details. * :ref:`USER-ATC ` * :ref:`USER-AWPMD ` * :ref:`USER-BOCS ` + * :ref:`USER-BROWNIAN ` * :ref:`USER-CGDNA ` * :ref:`USER-CGSDK ` * :ref:`USER-COLVARS ` + * :ref:`USER-DIELECTRIC ` * :ref:`USER-DIFFRACTION ` * :ref:`USER-DPD ` * :ref:`USER-DRUDE ` * :ref:`USER-EFF ` * :ref:`USER-FEP ` * :ref:`USER-H5MD ` + * :ref:`USER-HDNNP ` * :ref:`USER-INTEL ` * :ref:`USER-LB ` * :ref:`USER-MANIFOLD ` + * :ref:`USER-MDI ` * :ref:`USER-MEAMC ` * :ref:`USER-MESODPD ` * :ref:`USER-MESONT ` @@ -89,12 +94,14 @@ page gives those details. * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` * :ref:`USER-OMP ` + * :ref:`USER-PACE ` * :ref:`USER-PHONON ` * :ref:`USER-PLUMED ` * :ref:`USER-PTM ` * :ref:`USER-QMMM ` * :ref:`USER-QTB ` * :ref:`USER-QUIP ` + * :ref:`USER-RANN ` * :ref:`USER-REACTION ` * :ref:`USER-REAXC ` * :ref:`USER-SCAFACOS ` @@ -129,8 +136,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * `doc/PDF/pair_resquared_extra.pdf `_ * examples/ASPHERE * examples/ellipse -* https://lammps.sandia.gov/movies.html#line -* https://lammps.sandia.gov/movies.html#tri +* https://www.lammps.org/movies.html#line +* https://www.lammps.org/movies.html#tri ---------- @@ -326,7 +333,7 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * :doc:`package gpu ` * :doc:`Commands ` pages (:doc:`pair `, :doc:`kspace `) for styles followed by (g) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -352,11 +359,11 @@ potentials. * examples/granregion * examples/pour * bench/in.chute -* https://lammps.sandia.gov/pictures.html#jamming -* https://lammps.sandia.gov/movies.html#hopper -* https://lammps.sandia.gov/movies.html#dem -* https://lammps.sandia.gov/movies.html#brazil -* https://lammps.sandia.gov/movies.html#granregion +* https://www.lammps.org/pictures.html#jamming +* https://www.lammps.org/movies.html#hopper +* https://www.lammps.org/movies.html#dem +* https://www.lammps.org/movies.html#brazil +* https://www.lammps.org/movies.html#granregion ---------- @@ -443,7 +450,7 @@ time via the "-sf kk" or "-suffix kk" :doc:`command-line switches ` :ref:`USER-INTEL `, and :ref:`USER-OMP ` packages, which have styles optimized for CPUs, KNLs, and GPUs. -You must have a C++11 compatible compiler to use this package. +You must have a C++14 compatible compiler to use this package. KOKKOS makes extensive use of advanced C++ features, which can expose compiler bugs, especially when compiling for maximum performance at high optimization levels. Please see the file @@ -475,7 +482,7 @@ This package has :ref:`specific installation instructions ` on the :doc: * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (k) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -584,7 +591,7 @@ MC package Several fixes and a pair style that have Monte Carlo (MC) or MC-like attributes. These include fixes for creating, breaking, and swapping bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) in conjunction with dynamics. +(GCMC) or similar processes in conjunction with dynamics. **Supporting info:** @@ -592,10 +599,14 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix atom/swap ` * :doc:`fix bond/break ` * :doc:`fix bond/create ` +* :doc:`fix bond/create/angle ` * :doc:`fix bond/swap ` +* :doc:`fix charge/regulation ` * :doc:`fix gcmc ` +* :doc:`fix tfmc ` +* :doc:`fix widom ` * :doc:`pair_style dsmc ` -* https://lammps.sandia.gov/movies.html#gcmc +* https://www.lammps.org/movies.html#gcmc ---------- @@ -652,8 +663,8 @@ listing, "ls src/MISC", to see the list of commands. * :doc:`fix viscosity ` * examples/KAPPA * examples/VISCOSITY -* https://lammps.sandia.gov/pictures.html#ttm -* https://lammps.sandia.gov/movies.html#evaporation +* https://www.lammps.org/pictures.html#ttm +* https://www.lammps.org/movies.html#evaporation ---------- @@ -808,7 +819,7 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * :doc:`OPT package ` * :doc:`Section 2.6 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -839,7 +850,29 @@ Foster (UTSA). * :doc:`compute damage/atom ` * :doc:`compute plasticity/atom ` * examples/peri -* https://lammps.sandia.gov/movies.html#peri +* https://www.lammps.org/movies.html#peri + +---------- + +.. _PKG-PLUGIN: + +PLUGIN package +-------------- + +**Contents:** + +A :doc:`plugin ` command that can load and unload several +kind of styles in LAMMPS from shared object files at runtime without +having to recompile and relink LAMMPS. + +**Authors:** Axel Kohlmeyer (Temple U) + +**Supporting info:** + +* src/PLUGIN: filenames -> commands +* :doc:`plugin command ` +* :doc:`Information on writing plugins ` +* examples/plugin ---------- @@ -978,8 +1011,8 @@ Also several computes which calculate properties of rigid bodies. * examples/ASPHERE * examples/rigid * bench/in.rhodo -* https://lammps.sandia.gov/movies.html#box -* https://lammps.sandia.gov/movies.html#star +* https://www.lammps.org/movies.html#box +* https://www.lammps.org/movies.html#star ---------- @@ -1080,9 +1113,9 @@ colloidal particles. * :doc:`fix wall/srd ` * examples/srd * examples/ASPHERE -* https://lammps.sandia.gov/movies.html#tri -* https://lammps.sandia.gov/movies.html#line -* https://lammps.sandia.gov/movies.html#poly +* https://www.lammps.org/movies.html#tri +* https://www.lammps.org/movies.html#line +* https://www.lammps.org/movies.html#poly ---------- @@ -1174,7 +1207,7 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-ATC/README * :doc:`fix atc ` * examples/USER/atc -* https://lammps.sandia.gov/pictures.html#atc +* https://www.lammps.org/pictures.html#atc ---------- @@ -1238,6 +1271,26 @@ Example inputs are in the examples/USER/bocs folder. ---------- +.. _PKG-USER-BROWNIAN: + +USER-BROWNIAN package +--------------------- + +**Contents:** + +This package provides :doc:`fix brownian, fix brownian/sphere, and +fix brownian/asphere ` as well as +:doc:`fix propel/self ` which allow to do Brownian +Dynamics time integration of point, spherical and aspherical particles +and also support self-propelled particles. + +**Authors:** Sam Cameron (University of Bristol), +Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) + +Example inputs are in the examples/USER/brownian folder. + +---------- + .. _PKG-USER-CGDNA: USER-CGDNA package @@ -1287,7 +1340,7 @@ acids. * :doc:`pair_style lj/sdk/\* ` * :doc:`angle_style sdk ` * examples/USER/cgsdk -* https://lammps.sandia.gov/pictures.html#cg +* https://www.lammps.org/pictures.html#cg ---------- @@ -1326,34 +1379,26 @@ This package has :ref:`specific installation instructions ` on the ---------- -.. _PKG-USER-PLUMED: +.. _PKG-USER-DIELECTRIC: -USER-PLUMED package -------------------- +USER-DIELECTRIC package +------------------------ **Contents:** -The fix plumed command allows you to use the PLUMED free energy plugin -for molecular dynamics to analyze and bias your LAMMPS trajectory on -the fly. The PLUMED library is called from within the LAMMPS input -script by using the :doc:`fix plumed ` command. +An atom style, multiple pair styles, several fixes, Kspace styles and a +compute for simulating systems using boundary element solvers for +computing the induced charges at the interface between two media with +different dielectric constants. -**Authors:** The :ref:`PLUMED library ` is written and maintained by -Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth -Tribello. - -.. _PLUMED: https://www.plumed.org - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. +**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U) **Supporting info:** -* src/USER-PLUMED/README -* lib/plumed/README -* :doc:`fix plumed ` -* examples/USER/plumed +* src/USER-DIELECTRIC: filenames -> commands +* :doc:`compute efield/atom ` +* TODO: add all styles +* examples/USER/dielectric ---------- @@ -1484,7 +1529,7 @@ tools/eff; see its README file. * examples/USER/eff * tools/eff/README * tools/eff -* https://lammps.sandia.gov/movies.html#eff +* https://www.lammps.org/movies.html#eff ---------- @@ -1549,6 +1594,39 @@ This package has :ref:`specific installation instructions ` on the :d ---------- +.. _PKG-USER-HDNNP: + +USER-HDNNP package +------------------ + +**Contents:** + +A :doc:`pair_style hdnnp ` command which allows to use +high-dimensional neural network potentials (HDNNPs), a form of machine learning +potentials. HDNNPs must be carefully trained prior to their application in a +molecular dynamics simulation. + +.. _n2p2: https://github.com/CompPhysVienna/n2p2 + +To use this package you must have the `n2p2 `_ library installed and +compiled on your system. + +**Author:** Andreas Singraber + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/USER-HDNNP: filenames -> commands +* src/USER-HDNNP/README +* lib/hdnnp/README +* :doc:`pair_style hdnnp ` +* examples/USER/hdnnp + +---------- + .. _PKG-USER-INTEL: USER-INTEL package @@ -1593,7 +1671,7 @@ This package has :ref:`specific installation instructions ` on the : * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) * src/USER-INTEL/TEST -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -1698,7 +1776,29 @@ Waltham, MA, USA) * :doc:`fix nve/manifold/rattle ` * :doc:`fix nvt/manifold/rattle ` * examples/USER/manifold -* https://lammps.sandia.gov/movies.html#manifold +* https://www.lammps.org/movies.html#manifold + +---------- + +.. _PKG-USER-MDI: + +USER-MDI package +---------------- + +**Contents:** + +A LAMMPS command and fix to allow client-server coupling of LAMMPS to +other atomic or molecular simulation codes via the `MolSSI Driver Interface +(MDI) library `_. + +**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com + +**Supporting info:** + +* src/USER-MDI/README +* :doc:`mdi/engine ` +* :doc:`fix mdi/engine ` +* examples/USER/mdi ---------- @@ -1754,10 +1854,7 @@ algorithm. * :doc:`pair_style tdpd ` * :doc:`fix mvv/dpd ` * examples/USER/mesodpd -* https://lammps.sandia.gov/movies.html#mesodpd - -* examples/USER/meso -* http://lammps.sandia.gov/movies.html#mesodpd +* https://www.lammps.org/movies.html#mesodpd ---------- @@ -1973,7 +2070,47 @@ This package has :ref:`specific installation instructions ` on the :do * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (o) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site + +---------- + +.. _PKG-USER-PACE: + +USER-PACE package +------------------- + +**Contents:** + +A pair style for the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. The USER-PACE +package provides an efficient implementation for running simulations +with ACE potentials. + +**Authors:** + +This package was written by Yury Lysogorskiy^1, +Cas van der Oord^2, Anton Bochkarev^1, +Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, +Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. + + ^1: Ruhr-University Bochum, Bochum, Germany + + ^2: University of Cambridge, Cambridge, United Kingdom + + ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + + ^4: University of British Columbia, Vancouver, BC, Canada + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/USER-PACE: filenames -> commands +* :doc:`pair_style pace ` +* examples/USER/pace ---------- @@ -2005,6 +2142,35 @@ and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" ---------- +.. _PKG-USER-PLUMED: + +USER-PLUMED package +------------------- + +**Contents:** + +The fix plumed command allows you to use the PLUMED free energy plugin +for molecular dynamics to analyze and bias your LAMMPS trajectory on +the fly. The PLUMED library is called from within the LAMMPS input +script by using the :doc:`fix plumed ` command. + +**Authors:** The `PLUMED library `_ is written +and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni, +and Gareth Tribello. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/USER-PLUMED/README +* lib/plumed/README +* :doc:`fix plumed ` +* examples/USER/plumed + +---------- + .. _PKG-USER-PTM: USER-PTM package @@ -2131,6 +2297,31 @@ This package has :ref:`specific installation instructions ` on the :d ---------- +.. _PKG-USER-RANN: + +USER-RANN package +----------------- + +**Contents:** + +A pair style for using rapid atomistic neural network (RANN) potentials. +These neural network potentials work by first generating a series of symmetry +functions from the neighbor list and then using these values as the input layer +of a neural network. + +**Authors:** + +This package was written by Christopher Barrett +with contributions by Doyl Dickel, Mississippi State University. + +**Supporting info:** + +* src/USER-RANN: filenames -> commands +* :doc:`pair_style rann ` +* examples/USER/rann + +---------- + .. _PKG-USER-REACTION: USER-REACTION package @@ -2156,8 +2347,8 @@ molecules, and chiral-sensitive reactions. * src/USER-REACTION/README * :doc:`fix bond/react ` * examples/USER/reaction -* `2017 LAMMPS Workshop `_ -* `2019 LAMMPS Workshop `_ +* `2017 LAMMPS Workshop `_ +* `2019 LAMMPS Workshop `_ * reacter.org ---------- @@ -2284,7 +2475,7 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-SMD/README * doc/PDF/SMD_LAMMPS_userguide.pdf * examples/USER/smd -* https://lammps.sandia.gov/movies.html#smd +* https://www.lammps.org/movies.html#smd ---------- @@ -2341,7 +2532,7 @@ Dynamics, Ernst Mach Institute, Germany). * src/USER-SPH/README * doc/PDF/SPH_LAMMPS_userguide.pdf * examples/USER/sph -* https://lammps.sandia.gov/movies.html#sph +* https://www.lammps.org/movies.html#sph ---------- @@ -2456,6 +2647,6 @@ which discuss the `QuickFF `_ methodology. * :doc:`bond_style mm3 ` * :doc:`improper_style distharm ` * :doc:`improper_style sqdistharm ` -* :doc:`pair_style mm3/switch3/coulgauss/long ` +* :doc:`pair_style mm3/switch3/coulgauss/long ` * :doc:`pair_style lj/switch3/coulgauss/long ` * examples/USER/yaff diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index ab9be69ab3..8fc1e7df7a 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -39,13 +39,13 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style lj/.../dipole ` | dipole | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | +| :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`GRANULAR ` | granular systems | :doc:`Howto granular ` | pour | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`KIM ` | OpenKIM wrapper | :doc:`pair_style kim ` | kim | ext | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | +| :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace_style ` | peptide | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ @@ -67,10 +67,12 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`MSCG ` | multi-scale coarse-graining wrapper | :doc:`fix mscg ` | mscg | ext | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | +| :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`PLUGIN ` | Plugin loader command | :doc:`plugin ` | plugins | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`PYTHON ` | embed Python code in an input script | :doc:`python ` | python | sys | diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index a3efaf15c8..89d740939e 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -39,12 +39,16 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-BROWNIAN ` | Brownian dynamics and self-propelled particles | :doc:`fix brownian `, :doc:`fix propel/self ` | USER/brownian | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-DIELECTRIC ` | dielectric boundary solvers and force styles | :doc:`compute efield/atom ` | USER/dielectric | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-DPD ` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no | @@ -57,12 +61,16 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | +| :ref:`USER-HDNNP ` | High-dimensional neural network potentials | :doc:`pair_style hdnnp ` | USER/hdnnp | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MDI ` | client-server coupling | :doc:`MDI Howto ` | USER/mdi | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | @@ -79,7 +87,9 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PACE ` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace ` | USER/pace | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ @@ -93,6 +103,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-RANN ` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann ` | USER/rann | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 134d3e22d2..6b224bbf40 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -377,14 +377,6 @@ make MPI calls directly from Python in your script, if you desire. We have tested this with `MPI for Python `_ (aka mpi4py) and you will find installation instruction for it below. -.. note:: - - Older LAMMPS versions were also tested with `PyPar `_ - but we can no longer test it, since it does not work with the Python - (3.x) versions on our test servers. Since there have been no updates - to PyPar visible in its repository since November 2016 we have to assume - it is no longer maintained. - Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as follows: diff --git a/doc/src/Python_module.rst b/doc/src/Python_module.rst index d2564986de..c19d4b0345 100644 --- a/doc/src/Python_module.rst +++ b/doc/src/Python_module.rst @@ -142,7 +142,7 @@ Style Constants Type Constants -------------- -.. py:data:: LMP_TYPE_SCALAR, LMP_TYLE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS +.. py:data:: LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS :type: int Constants in the :py:mod:`lammps` module to select what type of data diff --git a/doc/src/Python_neighbor.rst b/doc/src/Python_neighbor.rst index cba117ad20..00c4cc8996 100644 --- a/doc/src/Python_neighbor.rst +++ b/doc/src/Python_neighbor.rst @@ -1,6 +1,43 @@ Neighbor list access ==================== +Access to neighbor lists is handled through a couple of wrapper classes +that allows to treat it like either a python list or a NumPy array. The +access procedure is similar to that of the C-library interface: use one +of the "find" functions to look up the index of the neighbor list in the +global table of neighbor lists and then get access to the neighbor list +data. The code sample below demonstrates reading the neighbor list data +using the NumPy access method. + +.. code-block:: python + + from lammps import lammps + import numpy as np + + lmp = lammps() + lmp.commands_string(""" + region box block -2 2 -2 2 -2 2 + lattice fcc 1.0 + create_box 1 box + create_atoms 1 box + mass 1 1.0 + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 + run 0 post no""") + + # look up the neighbor list + nlidx = lmp.find_pair_neighlist('lj/cut') + nl = lmp.numpy.get_neighlist(nlidx) + tags = lmp.extract_atom('id') + print("half neighbor list with {} entries".format(nl.size)) + # print neighbor list contents + for i in range(0,nl.size): + idx, nlist = nl.get(i) + print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size)) + if nlist.size > 0: + for n in np.nditer(nlist): + print(" atom {} with ID {}".format(n,tags[n])) + **Methods:** * :py:meth:`lammps.get_neighlist() `: Get neighbor list for given index diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 25756d9be0..d8adfcc5be 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -10,6 +10,7 @@ letter abbreviation can be used: * :ref:`-i or -in ` * :ref:`-k or -kokkos ` * :ref:`-l or -log ` +* :ref:`-mdi ` * :ref:`-m or -mpicolor ` * :ref:`-c or -cite ` * :ref:`-nc or -nocite ` @@ -196,9 +197,23 @@ Option -plog will override the name of the partition log files file.N. ---------- +.. _mdi: + +**-mdi 'multiple flags'** + +This flag is only recognized and used when LAMMPS has support for the MolSSI +Driver Interface (MDI) included as part of the :ref:`USER-MDI ` +package. This flag is specific to the MDI library and controls how LAMMPS +interacts with MDI. There are usually multiple flags that have to follow it +and those have to be placed in quotation marks. For more information about +how to launch LAMMPS in MDI client/server mode please refer to the +:doc:`MDI Howto `. + +---------- + .. _mpicolor: -**-mpicolor** color +**-mpicolor color** If used, this must be the first command-line argument after the LAMMPS executable name. It is only used when LAMMPS is launched by an mpirun @@ -223,7 +238,7 @@ links with from the lib/message directory. See the .. _cite: -**-cite style or file name** +**-cite style** or **file name** Select how and where to output a reminder about citing contributions to the LAMMPS code that were used during the run. Available styles are diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index 0343e123b9..8813d6d59e 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -7,7 +7,7 @@ To run a serial (non-MPI) executable, follow these steps: then typing "cmd". * Move to the directory where you have your input script, (e.g. by typing: cd "Documents"). -* At the command prompt, type "lmp_serial -in in.file", where +* At the command prompt, type "lmp -in in.file", where in.file is the name of your LAMMPS input script. Note that the serial executable includes support for multi-threading @@ -16,7 +16,7 @@ parallelization from the styles in the USER-OMP packages. To run with .. code-block:: bash - lmp_serial -in in.lj -pk omp 4 -sf omp + lmp -in in.lj -pk omp 4 -sf omp ---------- @@ -41,15 +41,17 @@ into the MPICH2 installation directory, then into the sub-directory * Move to the directory where you have your input file (e.g. by typing: cd "Documents"). -Then type something like this: +Then you can run the executable in serial like in the example above +or in parallel using MPI with one of the following commands: .. code-block:: bash - mpiexec -localonly 4 lmp_mpi -in in.file - mpiexec -np 4 lmp_mpi -in in.file + mpiexec -localonly 4 lmp -in in.file + mpiexec -np 4 lmp -in in.file where in.file is the name of your LAMMPS input script. For the latter -case, you may be prompted to enter your password. +case, you may be prompted to enter the password that you set during +installation of the MPI library software. In this mode, output may not immediately show up on the screen, so if your input script takes a long time to execute, you may need to be @@ -60,11 +62,12 @@ something like this: .. code-block:: bash - lmp_mpi -in in.lj + lmp -in in.lj Note that the parallel executable also includes OpenMP multi-threading, which can be combined with MPI using something like: .. code-block:: bash - mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp + mpiexec -localonly 2 lmp -in in.lj -pk omp 2 -sf omp + diff --git a/doc/src/Speed.rst b/doc/src/Speed.rst index 0528ff32d8..ccabc0adb6 100644 --- a/doc/src/Speed.rst +++ b/doc/src/Speed.rst @@ -12,7 +12,7 @@ accelerator packages provided with LAMMPS that contain code optimized for certain kinds of hardware, including multi-core CPUs, GPUs, and Intel Xeon Phi co-processors. -The `Benchmark page `_ of the LAMMPS +The `Benchmark page `_ of the LAMMPS web site gives performance results for the various accelerator packages discussed on the :doc:`Speed packages ` doc page, for several of the standard LAMMPS benchmark problems, as a diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst index 66db03e360..aa6128894a 100644 --- a/doc/src/Speed_bench.rst +++ b/doc/src/Speed_bench.rst @@ -1,7 +1,7 @@ Benchmarks ========== -Current LAMMPS performance is discussed on the `Benchmarks page `_ of the `LAMMPS website `_ +Current LAMMPS performance is discussed on the `Benchmarks page `_ of the `LAMMPS website `_ where timings and parallel efficiency are listed. The page has several sections, which are briefly described below: @@ -43,11 +43,11 @@ to build LAMMPS and run on that kind of hardware. The bench/POTENTIALS directory has input files which correspond to the table of results on the -`Potentials `_ section of +`Potentials `_ section of the Benchmarks web page. So you can also run those test problems on your machine. -The `billion-atom `_ section +The `billion-atom `_ section of the Benchmarks web page has performance data for very large benchmark runs of simple Lennard-Jones (LJ) models, which use the bench/in.lj input script. @@ -73,4 +73,4 @@ estimate parallel performance for multi-node runs using the same logic as for all-MPI mode, except that now you will typically need many more atoms/node to achieve good scalability. -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 709a3ad3bb..2cb8c08fd5 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -35,8 +35,8 @@ Coulombics. It has the following general features: To compile and use this package in CUDA mode, you currently need to have an NVIDIA GPU and install the corresponding NVIDIA CUDA -toolkit software on your system (this is primarily tested on Linux -and completely unsupported on Windows): +toolkit software on your system (this is only tested on Linux +and unsupported on Windows): * Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information * Go to http://www.nvidia.com/object/cuda_get.html @@ -152,7 +152,7 @@ in OpenCL mode on CPUs (which uses vectorization and multithreading) is usually resulting in inferior performance compared to using LAMMPS' native threading and vectorization support in the USER-OMP and USER-INTEL packages. -See the `Benchmark page `_ of the +See the `Benchmark page `_ of the LAMMPS web site for performance of the GPU package on various hardware, including the Titan HPC platform at ORNL. diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 708678e537..c3f8945c62 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -27,7 +27,7 @@ GPUs) and HIP (for AMD GPUs). You choose the mode at build time to produce an executable compatible with a specific hardware. .. admonition:: C++14 support - :class: note + :class: note Kokkos requires using a compiler that supports the c++14 standard. For some compilers, it may be necessary to add a flag to enable c++14 support. @@ -406,7 +406,7 @@ Generally speaking, the following rules of thumb apply: package also can increase the vector length of vector instructions by switching to single or mixed precision mode. -See the `Benchmark page `_ of the +See the `Benchmark page `_ of the LAMMPS web site for performance of the KOKKOS package on different hardware. diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index 6210242413..f5da991f0b 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -145,7 +145,7 @@ sub-directories with Make.py commands and input scripts for using all the accelerator packages on various machines. See the README files in those directories. -As mentioned above, the `Benchmark page `_ of the LAMMPS web site gives +As mentioned above, the `Benchmark page `_ of the LAMMPS web site gives performance results for the various accelerator packages for several of the standard LAMMPS benchmark problems, as a function of problem size and number of compute nodes, on different hardware platforms. diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 376489dcce..4d46d32037 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -6,15 +6,15 @@ molecular dynamics computations. Additional pre- and post-processing steps are often necessary to setup and analyze a simulation. A list of such tools can be found on the `LAMMPS webpage `_ at these links: -* `Pre/Post processing `_ -* `Offsite LAMMPS packages & tools `_ +* `Pre/Post processing `_ +* `Offsite LAMMPS packages & tools `_ * `Pizza.py toolkit `_ The last link for `Pizza.py `_ is a Python-based tool developed at Sandia which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. -.. _lws: https://lammps.sandia.gov +.. _lws: https://www.lammps.org .. _pizza: https://pizza.sandia.gov .. _python: https://www.python.org @@ -94,6 +94,7 @@ Miscellaneous tools * :ref:`kate ` * :ref:`LAMMPS shell ` * :ref:`LAMMPS magic patterns for file(1) ` + * :ref:`Offline build tool ` * :ref:`singularity ` * :ref:`SWIG interface ` * :ref:`vim ` @@ -756,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information. ---------- +.. _offline: + +Scripts for building LAMMPS when offline +---------------------------------------- + +In some situations it might be necessary to build LAMMPS on a system +without direct internet access. The scripts in ``tools/offline`` folder +allow you to pre-load external dependencies for both the documentation +build and for building LAMMPS with CMake. + +It does so by + + #. downloading necessary ``pip`` packages, + #. cloning ``git`` repositories + #. downloading tarballs + +to a designated cache folder. + +As of April 2021, all of these downloads make up around 600MB. By +default, the offline scripts will download everything into the +``$HOME/.cache/lammps`` folder, but this can be changed by setting the +``LAMMPS_CACHING_DIR`` environment variable. + +Once the caches have been initialized, they can be used for building the +LAMMPS documentation or compiling LAMMPS using CMake on an offline +system. + +The ``use_caches.sh`` script must be sourced into the current shell +to initialize the offline build environment. Note that it must use +the same ``LAMMPS_CACHING_DIR``. This script does the following: + + #. Set up environment variables that modify the behavior of both, + ``pip`` and ``git`` + #. Start a simple local HTTP server using Python to host files for CMake + +Afterwards, it will print out instruction on how to modify the CMake +command line to make sure it uses the local HTTP server. + +To undo the environment changes and shutdown the local HTTP server, +run the ``deactivate_caches`` command. + +Examples +^^^^^^^^ + +For all of the examples below, you first need to create the cache, which +requires an internet connection. + +.. code-block:: bash + + ./tools/offline/init_caches.sh + +Afterwards, you can disconnect or copy the contents of the +``LAMMPS_CACHING_DIR`` folder to an offline system. + +Documentation Build +^^^^^^^^^^^^^^^^^^^ + +The documentation build will create a new virtual environment that +typically first installs dependencies from ``pip``. With the offline +environment loaded, these installations will instead grab the necessary +packages from your local cache. + +.. code-block:: bash + + # if LAMMPS_CACHING_DIR is different from default, make sure to set it first + # export LAMMPS_CACHING_DIR=path/to/folder + source tools/offline/use_caches.sh + cd doc/ + make html + + deactivate_caches + +CMake Build +^^^^^^^^^^^ + +When compiling certain packages with external dependencies, the CMake +build system will download necessary files or sources from the web. For +more flexibility the CMake configuration allows users to specify the URL +of each of these dependencies. What the ``init_caches.sh`` script does +is create a CMake "preset" file, which sets the URLs for all of the known +dependencies and redirects the download to the local cache. + +.. code-block:: bash + + # if LAMMPS_CACHING_DIR is different from default, make sure to set it first + # export LAMMPS_CACHING_DIR=path/to/folder + source tools/offline/use_caches.sh + + mkdir build + cd build + cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake + make -j 8 + + deactivate_caches + +---------- + .. _phonon: phonon tool diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 71c2caa3f0..4983745618 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -24,20 +24,17 @@ Examples Description """"""""""" -The *cosine/periodic* angle style uses the following potential, which -is commonly used in the :doc:`DREIDING ` force field, -particularly for organometallic systems where :math:`n` = 4 might be used +The *cosine/periodic* angle style uses the following potential, which may be +particularly used for organometallic systems where :math:`n` = 4 might be used for an octahedral complex and :math:`n` = 3 might be used for a trigonal center: .. math:: - E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] + E = \frac{2.0}{n^2} * C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type. -See :ref:`(Mayo) ` for a description of the DREIDING force field - The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` @@ -47,10 +44,9 @@ or :doc:`read_restart ` commands: * :math:`B` = 1 or -1 * :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity -Note that the prefactor :math:`C` is specified and not the overall force -constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the -linear geometry. When :math:`B = -1`, it leads to a maximum for the linear -geometry. +Note that the prefactor :math:`C` is specified as coefficient and not the overall force +constant :math:`K = \frac{2 C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the +linear geometry. When :math:`B = -1`, it leads to a maximum for the linear geometry. ---------- @@ -75,9 +71,3 @@ Default none ----------- - -.. _cosine-Mayo: - -**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index 4a6a1debe9..d674eb61d8 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -30,8 +30,11 @@ The *cosine/squared* angle style uses the potential E = K [\cos(\theta) - \cos(\theta_0)]^2 -where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a -prefactor. Note that the usual 1/2 factor is included in :math:`K`. +, which is commonly used in the :doc:`DREIDING ` force field, +where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` +is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. + +See :ref:`(Mayo) ` for a description of the DREIDING force field. The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in @@ -66,3 +69,10 @@ Default """"""" none + +---------- + +.. _cosine-Mayo: + +**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index cad9f5a82f..b8aeae780b 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -69,7 +69,6 @@ parenthesized comments): HAM (keyword is the first text on line) N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters) (blank line) - N 181 FP 0 0 (N, FP parameters) 1 0.0 200.5 2.5 (index, angle, energy, derivative) 2 1.0 198.0 2.5 ... diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index a4e4ec1500..c142fb6519 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -80,7 +80,7 @@ LAMMPS commands require a map, even for atomic systems, and will generate an error if one does not exist. The *map* keyword thus allows you to force the creation of a map. The *yes* value will create either an *array* or *hash* style map, as explained in the next -paragraph. The *array* and *hash* values create an atom-style or +paragraph. The *array* and *hash* values create an array-style or hash-style map respectively. For an *array*\ -style map, each processor stores a lookup table of diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index a250f44b25..1b5aaccb9a 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -27,7 +27,7 @@ Syntax template-ID = ID of molecule template specified in a separate :doc:`molecule ` command *hybrid* args = list of one or more sub-styles, each with their args -* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* +* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* or *spin/kk* Examples """""""" @@ -88,6 +88,8 @@ quantities. +--------------+-----------------------------------------------------+--------------------------------------+ | *charge* | charge | atomic system with charges | +--------------+-----------------------------------------------------+--------------------------------------+ +| *dielectric* | dipole, area, curvature | system with surface polarization | ++--------------+-----------------------------------------------------+--------------------------------------+ | *dipole* | charge and dipole moment | system with dipolar particles | +--------------+-----------------------------------------------------+--------------------------------------+ | *dpd* | internal temperature and internal energies | DPD particles | @@ -166,6 +168,17 @@ a point particle. If it is an ellipsoid, it also stores a shape vector with the 3 diameters of the ellipsoid and a quaternion 4-vector with its orientation. +For the *dielectric* style, each particle can be either a physical +particle (e.g. an ion), or an interface particle representing a boundary +element. For physical particles, the per-particle properties are +the same as atom_style full. For interface particles, in addition to +these properties, each particle also has an area, a normal unit vector, +a mean local curvature, the mean and difference of the dielectric constants +of two sides of the interface, and the local dielectric constant at the +boundary element. The distinction between the physical and interface +particles is only meaningful when :doc:`fix polarize ` +commands are applied to the interface particles. + For the *dipole* style, a point dipole is defined for each point particle. Note that if you wish the particles to be finite-size spheres as in a Stockmayer potential for a dipolar fluid, so that the diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 07ea82eeba..5d42fabb21 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -257,7 +257,7 @@ factor, similar to how the :doc:`fix balance shift ` command operates. The *dimstr* argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, +an "x" or "y" or "z". Each character can appear zero or one time, since there is no advantage to balancing on a dimension more than once. You should normally only list dimensions where you expect there to be a density variation in the particles. @@ -285,7 +285,7 @@ plane gets closer to the target value. After the balanced plane positions are determined, if any pair of adjacent planes are closer together than the neighbor skin distance -(as specified by the :doc`neigh_modify ` command), then +(as specified by the :doc:`neigh_modify ` command), then the plane positions are shifted to separate them by at least this amount. This is to prevent particles being lost when dynamics are run with processor sub-domains that are too narrow in one or more diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 864c544fed..27b370c941 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -11,13 +11,17 @@ Syntax comm_modify keyword value ... * zero or more keyword/value pairs may be appended -* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel* +* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel* .. parsed-literal:: - *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances + *mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances *cutoff* value = Rcut (distance units) = communicate atoms from this far away - *cutoff/multi* type value + *cutoff/multi* collection value + collection = atom collection or collection range (supports asterisk notation) + value = Rcut (distance units) = communicate atoms for selected types from this far away + *reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style + *cutoff/multi/old* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away *group* value = group-ID = only communicate atoms in the group @@ -28,9 +32,9 @@ Examples .. code-block:: LAMMPS - comm_modify mode multi + comm_modify mode multi reduce/multi comm_modify mode multi group solvent - comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 + comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes comm_modify mode single cutoff 5.0 vel yes comm_modify cutoff/multi * 0.0 @@ -62,12 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor cutoff across all atom type pairs. For many systems this is an efficient algorithm, but for systems with -widely varying cutoffs for different type pairs, the *multi* mode can -be faster. In this case, each atom type is assigned its own distance +widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can +be faster. In *multi*, each atom is assigned to a collection which should +correspond to a set of atoms with similar interaction cutoffs. +In this case, each atom collection is assigned its own distance cutoff for communication purposes, and fewer atoms will be -communicated. See the :doc:`neighbor multi ` command for a -neighbor list construction option that may also be beneficial for -simulations of this kind. +communicated. in *multi/old*, a similar technique is used but atoms +are grouped by atom type. See the :doc:`neighbor multi ` and +:doc:`neighbor multi/old ` commands for +neighbor list construction options that may also be beneficial for +simulations of this kind. The *multi* communication mode is only compatible +with the *multi* neighbor style. The *multi/old* communication mode is comparable +with both the *multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance for communication mode *single*\ , which is the distance from the borders @@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the communication cutoff used. The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to -communication mode *multi* instead. Since in this case the communication -cutoffs are determined per atom type, a type specifier is needed and -cutoff for one or multiple types can be extended. Also ranges of types -using the usual asterisk notation can be given. For granular pair styles, -the default cutoff is set to the sum of the current maximum atomic radii -for each type. +communication mode *multi* instead. Since the communication cutoffs are +determined per atom collections, a collection specifier is needed and +cutoff for one or multiple collections can be extended. Also ranges of +collections using the usual asterisk notation can be given. Collections +are indexed from 1 to N where N is the total number of collections. +Note that the arguments for *cutoff/multi* are parsed right before each +simulation to account for potential changes in the number of +collections. Custom cutoffs are preserved between runs but if +collections are redefined, one may want to re-specify the communication +cutoffs. For granular pair styles,the default cutoff is set to the sum +of the current maximum atomic radii for each collection. The +*cutoff/multi/old* option is similar to *cutoff/multi* except it +operates on atom types as opposed to collections. + +The *reduce/multi* option applies to *multi* and sets the communication +cutoff for a particle equal to the maximum interaction distance between particles +in the same collection. This reduces the number of +ghost atoms that need to be communicated. This method is only compatible with the +*multi* neighbor style and requires a half neighbor list and Newton on. +See the :doc:`neighbor multi ` command for more information. These are simulation scenarios in which it may be useful or even necessary to set a ghost cutoff > neighbor cutoff: @@ -123,7 +147,7 @@ ghost cutoff should be set. In the last scenario, a :doc:`fix ` or :doc:`compute ` or :doc:`pairwise potential ` needs to calculate with ghost atoms beyond the normal pairwise cutoff for some computation it -performs (e.g. locate neighbors of ghost atoms in a multibody pair +performs (e.g. locate neighbors of ghost atoms in a manybody pair potential). Setting the ghost cutoff appropriately can insure it will find the needed atoms. diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index 2ec20ac220..75affe7ce6 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -59,6 +59,7 @@ Commands lattice log mass + mdi_engine message min_modify min_spin @@ -77,6 +78,7 @@ Commands pair_style pair_write partition + plugin prd print processors diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 4da3e4ebe6..afe54a69be 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -193,11 +193,13 @@ The individual style names on the :doc:`Commands compute ` doc * :doc:`dihedral ` - energy of each dihedral sub-style * :doc:`dihedral/local ` - angle of each dihedral * :doc:`dilatation/atom ` - Peridynamic dilatation for each atom +* :doc:`dipole ` - dipole vector and total dipole * :doc:`dipole/chunk ` - dipole vector and total dipole for each chunk * :doc:`displace/atom ` - displacement of each atom * :doc:`dpd ` - * :doc:`dpd/atom ` - * :doc:`edpd/temp/atom ` - per-atom temperature for each eDPD particle in a group +* :doc:`efield/atom ` - * :doc:`entropy/atom ` - pair entropy fingerprint of each atom * :doc:`erotate/asphere ` - rotational energy of aspherical particles * :doc:`erotate/rigid ` - rotational energy of rigid bodies diff --git a/doc/src/compute_dipole.rst b/doc/src/compute_dipole.rst new file mode 100644 index 0000000000..c0e17f27d3 --- /dev/null +++ b/doc/src/compute_dipole.rst @@ -0,0 +1,72 @@ +.. index:: compute dipole + +compute dipole command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID dipole charge-correction + +* ID, group-ID are documented in :doc:`compute ` command +* dipole = style name of this compute command +* charge-correction = *mass* or *geometry*\ , use COM or geometric center for charged chunk correction (optional) + +Examples +"""""""" + +.. code-block:: LAMMPS + + compute 1 fluid dipole + compute dw water dipole geometry + +Description +""""""""""" + +Define a computation that calculates the dipole vector and total dipole +for a group of atoms. + +This compute calculates the x,y,z coordinates of the dipole vector +and the total dipole moment for the atoms in the compute group. +This includes all effects due to atoms passing through periodic boundaries. +For a group with a net charge the resulting dipole is made position independent +by subtracting the position vector of the center of mass or geometric center +times the net charge from the computed dipole vector. Both per-atom charges +and per-atom dipole moments, if present, contribute to the computed dipole. + +.. note:: + + The coordinates of an atom contribute to the dipole in "unwrapped" + form, by using the image flags associated with each atom. See the + :doc:`dump custom ` command for a discussion of "unwrapped" + coordinates. See the Atoms section of the :doc:`read_data + ` command for a discussion of image flags and how they are + set for each atom. You can reset the image flags (e.g. to 0) before + invoking this compute by using the :doc:`set image ` command. + +Output info +""""""""""" + +This compute calculations a global scalar containing the magnitude of +the computed dipole moment and a global vector of length 3 with the +dipole vector. See the :doc:`Howto output ` doc page for +an overview of LAMMPS output options. + +The computed values are "intensive". The array values will be in +dipole units, i.e. charge units times distance :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute dipole/chunk ` + +Default +""""""" + +Using the center of mass is the default setting for the net charge correction. diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index d1bc5de4c9..4207d3d180 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -29,37 +29,41 @@ Description Define a computation that calculates the dipole vector and total dipole for multiple chunks of atoms. -In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` and :doc:`Howto chunk ` -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute +chunk/atom ` command, which assigns each atom to a +single chunk (or no chunk). The ID for this command is specified as +chunkID. For example, a single chunk could be the atoms in a molecule +or atoms in a spatial bin. See the :doc:`compute chunk/atom +` and :doc:`Howto chunk ` doc pages for +details of how chunks can be defined and examples of how they can be +used to measure properties of a system. -This compute calculates the x,y,z coordinates of the dipole vector -and the total dipole moment for each chunk, which includes all effects -due to atoms passing through periodic boundaries. For chunks with a net +This compute calculates the x,y,z coordinates of the dipole vector and +the total dipole moment for each chunk, which includes all effects due +to atoms passing through periodic boundaries. For chunks with a net charge the resulting dipole is made position independent by subtracting the position vector of the center of mass or geometric center times the -net charge from the computed dipole vector. +net charge from the computed dipole vector. Both per-atom charges and +per-atom dipole moments, if present, contribute to the computed dipole. Note that only atoms in the specified group contribute to the calculation. The :doc:`compute chunk/atom ` command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. +defines its own group; atoms will have a chunk ID = 0 if they are not in +that group, signifying they are not assigned to a chunk, and will thus +also not contribute to this calculation. You can specify the "all" +group for this command if you simply want to include atoms with non-zero +chunk IDs. .. note:: - The coordinates of an atom contribute to the chunk's - dipole in "unwrapped" form, by using the image flags - associated with each atom. See the :doc:`dump custom ` command - for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read_data ` command for a discussion of image flags + The coordinates of an atom contribute to the chunk's dipole in + "unwrapped" form, by using the image flags associated with each atom. + See the :doc:`dump custom ` command for a discussion of + "unwrapped" coordinates. See the Atoms section of the + :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags - (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + (e.g. to 0) before invoking this compute by using the :doc:`set image + ` command. The simplest way to output the results of the compute com/chunk calculation to a file is to use the :doc:`fix ave/time ` @@ -75,11 +79,12 @@ Output info """"""""""" This compute calculates a global array where the number of rows = the -number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = -4 for the x,y,z dipole vector components and the total dipole of each +number of chunks *Nchunk* as calculated by the specified :doc:`compute +chunk/atom ` command. The number of columns = 4 for +the x,y,z dipole vector components and the total dipole of each chunk. These values can be accessed by any command that uses global -array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output -options. +array values from a compute as input. See the :doc:`Howto output +` doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in dipole units, i.e. charge units times distance :doc:`units `. @@ -91,9 +96,11 @@ Restrictions Related commands """""""""""""""" -:doc:`compute com/chunk ` +:doc:`compute com/chunk `, +:doc:`compute dipole ` Default """"""" -none +Using the center of mass is the default setting for the net charge correction. + diff --git a/doc/src/compute_efield_atom.rst b/doc/src/compute_efield_atom.rst new file mode 100644 index 0000000000..1e87ad2556 --- /dev/null +++ b/doc/src/compute_efield_atom.rst @@ -0,0 +1,67 @@ +.. index:: compute efield/atom + +compute efield/atom command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID efield/atom + +* ID, group-ID are documented in :doc:`compute ` command +* efield/atom = style name of this compute command + +Examples +"""""""" + +.. code-block:: LAMMPS + + compute 1 all efield/atom + compute 1 all efield/atom pair yes kspace no + +Description +""""""""""" + +Define a computation that calculates the electric field at each atom in a group. +The compute should only enabled with pair and kspace styles that are provided +by the USER-DIELECTRIC package because only these styles compute the per-atom +electric field at every time step. + +The electric field is a 3-component vector. The value of the electric field +components will be 0.0 for atoms not in the specified compute group. + +---------- + +The keyword/value option pairs are used in the following ways. + +For the *pair* and *kspace* keywords, the real-space and reciprocal-space +contributions to the electric field can be turned off and on. + + +Output info +""""""""""" + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +the :doc:`Howto output ` doc page for an overview of +LAMMPS output options. + +The per-atom vector values will be in electric field :doc:`units `. + +Restrictions +"""""""""""" +This compute is part of the USER-DIELECTRIC package. It is only enabled if +LAMMPS was built with that package. + +Related commands +"""""""""""""""" + +:doc:`dump custom ` + +Default +""""""" + +The option defaults are pair = yes and kspace = yes. + diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index 279148a55d..ef908acfc0 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -48,6 +48,8 @@ Examples compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes compute 1 all fep 300 atom charge 2 v_delta +Example input scripts available: examples/USER/fep + Description """"""""""" diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index f69f70daba..3c98208261 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -46,13 +46,14 @@ system volume (or area in 2d). The second term is the virial, equal to -dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body, many-body, and long-range interactions, where :math:`r_i` and :math:`f_i` are the position and force vector of atom *i*, and the black -dot indicates a dot product. When periodic boundary conditions are -used, N' necessarily includes periodic image (ghost) atoms outside the -central box, and the position and force vectors of ghost atoms are thus -included in the summation. When periodic boundary conditions are not -used, N' = N = the number of atoms in the system. :doc:`Fixes ` -that impose constraints (e.g. the :doc:`fix shake ` command) -also contribute to the virial term. +dot indicates a dot product. This is computed in parallel for each +sub-domain and then summed over all parallel processes. Thus N' +necessarily includes atoms from neighboring sub-domains (so-called ghost +atoms) and the position and force vectors of ghost atoms are thus +included in the summation. Only when running in serial and without +periodic boundary conditions is N' = N = the number of atoms in the +system. :doc:`Fixes ` that impose constraints (e.g. the :doc:`fix +shake ` command) may also contribute to the virial term. A symmetric pressure tensor, stored as a 6-element vector, is also calculated by this compute. The 6 components of the vector are diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 418f2e1e5d..7e0f5f6555 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -20,6 +20,8 @@ Examples compute TDRUDE all temp/drude +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index bf3cf4902a..4301824b40 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -113,7 +113,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`quadratic ` - dihedral with quadratic term in angle * :doc:`spherical ` - dihedral which includes angle terms to avoid singularities * :doc:`table ` - tabulated dihedral -* :doc:`table/cut ` - tabulated dihedral with analytic cutoff +* :doc:`table/cut ` - tabulated dihedral with analytic cutoff ---------- diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index ff3e61baee..a456fecebd 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -1,19 +1,24 @@ .. index:: dihedral_style table .. index:: dihedral_style table/omp +.. index:: dihedral_style table/cut dihedral_style table command ============================ Accelerator Variants: *table/omp* +dihedral_style table/cut command +================================ + Syntax """""" .. code-block:: LAMMPS - dihedral_style table style Ntable + dihedral_style style interpolation Ntable -* style = *linear* or *spline* = method of interpolation +* style = *table* or *table/cut* +* interpolation = *linear* or *spline* = method of interpolation * Ntable = size of the internal lookup table Examples @@ -26,13 +31,21 @@ Examples dihedral_coeff 1 file.table DIH_TABLE1 dihedral_coeff 2 file.table DIH_TABLE2 + dihedral_style table/cut spline 400 + dihedral_style table/cut linear 1000 + dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1 + dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 + Description """"""""""" -The *table* dihedral style creates interpolation tables of length -*Ntable* from dihedral potential and derivative values listed in a -file(s) as a function of the dihedral angle "phi". The files are read -by the :doc:`dihedral_coeff ` command. +The *table* and *table/cut* dihedral styles create interpolation tables +of length *Ntable* from dihedral potential and derivative values listed +in a file(s) as a function of the dihedral angle "phi". The files are +read by the :doc:`dihedral_coeff ` command. For +dihedral style *table/cut* additionally an analytic cutoff that is +quadratic in the bond-angle (theta) is applied in order to regularize +the dihedral interaction. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and derivative values at each of @@ -51,16 +64,53 @@ interpolated table. For a given dihedral angle (phi), the appropriate coefficients are chosen from this list, and a cubic polynomial is used to compute the energy and the derivative at this angle. -The following coefficients must be defined for each dihedral type via -the :doc:`dihedral_coeff ` command as in the example -above. +For dihedral style *table* the following coefficients must be defined +for each dihedral type via the :doc:`dihedral_coeff ` +command as in the example above. * filename * keyword -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. +The filename specifies a file containing tabulated energy and derivative +values. The keyword specifies which section of the file to read. The +format of this file is the same for both dihedral styles and described +below. + +For dihedral style *table/cut* the following coefficients must be +defined for each dihedral type via the :doc:`dihedral_coeff +` command as in the example above. + +* style (aat) +* cutoff prefactor +* cutoff angle1 +* cutoff angle2 +* filename +* keyword + +The cutoff dihedral style uses a tabulated dihedral interaction with a +cutoff function: + +.. math:: + + f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ + f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 + +The cutoff specifies an prefactor to the cutoff function. While this +value would ordinarily equal 1 there may be situations where the value +should change. + +The cutoff :math:`\theta_1` specifies the angle (in degrees) below which +the dihedral interaction is unmodified, i.e. the cutoff function is 1. + +The cutoff function is applied between :math:`\theta_1` and +:math:`\theta_2`, which is the angle at which the cutoff function drops +to zero. The value of zero effectively "turns off" the dihedral +interaction. + +The filename specifies a file containing tabulated energy and derivative +values. The keyword specifies which section of the file to read. The +format of this file is the same for both dihedral styles and described +below. ---------- @@ -182,18 +232,19 @@ that matches the specified keyword. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -This dihedral style writes the settings for the "dihedral_style table" -command to :doc:`binary restart files `, so a dihedral_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, +These dihedral styles write the settings for the "dihedral_style table" +or "dihedral_style table/cut" command to :doc:`binary restart files +`, so a dihedral_style command does not need to specified in an +input script that reads a restart file. However, the coefficient +information loaded from the table file(s) is not stored in the restart +file, since it is tabulated in the potential files. Thus, suitable dihedral_coeff commands do need to be specified in the restart input -script. +script after reading the restart file. Restrictions """""""""""" -This dihedral style can only be used if LAMMPS was built with the +These dihedral styles can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst deleted file mode 100644 index a29844da19..0000000000 --- a/doc/src/dihedral_table_cut.rst +++ /dev/null @@ -1,229 +0,0 @@ -.. index:: dihedral_style table/cut - -dihedral_style table/cut command -================================ - -Syntax -"""""" - -.. code-block:: LAMMPS - - dihedral_style table/cut style Ntable - -* style = *linear* or *spline* = method of interpolation -* Ntable = size of the internal lookup table - -Examples -"""""""" - -.. code-block:: LAMMPS - - dihedral_style table/cut spline 400 - dihedral_style table/cut linear 1000 - dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1 - dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 - -Description -""""""""""" - -The *table/cut* dihedral style creates interpolation tables of length -*Ntable* from dihedral potential and derivative values listed in a -file(s) as a function of the dihedral angle "phi". In addition, an -analytic cutoff that is quadratic in the bond-angle (theta) is applied -in order to regularize the dihedral interaction. The dihedral table -files are read by the :doc:`dihedral_coeff ` command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -*Ntable* dihedral angles. During a simulation, these tables are used -to interpolate energy and force values on individual atoms as -needed. The interpolation is done in one of 2 styles: *linear* or -*spline*\ . - -For the *linear* style, the dihedral angle (phi) is used to find 2 -surrounding table values from which an energy or its derivative is -computed by linear interpolation. - -For the *spline* style, cubic spline coefficients are computed and -stored at each of the *Ntable* evenly-spaced values in the -interpolated table. For a given dihedral angle (phi), the appropriate -coefficients are chosen from this list, and a cubic polynomial is used -to compute the energy and the derivative at this angle. - -The following coefficients must be defined for each dihedral type via -the :doc:`dihedral_coeff ` command as in the example -above. - -* style (aat) -* cutoff prefactor -* cutoff angle1 -* cutoff angle2 -* filename -* keyword - -The cutoff dihedral style uses a tabulated dihedral interaction with a -cutoff function: - -.. math:: - - f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ - f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 - -The cutoff specifies an prefactor to the cutoff function. While this value -would ordinarily equal 1 there may be situations where the value should change. - -The cutoff :math:`\theta_1` specifies the angle (in degrees) below which the dihedral -interaction is unmodified, i.e. the cutoff function is 1. - -The cutoff function is applied between :math:`\theta_1` and :math:`\theta_2`, which is -the angle at which the cutoff function drops to zero. The value of zero effectively -"turns off" the dihedral interaction. - -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. - ----------- - -The format of a tabulated file is as follows (without the -parenthesized comments). It can begin with one or more comment -or blank lines. - -.. parsed-literal:: - - # Table of the potential and its negative derivative - - DIH_TABLE1 (keyword is the first text on line) - N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F) - (blank line) - 1 -168.0 -1.40351172223 0.0423346818422 - 2 -156.0 -1.70447981034 0.00811786522531 - 3 -144.0 -1.62956100432 -0.0184129719987 - ... - 30 180.0 -0.707106781187 0.0719306095245 - - # Example 2: table of the potential. Forces omitted - - DIH_TABLE2 - N 30 NOF CHECKU testU.dat CHECKF testF.dat - - 1 -168.0 -1.40351172223 - 2 -156.0 -1.70447981034 - 3 -144.0 -1.62956100432 - ... - 30 180.0 -0.707106781187 - -A section begins with a non-blank line whose first character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -:doc:`dihedral_coeff ` command. The next line lists (in -any order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -Following a blank line, the next N lines list the tabulated values. On -each line, the first value is the index from 1 to N, the second value is -the angle value, the third value is the energy (in energy units), and -the fourth is -dE/d(phi) also in energy units). The third term is the -energy of the 4-atom configuration for the specified angle. The fourth -term (when present) is the negative derivative of the energy with -respect to the angle (in degrees, or radians depending on whether the -user selected DEGREES or RADIANS). Thus the units of the last term -are still energy, not force. The dihedral angle values must increase -from one line to the next. - -Dihedral table splines are cyclic. There is no discontinuity at 180 -degrees (or at any other angle). Although in the examples above, the -angles range from -180 to 180 degrees, in general, the first angle in -the list can have any value (positive, zero, or negative). However -the *range* of angles represented in the table must be *strictly* less -than 360 degrees (2pi radians) to avoid angle overlap. (You may not -supply entries in the table for both 180 and -180, for example.) If -the user's table covers only a narrow range of dihedral angles, -strange numerical behavior can occur in the large remaining gap. - -**Parameters:** - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the :doc:`dihedral_style table ` command. -Let *Ntable* is the number of table entries requested dihedral_style -command, and let *Nfile* be the parameter following "N" in the -tabulated file ("30" in the sparse example above). What LAMMPS does -is a preliminary interpolation by creating splines using the *Nfile* -tabulated values as nodal points. It uses these to interpolate as -needed to generate energy and derivative values at *Ntable* different -points (which are evenly spaced over a 360 degree range, even if the -angles in the file are not). The resulting tables of length *Ntable* -are then used as described above, when computing energy and force for -individual dihedral angles and their atoms. This means that if you -want the interpolation tables of length *Ntable* to match exactly what -is in the tabulated file (with effectively nopreliminary -interpolation), you should set *Ntable* = *Nfile*\ . To insure the -nodal points in the user's file are aligned with the interpolated -table entries, the angles in the table should be integer multiples of -360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your -choice of angle units). - -The optional "NOF" keyword allows the user to omit the forces -(negative energy derivatives) from the table file (normally located in -the fourth column). In their place, forces will be calculated -automatically by differentiating the potential energy function -indicated by the third column of the table (using either linear or -spline interpolation). - -The optional "DEGREES" keyword allows the user to specify angles in -degrees instead of radians (default). - -The optional "RADIANS" keyword allows the user to specify angles in -radians instead of degrees. (Note: This changes the way the forces -are scaled in the fourth column of the data file.) - -The optional "CHECKU" keyword is followed by a filename. This allows -the user to save all of the *Ntable* different entries in the -interpolated energy table to a file to make sure that the interpolated -function agrees with the user's expectations. (Note: You can -temporarily increase the *Ntable* parameter to a high value for this -purpose. "\ *Ntable*\ " is explained above.) - -The optional "CHECKF" keyword is analogous to the "CHECKU" keyword. -It is followed by a filename, and it allows the user to check the -interpolated force table. This option is available even if the user -selected the "NOF" option. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds one -that matches the specified keyword. - -Restart, fix_modify, output, run start/stop, minimize info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -This dihedral style writes the settings for the "dihedral_style table/cut" -command to :doc:`binary restart files `, so a dihedral_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -dihedral_coeff commands do need to be specified in the restart input -script. - -Restrictions -"""""""""""" - -This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc -page for more info. - -Related commands -"""""""""""""""" - -:doc:`dihedral_coeff `, :doc:`dihedral_style table ` - -Default -""""""" - -none - -.. _dihedralcut-Salerno: - -**(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018). diff --git a/doc/src/dump.rst b/doc/src/dump.rst index c94d9a8007..a5f11a792a 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -349,7 +349,7 @@ the box size stored with the snapshot. The *xtc* style writes XTC files, a compressed trajectory format used by the GROMACS molecular dynamics package, and described -`here `_. +`here `_. The precision used in XTC files can be adjusted via the :doc:`dump_modify ` command. The default value of 1000 means that coordinates are stored to 1/1000 nanometer accuracy. XTC diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 753cce703c..07f00c4030 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -308,9 +308,9 @@ performed with dump style *xtc*\ . ---------- -The *format* keyword can be used to change the default numeric format -output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and -*xyz* styles, and their MPIIO variants. Only the *line* or *none* +The *format* keyword can be used to change the default numeric format output +by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and +*xyz* styles, and their MPIIO variants. Only the *line* or *none* options can be used with the *atom* and *xyz* styles. All the specified format strings are C-style formats, e.g. as used by @@ -362,7 +362,7 @@ settings, reverting all values to their default format. compute 1 all property/local batom1 batom2 dump 1 all local 100 tmp.bonds index c_1[1] c_1[2] - dump_modify 1 format "%d %0.0f %0.0f" + dump_modify 1 format line "%d %0.0f %0.0f" will output the two atom IDs for atoms in each bond as integers. If the dump_modify command were omitted, they would appear as diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 2e516faa4e..b4ac1e5e45 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -182,6 +182,9 @@ accelerated styles exist. * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`aveforce ` - add an averaged force to each atom * :doc:`balance ` - perform dynamic load-balancing +* :doc:`brownian ` - overdamped translational brownian motion +* :doc:`brownian/asphere ` - overdamped translational and rotational brownian motion for ellipsoids +* :doc:`brownian/sphere ` - overdamped translational and rotational brownian motion for spheres * :doc:`bocs ` - NPT style time integration with pressure correction * :doc:`bond/break ` - break bonds on the fly * :doc:`bond/create ` - create bonds on the fly @@ -189,6 +192,7 @@ accelerated styles exist. * :doc:`bond/react ` - apply topology changes to model reactions * :doc:`bond/swap ` - Monte Carlo bond swapping * :doc:`box/relax ` - relax box size during energy minimization +* :doc:`charge/regulation ` - Monte Carlo sampling of charge regulation * :doc:`client/md ` - MD client for client/server simulations * :doc:`cmap ` - enables CMAP cross-terms of the CHARMM force field * :doc:`colvars ` - interface to the collective variables "Colvars" library @@ -240,6 +244,7 @@ accelerated styles exist. * :doc:`lb/viscous ` - * :doc:`lineforce ` - constrain atoms to move in a line * :doc:`manifoldforce ` - restrain atoms to a manifold during minimization +* :doc:`mdi/engine ` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI) * :doc:`meso/move ` - move mesoscopic SPH/SDPD particles in a prescribed fashion * :doc:`momentum ` - zero the linear and/or angular momentum of a group of atoms * :doc:`momentum/chunk ` - zero the linear and/or angular momentum of a chunk of atoms @@ -300,6 +305,9 @@ accelerated styles exist. * :doc:`planeforce ` - constrain atoms to move in a plane * :doc:`plumed ` - wrapper on PLUMED free energy library * :doc:`poems ` - constrain clusters of atoms to move as coupled rigid bodies +* :doc:`polarize/bem/gmres ` - +* :doc:`polarize/bem/icc ` - +* :doc:`polarize/functional ` - * :doc:`pour ` - pour new atoms/molecules into a granular simulation domain * :doc:`precession/spin ` - * :doc:`press/berendsen ` - pressure control by Berendsen barostat diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index b45ac80429..81a34ab75e 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -56,6 +56,9 @@ Examples fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes fix 1 all adapt/fep 10 atom diameter 1 v_size + +Example input scripts available: examples/USER/fep + Description """"""""""" diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index d2dbaa320a..ce7fcd1fca 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -307,7 +307,9 @@ atoms in the chunk. The averaged output value for the chunk on the average over atoms across the entire *Nfreq* timescale. For the *density/number* and *density/mass* values, the volume (bin volume or system volume) used in the final normalization will be the volume at -the final *Nfreq* timestep. +the final *Nfreq* timestep. For the *temp* values, degrees of freedom and +kinetic energy are summed separately across the entire *Nfreq* timescale, and +the output value is calculated by dividing those two sums. If the *norm* setting is *sample*\ , the chunk value is summed over atoms for each sample, as is the count, and an "average sample value" diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index d50112ac48..3a2857f383 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -138,8 +138,8 @@ vector or columns of the array had been listed one by one. E.g. these .. code-block:: LAMMPS compute myCOM all com/chunk - fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector - fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector + fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector + fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector If the fix ave/histo/weight command is used, exactly two values must be specified. If the values are vectors, they must be the same diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 1875ab744f..8bab8ebefc 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -216,7 +216,7 @@ above. It changes the positions of cutting planes between processors in an iterative fashion, seeking to reduce the imbalance factor. The *dimstr* argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, +an "x" or "y" or "z". Each character can appear zero or one time, since there is no advantage to balancing on a dimension more than once. You should normally only list dimensions where you expect there to be a density variation in the particles. diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 5291aff81b..c421185d87 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -17,7 +17,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command. * bond/react = style name of this fix command * the common keyword/values may be appended directly after 'bond/react' -* this applies to all reaction specifications (below) +* common keywords apply to all reaction specifications * common_keyword = *stabilization* or *reset_mol_ids* .. parsed-literal:: @@ -328,8 +328,8 @@ keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose handedness should be enforced. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, there are -five types of constraints available, as discussed below: 'distance', -'angle', 'dihedral', 'arrhenius', and 'rmsd'. +six types of constraints available, as discussed below: 'distance', +'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'. A sample map file is given below: @@ -500,6 +500,45 @@ example, the molecule fragment could consist of only the backbone atoms of a polymer chain. This constraint can be used to enforce a specific relative position and orientation between reacting molecules. +The constraint of type 'custom' has the following syntax: + +.. parsed-literal:: + + custom *varstring* + +where 'custom' is the required keyword, and *varstring* is a +variable expression. The expression must be a valid equal-style +variable formula that can be read by the :doc:`variable ` command, +after any special reaction functions are evaluated. If the resulting +expression is zero, the reaction is prevented from occurring; +otherwise, it is permitted to occur. There are two special reaction +functions available, 'rxnsum' and 'rxnave'. These functions operate +over the atoms in a given reaction site, and have one mandatory +argument and one optional argument. The mandatory argument is the +identifier for an atom-style variable. The second, optional argument +is the name of a molecule fragment in the pre-reaction template, and +can be used to operate over a subset of atoms in the reaction site. +The 'rxnsum' function sums the atom-style variable over the reaction +site, while the 'rxnave' returns the average value. For example, a +constraint on the total potential energy of atoms involved in the +reaction can be imposed as follows: + +.. code-block:: LAMMPS + + compute 1 all pe/atom # in LAMMPS input script + variable my_pe atom c_1 # in LAMMPS input script + +.. code-block:: LAMMPS + + custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file + +The above example prevents the reaction from occurring unless the +total potential energy of the reaction site is above 100. The variable +expression can be interpreted as the probability of the reaction +occurring by using an inequality and the 'random(x,y,z)' function +available as an equal-style variable input, similar to the 'arrhenius' +constraint above. + By default, all constraints must be satisfied for the reaction to occur. In other words, constraints are evaluated as a series of logical values using the logical AND operator "&&". More complex logic diff --git a/doc/src/fix_brownian.rst b/doc/src/fix_brownian.rst new file mode 100644 index 0000000000..d032346617 --- /dev/null +++ b/doc/src/fix_brownian.rst @@ -0,0 +1,216 @@ +.. index:: fix brownian +.. index:: fix brownian/sphere +.. index:: fix brownian/asphere + +fix brownian command +=========================== + +fix brownian/sphere command +=========================== + +fix brownian/sphere command +=========================== + + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style_name temp seed keyword args + +* ID, group-ID are documented in :doc:`fix ` command +* style_name = *brownian* or *brownian/sphere* or *brownian/asphere* +* temp = temperature +* seed = random number generator seed +* one or more keyword/value pairs may be appended +* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t* + + .. parsed-literal:: + + *rng* value = *uniform* or *gaussian* or *none* + *uniform* = use uniform random number generator + *gaussian* = use gaussian random number generator + *none* = turn off noise + *dipole* value = *mux* and *muy* and *muz* for *brownian/asphere* + *mux*, *muy*, and *muz* = update orientation of dipole having direction (*mux*,*muy*,*muz*) in body frame of rigid body + *gamma_r_eigen* values = *gr1* and *gr2* and *gr3* for *brownian/asphere* + *gr1*, *gr2*, and *gr3* = diagonal entries of body frame rotational friction tensor + *gamma_r* values = *gr* for *brownian/sphere* + *gr* = magnitude of the (isotropic) rotational friction tensor + *gamma_t_eigen* values = *gt1* and *gt2* and *gt3* for *brownian/asphere* + *gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor + *gamma_t* values = *gt* for *brownian* and *brownian/sphere* + *gt* = magnitude of the (isotropic) translational friction tensor + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all brownian 1.0 12908410 gamma_t 1.0 + fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian + fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0 + fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none + fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian + fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0 + + +Description +""""""""""" + +Perform Brownian Dynamics time integration to update position, velocity, +dipole orientation (for spheres) and quaternion orientation (for +ellipsoids, with optional dipole update as well) of all particles in the +fix group in each timestep. Brownian Dynamics uses Newton's laws of +motion in the limit that inertial forces are negligible compared to +viscous forces. The stochastic equation of motion for the center of mass +positions is + +.. math:: + + d\mathbf{r} = \mathbf{\gamma}_t^{-1}\mathbf{F}dt+\sqrt{2k_BT}\mathbf{\gamma}_t^{-1/2}d\mathbf{W}_t, + +in the lab-frame (i.e. :math:`\mathbf{\gamma}_t` is not diagonal, but +only depends on orientation and so the noise is still additive). + +The rotational motion for the spherical and ellipsoidal particles is not +as simple an expression, but is chosen to replicate the Boltzmann +distribution for the case of conservative torques (see :ref:`(Ilie) +` or :ref:`(Delong) `). + +For the style *brownian*, only the positions of the particles are +updated. This is therefore suitable for point particle simulations. + +For the style *brownian/sphere*, the positions of the particles are +updated, and a dipole slaved to the spherical orientation is also +updated. This style therefore requires the hybrid atom style +:doc:`atom_style dipole ` and :doc:`atom_style sphere +`. + +For the style *brownian/asphere*, the center of mass positions and the +quaternions of ellipsoidal particles are updated. This fix style is +suitable for equations of motion where the rotational and translational +friction tensors can be diagonalized in a certain (body) reference frame. + + +--------- + +.. note:: + + This integrator does not by default assume a relationship between the + rotational and translational friction tensors, though such a relationship + should exist in the case of no-slip boundary conditions between the particles and + the surrounding (implicit) solvent. E.g. in the case of spherical particles, + the condition :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly + accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where + :math:`\sigma` is the spherical diameter). A similar (though more complex) + relationship holds for ellipsoids and rod-like particles. + +--------- + +.. note:: + + Temperature computation using the :doc:`compute temp ` + will not correctly compute temperature of these overdamped dynamics + since we are explicitly neglecting inertial effects. + Furthermore, this time integrator does not add the stochastic terms or + viscous terms to the force and/or torques. Rather, they are just added + in to the equations of motion to update the degrees of freedom. + +--------- + + +If the *rng* keyword is used with the *uniform* value, then the noise +is generated from a uniform distribution (see +:ref:`(Dunweg) ` for why this works). This is the same method +of noise generation as used in :doc:`fix_langevin `. + +If the *rng* keyword is used with the *gaussian* value, then the noise +is generated from a gaussian distribution. Typically this added +complexity is unnecessary, and one should be fine using the *uniform* +value for reasons argued in :ref:`(Dunweg) `. + +If the *rng* keyword is used with the *none* value, then the noise +terms are set to zero. + +The *gamma_t* keyword sets the (isotropic) translational viscous damping. +Required for (and only compatible with) *brownian* and *brownian/sphere*. +The units of *gamma_t* are mass/time. + +The *gamma_r* keyword sets the (isotropic) rotational viscous damping. +Required for (and only compatible with) *brownian/sphere*. +The units of *gamma_r* are mass*length**2/time. + +The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of +the rotational and viscous damping tensors (having the same units as +their isotropic counterparts). Required for (and only compatible with) +*brownian/asphere*. For a 2D system, the first two values of *gamma_r_eigen* +must be inf (only rotation in xy plane), and the third value of *gamma_t_eigen* +must be inf (only diffusion in xy plane). + +If the *dipole* keyword is used, then the dipole moments of the particles +are updated as described above. Only compatible with *brownian/asphere* +(as *brownian/sphere* updates dipoles automatically). + +---------- + +.. note:: + For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and + *gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the + *brownian/sphere* style with *gamma_t* = x and *gamma_r* = y. + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. +No global or per-atom quantities are stored +by this fix for access by various :doc:`output commands `. + + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. + +Restrictions +"""""""""""" + +The style *brownian/sphere* fix requires that atoms store torque and angular velocity (omega) +as defined by the :doc:`atom_style sphere ` command. +The style *brownian/asphere* fix requires that atoms store torque and quaternions +as defined by the :doc:`atom_style ellipsoid ` command. +If the *dipole* keyword is used, they must also store a dipole moment +as defined by the :doc:`atom_style dipole ` command. + +This fix is part of the USER-BROWNIAN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` +doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`fix propel/self `, +:doc:`fix langevin `, :doc:`fix nve/sphere `, + +Default +""""""" + +The default for *rng* is *uniform*. The default for the rotational and translational friction +tensors are the identity tensor. + +---------- + +.. _Ilie1: + +**(Ilie)** Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015). + +.. _Delong1: + +**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015) + +.. _Dunweg7: + +**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst new file mode 100644 index 0000000000..06c1d92b79 --- /dev/null +++ b/doc/src/fix_charge_regulation.rst @@ -0,0 +1,276 @@ + +.. index:: fix charge/regulation + +fix charge/regulation command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID charge/regulation cation_type anion_type keyword value(s) + +* ID, group-ID are documented in fix command +* charge/regulation = style name of this fix command +* cation_type = atom type of free cations +* anion_type = atom type of free anions + +* zero or more keyword/value pairs may be appended + + .. parsed-literal:: + + keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves* + *pH* value = pH of the solution (can be specified as an equal-style variable) + *pKa* value = acid dissociation constant + *pKb* value = base dissociation constant + *pIp* value = chemical potential of free cations + *pIm* value = chemical potential of free anions + *pKs* value = solution self-dissociation constant + *acid_type* = atom type of acid groups + *base_type* = atom type of base groups + *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers) + *temp* value = temperature + *tempfixid* value = fix ID of temperature thermostat + *nevery* value = invoke this fix every nevery steps + *nmc* value = number of charge regulation MC moves to attempt every nevery steps + *xrd* value = cutoff distance for acid/base reaction + *seed* value = random # seed (positive integer) + *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0") + *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups. + *onlysalt* values = flag charge_cation charge_anion. + flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion) + charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes) + *pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI) + +Examples +"""""""" +.. code-block:: LAMMPS + + fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT + + fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0 + +Description +""""""""""" + +This fix performs Monte Carlo (MC) sampling of charge regulation and +exchange of ions with a reservoir as discussed in :ref:`(Curk1) ` +and :ref:`(Curk2) `. The implemented method is largely analogous +to the grand-reaction ensemble method in :ref:`(Landsgesell) +`. The implementation is parallelized, compatible with +existing LAMMPS functionalities, and applicable to any system utilizing +discrete, ionizable groups or surface sites. + +Specifically, the fix implements the following three types of MC moves, +which discretely change the charge state of individual particles and +insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons +\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons +\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons +Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. In the former two types of +reactions, Monte Carlo moves alter the charge value of specific atoms +(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a +counterion to preserve the charge neutrality of the system, modeling the +dissociation/association process. The last type of reaction performs +grand canonical MC exchange of ion pairs with a (fictitious) reservoir. + +In our implementation "acid" refers to particles that can attain charge +:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, +whereas the MC exchange of free ions allows any integer charge values of +:math:`{Z^+}` and :math:`{Z^-}`. + +Here we provide several practical examples for modeling charge +regulation effects in solvated systems. An acid ionization reaction +(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be +defined via a single line in the input file + +.. code-block:: LAMMPS + + fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 + +where the fix attempts to charge :math:`\mathrm{A}` (discharge +:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and +insert (delete) a proton (atom type 2). Besides, the fix implements +self-ionization reaction of water :math:`\emptyset \rightleftharpoons +\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly +inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of +both protons and hydroxyl ions is low, resulting in a relatively low +acceptance rate of MC moves. + +A more efficient way is to allow salt ions to participate in ionization +reactions, which can be easily achieved via + +.. code-block:: LAMMPS + + fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 + +where particles of atom type 4 and 5 are the salt cations and anions, +both at chemical potential pI=2.0, see :ref:`(Curk1) ` and +:ref:`(Landsgesell) ` for more details. + + + Similarly, we could have simultaneously added a base ionization reaction + (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) + +.. code-block:: LAMMPS + + fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 + +where the fix will attempt to charge :math:`\mathrm{B}` (discharge +:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and +insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If +neither the acid or the base type is specified, for example, + +.. code-block:: LAMMPS + + fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0 + +the fix simply inserts or deletes an ion pair of a free cation (atom +type 4) and a free anion (atom type 5) as done in a conventional +grand-canonical MC simulation. + + +The fix is compatible with LAMMPS sub-packages such as *molecule* or +*rigid*. That said, the acid and base particles can be part of larger +molecules or rigid bodies. Free ions that are inserted to or deleted +from the system must be defined as single particles (no bonded +interactions allowed) and cannot be part of larger molecules or rigid +bodies. If *molecule* package is used, all inserted ions have a molecule +ID equal to zero. + +Note that LAMMPS implicitly assumes a constant number of particles +(degrees of freedom). Since using this fix alters the total number of +particles during the simulation, any thermostat used by LAMMPS, such as +NVT or Langevin, must use a dynamic calculation of system +temperature. This can be achieved by specifying a dynamic temperature +compute (e.g. dtemp) and using it with the desired thermostat, e.g. a +Langevin thermostat: + +.. code-block:: LAMMPS + + compute dtemp all temp + compute_modify dtemp dynamic yes + fix fT all langevin 1.0 1.0 1.0 123 + fix_modify fT temp dtemp + +The chemical potential units (e.g. pH) are in the standard log10 +representation assuming reference concentration :math:`\rho_0 = +\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit +conversion, the length (in nanometers) of the LAMMPS unit length must be +specified via *lunit_nm* (default is set to the Bjerrum length in water +at room temperature *lunit_nm* = 0.71nm). For example, in the dilute +ideal solution limit, the concentration of free ions will be +:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. + +The temperature used in MC acceptance probability is set by *temp*. This +temperature should be the same as the temperature set by the molecular +dynamics thermostat. For most purposes, it is probably best to use +*tempfixid* keyword which dynamically sets the temperature equal to the +chosen MD thermostat temperature, in the example above we assumed the +thermostat fix-ID is *fT*. The inserted particles attain a random +velocity corresponding to the specified temperature. Using *tempfixid* +overrides any fixed temperature set by *temp*. + +The *xrd* keyword can be used to restrict the inserted/deleted +counterions to a specific radial distance from an acid or base particle +that is currently participating in a reaction. This can be used to +simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* / +2, where *L* is the smallest box dimension, the radial restriction is +automatically turned off and free ion can be inserted or deleted +anywhere in the simulation box. + +If the *tag yes* is used, every inserted atom gets a unique tag ID, +otherwise, the tag of every inserted atom is set to 0. *tag yes* might +cause an integer overflow in very long simulations since the tags are +unique to every particle and thus increase with every successful +particle insertion. + +The *pmcmoves* keyword sets the relative probability of attempting the +three types of MC moves (reactions): acid charging, base charging, and +ion pair exchange. The fix only attempts to perform particle charging +MC moves if *acid_type* or *base_type* is defined. Otherwise fix only +performs free ion insertion/deletion. For example, if *acid_type* is not +defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is +automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33, +the vector would be normalized to [0,0.5,0.5]. + +The *only_salt* option can be used to perform multivalent +grand-canonical ion-exchange moves. If *only_salt yes* is used, no +charge exchange is performed, only ion insertion/deletion (*pmcmoves* is +set to [0,0,1]), but ions can be multivalent. In the example above, an +MC move would consist of three ion insertion/deletion to preserve the +charge neutrality of the system. + +The *group* keyword can be used to add inserted particles to a specific +group-ID. All inserted particles are automatically added to group *all*. + + +Output +"""""" + +This fix computes a global vector of length 8, which can be accessed by +various output commands. The vector values are the following global +quantities: + +* 1 = cumulative MC attempts +* 2 = cumulative MC successes +* 3 = current # of neutral acid atoms +* 4 = current # of -1 charged acid atoms +* 5 = current # of neutral base atoms +* 6 = current # of +1 charged base atoms +* 7 = current # of free cations +* 8 = current # of free anions + + +Restrictions +"""""""""""" + +This fix is part of the MC package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` doc page for more info. + +The :doc:`atom_style `, used must contain the charge +property, for example, the style could be *charge* or *full*. Only +usable for 3D simulations. Atoms specified as free ions cannot be part +of rigid bodies or molecules and cannot have bonding interactions. The +scheme is limited to integer charges, any atoms with non-integer charges +will not be considered by the fix. + +All interaction potentials used must be continuous, otherwise the MD +integration and the particle exchange MC moves do not correspond to the +same equilibrium ensemble. For example, if an lj/cut pair style is used, +the LJ potential must be shifted so that it vanishes at the cutoff. This +can be easily achieved using the :doc:`pair_modify ` +command, i.e., by using: *pair_modify shift yes*. + +.. note:: + + Region restrictions are not yet implemented. + +Related commands +"""""""""""""""" + +:doc:`fix gcmc `, +:doc:`fix atom/swap ` + +Default +""""""" + +pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; +acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = +100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = +[1/3, 1/3, 1/3], group-ID = all + +---------- + +.. _Curk1: + +**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021). + +.. _Curk2: + +**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021) + +.. _Landsgesell: + +**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020). diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index 892fd4ab41..e6e8d0c627 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -127,6 +127,11 @@ the :doc:`run ` command. The forces due to this fix are imposed during an energy minimization, invoked by the :doc:`minimize ` command. +The :doc:`fix_modify ` *respa* option is supported by this +fix. This allows to set at which level of the :doc:`r-RESPA +` integrator the fix is adding its forces. Default is the +outermost level. + .. note:: If you want the potential energy associated with the CMAP terms diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index 385a847749..a879f1594b 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -22,6 +22,8 @@ Examples fix 1 all drude 1 1 0 1 0 2 2 2 fix 1 all drude C C N C N D D D +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 792b041576..28d57306ea 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -25,6 +25,8 @@ Examples fix 3 all drude/transform/direct fix 1 all drude/transform/inverse +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index e57f1889e1..85702b909f 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -92,6 +92,11 @@ The :doc:`thermo_modify ` *press* option is supported by this fix to add the rescaled kinetic pressure as part of :doc:`thermodynamic output `. +This fix computes a global scalar which can be accessed by various +:doc:`output commands `. The scalar is the effective +temperature :math:`T_{eff}`. The scalar value calculated by this +fix is "intensive". + Restrictions """""""""""" diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 964132518d..06f068bb7d 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -115,6 +115,18 @@ The version with "bondmax" will just run somewhat faster, due to less overhead in computing bond lengths and not storing them in a separate compute. +A variable can be used to implement a large variety of conditions, +including to stop when a specific file exists. Example: + +.. code-block:: LAMMPS + + variable exit equal is_file(EXIT) + fix 10 all halt 100 v_exit != 0 error soft + +Will stop the current run command when a file ``EXIT`` is created +in the current working directory. The condition can be cleared +by removing the file through the :doc:`shell ` command. + The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "\|\^". In this context, XOR means that if either the attribute or avalue is diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index ad5a876712..c075a56549 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -35,6 +35,8 @@ Examples fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451 fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_mdi_engine.rst b/doc/src/fix_mdi_engine.rst new file mode 100644 index 0000000000..76506f3e19 --- /dev/null +++ b/doc/src/fix_mdi_engine.rst @@ -0,0 +1,59 @@ +.. index:: fix mdi/engine + +fix mdi/engine command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID mdi/engine + +* ID, group-ID are documented in :doc:`fix ` command +* mdi/engine = style name of this fix command + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all mdi/engine + +Description +""""""""""" + +This fix is used along with the :doc:`mdi/engine ` command +to enable LAMMPS to use the `MDI Library +`_ to run as +an MDI engine. The fix provides hooks that enable MDI driver codes to +communicate with LAMMPS at various points within a LAMMPS timestep. + +It is not generally necessary to add this fix to a LAMMPS input file, +even when using the :doc:`mdi/engine ` command. If the +:doc:`mdi/engine ` command is executed and this fix is not +present, it will automatically be added and applied as a new fix for +all atoms for the duration of the command. Thus it is only necessary +to add this fix to an input file when you want to modify the group-ID +or the ordering of this fix relative to other fixes in the input script. + +For more information about running LAMMPS as an MDI engine, see the +:doc:`mdi/engine ` command and the :doc:`Howto mdi +` doc page. + +Restrictions +"""""""""""" + +This command is part of the USER-MDI package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`mdi/engine ` + +Default +""""""" + +none diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst new file mode 100644 index 0000000000..2c499fce3c --- /dev/null +++ b/doc/src/fix_polarize.rst @@ -0,0 +1,113 @@ +.. index:: fix polarize/bem/gmres +.. index:: fix polarize/bem/icc +.. index:: fix polarize/functional + +fix polarize/bem/gmres command +============================== + +fix polarize/bem/icc command +============================ + +fix polarize/functional command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style nevery tolerance ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *polarize/bem/gmres* or *polarize/bem/icc* or *polarize/functional* +* Nevery = this fixed is invoked every this many timesteps +* tolerance = the tolerance for the iterative solver to stop + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 2 all polarize/bem/gmres 5 0.0001 + fix 1 interface polarize/bem/icc 1 0.0001 + fix 3 all polarize/functional 1 0.001 + +Description +""""""""""" + +These fixes compute induced charges at the interface between two +impermeable media with different dielectric constants. + +There are some example scripts for using this fix +with LAMMPS in the examples/USER/dielectric directory. + +---------- + +For fix *polarize/bem/gmres* and fix *polarize/bem/icc* the induced +charges of the atoms in the specified group, which are the vertices on +the interface, are computed using the equation: + +..math:: + + \sigma_b(\mathbf{s}) = \dfrac{1 - \bar{\epsilon}}{\bar{\epsilon}} + \sigma_f(\mathbf{s}) - \epsilon_0 \dfrac{\Delta \epsilon}{\bar{\epsilon}} + \mathbf{E}(\mathbf{s}) \cdot \mathbf{n}(\mathbf{s}) + +* :math:`\sigma_b` is the induced charge density at the interface vertex :math:`\mathbf{s}`. +* :math:`\bar{\epsilon}` is the mean dielectric constant at the interface vertex: :math:`\bar{\epsilon} = (\epsilon_1 + \epsilon_2)/2`. +* :math:`\Delta \epsilon` is the dielectric constant difference at the interface vertex: :math:`\Delta \epsilon = \epsilon_1 - \epsilon_2` +* :math:`\sigma_f` is the free charge density at the interface vertex +* :math:`\mathbf{E}(\mathbf{s})` is the electrical field at the vertex +* :math:`\mathbf{n}(\mathbf{s})` is the unit normal vector at the vertex pointing from medium with :math:`\epsilon_2` to that with :math:`\epsilon_1` + +Fix *polarize/bem/gmres* employs the Generalized Minimum Residual (GMRES) +as described in :ref:`(Barros) ` to solve :math:`\sigma_b`. + +Fix *polarize/bem/icc* employs the successive over-relaxation algorithm +as described in :ref:`(Tyagi) ` to solve :math:`\sigma_b`. + +Fix *polarize/functional* ... + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +... + +Restrictions +"""""""""""" + +These fixes are part of the USER-DIELECTRIC package. It is only enabled +if LAMMPS was built with that package, which requires that also the +KSPACE package is installed. See the :doc:`Build package +` doc page for more info. + + +Related commands +"""""""""""""""" + +:doc:`compute efield/atom ` + +Default +""""""" + +None. + +---------- + +.. _Barros: + +**(Barros)** Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014) + +.. _Tyagi: + +**(Tyagi)** Tyagi, Suzen, Sega, Barbosa, Kantorovich, Holm, J Chem Phys, 132, 154112 (2010) + +.. _Jadhao: + +**(Jadhao)** Jadhao, Solis, Olvera de la Cruz, J Chem Phys, 138, 054119 (2013) + +.. _NguyenTD: + +**(NguyenTD)** Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Comput Phys Commun 241, 80-19 (2019) + diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 5e818374a0..6a563bc32f 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -12,7 +12,7 @@ Syntax * ID, group are documented in :doc:`fix ` command * precession/spin = style name of this fix command -* style = *zeeman* or *anisotropy* or *cubic* +* style = *zeeman* or *anisotropy* or *cubic* or *stt* .. parsed-literal:: @@ -22,12 +22,12 @@ Syntax *anisotropy* args = K x y z K = intensity of the magnetic anisotropy (in eV) x y z = vector direction of the anisotropy - - .. parsed-literal:: - *cubic* args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z K1 and K2c = intensity of the magnetic anisotropy (in eV) n1x to n3z = three direction vectors of the cubic anisotropy + *stt* args = J x y z + J = intensity of the spin-transfer torque field + x y z = vector direction of the field Examples """""""" @@ -125,6 +125,11 @@ axis along the :math:`(1 1 1)`-type cube diagonals). :math:`K_2^c > diagonals. See chapter 2 of :ref:`(Skomski) ` for more details on cubic anisotropies. +Style *stt* is used to simulate the interaction between the spins and +a spin-transfer torque. +See equation (7) of :ref:`(Chirac) ` for more details about the +implemented spin-transfer torque term. + In all cases, the choice of :math:`(x y z)` only imposes the vector directions for the forces. Only the direction of the vector is important; its length is ignored (the entered vectors are @@ -132,6 +137,16 @@ normalized). Those styles can be combined within one single command line. +.. note:: + + The norm of all vectors defined with the precession/spin command + have to be non-zero. For example, defining + "fix 1 all precession/spin zeeman 0.1 0.0 0.0 0.0" would result + in an error message. + Since those vector components are used to compute the inverse of the + field (or anisotropy) vector norm, setting a zero-vector would result + in a division by zero. + ---------- Restart, fix_modify, output, run start/stop, minimize info @@ -162,11 +177,6 @@ is only enabled if LAMMPS was built with this package, and if the atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. -The *precession/spin* style can only be declared once. If more than -one precession type (for example combining an anisotropy and a Zeeman -interactions) has to be declared, they have to be chained in the same -command line (as shown in the examples above). - Related commands """""""""""""""" @@ -184,3 +194,9 @@ none **(Skomski)** Skomski, R. (2008). Simple models of magnetism. Oxford University Press. + +.. _Chirac1: + +**(Chirac)** Chirac, Theophile, et al. Ultrafast antiferromagnetic +switching in NiO induced by spin transfer torques. +Physical Review B 102.13 (2020): 134415. diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index 3a1bfb3166..ddc96817f9 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -8,52 +8,121 @@ Syntax .. parsed-literal:: - fix ID group-ID propel/self mode magnitude keyword values ... + fix ID group-ID propel/self mode magnitude keyword values * ID, group-ID are documented in :doc:`fix ` command * propel/self = style name of this fix command -* mode = velocity or quat -* magnitude = magnitude of the active force -* one or more keyword/value pairs may be appended to args -* keyword = *types* +* mode = *dipole* or *velocity* or *quat* +* magnitude = magnitude of self-propulsion force +* zero or one keyword/value pairs may be appended +* keyword = *qvector* + + .. parsed-literal:: + + *qvector* value = direction of force in ellipsoid frame + *sx*, *sy*, *sz* = components of *qvector* - *types* values = one or more atom types Examples """""""" .. code-block:: LAMMPS - fix active_group all propel/self velocity 1.0 - fix constant_velocity all viscous 1.0 - - fix active_group all propel/self quat 1.0 - - fix active all propel/self quat 1.0 types 1 2 4 + fix active all propel/self dipole 40.0 + fix active all propel/self velocity 10.0 + fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0 Description """"""""""" -Adds a force of a constant magnitude to each atom in the group. The nature in -which the force is added depends on the mode. +Add a force to each atom in the group due to a self-propulsion force. The +force is given by -For *mode* = *velocity*, the active force acts along the velocity vector of -each atom. This can be interpreted as a velocity-dependent friction, -such as proposed by :ref:`(Erdmann) `. +.. math:: -For *mode* = *quat* the force is applied along the axis obtained -by rotating the x-axis along the atom's quaternion. In other words, the -force is along the x-axis in the atom's body frame. This mode requires -all atoms in the group to have a quaternion, so atom_style should -either be ellipsoid or body. In combination with Langevin thermostat -for translation and rotation in the overdamped regime, the quaternion -mode corresponds to the active Brownian particle model introduced by -:ref:`(Henkes) `, :ref:`(Bialke) ` and :ref:`(Fily) -`. + F_i = f_P e_i -By default, this fix is applied to all atoms in the group. You can -override this behavior by specifying the atom types the fix should work -on through the *types* keyword. +where *i* is the particle the force is being applied to, :math:`f_P` +is the magnitude of the force, and :math:`e_i` is the vector direction +of the force. The specification of :math:`e_i` is based on which of the +three keywords (*dipole* or *velocity* or *quat*) one selects. + +For mode *dipole*, :math:`e_i` is just equal to +the dipole vectors of the atoms in the group. Therefore, if the dipoles +are not unit vectors, the :math:`e_i` will not be unit vectors. + +.. note:: + + If another command changes the magnitude of the dipole, this force will + change accordingly (since :math:`|e_i|` will change, which is physically + equivalent to re-scaling :math:`f_P` while keeping :math:`|e_i|` constant), + and no warning will be provided by LAMMPS. This is almost never what you + want, so ensure you are not changing dipole magnitudes with another LAMMPS + fix or pair style. Furthermore, self-propulsion forces (almost) always + set :math:`e_i` to be a unit vector for all times, so it's best to set + all the dipole magnitudes to 1.0 unless you have a good reason not to + (see the :doc:`set ` command on how to do this). + +For mode *velocity*, :math:`e_i` points in the direction +of the current velocity (a unit-vector). This can be interpreted as a +velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) `. + +For mode *quat*, :math:`e_i` points in the direction of a unit +vector, oriented in the coordinate frame of the ellipsoidal particles, +which defaults to point along the x-direction. This default behavior +can be changed by via the *quatvec* keyword. + +The optional *quatvec* keyword specifies the direction of self-propulsion +via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are +defined within the coordinate frame of the atom's +ellipsoid. For instance, for an ellipsoid with long axis along +its x-direction, if one wanted the self-propulsion force to also +be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal +to zero. This keyword may only be specified for mode *quat*. + +.. note:: + + In using keyword *quatvec*, the three arguments *sx*, + *sy*, and *sz* will be automatically normalized to components + of a unit vector internally to avoid users having to explicitly + do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i` + will always be of unit length. + + +Along with adding a force contribution, this fix can also +contribute to the virial (pressure) of the system, defined as +:math:`f_P \sum_i /(d V)`, where :math:`r_i` is the +*unwrapped* coordinate of particle i in the case of periodic +boundary conditions. See :ref:`(Winkler) ` for a +discussion of this active pressure contribution. + +For modes *dipole* and *quat*, this fix is by default +included in pressure computations. + +For mode *velocity*, this fix is by default not included +in pressure computations. + + +.. note:: + + In contrast to equilibrium systems, pressure of active systems + in general depends on the geometry of the container. + The active pressure contribution as calculated in this fix + is only valid for certain boundary conditions (spherical + walls, rectangular walls, or periodic boundary conditions). + For other geometries, the pressure must be measured via + explicit calculation of the force per unit area on a wall, + and so one must not calculate it using this fix. + (Use :doc:`fix_modify ` as described below + to turn off the virial contribution of this fix). Again, + see :ref:`(Winkler) ` for discussion of why this + is the case. + + Furthermore, when dealing with active systems, the temperature + is no longer well defined. Therefore, one should ensure that + the *virial* flag is used in the + :doc:`compute pressure ` command (turning + off temperature contributions). ---------- @@ -62,40 +131,48 @@ Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to :doc:`binary restart files `. -This fix is not imposed during minimization. +The :doc:`fix_modify ` *virial* option is supported by this +fix to add the contribution due to the added forces on atoms to the +system's virial as part of :doc:`thermodynamic output `. +The default is *virial yes* for keywords *dipole* and *quat*. The +default is *virial no* for keyword *velocity*. + + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + Restrictions """""""""""" -In quat mode, this fix makes use of per-atom quaternions to take -into account the fact that the orientation can rotate and hence the -direction of the active force can change. The quat mode -of this fix only works with atom_style ellipsoid. +With keyword *dipole*, this fix only works when the DIPOLE package is enabled. +See the :doc:`Build package ` doc page for more info. + +This fix is part of the USER-BROWNIAN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` +doc page for more info. + Related commands """""""""""""""" -:doc:`fix setforce `, :doc:`fix addforce ` - -.. _Erdmann: - -**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, -Eur. Phys. J. B 15, 105-113, 2000. - -.. _Henkes: - -**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011. - -.. _Bialke: - -**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012. - -.. _Fily: - -**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012. +:doc:`fix efield ` , :doc:`fix setforce `, +:doc:`fix addforce ` Default """"""" -types +none +---------- + + +.. _Erdmann1: + +**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, +Eur. Phys. J. B 15, 105-113, 2000. + + +.. _Winkler1: + +**(Winkler)** Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015). diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 56fde059e8..c655076ce8 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -56,27 +56,28 @@ Examples Description """"""""""" -Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) ` (also known -as the matrix inversion method) and in :ref:`(Rick and Stuart) ` (also -known as the extended Lagrangian method) based on the -electronegativity equilization principle. +Perform the charge equilibration (QEq) method as described in +:ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) +` (also known as the matrix inversion method) and in +:ref:`(Rick and Stuart) ` (also known as the extended Lagrangian +method) based on the electronegativity equilization principle. These fixes can be used with any :doc:`pair style ` in LAMMPS, so long as per-atom charges are defined. The most typical use-case is in conjunction with a :doc:`pair style ` that performs charge equilibration periodically (e.g. every timestep), such -as the ReaxFF or Streitz-Mintmire potential. -But these fixes can also be used with -potentials that normally assume per-atom charges are fixed, e.g. a -:doc:`Buckingham ` or :doc:`LJ/Coulombic ` potential. +as the ReaxFF or Streitz-Mintmire potential. But these fixes can also +be used with potentials that normally assume per-atom charges are fixed, +e.g. a :doc:`Buckingham ` or :doc:`LJ/Coulombic ` +potential. -Because the charge equilibration calculation is effectively -independent of the pair style, these fixes can also be used to perform -a one-time assignment of charges to atoms. For example, you could -define the QEq fix, perform a zero-timestep run via the :doc:`run ` -command without any pair style defined which would set per-atom -charges (based on the current atom configuration), then remove the fix -via the :doc:`unfix ` command before performing further dynamics. +Because the charge equilibration calculation is effectively independent +of the pair style, these fixes can also be used to perform a one-time +assignment of charges to atoms. For example, you could define the QEq +fix, perform a zero-timestep run via the :doc:`run ` command +without any pair style defined which would set per-atom charges (based +on the current atom configuration), then remove the fix via the +:doc:`unfix ` command before performing further dynamics. .. note:: @@ -87,11 +88,14 @@ via the :doc:`unfix ` command before performing further dynamics. .. note:: - The :doc:`fix qeq/comb ` command must still be used - to perform charge equilibration with the :doc:`COMB potential `. The :doc:`fix qeq/reax ` - command can be used to perform charge equilibration with the :doc:`ReaxFF force field `, although fix qeq/shielded yields the - same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance* - are the same. Eventually the fix qeq/reax command will be deprecated. + The :doc:`fix qeq/comb ` command must still be used to + perform charge equilibration with the :doc:`COMB potential + `. The :doc:`fix qeq/reax ` command can be + used to perform charge equilibration with the :doc:`ReaxFF force + field `, although fix qeq/shielded yields the same + results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance* + are the same. Eventually the fix qeq/reax command will be + deprecated. The QEq method minimizes the electrostatic energy of the system (or equalizes the derivative of energy with respect to charge of all the @@ -134,55 +138,57 @@ usually a good number. The *qeq/shielded* style describes partial charges on atoms also as point charges, but uses a shielded Coulomb potential to describe the interaction between a pair of charged particles. Interaction through -the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field ` paper. The shielding accounts for charge overlap +the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force +field ` paper. The shielding accounts for charge overlap between charged particles at small separation. This style is the same -as :doc:`fix qeq/reax `, and can be used with :doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and *gamma* -parameters from the *qfile* file are used. When using the string -*reax/c* as filename, these parameters are extracted directly from -an active *reax/c* pair style. This style solves partial -charges on atoms via the matrix inversion method. A tolerance of -1.0e-6 is usually a good number. +as :doc:`fix qeq/reax `, and can be used with +:doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and +*gamma* parameters from the *qfile* file are used. When using the string +*reax/c* as filename, these parameters are extracted directly from an +active *reax/c* pair style. This style solves partial charges on atoms +via the matrix inversion method. A tolerance of 1.0e-6 is usually a +good number. The *qeq/slater* style describes partial charges on atoms as spherical charge densities centered around atoms via the Slater 1\ *s* orbital, so -that the interaction between a pair of charged particles is the -product of two Slater 1\ *s* orbitals. The expression for the Slater -1\ *s* orbital is given under equation (6) of the -:ref:`Streitz-Mintmire ` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and -*qcore* parameters from the *qfile* file are used. When using the string +that the interaction between a pair of charged particles is the product +of two Slater 1\ *s* orbitals. The expression for the Slater 1\ *s* +orbital is given under equation (6) of the :ref:`Streitz-Mintmire +` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore* +parameters from the *qfile* file are used. When using the string *coul/streitz* as filename, these parameters are extracted directly from -an active *coul/streitz* pair style. This style solves -partial charges on atoms via the matrix inversion method. A tolerance -of 1.0e-6 is usually a good number. Keyword *alpha* can be used to -change the Slater type orbital exponent. +an active *coul/streitz* pair style. This style solves partial charges +on atoms via the matrix inversion method. A tolerance of 1.0e-6 is +usually a good number. Keyword *alpha* can be used to change the Slater +type orbital exponent. The *qeq/dynamic* style describes partial charges on atoms as point -charges that interact through 1/r, but the extended Lagrangian method -is used to solve partial charges on atoms. Only the *chi* and *eta* +charges that interact through 1/r, but the extended Lagrangian method is +used to solve partial charges on atoms. Only the *chi* and *eta* parameters from the *qfile* file are used. Note that Coulomb -catastrophe can occur if repulsion between the pair of charged -particles is too weak. A tolerance of 1.0e-3 is usually a good -number. Keyword *qdamp* can be used to change the damping factor, while -keyword *qstep* can be used to change the time step size. +catastrophe can occur if repulsion between the pair of charged particles +is too weak. A tolerance of 1.0e-3 is usually a good number. Keyword +*qdamp* can be used to change the damping factor, while keyword *qstep* +can be used to change the time step size. -The :ref:`\ *qeq/fire*\ ` style describes the same charge model and charge -solver as the *qeq/dynamic* style, but employs a FIRE minimization -algorithm to solve for equilibrium charges. -Keyword *qdamp* can be used to change the damping factor, while -keyword *qstep* can be used to change the time step size. +The :ref:`\ *qeq/fire*\ ` style describes the same charge model +and charge solver as the *qeq/dynamic* style, but employs a FIRE +minimization algorithm to solve for equilibrium charges. Keyword +*qdamp* can be used to change the damping factor, while keyword *qstep* +can be used to change the time step size. Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe different charge models, whereas the matrix inversion method and the extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are different solvers. -Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe -charges as point charges that interact through 1/r relationship, but -solve partial charges on atoms using different solvers. These three -styles should yield comparable results if -the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the -same. Style *qeq/point* is typically faster, *qeq/dynamic* scales -better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . +Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all +describe charges as point charges that interact through 1/r +relationship, but solve partial charges on atoms using different +solvers. These three styles should yield comparable results if the QEq +parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same. +Style *qeq/point* is typically faster, *qeq/dynamic* scales better on +larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . .. note:: @@ -200,9 +206,11 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about these fixes is written to :doc:`binary restart files `. No global scalar or vector or per-atom -quantities are stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used -with the *start/stop* keywords of the :doc:`run ` command. +No information about these fixes is written to :doc:`binary restart +files `. No global scalar or vector or per-atom quantities are +stored by these fixes for access by various :doc:`output commands +`. No parameter of these fixes can be used with the +*start/stop* keywords of the :doc:`run ` command. Thexe fixes are invoked during :doc:`energy minimization `. @@ -210,7 +218,8 @@ Restrictions """""""""""" These fixes are part of the QEQ package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index f3a10df321..4ff260f575 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -238,7 +238,7 @@ warning is generated. .. note:: - The fix srd command can be used with simulations the size and/or + The fix srd command can be used with simulations where the size and/or shape of the simulation box changes. This can be due to non-periodic boundary conditions or the use of fixes such as the :doc:`fix deform ` or :doc:`fix wall/srd ` commands to impose a shear on an SRD fluid or an interaction with an external diff --git a/doc/src/fix_tgnh_drude.rst b/doc/src/fix_tgnh_drude.rst index 1854655a82..a6e9832833 100644 --- a/doc/src/fix_tgnh_drude.rst +++ b/doc/src/fix_tgnh_drude.rst @@ -62,6 +62,8 @@ Examples fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0 fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 1eefc4aeae..57bec679e4 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -29,6 +29,7 @@ Syntax gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) xmu = static yield criterion (unitless value between 0.0 and 1.0e4) dampflag = 0 or 1 if tangential damping force is excluded or included + optional keyword = *limit_damping*, limit damping to prevent attractive interaction .. parsed-literal:: @@ -95,7 +96,8 @@ Specifically, delta = radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact = RiRj/Ri+Rj is set to the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 9ed5bb7bcc..35995fedf0 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -65,7 +65,7 @@ non-granular particles and simpler wall geometries, respectively. Here are snapshots of example models using this command. Corresponding input scripts can be found in examples/granregion. Movies of these -simulations are `here on the Movies page `_ +simulations are `here on the Movies page `_ of the LAMMPS web site. .. |wallgran1| image:: img/gran_funnel.png @@ -181,7 +181,8 @@ radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact is just the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 59f5b7f27c..01ad15a08e 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -16,6 +16,7 @@ .. index:: kspace_style pppm/disp/tip4p .. index:: kspace_style pppm/disp/tip4p/omp .. index:: kspace_style pppm/disp/intel +.. index:: kspace_style pppm/dielectric .. index:: kspace_style pppm/cg/omp .. index:: kspace_style pppm/stagger .. index:: kspace_style pppm/tip4p @@ -24,6 +25,7 @@ .. index:: kspace_style msm/omp .. index:: kspace_style msm/cg .. index:: kspace_style msm/cg/omp +.. index:: kspace_style msm/dielectric .. index:: kspace_style scafacos kspace_style command @@ -36,7 +38,7 @@ Syntax kspace_style style value -* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos* +* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos* .. parsed-literal:: @@ -87,6 +89,8 @@ Syntax accuracy = desired relative error in forces *pppm/stagger* value = accuracy accuracy = desired relative error in forces + *pppm/dielectric* value = accuracy + accuracy = desired relative error in forces *msm* value = accuracy accuracy = desired relative error in forces *msm/cg* value = accuracy (smallq) @@ -97,6 +101,8 @@ Syntax *msm/cg/omp* value = accuracy (smallq) accuracy = desired relative error in forces smallq = cutoff for charges to be considered (optional) (charge units) + *msm/dielectric* value = accuracy + accuracy = desired relative error in forces *scafacos* values = method accuracy method = fmm or p2nfft or p3m or ewald or direct accuracy = desired relative error in forces @@ -278,7 +284,7 @@ pressure simulation with MSM will cause the code to run slower. ---------- The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library `_ which provides a variety of solver -methods which can be used with LAMMPS. The paper by :ref:`(Who) ` +methods which can be used with LAMMPS. The paper by :ref:`(Sutman) ` gives an overview of ScaFaCoS. ScaFaCoS was developed by a consortium of German research facilities @@ -435,8 +441,14 @@ non-orthogonal (triclinic symmetry) simulation boxes. However, triclinic simulation cells may not yet be supported by all suffix versions of these styles. -All of the kspace styles are part of the KSPACE package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +Most of the base kspace styles are part of the KSPACE package. They are +only enabled if LAMMPS was built with that package. See the :doc:`Build +package ` doc page for more info. + +The *msm/dielectric* and *pppm/dielectric* kspace styles are part of the +USER-DIELECTRIC package. They are only enabled if LAMMPS was built with +that package **and** the KSPACE package. See the :doc:`Build package +` doc page for more info. For MSM, a simulation must be 3d and one can use any combination of periodic, non-periodic, or shrink-wrapped boundaries (specified using @@ -550,7 +562,7 @@ Illinois at Urbana-Champaign, (2006). **(Cerda)** Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008) -.. _Who2012: +.. _Sutmann2014: -**(Who)** Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 -(2012). +**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems. + In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014. diff --git a/doc/src/mdi_engine.rst b/doc/src/mdi_engine.rst new file mode 100644 index 0000000000..b39999606d --- /dev/null +++ b/doc/src/mdi_engine.rst @@ -0,0 +1,88 @@ +.. index:: mdi/engine + +mdi_engine command +================== + +Syntax +"""""" + +.. parsed-literal:: + + mdi_engine + +Description +""""""""""" + +This command is used to have LAMMPS act as a server with another +client code to effectively couple the two codes together in +client/server mode. + +More specifically, this command causes LAMMPS to begin using the `MDI +Library `_ +to run as an MDI engine (server), responding to commands made by an +external MDI driver code (client). See the :doc:`Howto mdi +` doc page for more information about how LAMMPS can work +as both an MDI driver or engine. + +General information about launching codes that communicate using the +MDI Library can be found in the `corresponding page +`_ +of the MDI Library's documentation. + +---------- + +This command should typically be used in an input script after LAMMPS +has setup the system it is going to model in collaboration with the +driver code. Depending on how the driver code tells the LAMMPS engine +to exit, other commands can be executed after this command, but +typically it should be used at the end of the LAMMPS input script. + +To act as a MD-based MDI engine, this is the list of MDI commands from +a driver code which LAMMPS currently recognizes. See more details +about these commands in the `MDI library documentation +`_ +.. NOTE: Taylor - is this the best link for this info? Can we flesh this +.. out with the full list of supported commands? Maybe the distinction +.. of what "node" the commands refer to is not needed in this table? + +.. list-table:: + :widths: 20 80 + :header-rows: 1 + + * - Command name + - Action + * - >NATOMS + - Driver sends the number of atoms in the system + * - FORCES + - Driver sends 3*N double-precision atom forces + * - ` doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`fix mdi/engine ` + +Default +""""""" + +None diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 2618953dd7..25c2c2ac77 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -14,7 +14,7 @@ Syntax .. parsed-literal:: - keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* + keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval* *delay* value = N N = delay building until this many steps since last build *every* value = M @@ -47,6 +47,12 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) + *collection/type* values = N arg1 ... argN + N = number of custom collections + arg = N separate lists of types (see below) + *collection/interval* values = N arg1 ... argN + N = number of custom collections + arg = N separate cutoffs for intervals (see below) Examples """""""" @@ -58,6 +64,8 @@ Examples neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 neigh_modify exclude molecule/intra rigid + neigh_modify collection/type 2 1*2,5 3*4 + neigh_modify collection/interval 2 1.0 10.0 Description """"""""""" @@ -188,8 +196,9 @@ atom can have. The *binsize* option allows you to specify what size of bins will be used in neighbor list construction to sort and find neighboring atoms. By default, for :doc:`neighbor style bin `, LAMMPS uses bins -that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, the bins are 1/2 the size of the minimum pair -cutoff. Typically these are good values for minimizing the time for +that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, +the bins are 1/2 the size of the collection interaction cutoff. +Typically these are good values for minimizing the time for neighbor list construction. This setting overrides the default. If you make it too big, there is little overhead due to looping over bins, but more atoms are checked. If you make it too @@ -197,6 +206,31 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. +The *collection/type* option allows you to define collections of atom +types, used by the *multi* neighbor mode. By grouping atom types with +similar physical size or interaction cutoff lengths, one may be able +to improve performance by reducing +overhead. You must first specify the number of collections N to be +defined followed by N lists of types. Each list consists of a series of type +ranges separated by commas. The range can be specified as a +single numeric value, or a wildcard asterisk can be used to specify a range +of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For +example, if M = the number of atom types, then an asterisk with no numeric +values means all types from 1 to M. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to M +(inclusive). A middle asterisk means all types from m to n (inclusive). +Note that all atom types must be included in exactly one of the N collections. + +The *collection/interval* option provides a similar capability. This +command allows a user to define collections by specifying a series of +cutoff intervals. LAMMPS will automatically sort atoms into these +intervals based on their type-dependent cutoffs or their finite size. +You must first specify the number of collections N to be defined +followed by N values representing the upper cutoff of each interval. +This command is particularly useful for granular pair styles where the +interaction distance of particles depends on their radius and may not +depend on their atom type. + Restrictions """""""""""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 98ee0d0b6a..1b10ec8998 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -11,7 +11,7 @@ Syntax neighbor skin style * skin = extra distance beyond force cutoff (distance units) -* style = *bin* or *nsq* or *multi* +* style = *bin* or *nsq* or *multi* or *multi/old* Examples """""""" @@ -55,14 +55,31 @@ For the *bin* style, the bin size is set to 1/2 of the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but -other type pairs have a much shorter cutoff. For style *multi* the -bin size is set to 1/2 of the shortest cutoff distance and multiple -sets of bins are defined to search over for different atom types. +other type pairs have a much shorter cutoff. The *multi* style uses +different sized bins for collections of different sized particles, where +"size" may mean the physical size of the particle or its cutoff +distance for interacting with other particles. Different +sets of bins are then used to construct the neighbor lists as as further +described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. -See the :doc:`comm_modify mode multi ` command for a -communication option that may also be beneficial for simulations of -this kind. +may be much faster. By default, each atom type defines a separate +collection of particles. For systems where two or more atom types +have the same size (either physical size or cutoff distance), the +definition of collections can be customized, which can result in less +overhead and faster performance. See the :doc:`neigh_modify ` +command for how to define custom collections. Whether the collection +definition is customized or not, also see the +:doc:`comm_modify mode multi ` command for communication +options that further improve performance in a manner consistent with +neighbor style multi. + +An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest +cutoff distance and multiple sets of bins are defined to search over for +different atom types. This algorithm used to be the default *multi* +algorithm in LAMMPS but was found to be significantly slower than the new +approach. For now we are keeping the old option in case there are use cases +where multi/old outperforms the new multi style. + The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are @@ -90,3 +107,9 @@ Default | 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm | 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm | + +---------- + +.. _bytype-Shire: + +**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020). diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 0508bf16ef..f566d41e2c 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -385,7 +385,12 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` setting to be "on" for pair interactions. -The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the +Pair style bop is not compatible with being used as a sub-style with +doc:`hybrid pair styles `. Pair style bop is also not +compatible with :doc:`multi-cutoff neighbor lists ` or +:doc:`multi-cutoff communitcation `. + +The .bop.table potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the BOP potential with any LAMMPS units, but you would need to create your own BOP potential file with coefficients listed in the diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 4def43647f..b8303622aa 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -10,6 +10,8 @@ .. index:: pair_style coul/dsf/gpu .. index:: pair_style coul/dsf/kk .. index:: pair_style coul/dsf/omp +.. index:: pair_style coul/cut/global +.. index:: pair_style coul/cut/global/omp .. index:: pair_style coul/long .. index:: pair_style coul/long/omp .. index:: pair_style coul/long/kk @@ -40,6 +42,11 @@ pair_style coul/dsf command Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp* +pair_style coul/cut/global command +================================== + +Accelerator Variants: *coul/cut/omp* + pair_style coul/long command ============================ @@ -76,8 +83,8 @@ Syntax pair_style coul/cut cutoff pair_style coul/debye kappa cutoff pair_style coul/dsf alpha cutoff + pair_style coul/cut/global cutoff pair_style coul/long cutoff - pair_style coul/long/gpu cutoff pair_style coul/wolf alpha cutoff pair_style coul/streitz cutoff keyword alpha pair_style tip4p/cut otype htype btype atype qdist cutoff @@ -245,6 +252,11 @@ Streitz-Mintmire parameterization for the material being modeled. ---------- +Pair style *coul/cut/global* computes the same Coulombic interactions +as style *coul/cut* except that it allows only a single global cutoff +and thus makes it compatible for use in combination with long-range +coulomb styles in :doc:`hybrid pair styles `. + Styles *coul/long* and *coul/msm* compute the same Coulombic interactions as style *coul/cut* except that an additional damping factor is applied so it can be used in conjunction with the diff --git a/doc/src/pair_coul_tt.rst b/doc/src/pair_coul_tt.rst index 11b4e72a60..b01d46d7ae 100644 --- a/doc/src/pair_coul_tt.rst +++ b/doc/src/pair_coul_tt.rst @@ -29,6 +29,7 @@ Examples pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0 pair_coeff 1 3* coul/tt 4.5 1.0 4 +Example input scripts available: examples/USER/drude Description """"""""""" diff --git a/doc/src/pair_dielectric.rst b/doc/src/pair_dielectric.rst new file mode 100644 index 0000000000..f98cfce976 --- /dev/null +++ b/doc/src/pair_dielectric.rst @@ -0,0 +1,357 @@ +.. index:: pair_style coul/cut/dielectric +.. index:: pair_style coul/long/dielectric +.. index:: pair_style lj/cut/coul/cut/dielectric +.. index:: pair_style lj/cut/coul/cut/dielectric/omp +.. index:: pair_style lj/cut/coul/debye/dielectric +.. index:: pair_style lj/cut/coul/long/dielectric +.. index:: pair_style lj/cut/coul/long/dielectric/omp +.. index:: pair_style lj/cut/coul/msm/dielectric +.. index:: pair_style lj/long/coul/long/dielectric + +pair_style coul/cut/dielectric command +====================================== + +pair_style coul/long/dielectric command +======================================= + +pair_style lj/cut/coul/cut/dielectric command +============================================= + +Accelerator Variants: *lj/cut/coul/cut/dielectric/omp* + +pair_style lj/cut/coul/debye/dielectric command +=============================================== + +pair_style lj/cut/coul/long/dielectric command +============================================== + +Accelerator Variants: *lj/cut/coul/long/dielectric/omp* + +pair_style lj/cut/coul/msm/dielectric command +============================================== + +pair_style lj/long/coul/long/dielectric command +=============================================== + +Syntax +"""""" + +TODO FIX the rest of the file + +.. code-block:: LAMMPS + + pair_style lj/cut/dipole/cut cutoff (cutoff2) + pair_style lj/sf/dipole/sf cutoff (cutoff2) + pair_style lj/cut/dipole/long cutoff (cutoff2) + pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) + +* cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) +* cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) +* flag_lj = *long* or *cut* or *off* + + .. parsed-literal:: + + *long* = use long-range damping on dispersion 1/r\^6 term + *cut* = use a cutoff on dispersion 1/r\^6 term + *off* = omit disperion 1/r\^6 term entirely + +* flag_coul = *long* or *off* + + .. parsed-literal:: + + *long* = use long-range damping on Coulombic 1/r and point-dipole terms + *off* = omit Coulombic and point-dipole terms entirely + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style lj/cut/dipole/cut 10.0 + pair_coeff * * 1.0 1.0 + pair_coeff 2 3 1.0 1.0 2.5 4.0 + + pair_style lj/sf/dipole/sf 9.0 + pair_coeff * * 1.0 1.0 + pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5 + pair_coeff 2 3 1.0 1.0 2.5 4.0 + + pair_style lj/cut/dipole/long 10.0 + pair_coeff * * 1.0 1.0 + pair_coeff 2 3 1.0 1.0 2.5 4.0 + + pair_style lj/long/dipole/long long long 3.5 10.0 + pair_coeff * * 1.0 1.0 + pair_coeff 2 3 1.0 1.0 2.5 4.0 + +Description +""""""""""" + +Style *lj/cut/dipole/cut* computes interactions between pairs of particles +that each have a charge and/or a point dipole moment. In addition to +the usual Lennard-Jones interaction between the particles (Elj) the +charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp) +interactions are computed by these formulas for the energy (E), force +(F), and torque (T) between particles I and J. + +.. math:: + + E_{LJ} = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^6 \right] \\ + E_{qq} = & \frac{q_i q_j}{r} \\ + E_{qp} = & \frac{q}{r^3} (p \bullet \vec{r}) \\ + E_{pp} = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) - + \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r}) \\ + & \\ + F_{qq} = & \frac{q_i q_j}{r^3} \vec{r} \\ + F_{qp} = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5} + (\vec{p} \bullet \vec{r}) \vec{r} \\ + F_{pp} = & \frac{3}{r^5} (\vec{p_i} \bullet \vec{p_j}) \vec{r} - + \frac{15}{r^7} (\vec{p_i} \bullet \vec{r}) + (\vec{p_j} \bullet \vec{r}) \vec{r} + + \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + + (\vec{p_i} \bullet \vec{r}) \vec{p_j} \right] \\ + & \\ + T_{pq} = T_{ij} = & \frac{q_j}{r^3} (\vec{p_i} \times \vec{r}) \\ + T_{qp} = T_{ji} = & - \frac{q_i}{r^3} (\vec{p_j} \times \vec{r}) \\ + T_{pp} = T_{ij} = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) + + \frac{3}{r^5} (\vec{p_j} \bullet \vec{r}) + (\vec{p_i} \times \vec{r}) \\ + T_{pp} = T_{ji} = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) + + \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) + (\vec{p_j} \times \vec{r}) + +where :math:`q_i` and :math:`q_j` are the charges on the two particles, +:math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole moment vectors of +the two particles, r is their separation distance, and the vector r = +Ri - Rj is the separation vector between the two particles. Note that +Eqq and Fqq are simply Coulombic energy and force, Fij = -Fji as +symmetric forces, and Tij != -Tji since the torques do not act +symmetrically. These formulas are discussed in :ref:`(Allen) ` +and in :ref:`(Toukmaji) `. + +Also note, that in the code, all of these terms (except Elj) have a +:math:`C/\epsilon` prefactor, the same as the Coulombic term in the LJ + +Coulombic pair styles discussed :doc:`here `. C is an +energy-conversion constant and epsilon is the dielectric constant +which can be set by the :doc:`dielectric ` command. The +same is true of the equations that follow for other dipole pair +styles. + +Style *lj/sf/dipole/sf* computes "shifted-force" interactions between +pairs of particles that each have a charge and/or a point dipole +moment. In general, a shifted-force potential is a (slightly) modified +potential containing extra terms that make both the energy and its +derivative go to zero at the cutoff distance; this removes +(cutoff-related) problems in energy conservation and any numerical +instability in the equations of motion :ref:`(Allen) `. Shifted-force +interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq), +charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp) +potentials are computed by these formulas for the energy (E), force +(F), and torque (T) between particles I and J: + +.. math:: + + E_{LJ} = & 4\epsilon \left\{ \left[ \left( \frac{\sigma}{r} \right)^{\!12} - + \left( \frac{\sigma}{r} \right)^{\!6} \right] + + \left[ 6\left( \frac{\sigma}{r_c} \right)^{\!12} - + 3\left(\frac{\sigma}{r_c}\right)^{\!6}\right]\left(\frac{r}{r_c}\right)^{\!2} + - 7\left( \frac{\sigma}{r_c} \right)^{\!12} + + 4\left( \frac{\sigma}{r_c} \right)^{\!6}\right\} \\ + E_{qq} = & \frac{q_i q_j}{r}\left(1-\frac{r}{r_c}\right)^{\!2} \\ + E_{pq} = & E_{ji} = -\frac{q}{r^3} \left[ 1 - + 3\left(\frac{r}{r_c}\right)^{\!2} + + 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\ + E_{qp} = & E_{ij} = \frac{q}{r^3} \left[ 1 - + 3\left(\frac{r}{r_c}\right)^{\!2} + + 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\ + E_{pp} = & \left[1-4\left(\frac{r}{r_c}\right)^{\!3} + + 3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3} + (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5} + (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\right] \\ + & \\ + + F_{LJ} = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} - + 24\epsilon \left(\frac{\sigma}{r}\right)^{\!6} \right]\frac{1}{r^2} - + \left[48\epsilon \left(\frac{\sigma}{r_c}\right)^{\!12} - 24\epsilon + \left(\frac{\sigma}{r_c}\right)^{\!6} \right]\frac{1}{r_c^2}\right\}\vec{r}\\ + F_{qq} = & \frac{q_i q_j}{r}\left(\frac{1}{r^2} - + \frac{1}{r_c^2}\right)\vec{r} \\ + F_{pq} = & F_{ij } = -\frac{3q}{r^5} \left[ 1 - + \left(\frac{r}{r_c}\right)^{\!2}\right](\vec{p}\bullet\vec{r})\vec{r} + + \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + + 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ + F_{qp} = & F_{ij} = \frac{3q}{r^5} \left[ 1 - + \left(\frac{r}{r_c}\right)^{\!2}\right] (\vec{p}\bullet\vec{r})\vec{r} - + \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + + 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ + F_{pp} = &\frac{3}{r^5}\Bigg\{\left[1-\left(\frac{r}{r_c}\right)^{\!4}\right] + \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r}) + (\vec{p_j} \bullet \vec{r})\right] \vec{r} + \\ + & \left[1 - + 4\left(\frac{r}{r_c}\right)^{\!3}+3\left(\frac{r}{r_c}\right)^{\!4}\right] + \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r}) + \vec{p_j} -\frac{2}{r^2} (\vec{p_i} \bullet \vec{r}) + (\vec{p_j} \bullet \vec{r})\vec{r}\right] \Bigg\} + +.. math:: + + T_{pq} = T_{ij} = & \frac{q_j}{r^3} \left[ 1 - + 3\left(\frac{r}{r_c}\right)^{\!2} + + 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p_i}\times\vec{r}) \\ + T_{qp} = T_{ji} = & - \frac{q_i}{r^3} \left[ 1 - + 3\left(\frac{r}{r_c}\right)^{\!2} + + 2\left(\frac{r}{r_c}\right)^{\!3} \right] (\vec{p_j}\times\vec{r}) \\ + T_{pp} = T_{ij} = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + + e3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \times \vec{p_j}) + \\ + & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + + 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_j}\bullet\vec{r}) + (\vec{p_i} \times \vec{r}) \\ + T_{pp} = T_{ji} = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + + 3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p_j} \times \vec{p_i}) + \\ + & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + + 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r}) + (\vec{p_j} \times \vec{r}) + +where :math:`\epsilon` and :math:`\sigma` are the standard LJ +parameters, :math:`r_c` is the cutoff, :math:`q_i` and :math:`q_j` are +the charges on the two particles, :math:`\vec{p_i}` and +:math:`\vec{p_j}` are the dipole moment vectors of the two particles, r +is their separation distance, and the vector r = Ri - Rj is the +separation vector between the two particles. Note that Eqq and Fqq are +simply Coulombic energy and force, Fij = -Fji as symmetric forces, and +Tij != -Tji since the torques do not act symmetrically. The +shifted-force formula for the Lennard-Jones potential is reported in +:ref:`(Stoddard) `. The original (non-shifted) formulas for +the electrostatic potentials, forces and torques can be found in +:ref:`(Price) `. The shifted-force electrostatic potentials have +been obtained by applying equation 5.13 of :ref:`(Allen) `. The +formulas for the corresponding forces and torques have been obtained by +applying the 'chain rule' as in appendix C.3 of :ref:`(Allen) `. + +If one cutoff is specified in the pair_style command, it is used for +both the LJ and Coulombic (q,p) terms. If two cutoffs are specified, +they are used as cutoffs for the LJ and Coulombic (q,p) terms +respectively. This pair style also supports an optional *scale* keyword +as part of a pair_coeff statement, where the interactions can be +scaled according to this factor. This scale factor is also made available +for use with fix adapt. + +Style *lj/cut/dipole/long* computes long-range point-dipole +interactions as discussed in :ref:`(Toukmaji) `. Dipole-dipole, +dipole-charge, and charge-charge interactions are all supported, along +with the standard 12/6 Lennard-Jones interactions, which are computed +with a cutoff. A :doc:`kspace_style ` must be defined to +use this pair style. Currently, only :doc:`kspace_style ewald/disp ` support long-range point-dipole +interactions. + +Style *lj/long/dipole/long* also computes point-dipole interactions as +discussed in :ref:`(Toukmaji) `. Long-range dipole-dipole, +dipole-charge, and charge-charge interactions are all supported, along +with the standard 12/6 Lennard-Jones interactions. LJ interactions +can be cutoff or long-ranged. + +For style *lj/long/dipole/long*\ , if *flag_lj* is set to *long*\ , no +cutoff is used on the LJ 1/r\^6 dispersion term. The long-range +portion is calculated by using the :doc:`kspace_style ewald_disp ` command. The specified LJ cutoff then +determines which portion of the LJ interactions are computed directly +by the pair potential versus which part is computed in reciprocal +space via the Kspace style. If *flag_lj* is set to *cut*\ , the LJ +interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag_lj* is set to *off*\ , LJ interactions +are not computed at all. + +If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic or +dipole interactions. The long-range portion is calculated by using +*ewald_disp* of the :doc:`kspace_style ` command. If +*flag_coul* is set to *off*\ , Coulombic and dipole interactions are not +computed at all. + +Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole ` or the :doc:`fix nvt/sphere update dipole ` command to rotate the +dipole moments. The *omega* option on the :doc:`fix langevin ` command can be used to thermostat the +rotational motion. The :doc:`compute temp/sphere ` +command can be used to monitor the temperature, since it includes +rotational degrees of freedom. The :doc:`atom_style hybrid dipole sphere ` command should be used since +it defines the point dipoles and their rotational state. +The magnitude and orientation of the dipole moment for each particle +can be defined by the :doc:`set ` command or in the "Atoms" section +of the data file read in by the :doc:`read_data ` command. + +The following coefficients must be defined for each pair of atoms +types via the :doc:`pair_coeff ` command as in the examples +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands, or by mixing as described below: + +* :math:`\epsilon` (energy units) +* :math:`\sigma` (distance units) +* cutoff1 (distance units) +* cutoff2 (distance units) + +The latter 2 coefficients are optional. If not specified, the global +LJ and Coulombic cutoffs specified in the pair_style command are used. +If only one cutoff is specified, it is used as the cutoff for both LJ +and Coulombic interactions for this type pair. If both coefficients +are specified, they are used as the LJ and Coulombic cutoffs for this +type pair. + +---------- + +.. include:: accel_styles.rst + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distances for this pair style can be mixed. The default +mix value is *geometric*\ . See the "pair_modify" command for details. + +For atom type pairs I,J and I != J, the A, sigma, d1, and d2 +coefficients and cutoff distance for this pair style can be mixed. A +is an energy value mixed like a LJ epsilon. D1 and d2 are distance +values and are mixed like sigma. The default mix value is +*geometric*\ . See the "pair_modify" command for details. + +This pair style does not support the :doc:`pair_modify ` +shift option for the energy of the Lennard-Jones portion of the pair +interaction; such energy goes to zero at the cutoff by construction. + +The :doc:`pair_modify ` table option is not relevant +for this pair style. + +This pair style does not support the :doc:`pair_modify ` +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords. + +Restrictions +"""""""""""" + +The *lj/cut/dipole/cut*\ , *lj/cut/dipole/long*\ , and +*lj/long/dipole/long* styles are part of the DIPOLE package. They are +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. + +The *lj/sf/dipole/sf* style is part of the USER-MISC package. It is +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. + +Using dipole pair styles with *electron* :doc:`units ` is not +currently supported. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff `, :doc:`set `, :doc:`read_data `, +:doc:`fix nve/sphere `, :doc:`fix nvt/sphere ` + +Default +""""""" + +none + diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index d1d84407c4..62cf94786d 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -150,7 +150,7 @@ shifted to be 0.0 at the cutoff distance Rc. The :doc:`pair_modify ` table option is not relevant for these pair styles. -These pair style do not support the :doc:`pair_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst new file mode 100644 index 0000000000..cfc72fe84c --- /dev/null +++ b/doc/src/pair_dpd_ext.rst @@ -0,0 +1,138 @@ +.. index:: pair_style dpd/ext +.. index:: pair_style dpd/ext/tstat + +pair_style dpd/ext command +========================== + +pair_style dpd/ext/tstat command +================================ + +Syntax +"""""" + + +.. code-block:: LAMMPS + + pair_style dpd/ext T cutoff seed + pair_style dpd/ext/tstat Tstart Tstop cutoff seed + +* T = temperature (temperature units) +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +* cutoff = global cutoff for DPD interactions (distance units) +* seed = random # seed (positive integer) + +Examples +"""""""" + + +.. code-block:: LAMMPS + + pair_style dpd/ext 1.0 2.5 34387 + pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2 + pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2 + + pair_style dpd/ext/tstat 1.0 1.0 2.5 34387 + pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2 + pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2 + +Description +""""""""""" + +The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. + +Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. + +For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum +of 3 terms + +.. math:: + + \mathbf{f} = & f^C + f^D + f^R \qquad \qquad r < r_c \\ + f^C = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\ + f^D = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij} - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\ + f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ + w(r) = & 1 - r/r_c \\ + +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. + +For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. + +For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. + +For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. + +For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. + +For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: + +* A (force units) +* :math:`\gamma_{\perp}` (force/velocity units) +* :math:`\gamma_{\parallel}` (force/velocity units) +* :math:`s_{\perp}` (unitless) +* :math:`s_{\parallel}` (unitless) +* :math:`r_c` (distance units) + +The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. + + +For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. + +.. note:: + + If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. + +.. note:: + + The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force. + +---------- + + +**Mixing, shift, table, tail correction, restart, rRESPA info**\ : + +The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. + +The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. + +The :doc:`pair_modify ` table option is not relevant for the style *dpd/ext*. + +The style *dpd/ext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. + +The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. + +The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. + +---------- + + +Restrictions +"""""""""""" + +The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. + +The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. + +The pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart ` command for more details. + +Related commands +"""""""""""""""" + +:doc:`pair_style dpd `, :doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` + +**Default:** none + + +---------- + + +.. _Groot: + + + +**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). + +.. _Junghans: + + + +**(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008). diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 109ddfdf21..ce8227abeb 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -182,6 +182,8 @@ Examples pair_coeff * * 100.0 2.0 1.5 1.0 pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 +Example input scripts available: examples/USER/fep + Description """"""""""" @@ -363,7 +365,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info The different versions of the *lj/cut/soft* pair styles support mixing. For atom type pairs I,J and I != J, the :math:`\epsilon` and :math:`\sigma` -coefficients and cutoff distance for these pair style can be mixed. The default +coefficients and cutoff distance for these pair styles can be mixed. The default mix value is *geometric* for 12-6 styles. The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 19597b9018..448f3a26de 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -188,7 +188,7 @@ Restrictions The *gayberne* style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -These pair style require that atoms store torque and a quaternion to +These pair styles require that atoms store torque and a quaternion to represent their orientation, as defined by the :doc:`atom_style `. It also require they store a per-type :doc:`shape `. The particles cannot store a per-particle diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index d3f87839e8..fbcacb5c76 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -26,7 +26,7 @@ Syntax .. code-block:: LAMMPS - pair_style style Kn Kt gamma_n gamma_t xmu dampflag + pair_style style Kn Kt gamma_n gamma_t xmu dampflag keyword * style = *gran/hooke* or *gran/hooke/history* or *gran/hertz/history* * Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) @@ -36,6 +36,13 @@ Syntax * xmu = static yield criterion (unitless value between 0.0 and 1.0e4) * dampflag = 0 or 1 if tangential damping force is excluded or included +* keyword = *limit_damping* + + .. parsed-literal:: + + *limit_damping* value = none + limit damping to prevent attractive interaction + .. note:: Versions of LAMMPS before 9Jan09 had different style names for @@ -54,6 +61,8 @@ Examples pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1 pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 + pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 limit_damping + Description """"""""""" @@ -208,6 +217,12 @@ potential is used as a sub-style of :doc:`pair_style hybrid `, then pair_coeff command to determine which atoms interact via a granular potential. +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the *limit_damping* keyword is used, this option +will zero out the normal component of the force if there is an effective +attractive force. + ---------- .. include:: accel_styles.rst diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 80663b7d49..432fd29584 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -24,7 +24,7 @@ Examples pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity pair_style granular - pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 + pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 limit_damping pair_style granular pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji @@ -623,6 +623,14 @@ Finally, the twisting torque on each particle is given by: ---------- +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the optional *limit_damping* keyword is used, this option +will zero out the normal component of the force if there is an effective +attractive force. This keyword cannot be used with the JKR or DMT models. + +---------- + The *granular* pair style can reproduce the behavior of the *pair gran/\** styles with the appropriate settings (some very minor differences can be expected due to corrections in @@ -657,6 +665,12 @@ then LAMMPS will use that cutoff for the specified atom type combination, and automatically set pairwise cutoffs for the remaining atom types. +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the *limit_damping* keyword is used, this option +will zero out the normal component of the force if there is an effective +attractive force. This keyword cannot be used with the JKR or DMT models. + ---------- .. include:: accel_styles.rst diff --git a/doc/src/pair_hdnnp.rst b/doc/src/pair_hdnnp.rst new file mode 100644 index 0000000000..77a87642c4 --- /dev/null +++ b/doc/src/pair_hdnnp.rst @@ -0,0 +1,230 @@ +.. index:: pair_style hdnnp + +pair_style hdnnp command +======================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style hdnnp cutoff keyword value ... + +* cutoff = short-range cutoff of HDNNP (maximum symmetry function cutoff radius) +* zero or more keyword/value pairs may be appended +* keyword = *dir* or *showew* or *showewsum* or *maxew* or *resetew* or *cflength* or *cfenergy* +* value depends on the preceding keyword: + +.. parsed-literal:: + + *dir* value = directory + directory = Path to HDNNP configuration files + *showew* value = *yes* or *no* + *showewsum* value = summary + summary = Write EW summary every this many timesteps (*0* turns summary off) + *maxew* value = threshold + threshold = Maximum number of EWs allowed + *resetew* value = *yes* or *no* + *cflength* value = length + length = Length unit conversion factor + *cfenergy* value = energy + energy = Energy unit conversion factor + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style hdnnp 6.35 showew yes showewsum 100 maxew 1000 resetew yes cflength 1.8897261328 cfenergy 0.0367493254 + pair_coeff * * H O + + pair_style hdnnp 6.01 dir "./" showewsum 10000 + pair_coeff * * S Cu NULL Cu + +Description +""""""""""" + +This pair style adds an interaction based on the high-dimensional neural network +potential (HDNNP) method as presented in :ref:`(Behler and Parrinello 2007) +`. HDNNPs are machine learning potentials which require +careful training of neural networks prior to application in MD simulations. The +pair style uses an interface to the *n2p2* library :ref:`(Singraber, Behler and +Dellago 2019) ` which is available on Github +`here `__. Please see the *n2p2* +`documentation `__ for further details. +*n2p2* (and hence this pair style) is compatible with neural network potentials +trained with its own tools :ref:`(Singraber et al 2019) ` +and with `RuNNer `__. + +Only a single *pair_coeff* command with two asterisk wild-cards is used with this +pair style. Its additional arguments define the mapping of LAMMPS atom types to +n2p2 elements. + +.. code-block:: LAMMPS + + pair_coeff * * H O + +In the above example LAMMPS types 1 and 2 are mapped to the elements "H" and "O" +in n2p2, respectively. Multiple types may map to the same element, or some types +may not be mapped at all. For example, if the LAMMPS simulation has four atom +types, the command + +.. code-block:: LAMMPS + + pair_coeff * * H H O NULL + +maps atom types 1 and 2 to the element "H", type 3 to "O" and type 4 is not mapped +(indicated by NULL). Atoms mapped to NULL are ignored by the HDNNP calculation, +i.e. they do not contribute in any way to the evaluation of HDNNP energies and forces. +This may be useful in a setup with :doc:`hybrid pair styles `. + +---- + +The mandatory pair style argument *cutoff* must match the short-range cutoff radius +of the HDNNP. This corresponds to the maximum cutoff radius of all symmetry +functions (the atomic environment descriptors of HDNNPs) used. + +.. note:: + + The cutoff must be given in LAMMPS length units, even if the neural network + potential has been trained using a different unit system (see remarks about the + *cflength* and *cfenergy* keywords below for details). + +The numeric value may be slightly larger than the actual maximum symmetry +function cutoff radius (to account for rounding errors when converting units), +but must not be smaller. + +Use the *dir* keyword to specify the directory containing the HDNNP configuration +files. The directory must contain ``input.nn`` with neural network and symmetry +function setup, ``scaling.data`` with symmetry function scaling data and +``weights.???.data`` with weight parameters for each element. + +The keyword *showew* can be used to turn on/off the display of extrapolation +warnings (EWs) which are issued whenever a symmetry function value is out of +bounds defined by minimum/maximum values in ``scaling.data``. An extrapolation +warning may look like this: + +.. code-block:: LAMMPS + + ### NNP EXTRAPOLATION WARNING ### STRUCTURE: 0 ATOM: 119 ELEMENT: Cu SYMFUNC: 32 TYPE: 3 VALUE: 2.166E-02 MIN: 2.003E-05 MAX: 1.756E-02 + +stating that the value 2.166E-02 of symmetry function 32 of type 3 (Narrow Angular symmetry function), element Cu (see the log file for a symmetry function listing) was out +of bounds (maximum in ``scaling.data`` is 1.756E-02) for atom 119. Here, the +atom index refers to the LAMMPS tag (global index) and the structure index is +used to print out the MPI rank the atom belongs to. + +.. note:: + + The *showew* keyword should only be set to *yes* for debugging purposes. + Extrapolation warnings may add lots of overhead as they are communicated each + timestep. Also, if the simulation is run in a region where the HDNNP was not + correctly trained, lots of extrapolation warnings may clog log files and the + console. In a production run use *showewsum* instead. + +The keyword *showewsum* can be used to get an overview of extrapolation warnings +occurring during an MD simulation. The argument specifies the interval at which +extrapolation warning summaries are displayed and logged. An EW summary may look +like this: + +.. code-block:: LAMMPS + + ### NNP EW SUMMARY ### TS: 100 EW 11 EWPERSTEP 1.100E-01 + +Here, at timestep 100 the occurrence of 11 extrapolation warnings since the last +summary is reported, which corresponds to an EW rate of 0.11 per timestep. +Setting *showewsum* to 0 deactivates the EW summaries. + +A maximum number of allowed extrapolation warnings can be specified with the +*maxew* keyword. If the number of EWs exceeds the *maxew* argument the +simulation is stopped. Note however that this is merely an approximate threshold +since the check is only performed at the end of each timestep and each MPI +process counts individually to minimize communication overhead. + +The keyword *resetew* alters the behavior of the above mentioned *maxew* +threshold. If *resetew* is set to *yes* the threshold is applied on a +per-timestep basis and the internal EW counters are reset at the beginning of +each timestep. With *resetew* set to *no* the counters accumulate EWs along the +whole trajectory. + +If the training of a neural network potential has been performed with different +physical units for length and energy than those set in LAMMPS, it is still +possible to use the potential when the unit conversion factors are provided via +the *cflength* and *cfenergy* keywords. If for example, the HDNNP was +parameterized with Bohr and Hartree training data and symmetry function +parameters (i.e. distances and energies in "input.nn" are given in Bohr and +Hartree) but LAMMPS is set to use *metal* units (Angstrom and eV) the correct +conversion factors are: + +.. code-block:: LAMMPS + + cflength 1.8897261328 + + cfenergy 0.0367493254 + +Thus, arguments of *cflength* and *cfenergy* are the multiplicative factors +required to convert lengths and energies given in LAMMPS units to respective +quantities in native HDNNP units (1 Angstrom = 1.8897261328 Bohr, 1 eV = +0.0367493254 Hartree). + +---- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This style does not support mixing. The :doc:`pair_coeff ` command +should only be invoked with asterisk wild cards (see above). + +This style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This style does not write information to :doc:`binary restart files `. +Thus, you need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This style can only be used via the *pair* keyword of the :doc:`run_style respa +` command. It does not support the *inner*\ , *middle*\ , *outer* +keywords. + +Restrictions +"""""""""""" + +This pair style is part of the USER-HDNNP package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` doc +page for more info. + +Please report bugs and feature requests to the `n2p2 GitHub issue page +`__. + +Related commands +^^^^^^^^^^^^^^^^ + +:doc:`pair_coeff `, :doc:`pair_hybrid `, :doc:`units ` + +Default +^^^^^^^ + +The default options are *dir* = "hdnnp/", *showew* = yes, *showewsum* = 0, *maxew* += 0, *resetew* = no, *cflength* = 1.0, *cfenergy* = 1.0. + +---- + +.. _Behler_Parrinello_2007: + +**(Behler and Parrinello 2007)** `Behler, J.; Parrinello, M. Generalized +Neural-Network Representation of High-Dimensional Potential-Energy Surfaces. +Phys. Rev. Lett. 2007, 98 (14), 146401. +`__ + +.. _Singraber_Behler_Dellago_2019: + +**(Singraber, Behler and Dellago 2019)** `Singraber, A.; Behler, J.; Dellago, C. +Library-Based LAMMPS Implementation of High-Dimensional Neural Network +Potentials. J. Chem. Theory Comput. 2019, 15 (3), 1827-1840 +`__ + +.. _Singraber_et_al_2019: + +**(Singraber et al 2019)** `Singraber, A.; Morawietz, T.; Behler, J.; Dellago, +C. Parallel Multistream Training of High-Dimensional Neural Network Potentials. +J. Chem. Theory Comput. 2019, 15 (5), 3075-3092. +`__ diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 558c326175..f7de713c94 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -2,6 +2,7 @@ .. index:: pair_style hybrid/kk .. index:: pair_style hybrid/overlay .. index:: pair_style hybrid/overlay/kk +.. index:: pair_style hybrid/scaled pair_style hybrid command ========================= @@ -13,6 +14,9 @@ pair_style hybrid/overlay command Accelerator Variants: *hybrid/overlay/kk* +pair_style hybrid/scaled command +================================== + Syntax """""" @@ -20,8 +24,10 @@ Syntax pair_style hybrid style1 args style2 args ... pair_style hybrid/overlay style1 args style2 args ... + pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ... * style1,style2 = list of one or more pair styles and their arguments +* factor1,factor2 = scale factors for pair styles, may be a variable Examples """""""" @@ -37,47 +43,73 @@ Examples pair_coeff * * lj/cut 1.0 1.0 pair_coeff * * coul/long + pair_style hybrid/scaled 0.5 tersoff 0.5 sw + pair_coeff * * tersoff Si.tersoff Si + pair_coeff * * sw Si.sw Si + + variable one equal ramp(1.0,0.0) + variable two equal 1.0-v_one + pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5 + pair_coeff 1 1 lj/cut 1.0 1.0 2.5 + pair_coeff 1 1 morse 1.0 1.0 1.0 2.5 + Description """"""""""" -The *hybrid* and *hybrid/overlay* styles enable the use of multiple -pair styles in one simulation. With the *hybrid* style, exactly one -pair style is assigned to each pair of atom types. With the -*hybrid/overlay* style, one or more pair styles can be assigned to -each pair of atom types. The assignment of pair styles to type pairs -is made via the :doc:`pair_coeff ` command. +The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the +use of multiple pair styles in one simulation. With the *hybrid* style, +exactly one pair style is assigned to each pair of atom types. With the +*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can +be assigned to each pair of atom types. The assignment of pair styles +to type pairs is made via the :doc:`pair_coeff ` command. +The major difference between the *hybrid/overlay* and *hybrid/scaled* +styles is that the *hybrid/scaled* adds a scale factor for each +sub-style contribution to forces, energies and stresses. Because of the +added complexity, the *hybrid/scaled* style has more overhead and thus +may be slower than *hybrid/overlay*. Here are two examples of hybrid simulations. The *hybrid* style could -be used for a simulation of a metal droplet on a LJ surface. The -metal atoms interact with each other via an *eam* potential, the -surface atoms interact with each other via a *lj/cut* potential, and -the metal/surface interaction is also computed via a *lj/cut* -potential. The *hybrid/overlay* style could be used as in the second -example above, where multiple potentials are superposed in an additive -fashion to compute the interaction between atoms. In this example, -using *lj/cut* and *coul/long* together gives the same result as if -the *lj/cut/coul/long* potential were used by itself. In this case, -it would be more efficient to use the single combined potential, but -in general any combination of pair potentials can be used together in -to produce an interaction that is not encoded in any single pair_style +be used for a simulation of a metal droplet on a LJ surface. The metal +atoms interact with each other via an *eam* potential, the surface atoms +interact with each other via a *lj/cut* potential, and the metal/surface +interaction is also computed via a *lj/cut* potential. The +*hybrid/overlay* style could be used as in the second example above, +where multiple potentials are superposed in an additive fashion to +compute the interaction between atoms. In this example, using *lj/cut* +and *coul/long* together gives the same result as if the +*lj/cut/coul/long* potential were used by itself. In this case, it +would be more efficient to use the single combined potential, but in +general any combination of pair potentials can be used together in to +produce an interaction that is not encoded in any single pair_style file, e.g. adding Coulombic forces between granular particles. +If the *hybrid/scaled* style is used instead of *hybrid/overlay*\ , +contributions from sub-styles are weighted by their scale factors, which +may be fractional or even negative. Furthermore the scale factors may +be variables that may change during a simulation. This enables +switching smoothly between two different pair styles or two different +parameter sets during a run. + All pair styles that will be used are listed as "sub-styles" following -the *hybrid* or *hybrid/overlay* keyword, in any order. Each -sub-style's name is followed by its usual arguments, as illustrated in -the example above. See the doc pages of individual pair styles for a -listing and explanation of the appropriate arguments. +the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the +*hybrid/scaled* pair style, each sub-style is prefixed with a scale +factor. The scale factor is either a floating point number or an equal +style (or equivalent) variable. Each sub-style's name is followed by +its usual arguments, as illustrated in the examples above. See the doc +pages of the individual pair styles for a listing and explanation of the +appropriate arguments for them. Note that an individual pair style can be used multiple times as a -sub-style. For efficiency this should only be done if your model -requires it. E.g. if you have different regions of Si and C atoms and -wish to use a Tersoff potential for pure Si for one set of atoms, and -a Tersoff potential for pure C for the other set (presumably with some -third potential for Si-C interactions), then the sub-style *tersoff* -could be listed twice. But if you just want to use a Lennard-Jones or -other pairwise potential for several different atom type pairs in your -model, then you should just list the sub-style once and use the -pair_coeff command to assign parameters for the different type pairs. +sub-style. For efficiency reasons this should only be done if your +model requires it. E.g. if you have different regions of Si and C atoms +and wish to use a Tersoff potential for pure Si for one set of atoms, +and a Tersoff potential for pure C for the other set (presumably with +some third potential for Si-C interactions), then the sub-style +*tersoff* could be listed twice. But if you just want to use a +Lennard-Jones or other pairwise potential for several different atom +type pairs in your model, then you should just list the sub-style once +and use the pair_coeff command to assign parameters for the different +type pairs. .. note:: @@ -143,16 +175,16 @@ one sub-style. Just as with a simulation using a single pair style, if you specify the same atom type pair in a second pair_coeff command, the previous assignment will be overwritten. -For the *hybrid/overlay* style, each atom type pair I,J can be -assigned to one or more sub-styles. If you specify the same atom type -pair in a second pair_coeff command with a new sub-style, then the -second sub-style is added to the list of potentials that will be -calculated for two interacting atoms of those types. If you specify -the same atom type pair in a second pair_coeff command with a -sub-style that has already been defined for that pair of atoms, then -the new pair coefficients simply override the previous ones, as in the -normal usage of the pair_coeff command. E.g. these two sets of -commands are the same: +For the *hybrid/overlay* and *hybrid/scaled* styles, each atom type pair +I,J can be assigned to one or more sub-styles. If you specify the same +atom type pair in a second pair_coeff command with a new sub-style, then +the second sub-style is added to the list of potentials that will be +calculated for two interacting atoms of those types. If you specify the +same atom type pair in a second pair_coeff command with a sub-style that +has already been defined for that pair of atoms, then the new pair +coefficients simply override the previous ones, as in the normal usage +of the pair_coeff command. E.g. these two sets of commands are the +same: .. code-block:: LAMMPS @@ -166,42 +198,43 @@ commands are the same: Coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as described above, or in the -data file or restart files read by the :doc:`read_data ` or -:doc:`read_restart ` commands, or by mixing as described -below. +data file read by the :doc:`read_data ` commands, or by +mixing as described below. -For both the *hybrid* and *hybrid/overlay* styles, every atom type -pair I,J (where I <= J) must be assigned to at least one sub-style via -the :doc:`pair_coeff ` command as in the examples above, or -in the data file read by the :doc:`read_data `, or by mixing -as described below. +For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles, +every atom type pair I,J (where I <= J) must be assigned to at least one +sub-style via the :doc:`pair_coeff ` command as in the +examples above, or in the data file read by the :doc:`read_data +`, or by mixing as described below. Also all sub-styles +must be used at least once in a :doc:`pair_coeff ` command. If you want there to be no interactions between a particular pair of atom types, you have 3 choices. You can assign the type pair to some sub-style and use the :doc:`neigh_modify exclude type ` command. You can assign it to some sub-style and set the coefficients -so that there is effectively no interaction (e.g. epsilon = 0.0 in a -LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you -can use this form of the pair_coeff command in your input script: +so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ +potential). Or, for *hybrid*, *hybrid/overlay*, or *hybrid/scaled* +simulations, you can use this form of the pair_coeff command in your +input script: .. code-block:: LAMMPS - pair_coeff 2 3 none + pair_coeff 2 3 none or this form in the "Pair Coeffs" section of the data file: .. parsed-literal:: - 3 none + 3 none If an assignment to *none* is made in a simulation with the -*hybrid/overlay* pair style, it wipes out all previous assignments of -that atom type pair to sub-styles. +*hybrid/overlay* or *hybrid/scaled* pair style, it wipes out all +previous assignments of that pair of atom types to sub-styles. Note that you may need to use an :doc:`atom_style ` hybrid command in your input script, if atoms in the simulation will need attributes from several atom styles, due to using multiple pair -potentials. +styles with different requirements. ---------- @@ -210,8 +243,9 @@ for applying weightings that change the strength of pairwise interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the :doc:`special_bonds ` command. Different weights can be -assigned to different pair hybrid sub-styles via the :doc:`pair_modify special ` command. This allows multiple force fields -to be used in a model of a hybrid system, however, there is no consistent +assigned to different pair hybrid sub-styles via the :doc:`pair_modify +special ` command. This allows multiple force fields to be +used in a model of a hybrid system, however, there is no consistent approach to determine parameters automatically for the interactions between the two force fields, this is only recommended when particles described by the different force fields do not mix. @@ -223,7 +257,7 @@ then overrides them with 0.0 only for CHARMM: .. code-block:: LAMMPS special_bonds amber - pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 + pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 The this input achieves the same effect: @@ -231,7 +265,7 @@ The this input achieves the same effect: .. code-block:: LAMMPS special_bonds 0.0 0.0 0.1 - pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 + pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5 pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333 pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 @@ -245,7 +279,7 @@ effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA: .. code-block:: LAMMPS special_bonds lj/coul 1e-20 1e-20 0.5 - pair_hybrid tersoff lj/cut/coul/long 12.0 + pair_style hybrid tersoff lj/cut/coul/long 12.0 pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 For use with the various :doc:`compute \*/tally ` @@ -260,7 +294,10 @@ the specific syntax, requirements and restrictions. ---------- The potential energy contribution to the overall system due to an -individual sub-style can be accessed and output via the :doc:`compute pair ` command. +individual sub-style can be accessed and output via the :doc:`compute +pair ` command. Note that in the case of pair style +*hybrid/scaled* this is the **unscaled** potential energy of the +selected sub-style. ---------- @@ -282,28 +319,27 @@ Pair_style hybrid allows interactions between type pairs 2-2, 1-2, could even add a second interaction for 1-1 to be computed by another pair style, assuming pair_style hybrid/overlay is used. -But you should not, as a general rule, attempt to exclude the -many-body interactions for some subset of the type pairs within the -set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That -is not conceptually well-defined for many-body interactions, since the +But you should not, as a general rule, attempt to exclude the many-body +interactions for some subset of the type pairs within the set of 1,3,4 +interactions, e.g. exclude 1-1 or 1-3 interactions. That is not +conceptually well-defined for many-body interactions, since the potential will typically calculate energies and foces for small groups of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to -find the additional atoms in the group. It is typically non-physical -to think of excluding an interaction between a particular pair of -atoms when the potential computes 3-body or 4-body interactions. +find the additional atoms in the group. However, you can still use the pair_coeff none setting or the :doc:`neigh_modify exclude ` command to exclude certain type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body -potential, since it builds its list of 3-body, 4-body, etc -interactions from the pair list. You will need to think carefully as -to whether it produces a physically meaningful result for your model. +potential beyond the specific pairs, since it builds its list of 3-body, +4-body, etc interactions from the pair lists. You will need to think +**carefully** as to whether excluding such pairs produces a physically +meaningful result for your model. For example, imagine you have two atom types in your model, type 1 for atoms in one surface, and type 2 for atoms in the other, and you wish to use a Tersoff potential to compute interactions within each -surface, but not between surfaces. Then either of these two command +surface, but not between the surfaces. Then either of these two command sequences would implement that model: .. code-block:: LAMMPS @@ -320,9 +356,9 @@ Either way, only neighbor lists with 1-1 or 2-2 interactions would be passed to the Tersoff potential, which means it would compute no 3-body interactions containing both type 1 and 2 atoms. -Here is another example, using hybrid/overlay, to use 2 many-body -potentials together, in an overlapping manner. Imagine you have CNT -(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C +Here is another example to use 2 many-body potentials together in an +overlapping manner using hybrid/overlay. Imagine you have CNT (C atoms) +on a Si surface. You want to use Tersoff for Si/Si and Si/C interactions, and AIREBO for C/C interactions. Si atoms are type 1; C atoms are type 2. Something like this will work: @@ -333,9 +369,9 @@ atoms are type 2. Something like this will work: pair_coeff * * airebo CH.airebo NULL C Note that to prevent the Tersoff potential from computing C/C -interactions, you would need to modify the SiC.tersoff file to turn -off C/C interaction, i.e. by setting the appropriate coefficients to -0.0. +interactions, you would need to **modify** the SiC.tersoff potential +file to turn off C/C interaction, i.e. by setting the appropriate +coefficients to 0.0. ---------- @@ -343,18 +379,19 @@ Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc -page. +page. Pair style *hybrid/scaled* does (currently) not support the +*gpu*, *omp*, *kk*, or *intel* suffix. -Since the *hybrid* and *hybrid/overlay* styles delegate computation to -the individual sub-styles, the suffix versions of the *hybrid* and -*hybrid/overlay* styles are used to propagate the corresponding suffix -to all sub-styles, if those versions exist. Otherwise the -non-accelerated version will be used. +Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles delegate +computation to the individual sub-styles, the suffix versions of the +*hybrid* and *hybrid/overlay* styles are used to propagate the +corresponding suffix to all sub-styles, if those versions +exist. Otherwise the non-accelerated version will be used. -The individual accelerated sub-styles are part of the GPU, USER-OMP -and OPT packages, respectively. They are only enabled if LAMMPS was -built with those packages. See the :doc:`Build package ` -doc page for more info. +The individual accelerated sub-styles are part of the GPU, KOKKOS, +USER-INTEL, USER-OMP, and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :doc:`Build +package ` doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the @@ -372,28 +409,35 @@ Any pair potential settings made via the :doc:`pair_modify ` command are passed along to all sub-styles of the hybrid potential. -For atom type pairs I,J and I != J, if the sub-style assigned to I,I -and J,J is the same, and if the sub-style allows for mixing, then the +For atom type pairs I,J and I != J, if the sub-style assigned to I,I and +J,J is the same, and if the sub-style allows for mixing, then the coefficients for I,J can be mixed. This means you do not have to specify a pair_coeff command for I,J since the I,J type pair will be -assigned automatically to the sub-style defined for both I,I and J,J -and its coefficients generated by the mixing rule used by that -sub-style. For the *hybrid/overlay* style, there is an additional -requirement that both the I,I and J,J pairs are assigned to a single -sub-style. See the "pair_modify" command for details of mixing rules. -See the See the doc page for the sub-style to see if allows for -mixing. +assigned automatically to the sub-style defined for both I,I and J,J and +its coefficients generated by the mixing rule used by that sub-style. +For the *hybrid/overlay* and *hybrid/scaled* style, there is an +additional requirement that both the I,I and J,J pairs are assigned to a +single sub-style. If this requirement is not met, no I,J coeffs will be +generated, even if the sub-styles support mixing, and I,J pair +coefficients must be explicitly defined. + +See the :doc:`pair_modify ` command for +details of mixing rules. See the See the doc page for the sub-style to +see if allows for mixing. The hybrid pair styles supports the :doc:`pair_modify ` shift, table, and tail options for an I,J pair interaction, if the associated sub-style supports it. -For the hybrid pair styles, the list of sub-styles and their -respective settings are written to :doc:`binary restart files `, so a :doc:`pair_style ` command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file. Thus, pair_coeff commands need to be re-specified in the -restart input script. +For the hybrid pair styles, the list of sub-styles and their respective +settings are written to :doc:`binary restart files `, so a +:doc:`pair_style ` command does not need to specified in an +input script that reads a restart file. However, the coefficient +information is not stored in the restart file. Thus, pair_coeff +commands need to be re-specified in the restart input script. For pair +style *hybrid/scaled* also the names of any variables used as scale +factors are restored, but not the variables themselves, so those may +need to be redefined when continuing from a restart. These pair styles support the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, if @@ -409,6 +453,12 @@ e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must insure that the short-range Coulombic cutoff used by each of these long pair styles is the same or else LAMMPS will generate an error. +Pair style *hybrid/scaled* currently only works for non-accelerated +pair styles and pair styles from the OPT package. + +When using pair styles from the GPU package they must not be listed +multiple times. LAMMPS will detect this and abort. + Related commands """""""""""""""" diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 6c9817cd5e..858b0eb984 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -36,7 +36,7 @@ No simplification is made, .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\ + V_{ij} = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) \right ] - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \\ \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\ \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\ f(\rho) & = e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n} diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index 942ef85836..bd02221074 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -33,7 +33,7 @@ which is to take all normals along the z-axis. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\ + V_{ij} = & e^{-\lambda(r_{ij} -z_0)} \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\ \rho_{ij}^2 = & \rho_{ji}^2 = x_{ij}^2 + y_{ij}^2 \qquad \qquad (\mathbf{n}_i \equiv \mathbf{\hat{z}}) \\ f(\rho) = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right)^{2n} diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst index 4f55f3b14e..5f3b4e48e7 100644 --- a/doc/src/pair_lj_cut_tip4p.rst +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -145,6 +145,22 @@ specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. +.. warning:: + + Because of how these pair styles implement the coulomb interactions + by implicitly defining a fourth site for the negative charge + of the TIP4P and similar water models, special care must be taken + when using these pair styles with other computations that also use + charges. Unless they are specially set up to also handle the implicit + definition of the 4th site, results are likely incorrect. Example: + :doc:`compute dipole/chunk `. For the same + reason, when using one of these pair styles with + :doc:`pair_style hybrid `, **all** coulomb interactions + should be handled by a single sub-style with TIP4P support. All other + instances and styles will "see" the M point charges at the position + of the Oxygen atom and thus compute incorrect forces and energies. + LAMMPS will print a warning when it detects one of these issues. + ---------- A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 7ba12c89ba..a77eefd023 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -1,10 +1,11 @@ .. index:: pair_style lj/smooth +.. index:: pair_style lj/smooth/gpu .. index:: pair_style lj/smooth/omp pair_style lj/smooth command ============================ -Accelerator Variants: *lj/smooth/omp* +Accelerator Variants: *lj/smooth/gpu*, *lj/smooth/omp* Syntax """""" diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index f791b9836b..6b918c1071 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -1,8 +1,12 @@ .. index:: pair_style lj/switch3/coulgauss/long +.. index:: pair_style mm3/switch3/coulgauss/long pair_style lj/switch3/coulgauss/long command ============================================ +pair_style mm3/switch3/coulgauss/long command +============================================= + Syntax """""" @@ -10,7 +14,7 @@ Syntax pair_style style args -* style = *lj/switch3/coulgauss/long* +* style = *lj/switch3/coulgauss/long* or *mm3/switch3/coulgauss/long* * args = list of arguments for a particular style .. parsed-literal:: @@ -20,6 +24,11 @@ Syntax cutoff2 = global cutoff for Coulombic (optional) (distance units) width = width parameter of the smoothing function (distance units) + *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width + cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + width = width parameter of the smoothing function (distance units) + Examples """""""" @@ -31,6 +40,12 @@ Examples pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0 pair_coeff 1 0.2 2.5 1.2 + pair_style mm3/switch3/coulgauss/long 12.0 3.0 + pair_coeff 1 0.2 2.5 1.2 + + pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0 + pair_coeff 1 0.2 2.5 1.2 + Description """"""""""" @@ -41,8 +56,17 @@ vdW potential E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right] -, which goes smoothly to zero at the cutoff r_c as defined -by the switching function +The *mm3/switch3/coulgauss/long* style evaluates the MM3 +vdW potential :ref:`(Allinger) ` + +.. math:: + + E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ + r_{v,ij} & = r_{v,i} + r_{v,j} \\ + \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} + +Both potentials go smoothly to zero at the cutoff r_c as defined by the +switching function .. math:: @@ -85,14 +109,35 @@ commands: Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/long pair styles can be mixed. +The default mix value is *geometric*\ . See the "pair_modify" command +for details. + Shifting the potential energy is not necessary because the switching function ensures that the potential is zero at the cut-off. +These pair styles support the :doc:`pair_modify ` table and +options since they can tabulate the short-range portion of the +long-range Coulombic interactions. + +Thes pair styles do not support the :doc:`pair_modify ` +tail option for adding a long-range tail correction to the +Lennard-Jones portion of the energy and pressure. + +These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +These pair styles can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. They do not support the +*inner*\ , *middle*\ , *outer* keywords. + Restrictions """""""""""" -These styles are part of the USER-YAFF package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These styles are part of the USER-YAFF package. They are only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 1efdfa8b45..6bb259a10d 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -238,7 +238,7 @@ Example scripts """"""""""""""" There are example scripts for using all these pair styles in -examples/USER/meso. The example for an eDPD simulation models heat +examples/USER/mesodpd. The example for an eDPD simulation models heat conduction with source terms analog of periodic Poiseuille flow problem. The setup follows Fig.12 in :ref:`(Li2014_JCP) `. The output of the short eDPD simulation (about 2 minutes on a single core) diff --git a/doc/src/pair_mliap.rst b/doc/src/pair_mliap.rst index c40b911087..73ebe48856 100644 --- a/doc/src/pair_mliap.rst +++ b/doc/src/pair_mliap.rst @@ -19,7 +19,7 @@ Syntax style = *linear* or *quadratic* or *nn* or *mliappy* filename = name of file containing model definitions *descriptor* values = style filename - style = *sna* + style = *sna* or *so3* filename = name of file containing descriptor definitions Examples @@ -29,65 +29,70 @@ Examples pair_style mliap model linear InP.mliap.model descriptor sna InP.mliap.descriptor pair_style mliap model quadratic W.mliap.model descriptor sna W.mliap.descriptor + pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor pair_coeff * * In P Description """"""""""" Pair style *mliap* provides a general interface to families of -machine-learning interatomic potentials. It allows separate -definitions of the interatomic potential functional form (*model*) -and the geometric quantities that characterize the atomic positions -(*descriptor*). By defining *model* and *descriptor* separately, -it is possible to use many different models with a given descriptor, -or many different descriptors with a given model. The -pair style currently supports just one descriptor style, but it is -is straightforward to add new descriptor styles. -The SNAP descriptor style *sna* is the same as that used by :doc:`pair_style snap `, -including the linear, quadratic, and chem variants. -The available models are *linear*, *quadratic*, *nn*, and *mliappy*. -The *mliappy* style can be used to couple python models, -e.g. PyTorch neural network energy models, and requires building -LAMMPS with the PYTHON package (see below). -In order to train a model, it is useful to know the gradient or derivative -of energy, force, and stress w.r.t. model parameters. This information -can be accessed using the related :doc:`compute mliap ` command. +machine-learning interatomic potentials. It allows separate definitions +of the interatomic potential functional form (*model*) and the geometric +quantities that characterize the atomic positions (*descriptor*). By +defining *model* and *descriptor* separately, it is possible to use many +different models with a given descriptor, or many different descriptors +with a given model. The pair style currently supports only *sna* and *so3* +descriptor styles, but it is is straightforward to add new descriptor +styles. -The pair_style *mliap* command must be followed by two keywords -*model* and *descriptor* in either order. A single -*pair_coeff* command is also required. The first 2 arguments -must be \* \* so as to span all LAMMPS atom types. -This is followed by a list of N arguments -that specify the mapping of MLIAP -element names to LAMMPS atom types, -where N is the number of LAMMPS atom types. +The SNAP descriptor style *sna* is the same as that used by +:doc:`pair_style snap `, including the linear, quadratic, and +chem variants. The available models are *linear*, *quadratic*, *nn*, +and *mliappy*. The *mliappy* style can be used to couple python models, +e.g. PyTorch neural network energy models, and requires building LAMMPS +with the PYTHON package (see below). In order to train a model, it is +useful to know the gradient or derivative of energy, force, and stress +w.r.t. model parameters. This information can be accessed using the +related :doc:`compute mliap ` command. -The *model* keyword is followed by the model style. This is followed -by a single argument specifying the model filename containing the -parameters for a set of elements. -The model filename usually ends in the *.mliap.model* extension. -It may contain parameters for many elements. The only requirement is that it -contain at least those element names appearing in the -*pair_coeff* command. +The descriptor style *so3* is a descriptor that is derived from the +the smooth SO(3) power spectrum with the explicit inclusion of a radial +basis :ref:`(Bartok) ` and :ref:`(Zagaceta) `. +The available models are *linear* and *nn*. -The top of the model file can contain any number of blank and comment lines (start with #), -but follows a strict format after that. The first non-blank non-comment -line must contain two integers: +The pair_style *mliap* command must be followed by two keywords *model* +and *descriptor* in either order. A single *pair_coeff* command is also +required. The first 2 arguments must be \* \* so as to span all LAMMPS +atom types. This is followed by a list of N arguments that specify the +mapping of MLIAP element names to LAMMPS atom types, where N is the +number of LAMMPS atom types. + +The *model* keyword is followed by the model style. This is followed by +a single argument specifying the model filename containing the +parameters for a set of elements. The model filename usually ends in +the *.mliap.model* extension. It may contain parameters for many +elements. The only requirement is that it contain at least those element +names appearing in the *pair_coeff* command. + +The top of the model file can contain any number of blank and comment +lines (start with #), but follows a strict format after that. The first +non-blank non-comment line must contain two integers: * nelems = Number of elements * nparams = Number of parameters -When the *model* keyword is *linear* or *quadratic*, -this is followed by one block for each of the *nelem* elements. -Each block consists of *nparams* parameters, one per line. -Note that this format is similar, but not identical to that used -for the :doc:`pair_style snap ` coefficient file. -Specifically, the line containing the element weight and radius is omitted, -since these are handled by the *descriptor*. +When the *model* keyword is *linear* or *quadratic*, this is followed by +one block for each of the *nelem* elements. Each block consists of +*nparams* parameters, one per line. Note that this format is similar, +but not identical to that used for the :doc:`pair_style snap +` coefficient file. Specifically, the line containing the +element weight and radius is omitted, since these are handled by the +*descriptor*. -When the *model* keyword is *nn* (neural networks), the model file can contain -blank and comment lines (start with #) anywhere. The second non-blank non-comment -line must contain the string NET, followed by two integers: +When the *model* keyword is *nn* (neural networks), the model file can +contain blank and comment lines (start with #) anywhere. The second +non-blank non-comment line must contain the string NET, followed by two +integers: * ndescriptors = Number of descriptors * nlayers = Number of layers (including the hidden layers and the output layer) @@ -97,54 +102,71 @@ and followed by a sequence of a string and an integer for each layer: * Activation function (linear, sigmoid, tanh or relu) * nnodes = Number of nodes -This is followed by one block for each of the *nelem* elements. Each block consists -of *scale0* minimum value, *scale1* (maximum - minimum) value, -in order to normalize the descriptors, followed by *nparams* parameters, -including *bias* and *weights* of the model, starting with the first node of the first layer -and so on, with a maximum of 30 values per line. +This is followed by one block for each of the *nelem* elements. Each +block consists of *scale0* minimum value, *scale1* (maximum - minimum) +value, in order to normalize the descriptors, followed by *nparams* +parameters, including *bias* and *weights* of the model, starting with +the first node of the first layer and so on, with a maximum of 30 values +per line. -Notes on mliappy models: -When the *model* keyword is *mliappy*, the filename should end in '.pt', -'.pth' for pytorch models, or be a pickle file. To load a model from -memory (i.e. an existing python object), specify the filename as -"LATER", and then call `lammps.mliap.load_model(model)` from python -before using the pair style. When using lammps via the library mode, you will need to call -`lammps.mliappy.activate_mliappy(lmp)` on the active lammps object -before the pair style is defined. This call locates and loads the mliap-specific -python module that is built into lammps. +The detail of *nn* module implementation can be found at :ref:`(Yanxon) `. + +.. admonition:: Notes on mliappy models + + When the *model* keyword is *mliappy*, the filename should end in '.pt', + '.pth' for pytorch models, or be a pickle file. To load a model from + memory (i.e. an existing python object), specify the filename as + "LATER", and then call `lammps.mliap.load_model(model)` from python + before using the pair style. When using lammps via the library mode, you + will need to call `lammps.mliappy.activate_mliappy(lmp)` on the active + lammps object before the pair style is defined. This call locates and + loads the mliap-specific python module that is built into lammps. The *descriptor* keyword is followed by a descriptor style, and additional arguments. -Currently the only descriptor style is *sna*, indicating the bispectrum component -descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of -:doc:`pair_style snap `. -A single additional argument specifies the descriptor filename -containing the parameters and setting used by the SNAP descriptor. -The descriptor filename usually ends in the *.mliap.descriptor* extension. +Currently two descriptor styles are available: *sna* and *so3*. + +- *sna* indicates the bispectrum component descriptors used by the Spectral + Neighbor Analysis Potential (SNAP) potentials of :doc:`pair_style snap + `. A single additional argument specifies the descriptor + filename containing the parameters and setting used by the SNAP + descriptor. The descriptor filename usually ends in the + *.mliap.descriptor* extension. + +- *so3* indicated the power spectrum component descriptors. A single additional + argument specifies the descriptor filename containing the parameters and setting. The SNAP descriptor file closely follows the format of the -:doc:`pair_style snap ` parameter file. -The file can contain blank and comment lines (start -with #) anywhere. Each non-blank non-comment line must contain one -keyword/value pair. The required keywords are *rcutfac* and -*twojmax*\ . There are many optional keywords that are described -on the :doc:`pair_style snap ` doc page. -In addition, the SNAP descriptor file must contain -the *nelems*, *elems*, *radelems*, and *welems* keywords. -The *nelems* keyword specifies the number of elements -provided in the other three keywords. -The *elems* keyword is followed by a list of *nelems* -element names that must include the element -names appearing in the *pair_coeff* command, -but can contain other names too. -Similarly, the *radelems* and *welems* keywords are -followed by lists of *nelems* numbers giving the element radius -and element weight of each element. Obviously, the order -in which the elements are listed must be consistent for all -three keywords. +:doc:`pair_style snap ` parameter file. The file can contain +blank and comment lines (start with #) anywhere. Each non-blank +non-comment line must contain one keyword/value pair. The required +keywords are *rcutfac* and *twojmax*\ . There are many optional keywords +that are described on the :doc:`pair_style snap ` doc page. +In addition, the SNAP descriptor file must contain the *nelems*, +*elems*, *radelems*, and *welems* keywords. The *nelems* keyword +specifies the number of elements provided in the other three keywords. +The *elems* keyword is followed by a list of *nelems* element names that +must include the element names appearing in the *pair_coeff* command, +but can contain other names too. Similarly, the *radelems* and *welems* +keywords are followed by lists of *nelems* numbers giving the element +radius and element weight of each element. Obviously, the order in which +the elements are listed must be consistent for all three keywords. + +The SO3 descriptor file is similar to the SNAP descriptor except that it +contains a few more arguments (e.g., *nmax* and *alpha*). The preparation +of SO3 descriptor and model files can be done with the +`Pyxtal_FF `_ package. See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for these *model* and *descriptor* files. +.. note:: + + To significantly reduce SO3 descriptor/force calculation time, + some properties are pre-computed and reused during the calculation. + These can consume a significant amount of RAM for simulations of + larger systems since their size depends on the total number of + neighbors per MPI process. + Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" @@ -156,9 +178,10 @@ specify a pair_coeff command with I != J arguments for this style. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential files. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the @@ -169,11 +192,11 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the MLIAP package. It is only enabled if LAMMPS -was built with that package. In addition, building LAMMPS with the MLIAP package -requires building LAMMPS with the SNAP package. -The *mliappy* model requires building LAMMPS with the PYTHON package. -See the :doc:`Build package ` doc page for more info. +This pair style is part of the MLIAP package. It is only enabled if +LAMMPS was built with that package. In addition, building LAMMPS with +the MLIAP package requires building LAMMPS with the SNAP package. The +*mliappy* model requires building LAMMPS with the PYTHON package. See +the :doc:`Build package ` doc page for more info. Related commands @@ -185,3 +208,19 @@ Default """"""" none + +---------- + +.. _Bartok2013: + +**(Bartok2013)** Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013). + +.. _Zagaceta2020: + +**(Zagaceta2020)** Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020). + +.. _Yanxon2020: + +**(Yanxon2020)** Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020). + + diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst deleted file mode 100644 index 798df0bf7a..0000000000 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ /dev/null @@ -1,109 +0,0 @@ -.. index:: pair_style mm3/switch3/coulgauss/long - -pair_style mm3/switch3/coulgauss/long command -============================================= - -Syntax -"""""" - -.. code-block:: LAMMPS - - pair_style style args - -* style = *mm3/switch3/coulgauss/long* -* args = list of arguments for a particular style - -.. parsed-literal:: - - *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width - cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - width = width parameter of the smoothing function (distance units) - -Examples -"""""""" - -.. code-block:: LAMMPS - - pair_style mm3/switch3/coulgauss/long 12.0 3.0 - pair_coeff 1 0.2 2.5 1.2 - - pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0 - pair_coeff 1 0.2 2.5 1.2 - -Description -""""""""""" - -The *mm3/switch3/coulgauss/long* style evaluates the MM3 -vdW potential :ref:`(Allinger) ` - -.. math:: - - E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ - r_{v,ij} & = r_{v,i} + r_{v,j} \\ - \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} - -, which goes smoothly to zero at the cutoff r_c as defined -by the switching function - -.. math:: - - S_3(r) = \left\lbrace \begin{array}{ll} - 1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\ - 3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\ - 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c} - \end{array} \right. - -where w is the width defined in the arguments. This potential -is combined with Coulomb interaction between Gaussian charge densities: - -.. math:: - - E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}} - -where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, -epsilon is the dielectric constant which can be set by the -:doc:`dielectric ` command, ::math:`\gamma_i` and -:math:`\gamma_j` are the widths of the Gaussian charge distribution and -erf() is the error-function. This style has to be used in conjunction -with the :doc:`kspace_style ` command - -If one cutoff is specified it is used for both the vdW and Coulomb -terms. If two cutoffs are specified, the first is used as the cutoff -for the vdW terms, and the second is the cutoff for the Coulombic term. - -The following coefficients must be defined for each pair of atoms -types via the :doc:`pair_coeff ` command as in the examples -above, or in the data file or restart files read by the -:doc:`read_data ` or :doc:`read_restart ` -commands: - -* :math:`\epsilon` (energy) -* :math:`r_v` (distance) -* :math:`\gamma` (distance) - ----------- - -Mixing, shift, table, tail correction, restart, rRESPA info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -Mixing rules are fixed for this style as defined above. - -Shifting the potential energy is not necessary because the switching -function ensures that the potential is zero at the cut-off. - -Restrictions -"""""""""""" - -These styles are part of the USER-YAFF package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - -Related commands -"""""""""""""""" - -:doc:`pair_coeff ` - -Default -""""""" - -none diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst new file mode 100644 index 0000000000..56ae0f32dc --- /dev/null +++ b/doc/src/pair_pace.rst @@ -0,0 +1,114 @@ +.. index:: pair_style pace + +pair_style pace command +======================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style pace ... keyword values ... + +* an optional keyword may be appended +* keyword = *product* or *recursive* + + .. parsed-literal:: + + *product* = use product algorithm for basis functions + *recursive* = use recursive algorithm for basis functions + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style pace + pair_style pace product + pair_coeff * * Cu-PBE-core-rep.ace Cu + +Description +""""""""""" + +Pair style *pace* computes interactions using the Atomic Cluster +Expansion (ACE), which is a general expansion of the atomic energy in +multi-body basis functions. :ref:`(Drautz) `. +The *pace* pair style +provides an efficient implementation that +is described in this paper :ref:`(Lysogorskiy) `. + +In ACE, the total energy is decomposed into a sum over +atomic energies. The energy of atom *i* is expressed as a +linear or non-linear function of one or more density functions. +By projecting the +density onto a local atomic base, the lowest order contributions +to the energy can be expressed as a set of scalar polynomials in +basis function contributions summed over neighbor atoms. + +Only a single pair_coeff command is used with the *pace* style which +specifies an ACE coefficient file followed by N additional arguments +specifying the mapping of ACE elements to LAMMPS atom types, +where N is the number of LAMMPS atom types: + +* ACE coefficient file +* N element names = mapping of ACE elements to atom types + +Only a single pair_coeff command is used with the *pace* style which +specifies an ACE file that fully defines the potential. +Note that unlike for other potentials, cutoffs are +not set in the pair_style or pair_coeff command; they are specified in +the ACE file. + +The pair_style *pace* command may be followed by an optional keyword +*product* or *recursive*, which determines which of two algorithms +is used for the calculation of basis functions and derivatives. +The default is *recursive*. + +See the :doc:`pair_coeff ` doc page for alternate ways +to specify the path for the ACE coefficient file. + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS with +user-specifiable parameters as described above. You never need to +specify a pair_coeff command with I != J arguments for this style. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This pair style is part of the USER-PACE package. It is only enabled if LAMMPS +was built with that package. +See the :doc:`Build package ` doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_style snap ` + +Default +""""""" + +recursive + +.. _Drautz20191: + +**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019). + +.. _Lysogorskiy20211: + +**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021). diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index 6abe037581..3df70a017c 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -319,7 +319,7 @@ This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This pair potential requires the :doc:`newtion ` setting to be +This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. The potential files provided with LAMMPS (see the potentials directory) diff --git a/doc/src/pair_rann.rst b/doc/src/pair_rann.rst new file mode 100644 index 0000000000..4177bae0c7 --- /dev/null +++ b/doc/src/pair_rann.rst @@ -0,0 +1,412 @@ +.. index:: pair_style rann + +pair_style rann command +======================= + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style rann + pair_coeff file Type1_element Type2_element Type3_element... + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style rann + pair_coeff ** Mg.rann Mg + pair_coeff ** MgAlalloy.rann Mg Mg Al Mg + +Description +""""""""""" + +Pair style *rann* computes pairwise interactions for a variety of +materials using rapid atomistic neural network (RANN) potentials +(:ref:`Dickel ` , :ref:`Nitol `). Neural network +potentials work by first generating a series of symmetry functions +i.e. structural fingerprints from the neighbor list and then using these +values as the input layer of a neural network. There is a single output +neuron in the final layer which is the energy. Atomic forces are found +by analytical derivatives computed via back-propagation. For alloy +systems, each element has a unique network. + +Potential file syntax +""""""""""""""""""""" + +The RANN potential is defined by a single text file which contains all +the fitting parameters for the alloy system. The potential file also +defines the active fingerprints, network architecture, activation +functions, etc. The potential file is divided into several sections +which are identified by one of the following keywords: + +* atomtypes +* mass +* fingerprintsperelement +* fingerprints +* fingerprintconstants +* screening (optional) +* networklayers +* layersize +* weight +* bias +* activationfunctions +* calibrationparameters (ignored) + +The '#' character is treated as a comment marker, similar to LAMMPS +input scripts. Sections are not required to follow a rigid ordering, +but do require previous definition of prerequisite information. E.g., +fingerprintconstants for a particular fingerprint must follow the +fingerprints definition; layersize for a particular layer must follow +the declaration of network layers. + +*atomtypes* are defined as follows using element keywords separated by spaces. + +.. code-block:: + + atomtypes: + Fe Mg Al etc. + +*mass* must be specified for each element keyword as follows: + +.. code-block:: + + mass:Mg: + 24.305 + mass:Fe: + 55.847 + mass:Al: + 26.982 + +*fingerprintsperelement* specifies how many fingerprints are active for +computing the energy of a given atom. This number must be specified for +each element keyword. Active elements for each fingerprint depend upon +the type of the central atom and the neighboring atoms. Pairwise +fingerprints may be defined for a Mg atom based exclusively on its Al +neighbors, for example. Bond fingerprints may use two neighbor lists of +different element types. In computing fingerprintsperelement from all +defined fingerprints, only the fingerprints defined for atoms of a +particular element should be considered, regardless of the elements used +in its neighbor list. In the following code, for example, some +fingerprints may compute pairwise fingerprints summing contributions +about Fe atoms based on a neighbor list of exclusively Al atoms, but if +there are no fingerprints summing contributions of all neighbors about a +central Al atom, then fingerprintsperelement of Al is zero: + +.. code-block:: + + fingerprintsperelement:Mg: + 5 + fingerprintsperelement:Fe: + 2 + fingerprintsperelement:Al: + 0 + +*fingerprints* specifies the active fingerprints for a certain element +combination. Pair fingerprints are specified for two elements, while +bond fingerprints are specified for three elements. Only one +fingerprints header should be used for an individual combination of +elements. The ordering of the fingerprints in the network input layer +is determined by the order of element combinations specified by +subsequent *fingerprints* lines, and the order of the fingerprints +defined for each element combination. Multiple fingerprints of the same +style or different ones may be specified. If the same style and element +combination is used for multiple fingerprints, they should have +different id numbers. The first element specifies the atoms for which +this fingerprint is computed while the other(s) specify which atoms to +use in the neighbor lists for the computation. Switching the second and +third element type in bond fingerprints has no effect on the +computation: + +.. code-block:: + + fingerprints:Mg_Mg: + radial_0 radialscreened_0 radial_1 + fingerprints:Mg_Al_Fe: + bond_0 bondspin_0 + fingerprints:Mg_Al: + radial_0 radialscreened_0 + +The following fingerprint styles are currently defined. See the +:ref:`formulation section ` below for their definitions: + +* radial +* radialscreened +* radialspin +* radialscreenedspin +* bond +* bondscreened +* bondspin +* bondscreenedspin + +*fingerprintconstants* specifies the meta-parameters for a defined fingerprint. For all radial styles, re, rc, +alpha, dr, o, and n must be specified. re should usually be the stable interatomic distance, rc is the cutoff +radius, dr is the cutoff smoothing distance, o is the lowest radial power term (which may be negative), and n +is the highest power term. The total length of the fingerprint vector is (n-o+1). alpha is a list of decay parameters +used for exponential decay of radial contributions. It may be set proportionally to the bulk modulus similarly +to MEAM potentials, but other values may provided better fitting in special cases. Bond style fingerprints require +specification of re, rc, alphak, dr, k, and m. Here m is the power of the bond cosines and k is the number of +decay parameters. Cosine powers go from 0 to m-1 and are each computed for all values of alphak. Thus the total +length of the fingerprint vector is m*k. + +.. code-block:: + + fingerprintconstants:Mg_Mg:radialscreened_0:re: + 3.193592 + fingerprintconstants:Mg_Mg:radialscreened_0:rc: + 6.000000 + fingerprintconstants:Mg_Mg:radialscreened_0:alpha: + 5.520000 5.520000 5.520000 5.520000 5.520000 + fingerprintconstants:Mg_Mg:radialscreened_0:dr: + 2.806408 + fingerprintconstants:Mg_Mg:radialscreened_0:o: + -1 + fingerprintconstants:Mg_Mg:radialscreened_0:n: + 3 + +*screening* specifies the Cmax and Cmin values used in the screening +fingerprints. Contributions form neighbors to the fingerprint are +omitted if they are blocked by a closer neighbor, and reduced if they +are partially blocked. Larger values of Cmin correspond to neighbors +being blocked more easily. Cmax cannot be greater than 3, and Cmin +cannot be greater than Cmax or less than zero. Screening may be omitted +in which case the default values Cmax = 2.8, Cmin = 0.8 are used. Since +screening is a bond computation, it is specified separately for each +combination of three elements in which the latter two may be +interchanged with no effect. + +.. code-block:: + + screening:Mg_Mg_Mg:Cmax: + 2.700000 + screening:Mg_Mg_Mg:Cmin: + 0.400000 + +*networklayers* species the size of the neural network for each atom. +It counts both the input and output layer and so is 2 + \. + +.. code-block:: + + networklayers:Mg: + 3 + +*layersize* specifies the length of each layer, including the input +layer and output layer. The input layer is layer 0. The size of the +input layer size must match the summed length of all the fingerprints +for that element, and the output layer size must be 1: + +.. code-block:: + + layersize:Mg:0: + 14 + layersize:Mg:1: + 20 + layersize:Mg:2: + 1 + + +*weight* specifies the weight for a given element and layer. Weight +cannot be specified for the output layer. The weight of layer i is a +*m* x *n* matrix where *m* is the layer size of *i* and *n* is the layer size of +*i*\ +1: + +.. code-block:: + + weight:Mg:0: + w11 w12 w13 ... + w21 w22 w23 ... + ... + +*bias* specifies the bias for a given element and layer. Bias cannot be +specified for the output layer. The bias of layer i is a nx1 vector +where n is the layer size of i+1: + +.. code-block:: + + bias:Mg:0: + b1 + b2 + b3 + ... + +*activationfunctions* specifies the activation function for a given +element and layer. Activation functions cannot be specified for the +output layer: + +.. code-block:: + + activationfunctions:Mg:0: + sigI + activationfunctions:Mg:1: + linear + +The following activation styles are currently specified. See the +:ref:`formulation section ` below for their definitions. + +* sigI + +* linear + +*calibrationparameters* specifies a number of parameters used to calibrate the potential. These are ignored +by LAMMPS. + +Formulation +""""""""""" + +In the RANN formulation, the total energy of a system of atoms +is given by: + +.. math:: + + E = \sum_{\alpha} E^{\alpha}\\\\ + E^{\alpha} = {}^{N}\!A^{\alpha}\\\\ + {}^{n+1}\!A_i^{\alpha} = {}^{n}\!F\left({}^{n}\!W_{ij}{\;}^{n}\!A_j^{\alpha}+{}^{n}\!B_i\right)\\\\ + {}^{0}\!A_i^{\alpha} = \left[\begin{array}{c} {}^1\!S\!f^\alpha\\ {}^2\!S\!f^\alpha \\...\\\end{array}\right] + +Here :math:`E^\alpha` is the energy of atom :math:`\alpha`, +:math:`{}^n\!F()`, :math:`{}^n\!W_{ij}` and :math:`{}^n\!B_i` are the +activation function, weight matrix and bias vector of the n-th layer +respectively. The inputs to the first layer are a collection of +structural fingerprints which are collected and reshaped into a single +long vector. The individual fingerprints may be defined in any order +and have various shapes and sizes. Multiple fingerprints of the same +type and varying parameters may also be defined in the input layer. + +Eight types of structural fingerprints are currently defined. In the +following, :math:`\beta` and :math:`\gamma` span the full neighbor list +of atom :math:`\alpha`. :math:`\delta_i` are decay meta-parameters, and +:math:`r_e` is a meta-parameter roughly proportional to the first +neighbor distance. :math:`r_c` and :math:`dr` are the neighbor cutoff +distance and cutoff smoothing distance respectively. +:math:`S^{\alpha\beta}` is the MEAM screening function :ref:`(Baskes) +`, :math:`s_i^\alpha` and :math:`s_i^\beta` are the atom spin +vectors :ref:`(Tranchida) `. :math:`r^{\alpha\beta}` is the +distance from atom :math:`\alpha` to atom :math:`\beta`, and +:math:`\theta^{\alpha\beta\gamma}` is the bond angle: + +.. math :: + + cos\left(\theta^{\alpha\beta\gamma}\right)=\frac{\mathbf{r}^{\alpha\beta} \cdot \mathbf{r}^{\alpha\gamma}}{r^{\alpha\beta}r^{\alpha\gamma}} + +:math:`S^{\alpha\beta}` is defined as :ref:`(Baskes) `: + +.. math:: + + X^{\gamma\beta} = \left(\frac{r^{\gamma\beta}}{r^{\alpha\beta}}\right)^2\\ + \\ + X^{\alpha\gamma} = \left(\frac{r^{\alpha\gamma}}{r^{\alpha\beta}}\right)^2\\ + \\ + C = \frac{2\left(X^{\alpha\gamma}+X^{\gamma\beta}\right)-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2-1}{1-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2}\\ + \\ + f_c(x) = \left[\begin{array}{l} 1 \; \: x \geq 1\\ \left(1-\left(1-x\right)^4\right)^2 \; \: 0` - turn off pairwise interactions * :doc:`hybrid ` - multiple styles of pairwise interactions * :doc:`hybrid/overlay ` - multiple styles of superposed pairwise interactions +* :doc:`hybrid/scaled ` - multiple styles of scaled superposed pairwise interactions * :doc:`zero ` - neighbor list but no interactions * :doc:`adp ` - angular dependent potential (ADP) of Mishin -* :doc:`agni ` - machine learned potential mapping atomic environment to forces +* :doc:`agni ` - AGNI machine-learning potential * :doc:`airebo ` - AIREBO potential of Stuart * :doc:`airebo/morse ` - AIREBO with Morse instead of LJ * :doc:`atm ` - Axilrod-Teller-Muto potential @@ -132,12 +133,15 @@ accelerated styles exist. * :doc:`comb3 ` - charge-optimized many-body (COMB3) potential * :doc:`cosine/squared ` - Cooke-Kremer-Deserno membrane model potential * :doc:`coul/cut ` - cutoff Coulomb potential +* :doc:`coul/cut/dielectric ` - +* :doc:`coul/cut/global ` - cutoff Coulomb potential * :doc:`coul/cut/soft ` - Coulomb potential with a soft core * :doc:`coul/debye ` - cutoff Coulomb potential with Debye screening * :doc:`coul/diel ` - Coulomb potential with dielectric permittivity * :doc:`coul/dsf ` - Coulomb with damped-shifted-force model * :doc:`coul/long ` - long-range Coulomb potential * :doc:`coul/long/cs ` - long-range Coulomb potential and core/shell +* :doc:`coul/long/dielectric ` - * :doc:`coul/long/soft ` - long-range Coulomb potential with a soft core * :doc:`coul/msm ` - long-range MSM Coulomb * :doc:`coul/slater/cut ` - smeared out Coulomb @@ -148,6 +152,8 @@ accelerated styles exist. * :doc:`coul/wolf ` - Coulomb via Wolf potential * :doc:`coul/wolf/cs ` - Coulomb via Wolf potential with core/shell adjustments * :doc:`dpd ` - dissipative particle dynamics (DPD) +* :doc:`dpd/ext ` - generalized force field for DPD +* :doc:`dpd/ext/tstat ` - pair-wise DPD thermostatting with generalized force field * :doc:`dpd/fdt ` - DPD for constant temperature and pressure * :doc:`dpd/fdt/energy ` - DPD for constant energy and enthalpy * :doc:`dpd/tstat ` - pair-wise DPD thermostatting @@ -178,6 +184,7 @@ accelerated styles exist. * :doc:`gw/zbl ` - Gao-Weber potential with a repulsive ZBL core * :doc:`hbond/dreiding/lj ` - DREIDING hydrogen bonding LJ potential * :doc:`hbond/dreiding/morse ` - DREIDING hydrogen bonding Morse potential +* :doc:`hdnnp ` - High-dimensional neural network potential * :doc:`ilp/graphene/hbn ` - registry-dependent interlayer potential (ILP) * :doc:`kim ` - interface to potentials provided by KIM project * :doc:`kolmogorov/crespi/full ` - Kolmogorov-Crespi (KC) potential with no simplifications @@ -204,13 +211,17 @@ accelerated styles exist. * :doc:`lj/cubic ` - LJ with cubic after inflection point * :doc:`lj/cut ` - cutoff Lennard-Jones potential without Coulomb * :doc:`lj/cut/coul/cut ` - LJ with cutoff Coulomb +* :doc:`lj/cut/coul/cut/dielectric ` - * :doc:`lj/cut/coul/cut/soft ` - LJ with cutoff Coulomb with a soft core * :doc:`lj/cut/coul/debye ` - LJ with Debye screening added to Coulomb +* :doc:`lj/cut/coul/debye/dielectric ` - * :doc:`lj/cut/coul/dsf ` - LJ with Coulomb via damped shifted forces * :doc:`lj/cut/coul/long ` - LJ with long-range Coulomb * :doc:`lj/cut/coul/long/cs ` - LJ with long-range Coulomb with core/shell adjustments +* :doc:`lj/cut/coul/long/dielectric ` - * :doc:`lj/cut/coul/long/soft ` - LJ with long-range Coulomb with a soft core * :doc:`lj/cut/coul/msm ` - LJ with long-range MSM Coulomb +* :doc:`lj/cut/coul/msm/dielectric ` - * :doc:`lj/cut/coul/wolf ` - LJ with Coulomb via Wolf potential * :doc:`lj/cut/dipole/cut ` - point dipoles with cutoff * :doc:`lj/cut/dipole/long ` - point dipoles with long-range Ewald @@ -224,6 +235,7 @@ accelerated styles exist. * :doc:`lj/gromacs ` - GROMACS-style Lennard-Jones potential * :doc:`lj/gromacs/coul/gromacs ` - GROMACS-style LJ and Coulomb potential * :doc:`lj/long/coul/long ` - long-range LJ and long-range Coulomb +* :doc:`lj/long/coul/long/dielectric ` - * :doc:`lj/long/dipole/long ` - long-range LJ and long-range point dipoles * :doc:`lj/long/tip4p/long ` - long-range LJ and long-range Coulomb for TIP4P water * :doc:`lj/mdf ` - LJ potential with a taper function @@ -250,7 +262,7 @@ accelerated styles exist. * :doc:`mgpt ` - simplified model generalized pseudopotential theory (MGPT) potential * :doc:`mesont/tpm ` - nanotubes mesoscopic force field * :doc:`mie/cut ` - Mie potential -* :doc:`mm3/switch3/coulgauss/long ` - smoothed MM3 vdW potential with Gaussian electrostatics +* :doc:`mm3/switch3/coulgauss/long ` - smoothed MM3 vdW potential with Gaussian electrostatics * :doc:`momb ` - Many-Body Metal-Organic (MOMB) force field * :doc:`morse ` - Morse potential * :doc:`morse/smooth/linear ` - linear smoothed Morse potential @@ -278,6 +290,7 @@ accelerated styles exist. * :doc:`oxrna2/hbond ` - * :doc:`oxrna2/stk ` - * :doc:`oxrna2/xstk ` - +* :doc:`pace ` - Atomic Cluster Expansion (ACE) machine-learning potential * :doc:`peri/eps ` - peridynamic EPS potential * :doc:`peri/lps ` - peridynamic LPS potential * :doc:`peri/pmb ` - peridynamic PMB potential @@ -285,6 +298,7 @@ accelerated styles exist. * :doc:`polymorphic ` - polymorphic 3-body potential * :doc:`python ` - * :doc:`quip ` - +* :doc:`rann ` - * :doc:`reax/c ` - ReaxFF potential in C * :doc:`rebo ` - second generation REBO potential of Brenner * :doc:`resquared ` - Everaers RE-Squared ellipsoidal potential @@ -295,7 +309,7 @@ accelerated styles exist. * :doc:`smd/ulsph ` - * :doc:`smtbq ` - * :doc:`mliap ` - Multiple styles of machine-learning potential -* :doc:`snap ` - SNAP quantum-accurate potential +* :doc:`snap ` - SNAP machine-learning potential * :doc:`soft ` - Soft (cosine) potential * :doc:`sph/heatconduction ` - * :doc:`sph/idealgas ` - diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index a8cf8ee044..183bab48c9 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -42,6 +42,8 @@ Examples pair_style lj/cut/thole/long 2.6 12.0 +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index aef401ec7c..9edb77ecbe 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -217,7 +217,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -These pair style are part of the MANYBODY package. They is only +These pair styles are part of the MANYBODY package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. These pair styles requires the :doc:`newton ` setting to be "on" diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst new file mode 100644 index 0000000000..02228636bc --- /dev/null +++ b/doc/src/plugin.rst @@ -0,0 +1,90 @@ +.. index:: plugin + +plugin command +============== + +Syntax +"""""" + +.. parsed-literal:: + + plugin command args + +* command = *load* or *unload* or *list* or *clear* +* args = list of arguments for a particular plugin command + + .. parsed-literal:: + + *load* file = load plugin(s) from shared object in *file* + *unload* style name = unload plugin *name* of style *style* + *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *compute* or *fix* or *region* or *command* + *list* = print a list of currently loaded plugins + *clear* = unload all currently loaded plugins + +Examples +"""""""" + +.. code-block:: LAMMPS + + plugin load morse2plugin.so + plugin unload pair morse2/omp + plugin unload command hello + plugin list + plugin clear + +Description +""""""""""" + +The plugin command allows to load (and unload) additional styles and +commands into a LAMMPS binary from so-called dynamic shared object (DSO) +files. This enables to add new functionality to an existing LAMMPS +binary without having to recompile and link the entire executable. + +The *load* command will load and initialize all plugins contained in the +plugin DSO with the given filename. A message with information the +plugin style and name and more will be printed. Individual DSO files +may contain multiple plugins. More details about how to write and +compile the plugin DSO is given in programmer's guide part of the manual +under :doc:`Developer_plugins`. + +The *unload* command will remove the given style or the given name from +the list of available styles. If the plugin style is currently in use, +that style instance will be deleted. + +The *list* command will print a list of the loaded plugins and their +styles and names. + +The *clear* command will unload all currently loaded plugins. + + +Restrictions +"""""""""""" + +The *plugin* command is part of the PLUGIN package. It is +only enabled if LAMMPS was built with that package. +See the :doc:`Build package ` doc page for +more info. Plugins are not available on Windows. + +For the loading of plugins to work the LAMMPS library must be +:ref:`compiled as a shared library `. If plugins +access functions or classes from a package, LAMMPS must have +been compiled with that package included. + +Plugins are dependent on the LAMMPS binary interface (ABI) +and particularly the MPI library used. So they are not guaranteed +to work when the plugin was compiled with a different MPI library +or different compilation settings or a different LAMMPS version. +There are no checks, so if there is a mismatch the plugin object +will either not load or data corruption and crashes may happen. + + +Related commands +"""""""""""""""" + +none + + +Default +""""""" + +none diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 5d74d9c28b..bd7c480af2 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -223,6 +223,9 @@ The structure of the data file is important, though many settings and sections are optional or can come in any order. See the examples directory for sample data files for different problems. +The file will be read line by line, but there is a limit of 254 +characters per line and characters beyond that limit will be ignored. + A data file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains a description of the file. Then lines are read one at a time. Lines diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index 7d51fba868..e9e23afba8 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -15,7 +15,7 @@ Syntax .. parsed-literal:: - keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump* + keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *post* or *dump* *first* args = Nfirst Nfirst = dump timestep to start on *last* args = Nlast @@ -28,6 +28,7 @@ Syntax Nstart = timestep on which pseudo run will start *stop* args = Nstop Nstop = timestep to which pseudo run will end + *post* value = *yes* or *no* *dump* args = same as :doc:`read_dump ` command starting with its field arguments Examples @@ -154,6 +155,10 @@ Also note that an error will occur if you read a snapshot from the dump file with a timestep value larger than the *stop* setting you have specified. +The *post* keyword can be used to minimize the output to the screen that +happens after a *rerun* command, similar to the post keyword of the +:doc:`run command `. It is set to *no* by default. + The *dump* keyword is required and must be the last keyword specified. Its arguments are passed internally to the :doc:`read_dump ` command. The first argument following the *dump* keyword should be @@ -226,4 +231,4 @@ Default The option defaults are first = 0, last = a huge value (effectively infinity), start = same as first, stop = same as last, every = 0, skip -= 1; += 1, post = no; diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 4439f7732c..1815a7cb76 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -11,12 +11,13 @@ Syntax thermo_modify keyword value ... * one or more keyword/value pairs may be listed -* keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press* +* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *format* or *temp* or *press* .. parsed-literal:: *lost* value = *error* or *warn* or *ignore* *lost/bond* value = *error* or *warn* or *ignore* + *warn* value = *ignore* or *reset* or *default* or a number *norm* value = *yes* or *no* *flush* value = *yes* or *no* *line* value = *one* or *multi* @@ -75,6 +76,43 @@ are drifting out of the box through a fixed boundary condition (see the :doc:`boundary ` command). In this case one atom may be deleted before the rest of the molecule is, on a later timestep. +The *warn* keyword allows you to control whether LAMMPS will print +warning messages and how many of them. Most warning messages are only +printed by MPI rank 0. They are usually pointing out important issues +that should be investigated, but LAMMPS cannot determine for +certain whether they are an indication of an error. + +Some warning messages are printed during a run (or immediately before) +each time a specific MPI rank encounters the issue, e.g. bonds that are +stretched too far or dihedrals in extreme configurations. These number +of these can quickly blow up the size of the log file and screen output. +Thus a limit of 100 warning messages is applied by default. The warning +count is applied to the entire input unless reset with a ``thermo_modify +warn reset`` command. If there are more warnings than the limit, LAMMPS +will print one final warning that it will not print any additional +warning messages. + +.. note:: + + The warning limit is enforced on either the per-processor count or + the total count across all processors. For efficiency reasons, + however, the total count is only updated at steps with thermodynamic + output. Thus when running on a large number of processors in + parallel, the total number of warnings printed can be significantly + larger than the given limit. + +Any number after the keyword *warn* will change the warning limit +accordingly. With the value *ignore* all warnings will be suppressed, +with the value *always* no limit will be applied and warnings will +always be printed, with the value *reset* the internal warning counter +will be reset to zero, and with the value *default*, the counter is +reset and the limit set to 100. An example usage of either *reset* or +*default* would be to re-enable warnings that were disabled or have +reached the limit during equilibration, where the warnings would be +acceptable while the system is still adjusting, but then change +to all warnings for the production run, where they would indicate +problems that would require a closer look at what is causing them. + The *norm* keyword determines whether various thermodynamic output values are normalized by the number of atoms or not, depending on whether it is set to *yes* or *no*\ . Different unit styles have @@ -183,9 +221,9 @@ Related commands Default """"""" -The option defaults are lost = error, norm = yes for unit style of -*lj*\ , norm = no for unit style of *real* and *metal*\ , flush = no, -and temp/press = compute IDs defined by thermo_style. +The option defaults are lost = error, warn = 100, norm = yes for unit +style of *lj*\ , norm = no for unit style of *real* and *metal*\ , +flush = no, and temp/press = compute IDs defined by thermo_style. The defaults for the line and format options depend on the thermo style. For styles "one" and "custom", the line and format defaults diff --git a/doc/src/units.rst b/doc/src/units.rst index 8ca29f4c49..3c0f4a220a 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -87,7 +87,7 @@ energy is a derived unit (in SI units you equivalently have the relation * charge = reduced LJ charge, where :math:`q^* = q \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon}}` * dipole = reduced LJ dipole, moment where :math:`\mu^* = \mu \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma^3 \epsilon}}` * electric field = force/charge, where :math:`E^* = E \frac{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon} \sigma}{\epsilon}` -* density = mass/volume, where :math:`\rho^* = \rho \sigma^{dim}` +* density = mass/volume, where :math:`\rho^* = \rho \frac{\sigma^{dim}}{m}` Note that for LJ units, the default mode of thermodynamic output via the :doc:`thermo_style ` command is to normalize all diff --git a/doc/src/variable.rst b/doc/src/variable.rst index ea6b7ef8ec..4747c492aa 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -65,8 +65,8 @@ Syntax bound(group,dir,region), gyration(group,region), ke(group,reigon), angmom(group,dim,region), torque(group,dim,region), inertia(group,dimdim,region), omega(group,dim,region) - special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) - feature functions = is_active(category,feature,exact), is_defined(category,id,exact) + special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name) + feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id) atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] @@ -363,12 +363,14 @@ variable, as discussed below. The rules for formatting the file are as follows. Each time a set of per-atom values is read, a non-blank line is searched for in the file. -A comment character "#" can be used anywhere on a line; text starting -with the comment character is stripped. Blank lines are skipped. The -first "word" of a non-blank line, delimited by white-space, is read as -the count N of per-atom lines to immediately follow. N can be the -total number of atoms in the system, or only a subset. The next N -lines have the following format +The file is read line by line but only up to 254 characters are used. +The rest are ignored. A comment character "#" can be used anywhere +on a line and all text following and the "#" character are ignored; +text starting with the comment character is stripped. Blank lines +are skipped. The first "word" of a non-blank line, delimited by +white-space, is read as the count N of per-atom lines to immediately +follow. N can be the total number of atoms in the system, or only a +subset. The next N lines have the following format .. parsed-literal:: @@ -429,7 +431,7 @@ argument. For *equal*\ -style variables the formula computes a scalar quantity, which becomes the value of the variable whenever it is evaluated. For *vector*\ -style variables the formula must compute a vector of quantities, which becomes the value of the variable whenever -it is evaluated. The calculated vector can be on length one, but it +it is evaluated. The calculated vector can be of length one, but it cannot be a simple scalar value like that produced by an equal-style compute. I.e. the formula for a vector-style variable must have at least one quantity in it that refers to a global vector produced by a @@ -821,6 +823,10 @@ Special Functions Special functions take specific kinds of arguments, meaning their arguments cannot be formulas themselves. +The is_file(x) function is a test whether 'x' is a (readable) file +and returns 1 in this case, otherwise it returns 0. For that 'x' +is taken as a literal string and must not have any blanks in it. + The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions each take 1 argument which is of the form "c_ID" or "c_ID[N]" or "f_ID" or "f_ID[N]" or "v_name". The first two are computes and the diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py old mode 100644 new mode 100755 index 64a1308601..5d4ee428e2 --- a/doc/utils/converters/lammpsdoc/rst_anchor_check.py +++ b/doc/utils/converters/lammpsdoc/rst_anchor_check.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python3 +#!/usr/bin/env python3 # LAMMPS Documentation Utilities # # Scan for duplicate anchor labels in documentation files diff --git a/doc/utils/converters/setup.py b/doc/utils/converters/setup.py index d85669bcc1..275c9b0c0b 100644 --- a/doc/utils/converters/setup.py +++ b/doc/utils/converters/setup.py @@ -1,7 +1,7 @@ from setuptools import setup setup(name='LAMMPS Documentation Utilities', - version='2.0.0', + version='2.0.1', description='Utilities to convert existing LAMMPS documentation text files into ReStructured Text', url='https://github.com/rbberger/lammps-doc-utils', author='Richard Berger', @@ -11,8 +11,6 @@ setup(name='LAMMPS Documentation Utilities', test_suite='nose.collector', tests_require=['nose'], entry_points = { - "console_scripts": ['txt2html = lammpsdoc.txt2html:main', - 'txt2rst = lammpsdoc.txt2rst:main', - 'rst_anchor_check = lammpsdoc.rst_anchor_check:main '] + "console_scripts": ['rst_anchor_check = lammpsdoc.rst_anchor_check:main '] }, ) diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index 00fa6ecfaf..9b8e106875 100644 --- a/doc/utils/requirements.txt +++ b/doc/utils/requirements.txt @@ -4,3 +4,4 @@ git+git://github.com/akohlmey/sphinx-fortran@parallel-read sphinx_tabs breathe Pygments +six diff --git a/doc/utils/sphinx-config/_static/css/lammps.css b/doc/utils/sphinx-config/_static/css/lammps.css index b69405365a..900054eeeb 100644 --- a/doc/utils/sphinx-config/_static/css/lammps.css +++ b/doc/utils/sphinx-config/_static/css/lammps.css @@ -35,6 +35,10 @@ hr { display: none; } +#command-reference.section h2 { + display: none; +} + .ui.tabular.menu .item { padding-right: 1em; padding-left: 1em; diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html index 3a5672093d..d658528368 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html @@ -65,7 +65,7 @@ {% elif show_source and has_source and sourcename %} {{ _('View page source') }} {% endif %} - Website + Website Commands {% endif %} diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html index 845f213a4c..703a3ace5d 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html @@ -38,10 +38,11 @@ {% if favicon %} {% endif %} - {# CANONICAL URL #} - {% if theme_canonical_url %} - - {% endif %} + + {#- CANONICAL URL #} + {%- if pageurl %} + + {%- endif -%} {# JAVASCRIPTS #} {%- block scripts %} @@ -134,14 +135,8 @@ {% if theme_display_version %} - {%- set nav_version = version %} - {% if READTHEDOCS and current_version %} - {%- set nav_version = current_version %} - {% endif %} - {% if nav_version %} -
Version: {{ nav_version }}
+
Version: {{ current_version }}
git info: {{ release }}
- {% endif %} {% endif %} {% include "searchbox.html" %} diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf b/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf index 37dc1185b7..444b1379f2 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf +++ b/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf @@ -4,7 +4,6 @@ stylesheet = css/theme.css pygments_style = default [options] -canonical_url = analytics_id = collapse_navigation = False sticky_navigation = False diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/versions.html b/doc/utils/sphinx-config/_themes/lammps_theme/versions.html index 7368659c43..f0ec4fea1a 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/versions.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/versions.html @@ -1,9 +1,9 @@ -{% if READTHEDOCS %} +{% if READTHEDOCS or display_manual_versions %} {# Add rst-badge after rst-versions for small badge style. #}
- Read the Docs - v: {{ current_version }} + Version + {{ current_version }}
@@ -20,14 +20,8 @@ {% endfor %}
- {# Translators: The phrase "Read the Docs" is not translated #} -
{{ _('On Read the Docs') }}
-
- {{ _('Project Home') }} -
-
- {{ _('Builds') }} -
+
Git Info
+
{{ release }}
diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index 17cb3c2395..68a61af009 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -15,6 +15,7 @@ import sys import os +from datetime import date has_enchant = False try: @@ -76,7 +77,7 @@ master_doc = 'Manual' # General information about the project. project = 'LAMMPS' -copyright = '2003-2020 Sandia Corporation' +copyright = '2003-{} Sandia Corporation'.format(date.today().year) def get_lammps_version(): import os @@ -99,6 +100,16 @@ def get_git_info(): pass return git_n_date +def get_git_commit(): + import subprocess,time + try: + commit = subprocess.run(['git','rev-parse','HEAD'],stdout=subprocess.PIPE,stderr=subprocess.PIPE) + if commit.returncode == 0: + return commit.stdout.decode() + except: + pass + return '' + # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. @@ -108,6 +119,8 @@ version = get_lammps_version() # The full version, including alpha/beta/rc tags. release = get_git_info() +git_commit = get_git_commit() + # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None @@ -241,7 +254,9 @@ html_show_sourcelink = False # Output file base name for HTML help builder. htmlhelp_basename = 'LAMMPSdoc' -html_add_permalinks = '' +html_permalinks = True + +html_baseurl = os.environ.get('LAMMPS_WEBSITE_BASEURL', '') if 'epub' in sys.argv: html_math_renderer = 'imgmath' @@ -348,7 +363,7 @@ with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The primary author of the code is Steve Plimpton, who can be emailed -at sjplimp@sandia.gov. The LAMMPS WWW Site at lammps.sandia.gov has +at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has more information about the code and its uses. """ @@ -389,3 +404,20 @@ breathe_domain_by_extension = { 'h' : 'cpp', 'cpp' : 'cpp', 'c' : 'c', } + +# allows showing multiple versions +try: + html_context +except NameError: + html_context = dict() + +is_website_build = os.environ.get('LAMMPS_WEBSITE_BUILD', '0') != '0' + +html_context['display_manual_versions'] = is_website_build +html_context['current_version'] = os.environ.get('LAMMPS_WEBSITE_BUILD_VERSION', version) +html_context['git_commit'] = git_commit +html_context['versions'] = [ + ('latest', 'https://docs.lammps.org/latest/'), + (version, 'https://docs.lammps.org/') +] +html_context['downloads'] = [('PDF', 'Manual.pdf')] diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 1d66028621..5d9b3eb8c1 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -23,6 +23,7 @@ acolor acos Acta actinide +activationfunctions acylindricity addforce Addington @@ -47,6 +48,7 @@ Agnolin Ai Aidan aij +aimd airebo Aj ajs @@ -74,6 +76,7 @@ allocaters allosws AlO Alonso +alphak alphashrink amap Amatrix @@ -101,6 +104,7 @@ anisotropic anisotropies anisotropy ansi +antiferromagnetic antiquewhite Antisymmetrized antisymmetry @@ -151,6 +155,7 @@ atomfile AtomicPairStyle atomID atomistic +atomtypes attogram attograms attrac @@ -183,8 +188,10 @@ Babaei backcolor backends Baczewski +Bagchi Bagi Bagnold +Bajaj Bkappa Bal balancer @@ -195,12 +202,15 @@ Ballenegger Bammann Banna Barashev +Barbosa +barnes barostat Barostats barostatted barostatting Barostatting Barrat +Barros Bartelt Bartels barycenter @@ -218,6 +228,7 @@ bdw Beckman Belak Bellott +bem benchmarking Bennet Berardi @@ -261,6 +272,7 @@ bitmask bitrate bitrates Bitzek +Bjerrum Blaise blanchedalmond blocksize @@ -268,6 +280,7 @@ blueviolet bn bni bo +Bochkarev Bochum bocs bodyflag @@ -282,6 +295,9 @@ BondAngle BondBond bondchk bondmax +bondscreened +bondscreenedspin +bondspin bondtype Bonet Bonomi @@ -309,6 +325,7 @@ br Branduardi Branicio brennan +Briels Brien Brilliantov Broadwell @@ -333,6 +350,8 @@ bz cadetblue Cagin calc +calibrationfunctions +calibrationparameters calibre caltech Caltech @@ -343,6 +362,7 @@ Cao Capolungo Caro cartesian +Cas CasP Caswell Cates @@ -502,6 +522,8 @@ coulgauss coulombic Coulombic Coulombics +counterion +counterions Courant covalent covalently @@ -620,6 +642,7 @@ delflag Dellago delocalization delocalized +Delong delr deltaHf Dendrimer @@ -659,6 +682,7 @@ diagonalized diagonalizers diagonalizing Diallo +Dickel diel differentiable diffusively @@ -703,6 +727,7 @@ dodgerblue dof doi Donadio +Donev dotc Doty doxygen @@ -710,6 +735,7 @@ doxygenclass doxygenfunction downarrow Doye +Doyl dpd DPD dpdTheta @@ -730,6 +756,7 @@ DRUDE dsf dsmc dt +dtemp dtgrow dtheta dtshrink @@ -758,7 +785,6 @@ Dyre Dzyaloshinskii Eaa Eaat -Eacn eam eangle earg @@ -878,6 +904,7 @@ equilibrates equilibrating equilibration Equilibria +equilibria equilization equipartitioning Ercolessi @@ -1017,6 +1044,7 @@ fmag fmass fmm fmt +fmtlib fmx fmy fmz @@ -1069,6 +1097,7 @@ fuer fx fy fz +Gabor Gahler gainsboro Galindo @@ -1131,9 +1160,11 @@ gmake gmask Gmask GMock +gmres gneb GNEB Goldfarb +Gompper Gonzalez-Melchor googlemail googletest @@ -1193,6 +1224,8 @@ Halperin Halver Hamaker Hamel +Hammerschmidt +Hanley haptic Hara Harpertown @@ -1211,7 +1244,10 @@ hbn hbnewflag hbond hcp +hdnnp +HDNNP heatconduction +Hebbeker Hebenstreit Hecht Heenen @@ -1254,6 +1290,7 @@ holonomic Homebrew hooke Hookean +hostname hotpink Houlle howto @@ -1279,6 +1316,7 @@ hy hydrophobicity hydrostatic hydrostatically +hydroxyl Hynninen Hyoungki hyperdynamics @@ -1309,6 +1347,7 @@ ijk ijkl ik Ikeshoji +Ilie ilmenau Ilmenau ilp @@ -1369,6 +1408,7 @@ ints inv invariants inversed +ionizable ionocovalent iostreams iparam @@ -1426,6 +1466,7 @@ Izvekov izz Izz Jacobsen +Jadhao Jadhav jagreat Jahn @@ -1481,6 +1522,7 @@ Kadiri Kai Kalia Kamberaj +Kantorovich Kapfer Karls Karlsruhe @@ -1548,6 +1590,8 @@ Koning Kooser Korn Koskinen +Koslowski +Kosovan Koster Kosztin Kp @@ -1588,11 +1632,13 @@ lammps Lammps LAMMPS lammpsplot +lammpsplugin Lampis Lamoureux Lanczos Lande Landron +Landsgesell langevin Langevin Langston @@ -1609,6 +1655,7 @@ Laupretre Lauriat lavenderblush lawngreen +layersize lB lbfgs lbl @@ -1707,6 +1754,7 @@ Lmpsdata lmptype LMT ln +localhost localTemp localvectors Loewen @@ -1730,10 +1778,13 @@ lpsapi lrt lsfftw ltbbmalloc +Lua lubricateU lucy -Lua Luding +Luijten +lunit +Lunkad Lussetti Lustig lval @@ -1742,6 +1793,7 @@ lx ly Lybrand lyon +Lysogorskiy Lyulin lz Maaravi @@ -1800,8 +1852,11 @@ Materias mathbf mathjax matlab +Matous matplotlib Matsubara +Matteo +Matteson Mattice Mattox Mattson @@ -1831,6 +1886,8 @@ mc McLachlan md mdf +MDI +mdi mdpd mDPD meam @@ -1862,6 +1919,7 @@ MEMALIGN membered memcheck Mendelev +Menon mer Meremianin Mersenne @@ -1985,6 +2043,7 @@ mpiio mpirun mplayer mps +Mrovec Mryglod mscg MSCG @@ -2019,6 +2078,7 @@ multiscale multisectioning multithreading Multithreading +multivalent Mundy Murdick Murtola @@ -2064,6 +2124,7 @@ Nanoletters nanomechanics nanometer nanometers +nanoparticle nanoparticles Nanotube nanotube @@ -2122,6 +2183,7 @@ nemd netcdf netstat Nettleton +networklayers Neumann Nevent nevery @@ -2153,8 +2215,10 @@ nimpropers nimpropertypes Nimpropertype Ninteger +NiO Nissila nist +Nitol nitride nitrides niu @@ -2164,6 +2228,7 @@ nl nlayers nlen Nlines +nlines nlo nlocal Nlocal @@ -2173,6 +2238,7 @@ nm Nm Nmax nmax +nmc Nmin nmin Nmols @@ -2254,6 +2320,7 @@ Ntype ntypes Ntypes nucleotides +nullptr num numa numactl @@ -2297,6 +2364,7 @@ Oleinik Olfason olivedrab Ollila +Olvera omegaDD omegax omegay @@ -2307,9 +2375,11 @@ OMP oneAPI onelevel oneway +onlysalt onn ons OO +Oord opencl openKIM openmp @@ -2330,6 +2400,7 @@ Orsi ortho orthonormal orthorhombic +Ortner oso Otype Ouldridge @@ -2389,6 +2460,8 @@ pbc pc pchain Pchain +pcmoves +pmcmoves Pdamp pdb pdf @@ -2433,6 +2506,7 @@ phosphide Phs Physica physik +pI Piaggi picocoulomb picocoulombs @@ -2444,7 +2518,9 @@ pid piecewise Pieniazek Pieter +pIm pimd +pIp Piola Pisarev Pishevar @@ -2459,6 +2535,9 @@ ploop PloS plt plumedfile +pKa +pKb +pKs pmb Pmolrotate Pmoltrans @@ -2502,6 +2581,7 @@ ppn pppm prd Prakash +Praprotnik pre Pre prec @@ -2560,7 +2640,6 @@ PyLammps pymbar pymodule pymol -pypar pythonic pytorch pyy @@ -2614,17 +2693,23 @@ qw qx qy qz +radialscreened +radialscreenedspin +radialspin radian radians Rafferty rahman Rahman +Ralf Raman ramped ramping Ramprasad Randisi randomizations +rann +RANN Raphson Rappe Ravelo @@ -2680,6 +2765,7 @@ representable Reproducibility reproducibility repuls +reqid rescale rescaled rescales @@ -2725,6 +2811,7 @@ Rij RIj Rik Rin +Rinaldi Rino RiRj Risi @@ -2784,6 +2871,7 @@ rst rstyle Rubensson Rubia +Rud Rudd Rudra Rudranarayan @@ -2792,6 +2880,8 @@ Runge runtime Rutuparna rx +rxnave +rxnsum ry rz Ryckaert @@ -2813,6 +2903,7 @@ Sandia sandybrown sanitizer Sanyal +Sarath sc scafacos SCAFACOS @@ -2892,8 +2983,10 @@ shrinkexceed Shugaev si SiC +Siegmund Siepmann Sievers +sigI sigmoid Sij Sikandar @@ -2903,6 +2996,7 @@ Sim Simov Simul simulations +Sinkovits Sinnott sinusoid sinusoidally @@ -3053,6 +3147,7 @@ surfactant surfactants Suter Sutmann +Suzen svn sw Swegat @@ -3062,6 +3157,7 @@ Swinburne Swol Swope Sx +sx sy Sy symplectic @@ -3071,6 +3167,7 @@ sysdim Syst systemd Sz +sz Tabbernor tabinner Tadmor @@ -3089,6 +3186,7 @@ Tanmoy Tartakovsky taskset taubi +taylor tb tchain Tchain @@ -3122,6 +3220,7 @@ th thb thei Theodorou +Theophile Theor thermalization thermalize @@ -3250,6 +3349,7 @@ twobody twojmax Tx txt +Tyagi typeI typeJ typeN @@ -3274,6 +3374,7 @@ Uleft uloop Ulomek ulsph +Ultrafast uMech umin Umin @@ -3309,6 +3410,7 @@ upenn upto Urbakh Urbana +Usabiaga usec uSemiParallel userguide @@ -3453,6 +3555,7 @@ Wikipedia Wildcard wildcard wildcards +Winkler Wirnsberger wirtes witin @@ -3464,6 +3567,7 @@ Worley Wriggers Wuppertal Wurtzite +Wysocki www wx Wx @@ -3517,6 +3621,7 @@ xz xzhou yaff yaml +Yanxon YAFF Yamada Yaser @@ -3549,11 +3654,13 @@ yx yy yz Zannoni +Zavattieri zbl ZBL Zc zcm Zeeman +zeeman Zemer Zepeda zflag @@ -3585,6 +3692,9 @@ zz Zm PowerShell filesystems +fingerprintconstants +fingerprintsperelement +Zagaceta zincblende Zstandard Zstd diff --git a/examples/ASPHERE/README b/examples/ASPHERE/README index ced5ead8c3..1aa9552bec 100644 --- a/examples/ASPHERE/README +++ b/examples/ASPHERE/README @@ -10,7 +10,7 @@ systems. Some of the directories include a Python script, which can be used with the Pizza.py tool to create the data file, e.g. for collections of rigid bodies. -The web site for Pizza.py is http://pizza.sandia.gov +The web site for Pizza.py is https://pizza.sandia.gov For example, If you have Pizza.py installed you can type "pizza.py -f box.py", which creates the data.box data file in the box dir. @@ -18,7 +18,7 @@ box.py", which creates the data.box data file in the box dir. If you uncomment the dump or dump image lines in the input scripts the runs will produce dump files or JPG images which you can view or animate. See the Movies page of the LAMMPS web site -(http://lammps.sandia.gov/movies.html), for animations of these +(https://www.lammps.org/movies.html), for animations of these scripts. Most were done using the dump image command. A few were done using the gl tool in Pizza.py; the Pizza.py scripts that do the animation are given in the directory, e.g. as line.viz.py. diff --git a/examples/ASPHERE/box/in.box b/examples/ASPHERE/box/in.box index 2ec09faf56..96b0605fc8 100644 --- a/examples/ASPHERE/box/in.box +++ b/examples/ASPHERE/box/in.box @@ -1,111 +1,111 @@ # SRD diffusion demo - rigid box particles -units lj -atom_style sphere -atom_modify map array first big -dimension 2 +units lj +atom_style sphere +atom_modify map array first big +dimension 2 # read in clusters of rigid bodies -fix molprop all property/atom mol -read_data data.box fix molprop NULL Molecules +fix molprop all property/atom mol ghost yes +read_data data.box fix molprop NULL Molecules + +set type 1 mass 1.0 +group big type 1 +velocity big create 1.44 87287 loop geom -set type 1 mass 1.0 -group big type 1 -velocity big create 1.44 87287 loop geom - # equilibrate big particles -pair_style soft 1.12 -pair_coeff 1 1 0.0 -pair_coeff 2 2 0.0 0.0 -pair_coeff 1 2 0.0 0.0 +pair_style soft 1.12 +pair_coeff 1 1 0.0 +pair_coeff 2 2 0.0 0.0 +pair_coeff 1 2 0.0 0.0 variable prefactor equal ramp(0,60) fix soft all adapt 1 pair soft a * * v_prefactor -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes -fix 1 big rigid molecule -fix 2 all enforce2d +fix 1 big rigid molecule +fix 2 all enforce2d -#dump 1 all atom 10 dump.box.equil +#dump 1 all atom 10 dump.box.equil -compute tbig all temp/sphere -thermo_modify temp tbig +compute tbig all temp/sphere +thermo_modify temp tbig -thermo 100 -run 1000 +thermo 100 +run 1000 -#undump 1 +#undump 1 unfix soft -unfix 1 -unfix 2 +unfix 1 +unfix 2 # add small particles as hi density lattice -region plane block INF INF INF INF -0.001 0.001 units box -lattice sq 85.0 -create_atoms 2 region plane +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 85.0 +create_atoms 2 region plane -set type 2 mass 0.1 -group small type 2 -velocity small create 1.0 593849 loop geom +set type 2 mass 0.1 +group small type 2 +velocity small create 1.0 593849 loop geom # delete overlaps # must set 1-2 cutoff to non-zero value -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 1.0 +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 1.0 -delete_atoms overlap 1.0 small big +delete_atoms overlap 1.0 small big # SRD run -reset_timestep 0 +reset_timestep 0 -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes -comm_modify mode multi group big vel yes -neigh_modify include big +comm_modify mode multi group big vel yes +neigh_modify include big # no pairwise interactions with small particles -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 # use fix SRD to push small particles out from inside big ones # if comment out, big particles won't see SRD particles -timestep 0.001 +timestep 0.001 -fix 1 big rigid molecule -fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & - search 0.2 collision slip inside ignore overlap yes -fix 3 all enforce2d +fix 1 big rigid molecule +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & + search 0.2 collision slip inside ignore overlap yes +fix 3 all enforce2d # diagnostics uncompute tbig -compute tbig big temp/sphere -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press & - f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & - f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +compute tbig big temp/sphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press & + f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & + f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] -thermo_modify temp tbig -thermo 1000 +thermo_modify temp tbig +thermo 1000 -#dump 1 all atom 1000 dump.box +#dump 1 all atom 1000 dump.box -#dump 1 all image 1000 image.*.jpg type type zoom 1.6 -#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 +#dump 1 all image 1000 image.*.jpg type type zoom 1.6 +#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 -run 100000 +run 10000 diff --git a/examples/ASPHERE/box/in.box.mp b/examples/ASPHERE/box/in.box.mp index 2953552595..d60b973d62 100644 --- a/examples/ASPHERE/box/in.box.mp +++ b/examples/ASPHERE/box/in.box.mp @@ -1,112 +1,112 @@ # SRD viscosity demo - rigid box particles -units lj -atom_style sphere -atom_modify map array first big -dimension 2 +units lj +atom_style sphere +atom_modify map array first big +dimension 2 # read in clusters of rigid bodies -fix molprop all property/atom mol -read_data data.box fix molprop NULL Molecules +fix molprop all property/atom mol ghost yes +read_data data.box fix molprop NULL Molecules + +set type 1 mass 1.0 +group big type 1 +velocity big create 1.44 87287 loop geom -set type 1 mass 1.0 -group big type 1 -velocity big create 1.44 87287 loop geom - # equilibrate big particles -pair_style soft 1.12 -pair_coeff 1 1 0.0 -pair_coeff 2 2 0.0 0.0 -pair_coeff 1 2 0.0 0.0 +pair_style soft 1.12 +pair_coeff 1 1 0.0 +pair_coeff 2 2 0.0 0.0 +pair_coeff 1 2 0.0 0.0 variable prefactor equal ramp(0,60) fix soft all adapt 1 pair soft a * * v_prefactor -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes -fix 1 big rigid molecule -fix 2 all enforce2d +fix 1 big rigid molecule +fix 2 all enforce2d -#dump 1 all atom 10 dump.box.equil +#dump 1 all atom 10 dump.box.equil -compute tbig all temp/sphere -thermo_modify temp tbig +compute tbig all temp/sphere +thermo_modify temp tbig -thermo 100 -run 1000 +thermo 100 +run 1000 -#undump 1 -unfix soft -unfix 1 -unfix 2 +#undump 1 +unfix soft +unfix 1 +unfix 2 # add small particles as hi density lattice -region plane block INF INF INF INF -0.001 0.001 units box -lattice sq 85.0 -create_atoms 2 region plane +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 85.0 +create_atoms 2 region plane -set type 2 mass 0.1 -group small type 2 -velocity small create 1.0 593849 loop geom +set type 2 mass 0.1 +group small type 2 +velocity small create 1.0 593849 loop geom # delete overlaps # must set 1-2 cutoff to non-zero value -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 1.0 +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 1.0 -delete_atoms overlap 1.0 small big +delete_atoms overlap 1.0 small big # SRD run -reset_timestep 0 +reset_timestep 0 -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes -comm_modify mode multi group big vel yes -neigh_modify include big +comm_modify mode multi group big vel yes +neigh_modify include big # no pairwise interactions with small particles -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 # use fix SRD to push small particles out from inside big ones # if comment out, big particles won't see SRD particles -timestep 0.001 +timestep 0.001 -fix 1 big rigid molecule -fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & - search 0.2 collision slip inside ignore overlap yes -fix 3 small viscosity 10 x y 50 -fix 4 all enforce2d +fix 1 big rigid molecule +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & + search 0.2 collision slip inside ignore overlap yes +fix 3 small viscosity 10 x y 50 +fix 4 all enforce2d # diagnostics uncompute tbig -compute tbig big temp/sphere -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press & - f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & - f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +compute tbig big temp/sphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press & + f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & + f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] -thermo_modify temp tbig -thermo 1000 +thermo_modify temp tbig +thermo 1000 -#dump 1 all atom 1000 dump.box.mp +#dump 1 all atom 1000 dump.box.mp -#dump 1 all image 1000 image.*.jpg type type zoom 1.6 -#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 +#dump 1 all image 1000 image.*.jpg type type zoom 1.6 +#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 -run 100000 +run 10000 diff --git a/examples/ASPHERE/box/log.17Jun21.box.g++.1 b/examples/ASPHERE/box/log.17Jun21.box.g++.1 new file mode 100644 index 0000000000..e3e4f79fcc --- /dev/null +++ b/examples/ASPHERE/box/log.17Jun21.box.g++.1 @@ -0,0 +1,309 @@ +LAMMPS (27 May 2021) + using 1 OpenMP thread(s) per MPI task +# SRD diffusion demo - rigid box particles + +units lj +atom_style sphere +atom_modify map array first big +dimension 2 + +# read in clusters of rigid bodies + +fix molprop all property/atom mol ghost yes +read_data data.box fix molprop NULL Molecules +Reading data file ... + orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 420 atoms + read_data CPU = 0.002 seconds + +set type 1 mass 1.0 +Setting atom values ... + 420 settings made for mass +group big type 1 +420 atoms in group big +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style soft 1.12 +pair_coeff 1 1 0.0 +pair_coeff 2 2 0.0 0.0 +pair_coeff 1 2 0.0 0.0 + +variable prefactor equal ramp(0,60) +fix soft all adapt 1 pair soft a * * v_prefactor + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 all enforce2d + +#dump 1 all atom 10 dump.box.equil + +compute tbig all temp/sphere +thermo_modify temp tbig + +thermo 100 +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42 + ghost atom cutoff = 1.42 + binsize = 0.71, bins = 54 54 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.570 | 5.570 | 5.570 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.4252596 0 0 0.14931291 -8.727261 + 100 4.7699234 3.4203218 0 3.9200281 0.63667047 + 200 14.850064 5.3315601 0 6.8872811 0.71533738 + 300 21.249889 7.2094878 0 9.4356667 1.0710181 + 400 24.551027 9.2008598 0 11.772872 1.0133205 + 500 23.999755 11.562353 0 14.076613 1.3275867 + 600 25.022182 13.731564 0 16.352935 1.0236907 + 700 26.601942 15.850142 0 18.637012 0.80166569 + 800 24.154216 18.395444 0 20.925886 1.7521839 + 900 27.3897 20.3322 0 23.201597 0.65472411 + 1000 27.381112 22.600716 0 25.469214 0.69152692 +Loop time of 0.0920079 on 1 procs for 1000 steps with 420 atoms + +Performance: 4695251.138 tau/day, 10868.637 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.029557 | 0.029557 | 0.029557 | 0.0 | 32.12 +Neigh | 0.011621 | 0.011621 | 0.011621 | 0.0 | 12.63 +Comm | 0.0041208 | 0.0041208 | 0.0041208 | 0.0 | 4.48 +Output | 0.00034363 | 0.00034363 | 0.00034363 | 0.0 | 0.37 +Modify | 0.042122 | 0.042122 | 0.042122 | 0.0 | 45.78 +Other | | 0.004243 | | | 4.61 + +Nlocal: 420.000 ave 420 max 420 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84.0000 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 562.000 ave 562 max 562 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 562 +Ave neighs/atom = 1.3380952 +Neighbor list builds = 158 +Dangerous builds = 0 + +#undump 1 +unfix soft +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 85.0 +Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523 +create_atoms 2 region plane +Created 124609 atoms + create_atoms CPU = 0.042 seconds + +set type 2 mass 0.1 +Setting atom values ... + 124609 settings made for mass +group small type 2 +124609 atoms in group small +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 1.0 + +delete_atoms overlap 1.0 small big +System init for delete_atoms ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 28 28 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308) +Deleted 51030 atoms, new total = 73999 + +# SRD run + +reset_timestep 0 + +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes + +comm_modify mode multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones +# if comment out, big particles won't see SRD particles + +timestep 0.001 + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes +fix 3 all enforce2d + +# diagnostics + +uncompute tbig +compute tbig big temp/sphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689) + +thermo_modify temp tbig +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483) +thermo 1000 + +#dump 1 all atom 1000 dump.box + +#dump 1 all image 1000 image.*.jpg type type zoom 1.6 +#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 + +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2 + +@Article{Intveld08, + author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest}, + title = {Accurate and Efficient Methods for Modeling Colloidal + Mixtures in an Explicit Solvent using Molecular Dynamics}, + journal = {Comp.~Phys.~Comm.}, + year = 2008, + volume = 179, + pages = {320--329} +} + +@article{Stratford2018, + author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin}, + title = {Implementation of multi-level contact detection in LAMMPS}, + year = {2018} +} + +@article{Shire2020, + author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin}, + title = {DEM simulations of polydisperse media: efficient contact + detection applied to investigate the quasi-static limit}, + journal = {Computational Particle Mechanics}, + year = {2020} +} + +- fix srd command: + +@Article{Petersen10, + author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk}, + title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.}, + year = 2010, + volume = 132, + pages = {174106} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +SRD info: + SRD/big particles = 73579 420 + big particle diameter max/min = 1.0000000 1.0000000 + SRD temperature & lamda = 1.0000000 0.063245553 + SRD max distance & max velocity = 0.25298221 12.649111 + SRD grid counts: 153 153 1 + SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000 + SRD per actual grid cell = 4.0557326 + SRD viscosity = 0.22929663 + big/SRD mass density ratio = 0.19661407 +WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845) + # of rescaled SRD velocities = 0 + ave/max small velocity = 4.1966772 7.7276214 + ave/max big velocity = 2.1275716 5.8359099 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 38.289379, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 75.37 | 75.37 | 75.37 Mbytes +Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] + 0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0 + 1000 3.7986429 16232 0.24173874 42.193535 42.591488 10.849557 10086 45 45 0 1004 51984 23409 16232 0.91196906 0 5 0 + 2000 1.4227624 16312 0.24027816 42.185099 42.334151 11.114609 10229 28 28 0 1829 51984 23409 16312 0.91266737 0 5 0 + 3000 1.2870561 16338 0.24012829 42.172911 42.307746 9.1532934 10247 29 29 0 2474 51984 23409 16338 0.92249481 0 5 0 + 4000 0.99207377 16354 0.23996323 42.174734 42.278665 13.010306 10390 42 42 0 3137 51984 23409 16354 0.93252257 0 5 0 + 5000 1.2778672 16234 0.24012389 42.1731 42.306972 11.375628 10158 39 39 0 3802 51984 23409 16234 0.93405963 0 7 0 + 6000 0.92241679 16273 0.23984728 42.161601 42.258235 9.4164757 10190 34 35 0 4514 51984 23409 16273 0.94347665 0 7 0 + 7000 1.4747828 16291 0.24015741 42.158375 42.312876 11.273642 10208 40 40 0 5231 51984 23409 16291 0.94315382 0 7 0 + 8000 1.143932 16385 0.23997671 42.1612 42.28104 11.518583 10409 31 31 0 5954 51984 23409 16385 0.94024078 0 7 0 + 9000 1.123729 16298 0.23981793 42.135341 42.253065 14.210625 10067 51 51 0 6654 51984 23409 16298 0.9463894 0 7 0 + 10000 1.0362924 16356 0.23977465 42.136875 42.245439 10.19621 10227 33 34 0 7437 51984 23409 16356 0.94188712 0 7 0 +Loop time of 41.8379 on 1 procs for 10000 steps with 73999 atoms + +Performance: 20651.124 tau/day, 239.018 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.44984 | 0.44984 | 0.44984 | 0.0 | 1.08 +Neigh | 0.11618 | 0.11618 | 0.11618 | 0.0 | 0.28 +Comm | 0.4757 | 0.4757 | 0.4757 | 0.0 | 1.14 +Output | 0.0035887 | 0.0035887 | 0.0035887 | 0.0 | 0.01 +Modify | 40.52 | 40.52 | 40.52 | 0.0 | 96.85 +Other | | 0.2722 | | | 0.65 + +Nlocal: 73999.0 ave 73999 max 73999 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 135.000 ave 135 max 135 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2407.00 ave 2407 max 2407 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2407 +Ave neighs/atom = 0.032527467 +Neighbor list builds = 500 +Dangerous builds = 0 +Total wall time: 0:00:45 diff --git a/examples/ASPHERE/box/log.17Jun21.box.g++.4 b/examples/ASPHERE/box/log.17Jun21.box.g++.4 new file mode 100644 index 0000000000..d530d04c3c --- /dev/null +++ b/examples/ASPHERE/box/log.17Jun21.box.g++.4 @@ -0,0 +1,309 @@ +LAMMPS (27 May 2021) + using 1 OpenMP thread(s) per MPI task +# SRD diffusion demo - rigid box particles + +units lj +atom_style sphere +atom_modify map array first big +dimension 2 + +# read in clusters of rigid bodies + +fix molprop all property/atom mol ghost yes +read_data data.box fix molprop NULL Molecules +Reading data file ... + orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 420 atoms + read_data CPU = 0.009 seconds + +set type 1 mass 1.0 +Setting atom values ... + 420 settings made for mass +group big type 1 +420 atoms in group big +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style soft 1.12 +pair_coeff 1 1 0.0 +pair_coeff 2 2 0.0 0.0 +pair_coeff 1 2 0.0 0.0 + +variable prefactor equal ramp(0,60) +fix soft all adapt 1 pair soft a * * v_prefactor + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 all enforce2d + +#dump 1 all atom 10 dump.box.equil + +compute tbig all temp/sphere +thermo_modify temp tbig + +thermo 100 +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42 + ghost atom cutoff = 1.42 + binsize = 0.71, bins = 54 54 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.558 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.4252596 0 0 0.14931291 -8.727261 + 100 4.7699234 3.4203218 0 3.9200281 0.63667047 + 200 14.850064 5.3315601 0 6.8872811 0.71533738 + 300 21.249889 7.2094878 0 9.4356667 1.0710181 + 400 24.551027 9.2008598 0 11.772872 1.0133205 + 500 23.999755 11.562353 0 14.076613 1.3275867 + 600 25.022182 13.731564 0 16.352935 1.0236907 + 700 26.601942 15.850142 0 18.637012 0.80166569 + 800 24.154216 18.395444 0 20.925886 1.7521839 + 900 27.3897 20.3322 0 23.201597 0.65472411 + 1000 27.381112 22.600716 0 25.469214 0.69152692 +Loop time of 0.102477 on 4 procs for 1000 steps with 420 atoms + +Performance: 4215597.184 tau/day, 9758.327 timesteps/s +87.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0086884 | 0.011084 | 0.012345 | 1.4 | 10.82 +Neigh | 0.0038968 | 0.0042393 | 0.0045272 | 0.4 | 4.14 +Comm | 0.028577 | 0.030455 | 0.032476 | 1.0 | 29.72 +Output | 0.00028127 | 0.00044494 | 0.0009265 | 0.0 | 0.43 +Modify | 0.041755 | 0.042937 | 0.044332 | 0.4 | 41.90 +Other | | 0.01332 | | | 13.00 + +Nlocal: 105.000 ave 130 max 77 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 39.0000 ave 49 max 21 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Neighs: 140.500 ave 180 max 105 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 562 +Ave neighs/atom = 1.3380952 +Neighbor list builds = 158 +Dangerous builds = 0 + +#undump 1 +unfix soft +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 85.0 +Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523 +create_atoms 2 region plane +Created 124609 atoms + create_atoms CPU = 0.025 seconds + +set type 2 mass 0.1 +Setting atom values ... + 124609 settings made for mass +group small type 2 +124609 atoms in group small +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 1.0 + +delete_atoms overlap 1.0 small big +System init for delete_atoms ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 28 28 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308) +Deleted 51030 atoms, new total = 73999 + +# SRD run + +reset_timestep 0 + +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes + +comm_modify mode multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones +# if comment out, big particles won't see SRD particles + +timestep 0.001 + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes +fix 3 all enforce2d + +# diagnostics + +uncompute tbig +compute tbig big temp/sphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689) + +thermo_modify temp tbig +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483) +thermo 1000 + +#dump 1 all atom 1000 dump.box + +#dump 1 all image 1000 image.*.jpg type type zoom 1.6 +#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 + +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2 + +@Article{Intveld08, + author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest}, + title = {Accurate and Efficient Methods for Modeling Colloidal + Mixtures in an Explicit Solvent using Molecular Dynamics}, + journal = {Comp.~Phys.~Comm.}, + year = 2008, + volume = 179, + pages = {320--329} +} + +@article{Stratford2018, + author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin}, + title = {Implementation of multi-level contact detection in LAMMPS}, + year = {2018} +} + +@article{Shire2020, + author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin}, + title = {DEM simulations of polydisperse media: efficient contact + detection applied to investigate the quasi-static limit}, + journal = {Computational Particle Mechanics}, + year = {2020} +} + +- fix srd command: + +@Article{Petersen10, + author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk}, + title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.}, + year = 2010, + volume = 132, + pages = {174106} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +SRD info: + SRD/big particles = 73579 420 + big particle diameter max/min = 1.0000000 1.0000000 + SRD temperature & lamda = 1.0000000 0.063245553 + SRD max distance & max velocity = 0.25298221 12.649111 + SRD grid counts: 153 153 1 + SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000 + SRD per actual grid cell = 4.0557326 + SRD viscosity = 0.22929663 + big/SRD mass density ratio = 0.19661407 +WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845) + # of rescaled SRD velocities = 0 + ave/max small velocity = 4.1966772 7.7276214 + ave/max big velocity = 2.1275716 5.8359099 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 38.289379, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 27.16 | 27.18 | 27.21 Mbytes +Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] + 0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0 + 1000 2.4803865 16183 0.24097572 42.197203 42.457053 10.685486 10313 34 34 0 1010 70756 23409 16183 0.91088084 0 10 0 + 2000 1.5192587 16288 0.2403558 42.18867 42.34783 12.991827 10247 51 51 0 1780 70756 23409 16288 0.91423542 0 10 0 + 3000 1.3453745 16254 0.24021083 42.181344 42.322288 10.311263 9901 36 36 0 2457 70756 23409 16254 0.92345925 0 10 0 + 4000 1.5208981 16348 0.24035467 42.188298 42.347631 11.118817 10195 32 33 2 3117 70756 23409 16348 0.93218296 0 10 0 + 5000 1.0700659 16291 0.2400755 42.186343 42.298445 9.3784033 10271 35 35 0 3810 70756 23409 16291 0.93211425 0 10 0 + 6000 1.0488908 16303 0.2400744 42.188368 42.298252 12.777782 10058 50 50 0 4557 70756 23409 16303 0.94151194 0 10 0 + 7000 1.331013 16244 0.24024721 42.189259 42.328698 10.953939 10388 36 36 0 5276 70756 23409 16244 0.94703063 0 10 0 + 8000 0.94738473 16321 0.23996282 42.179342 42.278592 11.767946 10161 41 41 0 5967 70756 23409 16321 0.94682195 0 10 0 + 9000 1.1009209 16291 0.24002765 42.17468 42.290015 8.045595 10584 33 33 0 6751 70756 23409 16291 0.94001295 0 10 0 + 10000 1.0564033 16282 0.23992848 42.161871 42.272542 12.284202 10257 40 40 0 7488 70756 23409 16282 0.94873736 0 10 0 +Loop time of 30.6515 on 4 procs for 10000 steps with 73999 atoms + +Performance: 28187.845 tau/day, 326.248 timesteps/s +90.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14666 | 0.20404 | 0.29182 | 13.1 | 0.67 +Neigh | 0.040061 | 0.050996 | 0.068192 | 4.8 | 0.17 +Comm | 1.087 | 1.2248 | 1.2747 | 7.2 | 4.00 +Output | 0.0024737 | 0.0037751 | 0.0060755 | 2.4 | 0.01 +Modify | 28.133 | 28.273 | 28.452 | 2.3 | 92.24 +Other | | 0.8951 | | | 2.92 + +Nlocal: 18499.8 ave 20267 max 16093 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 74.5000 ave 90 max 57 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Neighs: 590.250 ave 907 max 422 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 2361 +Ave neighs/atom = 0.031905837 +Neighbor list builds = 500 +Dangerous builds = 0 +Total wall time: 0:00:32 diff --git a/examples/ASPHERE/box/log.17Jun21.box.mp.g++.1 b/examples/ASPHERE/box/log.17Jun21.box.mp.g++.1 new file mode 100644 index 0000000000..02552a4c29 --- /dev/null +++ b/examples/ASPHERE/box/log.17Jun21.box.mp.g++.1 @@ -0,0 +1,310 @@ +LAMMPS (27 May 2021) + using 1 OpenMP thread(s) per MPI task +# SRD viscosity demo - rigid box particles + +units lj +atom_style sphere +atom_modify map array first big +dimension 2 + +# read in clusters of rigid bodies + +fix molprop all property/atom mol ghost yes +read_data data.box fix molprop NULL Molecules +Reading data file ... + orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 420 atoms + read_data CPU = 0.002 seconds + +set type 1 mass 1.0 +Setting atom values ... + 420 settings made for mass +group big type 1 +420 atoms in group big +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style soft 1.12 +pair_coeff 1 1 0.0 +pair_coeff 2 2 0.0 0.0 +pair_coeff 1 2 0.0 0.0 + +variable prefactor equal ramp(0,60) +fix soft all adapt 1 pair soft a * * v_prefactor + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 all enforce2d + +#dump 1 all atom 10 dump.box.equil + +compute tbig all temp/sphere +thermo_modify temp tbig + +thermo 100 +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42 + ghost atom cutoff = 1.42 + binsize = 0.71, bins = 54 54 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.570 | 5.570 | 5.570 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.4252596 0 0 0.14931291 -8.727261 + 100 4.7699234 3.4203218 0 3.9200281 0.63667047 + 200 14.850064 5.3315601 0 6.8872811 0.71533738 + 300 21.249889 7.2094878 0 9.4356667 1.0710181 + 400 24.551027 9.2008598 0 11.772872 1.0133205 + 500 23.999755 11.562353 0 14.076613 1.3275867 + 600 25.022182 13.731564 0 16.352935 1.0236907 + 700 26.601942 15.850142 0 18.637012 0.80166569 + 800 24.154216 18.395444 0 20.925886 1.7521839 + 900 27.3897 20.3322 0 23.201597 0.65472411 + 1000 27.381112 22.600716 0 25.469214 0.69152692 +Loop time of 0.0830324 on 1 procs for 1000 steps with 420 atoms + +Performance: 5202788.685 tau/day, 12043.492 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.027522 | 0.027522 | 0.027522 | 0.0 | 33.15 +Neigh | 0.011039 | 0.011039 | 0.011039 | 0.0 | 13.29 +Comm | 0.0034208 | 0.0034208 | 0.0034208 | 0.0 | 4.12 +Output | 0.00033641 | 0.00033641 | 0.00033641 | 0.0 | 0.41 +Modify | 0.037199 | 0.037199 | 0.037199 | 0.0 | 44.80 +Other | | 0.003515 | | | 4.23 + +Nlocal: 420.000 ave 420 max 420 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84.0000 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 562.000 ave 562 max 562 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 562 +Ave neighs/atom = 1.3380952 +Neighbor list builds = 158 +Dangerous builds = 0 + +#undump 1 +unfix soft +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 85.0 +Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523 +create_atoms 2 region plane +Created 124609 atoms + create_atoms CPU = 0.044 seconds + +set type 2 mass 0.1 +Setting atom values ... + 124609 settings made for mass +group small type 2 +124609 atoms in group small +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 1.0 + +delete_atoms overlap 1.0 small big +System init for delete_atoms ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 28 28 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308) +Deleted 51030 atoms, new total = 73999 + +# SRD run + +reset_timestep 0 + +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes + +comm_modify mode multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones +# if comment out, big particles won't see SRD particles + +timestep 0.001 + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes +fix 3 small viscosity 10 x y 50 +fix 4 all enforce2d + +# diagnostics + +uncompute tbig +compute tbig big temp/sphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689) + +thermo_modify temp tbig +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483) +thermo 1000 + +#dump 1 all atom 1000 dump.box.mp + +#dump 1 all image 1000 image.*.jpg type type zoom 1.6 +#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 + +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2 + +@Article{Intveld08, + author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest}, + title = {Accurate and Efficient Methods for Modeling Colloidal + Mixtures in an Explicit Solvent using Molecular Dynamics}, + journal = {Comp.~Phys.~Comm.}, + year = 2008, + volume = 179, + pages = {320--329} +} + +@article{Stratford2018, + author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin}, + title = {Implementation of multi-level contact detection in LAMMPS}, + year = {2018} +} + +@article{Shire2020, + author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin}, + title = {DEM simulations of polydisperse media: efficient contact + detection applied to investigate the quasi-static limit}, + journal = {Computational Particle Mechanics}, + year = {2020} +} + +- fix srd command: + +@Article{Petersen10, + author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk}, + title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.}, + year = 2010, + volume = 132, + pages = {174106} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +SRD info: + SRD/big particles = 73579 420 + big particle diameter max/min = 1.0000000 1.0000000 + SRD temperature & lamda = 1.0000000 0.063245553 + SRD max distance & max velocity = 0.25298221 12.649111 + SRD grid counts: 153 153 1 + SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000 + SRD per actual grid cell = 4.0557326 + SRD viscosity = 0.22929663 + big/SRD mass density ratio = 0.19661407 +WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845) + # of rescaled SRD velocities = 0 + ave/max small velocity = 4.1966772 7.7276214 + ave/max big velocity = 2.1275716 5.8359099 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 38.289379, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 75.37 | 75.37 | 75.37 Mbytes +Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] + 0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0 + 1000 2.9594916 16137 0.24127616 42.199945 42.509987 10.792325 10296 45 45 0 990 51984 23409 16137 0.90706131 0 10 0 + 2000 1.7108824 16274 0.24052684 42.198731 42.377967 9.5364607 10320 34 34 0 1741 51984 23409 16274 0.91369719 0 10 0 + 3000 1.3927232 16271 0.24024605 42.182589 42.328493 9.6211672 10122 29 29 0 2450 51984 23409 16271 0.92150155 0 10 0 + 4000 1.8264312 16304 0.24052774 42.186783 42.378124 9.2177883 10128 38 40 0 3114 51984 23409 16304 0.92089374 0 10 0 + 5000 1.6944513 16287 0.24043781 42.184766 42.36228 7.4352852 10198 31 31 0 3833 51984 23409 16287 0.92601496 0 10 0 + 6000 2.1923757 16301 0.24067781 42.174888 42.404565 11.864868 10340 39 39 0 4537 51984 23409 16301 0.93147673 0 10 0 + 7000 2.1699734 16292 0.24062985 42.168784 42.396114 9.6780093 9932 23 23 0 5290 51984 23409 16292 0.94127767 0 10 0 + 8000 2.8026605 16335 0.24100748 42.169037 42.462649 9.1457843 10044 38 38 0 6125 51984 23409 16335 0.93275263 0 10 0 + 9000 4.1434204 16297 0.24180594 42.169255 42.603328 12.358126 10095 37 37 0 6957 51984 23409 16297 0.9324244 0 10 0 + 10000 3.6168745 16237 0.24147749 42.166548 42.545459 9.1577014 10270 27 27 0 7779 51984 23409 16237 0.93952778 0 10 0 +Loop time of 40.9072 on 1 procs for 10000 steps with 73999 atoms + +Performance: 21120.990 tau/day, 244.456 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.44663 | 0.44663 | 0.44663 | 0.0 | 1.09 +Neigh | 0.11472 | 0.11472 | 0.11472 | 0.0 | 0.28 +Comm | 0.45946 | 0.45946 | 0.45946 | 0.0 | 1.12 +Output | 0.0036154 | 0.0036154 | 0.0036154 | 0.0 | 0.01 +Modify | 39.618 | 39.618 | 39.618 | 0.0 | 96.85 +Other | | 0.2648 | | | 0.65 + +Nlocal: 73999.0 ave 73999 max 73999 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 126.000 ave 126 max 126 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2406.00 ave 2406 max 2406 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2406 +Ave neighs/atom = 0.032513953 +Neighbor list builds = 500 +Dangerous builds = 0 +Total wall time: 0:00:44 diff --git a/examples/ASPHERE/box/log.17Jun21.box.mp.g++.4 b/examples/ASPHERE/box/log.17Jun21.box.mp.g++.4 new file mode 100644 index 0000000000..dfb28a8585 --- /dev/null +++ b/examples/ASPHERE/box/log.17Jun21.box.mp.g++.4 @@ -0,0 +1,310 @@ +LAMMPS (27 May 2021) + using 1 OpenMP thread(s) per MPI task +# SRD viscosity demo - rigid box particles + +units lj +atom_style sphere +atom_modify map array first big +dimension 2 + +# read in clusters of rigid bodies + +fix molprop all property/atom mol ghost yes +read_data data.box fix molprop NULL Molecules +Reading data file ... + orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 420 atoms + read_data CPU = 0.003 seconds + +set type 1 mass 1.0 +Setting atom values ... + 420 settings made for mass +group big type 1 +420 atoms in group big +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style soft 1.12 +pair_coeff 1 1 0.0 +pair_coeff 2 2 0.0 0.0 +pair_coeff 1 2 0.0 0.0 + +variable prefactor equal ramp(0,60) +fix soft all adapt 1 pair soft a * * v_prefactor + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 all enforce2d + +#dump 1 all atom 10 dump.box.equil + +compute tbig all temp/sphere +thermo_modify temp tbig + +thermo 100 +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42 + ghost atom cutoff = 1.42 + binsize = 0.71, bins = 54 54 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.558 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.4252596 0 0 0.14931291 -8.727261 + 100 4.7699234 3.4203218 0 3.9200281 0.63667047 + 200 14.850064 5.3315601 0 6.8872811 0.71533738 + 300 21.249889 7.2094878 0 9.4356667 1.0710181 + 400 24.551027 9.2008598 0 11.772872 1.0133205 + 500 23.999755 11.562353 0 14.076613 1.3275867 + 600 25.022182 13.731564 0 16.352935 1.0236907 + 700 26.601942 15.850142 0 18.637012 0.80166569 + 800 24.154216 18.395444 0 20.925886 1.7521839 + 900 27.3897 20.3322 0 23.201597 0.65472411 + 1000 27.381112 22.600716 0 25.469214 0.69152692 +Loop time of 0.0821786 on 4 procs for 1000 steps with 420 atoms + +Performance: 5256844.414 tau/day, 12168.621 timesteps/s +92.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0096035 | 0.011958 | 0.014498 | 1.7 | 14.55 +Neigh | 0.0039157 | 0.0041593 | 0.0045318 | 0.4 | 5.06 +Comm | 0.021053 | 0.022374 | 0.024067 | 0.8 | 27.23 +Output | 0.00024565 | 0.00085109 | 0.0026608 | 0.0 | 1.04 +Modify | 0.031525 | 0.034215 | 0.036481 | 1.2 | 41.63 +Other | | 0.008622 | | | 10.49 + +Nlocal: 105.000 ave 130 max 77 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 39.0000 ave 49 max 21 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Neighs: 140.500 ave 180 max 105 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 562 +Ave neighs/atom = 1.3380952 +Neighbor list builds = 158 +Dangerous builds = 0 + +#undump 1 +unfix soft +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 85.0 +Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523 +create_atoms 2 region plane +Created 124609 atoms + create_atoms CPU = 0.020 seconds + +set type 2 mass 0.1 +Setting atom values ... + 124609 settings made for mass +group small type 2 +124609 atoms in group small +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 1.0 + +delete_atoms overlap 1.0 small big +System init for delete_atoms ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 28 28 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308) +Deleted 51030 atoms, new total = 73999 + +# SRD run + +reset_timestep 0 + +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes + +comm_modify mode multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones +# if comment out, big particles won't see SRD particles + +timestep 0.001 + +fix 1 big rigid molecule + 30 rigid bodies with 420 atoms +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes +fix 3 small viscosity 10 x y 50 +fix 4 all enforce2d + +# diagnostics + +uncompute tbig +compute tbig big temp/sphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689) + +thermo_modify temp tbig +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483) +thermo 1000 + +#dump 1 all atom 1000 dump.box.mp + +#dump 1 all image 1000 image.*.jpg type type zoom 1.6 +#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 + +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2 + +@Article{Intveld08, + author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest}, + title = {Accurate and Efficient Methods for Modeling Colloidal + Mixtures in an Explicit Solvent using Molecular Dynamics}, + journal = {Comp.~Phys.~Comm.}, + year = 2008, + volume = 179, + pages = {320--329} +} + +@article{Stratford2018, + author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin}, + title = {Implementation of multi-level contact detection in LAMMPS}, + year = {2018} +} + +@article{Shire2020, + author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin}, + title = {DEM simulations of polydisperse media: efficient contact + detection applied to investigate the quasi-static limit}, + journal = {Computational Particle Mechanics}, + year = {2020} +} + +- fix srd command: + +@Article{Petersen10, + author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk}, + title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.}, + year = 2010, + volume = 132, + pages = {174106} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +SRD info: + SRD/big particles = 73579 420 + big particle diameter max/min = 1.0000000 1.0000000 + SRD temperature & lamda = 1.0000000 0.063245553 + SRD max distance & max velocity = 0.25298221 12.649111 + SRD grid counts: 153 153 1 + SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000 + SRD per actual grid cell = 4.0557326 + SRD viscosity = 0.22929663 + big/SRD mass density ratio = 0.19661407 +WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845) + # of rescaled SRD velocities = 0 + ave/max small velocity = 4.1966772 7.7276214 + ave/max big velocity = 2.1275716 5.8359099 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 38.289379, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 27.16 | 27.18 | 27.21 Mbytes +Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] + 0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0 + 1000 3.1072437 16288 0.24129297 42.187428 42.512949 11.859485 10412 35 35 0 1004 70756 23409 16288 0.91643759 0 66 0 + 2000 2.1718238 16265 0.24069263 42.179651 42.407175 11.539339 10224 48 48 0 1797 70756 23409 16265 0.91071196 0 66 0 + 3000 1.5732455 16326 0.24032934 42.178352 42.343168 10.457457 10058 45 45 0 2517 70756 23409 16326 0.91928964 0 66 0 + 4000 2.3482192 16229 0.24085032 42.188956 42.43496 10.606093 10150 43 43 0 3181 70756 23409 16229 0.91913606 0 66 0 + 5000 2.5996379 16333 0.2410073 42.190274 42.462617 11.204793 10528 38 38 0 3885 70756 23409 16333 0.9241125 0 66 0 + 6000 2.4105417 16271 0.24084161 42.180891 42.433424 9.8492284 10088 30 30 0 4620 70756 23409 16271 0.93147983 0 66 0 + 7000 2.2377455 16250 0.24081836 42.194898 42.429329 9.2171742 10091 34 34 0 5351 70756 23409 16250 0.92985862 0 66 0 + 8000 2.9660933 16303 0.24115329 42.177606 42.48834 9.4008156 10139 39 39 0 6167 70756 23409 16303 0.92973123 0 66 0 + 9000 2.9430592 16287 0.24114154 42.177948 42.486269 10.347006 10329 41 41 0 6957 70756 23409 16287 0.93491985 0 66 0 + 10000 2.9059731 16336 0.2410888 42.172541 42.476977 8.1176194 10272 31 31 0 7736 70756 23409 16336 0.94200526 0 66 0 +Loop time of 24.5198 on 4 procs for 10000 steps with 73999 atoms + +Performance: 35236.804 tau/day, 407.833 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14222 | 0.18851 | 0.26138 | 11.1 | 0.77 +Neigh | 0.039759 | 0.047049 | 0.058019 | 3.3 | 0.19 +Comm | 0.58081 | 0.65008 | 0.68833 | 5.4 | 2.65 +Output | 0.0024264 | 0.0030395 | 0.0048751 | 1.9 | 0.01 +Modify | 23.123 | 23.276 | 23.388 | 2.3 | 94.93 +Other | | 0.3547 | | | 1.45 + +Nlocal: 18499.8 ave 19805 max 17016 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 71.0000 ave 86 max 62 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Neighs: 604.000 ave 818 max 455 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 2416 +Ave neighs/atom = 0.032649090 +Neighbor list builds = 500 +Dangerous builds = 0 +Total wall time: 0:00:26 diff --git a/examples/ASPHERE/box/log.1Feb14.box.g++.8 b/examples/ASPHERE/box/log.1Feb14.box.g++.8 deleted file mode 100644 index cb21e806fe..0000000000 --- a/examples/ASPHERE/box/log.1Feb14.box.g++.8 +++ /dev/null @@ -1,290 +0,0 @@ -LAMMPS (1 Feb 2014) -# SRD diffusion demo - rigid box particles - -units lj -atom_style sphere -atom_modify map array first big -dimension 2 - -# read in clusters of rigid bodies - -fix molprop all property/atom mol -read_data data.box fix molprop NULL Molecules - orthogonal box = (-19.1447 -19.1447 -0.5) to (19.1447 19.1447 0.5) - 4 by 2 by 1 MPI processor grid - reading atoms ... - 420 atoms - -set type 1 mass 1.0 - 420 settings made for mass -group big type 1 -420 atoms in group big -velocity big create 1.44 87287 loop geom - -# equilibrate big particles - -pair_style soft 1.12 -pair_coeff 1 1 0.0 -pair_coeff 2 2 0.0 0.0 -pair_coeff 1 2 0.0 0.0 - -variable prefactor equal ramp(0,60) -fix soft all adapt 1 pair soft a * * v_prefactor - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 big rigid molecule -30 rigid bodies with 420 atoms -fix 2 all enforce2d - -#dump 1 all atom 10 dump.box.equil - -thermo 100 -run 1000 -Memory usage per processor = 0.443012 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 0 0 0 -8.770036 - 100 0 3.4203218 0 3.4203218 0.49351517 - 200 0 5.3315601 0 5.3315601 0.26965614 - 300 0 7.2094878 0 7.2094878 0.43326479 - 400 0 9.2008598 0 9.2008598 0.27649318 - 500 0 11.562353 0 11.562353 0.60730421 - 600 0 13.731564 0 13.731564 0.27272312 - 700 0 15.850142 0 15.850142 0.0032862218 - 800 0 18.395444 0 18.395444 1.0272658 - 900 0 20.3322 0 20.3322 -0.16729762 - 1000 0 22.600716 0 22.600716 -0.13023705 -Loop time of 0.0534293 on 8 procs for 1000 steps with 420 atoms - -Pair time (%) = 0.00388658 (7.27425) -Neigh time (%) = 0.0012759 (2.38801) -Comm time (%) = 0.0151907 (28.4315) -Outpt time (%) = 0.000330567 (0.618701) -Other time (%) = 0.0327455 (61.2876) - -Nlocal: 52.5 ave 67 max 35 min -Histogram: 1 1 1 0 1 0 0 1 1 2 -Nghost: 30.625 ave 41 max 17 min -Histogram: 1 0 0 1 1 1 2 0 1 1 -Neighs: 70.25 ave 90 max 44 min -Histogram: 2 0 0 1 1 0 1 0 0 3 - -Total # of neighbors = 562 -Ave neighs/atom = 1.3381 -Neighbor list builds = 158 -Dangerous builds = 0 - -#undump 1 -unfix soft -unfix 1 -unfix 2 - -# add small particles as hi density lattice - -region plane block INF INF INF INF -0.001 0.001 units box -lattice sq 85.0 -Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 -create_atoms 2 region plane -Created 124609 atoms - -set type 2 mass 0.1 - 124609 settings made for mass -group small type 2 -124609 atoms in group small -velocity small create 1.0 593849 loop geom - -# delete overlaps -# must set 1-2 cutoff to non-zero value - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 1.0 - -delete_atoms overlap 1.0 small big -Deleted 51030 atoms, new total = 73999 - -# SRD run - -reset_timestep 0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -communicate multi group big vel yes -neigh_modify include big - -# no pairwise interactions with small particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -# use fix SRD to push small particles out from inside big ones -# if comment out, big particles won't see SRD particles - -timestep 0.001 - -fix 1 big rigid molecule -30 rigid bodies with 420 atoms -fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes -fix 3 all enforce2d - -# diagnostics - -compute tbig big temp/sphere -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] - -thermo_modify temp tbig -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439) -thermo 1000 - -#dump 1 all atom 1000 dump.box - -#dump 1 all image 1000 image.*.jpg type type zoom 1.6 -#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 - -run 100000 -SRD info: - SRD/big particles = 73579 420 - big particle diameter max/min = 1 1 - SRD temperature & lamda = 1 0.0632456 - SRD max distance & max velocity = 0.252982 12.6491 - SRD grid counts: 153 153 1 - SRD grid size: request, actual (xyz) = 0.25, 0.250257 0.250257 1 - SRD per actual grid cell = 4.05573 - SRD viscosity = 0.229297 - big/SRD mass density ratio = 0.196614 -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875) - # of rescaled SRD velocities = 0 - ave/max small velocity = 4.19668 7.72762 - ave/max big velocity = 2.12757 5.83591 -Memory usage per processor = 14.2707 Mbytes -Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12] - 0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0 - 1000 3.4640099 16291 0.24158286 42.201127 42.564024 10.312083 10282 38 38 0 957 90440 23409 16291 0.91054529 0 69 0 - 2000 1.4820124 16228 0.24022248 42.169082 42.324341 9.5969069 10066 30 30 0 1726 90440 23409 16228 0.91140743 0 69 0 - 3000 1.3797075 16198 0.24017061 42.170661 42.315202 11.093574 10151 43 43 0 2410 90440 23409 16198 0.91909014 0 69 0 - 4000 1.3403741 16287 0.24014493 42.170257 42.310677 10.101336 10172 38 38 0 3094 90440 23409 16287 0.92752333 0 69 0 - 5000 1.0444432 16295 0.2399965 42.175108 42.284525 9.5498999 10375 26 26 0 3799 90440 23409 16295 0.93506273 0 69 0 - 6000 0.78295352 16299 0.2398933 42.184319 42.266343 9.535916 10090 37 37 0 4563 90440 23409 16299 0.93041308 0 69 0 - 7000 1.1675613 16333 0.24006565 42.174393 42.296709 11.594065 10426 37 37 0 5266 90440 23409 16333 0.94031182 0 69 0 - 8000 1.1343357 16302 0.24001364 42.168711 42.287546 9.8091173 9979 39 39 0 5993 90440 23409 16302 0.94116994 0 69 0 - 9000 1.4165164 16306 0.24010969 42.156072 42.304469 10.736953 10191 38 39 1 6683 90440 23409 16306 0.93957787 0 69 0 - 10000 0.63657628 16306 0.23958347 42.145066 42.211755 6.3923231 10115 37 37 0 7409 90440 23409 16306 0.9420945 0 69 0 - 11000 0.9421837 16286 0.23976832 42.145619 42.244324 9.9611184 10079 45 45 0 8122 90440 23409 16286 0.94240902 0 69 0 - 12000 0.9735159 16295 0.23980202 42.148274 42.250262 11.862106 10345 36 36 0 8854 90440 23409 16295 0.94994179 0 69 0 - 13000 0.93356977 16392 0.23970059 42.134589 42.232391 11.29915 10321 41 41 0 9607 90440 23409 16392 0.94747955 0 69 0 - 14000 1.0596151 16306 0.2397451 42.129226 42.240233 12.305503 10075 37 37 0 10323 90440 23409 16306 0.94857373 0 69 0 - 15000 1.4275311 16285 0.23986502 42.11181 42.261361 8.6785032 9963 43 43 0 11054 90440 23409 16285 0.95130035 0 69 0 - 16000 1.1798179 16367 0.23973717 42.115236 42.238836 9.7201163 10138 38 38 0 11785 90440 23409 16367 0.94838949 0 69 0 - 17000 1.2809316 16368 0.23978706 42.113433 42.247626 7.4568393 10239 31 31 0 12545 90440 23409 16368 0.94818482 0 69 0 - 18000 1.0552359 16355 0.23962676 42.108834 42.219382 11.024507 10270 39 39 0 13350 90440 23409 16355 0.94825339 0 69 0 - 19000 1.1373204 16343 0.23964456 42.103371 42.222519 9.1505749 10245 37 37 0 14198 90440 23409 16343 0.94776971 0 69 0 - 20000 0.89607862 16295 0.23962161 42.1246 42.218475 8.377591 10173 48 48 0 14985 90440 23409 16295 0.95836326 0 69 0 - 21000 0.93823225 16323 0.23958542 42.113808 42.212099 9.9128627 10398 39 39 0 15722 90440 23409 16323 0.94732512 0 69 0 - 22000 1.0132051 16270 0.23958637 42.106121 42.212267 12.521464 10414 37 37 1 16538 90440 23409 16270 0.94611956 0 69 0 - 23000 1.2399208 16420 0.2396696 42.097034 42.226931 9.1607507 10169 32 32 0 17263 90440 23409 16420 0.95141771 0 69 0 - 24000 1.2359103 16395 0.23957354 42.080529 42.210006 10.051289 10225 34 34 1 18057 90440 23409 16395 0.95487046 0 69 0 - 25000 0.96280337 16322 0.23944374 42.086271 42.187136 11.818136 10183 40 40 0 18818 90440 23409 16322 0.95691179 0 69 0 - 26000 0.83139747 16344 0.23940306 42.09287 42.179968 10.844701 10090 38 38 0 19555 90440 23409 16344 0.95332651 0 69 0 - 27000 1.107274 16270 0.23949948 42.080957 42.196957 14.435937 10028 46 46 0 20355 90440 23409 16270 0.95321506 0 69 0 - 28000 1.0892583 16399 0.23938721 42.063064 42.177177 9.3768225 10011 38 38 0 21195 90440 23409 16399 0.95935372 0 69 0 - 29000 1.1099534 16320 0.23940855 42.064655 42.180936 8.8044985 9919 34 34 0 22020 90440 23409 16320 0.95465302 0 69 0 - 30000 1.0119272 16302 0.23934223 42.06324 42.169252 12.13721 10160 47 47 0 22750 90440 23409 16302 0.94922806 0 69 0 - 31000 0.9567755 16335 0.23916982 42.038642 42.138875 8.3903033 10007 30 30 0 23497 90440 23409 16335 0.95223124 0 69 0 - 32000 0.86048362 16291 0.23910468 42.037252 42.127398 11.646647 10347 41 41 0 24266 90440 23409 16291 0.95484469 0 69 0 - 33000 1.1129645 16284 0.23928206 42.042053 42.15865 9.0389494 9909 33 33 0 25073 90440 23409 16284 0.96246044 0 69 0 - 34000 1.0741874 16303 0.23920774 42.033022 42.145556 12.710332 10125 35 35 0 25845 90440 23409 16303 0.95343962 0 69 0 - 35000 0.87606515 16293 0.23916564 42.046361 42.138139 13.784203 10044 42 42 0 26569 90440 23409 16293 0.95827172 0 69 0 - 36000 0.8268686 16315 0.23912916 42.045087 42.131712 13.474499 10240 43 44 0 27324 90440 23409 16315 0.9539089 0 69 0 - 37000 1.1732368 16336 0.23930076 42.039035 42.161945 8.7392785 9996 34 34 0 28094 90440 23409 16336 0.95672234 0 69 0 - 38000 1.089263 16323 0.2391967 42.029498 42.143611 9.464664 10104 39 39 0 28856 90440 23409 16323 0.95362271 0 69 0 - 39000 1.06444 16335 0.23919427 42.03167 42.143183 10.036973 9961 36 36 0 29607 90440 23409 16335 0.95464483 0 69 0 - 40000 1.1390869 16376 0.23927054 42.037288 42.156621 9.8133871 10206 38 38 0 30409 90440 23409 16376 0.95191201 0 69 0 - 41000 0.76020035 16347 0.23906101 42.040064 42.119704 10.826738 10406 41 41 0 31195 90440 23409 16347 0.94685002 0 69 0 - 42000 1.3087439 16311 0.23945151 42.051398 42.188505 11.375199 10219 45 45 0 31938 90440 23409 16311 0.95326292 0 69 0 - 43000 0.98306175 16313 0.23923796 42.047893 42.15088 10.536429 10269 47 47 0 32660 90440 23409 16313 0.94791465 0 69 0 - 44000 1.1067947 16299 0.23929754 42.045427 42.161377 10.366386 10166 33 33 0 33471 90440 23409 16299 0.9520033 0 69 0 - 45000 1.1754605 16269 0.2394174 42.059352 42.182496 7.898603 9985 37 37 0 34245 90440 23409 16269 0.95500544 0 69 0 - 46000 0.93860976 16272 0.23926541 42.057387 42.155717 11.566786 10108 35 35 0 35050 90440 23409 16272 0.95183186 0 69 0 - 47000 1.3576761 16315 0.23942 42.040721 42.182954 10.037574 9902 33 33 0 35807 90440 23409 16315 0.95525561 0 69 0 - 48000 1.3465813 16308 0.23938501 42.035719 42.176789 8.9584586 9830 33 33 0 36625 90440 23409 16308 0.95044669 0 69 0 - 49000 0.93823974 16340 0.23917669 42.041793 42.140085 10.474409 9930 35 35 0 37393 90440 23409 16340 0.94869206 0 69 0 - 50000 1.0643183 16332 0.23923523 42.0389 42.1504 8.9372951 9886 43 43 0 38182 90440 23409 16332 0.94865149 0 69 0 - 51000 0.87518396 16310 0.23914944 42.043598 42.135284 11.284535 9695 40 40 0 38995 90440 23409 16310 0.9560088 0 69 0 - 52000 1.1910982 16336 0.23929054 42.035364 42.160145 12.437325 9961 44 44 0 39787 90440 23409 16336 0.95735399 0 69 0 - 53000 1.0023949 16384 0.23923896 42.046043 42.151056 10.386358 9859 36 36 0 40569 90440 23409 16384 0.95693245 0 69 0 - 54000 0.98715708 16261 0.23921241 42.042962 42.146379 9.9941499 10027 35 35 0 41343 90440 23409 16261 0.951038 0 69 0 - 55000 1.0004435 16299 0.23914811 42.030241 42.135049 12.345206 9830 47 48 0 42056 90440 23409 16299 0.95562154 0 69 0 - 56000 1.0479458 16296 0.23914874 42.025377 42.135162 11.587952 9801 39 39 0 42915 90440 23409 16296 0.94868699 0 69 0 - 57000 0.94369119 16319 0.23902076 42.013749 42.112612 10.195934 9764 46 46 0 43652 90440 23409 16319 0.95438171 0 69 0 - 58000 1.1549569 16347 0.23924582 42.031269 42.152265 9.511812 9910 41 41 0 44366 90440 23409 16347 0.9484367 0 69 0 - 59000 0.81453047 16402 0.23895926 42.016445 42.101776 10.359564 9967 46 46 0 45115 90440 23409 16402 0.95256147 0 69 0 - 60000 0.9253868 16360 0.23897085 42.006873 42.103818 12.308731 9839 44 44 0 45872 90440 23409 16360 0.95753176 0 69 0 - 61000 0.95173279 16298 0.23908799 42.024752 42.124457 10.985428 9848 45 45 0 46621 90440 23409 16298 0.95937218 0 69 0 - 62000 1.0168886 16273 0.23910318 42.020603 42.127134 13.493586 9842 41 41 0 47356 90440 23409 16273 0.95720763 0 69 0 - 63000 0.59853847 16306 0.23888991 42.026854 42.089558 11.654045 10030 47 47 0 48152 90440 23409 16306 0.95164201 0 69 0 - 64000 0.88165231 16295 0.23904152 42.023907 42.11627 8.6017877 9808 31 31 0 48944 90440 23409 16295 0.95791125 0 69 0 - 65000 0.83089386 16306 0.23895929 42.014736 42.101782 11.57787 10042 51 51 0 49729 90440 23409 16306 0.95848466 0 69 0 - 66000 1.1172469 16324 0.23919188 42.025716 42.142761 11.423941 9802 55 55 0 50498 90440 23409 16324 0.94666759 0 69 0 - 67000 0.97470955 16356 0.23903681 42.013327 42.11544 11.345125 10043 40 40 0 51251 90440 23409 16356 0.95264876 0 69 0 - 68000 0.90592443 16274 0.23906764 42.025966 42.120872 11.050097 9782 44 44 0 52009 90440 23409 16274 0.95334971 0 69 0 - 69000 1.0820724 16352 0.23920813 42.032265 42.145625 11.892518 9803 43 43 0 52800 90440 23409 16352 0.95290952 0 69 0 - 70000 1.0413192 16301 0.23929529 42.051891 42.160982 13.193444 9847 48 48 0 53595 90440 23409 16301 0.95613844 0 69 0 - 71000 0.95433723 16430 0.23919345 42.04306 42.143038 12.116035 9898 46 46 0 54350 90440 23409 16430 0.95532726 0 69 0 - 72000 0.80923962 16318 0.23909626 42.041137 42.125915 10.240888 9800 37 37 0 55133 90440 23409 16318 0.95196829 0 69 0 - 73000 0.93773964 16330 0.23920083 42.046099 42.144338 13.100955 9780 37 37 0 55931 90440 23409 16330 0.95075325 0 69 0 - 74000 1.0547823 16296 0.23913003 42.021364 42.131865 12.215247 10308 45 45 0 56705 90440 23409 16296 0.95515593 0 69 0 - 75000 0.74939607 16287 0.23910386 42.048745 42.127253 10.270685 10092 43 43 0 57457 90440 23409 16287 0.95365363 0 69 0 - 76000 0.95221448 16326 0.23921923 42.047825 42.147581 10.33549 10191 47 47 0 58254 90440 23409 16326 0.95389896 0 69 0 - 77000 0.94854568 16249 0.23925669 42.054809 42.15418 10.317964 10055 35 35 1 59026 90440 23409 16249 0.95716276 0 69 0 - 78000 1.2663624 16282 0.23949043 42.062695 42.195362 10.496265 9893 41 41 0 59780 90440 23409 16282 0.94847998 0 69 0 - 79000 0.98933199 16264 0.2392933 42.056987 42.160631 12.876564 9946 41 41 0 60518 90440 23409 16264 0.95354593 0 69 0 - 80000 0.8212992 16341 0.23927469 42.07131 42.157351 8.5608431 9838 40 40 0 61296 90440 23409 16341 0.95234534 0 69 0 - 81000 0.98231967 16339 0.23928757 42.056712 42.159622 11.491156 10104 37 38 0 62061 90440 23409 16339 0.94886686 0 69 0 - 82000 0.99158973 16299 0.23925843 42.050607 42.154488 9.4538952 10047 37 37 0 62852 90440 23409 16299 0.95656275 0 69 0 - 83000 1.2341517 16344 0.239348 42.040977 42.170269 10.524371 9784 37 37 0 63608 90440 23409 16344 0.94780456 0 69 0 - 84000 1.1753084 16288 0.23928447 42.035947 42.159074 9.1748883 9831 37 37 0 64314 90440 23409 16288 0.94217045 0 69 0 - 85000 0.84912682 16310 0.23915288 42.046935 42.135891 11.43337 9890 42 42 0 64992 90440 23409 16310 0.9423407 0 69 0 - 86000 0.88939653 16275 0.23909757 42.032971 42.126146 12.34417 9961 46 46 0 65677 90440 23409 16275 0.93887016 0 69 0 - 87000 1.1303842 16248 0.23922093 42.029458 42.147879 11.934641 9945 47 47 0 66417 90440 23409 16248 0.93840688 0 69 0 - 88000 1.2294052 16326 0.23916023 42.00839 42.137185 9.7233305 9838 35 36 0 67149 90440 23409 16326 0.94945034 0 69 0 - 89000 1.0455638 16345 0.23918575 42.032147 42.141682 8.6325214 9871 35 35 0 67855 90440 23409 16345 0.94891424 0 69 0 - 90000 0.79047982 16288 0.23897011 42.020876 42.103688 10.271997 10053 45 45 0 68551 90440 23409 16288 0.94963234 0 69 0 - 91000 0.85451256 16320 0.23898107 42.016098 42.105619 12.567859 10053 42 42 0 69246 90440 23409 16320 0.9506585 0 69 0 - 92000 1.1082033 16363 0.23917252 42.023254 42.139351 11.730554 9858 46 46 0 70046 90440 23409 16363 0.95352701 0 69 0 - 93000 0.90368051 16312 0.23897927 42.010631 42.105303 10.70167 9793 37 37 0 70824 90440 23409 16312 0.95992717 0 69 0 - 94000 0.95749706 16350 0.23909592 42.025545 42.125855 10.174353 9970 42 42 0 71646 90440 23409 16350 0.95082103 0 69 0 - 95000 0.90723392 16298 0.23898239 42.010809 42.105853 11.561525 9938 33 33 0 72414 90440 23409 16298 0.94768554 0 69 0 - 96000 1.0249944 16288 0.23910408 42.019912 42.127292 10.755062 9945 38 38 0 73184 90440 23409 16288 0.94637131 0 69 0 - 97000 0.96263604 16339 0.23911151 42.027754 42.128601 9.9303923 9816 36 36 0 73853 90440 23409 16339 0.94851816 0 69 0 - 98000 0.93105892 16301 0.23897506 42.00702 42.10456 12.088691 9933 39 39 0 74604 90440 23409 16301 0.94785265 0 69 0 - 99000 1.2448977 16286 0.23920972 42.015487 42.145905 11.565661 10001 51 51 0 75328 90440 23409 16286 0.9483854 0 69 0 - 100000 0.95492648 16337 0.23919603 42.043453 42.143492 11.223512 9793 32 32 0 76045 90440 23409 16337 0.95143273 0 69 0 -Loop time of 51.3335 on 8 procs for 100000 steps with 73999 atoms - -Pair time (%) = 0.586967 (1.14344) -Neigh time (%) = 3.95145 (7.69761) -Comm time (%) = 2.97199 (5.78957) -Outpt time (%) = 0.0085291 (0.0166151) -Other time (%) = 43.8145 (85.3528) - -Nlocal: 9249.88 ave 10642 max 7533 min -Histogram: 1 0 0 1 1 1 2 0 1 1 -Nghost: 57.375 ave 89 max 34 min -Histogram: 1 2 0 1 1 0 2 0 0 1 -Neighs: 335.875 ave 616 max 209 min -Histogram: 2 1 0 3 1 0 0 0 0 1 - -Total # of neighbors = 2687 -Ave neighs/atom = 0.0363113 -Neighbor list builds = 5000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/ASPHERE/box/log.1Feb14.box.mp.g++.8 b/examples/ASPHERE/box/log.1Feb14.box.mp.g++.8 deleted file mode 100644 index 1613729eca..0000000000 --- a/examples/ASPHERE/box/log.1Feb14.box.mp.g++.8 +++ /dev/null @@ -1,291 +0,0 @@ -LAMMPS (1 Feb 2014) -# SRD viscosity demo - rigid box particles - -units lj -atom_style sphere -atom_modify map array first big -dimension 2 - -# read in clusters of rigid bodies - -fix molprop all property/atom mol -read_data data.box fix molprop NULL Molecules - orthogonal box = (-19.1447 -19.1447 -0.5) to (19.1447 19.1447 0.5) - 4 by 2 by 1 MPI processor grid - reading atoms ... - 420 atoms - -set type 1 mass 1.0 - 420 settings made for mass -group big type 1 -420 atoms in group big -velocity big create 1.44 87287 loop geom - -# equilibrate big particles - -pair_style soft 1.12 -pair_coeff 1 1 0.0 -pair_coeff 2 2 0.0 0.0 -pair_coeff 1 2 0.0 0.0 - -variable prefactor equal ramp(0,60) -fix soft all adapt 1 pair soft a * * v_prefactor - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 big rigid molecule -30 rigid bodies with 420 atoms -fix 2 all enforce2d - -#dump 1 all atom 10 dump.box.equil - -thermo 100 -run 1000 -Memory usage per processor = 0.443012 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 0 0 0 -8.770036 - 100 0 3.4203218 0 3.4203218 0.49351517 - 200 0 5.3315601 0 5.3315601 0.26965614 - 300 0 7.2094878 0 7.2094878 0.43326479 - 400 0 9.2008598 0 9.2008598 0.27649318 - 500 0 11.562353 0 11.562353 0.60730421 - 600 0 13.731564 0 13.731564 0.27272312 - 700 0 15.850142 0 15.850142 0.0032862218 - 800 0 18.395444 0 18.395444 1.0272658 - 900 0 20.3322 0 20.3322 -0.16729762 - 1000 0 22.600716 0 22.600716 -0.13023705 -Loop time of 0.0540034 on 8 procs for 1000 steps with 420 atoms - -Pair time (%) = 0.00388333 (7.1909) -Neigh time (%) = 0.0012731 (2.35743) -Comm time (%) = 0.0160792 (29.7743) -Outpt time (%) = 0.000274509 (0.508318) -Other time (%) = 0.0324934 (60.169) - -Nlocal: 52.5 ave 67 max 35 min -Histogram: 1 1 1 0 1 0 0 1 1 2 -Nghost: 30.625 ave 41 max 17 min -Histogram: 1 0 0 1 1 1 2 0 1 1 -Neighs: 70.25 ave 90 max 44 min -Histogram: 2 0 0 1 1 0 1 0 0 3 - -Total # of neighbors = 562 -Ave neighs/atom = 1.3381 -Neighbor list builds = 158 -Dangerous builds = 0 - -#undump 1 -unfix soft -unfix 1 -unfix 2 - -# add small particles as hi density lattice - -region plane block INF INF INF INF -0.001 0.001 units box -lattice sq 85.0 -Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 -create_atoms 2 region plane -Created 124609 atoms - -set type 2 mass 0.1 - 124609 settings made for mass -group small type 2 -124609 atoms in group small -velocity small create 1.0 593849 loop geom - -# delete overlaps -# must set 1-2 cutoff to non-zero value - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 1.0 - -delete_atoms overlap 1.0 small big -Deleted 51030 atoms, new total = 73999 - -# SRD run - -reset_timestep 0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -communicate multi group big vel yes -neigh_modify include big - -# no pairwise interactions with small particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -# use fix SRD to push small particles out from inside big ones -# if comment out, big particles won't see SRD particles - -timestep 0.001 - -fix 1 big rigid molecule -30 rigid bodies with 420 atoms -fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes -fix 3 small viscosity 10 x y 50 -fix 4 all enforce2d - -# diagnostics - -compute tbig big temp/sphere -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] - -thermo_modify temp tbig -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439) -thermo 1000 - -#dump 1 all atom 1000 dump.box.mp - -#dump 1 all image 1000 image.*.jpg type type zoom 1.6 -#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 - -run 100000 -SRD info: - SRD/big particles = 73579 420 - big particle diameter max/min = 1 1 - SRD temperature & lamda = 1 0.0632456 - SRD max distance & max velocity = 0.252982 12.6491 - SRD grid counts: 153 153 1 - SRD grid size: request, actual (xyz) = 0.25, 0.250257 0.250257 1 - SRD per actual grid cell = 4.05573 - SRD viscosity = 0.229297 - big/SRD mass density ratio = 0.196614 -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875) - # of rescaled SRD velocities = 0 - ave/max small velocity = 4.19668 7.72762 - ave/max big velocity = 2.12757 5.83591 -Memory usage per processor = 14.2707 Mbytes -Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12] - 0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0 - 1000 3.0049838 16229 0.24126663 42.1935 42.508307 10.275827 10158 39 39 0 970 90440 23409 16229 0.90908897 0 5 0 - 2000 2.1454941 16282 0.24068985 42.18192 42.406686 8.3551805 10114 39 39 0 1766 90440 23409 16282 0.91411077 0 5 0 - 3000 1.7194781 16297 0.24043991 42.182513 42.362649 9.0500757 10293 35 35 0 2454 90440 23409 16297 0.91613392 0 5 0 - 4000 1.9700398 16189 0.24063155 42.190029 42.396415 11.380017 10043 27 28 0 3083 90440 23409 16189 0.92535621 0 5 0 - 5000 2.2262815 16301 0.24071918 42.178625 42.411854 10.059361 10169 29 29 0 3730 90440 23409 16301 0.92861813 0 5 0 - 6000 2.2291507 16232 0.24063671 42.163793 42.397323 7.276142 9899 40 40 0 4445 90440 23409 16232 0.93275834 0 5 0 - 7000 2.7841984 16212 0.2407729 42.129641 42.421319 10.838996 10144 39 39 0 5148 90440 23409 16212 0.93329636 0 5 0 - 8000 3.1799279 16294 0.24102189 42.132053 42.465189 9.3204165 10068 31 31 0 5897 90440 23409 16294 0.93229671 0 5 0 - 9000 3.6101913 16308 0.24126974 42.130646 42.508857 9.9117415 10113 30 30 0 6716 90440 23409 16308 0.93107227 0 5 0 - 10000 4.1022731 16319 0.24161934 42.140689 42.570451 9.8799373 10205 34 34 0 7480 90440 23409 16319 0.92489062 0 5 0 - 11000 4.2790298 16269 0.2417129 42.138657 42.586936 10.14836 10002 37 37 2 8283 90440 23409 16269 0.92331323 0 10 0 - 12000 4.4299614 16323 0.24179577 42.137445 42.601537 11.786696 10068 37 37 1 9085 90440 23409 16323 0.93507414 0 10 0 - 13000 4.1451629 16263 0.24166347 42.143972 42.578227 7.5907603 9931 27 27 0 9967 90440 23409 16263 0.93269278 0 10 0 - 14000 5.0478037 16299 0.24222245 42.147894 42.676711 9.616107 10010 39 39 0 10856 90440 23409 16299 0.93132197 0 10 0 - 15000 4.9761523 16318 0.24208522 42.131222 42.652533 10.028283 10181 45 45 0 11744 90440 23409 16318 0.92914494 0 10 0 - 16000 5.0281695 16300 0.24209471 42.127445 42.654206 13.025657 10410 38 38 0 12657 90440 23409 16300 0.9322983 0 10 0 - 17000 6.0553511 16294 0.24278108 42.140765 42.775135 8.3971756 9898 31 31 0 13606 90440 23409 16294 0.93207864 0 10 0 - 18000 5.8870865 16349 0.24261355 42.128876 42.745619 9.4579631 9872 33 33 0 14510 90440 23409 16349 0.92911772 0 10 0 - 19000 6.19767 16260 0.2425369 42.082834 42.732114 10.497489 10068 37 37 0 15478 90440 23409 16260 0.9258668 0 10 0 - 20000 5.0588231 16330 0.24187554 42.085618 42.61559 9.3582625 9935 35 35 0 16470 90440 23409 16330 0.92639501 0 10 0 - 21000 6.4272357 16337 0.24285051 42.11404 42.78737 11.339789 9973 38 38 0 17363 90440 23409 16337 0.91830732 0 10 0 - 22000 6.3660195 16301 0.24257121 42.071243 42.738159 10.340724 9855 41 41 0 18300 90440 23409 16301 0.92735973 0 13 0 - 23000 5.9141967 16265 0.24245321 42.097787 42.71737 10.888473 9874 46 46 0 19294 90440 23409 16265 0.92958577 0 13 0 - 24000 7.3326392 16305 0.24333743 42.104977 42.873159 8.159204 9831 32 32 0 20337 90440 23409 16305 0.92498949 0 13 0 - 25000 7.8712498 16317 0.24365329 42.104202 42.928809 13.3861 10107 51 52 0 21343 90440 23409 16317 0.92093733 0 13 0 - 26000 7.6909446 16302 0.24354679 42.104327 42.910045 9.3626418 10101 45 45 0 22390 90440 23409 16302 0.91881953 0 13 0 - 27000 7.7525711 16296 0.24366541 42.11877 42.930944 9.3545743 9869 31 31 0 23458 90440 23409 16296 0.92276633 0 13 0 - 28000 7.8688635 16287 0.24363999 42.102109 42.926466 9.6143934 10023 37 37 0 24515 90440 23409 16287 0.92561111 0 13 0 - 29000 8.1116441 16298 0.24396496 42.13393 42.983722 9.8457785 10018 37 37 0 25571 90440 23409 16298 0.92896968 0 13 0 - 30000 7.5432306 16233 0.24356273 42.12261 42.912853 10.484741 9978 33 33 0 26714 90440 23409 16233 0.92084331 0 13 0 - 31000 7.9849131 16251 0.24395097 42.144741 42.981256 8.728219 9926 36 36 0 27794 90440 23409 16251 0.91985968 0 13 0 - 32000 8.8200827 16255 0.24461412 42.174088 43.098096 9.4477224 10118 31 31 0 28911 90440 23409 16255 0.92764378 0 13 0 - 33000 9.0462578 16266 0.24476502 42.176979 43.124682 9.0256529 9948 41 41 0 30010 90440 23409 16266 0.92496675 0 13 0 - 34000 11.115911 16273 0.24591951 42.163566 43.32809 10.89006 10013 35 35 1 31155 90440 23409 16273 0.9209011 0 59 0 - 35000 9.5287387 16348 0.24494148 42.157524 43.155772 9.1589486 10058 33 33 0 32262 90440 23409 16348 0.91852697 0 59 0 - 36000 8.6525285 16271 0.24454224 42.178976 43.085431 9.6115865 9936 39 39 0 33447 90440 23409 16271 0.91738637 0 59 0 - 37000 9.3244405 16237 0.24490339 42.172216 43.149062 11.766374 10057 49 49 0 34660 90440 23409 16237 0.92209291 0 59 0 - 38000 9.2952308 16272 0.24496591 42.186292 43.160078 9.5173055 10039 32 32 1 35916 90440 23409 16272 0.91915422 0 59 0 - 39000 10.12307 16312 0.24550971 42.195376 43.255888 10.678168 9989 43 43 1 37116 90440 23409 16312 0.92499805 0 59 0 - 40000 11.051307 16266 0.24606279 42.195578 43.353334 10.078073 9867 37 37 0 38363 90440 23409 16266 0.9229677 0 59 0 - 41000 10.400692 16313 0.24566631 42.193882 43.283479 9.2181368 10040 39 39 0 39612 90440 23409 16313 0.92195363 0 59 0 - 42000 9.0646248 16277 0.24487452 42.194348 43.143975 8.2531891 10173 37 37 0 40821 90440 23409 16277 0.91941681 0 59 0 - 43000 9.8646504 16258 0.24532194 42.189366 43.222806 10.34072 10037 37 37 0 42068 90440 23409 16258 0.91264623 0 59 0 - 44000 10.441846 16296 0.24553053 42.165649 43.259556 12.147264 10299 31 31 0 43277 90440 23409 16296 0.91599514 0 59 0 - 45000 10.458302 16261 0.24544296 42.148496 43.244128 8.8999271 10208 26 26 0 44492 90440 23409 16261 0.91716968 0 59 0 - 46000 10.117248 16269 0.24511999 42.127322 43.187224 9.0053892 10132 36 36 0 45691 90440 23409 16269 0.91327538 0 59 0 - 47000 9.6094606 16247 0.24494761 42.150148 43.156854 11.844069 9936 43 43 0 46930 90440 23409 16247 0.91513796 0 59 0 - 48000 12.544005 16250 0.24661869 42.137144 43.451278 14.420938 9999 43 43 0 48233 90440 23409 16250 0.91642267 0 59 0 - 49000 11.948168 16257 0.24628573 42.140902 43.392614 8.653163 10093 38 38 0 49517 90440 23409 16257 0.90604463 0 59 0 - 50000 12.315254 16233 0.2466687 42.16992 43.460089 9.1125366 10050 39 39 0 50806 90440 23409 16233 0.90490961 0 59 0 - 51000 11.364234 16265 0.24609762 42.168932 43.359471 9.8694192 9860 37 37 0 52074 90440 23409 16265 0.909623 0 59 0 - 52000 10.627787 16231 0.24578998 42.191882 43.305269 10.869196 9877 33 33 0 53420 90440 23409 16231 0.90981484 0 59 0 - 53000 11.809423 16261 0.24656286 42.204263 43.441441 13.38992 9828 39 39 0 54766 90440 23409 16261 0.90710704 0 59 0 - 54000 10.63283 16251 0.24554697 42.148537 43.262453 10.181102 10098 29 29 0 56085 90440 23409 16251 0.90800902 0 59 0 - 55000 10.803075 16254 0.24562954 42.145251 43.277002 7.9856721 9964 26 26 0 57451 90440 23409 16254 0.90786888 0 59 0 - 56000 10.844803 16274 0.2458735 42.183861 43.319983 9.9407901 10031 36 36 0 58695 90440 23409 16274 0.89847818 0 59 0 - 57000 10.623373 16218 0.24574768 42.184891 43.297816 12.015798 9792 43 43 0 60012 90440 23409 16218 0.90944412 0 59 0 - 58000 10.679964 16262 0.24583434 42.194231 43.313084 11.651504 9776 45 45 0 61295 90440 23409 16262 0.90511687 0 59 0 - 59000 10.35931 16278 0.24567475 42.199706 43.284967 10.599471 10069 30 30 1 62506 90440 23409 16278 0.90064789 0 59 0 - 60000 12.034078 16208 0.24677506 42.218115 43.478828 10.511331 9936 31 31 0 63825 90440 23409 16208 0.90250225 0 59 0 - 61000 11.915856 16208 0.24666669 42.211407 43.459734 11.982448 10227 34 34 0 65189 90440 23409 16208 0.90006711 0 59 0 - 62000 11.388719 16269 0.24635856 42.212341 43.405445 8.4867265 9991 29 29 0 66502 90440 23409 16269 0.90418592 0 59 0 - 63000 10.513272 16243 0.24593174 42.228854 43.330244 9.2843187 10133 39 39 0 67836 90440 23409 16243 0.91282932 0 59 0 - 64000 11.465761 16203 0.24638806 42.209467 43.410642 8.8736184 10023 38 39 0 69216 90440 23409 16203 0.90742452 0 59 0 - 65000 9.9798452 16292 0.24547666 42.204557 43.250064 12.475112 9766 36 36 0 70559 90440 23409 16292 0.90921789 0 59 0 - 66000 12.184131 16177 0.2468175 42.209872 43.486305 8.4442171 10049 33 33 0 71851 90440 23409 16177 0.90771921 0 59 0 - 67000 11.845593 16250 0.24645726 42.181869 43.422835 8.2359478 9678 33 33 0 73241 90440 23409 16250 0.9069606 0 59 0 - 68000 10.616202 16220 0.2456631 42.17074 43.282913 7.6844013 9954 28 28 0 74707 90440 23409 16220 0.90830051 0 59 0 - 69000 11.708481 16174 0.246425 42.190549 43.417152 9.6601201 10019 34 34 0 76143 90440 23409 16174 0.90853993 0 59 0 - 70000 13.149115 16175 0.24730865 42.195313 43.57284 7.8721271 9794 31 31 0 77520 90440 23409 16175 0.90460472 0 59 0 - 71000 12.420743 16210 0.24676949 42.176626 43.477846 10.370102 9886 36 36 0 78901 90440 23409 16210 0.90567986 0 59 0 - 72000 13.424842 16222 0.24726211 42.158228 43.56464 10.837461 9892 36 36 0 80221 90440 23409 16222 0.90896224 0 59 0 - 73000 12.983985 16177 0.2470467 42.16646 43.526687 7.3246122 9975 31 31 0 81578 90440 23409 16177 0.90172487 0 59 0 - 74000 11.873207 16217 0.24644792 42.177329 43.421189 11.257297 9937 40 40 0 83004 90440 23409 16217 0.9069376 0 59 0 - 75000 11.719883 16219 0.24631358 42.169723 43.397521 8.2731229 10281 28 28 0 84503 90440 23409 16219 0.90087971 0 59 0 - 76000 11.648725 16220 0.24633978 42.181793 43.402136 11.364684 9961 31 31 0 85910 90440 23409 16220 0.90445518 0 59 0 - 77000 11.315159 16169 0.24618794 42.189986 43.375384 10.639734 9853 35 35 0 87272 90440 23409 16169 0.90967681 0 59 0 - 78000 11.026923 16262 0.2459278 42.17435 43.329551 9.3461335 10068 36 36 0 88765 90440 23409 16262 0.90250223 0 59 0 - 79000 11.923316 16205 0.24657893 42.195162 43.444272 8.3200696 9914 29 29 1 90167 90440 23409 16205 0.89792511 0 59 0 - 80000 12.28723 16233 0.246793 42.194756 43.481989 9.8594414 9898 41 41 0 91543 90440 23409 16233 0.89920018 0 59 0 - 81000 12.657271 16252 0.24700788 42.193847 43.519847 9.5478351 10045 38 38 0 92888 90440 23409 16252 0.90032559 0 59 0 - 82000 10.415047 16249 0.24563975 42.1877 43.2788 8.4502786 9729 30 30 0 94355 90440 23409 16249 0.90516702 0 59 0 - 83000 13.038087 16237 0.24718282 42.184776 43.550671 10.813181 9834 48 48 0 95792 90440 23409 16237 0.90160106 0 59 0 - 84000 11.994728 16253 0.24664911 42.200046 43.456637 10.907779 9632 48 48 0 97203 90440 23409 16253 0.90075335 0 59 0 - 85000 11.560331 16253 0.24626448 42.177788 43.38887 9.8019244 9637 27 27 0 98581 90440 23409 16253 0.90204694 0 59 0 - 86000 12.294346 16214 0.2466302 42.165325 43.453305 8.4731319 9776 30 30 1 100022 90440 23409 16214 0.8976977 0 59 0 - 87000 11.439691 16227 0.24593937 42.133145 43.331589 11.138197 9408 35 35 0 101446 90440 23409 16227 0.90678956 0 59 0 - 88000 12.269451 16218 0.24642733 42.132191 43.417562 9.2022903 9627 28 28 0 102882 90440 23409 16218 0.89354177 0 59 0 - 89000 11.630085 16281 0.24612243 42.145453 43.363843 9.4906584 9713 45 45 0 104390 90440 23409 16281 0.90416008 0 59 0 - 90000 12.068036 16226 0.24636746 42.142743 43.407014 13.55402 9721 30 30 1 105786 90440 23409 16226 0.90693102 0 59 0 - 91000 11.423374 16180 0.24593187 42.133533 43.330267 11.12182 9490 33 33 0 107319 90440 23409 16180 0.89908597 0 59 0 - 92000 11.759782 16253 0.24594059 42.099827 43.331804 8.5785997 9808 36 37 0 108822 90440 23409 16253 0.90323757 0 59 0 - 93000 12.860286 16203 0.24670999 42.120094 43.467362 9.7352723 9342 32 32 0 110320 90440 23409 16203 0.89837993 0 59 0 - 94000 12.65067 16201 0.24650827 42.106515 43.431823 11.726981 9708 37 37 0 111721 90440 23409 16201 0.90153973 0 59 0 - 95000 12.938398 16301 0.2467405 42.117288 43.472739 13.229664 9490 42 42 0 113106 90440 23409 16301 0.89222858 0 59 0 - 96000 13.125 16243 0.24672164 42.094416 43.469416 11.492955 9666 43 43 0 114441 90440 23409 16243 0.89369219 0 59 0 - 97000 14.779601 16270 0.24775001 42.102263 43.650602 9.7132418 9517 31 31 0 115831 90440 23409 16270 0.88854614 0 59 0 - 98000 15.427308 16254 0.24808383 42.093224 43.709418 11.821283 9510 36 37 0 117263 90440 23409 16254 0.88982996 0 59 0 - 99000 16.212104 16248 0.24846852 42.078784 43.777195 10.786344 9807 37 37 0 118659 90440 23409 16248 0.89136464 0 59 0 - 100000 15.896 16229 0.24841013 42.101613 43.766908 10.836017 9640 28 28 0 120081 90440 23409 16229 0.90018614 0 59 0 -Loop time of 53.3125 on 8 procs for 100000 steps with 73999 atoms - -Pair time (%) = 0.559711 (1.04987) -Neigh time (%) = 3.94754 (7.40453) -Comm time (%) = 3.46588 (6.50106) -Outpt time (%) = 0.00787139 (0.0147646) -Other time (%) = 45.3315 (85.0298) - -Nlocal: 9249.88 ave 10477 max 8359 min -Histogram: 1 2 1 1 0 1 0 0 0 2 -Nghost: 54 ave 65 max 45 min -Histogram: 2 1 0 0 1 1 0 2 0 1 -Neighs: 316.875 ave 387 max 170 min -Histogram: 1 0 0 0 1 0 0 4 0 2 - -Total # of neighbors = 2535 -Ave neighs/atom = 0.0342572 -Neighbor list builds = 5000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/ASPHERE/dimer/in.dimer b/examples/ASPHERE/dimer/in.dimer index 9e514d83f1..224db9937d 100644 --- a/examples/ASPHERE/dimer/in.dimer +++ b/examples/ASPHERE/dimer/in.dimer @@ -61,7 +61,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/dimer/in.dimer.mp b/examples/ASPHERE/dimer/in.dimer.mp index 2970df022b..a637acaf87 100644 --- a/examples/ASPHERE/dimer/in.dimer.mp +++ b/examples/ASPHERE/dimer/in.dimer.mp @@ -61,7 +61,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid b/examples/ASPHERE/ellipsoid/in.ellipsoid index 241f010771..5e9a20f6e0 100644 --- a/examples/ASPHERE/ellipsoid/in.ellipsoid +++ b/examples/ASPHERE/ellipsoid/in.ellipsoid @@ -72,7 +72,7 @@ delete_atoms overlap 1.6 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp index 52c30db0a9..7ce01ad4e1 100644 --- a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp +++ b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp @@ -72,7 +72,7 @@ delete_atoms overlap 1.6 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/line/in.line.srd b/examples/ASPHERE/line/in.line.srd index 6ec1998d31..a32bde0b76 100644 --- a/examples/ASPHERE/line/in.line.srd +++ b/examples/ASPHERE/line/in.line.srd @@ -34,7 +34,7 @@ reset_timestep 0 velocity small create 1.44 87287 loop geom -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes neigh_modify exclude molecule/intra big include big diff --git a/examples/ASPHERE/poly/in.poly b/examples/ASPHERE/poly/in.poly index 3496a774bb..68bd2a6bbc 100644 --- a/examples/ASPHERE/poly/in.poly +++ b/examples/ASPHERE/poly/in.poly @@ -70,7 +70,7 @@ delete_atoms overlap 1.0 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/poly/in.poly.mp b/examples/ASPHERE/poly/in.poly.mp index 1c6a1faee3..8fa5d24a55 100644 --- a/examples/ASPHERE/poly/in.poly.mp +++ b/examples/ASPHERE/poly/in.poly.mp @@ -70,7 +70,7 @@ delete_atoms overlap 1.0 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/star/in.star b/examples/ASPHERE/star/in.star index 6711e7a0a7..a098810199 100644 --- a/examples/ASPHERE/star/in.star +++ b/examples/ASPHERE/star/in.star @@ -67,7 +67,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/star/in.star.mp b/examples/ASPHERE/star/in.star.mp index de5f23dfb6..53cb924e42 100644 --- a/examples/ASPHERE/star/in.star.mp +++ b/examples/ASPHERE/star/in.star.mp @@ -67,7 +67,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/examples/ASPHERE/tri/in.tri.srd b/examples/ASPHERE/tri/in.tri.srd index e7ef6ef59a..9bfc9d7b65 100644 --- a/examples/ASPHERE/tri/in.tri.srd +++ b/examples/ASPHERE/tri/in.tri.srd @@ -33,7 +33,7 @@ reset_timestep 0 velocity small create 1.44 87287 loop geom -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes neigh_modify exclude molecule/intra big include big diff --git a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp index 6f2f951a39..8b6a257755 100644 --- a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp +++ b/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp @@ -1,6 +1,6 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/ + https://www.lammps.org/ Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp index 6f2f951a39..8b6a257755 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp @@ -1,6 +1,6 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/ + https://www.lammps.org/ Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp index 131dc8696c..5f94363346 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp @@ -1,6 +1,6 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/ + https://www.lammps.org/ Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp index 0ceead08c2..27d356f264 100644 --- a/examples/COUPLE/lammps_mc/mc.cpp +++ b/examples/COUPLE/lammps_mc/mc.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov ------------------------------------------------------------------------- */ diff --git a/examples/COUPLE/lammps_mc/mc.h b/examples/COUPLE/lammps_mc/mc.h index e9d88523fc..fd3eff24f8 100644 --- a/examples/COUPLE/lammps_mc/mc.h +++ b/examples/COUPLE/lammps_mc/mc.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov ------------------------------------------------------------------------- */ diff --git a/examples/COUPLE/lammps_mc/random_park.cpp b/examples/COUPLE/lammps_mc/random_park.cpp index f08d3a4894..1c9018dee3 100644 --- a/examples/COUPLE/lammps_mc/random_park.cpp +++ b/examples/COUPLE/lammps_mc/random_park.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/lammps_mc/random_park.h b/examples/COUPLE/lammps_mc/random_park.h index 0dc2081768..c4dfa40ee4 100644 --- a/examples/COUPLE/lammps_mc/random_park.h +++ b/examples/COUPLE/lammps_mc/random_park.h @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/lammps_nwchem/nwchem_wrap.py b/examples/COUPLE/lammps_nwchem/nwchem_wrap.py index 6fddc35da8..28b7239f8f 100644 --- a/examples/COUPLE/lammps_nwchem/nwchem_wrap.py +++ b/examples/COUPLE/lammps_nwchem/nwchem_wrap.py @@ -2,7 +2,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator -# http://lammps.sandia.gov, Sandia National Laboratories +# https://www.lammps.org/ Sandia National Laboratories # Steve Plimpton, sjplimp@sandia.gov # ---------------------------------------------------------------------- diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py index 1e2c52aa46..bef8e899b9 100644 --- a/examples/COUPLE/lammps_vasp/vasp_wrap.py +++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py @@ -2,7 +2,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator -# http://lammps.sandia.gov, Sandia National Laboratories +# https://www.lammps.org/ Sandia National Laboratories # Steve Plimpton, sjplimp@sandia.gov # ---------------------------------------------------------------------- diff --git a/examples/COUPLE/multiple/multiple.cpp b/examples/COUPLE/multiple/multiple.cpp index e61f17031f..5e875bf879 100644 --- a/examples/COUPLE/multiple/multiple.cpp +++ b/examples/COUPLE/multiple/multiple.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/ + https://www.lammps.org/ Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/plugin/liblammpsplugin.c b/examples/COUPLE/plugin/liblammpsplugin.c index a66d87dfcc..474b0a86c2 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.c +++ b/examples/COUPLE/plugin/liblammpsplugin.c @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/plugin/liblammpsplugin.h b/examples/COUPLE/plugin/liblammpsplugin.h index 83d0dfa557..c70316d8e6 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.h +++ b/examples/COUPLE/plugin/liblammpsplugin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/COUPLE/simple/simple.cpp b/examples/COUPLE/simple/simple.cpp index f5ce7d91f3..c05266975e 100644 --- a/examples/COUPLE/simple/simple.cpp +++ b/examples/COUPLE/simple/simple.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/ + https://www.lammps.org/ Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/ELASTIC/compliance.py b/examples/ELASTIC/compliance.py index 6ef35be553..47f680abb4 100755 --- a/examples/ELASTIC/compliance.py +++ b/examples/ELASTIC/compliance.py @@ -1,13 +1,14 @@ #!/usr/bin/env python # This file reads in the file log.lammps generated by the script ELASTIC/in.elastic -# It prints out the 6x6 tensor of elastic constants Cij +# It prints out the 6x6 tensor of elastic constants Cij # followed by the 6x6 tensor of compliance constants Sij # It uses the same conventions as described in: -# Sprik, Impey and Klein PRB (1984). +# Sprik, Impey and Klein PRB (1984). # The units of Cij are whatever was used in log.lammps (usually GPa) # The units of Sij are the inverse of that (usually 1/GPa) +from __future__ import print_function from numpy import zeros from numpy.linalg import inv @@ -44,9 +45,8 @@ cindices[20] = (4,5) # open logfile -logfile = open("log.lammps",'r') - -txt = logfile.read() +with open("log.lammps",'r') as logfile: + txt = logfile.read() # search for 21 elastic constants @@ -56,7 +56,7 @@ s2 = 0 for ival in range(nvals): s1 = txt.find(valstr,s2) if (s1 == -1): - print "Failed to find elastic constants in log file" + print("Failed to find elastic constants in log file") exit(1) s1 += 1 s2 = txt.find("\n",s1) @@ -67,18 +67,18 @@ for ival in range(nvals): c[i1,i2] = float(words[valpos]) c[i2,i1] = c[i1,i2] -print "C tensor [GPa]" +print("C tensor [GPa]") for i in range(6): for j in range(6): - print "%10.8g " % c[i][j], - print - + print("%10.8g " % c[i][j], end="") + print() + # apply factor of 2 to columns of off-diagonal elements for i in range(6): for j in range(3,6): c[i][j] *= 2.0 - + s = inv(c) # apply factor of 1/2 to columns of off-diagonal elements @@ -86,10 +86,9 @@ s = inv(c) for i in range(6): for j in range(3,6): s[i][j] *= 0.5 - -print "S tensor [1/GPa]" + +print("S tensor [1/GPa]") for i in range(6): for j in range(6): - print "%10.8g " % s[i][j], - print - + print("%10.8g " % s[i][j], end="") + print() diff --git a/examples/README b/examples/README index 074a1cfaf3..9efac36a47 100644 --- a/examples/README +++ b/examples/README @@ -37,7 +37,7 @@ produce dump snapshots of the running simulation in any of 3 formats. If you uncomment the dump command in the input script, a text dump file will be produced, which can be animated by various visualization -programs (see http://lammps.sandia.gov/viz.html) such as Ovito, VMD, +programs (see https://www.lammps.org/viz.html) such as Ovito, VMD, or AtomEye. If you uncomment the dump image command in the input script, and diff --git a/examples/SPIN/test_problems/README b/examples/SPIN/test_problems/README index 0a1362ec9c..17e0935a35 100644 --- a/examples/SPIN/test_problems/README +++ b/examples/SPIN/test_problems/README @@ -45,3 +45,14 @@ directory. results (computed by the python script). Note: This example is a reworked version of a test problem provided by Martin Kroger (ETHZ). + +- validation_nve: + simulates a small assembly of magnetic atoms (54). The atoms are + coupled by an exchange interaction and a mechanical potential + (EAM here). + This example represents an NVE run: the total energy of the + system is preserved, whereas the spin and lattice energy + reservoirs are exchanging energy. + Run as: ./run-test-nve.sh + Output: res_lammps.dat contains the data. The results are displayed + by nve_spin_lattice.pdf. diff --git a/examples/SPIN/test_problems/run_all.sh b/examples/SPIN/test_problems/run_all.sh new file mode 100755 index 0000000000..fb682e3ef5 --- /dev/null +++ b/examples/SPIN/test_problems/run_all.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# test 1: damping and exchange +cd validation_damped_exchange/ +./run-test-exchange.sh +rm dump.data res_lammps.dat res_llg.dat +cd .. + +# test 2: damping and Zeeman +cd validation_damped_precession/ +./run-test-prec.sh +rm res_lammps.dat res_llg.dat +cd .. + +# test 3: langevin, damping and Zeeman +cd validation_langevin_precession/ +./run-test-prec.sh +rm average_spin test-prec-spin.in res_lammps.dat res_langevin.dat +cd .. + +# test 4: NVE run, test Etot preservation +cd validation_nve/ +./run-test-nve.sh +rm nve_spin_lattice.pdf res_lammps.dat +cd .. diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py index 5b93ac5c2d..a4cba3a940 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py +++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py @@ -6,7 +6,7 @@ import matplotlib.pyplot as plt import mpmath as mp hbar=0.658212 # Planck's constant (eV.fs/rad) -# J0=0.05 # per-neighbor exchange interaction (eV) +J0=0.05 # per-neighbor exchange interaction (eV) # exchange interaction parameters J1 = 11.254 # in eV diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh index bd878a52de..9d00318473 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh +++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh @@ -3,9 +3,15 @@ # clean old res rm res_*.dat -# compute Lammps +# test standard Lammps ./../../../../src/lmp_serial \ -in test-spin-precession.in + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in index 9dfb4a98d6..c195c046ec 100644 --- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in @@ -2,8 +2,10 @@ units metal atom_style spin +# atom_style spin/kk atom_modify map array boundary f f f +shell echo "test1" atom_modify map array lattice sc 3.0 diff --git a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh index 8609179376..e7a943beef 100755 --- a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh +++ b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh @@ -3,9 +3,15 @@ # clean old res rm res_*.dat -# compute Lammps +# test standard Lammps ./../../../../src/lmp_serial \ -in test-spin-precession.in + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in index b8e943e579..56abdded15 100644 --- a/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in @@ -2,6 +2,7 @@ units metal atom_style spin +# atom_style spin/kk atom_modify map array boundary f f f diff --git a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh index bcdd337903..ecdbb2c156 100755 --- a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh +++ b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh @@ -12,7 +12,14 @@ do temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)" sed s/temperature/${temp}/g test-prec-spin.template > \ test-prec-spin.in + + # test standard Lammps ./../../../../src/lmp_serial -in test-prec-spin.in + + # test spin/kk with Kokkos Lammps + # mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ + # -k on -sf kk -in test-prec-spin.in + Hz="$(tail -n 1 average_spin | awk -F " " '{print $3}')" sz="$(tail -n 1 average_spin | awk -F " " '{print $5}')" en="$(tail -n 1 average_spin | awk -F " " '{print $6}')" diff --git a/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template b/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template index 52f6a105ea..bec7126e69 100644 --- a/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template +++ b/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template @@ -2,6 +2,7 @@ units metal atom_style spin +# atom_style spin/kk atom_modify map array boundary p p p diff --git a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve index f00fb1ec12..38c669e166 100644 --- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve +++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p @@ -46,4 +47,8 @@ variable tmag equal c_out_mag[6] thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo 200 +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + run 100000 +# run 1 diff --git a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh index 18cedd9503..04d3d60847 100755 --- a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh +++ b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh @@ -3,9 +3,14 @@ # clean old res rm res_*.dat -# compute Lammps -./../../../../src/lmp_serial \ - -in in.spin.iron-nve +# test standard Lammps +../../../../src/lmp_serial -in in.spin.iron-nve + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.iron-nve + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice index 2375c0ff8d..a1f739fe54 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p @@ -30,8 +31,8 @@ neighbor 0.1 bin neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin 200.0 200.0 1.0 48279 -fix 3 all langevin/spin 0.0 0.00001 321 +fix 2 all langevin 200.0 200.0 0.1 48279 +fix 3 all langevin/spin 0.0 0.0 321 fix 4 all nve/spin lattice moving timestep 0.001 diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin index 6b65df7109..102f76a2a6 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p @@ -21,16 +22,19 @@ mass 1 55.845 set group all spin 2.2 0.0 0.0 1.0 velocity all create 0 4928459 rot yes dist gaussian -pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +# pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841 +pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0 neighbor 0.1 bin neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 200.0 0.01 321 -fix 3 all nve/spin lattice moving +fix 2 all langevin 0.0 0.0 0.0 48279 +fix 3 all langevin/spin 200.0 0.01 321 +fix 4 all nve/spin lattice moving timestep 0.001 # compute and output options diff --git a/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh b/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh index d3abbbe1a5..1372e1bd2c 100755 --- a/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh +++ b/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh @@ -3,16 +3,32 @@ # clean old res rm res_*.dat -# compute NVT Spin -> Lattice +### compute NVT Spin -> Lattice + +# test standard Lammps ./../../../../src/lmp_serial -in in.spin.nvt_spin + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.nvt_spin + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" en="$(echo "$en-$in" | bc -l)" tail -n +$in log.lammps | head -n $en > res_nvt_spin.dat -# compute NVT Lattice -> Spin +### compute NVT Lattice -> Spin + +# test standard Lammps ./../../../../src/lmp_serial -in in.spin.nvt_lattice + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.nvt_lattice + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/USER/brownian/2d_velocity/in2d.velocity b/examples/USER/brownian/2d_velocity/in2d.velocity new file mode 100644 index 0000000000..fcfae0554b --- /dev/null +++ b/examples/USER/brownian/2d_velocity/in2d.velocity @@ -0,0 +1,53 @@ +##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. ##### + +variable gamma_t equal 1.0 +variable temp equal 1.0 +variable seed equal 1974019 +variable fp equal 4.0 +variable params string ${gamma_t}_${temp}_${fp} + +units lj +dimension 2 +newton off + +lattice sq 0.4 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix step all brownian ${temp} ${seed} gamma_t ${gamma_t} +fix vel all propel/self velocity ${fp} +fix 2 all enforce2d +fix_modify vel virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 500 +run 5000 +reset_timestep 0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] c_press + +timestep 0.00001 +thermo 1000 + +# main run +run 12000 + + diff --git a/examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.1 b/examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.1 new file mode 100644 index 0000000000..a5a58ba9f0 --- /dev/null +++ b/examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.1 @@ -0,0 +1,151 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. ##### + +variable gamma_t equal 1.0 +variable temp equal 1.0 +variable seed equal 1974019 +variable fp equal 4.0 +variable params string ${gamma_t}_${temp}_${fp} +variable params string 1_${temp}_${fp} +variable params string 1_1_${fp} +variable params string 1_1_4 + +units lj +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1024 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix step all brownian ${temp} ${seed} gamma_t ${gamma_t} +fix step all brownian 1 ${seed} gamma_t ${gamma_t} +fix step all brownian 1 1974019 gamma_t ${gamma_t} +fix step all brownian 1 1974019 gamma_t 1 +fix vel all propel/self velocity ${fp} +fix vel all propel/self velocity 4 +fix 2 all enforce2d +fix_modify vel virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 500 +run 5000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes +Step Temp E_pair c_press + 0 1 0 -0.18336111 + 500 2.0519273e+10 0 -0.048238222 + 1000 1.9821717e+10 0 -0.4711053 + 1500 1.9697609e+10 0 -0.13539588 + 2000 2.0209443e+10 0 0.0094958039 + 2500 1.9591299e+10 0 0.40117118 + 3000 2.089566e+10 0 -0.036548251 + 3500 1.978692e+10 0 0.28282578 + 4000 2.0657848e+10 0 0.17618064 + 4500 2.0837353e+10 0 -0.080724651 + 5000 2.0348316e+10 0 -0.17471195 +Loop time of 0.575164 on 1 procs for 5000 steps with 1024 atoms + +Performance: 0.075 tau/day, 8693.168 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0036819 | 0.0036819 | 0.0036819 | 0.0 | 0.64 +Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05 +Modify | 0.51999 | 0.51999 | 0.51999 | 0.0 | 90.41 +Other | | 0.05121 | | | 8.90 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 65.0000 ave 65 max 65 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] c_press + +timestep 0.00001 +thermo 1000 + +# main run +run 12000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 2.0328444e+10 0 0 0 0 0 -0.17471195 + 1000 197017.59 0 0.018147562 0.019839233 0 0.037986796 -0.71897807 + 2000 197030.23 0 0.03909867 0.041721342 0 0.080820011 -0.30051929 + 3000 201997.2 0 0.065694399 0.06235257 0 0.12804697 -0.85167039 + 4000 199927.76 0 0.085698715 0.080328815 0 0.16602753 0.18493117 + 5000 198665.7 0 0.10896054 0.097021266 0 0.2059818 -0.090735406 + 6000 199277.78 0 0.13081111 0.11724814 0 0.24805925 -0.18189034 + 7000 199850.54 0 0.14721838 0.13806858 0 0.28528696 0.11334674 + 8000 191577.11 0 0.16582149 0.15935853 0 0.32518002 -0.73284569 + 9000 197331.29 0 0.17995704 0.18652927 0 0.3664863 -0.015558407 + 10000 197048.17 0 0.2034106 0.20329856 0 0.40670916 0.36985211 + 11000 200105.54 0 0.21809835 0.21966463 0 0.43776298 0.36437 + 12000 203180.39 0 0.23810386 0.23666184 0 0.47476569 -0.072006034 +Loop time of 1.37465 on 1 procs for 12000 steps with 1024 atoms + +Performance: 7542.303 tau/day, 8729.517 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.01 +Comm | 0.0024607 | 0.0024607 | 0.0024607 | 0.0 | 0.18 +Output | 0.00068665 | 0.00068665 | 0.00068665 | 0.0 | 0.05 +Modify | 1.2479 | 1.2479 | 1.2479 | 0.0 | 90.78 +Other | | 0.1235 | | | 8.98 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 15 +Dangerous builds = 0 + + +Total wall time: 0:00:01 diff --git a/examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 b/examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 new file mode 100644 index 0000000000..df9ff24070 --- /dev/null +++ b/examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 @@ -0,0 +1,151 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. ##### + +variable gamma_t equal 1.0 +variable temp equal 1.0 +variable seed equal 1974019 +variable fp equal 4.0 +variable params string ${gamma_t}_${temp}_${fp} +variable params string 1_${temp}_${fp} +variable params string 1_1_${fp} +variable params string 1_1_4 + +units lj +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 1024 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix step all brownian ${temp} ${seed} gamma_t ${gamma_t} +fix step all brownian 1 ${seed} gamma_t ${gamma_t} +fix step all brownian 1 1974019 gamma_t ${gamma_t} +fix step all brownian 1 1974019 gamma_t 1 +fix vel all propel/self velocity ${fp} +fix vel all propel/self velocity 4 +fix 2 all enforce2d +fix_modify vel virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 500 +run 5000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes +Step Temp E_pair c_press + 0 1 0 -0.18336111 + 500 1.9862591e+10 0 -0.32013566 + 1000 2.0093184e+10 0 -0.36609742 + 1500 1.9562283e+10 0 -0.53349351 + 2000 1.9903977e+10 0 0.63783249 + 2500 2.0260128e+10 0 0.30046413 + 3000 1.9948065e+10 0 -0.63093105 + 3500 1.9507486e+10 0 0.48762848 + 4000 2.0049087e+10 0 0.40289309 + 4500 1.9975813e+10 0 0.57649363 + 5000 2.0129291e+10 0 -0.41288352 +Loop time of 0.238949 on 4 procs for 5000 steps with 1024 atoms + +Performance: 0.181 tau/day, 20924.952 timesteps/s +92.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0080078 | 0.024718 | 0.031782 | 6.2 | 10.34 +Output | 0.0001812 | 0.00029999 | 0.00063467 | 0.0 | 0.13 +Modify | 0.13401 | 0.14401 | 0.15438 | 2.4 | 60.27 +Other | | 0.06992 | | | 29.26 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 33.0000 ave 33 max 33 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] c_press + +timestep 0.00001 +thermo 1000 + +# main run +run 12000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 2.0109634e+10 0 0 0 0 0 -0.41288352 + 1000 195711.46 0 0.020076462 0.020523099 0 0.040599561 -0.32125126 + 2000 203263.85 0 0.039242992 0.039661282 0 0.078904274 0.11008705 + 3000 197417.54 0 0.064938128 0.057716419 0 0.12265455 0.16967601 + 4000 200505.97 0 0.086511225 0.074975267 0 0.16148649 0.31338473 + 5000 199373.77 0 0.10583263 0.098175658 0 0.20400829 0.34205791 + 6000 192881.14 0 0.12152088 0.11706037 0 0.23858125 -0.27870467 + 7000 203045.3 0 0.1383248 0.13629503 0 0.27461983 -0.046936646 + 8000 198544.08 0 0.16064738 0.1582206 0 0.31886798 -0.18803452 + 9000 205450.74 0 0.17926529 0.1829047 0 0.36216999 0.47191228 + 10000 200371.73 0 0.20084273 0.20365189 0 0.40449463 0.093098262 + 11000 202911.93 0 0.21569236 0.22221715 0 0.43790952 -0.38430031 + 12000 192590.04 0 0.24041439 0.24114487 0 0.48155926 -0.1677052 +Loop time of 0.443026 on 4 procs for 12000 steps with 1024 atoms + +Performance: 23402.683 tau/day, 27086.439 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 3.2663e-05 | 3.3855e-05 | 3.4809e-05 | 0.0 | 0.01 +Comm | 0.0030291 | 0.0030628 | 0.0030825 | 0.0 | 0.69 +Output | 0.00027895 | 0.00051624 | 0.001184 | 0.0 | 0.12 +Modify | 0.31607 | 0.33372 | 0.37391 | 4.0 | 75.33 +Other | | 0.1057 | | | 23.86 + +Nlocal: 256.000 ave 259 max 253 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 15 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/examples/USER/brownian/asphere/in2d.ellipsoid b/examples/USER/brownian/asphere/in2d.ellipsoid new file mode 100644 index 0000000000..4b1a88bba7 --- /dev/null +++ b/examples/USER/brownian/asphere/in2d.ellipsoid @@ -0,0 +1,54 @@ +##### overdamped dynamics of non-interacting ellipsoids in 2D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 1.0 +variable gamma_r_1 string inf +variable gamma_r_2 string inf +variable gamma_r_3 string 0.1 +variable gamma_t_1 string 5.0 +variable gamma_t_2 string 7.0 +variable gamma_t_3 string inf +variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} + +units lj +atom_style hybrid dipole ellipsoid +dimension 2 +newton off + +lattice sq 0.4 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * shape 3.0 1.0 1.0 +set type * quat/random ${seed} +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} & + gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} & + gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} & + dipole 1.0 0.0 0.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type & +# x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 diff --git a/examples/USER/brownian/asphere/in3d.ellipsoid b/examples/USER/brownian/asphere/in3d.ellipsoid new file mode 100644 index 0000000000..34f2684ee7 --- /dev/null +++ b/examples/USER/brownian/asphere/in3d.ellipsoid @@ -0,0 +1,54 @@ +##### overdamped dynamics of non-interacting ellipsoids in 3D ##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_r_1 string 2.0 +variable gamma_r_2 string 0.25 +variable gamma_r_3 string 0.1 +variable gamma_t_1 string 5.0 +variable gamma_t_2 string 7.0 +variable gamma_t_3 string 9.0 +variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} + +units lj +atom_style hybrid dipole ellipsoid +dimension 3 +newton off + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * shape 3.0 1.0 1.0 +set type * quat/random ${seed} +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} & + gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} & + gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} & + dipole 1.0 0.0 0.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type & +# x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 diff --git a/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.1 b/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.1 new file mode 100644 index 0000000000..619ab937c9 --- /dev/null +++ b/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.1 @@ -0,0 +1,145 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of non-interacting ellipsoids in 2D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 1.0 +variable gamma_r_1 string inf +variable gamma_r_2 string inf +variable gamma_r_3 string 0.1 +variable gamma_t_1 string 5.0 +variable gamma_t_2 string 7.0 +variable gamma_t_3 string inf +variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf + +units lj +atom_style hybrid dipole ellipsoid +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.005 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 3600 settings made for dipole/random +set type * shape 3.0 1.0 1.0 +Setting atom values ... + 3600 settings made for shape +set type * quat/random ${seed} +set type * quat/random 198098 +Setting atom values ... + 3600 settings made for quat/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 5.114 | 5.114 | 5.114 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 0.99972222 0 0 0 0 0 + 100 34376.187 0 0.00034728749 0.00034318997 0 0.00069047747 + 200 36135.708 0 0.00067452936 0.0006818928 0 0.0013564222 + 300 34444.929 0 0.0010189319 0.00099849203 0 0.002017424 + 400 35668.312 0 0.0013648699 0.0013311884 0 0.0026960583 + 500 35388.615 0 0.0017330203 0.0016077184 0 0.0033407387 + 600 35180.065 0 0.002052223 0.0019394635 0 0.0039916865 + 700 34035.38 0 0.0024329956 0.0022664905 0 0.0046994861 + 800 34581.664 0 0.002783885 0.0025794872 0 0.0053633723 + 900 34579.945 0 0.003163442 0.0029351952 0 0.0060986372 + 1000 34158.066 0 0.0035589034 0.0032627605 0 0.0068216639 + 1100 33453.827 0 0.0038861895 0.003565372 0 0.0074515615 + 1200 33608.06 0 0.0041325698 0.0038943268 0 0.0080268966 + 1300 34381.633 0 0.004405682 0.0043294156 0 0.0087350976 + 1400 32925.746 0 0.0047383547 0.0046803517 0 0.0094187065 + 1500 34809.764 0 0.0051149571 0.0049309746 0 0.010045932 + 1600 33580.096 0 0.0054893472 0.0052465377 0 0.010735885 + 1700 34596.275 0 0.00581894 0.0056500316 0 0.011468972 + 1800 33926.736 0 0.0062129617 0.0059796125 0 0.012192574 + 1900 35577.131 0 0.0065668637 0.0062530163 0 0.01281988 + 2000 34224.967 0 0.0070005917 0.006598912 0 0.013599504 + 2100 33991.406 0 0.0073134826 0.0069119252 0 0.014225408 + 2200 34647.054 0 0.007659301 0.0073434715 0 0.015002772 + 2300 33956.835 0 0.007965191 0.0076318537 0 0.015597045 + 2400 35272.549 0 0.0082467116 0.007929202 0 0.016175914 + 2500 33901.494 0 0.0086251299 0.0082790757 0 0.016904206 + 2600 34138.227 0 0.0089419364 0.0086639744 0 0.017605911 + 2700 33691.013 0 0.0093083376 0.0090219118 0 0.018330249 + 2800 34716.817 0 0.0095840095 0.0094118945 0 0.018995904 + 2900 34473.982 0 0.0099773501 0.0098167668 0 0.019794117 + 3000 33406.776 0 0.010391969 0.010098625 0 0.020490594 +Loop time of 3.67112 on 1 procs for 3000 steps with 3600 atoms + +Performance: 706.051 tau/day, 817.189 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.037973 | 0.037973 | 0.037973 | 0.0 | 1.03 +Output | 0.0040674 | 0.0040674 | 0.0040674 | 0.0 | 0.11 +Modify | 3.515 | 3.515 | 3.515 | 0.0 | 95.75 +Other | | 0.1141 | | | 3.11 + +Nlocal: 3600.00 ave 3600 max 3600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 121.000 ave 121 max 121 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.4 b/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.4 new file mode 100644 index 0000000000..b3da385dda --- /dev/null +++ b/examples/USER/brownian/asphere/log.11May2021.in2d.ellipsoid.g++.4 @@ -0,0 +1,145 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of non-interacting ellipsoids in 2D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 1.0 +variable gamma_r_1 string inf +variable gamma_r_2 string inf +variable gamma_r_3 string 0.1 +variable gamma_t_1 string 5.0 +variable gamma_t_2 string 7.0 +variable gamma_t_3 string inf +variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3} +variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf + +units lj +atom_style hybrid dipole ellipsoid +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.007 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 3600 settings made for dipole/random +set type * shape 3.0 1.0 1.0 +Setting atom values ... + 3600 settings made for shape +set type * quat/random ${seed} +set type * quat/random 198098 +Setting atom values ... + 3600 settings made for quat/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 5.102 | 5.102 | 5.102 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 0.99972222 0 0 0 0 0 + 100 33874.438 0 0.0003458147 0.00033165629 0 0.00067747099 + 200 34893.188 0 0.00066290209 0.00068146332 0 0.0013443654 + 300 34494.226 0 0.0010064902 0.0010276646 0 0.0020341548 + 400 34537.887 0 0.0013457339 0.0014057042 0 0.0027514381 + 500 34458.46 0 0.0017006949 0.0017120083 0 0.0034127033 + 600 33229.977 0 0.0020841613 0.0020485346 0 0.0041326959 + 700 33288.631 0 0.0024270272 0.0023673304 0 0.0047943576 + 800 35317.512 0 0.0027924435 0.0026950912 0 0.0054875347 + 900 33094.299 0 0.0031503627 0.0030789319 0 0.0062292946 + 1000 35801.751 0 0.003489398 0.0034594626 0 0.0069488607 + 1100 33427.701 0 0.0038547506 0.0038375809 0 0.0076923316 + 1200 34675.07 0 0.0041824195 0.0042017298 0 0.0083841493 + 1300 33080.294 0 0.0045258945 0.0045816356 0 0.0091075301 + 1400 34927.288 0 0.0048252992 0.0049215701 0 0.0097468693 + 1500 34338.558 0 0.0051959155 0.0053020102 0 0.010497926 + 1600 34686.248 0 0.0055111463 0.0056220225 0 0.011133169 + 1700 34336.158 0 0.0059240394 0.0059060319 0 0.011830071 + 1800 34315.859 0 0.0063027944 0.0063004467 0 0.012603241 + 1900 35096.721 0 0.0066098525 0.00672222 0 0.013332073 + 2000 33544.18 0 0.0069401261 0.007074124 0 0.01401425 + 2100 33863.219 0 0.0072726502 0.0074175954 0 0.014690246 + 2200 34705.892 0 0.0075586722 0.0077552683 0 0.015313941 + 2300 34025.357 0 0.0079046728 0.0081760519 0 0.016080725 + 2400 34741.849 0 0.008252969 0.0085203087 0 0.016773278 + 2500 34406.959 0 0.0085370091 0.0088556377 0 0.017392647 + 2600 34062.63 0 0.0088134153 0.0092536326 0 0.018067048 + 2700 34677.666 0 0.0090592854 0.0096225881 0 0.018681874 + 2800 33464.216 0 0.0093984162 0.0099647695 0 0.019363186 + 2900 32920.721 0 0.0098222985 0.010366517 0 0.020188816 + 3000 34539.66 0 0.010133317 0.01068102 0 0.020814337 +Loop time of 1.12143 on 4 procs for 3000 steps with 3600 atoms + +Performance: 2311.341 tau/day, 2675.163 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.036017 | 0.042828 | 0.051558 | 2.7 | 3.82 +Output | 0.0012608 | 0.0025993 | 0.0063775 | 4.3 | 0.23 +Modify | 0.9002 | 0.93095 | 0.99546 | 3.9 | 83.01 +Other | | 0.1451 | | | 12.93 + +Nlocal: 900.000 ave 900 max 900 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 61.0000 ave 61 max 61 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.1 b/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.1 new file mode 100644 index 0000000000..a193fc98e2 --- /dev/null +++ b/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.1 @@ -0,0 +1,145 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of non-interacting ellipsoids in 3D ##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_r_1 string 2.0 +variable gamma_r_2 string 0.25 +variable gamma_r_3 string 0.1 +variable gamma_t_1 string 5.0 +variable gamma_t_2 string 7.0 +variable gamma_t_3 string 9.0 +variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0 + +units lj +atom_style hybrid dipole ellipsoid +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.005 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 4096 settings made for dipole/random +set type * shape 3.0 1.0 1.0 +Setting atom values ... + 4096 settings made for shape +set type * quat/random ${seed} +set type * quat/random 198098 +Setting atom values ... + 4096 settings made for quat/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 5.219 | 5.219 | 5.219 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 1.4996338 0 0 0 0 0 + 100 45690.838 0 0.00029994317 0.00029953902 0.00030002809 0.00089951027 + 200 45571.166 0 0.00061376797 0.00060955238 0.00061153551 0.0018348559 + 300 44693.418 0 0.00093058034 0.00089383536 0.00091554588 0.0027399616 + 400 44831.846 0 0.001250227 0.0012230128 0.0012120517 0.0036852914 + 500 45028.015 0 0.0015448869 0.0015339549 0.0014978843 0.0045767262 + 600 45895.442 0 0.0018621952 0.0018169905 0.0018352784 0.0055144641 + 700 45858.744 0 0.0021617097 0.0021137714 0.0021360394 0.0064115206 + 800 45155.215 0 0.002428445 0.0024288837 0.0024516737 0.0073090023 + 900 45427.427 0 0.0027265978 0.0027662531 0.0027329878 0.0082258387 + 1000 45398.166 0 0.0030685345 0.0030805014 0.0029765916 0.0091256275 + 1100 44622.428 0 0.0033766954 0.0033976168 0.0032745406 0.010048853 + 1200 45500.277 0 0.0036410565 0.0036840528 0.0035831659 0.010908275 + 1300 45265.8 0 0.0039143146 0.0039419334 0.0038761633 0.011732411 + 1400 45482.435 0 0.0042006542 0.0043373651 0.004164002 0.012702021 + 1500 45126.629 0 0.0044647379 0.0046021855 0.004487041 0.013553965 + 1600 45178.172 0 0.0047726618 0.0049110287 0.0048012671 0.014484958 + 1700 44918.685 0 0.005104787 0.0052522662 0.0050844375 0.015441491 + 1800 44776.678 0 0.0054395368 0.0056092038 0.0054623875 0.016511128 + 1900 46035.987 0 0.0057735872 0.0059357043 0.0057296009 0.017438892 + 2000 45436.517 0 0.0060837459 0.0063485717 0.0059769119 0.018409229 + 2100 45871.502 0 0.0063736337 0.0066551978 0.0063077439 0.019336575 + 2200 45511.847 0 0.0066419141 0.0069700452 0.0065553318 0.020167291 + 2300 45597.047 0 0.0069251517 0.0073015716 0.0068945654 0.021121289 + 2400 44832.007 0 0.0071894253 0.0076238221 0.0071638554 0.021977103 + 2500 45668.42 0 0.0074351304 0.0079594991 0.0075390719 0.022933701 + 2600 45248.483 0 0.007781496 0.008293944 0.0077956068 0.023871047 + 2700 45308.515 0 0.0080302993 0.0086329679 0.0081457335 0.024809001 + 2800 45637.72 0 0.0083889026 0.0089173198 0.0086032427 0.025909465 + 2900 45909.343 0 0.0087169392 0.009181179 0.0088778569 0.026775975 + 3000 45213.613 0 0.0090508891 0.0094253485 0.0092660321 0.02774227 +Loop time of 4.13937 on 1 procs for 3000 steps with 4096 atoms + +Performance: 626.183 tau/day, 724.749 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.24709 | 0.24709 | 0.24709 | 0.0 | 5.97 +Output | 0.004636 | 0.004636 | 0.004636 | 0.0 | 0.11 +Modify | 3.7604 | 3.7604 | 3.7604 | 0.0 | 90.85 +Other | | 0.1272 | | | 3.07 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 817.000 ave 817 max 817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.4 b/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.4 new file mode 100644 index 0000000000..7f6d8a81f0 --- /dev/null +++ b/examples/USER/brownian/asphere/log.11May2021.in3d.ellipsoid.g++.4 @@ -0,0 +1,145 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of non-interacting ellipsoids in 3D ##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_r_1 string 2.0 +variable gamma_r_2 string 0.25 +variable gamma_r_3 string 0.1 +variable gamma_t_1 string 5.0 +variable gamma_t_2 string 7.0 +variable gamma_t_3 string 9.0 +variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3} +variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0 + +units lj +atom_style hybrid dipole ellipsoid +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 2 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 4096 settings made for dipole/random +set type * shape 3.0 1.0 1.0 +Setting atom values ... + 4096 settings made for shape +set type * quat/random ${seed} +set type * quat/random 198098 +Setting atom values ... + 4096 settings made for quat/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0 +fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 5.152 | 5.152 | 5.152 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 1.4996338 0 0 0 0 0 + 100 45236.508 0 0.00030817418 0.00030717742 0.0003019227 0.0009172743 + 200 45564.566 0 0.00062027526 0.00062110132 0.0006080391 0.0018494157 + 300 46232.801 0 0.00091155216 0.00094473459 0.00093009391 0.0027863807 + 400 45250.414 0 0.0011980791 0.0012538262 0.0012201461 0.0036720513 + 500 45217.133 0 0.0015186813 0.0015752994 0.001509437 0.0046034177 + 600 45531.276 0 0.0018194588 0.0019243758 0.0018209246 0.0055647592 + 700 44834.624 0 0.0021277747 0.0022417115 0.0021352036 0.0065046898 + 800 45413.998 0 0.0024558838 0.0025741787 0.0024088704 0.0074389329 + 900 45668.624 0 0.0027366171 0.002858242 0.0027580782 0.0083529374 + 1000 45809.223 0 0.0030331425 0.003186293 0.0030414906 0.0092609261 + 1100 45193.019 0 0.0033199824 0.0034668659 0.003298885 0.010085733 + 1200 44522.927 0 0.0036503132 0.0037490684 0.0036089852 0.011008367 + 1300 45214.567 0 0.0039958617 0.0040881934 0.0038709079 0.011954963 + 1400 45217.997 0 0.004276499 0.0044624985 0.0041104891 0.012849487 + 1500 45497.171 0 0.0045943272 0.0047116875 0.0044113504 0.013717365 + 1600 45905.187 0 0.0049004996 0.0049982014 0.0047394999 0.014638201 + 1700 45551.346 0 0.0051540939 0.0053187249 0.0050861052 0.015558924 + 1800 45347.782 0 0.0054101891 0.0056306 0.0053515873 0.016392376 + 1900 45107.895 0 0.005743705 0.0059584896 0.0056220384 0.017324233 + 2000 45043.389 0 0.0059803588 0.006230449 0.005911555 0.018122363 + 2100 45433.293 0 0.0062610364 0.0066140744 0.0062152977 0.019090408 + 2200 45804.217 0 0.0064995183 0.0068831274 0.0064971789 0.019879825 + 2300 45697.516 0 0.0067910846 0.0071845673 0.0068046192 0.020780271 + 2400 45447.422 0 0.0071022706 0.0074743709 0.0070983185 0.02167496 + 2500 45395.18 0 0.0073817023 0.0077467991 0.0074263196 0.022554821 + 2600 45943.044 0 0.0075953233 0.007997707 0.0076508583 0.023243889 + 2700 45859.978 0 0.0079082128 0.0082090043 0.0078853376 0.024002555 + 2800 45822.007 0 0.0082607534 0.0084510061 0.0081985549 0.024910314 + 2900 45438.456 0 0.0085958203 0.0088807705 0.0084755353 0.025952126 + 3000 45060.957 0 0.0089017992 0.0090966159 0.0086718875 0.026670303 +Loop time of 1.23282 on 4 procs for 3000 steps with 4096 atoms + +Performance: 2102.502 tau/day, 2433.452 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 8.5831e-06 | 8.5831e-06 | 8.5831e-06 | 0.0 | 0.00 +Comm | 0.10931 | 0.11473 | 0.11748 | 0.9 | 9.31 +Output | 0.001375 | 0.0018924 | 0.0034099 | 2.0 | 0.15 +Modify | 0.97744 | 0.99158 | 1.0089 | 1.3 | 80.43 +Other | | 0.1246 | | | 10.11 + +Nlocal: 1024.00 ave 1035 max 1016 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/brownian/point/in2d.point b/examples/USER/brownian/point/in2d.point new file mode 100644 index 0000000000..bf790f8fc2 --- /dev/null +++ b/examples/USER/brownian/point/in2d.point @@ -0,0 +1,43 @@ +##### dynamics of non-interacting point particles in 2D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 5.0 +variable gamma_t string 1.0 +variable params string ${rng}_${temp}_${gamma_t} + +units lj +atom_style atomic +dimension 2 +newton off + +lattice sq 0.4 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t} + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type & +# x y z xu yu zu fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 diff --git a/examples/USER/brownian/point/in3d.point b/examples/USER/brownian/point/in3d.point new file mode 100644 index 0000000000..974f08866d --- /dev/null +++ b/examples/USER/brownian/point/in3d.point @@ -0,0 +1,44 @@ +##### overdamped dynamics of non-interacting point particles in 3D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 5.0 +variable gamma_t string 1.0 +variable params string ${rng}_${temp}_${gamma_t} + +units lj +atom_style atomic +dimension 3 +newton off + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t} + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type & +# x y z xu yu zu fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 + diff --git a/examples/USER/brownian/point/log.11May2021.in2d.point.g++.1 b/examples/USER/brownian/point/log.11May2021.in2d.point.g++.1 new file mode 100644 index 0000000000..b875ccedad --- /dev/null +++ b/examples/USER/brownian/point/log.11May2021.in2d.point.g++.1 @@ -0,0 +1,119 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### dynamics of non-interacting point particles in 2D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 5.0 +variable gamma_t string 1.0 +variable params string ${rng}_${temp}_${gamma_t} +variable params string gaussian_${temp}_${gamma_t} +variable params string gaussian_5.0_${gamma_t} +variable params string gaussian_5.0_1.0 + +units lj +atom_style atomic +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.003 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 0.99972222 0 0 0 0 0 + 100 1022861.2 0 0.010252464 0.0095481044 0 0.019800568 + 200 986781.19 0 0.020552091 0.019485252 0 0.040037343 + 300 1030219 0 0.030642552 0.028377678 0 0.05902023 + 400 1003322.5 0 0.040610693 0.038179284 0 0.078789978 + 500 989343.12 0 0.049978908 0.047445856 0 0.097424764 + 600 1029781.3 0 0.059551719 0.057941149 0 0.11749287 + 700 999447.72 0 0.06979546 0.067552325 0 0.13734778 + 800 995373.97 0 0.080049251 0.078006344 0 0.1580556 + 900 1011991.4 0 0.089753134 0.087065214 0 0.17681835 + 1000 1006017.1 0 0.10041092 0.097934217 0 0.19834514 + 1100 997762.63 0 0.11229742 0.10841547 0 0.22071289 + 1200 1011707.8 0 0.12006388 0.1190115 0 0.23907538 + 1300 1012099.1 0 0.13097486 0.12996632 0 0.26094117 + 1400 997602.43 0 0.14345778 0.13830585 0 0.28176362 + 1500 1005358.1 0 0.15441686 0.14927539 0 0.30369225 + 1600 1007081.8 0 0.16496828 0.15936363 0 0.3243319 + 1700 990284.9 0 0.1747286 0.16818246 0 0.34291106 + 1800 969006.97 0 0.18228778 0.17972813 0 0.3620159 + 1900 998066.69 0 0.19338277 0.19226121 0 0.38564397 + 2000 972300.66 0 0.20352485 0.20145928 0 0.40498413 + 2100 985025.88 0 0.21283854 0.21090075 0 0.42373929 + 2200 1010964.6 0 0.22279055 0.22110734 0 0.44389789 + 2300 975819.44 0 0.23128131 0.23226488 0 0.46354619 + 2400 977043.53 0 0.24284105 0.24301689 0 0.48585794 + 2500 969708.21 0 0.25415238 0.25354284 0 0.50769522 + 2600 981969.5 0 0.26457173 0.26318018 0 0.52775192 + 2700 987261.1 0 0.27497004 0.27761213 0 0.55258218 + 2800 1005751.1 0 0.28530448 0.28715428 0 0.57245876 + 2900 975930.11 0 0.29394811 0.29896948 0 0.59291759 + 3000 997388.08 0 0.30674701 0.31193573 0 0.61868274 +Loop time of 1.501 on 1 procs for 3000 steps with 3600 atoms + +Performance: 1726.852 tau/day, 1998.672 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00059271 | 0.00059271 | 0.00059271 | 0.0 | 0.04 +Comm | 0.0055437 | 0.0055437 | 0.0055437 | 0.0 | 0.37 +Output | 0.0039999 | 0.0039999 | 0.0039999 | 0.0 | 0.27 +Modify | 1.3852 | 1.3852 | 1.3852 | 0.0 | 92.28 +Other | | 0.1057 | | | 7.04 + +Nlocal: 3600.00 ave 3600 max 3600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 21 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/USER/brownian/point/log.11May2021.in2d.point.g++.4 b/examples/USER/brownian/point/log.11May2021.in2d.point.g++.4 new file mode 100644 index 0000000000..d12d71118e --- /dev/null +++ b/examples/USER/brownian/point/log.11May2021.in2d.point.g++.4 @@ -0,0 +1,119 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### dynamics of non-interacting point particles in 2D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 5.0 +variable gamma_t string 1.0 +variable params string ${rng}_${temp}_${gamma_t} +variable params string gaussian_${temp}_${gamma_t} +variable params string gaussian_5.0_${gamma_t} +variable params string gaussian_5.0_1.0 + +units lj +atom_style atomic +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 0.99972222 0 0 0 0 0 + 100 1017972.1 0 0.010094052 0.0097502899 0 0.019844342 + 200 1004552.1 0 0.020125116 0.01957629 0 0.039701406 + 300 1017712.9 0 0.030271373 0.029411656 0 0.059683029 + 400 1016693.8 0 0.040610061 0.038605869 0 0.07921593 + 500 999527.84 0 0.049451389 0.049042225 0 0.098493614 + 600 961157.92 0 0.059691948 0.059033176 0 0.11872512 + 700 1006804.9 0 0.071205977 0.069972106 0 0.14117808 + 800 1007321.8 0 0.081136977 0.079825976 0 0.16096295 + 900 1002801.7 0 0.091236148 0.090833816 0 0.18206996 + 1000 1010134.7 0 0.10091362 0.10023906 0 0.20115269 + 1100 990246.55 0 0.1118367 0.11141049 0 0.22324719 + 1200 1010555.5 0 0.12091736 0.12355456 0 0.24447192 + 1300 997117.19 0 0.13099592 0.13292775 0 0.26392367 + 1400 1020817.1 0 0.14167961 0.14172898 0 0.28340859 + 1500 1015048.1 0 0.15225884 0.15162948 0 0.30388833 + 1600 990291.98 0 0.16460973 0.16251919 0 0.32712891 + 1700 980848.58 0 0.17380313 0.17351201 0 0.34731513 + 1800 1000673.8 0 0.18383991 0.18175453 0 0.36559445 + 1900 1009388.9 0 0.19411523 0.19367453 0 0.38778976 + 2000 1005935.9 0 0.2015342 0.20585359 0 0.40738779 + 2100 985500.56 0 0.21161056 0.21238463 0 0.42399519 + 2200 997241.34 0 0.21841986 0.22117922 0 0.43959908 + 2300 1011672.3 0 0.22688099 0.23155741 0 0.4584384 + 2400 989837.68 0 0.23849839 0.24219 0 0.48068839 + 2500 1035706.8 0 0.24541408 0.24947563 0 0.49488971 + 2600 992370.08 0 0.25537803 0.25758332 0 0.51296135 + 2700 990586.56 0 0.26542605 0.26762286 0 0.53304892 + 2800 1002767.3 0 0.27570392 0.27874972 0 0.55445363 + 2900 995307.27 0 0.28580946 0.29115624 0 0.5769657 + 3000 1024317.7 0 0.29493208 0.30208924 0 0.59702132 +Loop time of 0.413047 on 4 procs for 3000 steps with 3600 atoms + +Performance: 6275.312 tau/day, 7263.093 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00016236 | 0.00016338 | 0.00016403 | 0.0 | 0.04 +Comm | 0.0026367 | 0.0030084 | 0.0031497 | 0.4 | 0.73 +Output | 0.0011849 | 0.0013574 | 0.0018065 | 0.7 | 0.33 +Modify | 0.34447 | 0.35223 | 0.36357 | 1.2 | 85.28 +Other | | 0.05629 | | | 13.63 + +Nlocal: 900.000 ave 906 max 891 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 22 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/brownian/point/log.11May2021.in3d.point.g++.1 b/examples/USER/brownian/point/log.11May2021.in3d.point.g++.1 new file mode 100644 index 0000000000..febb7657e7 --- /dev/null +++ b/examples/USER/brownian/point/log.11May2021.in3d.point.g++.1 @@ -0,0 +1,119 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of non-interacting point particles in 3D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 5.0 +variable gamma_t string 1.0 +variable params string ${rng}_${temp}_${gamma_t} +variable params string gaussian_${temp}_${gamma_t} +variable params string gaussian_5.0_${gamma_t} +variable params string gaussian_5.0_1.0 + +units lj +atom_style atomic +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.694 | 2.694 | 2.694 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 1.4996338 0 0 0 0 0 + 100 1500286.3 0 0.0098123603 0.010352169 0.010242435 0.030406964 + 200 1488308 0 0.019934427 0.019968198 0.020471735 0.06037436 + 300 1484472.4 0 0.029397156 0.030749312 0.030121294 0.090267762 + 400 1517938.7 0 0.039217504 0.041440617 0.040512943 0.12117106 + 500 1492769.5 0 0.04890343 0.051561801 0.050614941 0.15108017 + 600 1510159.6 0 0.059770181 0.061650364 0.061298117 0.18271866 + 700 1485424.1 0 0.070537955 0.071144877 0.071141546 0.21282438 + 800 1496377.2 0 0.081291995 0.082546059 0.080653381 0.24449144 + 900 1484409.1 0 0.090940427 0.093298981 0.091328056 0.27556746 + 1000 1503322.4 0 0.10176921 0.10246052 0.10151773 0.30574747 + 1100 1503322.4 0 0.11295993 0.11052632 0.11053406 0.33402031 + 1200 1489236.2 0 0.12509723 0.11961982 0.12146498 0.36618203 + 1300 1476050.3 0 0.13449034 0.12941323 0.1309765 0.39488007 + 1400 1520818.7 0 0.14613571 0.13788044 0.14083944 0.42485558 + 1500 1498936.4 0 0.15752286 0.15057712 0.15063399 0.45873397 + 1600 1507524.1 0 0.16793678 0.16095681 0.16063531 0.4895289 + 1700 1480581.2 0 0.17748019 0.172614 0.16922383 0.51931802 + 1800 1505353.6 0 0.18850931 0.18304171 0.18063119 0.55218221 + 1900 1491234.7 0 0.19836402 0.19306339 0.1929707 0.58439811 + 2000 1519868.8 0 0.20698191 0.20211344 0.20328302 0.61237838 + 2100 1493919.5 0 0.21453524 0.21186097 0.21423293 0.64062914 + 2200 1517098.6 0 0.2257338 0.22381647 0.22474081 0.67429108 + 2300 1481270.7 0 0.23499747 0.23348379 0.23498244 0.70346369 + 2400 1495445.1 0 0.24535894 0.24290239 0.24229161 0.73055293 + 2500 1522839.3 0 0.25695938 0.25109669 0.25214541 0.76020148 + 2600 1518697.4 0 0.26680819 0.26120216 0.2604112 0.78842155 + 2700 1529283.1 0 0.27524422 0.26942681 0.27148042 0.81615146 + 2800 1500557.5 0 0.28436226 0.27957592 0.27935619 0.84329437 + 2900 1509711.1 0 0.2948528 0.28562401 0.29055956 0.87103637 + 3000 1522712.8 0 0.30347033 0.2975063 0.30121685 0.90219348 +Loop time of 2.35056 on 1 procs for 3000 steps with 4096 atoms + +Performance: 1102.718 tau/day, 1276.293 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00077772 | 0.00077772 | 0.00077772 | 0.0 | 0.03 +Comm | 0.010985 | 0.010985 | 0.010985 | 0.0 | 0.47 +Output | 0.0045807 | 0.0045807 | 0.0045807 | 0.0 | 0.19 +Modify | 2.2116 | 2.2116 | 2.2116 | 0.0 | 94.09 +Other | | 0.1226 | | | 5.22 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 24 +Dangerous builds = 0 + +Total wall time: 0:00:02 diff --git a/examples/USER/brownian/point/log.11May2021.in3d.point.g++.4 b/examples/USER/brownian/point/log.11May2021.in3d.point.g++.4 new file mode 100644 index 0000000000..6a41a12f0f --- /dev/null +++ b/examples/USER/brownian/point/log.11May2021.in3d.point.g++.4 @@ -0,0 +1,119 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of non-interacting point particles in 3D ##### + +variable rng string gaussian +variable seed string 198098 +variable temp string 5.0 +variable gamma_t string 1.0 +variable params string ${rng}_${temp}_${gamma_t} +variable params string gaussian_${temp}_${gamma_t} +variable params string gaussian_5.0_${gamma_t} +variable params string gaussian_5.0_1.0 + +units lj +atom_style atomic +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 2 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t} +fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.672 | 2.672 | 2.672 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 1.4996338 0 0 0 0 0 + 100 1515328.2 0 0.010465453 0.010044629 0.0097242319 0.030234314 + 200 1510820.8 0 0.020658886 0.019954762 0.020008864 0.060622512 + 300 1482006.5 0 0.030402195 0.029802874 0.030047586 0.090252655 + 400 1492228.5 0 0.039622543 0.038899144 0.040381854 0.11890354 + 500 1494985.5 0 0.050523465 0.050022913 0.050186478 0.15073286 + 600 1516047.4 0 0.061111845 0.061433818 0.059195364 0.18174103 + 700 1510021.8 0 0.071636778 0.072829755 0.06946406 0.21393059 + 800 1505964.7 0 0.08240965 0.08433785 0.078799851 0.24554735 + 900 1491035.9 0 0.093659937 0.094517749 0.08812559 0.27630328 + 1000 1516599.6 0 0.10436496 0.10431759 0.097480868 0.30616342 + 1100 1495170.3 0 0.11468757 0.111397 0.1069763 0.33306087 + 1200 1500630.6 0 0.12360977 0.12264534 0.11583999 0.3620951 + 1300 1474889.5 0 0.13432447 0.13471694 0.12702491 0.39606632 + 1400 1487145.8 0 0.14573239 0.14431493 0.13669403 0.42674135 + 1500 1519496.7 0 0.15610742 0.15505416 0.14600182 0.4571634 + 1600 1525674.1 0 0.16728653 0.1649354 0.15562133 0.48784325 + 1700 1540725.4 0 0.17846447 0.17666562 0.16531781 0.52044791 + 1800 1512334.8 0 0.18872753 0.18538847 0.17450009 0.54861609 + 1900 1498371.4 0 0.19688928 0.19333299 0.18581712 0.5760394 + 2000 1546459.4 0 0.20955053 0.20243854 0.19613897 0.60812803 + 2100 1509712.9 0 0.21922567 0.20940597 0.20567239 0.63430404 + 2200 1509630.4 0 0.23067999 0.21856734 0.21619911 0.66544645 + 2300 1483929.1 0 0.24160803 0.231048 0.22617193 0.69882797 + 2400 1488492.1 0 0.25399491 0.24082678 0.23972356 0.73454526 + 2500 1508107.9 0 0.26608734 0.25316913 0.2486814 0.76793787 + 2600 1511952.1 0 0.27523956 0.2623673 0.25706539 0.79467225 + 2700 1488888.8 0 0.28518299 0.27425585 0.26728622 0.82672506 + 2800 1515428.4 0 0.29595429 0.28589969 0.27781327 0.85966725 + 2900 1504312.1 0 0.30393798 0.29533034 0.28725362 0.88652194 + 3000 1521521.3 0 0.31445132 0.30117607 0.29959324 0.91522062 +Loop time of 0.708196 on 4 procs for 3000 steps with 4096 atoms + +Performance: 3660.004 tau/day, 4236.115 timesteps/s +97.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00020647 | 0.00021023 | 0.0002141 | 0.0 | 0.03 +Comm | 0.0045607 | 0.0050649 | 0.0053098 | 0.4 | 0.72 +Output | 0.0013759 | 0.002265 | 0.0037355 | 1.9 | 0.32 +Modify | 0.57353 | 0.58931 | 0.6109 | 1.8 | 83.21 +Other | | 0.1113 | | | 15.72 + +Nlocal: 1024.00 ave 1043 max 1001 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 25 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/brownian/sphere/in2d.sphere b/examples/USER/brownian/sphere/in2d.sphere new file mode 100644 index 0000000000..a194f967cc --- /dev/null +++ b/examples/USER/brownian/sphere/in2d.sphere @@ -0,0 +1,45 @@ +##### overdamped dynamics of a sphere (with dipole attached to it) in 2D ##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_t string 5.0 +variable gamma_r string 0.7 +variable params string ${rng}_${temp}_${gamma_r}_${gamma_t} + +units lj +atom_style hybrid dipole sphere +dimension 2 +newton off + +lattice sq 0.4 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type & +# x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 diff --git a/examples/USER/brownian/sphere/in3d.sphere b/examples/USER/brownian/sphere/in3d.sphere new file mode 100644 index 0000000000..d3264ee450 --- /dev/null +++ b/examples/USER/brownian/sphere/in3d.sphere @@ -0,0 +1,45 @@ +##### overdamped dynamics of a sphere (with dipole attached to it) in 3D##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_t string 5.0 +variable gamma_r string 0.7 +variable params string ${rng}_${temp}_${gamma_r}_${gamma_t} + +units lj +atom_style hybrid dipole sphere +dimension 3 +newton off + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type & +# x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 diff --git a/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1 b/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1 new file mode 100644 index 0000000000..917f2b63fb --- /dev/null +++ b/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1 @@ -0,0 +1,126 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of a sphere (with dipole attached to it) in 2D ##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_t string 5.0 +variable gamma_r string 0.7 +variable params string ${rng}_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_1.0_${gamma_r}_${gamma_t} +variable params string uniform_1.0_0.7_${gamma_t} +variable params string uniform_1.0_0.7_5.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.005 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 3600 settings made for dipole/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 0.99972222 0 0 0 0 0 + 100 20867.136 0 0.00040006704 0.00039570887 0 0.00079577592 + 200 20835.491 0 0.00077560901 0.00080455484 0 0.0015801638 + 300 20813.122 0 0.0011737739 0.0012172689 0 0.0023910428 + 400 21137.397 0 0.0015587675 0.0016096093 0 0.0031683768 + 500 21167.188 0 0.0019294105 0.0020251322 0 0.0039545428 + 600 21345.908 0 0.0023105313 0.0024111742 0 0.0047217054 + 700 21086.272 0 0.0027236116 0.0027846006 0 0.0055082122 + 800 20840.906 0 0.0031505299 0.0031810732 0 0.0063316031 + 900 20916.456 0 0.0035525852 0.0035981301 0 0.0071507153 + 1000 20752.249 0 0.0039147929 0.0039791172 0 0.0078939101 + 1100 20643.612 0 0.0042977921 0.0043701484 0 0.0086679405 + 1200 21085.63 0 0.0045584242 0.0047475091 0 0.0093059332 + 1300 20900.794 0 0.0049718803 0.0051481706 0 0.010120051 + 1400 20980.731 0 0.0054234603 0.0054230724 0 0.010846533 + 1500 20916.308 0 0.0058502946 0.0058114313 0 0.011661726 + 1600 20949.786 0 0.0062258463 0.006208129 0 0.012433975 + 1700 20531.205 0 0.0066276219 0.006595921 0 0.013223543 + 1800 21418.472 0 0.0070077409 0.007030461 0 0.014038202 + 1900 21291.928 0 0.0074052208 0.0074333041 0 0.014838525 + 2000 20893.895 0 0.0077407477 0.007901402 0 0.01564215 + 2100 21218.001 0 0.0080384756 0.0082611258 0 0.016299601 + 2200 21116.189 0 0.0084325164 0.008617977 0 0.017050493 + 2300 20718.83 0 0.0089455345 0.0091768161 0 0.018122351 + 2400 20719.164 0 0.0093666455 0.0095272546 0 0.0188939 + 2500 20991.382 0 0.009706795 0.0098256506 0 0.019532446 + 2600 20515.74 0 0.0099247069 0.010329841 0 0.020254548 + 2700 21001.55 0 0.010448354 0.010693502 0 0.021141855 + 2800 21363.824 0 0.010990971 0.011142092 0 0.022133063 + 2900 20497.025 0 0.011399704 0.011504868 0 0.022904573 + 3000 20726.572 0 0.011785354 0.01187482 0 0.023660175 +Loop time of 1.76023 on 1 procs for 3000 steps with 3600 atoms + +Performance: 1472.538 tau/day, 1704.326 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.026518 | 0.026518 | 0.026518 | 0.0 | 1.51 +Output | 0.0040107 | 0.0040107 | 0.0040107 | 0.0 | 0.23 +Modify | 1.6194 | 1.6194 | 1.6194 | 0.0 | 92.00 +Other | | 0.1103 | | | 6.27 + +Nlocal: 3600.00 ave 3600 max 3600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 121.000 ave 121 max 121 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4 b/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4 new file mode 100644 index 0000000000..95602a809c --- /dev/null +++ b/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of a sphere (with dipole attached to it) in 2D ##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_t string 5.0 +variable gamma_r string 0.7 +variable params string ${rng}_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_1.0_${gamma_r}_${gamma_t} +variable params string uniform_1.0_0.7_${gamma_t} +variable params string uniform_1.0_0.7_5.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -30 30 -30 30 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 3600 settings made for dipole/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 0.99972222 0 0 0 0 0 + 100 21085.797 0 0.00042014118 0.00040399828 0 0.00082413946 + 200 20598.717 0 0.00081715618 0.00082613236 0 0.0016432885 + 300 21040.226 0 0.0012412527 0.0012520475 0 0.0024933002 + 400 21289.734 0 0.0016129899 0.001634482 0 0.003247472 + 500 20951.595 0 0.0020104279 0.0020197694 0 0.0040301973 + 600 20984.974 0 0.0023965593 0.0024277086 0 0.0048242679 + 700 21252.602 0 0.0028349303 0.0028407812 0 0.0056757114 + 800 20951.95 0 0.0032674595 0.0032573476 0 0.0065248071 + 900 20828.611 0 0.003647953 0.0036650963 0 0.0073130493 + 1000 21073.256 0 0.0040238604 0.0040103537 0 0.0080342142 + 1100 21104.396 0 0.0043694059 0.0044146515 0 0.0087840574 + 1200 20580.591 0 0.0047638237 0.0047646659 0 0.0095284896 + 1300 20667.623 0 0.0051512568 0.0051134445 0 0.010264701 + 1400 20466.72 0 0.0055921578 0.005517863 0 0.011110021 + 1500 20842.366 0 0.0059747304 0.0059374031 0 0.011912134 + 1600 20867.02 0 0.0065493697 0.0064163066 0 0.012965676 + 1700 21021.077 0 0.0070208005 0.0068164842 0 0.013837285 + 1800 21191.183 0 0.0073708939 0.0073226521 0 0.014693546 + 1900 20792.8 0 0.0076984189 0.0077400043 0 0.015438423 + 2000 21296.326 0 0.0081882545 0.0081503672 0 0.016338622 + 2100 21085.097 0 0.008596146 0.0086041272 0 0.017200273 + 2200 20506.523 0 0.0089905439 0.0091045462 0 0.01809509 + 2300 21068.555 0 0.0094163509 0.0094703314 0 0.018886682 + 2400 21128.867 0 0.0097349212 0.0098535832 0 0.019588504 + 2500 21009.514 0 0.010218059 0.010244621 0 0.020462679 + 2600 21177.52 0 0.01060437 0.010642719 0 0.021247089 + 2700 20832.56 0 0.011052623 0.011078899 0 0.022131522 + 2800 21298.053 0 0.011439708 0.011587702 0 0.023027411 + 2900 21002.28 0 0.011863624 0.01199682 0 0.023860443 + 3000 20737.939 0 0.012229608 0.012324579 0 0.024554186 +Loop time of 0.492798 on 4 procs for 3000 steps with 3600 atoms + +Performance: 5259.763 tau/day, 6087.689 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.018005 | 0.021524 | 0.025207 | 2.2 | 4.37 +Output | 0.0013187 | 0.0018334 | 0.0032332 | 1.9 | 0.37 +Modify | 0.37545 | 0.38775 | 0.40664 | 1.9 | 78.68 +Other | | 0.08169 | | | 16.58 + +Nlocal: 900.000 ave 900 max 900 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 61.0000 ave 61 max 61 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1 b/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1 new file mode 100644 index 0000000000..20048f96f1 --- /dev/null +++ b/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1 @@ -0,0 +1,126 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of a sphere (with dipole attached to it) in 3D##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_t string 5.0 +variable gamma_r string 0.7 +variable params string ${rng}_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_1.0_${gamma_r}_${gamma_t} +variable params string uniform_1.0_0.7_${gamma_t} +variable params string uniform_1.0_0.7_5.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.005 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 4096 settings made for dipole/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 1.4996338 0 0 0 0 0 + 100 32032.279 0 0.00040227568 0.00039159837 0.00040147813 0.0011953522 + 200 31673.093 0 0.00077657885 0.00077292327 0.00079963705 0.0023491392 + 300 31476.164 0 0.0011712083 0.0011606723 0.0012089537 0.0035408343 + 400 31911.374 0 0.0015803424 0.001562091 0.0016042321 0.0047466655 + 500 31182.011 0 0.0019677217 0.0019269105 0.0020015977 0.0058962298 + 600 31206.05 0 0.0023360975 0.0023134398 0.0024213372 0.0070708745 + 700 31278.057 0 0.0026966955 0.0027129858 0.0028721373 0.0082818187 + 800 31677.724 0 0.0031197964 0.003134834 0.0032726303 0.0095272607 + 900 31312.741 0 0.0035636612 0.0035573653 0.0037328373 0.010853864 + 1000 31426.075 0 0.0039774626 0.003952159 0.0041879386 0.01211756 + 1100 31361.699 0 0.0044256852 0.004320566 0.004638132 0.013384383 + 1200 31559.778 0 0.0048338539 0.0047210601 0.0050296056 0.01458452 + 1300 31716.797 0 0.0052239651 0.0050796723 0.0054794684 0.015783106 + 1400 31231.077 0 0.0055890568 0.005472377 0.0059264123 0.016987846 + 1500 31605.513 0 0.0059876582 0.0058974054 0.0063452478 0.018230311 + 1600 31551.402 0 0.006413094 0.0062665632 0.0067442106 0.019423868 + 1700 31725.868 0 0.0068244611 0.0067189707 0.0071424779 0.02068591 + 1800 31385.794 0 0.0071570297 0.0070502303 0.0075240296 0.02173129 + 1900 31754.094 0 0.0075638662 0.0074243015 0.0079935325 0.0229817 + 2000 31668.959 0 0.0080059944 0.0079019753 0.0084000614 0.024308031 + 2100 31781.994 0 0.0084108141 0.0082719077 0.0088004977 0.02548322 + 2200 31455.021 0 0.0088844434 0.0086931769 0.0091916929 0.026769313 + 2300 31273.079 0 0.0093155639 0.0091027782 0.0095364621 0.027954804 + 2400 31283.781 0 0.0098441686 0.0094496218 0.0099279073 0.029221698 + 2500 31758.315 0 0.010372129 0.0097843406 0.010334653 0.030491123 + 2600 31780.442 0 0.010770862 0.010313119 0.010637545 0.031721525 + 2700 31552.277 0 0.011268703 0.010693437 0.01110762 0.033069759 + 2800 31124.693 0 0.011661333 0.011100115 0.011480624 0.034242072 + 2900 31438.795 0 0.012068847 0.011346633 0.011842006 0.035257486 + 3000 31574.258 0 0.012482632 0.011691477 0.012210207 0.036384317 +Loop time of 2.8531 on 1 procs for 3000 steps with 4096 atoms + +Performance: 908.486 tau/day, 1051.488 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 3.2425e-05 | 3.2425e-05 | 3.2425e-05 | 0.0 | 0.00 +Comm | 0.13219 | 0.13219 | 0.13219 | 0.0 | 4.63 +Output | 0.0045686 | 0.0045686 | 0.0045686 | 0.0 | 0.16 +Modify | 2.5857 | 2.5857 | 2.5857 | 0.0 | 90.63 +Other | | 0.1307 | | | 4.58 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4 b/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4 new file mode 100644 index 0000000000..57dc6d5f11 --- /dev/null +++ b/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +##### overdamped dynamics of a sphere (with dipole attached to it) in 3D##### + +variable rng string uniform +variable seed string 198098 +variable temp string 1.0 +variable gamma_t string 5.0 +variable gamma_r string 0.7 +variable params string ${rng}_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_${temp}_${gamma_r}_${gamma_t} +variable params string uniform_1.0_${gamma_r}_${gamma_t} +variable params string uniform_1.0_0.7_${gamma_t} +variable params string uniform_1.0_0.7_5.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 2 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.006 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 198098 1.0 +Setting atom values ... + 4096 settings made for dipole/random +velocity all create 1.0 1 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +pair_style none + +fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t} +fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0 + +#initialisation for the main run + +# MSD +compute msd all msd + +thermo_style custom step ke pe c_msd[*] + +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 100 + +# main run +run 3000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] + 0 1.4996338 0 0 0 0 0 + 100 30882.707 0 0.00040787161 0.00039391576 0.00040796913 0.0012097565 + 200 31370.751 0 0.00081742036 0.00078240455 0.0008195167 0.0024193416 + 300 31469.51 0 0.0012118299 0.0011819412 0.0012477119 0.003641483 + 400 31696.58 0 0.0015540547 0.0015849689 0.0015836091 0.0047226327 + 500 31488.269 0 0.0019638041 0.0019659637 0.0020547832 0.005984551 + 600 30942.589 0 0.0023273784 0.0023572171 0.0024715245 0.00715612 + 700 31228.473 0 0.0027821732 0.002735338 0.0028734675 0.0083909787 + 800 31426.92 0 0.0031663838 0.0031092782 0.0033231014 0.0095987634 + 900 31447.595 0 0.003539588 0.003564381 0.003753036 0.010857005 + 1000 31363.911 0 0.0039854308 0.003937555 0.0041203919 0.012043378 + 1100 31522.958 0 0.0043009285 0.0043676491 0.0044799414 0.013148519 + 1200 31403.033 0 0.0046361199 0.0047513598 0.0049014974 0.014288977 + 1300 31752.182 0 0.0049824718 0.0051327113 0.0053130614 0.015428244 + 1400 31336.955 0 0.0054251445 0.0055442325 0.0057472998 0.016716677 + 1500 31224.306 0 0.0059295596 0.0059920697 0.0061375228 0.018059152 + 1600 31744.535 0 0.0063845142 0.0063600989 0.0064833215 0.019227935 + 1700 31472.081 0 0.0068360092 0.0067985824 0.0069464303 0.020581022 + 1800 31577.334 0 0.0073001079 0.0071355564 0.0073400543 0.021775719 + 1900 31521.234 0 0.0077178677 0.0074371106 0.007708008 0.022862986 + 2000 31045.148 0 0.0080515968 0.0078583776 0.0081000219 0.024009996 + 2100 31289.809 0 0.0084280175 0.0082322226 0.0084475904 0.02510783 + 2200 31505.455 0 0.008802925 0.0085708943 0.0087648194 0.026138639 + 2300 31882.722 0 0.0092223105 0.0089242925 0.0092643028 0.027410906 + 2400 31028.15 0 0.0095737559 0.0093585981 0.0096771837 0.028609538 + 2500 31581.041 0 0.0099316284 0.009785264 0.010100235 0.029817127 + 2600 31272.119 0 0.010332986 0.01007291 0.010474606 0.030880502 + 2700 31537.8 0 0.010751592 0.010565273 0.01093107 0.032247935 + 2800 31060.697 0 0.011156729 0.011010751 0.011260025 0.033427506 + 2900 31541.612 0 0.011542003 0.011499419 0.011642873 0.034684295 + 3000 31305.382 0 0.011876832 0.011866445 0.012052577 0.035795854 +Loop time of 1.00142 on 4 procs for 3000 steps with 4096 atoms + +Performance: 2588.329 tau/day, 2995.751 timesteps/s +95.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.084416 | 0.10685 | 0.12695 | 5.7 | 10.67 +Output | 0.001471 | 0.0019466 | 0.0033245 | 1.8 | 0.19 +Modify | 0.66585 | 0.70645 | 0.78995 | 6.0 | 70.54 +Other | | 0.1862 | | | 18.59 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 353.000 ave 353 max 353 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/brownian/spherical_ABP/in2d.abp b/examples/USER/brownian/spherical_ABP/in2d.abp new file mode 100644 index 0000000000..bd7dce13b6 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/in2d.abp @@ -0,0 +1,60 @@ +# 2D overdamped active brownian particle dynamics (ABP) +# with WCA potential + +variable gamma_t string 1.0 +variable gamma_r string 1.0 +variable temp string 1.0 +variable seed equal 1974019 +variable fp string 4.0 +variable params string ${temp}_${gamma_t}_${gamma_r}_${fp} + +units lj +atom_style hybrid dipole sphere +dimension 2 +newton off + +lattice sq 0.4 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + +# more careful with neighbors since higher diffusion in abps +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +# WCA potential (purely repulsive) +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.1224 +pair_modify shift yes + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +# self-propulsion force along the dipole direction +fix activity all propel/self dipole ${fp} +fix 2 all enforce2d + +compute press all pressure NULL virial + +thermo_style custom step pe ke c_press + +#equilibration +timestep 0.0000000001 +thermo 100 +run 5000 +reset_timestep 0 + + +# MSD +compute msd all msd + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 20000 diff --git a/examples/USER/brownian/spherical_ABP/in3d.ideal_abp b/examples/USER/brownian/spherical_ABP/in3d.ideal_abp new file mode 100644 index 0000000000..6a6575b510 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/in3d.ideal_abp @@ -0,0 +1,67 @@ +# 3D overdamped active brownian dynamics with no interactions + +variable gamma_t string 3.0 +variable gamma_r string 1.0 +variable temp string 1.0 +variable seed equal 1974019 +variable fp string 4.0 +variable params string ${temp}_${gamma_t}_${gamma_r}_${fp} + +units lj +atom_style hybrid dipole sphere +dimension 3 +newton off + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + +pair_style none + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +# self-propulsion force along the dipole direction +fix activity all propel/self dipole ${fp} + +compute press all pressure NULL virial + +thermo_style custom step ke pe c_press + +#equilibration +timestep 0.0000000001 +thermo 100 +run 5000 +reset_timestep 0 + +# MSD to demonstrate expected diffusive behaviour for ideal active +# brownian motion, which is +# +# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t +# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1) +# +# with d being simulation dimension +compute msd all msd + +thermo_style custom step ke pe c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 12000 + +# if you want to check that rotational diffusion is behaving as expected, +# uncomment next three lines for dump output and then plot , +# which should decay exponentially with timescale (d-1)*D_r (with d +# being simulation dimension) + +#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type & +# x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +#run 120000 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 b/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 new file mode 100644 index 0000000000..452d8a3d52 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 @@ -0,0 +1,221 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# 2D overdamped active brownian particle dynamics (ABP) +# with WCA potential + +variable gamma_t string 1.0 +variable gamma_r string 1.0 +variable temp string 1.0 +variable seed equal 1974019 +variable fp string 4.0 +variable params string ${temp}_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_1.0_${gamma_r}_${fp} +variable params string 1.0_1.0_1.0_${fp} +variable params string 1.0_1.0_1.0_4.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1024 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 1024 settings made for dipole/random +velocity all create 1.0 1 loop geom + +# more careful with neighbors since higher diffusion in abps +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +# WCA potential (purely repulsive) +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.1224 +pair_modify shift yes + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0 +# self-propulsion force along the dipole direction +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4.0 +fix 2 all enforce2d + +compute press all pressure NULL virial + +thermo_style custom step pe ke c_press + +#equilibration +timestep 0.0000000001 +thermo 100 +run 5000 +Neighbor list info ... + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.1224 + ghost atom cutoff = 2.1224 + binsize = 1.0612, bins = 48 48 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/2d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes +Step PotEng KinEng c_press + 0 0 0.99902344 -0.53979198 + 100 0 1.026585e+10 -0.5398101 + 200 0 1.0630628e+10 -0.53977393 + 300 0 1.03483e+10 -0.53977041 + 400 0 1.049279e+10 -0.53974314 + 500 0 1.0832067e+10 -0.53979451 + 600 0 1.0403632e+10 -0.53976233 + 700 0 1.0334726e+10 -0.53976174 + 800 0 1.0119596e+10 -0.53969338 + 900 0 1.0786136e+10 -0.53970415 + 1000 0 1.0539036e+10 -0.53974577 + 1100 0 1.0643695e+10 -0.53982431 + 1200 0 1.0234642e+10 -0.53976823 + 1300 0 1.036268e+10 -0.53981454 + 1400 0 1.0605702e+10 -0.53988117 + 1500 0 1.0517916e+10 -0.53989207 + 1600 0 1.0564482e+10 -0.53993016 + 1700 0 1.0460152e+10 -0.53984454 + 1800 0 1.0468566e+10 -0.53985574 + 1900 0 1.0474075e+10 -0.53985439 + 2000 0 1.0683568e+10 -0.53987349 + 2100 0 1.0269077e+10 -0.53990709 + 2200 0 1.0386943e+10 -0.53990068 + 2300 0 1.0406078e+10 -0.53978402 + 2400 0 1.0482072e+10 -0.53980757 + 2500 0 1.0442975e+10 -0.53982657 + 2600 0 1.0292103e+10 -0.53985533 + 2700 0 1.1106453e+10 -0.53991861 + 2800 0 1.0395289e+10 -0.53990138 + 2900 0 1.034021e+10 -0.53992375 + 3000 0 1.0434718e+10 -0.53995566 + 3100 0 1.0194094e+10 -0.53993997 + 3200 0 1.0411552e+10 -0.54000097 + 3300 0 1.0214175e+10 -0.53999884 + 3400 0 1.0434719e+10 -0.54000005 + 3500 0 1.0529638e+10 -0.53998281 + 3600 0 1.0406541e+10 -0.54000141 + 3700 0 1.0577151e+10 -0.54002354 + 3800 0 1.0488249e+10 -0.53996003 + 3900 0 1.0316153e+10 -0.54002024 + 4000 0 1.0491289e+10 -0.5400259 + 4100 0 1.0587981e+10 -0.5399811 + 4200 0 1.0332035e+10 -0.53997951 + 4300 0 1.0776469e+10 -0.53994151 + 4400 0 1.0982142e+10 -0.53983842 + 4500 0 1.0796919e+10 -0.5398414 + 4600 0 1.0324249e+10 -0.53979712 + 4700 0 1.0420899e+10 -0.53981967 + 4800 0 1.0274188e+10 -0.53976759 + 4900 0 1.0411535e+10 -0.5397757 + 5000 0 1.0399215e+10 -0.53980199 +Loop time of 1.34285 on 1 procs for 5000 steps with 1024 atoms + +Performance: 0.032 tau/day, 3723.422 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.25309 | 0.25309 | 0.25309 | 0.0 | 18.85 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.068734 | 0.068734 | 0.068734 | 0.0 | 5.12 +Output | 0.0012887 | 0.0012887 | 0.0012887 | 0.0 | 0.10 +Modify | 0.96552 | 0.96552 | 0.96552 | 0.0 | 71.90 +Other | | 0.05422 | | | 4.04 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 201.000 ave 201 max 201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2112.00 ave 2112 max 2112 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2112 +Ave neighs/atom = 2.0625000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +# MSD +compute msd all msd + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 20000 +Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 1.0409381e+10 0 0 0 0 0 -0.53980199 + 1000 107022.73 0.0080050427 0.020451432 0.021388798 0 0.04184023 -0.54900967 + 2000 107475.82 0.017262846 0.040669645 0.044251149 0 0.084920794 -0.42740968 + 3000 105388.35 0.042257875 0.062828995 0.05845782 0 0.12128682 -0.31792184 + 4000 106238.38 0.052733384 0.079036841 0.079396453 0 0.15843329 -0.24243699 + 5000 102904.54 0.088524456 0.095977642 0.099533961 0 0.1955116 -0.093468615 + 6000 105274.15 0.065334999 0.11591691 0.11675531 0 0.23267222 -0.21904478 + 7000 108903.41 0.06724271 0.13694218 0.13914947 0 0.27609164 -0.15913012 + 8000 101451.44 0.097201152 0.15704893 0.16178845 0 0.31883738 -0.055786965 + 9000 106808.72 0.084301668 0.18029391 0.175753 0 0.3560469 0.014898739 + 10000 107381.19 0.088583354 0.2000753 0.19569789 0 0.39577319 0.19417596 + 11000 102105.78 0.081066654 0.22042599 0.21914042 0 0.43956641 0.060574143 + 12000 105384.94 0.098716908 0.24382064 0.24673594 0 0.49055657 0.17067875 + 13000 107479.53 0.099989043 0.26942088 0.27207566 0 0.54149654 0.25514896 + 14000 102938.12 0.093252916 0.28529564 0.28698837 0 0.57228401 0.19976355 + 15000 104408.02 0.11900926 0.31291315 0.31195058 0 0.62486373 0.36956014 + 16000 103447.68 0.09627777 0.34145225 0.33159885 0 0.6730511 0.29857404 + 17000 108400.05 0.11433561 0.36561966 0.36068301 0 0.72630267 0.41922801 + 18000 103363.68 0.11040153 0.38709746 0.39228677 0 0.77938423 0.38111686 + 19000 103310.43 0.10660536 0.41406235 0.40975085 0 0.8238132 0.36022184 + 20000 102692.1 0.13517651 0.43870812 0.44138776 0 0.88009588 0.51144366 +Loop time of 5.66207 on 1 procs for 20000 steps with 1024 atoms + +Performance: 3051.889 tau/day, 3532.279 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3123 | 1.3123 | 1.3123 | 0.0 | 23.18 +Neigh | 0.011856 | 0.011856 | 0.011856 | 0.0 | 0.21 +Comm | 0.2747 | 0.2747 | 0.2747 | 0.0 | 4.85 +Output | 0.0011516 | 0.0011516 | 0.0011516 | 0.0 | 0.02 +Modify | 3.8451 | 3.8451 | 3.8451 | 0.0 | 67.91 +Other | | 0.2169 | | | 3.83 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 184.000 ave 184 max 184 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2558.00 ave 2558 max 2558 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2558 +Ave neighs/atom = 2.4980469 +Neighbor list builds = 23 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 b/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 new file mode 100644 index 0000000000..aa902fbe80 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 @@ -0,0 +1,221 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# 2D overdamped active brownian particle dynamics (ABP) +# with WCA potential + +variable gamma_t string 1.0 +variable gamma_r string 1.0 +variable temp string 1.0 +variable seed equal 1974019 +variable fp string 4.0 +variable params string ${temp}_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_1.0_${gamma_r}_${fp} +variable params string 1.0_1.0_1.0_${fp} +variable params string 1.0_1.0_1.0_4.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 2 +newton off + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 1024 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 1024 settings made for dipole/random +velocity all create 1.0 1 loop geom + +# more careful with neighbors since higher diffusion in abps +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + +# WCA potential (purely repulsive) +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.1224 +pair_modify shift yes + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0 +# self-propulsion force along the dipole direction +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4.0 +fix 2 all enforce2d + +compute press all pressure NULL virial + +thermo_style custom step pe ke c_press + +#equilibration +timestep 0.0000000001 +thermo 100 +run 5000 +Neighbor list info ... + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.1224 + ghost atom cutoff = 2.1224 + binsize = 1.0612, bins = 48 48 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/2d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes +Step PotEng KinEng c_press + 0 0 0.99902344 -0.53979198 + 100 0 1.0503521e+10 -0.53983092 + 200 0 1.0390343e+10 -0.5398287 + 300 0 1.0493441e+10 -0.53979247 + 400 0 1.0545991e+10 -0.53978678 + 500 0 1.0266398e+10 -0.53986297 + 600 0 1.0484775e+10 -0.53978746 + 700 0 1.0583596e+10 -0.53969114 + 800 0 1.0521919e+10 -0.53968754 + 900 0 1.0492019e+10 -0.53958643 + 1000 0 1.0298052e+10 -0.53949872 + 1100 0 1.0531424e+10 -0.53955431 + 1200 0 1.0635635e+10 -0.53960048 + 1300 0 1.0633405e+10 -0.53966331 + 1400 0 1.0195401e+10 -0.53968849 + 1500 0 1.0593758e+10 -0.53969763 + 1600 0 1.0425238e+10 -0.53971936 + 1700 0 1.0470017e+10 -0.53981957 + 1800 0 1.0545953e+10 -0.53987747 + 1900 0 1.0425015e+10 -0.53990412 + 2000 0 1.0655092e+10 -0.5399511 + 2100 0 1.0197224e+10 -0.53988687 + 2200 0 1.0448012e+10 -0.53986066 + 2300 0 1.0355268e+10 -0.53980415 + 2400 0 1.0246979e+10 -0.53979737 + 2500 0 1.0021539e+10 -0.5397919 + 2600 0 1.0200824e+10 -0.5397575 + 2700 0 1.0721591e+10 -0.53973512 + 2800 0 1.0354562e+10 -0.5397127 + 2900 0 1.0306795e+10 -0.5396946 + 3000 0 1.0301339e+10 -0.53968642 + 3100 0 1.0435826e+10 -0.53970945 + 3200 0 1.019524e+10 -0.53969746 + 3300 0 1.0550481e+10 -0.53967977 + 3400 0 1.0283446e+10 -0.53971102 + 3500 0 1.0956695e+10 -0.53976173 + 3600 0 1.0271033e+10 -0.53983632 + 3700 0 1.0389461e+10 -0.53977293 + 3800 0 1.0680515e+10 -0.53977425 + 3900 0 1.0072183e+10 -0.53982922 + 4000 0 1.0458036e+10 -0.53980042 + 4100 0 1.0588689e+10 -0.53971405 + 4200 0 1.0068308e+10 -0.5398033 + 4300 0 1.0502064e+10 -0.53981291 + 4400 0 1.0590544e+10 -0.5398346 + 4500 0 1.0411612e+10 -0.5397916 + 4600 0 1.0518596e+10 -0.53984868 + 4700 0 1.0386105e+10 -0.53977803 + 4800 0 1.029525e+10 -0.53970882 + 4900 0 1.0519112e+10 -0.53969616 + 5000 0 1.0335841e+10 -0.53976477 +Loop time of 0.471663 on 4 procs for 5000 steps with 1024 atoms + +Performance: 0.092 tau/day, 10600.781 timesteps/s +95.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.067099 | 0.07105 | 0.077898 | 1.6 | 15.06 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0581 | 0.066084 | 0.072322 | 2.0 | 14.01 +Output | 0.0014644 | 0.002618 | 0.0037239 | 1.6 | 0.56 +Modify | 0.24817 | 0.25719 | 0.26697 | 1.3 | 54.53 +Other | | 0.07472 | | | 15.84 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 105.000 ave 105 max 105 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 544.000 ave 544 max 544 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2176 +Ave neighs/atom = 2.1250000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +# MSD +compute msd all msd + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 20000 +Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 1.0345945e+10 0 0 0 0 0 -0.53976477 + 1000 100114.28 0.0029703577 0.020320684 0.020950989 0 0.041271673 -0.43948247 + 2000 106825.83 0.020969054 0.039616412 0.039459167 0 0.079075578 -0.22765541 + 3000 105287.4 0.037343571 0.056828177 0.058639835 0 0.11546801 -0.11728136 + 4000 104522.23 0.052237136 0.080264931 0.080863543 0 0.16112847 0.033230576 + 5000 103277.94 0.053791862 0.099188864 0.10141444 0 0.20060331 0.073591503 + 6000 104252.87 0.073304776 0.11964238 0.1215576 0 0.24119999 0.22062305 + 7000 105184.19 0.089054043 0.13691291 0.14216478 0 0.27907769 0.29015692 + 8000 104211.82 0.072577918 0.15820522 0.15658491 0 0.31479013 0.25908291 + 9000 99242.172 0.071616004 0.17658708 0.17479704 0 0.35138412 0.26305532 + 10000 105070.83 0.077009979 0.20175025 0.19871513 0 0.40046538 0.34120567 + 11000 106421.07 0.098623061 0.22472634 0.22671582 0 0.45144216 0.44021335 + 12000 103209.85 0.12032847 0.25004966 0.25368441 0 0.50373406 0.57344873 + 13000 107156.89 0.1058386 0.27283231 0.2744873 0 0.54731961 0.47957408 + 14000 108119.3 0.1204768 0.29333677 0.30054535 0 0.59388213 0.51832639 + 15000 105477.62 0.12510026 0.32217621 0.32806599 0 0.6502422 0.50174158 + 16000 106676.27 0.10893618 0.34980866 0.36031184 0 0.7101205 0.44769198 + 17000 103048.41 0.10625673 0.3781797 0.37970499 0 0.75788468 0.42803898 + 18000 109454.8 0.10555778 0.40997694 0.41396777 0 0.82394471 0.41380982 + 19000 107459.73 0.11267582 0.43757738 0.43577856 0 0.87335594 0.4917748 + 20000 101991.9 0.084279008 0.45363612 0.46278076 0 0.91641688 0.41707912 +Loop time of 1.80877 on 4 procs for 20000 steps with 1024 atoms + +Performance: 9553.439 tau/day, 11057.221 timesteps/s +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.34461 | 0.36424 | 0.40948 | 4.4 | 20.14 +Neigh | 0.0031493 | 0.003215 | 0.0032432 | 0.1 | 0.18 +Comm | 0.19538 | 0.20419 | 0.2104 | 1.2 | 11.29 +Output | 0.00054121 | 0.00087297 | 0.0018425 | 0.0 | 0.05 +Modify | 0.98335 | 1.0156 | 1.0791 | 3.8 | 56.15 +Other | | 0.2207 | | | 12.20 + +Nlocal: 256.000 ave 261 max 252 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 93.0000 ave 100 max 83 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Neighs: 662.250 ave 693 max 635 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 2649 +Ave neighs/atom = 2.5869141 +Neighbor list builds = 23 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 b/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 new file mode 100644 index 0000000000..0820471faa --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 @@ -0,0 +1,210 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# 3D overdamped active brownian dynamics with no interactions + +variable gamma_t string 3.0 +variable gamma_r string 1.0 +variable temp string 1.0 +variable seed equal 1974019 +variable fp string 4.0 +variable params string ${temp}_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_3.0_${gamma_r}_${fp} +variable params string 1.0_3.0_1.0_${fp} +variable params string 1.0_3.0_1.0_4.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.004 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 4096 settings made for dipole/random +velocity all create 1.0 1 loop geom + +pair_style none + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0 +# self-propulsion force along the dipole direction +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4.0 + +compute press all pressure NULL virial + +thermo_style custom step ke pe c_press + +#equilibration +timestep 0.0000000001 +thermo 100 +run 5000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes +Step KinEng PotEng c_press + 0 1.4996338 0 0.068021726 + 100 5.184227e+09 0 0.06801544 + 200 5.2165482e+09 0 0.068010729 + 300 5.2782092e+09 0 0.068009058 + 400 5.3244927e+09 0 0.068003481 + 500 5.2376606e+09 0 0.067998237 + 600 5.2735634e+09 0 0.067998037 + 700 5.2692439e+09 0 0.068025402 + 800 5.2667984e+09 0 0.068030143 + 900 5.242057e+09 0 0.0680246 + 1000 5.2557468e+09 0 0.068028348 + 1100 5.2975687e+09 0 0.068029528 + 1200 5.2081927e+09 0 0.068017542 + 1300 5.2636873e+09 0 0.068012572 + 1400 5.2187907e+09 0 0.06802049 + 1500 5.2349541e+09 0 0.0680373 + 1600 5.216092e+09 0 0.068056885 + 1700 5.2598019e+09 0 0.068069504 + 1800 5.2569065e+09 0 0.068065306 + 1900 5.2072055e+09 0 0.068074863 + 2000 5.2092961e+09 0 0.068061619 + 2100 5.2918572e+09 0 0.068076418 + 2200 5.2680626e+09 0 0.068072149 + 2300 5.242958e+09 0 0.06806486 + 2400 5.2494099e+09 0 0.06805038 + 2500 5.2055798e+09 0 0.068072194 + 2600 5.2264829e+09 0 0.068069312 + 2700 5.3557342e+09 0 0.068064812 + 2800 5.2186177e+09 0 0.068042942 + 2900 5.2652497e+09 0 0.068044214 + 3000 5.1894899e+09 0 0.068044801 + 3100 5.241524e+09 0 0.068056675 + 3200 5.1915006e+09 0 0.06805641 + 3300 5.2367825e+09 0 0.068049946 + 3400 5.2288011e+09 0 0.068060182 + 3500 5.2704335e+09 0 0.068070881 + 3600 5.2886558e+09 0 0.068050439 + 3700 5.1976022e+09 0 0.068045927 + 3800 5.1525512e+09 0 0.068054494 + 3900 5.2212395e+09 0 0.068061432 + 4000 5.2309575e+09 0 0.068070842 + 4100 5.2260184e+09 0 0.068078378 + 4200 5.2829349e+09 0 0.068071652 + 4300 5.2204917e+09 0 0.068083072 + 4400 5.255242e+09 0 0.068066175 + 4500 5.2435681e+09 0 0.068050802 + 4600 5.2483356e+09 0 0.06805658 + 4700 5.2365098e+09 0 0.068041845 + 4800 5.2254325e+09 0 0.068038583 + 4900 5.1842852e+09 0 0.068028401 + 5000 5.2240722e+09 0 0.068031544 +Loop time of 5.14275 on 1 procs for 5000 steps with 4096 atoms + +Performance: 0.008 tau/day, 972.242 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.26842 | 0.26842 | 0.26842 | 0.0 | 5.22 +Output | 0.0035088 | 0.0035088 | 0.0035088 | 0.0 | 0.07 +Modify | 4.6588 | 4.6588 | 4.6588 | 0.0 | 90.59 +Other | | 0.212 | | | 4.12 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 817.000 ave 817 max 817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + +# MSD to demonstrate expected diffusive behaviour for ideal active +# brownian motion, which is +# +# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t +# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1) +# +# with d being simulation dimension +compute msd all msd + +thermo_style custom step ke pe c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 12000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 5.2240722e+09 0 0 0 0 0 0.068031544 + 1000 52651.581 0 0.0066842466 0.0067977045 0.0066831353 0.020165086 0.060774985 + 2000 52835.806 0 0.013693443 0.014008773 0.013518945 0.041221161 0.094748037 + 3000 52097.629 0 0.020666918 0.021696789 0.020665685 0.063029392 0.10673866 + 4000 52579.452 0 0.028145318 0.028504548 0.02830967 0.084959536 0.13358122 + 5000 51255.456 0 0.035019271 0.034644123 0.03638843 0.10605182 0.13507609 + 6000 52730.035 0 0.041412307 0.042689213 0.043339117 0.12744064 0.16497663 + 7000 52247.642 0 0.048119396 0.050556395 0.050706527 0.14938232 0.16360301 + 8000 52169.849 0 0.055241196 0.058678631 0.059373122 0.17329295 0.1676169 + 9000 52520.526 0 0.063519587 0.066592779 0.066988842 0.19710121 0.17142694 + 10000 53519.297 0 0.07164814 0.074576535 0.075619236 0.22184391 0.15619444 + 11000 52937.293 0 0.077992504 0.083184462 0.082988794 0.24416576 0.15257327 + 12000 51762.283 0 0.085959749 0.090992292 0.08984213 0.26679417 0.15996211 +Loop time of 11.6748 on 1 procs for 12000 steps with 4096 atoms + +Performance: 888.063 tau/day, 1027.851 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0024164 | 0.0024164 | 0.0024164 | 0.0 | 0.02 +Comm | 0.048127 | 0.048127 | 0.048127 | 0.0 | 0.41 +Output | 0.0019393 | 0.0019393 | 0.0019393 | 0.0 | 0.02 +Modify | 11.12 | 11.12 | 11.12 | 0.0 | 95.24 +Other | | 0.5027 | | | 4.31 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 75 +Dangerous builds = 0 + +# if you want to check that rotational diffusion is behaving as expected, +# uncomment next three lines for dump output and then plot , +# which should decay exponentially with timescale (d-1)*D_r (with d +# being simulation dimension) + +#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +#run 120000 +Total wall time: 0:00:16 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 b/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 new file mode 100644 index 0000000000..c6e5b82090 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 @@ -0,0 +1,210 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# 3D overdamped active brownian dynamics with no interactions + +variable gamma_t string 3.0 +variable gamma_r string 1.0 +variable temp string 1.0 +variable seed equal 1974019 +variable fp string 4.0 +variable params string ${temp}_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_${gamma_t}_${gamma_r}_${fp} +variable params string 1.0_3.0_${gamma_r}_${fp} +variable params string 1.0_3.0_1.0_${fp} +variable params string 1.0_3.0_1.0_4.0 + +units lj +atom_style hybrid dipole sphere +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156) +dimension 3 +newton off + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 2 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 4096 settings made for dipole/random +velocity all create 1.0 1 loop geom + +pair_style none + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r} +fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0 +# self-propulsion force along the dipole direction +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4.0 + +compute press all pressure NULL virial + +thermo_style custom step ke pe c_press + +#equilibration +timestep 0.0000000001 +thermo 100 +run 5000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes +Step KinEng PotEng c_press + 0 1.4996338 0 0.068021726 + 100 5.2484581e+09 0 0.068010768 + 200 5.277936e+09 0 0.068024039 + 300 5.2651427e+09 0 0.068014821 + 400 5.2066432e+09 0 0.068027583 + 500 5.2250276e+09 0 0.068030242 + 600 5.239771e+09 0 0.068018406 + 700 5.1953674e+09 0 0.068017081 + 800 5.2097107e+09 0 0.068010167 + 900 5.2559863e+09 0 0.068012923 + 1000 5.2743197e+09 0 0.068017855 + 1100 5.1999741e+09 0 0.068014189 + 1200 5.3216344e+09 0 0.068005604 + 1300 5.2839264e+09 0 0.067982558 + 1400 5.2462761e+09 0 0.067977843 + 1500 5.2208208e+09 0 0.067979594 + 1600 5.2740284e+09 0 0.067972573 + 1700 5.1919692e+09 0 0.067974452 + 1800 5.2497614e+09 0 0.067966417 + 1900 5.2910442e+09 0 0.067976096 + 2000 5.27238e+09 0 0.067963979 + 2100 5.3305398e+09 0 0.06795661 + 2200 5.205471e+09 0 0.067970212 + 2300 5.1803713e+09 0 0.067931775 + 2400 5.2134311e+09 0 0.067941825 + 2500 5.2367424e+09 0 0.067963456 + 2600 5.2246738e+09 0 0.067957556 + 2700 5.2514573e+09 0 0.067960724 + 2800 5.2601577e+09 0 0.067965167 + 2900 5.2422855e+09 0 0.067956561 + 3000 5.1796674e+09 0 0.067946764 + 3100 5.2308189e+09 0 0.067946585 + 3200 5.1835395e+09 0 0.067951909 + 3300 5.2762112e+09 0 0.067963199 + 3400 5.3224133e+09 0 0.067944918 + 3500 5.2314242e+09 0 0.06795318 + 3600 5.2760337e+09 0 0.067958005 + 3700 5.2549349e+09 0 0.06795228 + 3800 5.3343065e+09 0 0.067944561 + 3900 5.2440993e+09 0 0.067947433 + 4000 5.2565026e+09 0 0.067962624 + 4100 5.1766738e+09 0 0.067949542 + 4200 5.2058437e+09 0 0.067959946 + 4300 5.2777775e+09 0 0.067945883 + 4400 5.2020331e+09 0 0.067953495 + 4500 5.1417619e+09 0 0.067944161 + 4600 5.2672994e+09 0 0.067936777 + 4700 5.222847e+09 0 0.067943025 + 4800 5.2467842e+09 0 0.06794191 + 4900 5.2784378e+09 0 0.067939495 + 5000 5.2563969e+09 0 0.067940246 +Loop time of 1.55848 on 4 procs for 5000 steps with 4096 atoms + +Performance: 0.028 tau/day, 3208.260 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.15304 | 0.15677 | 0.16459 | 1.2 | 10.06 +Output | 0.0012078 | 0.0021182 | 0.0047011 | 3.2 | 0.14 +Modify | 1.1966 | 1.2236 | 1.2761 | 2.8 | 78.51 +Other | | 0.176 | | | 11.29 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 353.000 ave 353 max 353 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + +# MSD to demonstrate expected diffusive behaviour for ideal active +# brownian motion, which is +# +# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t +# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1) +# +# with d being simulation dimension +compute msd all msd + +thermo_style custom step ke pe c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 12000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes +Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 5.2563969e+09 0 0 0 0 0 0.067940246 + 1000 52568.549 0 0.0067249858 0.0066478843 0.0066014231 0.019974293 0.066777589 + 2000 52836.937 0 0.013611101 0.013799663 0.013161144 0.040571907 0.066769693 + 3000 52129.467 0 0.020360834 0.02089829 0.01995025 0.061209374 0.060026879 + 4000 52075.177 0 0.027638751 0.028062314 0.026895904 0.082596969 0.078290387 + 5000 52203.996 0 0.034087112 0.034933104 0.033832559 0.10285278 0.083657551 + 6000 52986.764 0 0.041562413 0.042238976 0.040542538 0.12434393 0.11542014 + 7000 51941.229 0 0.049216989 0.049250201 0.047598008 0.1460652 0.13739893 + 8000 52618.713 0 0.057198947 0.057409217 0.05404895 0.16865711 0.13681938 + 9000 52501.332 0 0.066447829 0.065262287 0.062271789 0.19398191 0.14306596 + 10000 52545.628 0 0.073800792 0.072510553 0.070100713 0.21641206 0.14689578 + 11000 52416.561 0 0.081881868 0.080638809 0.078969817 0.24149049 0.15608324 + 12000 52271.578 0 0.090521937 0.088555992 0.08592156 0.26499949 0.1474981 +Loop time of 3.13506 on 4 procs for 12000 steps with 4096 atoms + +Performance: 3307.113 tau/day, 3827.677 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00060225 | 0.00060934 | 0.00061345 | 0.0 | 0.02 +Comm | 0.029197 | 0.029376 | 0.029582 | 0.1 | 0.94 +Output | 0.00060606 | 0.00087148 | 0.0016448 | 0.0 | 0.03 +Modify | 2.84 | 2.8773 | 2.8942 | 1.3 | 91.78 +Other | | 0.2269 | | | 7.24 + +Nlocal: 1024.00 ave 1037 max 999 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 73 +Dangerous builds = 0 + +# if you want to check that rotational diffusion is behaving as expected, +# uncomment next three lines for dump output and then plot , +# which should decay exponentially with timescale (d-1)*D_r (with d +# being simulation dimension) + +#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +#run 120000 +Total wall time: 0:00:04 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py index 131f51e9b4..2cd6f46aec 100644 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py @@ -2,7 +2,7 @@ """ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/USER/cgdna/util/generate.py b/examples/USER/cgdna/util/generate.py index e175455970..d2ba3ba980 100644 --- a/examples/USER/cgdna/util/generate.py +++ b/examples/USER/cgdna/util/generate.py @@ -2,7 +2,7 @@ """ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/examples/USER/cgsdk/sds-monolayer/in.sds-hybrid b/examples/USER/cgsdk/sds-monolayer/in.sds-hybrid index 3a9fcc13a9..eb3eca9c96 100644 --- a/examples/USER/cgsdk/sds-monolayer/in.sds-hybrid +++ b/examples/USER/cgsdk/sds-monolayer/in.sds-hybrid @@ -37,10 +37,11 @@ atom_modify first charged kspace_style pppm/cg 0.00001 kspace_modify order 3 -comm_modify mode multi neighbor 2.0 multi neigh_modify delay 4 every 2 check yes +comm_modify mode multi + timestep 10.0 fix 1 all nvt temp 310.0 310.0 100.0 diff --git a/examples/USER/dielectric/README b/examples/USER/dielectric/README new file mode 100644 index 0000000000..6cbb1e204d --- /dev/null +++ b/examples/USER/dielectric/README @@ -0,0 +1,44 @@ +This folder contains some example data and input scripts for the USER-DIELECTRIC package. Please refer to the following reference for more details: + +Nguyen TD, Li H, Bagchi D, Solis FJ, Olvera de la Cruz, Incorporating surface polarization effects into large-scale coarse-grained molecular dynamics simulation, Computer Physics Communications 2019, 241, 80--91. + +- data.confined : two point opposite charges confined between two interfaces (epsilon1=2/epsilon2=10/epsilon2=2) +- data.sphere : two point opposite charges outside a spherical interface (epsilon_in=1/epsilon2=10) + +- in.confined : read in data.confined +- in.nopbc : read in data.* files, using non-periodic boundary conditions, with a large cutoff + +For "atom_style dielectric" the Atoms section in the data file contains 15 following columns: + +id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature + +where + +* id, mol, type, q, x, y and z are similar to those in atom_style full + +* normx, normy and normz are the three components of the normal unit vector + of the interface at the boundary element (also called vertex, or patch). + For real charges (ions), these 3 values are irrelevant, + and can be anything (e.g. 0,0,1). normx, normy, and normz can be + accessed through mux, muy and muz as if they were dipole components. + +* ed = dielectric difference at the vertex along the normal vector direction. + For example, if (normx,normy,normz) points from medium with epsilon_in + to medium with epsilon_out, then ed = epsilon_out - epsilon_in + +* em = (epsilon_out + epsilon_in)/2: the mean dielectric value + +* epsilon = the local epsilon value at the vertex or at the ion. + For real charges, epsilon is the medium dielectric constant, + and q is the real (unscaled) charges. + For interface particles: + + if q is zero (zero surface charges), epsilon is set to be 1.0; + + if q is nonzero (charged surfaces), epsilon is set to be em + (the mean dielectric value above). + +* area_per_patch: the surface area of the patch (element). + For real charges, this value is irrelevant, can be 1.0. + +* curvature: surface mean curvature at the patch. + For example, for spherical interfaces, curvature = 1/spherical radius. + For planar interfaces, curvature = 0. diff --git a/examples/USER/dielectric/data.confined b/examples/USER/dielectric/data.confined new file mode 100644 index 0000000000..52afc2cf62 --- /dev/null +++ b/examples/USER/dielectric/data.confined @@ -0,0 +1,4019 @@ +LAMMPS data file: two oppositely charged ions confined between two walls + +4002 atoms +3 atom types + +0.0000000000000000e+00 4.0000006274935302e+01 xlo xhi +0.0000000000000000e+00 4.3301276792816687e+01 ylo yhi +0.0000000000000000e+00 4.0000000000000000e+01 zlo zhi + +Masses + +1 1 +2 1 +3 1 + +Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature + +1 0 1 0 0 0 9.99798 0 0 1 0.866 8 6 1 0 +2 0 1 0 0.500101 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +3 0 1 0 1.0002 0 9.99798 0 0 1 0.866 8 6 1 0 +4 0 1 0 1.5003 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +5 0 1 0 2.0004 0 9.99798 0 0 1 0.866 8 6 1 0 +6 0 1 0 2.50051 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +7 0 1 0 3.00061 0 9.99798 0 0 1 0.866 8 6 1 0 +8 0 1 0 3.50071 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +9 0 1 0 4.00081 0 9.99798 0 0 1 0.866 8 6 1 0 +10 0 1 0 4.50091 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +11 0 1 0 5.00101 0 9.99798 0 0 1 0.866 8 6 1 0 +12 0 1 0 5.50111 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +13 0 1 0 6.00121 0 9.99798 0 0 1 0.866 8 6 1 0 +14 0 1 0 6.50132 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +15 0 1 0 7.00142 0 9.99798 0 0 1 0.866 8 6 1 0 +16 0 1 0 7.50152 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +17 0 1 0 8.00162 0 9.99798 0 0 1 0.866 8 6 1 0 +18 0 1 0 8.50172 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +19 0 1 0 9.00182 0 9.99798 0 0 1 0.866 8 6 1 0 +20 0 1 0 9.50192 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +21 0 1 0 10.002 0 9.99798 0 0 1 0.866 8 6 1 0 +22 0 1 0 10.5021 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +23 0 1 0 11.0022 0 9.99798 0 0 1 0.866 8 6 1 0 +24 0 1 0 11.5023 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +25 0 1 0 12.0024 0 9.99798 0 0 1 0.866 8 6 1 0 +26 0 1 0 12.5025 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +27 0 1 0 13.0026 0 9.99798 0 0 1 0.866 8 6 1 0 +28 0 1 0 13.5027 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +29 0 1 0 14.0028 0 9.99798 0 0 1 0.866 8 6 1 0 +30 0 1 0 14.5029 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +31 0 1 0 15.003 0 9.99798 0 0 1 0.866 8 6 1 0 +32 0 1 0 15.5031 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +33 0 1 0 16.0032 0 9.99798 0 0 1 0.866 8 6 1 0 +34 0 1 0 16.5033 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +35 0 1 0 17.0034 0 9.99798 0 0 1 0.866 8 6 1 0 +36 0 1 0 17.5035 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +37 0 1 0 18.0036 0 9.99798 0 0 1 0.866 8 6 1 0 +38 0 1 0 18.5037 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +39 0 1 0 19.0038 0 9.99798 0 0 1 0.866 8 6 1 0 +40 0 1 0 19.5039 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +41 0 1 0 20.004 0 9.99798 0 0 1 0.866 8 6 1 0 +42 0 1 0 20.5041 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +43 0 1 0 21.0042 0 9.99798 0 0 1 0.866 8 6 1 0 +44 0 1 0 21.5043 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +45 0 1 0 22.0045 0 9.99798 0 0 1 0.866 8 6 1 0 +46 0 1 0 22.5046 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +47 0 1 0 23.0047 0 9.99798 0 0 1 0.866 8 6 1 0 +48 0 1 0 23.5048 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +49 0 1 0 24.0049 0 9.99798 0 0 1 0.866 8 6 1 0 +50 0 1 0 24.505 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +51 0 1 0 25.0051 0 9.99798 0 0 1 0.866 8 6 1 0 +52 0 1 0 25.5052 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +53 0 1 0 26.0053 0 9.99798 0 0 1 0.866 8 6 1 0 +54 0 1 0 26.5054 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +55 0 1 0 27.0055 0 9.99798 0 0 1 0.866 8 6 1 0 +56 0 1 0 27.5056 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +57 0 1 0 28.0057 0 9.99798 0 0 1 0.866 8 6 1 0 +58 0 1 0 28.5058 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +59 0 1 0 29.0059 0 9.99798 0 0 1 0.866 8 6 1 0 +60 0 1 0 29.506 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +61 0 1 0 30.0061 0 9.99798 0 0 1 0.866 8 6 1 0 +62 0 1 0 30.5062 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +63 0 1 0 31.0063 0 9.99798 0 0 1 0.866 8 6 1 0 +64 0 1 0 31.5064 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +65 0 1 0 32.0065 0 9.99798 0 0 1 0.866 8 6 1 0 +66 0 1 0 32.5066 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +67 0 1 0 33.0067 0 9.99798 0 0 1 0.866 8 6 1 0 +68 0 1 0 33.5068 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +69 0 1 0 34.0069 0 9.99798 0 0 1 0.866 8 6 1 0 +70 0 1 0 34.507 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +71 0 1 0 35.0071 0 9.99798 0 0 1 0.866 8 6 1 0 +72 0 1 0 35.5072 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +73 0 1 0 36.0073 0 9.99798 0 0 1 0.866 8 6 1 0 +74 0 1 0 36.5074 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +75 0 1 0 37.0075 0 9.99798 0 0 1 0.866 8 6 1 0 +76 0 1 0 37.5076 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +77 0 1 0 38.0077 0 9.99798 0 0 1 0.866 8 6 1 0 +78 0 1 0 38.5078 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +79 0 1 0 39.0079 0 9.99798 0 0 1 0.866 8 6 1 0 +80 0 1 0 39.508 0.866201 9.99798 0 0 1 0.866 8 6 1 0 +81 0 1 0 0 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +82 0 1 0 0.500101 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +83 0 1 0 1.0002 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +84 0 1 0 1.5003 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +85 0 1 0 2.0004 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +86 0 1 0 2.50051 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +87 0 1 0 3.00061 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +88 0 1 0 3.50071 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +89 0 1 0 4.00081 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +90 0 1 0 4.50091 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +91 0 1 0 5.00101 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +92 0 1 0 5.50111 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +93 0 1 0 6.00121 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +94 0 1 0 6.50132 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +95 0 1 0 7.00142 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +96 0 1 0 7.50152 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +97 0 1 0 8.00162 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +98 0 1 0 8.50172 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +99 0 1 0 9.00182 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +100 0 1 0 9.50192 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +101 0 1 0 10.002 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +102 0 1 0 10.5021 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +103 0 1 0 11.0022 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +104 0 1 0 11.5023 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +105 0 1 0 12.0024 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +106 0 1 0 12.5025 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +107 0 1 0 13.0026 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +108 0 1 0 13.5027 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +109 0 1 0 14.0028 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +110 0 1 0 14.5029 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +111 0 1 0 15.003 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +112 0 1 0 15.5031 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +113 0 1 0 16.0032 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +114 0 1 0 16.5033 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +115 0 1 0 17.0034 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +116 0 1 0 17.5035 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +117 0 1 0 18.0036 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +118 0 1 0 18.5037 2.5986 9.99798 0 0 1 0.866 8 6 1 0 +119 0 1 0 19.0038 1.7324 9.99798 0 0 1 0.866 8 6 1 0 +120 0 1 0 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30.0061 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1182 0 1 0 30.5062 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1183 0 1 0 31.0063 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1184 0 1 0 31.5064 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1185 0 1 0 32.0065 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1186 0 1 0 32.5066 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1187 0 1 0 33.0067 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1188 0 1 0 33.5068 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1189 0 1 0 34.0069 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1190 0 1 0 34.507 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1191 0 1 0 35.0071 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1192 0 1 0 35.5072 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1193 0 1 0 36.0073 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1194 0 1 0 36.5074 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1195 0 1 0 37.0075 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1196 0 1 0 37.5076 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1197 0 1 0 38.0077 24.2536 9.99798 0 0 1 0.866 8 6 1 0 +1198 0 1 0 38.5078 25.1198 9.99798 0 0 1 0.866 8 6 1 0 +1199 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8.00162 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1218 0 1 0 8.50172 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1219 0 1 0 9.00182 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1220 0 1 0 9.50192 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1221 0 1 0 10.002 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1222 0 1 0 10.5021 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1223 0 1 0 11.0022 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1224 0 1 0 11.5023 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1225 0 1 0 12.0024 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1226 0 1 0 12.5025 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1227 0 1 0 13.0026 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1228 0 1 0 13.5027 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1229 0 1 0 14.0028 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1230 0 1 0 14.5029 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1231 0 1 0 15.003 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1232 0 1 0 15.5031 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1233 0 1 0 16.0032 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1234 0 1 0 16.5033 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1235 0 1 0 17.0034 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1236 0 1 0 17.5035 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1237 0 1 0 18.0036 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1238 0 1 0 18.5037 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1239 0 1 0 19.0038 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1240 0 1 0 19.5039 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1241 0 1 0 20.004 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1242 0 1 0 20.5041 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1243 0 1 0 21.0042 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1244 0 1 0 21.5043 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1245 0 1 0 22.0045 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1246 0 1 0 22.5046 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1247 0 1 0 23.0047 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1248 0 1 0 23.5048 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1249 0 1 0 24.0049 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1250 0 1 0 24.505 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1251 0 1 0 25.0051 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1252 0 1 0 25.5052 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1253 0 1 0 26.0053 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1254 0 1 0 26.5054 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1255 0 1 0 27.0055 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1256 0 1 0 27.5056 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1257 0 1 0 28.0057 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1258 0 1 0 28.5058 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1259 0 1 0 29.0059 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1260 0 1 0 29.506 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1261 0 1 0 30.0061 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1262 0 1 0 30.5062 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1263 0 1 0 31.0063 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1264 0 1 0 31.5064 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1265 0 1 0 32.0065 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1266 0 1 0 32.5066 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1267 0 1 0 33.0067 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1268 0 1 0 33.5068 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1269 0 1 0 34.0069 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1270 0 1 0 34.507 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1271 0 1 0 35.0071 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1272 0 1 0 35.5072 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1273 0 1 0 36.0073 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1274 0 1 0 36.5074 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1275 0 1 0 37.0075 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1276 0 1 0 37.5076 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1277 0 1 0 38.0077 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1278 0 1 0 38.5078 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1279 0 1 0 39.0079 25.986 9.99798 0 0 1 0.866 8 6 1 0 +1280 0 1 0 39.508 26.8522 9.99798 0 0 1 0.866 8 6 1 0 +1281 0 1 0 0 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1282 0 1 0 0.500101 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1283 0 1 0 1.0002 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1284 0 1 0 1.5003 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1285 0 1 0 2.0004 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1286 0 1 0 2.50051 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1287 0 1 0 3.00061 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1288 0 1 0 3.50071 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1289 0 1 0 4.00081 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1290 0 1 0 4.50091 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1291 0 1 0 5.00101 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1292 0 1 0 5.50111 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1293 0 1 0 6.00121 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1294 0 1 0 6.50132 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1295 0 1 0 7.00142 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1296 0 1 0 7.50152 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1297 0 1 0 8.00162 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1298 0 1 0 8.50172 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1299 0 1 0 9.00182 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1300 0 1 0 9.50192 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1301 0 1 0 10.002 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1302 0 1 0 10.5021 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1303 0 1 0 11.0022 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1304 0 1 0 11.5023 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1305 0 1 0 12.0024 27.7184 9.99798 0 0 1 0.866 8 6 1 0 +1306 0 1 0 12.5025 28.5846 9.99798 0 0 1 0.866 8 6 1 0 +1307 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opposite charges + +2563 atoms +3 atom types + +0.000000 100.000000 xlo xhi +0.000000 100.000000 ylo yhi +0.000000 100.000000 zlo zhi + + +Masses + +1 1 +2 1 +3 1 + +Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature + +1 1 1 0 50 55.2573 41.4935 0 0.525731 -0.850651 0.490491 45 57.5 1 0 +2 1 1 0 50.4064 55.7206 41.8079 0.0406403 0.572055 -0.819208 0.490491 45 57.5 1 0 +3 1 1 0 49.5936 55.7206 41.8079 -0.0406403 0.572055 -0.819208 0.490491 45 57.5 1 0 +4 1 1 0 50.8109 56.1564 42.1616 0.081086 0.615642 -0.783843 0.490491 45 57.5 1 0 +5 1 1 0 50 56.1768 42.1357 0 0.617676 -0.786433 0.490491 45 57.5 1 0 +6 1 1 0 49.1891 56.1564 42.1616 -0.081086 0.615642 -0.783843 0.490491 45 57.5 1 0 +7 1 1 0 51.2114 56.5628 42.5527 0.121144 0.656282 -0.744727 0.490491 45 57.5 1 0 +8 1 1 0 50.4064 56.6088 42.5061 0.0406418 0.660883 -0.749387 0.490491 45 57.5 1 0 +9 1 1 0 51.6062 56.9378 42.9795 0.160622 0.69378 -0.702047 0.490491 45 57.5 1 0 +10 1 1 0 50.8057 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1 0 57.7258 45.9171 54.8624 0.772575 -0.408286 0.48624 0.490491 45 57.5 1 0 +2506 1 1 0 57.5794 45.3157 54.5399 0.757936 -0.46843 0.45399 0.490491 45 57.5 1 0 +2507 1 1 0 58.2518 46.962 54.7623 0.825175 -0.303801 0.476225 0.490491 45 57.5 1 0 +2508 1 1 0 58.1623 46.3397 54.4698 0.816233 -0.366027 0.446977 0.490491 45 57.5 1 0 +2509 1 1 0 58.0302 45.7287 54.156 0.803016 -0.427135 0.415597 0.490491 45 57.5 1 0 +2510 1 1 0 57.859 45.1429 53.8268 0.785899 -0.485712 0.382683 0.490491 45 57.5 1 0 +2511 1 1 0 57.4944 47.4482 56.1093 0.749435 -0.25518 0.610926 0.490491 45 57.5 1 0 +2512 1 1 0 57.9011 47.1968 55.4511 0.790112 -0.280319 0.545109 0.490491 45 57.5 1 0 +2513 1 1 0 57.4534 46.7786 55.8369 0.745339 -0.322141 0.583692 0.490491 45 57.5 1 0 +2514 1 1 0 53.8268 42.141 54.8571 0.382683 -0.785899 0.485712 0.490491 45 57.5 1 0 +2515 1 1 0 54.5399 42.4206 54.6843 0.45399 -0.757936 0.46843 0.490491 45 57.5 1 0 +2516 1 1 0 54.156 41.9698 54.2713 0.415597 -0.803016 0.427135 0.490491 45 57.5 1 0 +2517 1 1 0 55.225 42.747 54.4826 0.522499 -0.725299 0.448259 0.490491 45 57.5 1 0 +2518 1 1 0 54.8624 42.2742 54.0829 0.48624 -0.772575 0.408286 0.490491 45 57.5 1 0 +2519 1 1 0 55.8779 43.1181 54.2533 0.587785 -0.688191 0.425325 0.490491 45 57.5 1 0 +2520 1 1 0 55.5337 42.6229 53.8673 0.553372 -0.737712 0.38673 0.490491 45 57.5 1 0 +2521 1 1 0 55.1612 42.1655 53.4615 0.516122 -0.783452 0.346153 0.490491 45 57.5 1 0 +2522 1 1 0 54.4698 41.8377 53.6603 0.446977 -0.816233 0.366027 0.490491 45 57.5 1 0 +2523 1 1 0 54.7623 41.7482 53.038 0.476225 -0.825175 0.303801 0.490491 45 57.5 1 0 +2524 1 1 0 56.4945 43.5316 53.9977 0.649448 -0.64684 0.399769 0.490491 45 57.5 1 0 +2525 1 1 0 56.1919 43.0296 53.6159 0.619186 -0.697037 0.361591 0.490491 45 57.5 1 0 +2526 1 1 0 57.0711 43.985 53.7175 0.707107 -0.601501 0.371748 0.490491 45 57.5 1 0 +2527 1 1 0 56.7891 43.465 53.3469 0.678913 -0.653497 0.334691 0.490491 45 57.5 1 0 +2528 1 1 0 56.4741 42.9769 52.96 0.647412 -0.70231 0.296004 0.490491 45 57.5 1 0 +2529 1 1 0 57.6041 44.4755 53.4143 0.760406 -0.552454 0.341435 0.490491 45 57.5 1 0 +2530 1 1 0 57.3479 43.9426 53.0521 0.734794 -0.605742 0.305212 0.490491 45 57.5 1 0 +2531 1 1 0 57.0524 43.4338 52.6738 0.705236 -0.65662 0.267381 0.490491 45 57.5 1 0 +2532 1 1 0 56.7232 42.9602 52.289 0.672319 -0.703983 0.228899 0.490491 45 57.5 1 0 +2533 1 1 0 55.0421 41.6964 52.3723 0.504209 -0.830359 0.237228 0.490491 45 57.5 1 0 +2534 1 1 0 55.7125 42.0735 52.1302 0.571251 -0.79265 0.213023 0.490491 45 57.5 1 0 +2535 1 1 0 55.2913 41.6919 51.7253 0.529135 -0.830812 0.172532 0.490491 45 57.5 1 0 +2536 1 1 0 56.3458 42.5021 51.8743 0.634579 -0.749786 0.187432 0.490491 45 57.5 1 0 +2537 1 1 0 55.949 42.0983 51.4741 0.594895 -0.79017 0.147413 0.490491 45 57.5 1 0 +2538 1 1 0 55.5186 41.7289 51.0649 0.551859 -0.82711 0.106494 0.490491 45 57.5 1 0 +2539 1 1 0 55.8369 42.5466 53.2214 0.583692 -0.745339 0.322141 0.490491 45 57.5 1 0 +2540 1 1 0 56.1093 42.5056 52.5518 0.610926 -0.749435 0.25518 0.490491 45 57.5 1 0 +2541 1 1 0 55.4511 42.0989 52.8032 0.545109 -0.790112 0.280319 0.490491 45 57.5 1 0 +2542 1 1 0 55.3678 45.8573 57.3501 0.536784 -0.414272 0.735011 0.490491 45 57.5 1 0 +2543 1 1 0 55.8472 45.5604 56.7898 0.584716 -0.443957 0.678977 0.490491 45 57.5 1 0 +2544 1 1 0 56.2831 45.2908 56.1924 0.628313 -0.470917 0.619242 0.490491 45 57.5 1 0 +2545 1 1 0 55.6425 44.8662 56.4658 0.564254 -0.513375 0.646578 0.490491 45 57.5 1 0 +2546 1 1 0 55.1797 45.1479 57.0447 0.51797 -0.485208 0.704471 0.490491 45 57.5 1 0 +2547 1 1 0 54.9644 44.4758 56.6961 0.496441 -0.552418 0.669612 0.490491 45 57.5 1 0 +2548 1 1 0 56.6961 45.0356 55.5242 0.669612 -0.496441 0.552418 0.490491 45 57.5 1 0 +2549 1 1 0 57.0447 44.8203 54.8521 0.704471 -0.51797 0.485208 0.490491 45 57.5 1 0 +2550 1 1 0 56.4658 44.3575 55.1338 0.646578 -0.564254 0.513375 0.490491 45 57.5 1 0 +2551 1 1 0 57.3501 44.6322 54.1427 0.735011 -0.536784 0.414272 0.490491 45 57.5 1 0 +2552 1 1 0 56.7898 44.1528 54.4396 0.678977 -0.584716 0.443957 0.490491 45 57.5 1 0 +2553 1 1 0 56.1924 43.7169 54.7092 0.619242 -0.628313 0.470917 0.490491 45 57.5 1 0 +2554 1 1 0 54.7092 43.8076 56.2831 0.470917 -0.619242 0.628313 0.490491 45 57.5 1 0 +2555 1 1 0 55.1338 43.5342 55.6425 0.513375 -0.646578 0.564254 0.490491 45 57.5 1 0 +2556 1 1 0 54.4396 43.2102 55.8472 0.443957 -0.678977 0.584716 0.490491 45 57.5 1 0 +2557 1 1 0 55.5242 43.3039 54.9644 0.552418 -0.669612 0.496441 0.490491 45 57.5 1 0 +2558 1 1 0 54.8521 42.9553 55.1797 0.485208 -0.704471 0.51797 0.490491 45 57.5 1 0 +2559 1 1 0 54.1427 42.6499 55.3678 0.414272 -0.735011 0.536784 0.490491 45 57.5 1 0 +2560 1 1 0 56.0748 44.5935 55.8195 0.607478 -0.54065 0.581952 0.490491 45 57.5 1 0 +2561 1 1 0 55.8195 43.9252 55.4065 0.581952 -0.607478 0.54065 0.490491 45 57.5 1 0 +2562 1 1 0 55.4065 44.1805 56.0748 0.54065 -0.581952 0.607478 0.490491 45 57.5 1 0 +2563 2 2 1 50 50 62 0 0 1 0.490491 45 57.5 80 0 +2564 3 3 -1 50 50 38 0 0 1 0.490491 45 57.5 80 0 diff --git a/examples/USER/dielectric/in.confined b/examples/USER/dielectric/in.confined new file mode 100644 index 0000000000..c9ae6d712a --- /dev/null +++ b/examples/USER/dielectric/in.confined @@ -0,0 +1,83 @@ +# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1 +# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2 +# bottom interface: n = (0, 0, 1) +# top interface: n = (0, 0, -1) +# so that ed's are the same for both interfaces + +variable epsilon1 index 20 +variable epsilon2 index 8 + +variable data index data.confined + +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary p p f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable ed equal "v_epsilon2 - v_epsilon1" +variable em equal "(v_epsilon2 + v_epsilon1)/2" +variable epsilon equal 1.0 # epsilon at the patch, not used for now +variable area equal 0.866 # patch area, same as in the data file + +read_data ${data} + +group interface type 1 +group ions type 2 3 + +group cations type 2 +group anions type 3 + +# 1.0 = q * epsilon2 = qreal for cations +# -1.0 = q * epsilon2 = qreal for anions +variable qscale equal "1.0 / v_epsilon2" +set group cations charge ${qscale} +variable qscale equal "-1.0 / v_epsilon2" +set group anions charge ${qscale} + +pair_style lj/cut/coul/long/dielectric 1.122 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +kspace_style pppm/dielectric 0.0001 +kspace_modify slab 3.0 + +neigh_modify every 1 delay 0 check yes one 5000 + +#compute ef all efield/atom +dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +dump_modify 1 sort id + +dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] + +fix 1 ions nve + +if "${method} == gmres" then & + "fix 3 interface polarize/bem/gmres 1 1.0e-4" & + "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" & +elif "${method} == icc"& + "fix 3 interface polarize/bem/icc 1 1.0e-4 itr_max 50" & + "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" & +elif "${method} == dof" & + "fix 3 interface polarize/functional 1 0.001" & + "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" & +else & + "print 'Unsupported polarization solver' " + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair #f_3 +thermo_modify flush yes + +run 0 + + + + + diff --git a/examples/USER/dielectric/in.nopbc b/examples/USER/dielectric/in.nopbc new file mode 100644 index 0000000000..ada9af2bf5 --- /dev/null +++ b/examples/USER/dielectric/in.nopbc @@ -0,0 +1,51 @@ +# Interface +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary f f f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable data index data.sphere + +read_data ${data} + +group interface type 1 +group ions type 2 3 + +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +neigh_modify one 5000 + +#compute ef all efield/atom +dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] + +dump_modify 1 sort id + +fix 1 ions nve + +if "${method} == gmres" then & + "fix 3 interface polarize/bem/gmres 1 1.0e-4" & +elif "${method} == icc"& + "fix 3 interface polarize/bem/icc 1 1.0e-4" & +elif "${method} == dof" & + "fix 3 interface polarize/functional 1 1.0e-4" & +else & + "print 'Unsupported method for polarization' " + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair +thermo_modify flush yes + +run 0 + + + diff --git a/examples/USER/diffraction/Output/log.cite b/examples/USER/diffraction/Output/log.cite index 6a807fe927..51017908a0 100644 --- a/examples/USER/diffraction/Output/log.cite +++ b/examples/USER/diffraction/Output/log.cite @@ -1,5 +1,5 @@ This LAMMPS simulation made specific use of work described in the -following references. See http://lammps.sandia.gov/cite.html +following references. See https://www.lammps.org/cite.html for details. compute_xrd command: diff --git a/examples/USER/fep/README.md b/examples/USER/fep/README.md index 416af526e7..d8f0935115 100644 --- a/examples/USER/fep/README.md +++ b/examples/USER/fep/README.md @@ -9,6 +9,9 @@ to the final states. * `CH4hyd` -- free energy of hydration of methane (simple). FEP and FDTI methods. +* `SPCEhyd` -- free energy of hydration of SPCE water (simple). FEP + in separate steps for the LJ sites and the atomic charges. + * `CH4-CF4` -- free energy difference of transforming methane into perfluoromethane, in water (quite simple). FEP and BAR methods. diff --git a/examples/USER/fep/SPCEhyd/README.md b/examples/USER/fep/SPCEhyd/README.md new file mode 100644 index 0000000000..de30f0c19b --- /dev/null +++ b/examples/USER/fep/SPCEhyd/README.md @@ -0,0 +1,45 @@ +Free Energy of Hydration of SPCE Water +====================================== + +Example calculation of the free energy of hydration of water with +LAMMPS using *compute fep*, *fix adapt/fep* and *pair lj/cut/soft*. + +The Lennard-Jones sites and the electrostatic charges are +created/annihilated in separate runs, which simplifies the use of +*fix adapt/fep* and *compute fep*. The Lennard-Jones sites are handled +using soft core potentials (*pair lj/cut/soft*). Trajectories are at +constant NpT, so corrections for the fluctuating volume are included. + +The following directories contain input files and results for +calculations using free-energy perturbation (FEP): + +* `mols` -- molecule description files and force field database used + to create the initial configuration used for the simulations + `data.lmp` + +* `fep01` -- Calculation using FEP, multi-stage creation of one SPC/E + molecule, LJ and q. Results in `fep01-lj.fep` and `fep01-lj.fep` + +* `fep10` -- Calculation using FEP, multi-stage deletion of one SPC/E + molecule, q and LJ. Results in `fep10-q.fep` and `fep10-lj.fep` + +The Python script `fep.py` found in the +`tools` directory can be used to calculate the free-energy differences +corresponding to the transformations above: + + fep.py 300 < fep01-lj.fep + + fep.py 300 < fep01-q.fep + + fep.py 300 < fep10-q.fep + + fep.py 300 < fep10-lj.fep + +The outputs are in kcal/mol and can be compared with the experimental +value of -6.3 kcal/mol, or with a simulation value from the literature +of -6.7 kcal/mol +[Gonçalves, Stassen, Pure Appl Chem 76 (2004) 231](https://doi.org/10.1351/pac200476010231). + +These example calculations are for tutorial purposes only. The results +may not be of research quality (not enough sampling, size of the step +in lambda not optimized, etc.) diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep new file mode 100644 index 0000000000..67dc4bfd8d --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 0.00203701 17656.7 17717 +200000 0.0148799 17235.9 17669.1 +300000 0.0478517 16378 17736.4 +400000 0.100195 15034.8 17725.7 +500000 0.218866 12390.7 17698.7 +600000 0.371395 9907.37 17731.1 +700000 0.613593 7317.6 17750.5 +800000 0.895639 5984.39 17714.3 +900000 0.638838 8921.42 17726.2 +1000000 0.372214 11782.7 17728.6 +1100000 0.295555 12613 17730.3 +1200000 0.152975 15013.7 17792.5 +1300000 0.106403 15927.4 17737.2 +1400000 0.0570002 16875.1 17725.9 +1500000 0.0182185 17924.9 17790.8 +1600000 -0.0319612 19263.7 17775.1 +1700000 -0.0684472 20338.7 17786.9 +1800000 -0.0941487 21136.1 17764.8 +1900000 -0.132444 22374 17750.6 +2000000 -0.153928 23156.8 17744.8 diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-lj.out b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.out new file mode 100644 index 0000000000..3eaf2fd98c --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.out @@ -0,0 +1,592 @@ +LAMMPS (29 Oct 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.018 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +Setting atom values ... + 3 settings made for charge +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25066829 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030719151 + estimated relative force accuracy = 9.250981e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.477 | 9.489 | 9.507 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1344.7207 1251.046 93.67475 54.469999 30049.554 -30010.349 300 10284.691 24908.667 0.72058313 + 5000 28.694564 -5486.1043 1288.3881 -6774.4924 1379.4864 21688.643 -30296.277 308.95461 54.310852 17485.125 1.0265163 + 10000 60.154999 -5445.984 1289.4468 -6735.4308 1414.0583 21715.025 -30296.898 309.2085 479.66554 17890.87 1.003236 + 15000 93.146023 -5513.8313 1247.6759 -6761.5072 1299.4795 21790.371 -30301.687 299.19185 -508.0062 17325.35 1.0359828 + 20000 125.27418 -5449.2886 1284.4959 -6733.7844 1413.7763 21713.785 -30296.156 308.02126 590.93324 17813.863 1.0075729 + 25000 159.91521 -5488.9702 1263.558 -6752.5282 1419.1433 21691.575 -30298.164 303.00038 745.03072 17529.113 1.0239403 + 30000 192.99516 -5560.7692 1261.1821 -6821.9512 1417.204 21619.369 -30296.506 302.43062 247.03569 17579.175 1.0210243 + 35000 226.31455 -5475.9339 1217.5826 -6693.5164 1416.6051 21740.37 -30296.23 291.97549 585.78922 17897.211 1.0028805 + 40000 257.38113 -5547.1985 1242.3037 -6789.5022 1368.836 21696.099 -30299.114 297.90361 -308.25384 17644.122 1.017266 + 45000 290.1833 -5546.482 1247.5586 -6794.0405 1478.3456 21579.538 -30298.856 299.16372 1088.2882 17592.834 1.0202316 + 50000 323.27342 -5587.1305 1245.2866 -6832.4171 1494.5555 21518.708 -30301.175 298.6189 1294.6268 17477.389 1.0269707 + 55000 357.01676 -5579.512 1240.4584 -6819.9704 1395.6861 21642.898 -30295.857 297.46109 -99.93318 17770.807 1.0100141 + 60000 388.82447 -5489.9387 1234.3341 -6724.2728 1285.7293 21870.543 -30295.028 295.99251 -1147.8529 17885.706 1.0035257 + 65000 422.87575 -5552.7156 1212.0793 -6764.7949 1333.565 21754.173 -30298.11 290.65582 -712.18036 17669.638 1.015797 + 70000 457.6093 -5497.6045 1258.538 -6756.1425 1322.4574 21754.169 -30297.784 301.79659 -688.38797 17616.532 1.0188592 + 75000 491.97196 -5625.4891 1179.169 -6804.6581 1390.1744 21637.212 -30297.753 282.76395 42.978393 17500.681 1.0256038 + 80000 525.96216 -5522.0997 1232.6571 -6754.7568 1341.1534 21770.924 -30301.663 295.59035 -265.75148 17495.977 1.0258796 + 85000 559.772 -5429.8519 1249.9284 -6679.7803 1347.2093 21813.241 -30297.861 299.732 -111.81756 17957.604 0.9995078 + 90000 593.75975 -5560.9592 1265.0979 -6826.0571 1463.6326 21567.748 -30297.643 303.36965 599.30412 17830.144 1.0066528 + 95000 627.953 -5544.2442 1277.7084 -6821.9526 1407.1904 21633.729 -30299.133 306.39364 192.51289 17668.067 1.0158873 + 100000 662.08715 -5474.8467 1286.3434 -6761.1902 1377.3305 21690.898 -30299.316 308.46431 -161.00615 17888.012 1.0033963 +Loop time of 662.087 on 12 procs for 100000 steps with 1800 atoms + +Performance: 13.050 ns/day, 1.839 hours/ns, 151.038 timesteps/s +94.9% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 345.52 | 374.93 | 410.41 | 88.0 | 56.63 +Bond | 1.2655 | 1.3414 | 1.443 | 5.2 | 0.20 +Kspace | 99.52 | 135.77 | 165.42 | 148.0 | 20.51 +Neigh | 28.904 | 28.95 | 28.997 | 0.6 | 4.37 +Comm | 41.498 | 45.503 | 50.663 | 51.8 | 6.87 +Output | 0.0013665 | 0.0014183 | 0.0018614 | 0.4 | 0.00 +Modify | 49.685 | 64.033 | 72.601 | 117.1 | 9.67 +Other | | 11.56 | | | 1.75 + +Nlocal: 150.000 ave 169 max 133 min +Histogram: 1 2 1 1 2 1 0 3 0 1 +Nghost: 6036.17 ave 6092 max 5976 min +Histogram: 3 1 0 0 0 1 3 2 0 2 +Neighs: 86433.7 ave 96904 max 78425 min +Histogram: 3 1 1 0 2 1 1 0 1 2 + +Total # of neighbors = 1037204 +Ave neighs/atom = 576.22444 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4498 +Dangerous builds = 9 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25099061 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0035434233 + estimated relative force accuracy = 1.0670914e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + lj/cut/soft lambda 1-2 3-4 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.473 | 9.524 | 9.885 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda + 0 -5474.8313 1286.3434 -6761.1748 1377.3305 21729.814 -30338.216 308.46431 -145.89091 1.0033963 0 + 5000 -5501.3742 1227.5839 -6728.9581 1383.6091 21832.227 -30338.792 294.37381 197.29783 1.0066092 0.0025 + 10000 -5464.6748 1299.6003 -6764.2751 1422.869 21700.714 -30339.338 311.64329 911.1393 1.0308533 0.005 + 15000 -5570.8381 1254.6639 -6825.502 1432.6295 21661.321 -30337.889 300.86757 606.08029 1.0232505 0.0075 + 20000 -5517.9977 1279.1 -6797.0976 1408.873 21713.571 -30334.986 306.72733 71.014518 1.00536 0.01 + 25000 -5502.8662 1256.1509 -6759.0171 1354.4185 21819.904 -30335.966 301.22416 -280.3804 1.0121715 0.0125 + 30000 -5479.0987 1247.8675 -6726.9662 1413.5362 21734.153 -30338.534 299.23779 347.7292 1.0037264 0.015 + 35000 -5507.6469 1301.4131 -6809.06 1460.033 21614.564 -30336.109 312.07801 771.56011 1.0011707 0.0175 + 40000 -5487.2955 1295.7159 -6783.0113 1321.8494 21814.192 -30340.297 310.71181 -399.68468 1.0295009 0.02 + 45000 -5582.7908 1203.9957 -6786.7865 1428.232 21690.272 -30335.2 288.71737 516.0938 1.0238261 0.0225 + 50000 -5543.0112 1239.5077 -6782.5189 1442.8695 21660.077 -30336.998 297.23314 966.89878 1.0234172 0.025 + 55000 -5590.3604 1232.4497 -6822.8101 1322.5893 21772.961 -30338.359 295.54062 -790.54432 1.0210518 0.0275 + 60000 -5479.6266 1218.6941 -6698.3207 1363.233 21839.328 -30336.264 292.24204 102.67075 1.0069364 0.03 + 65000 -5492.8433 1277.3976 -6770.2409 1361.2794 21754.915 -30335.072 306.31909 -345.94035 1.0111736 0.0325 + 70000 -5564.9632 1256.2689 -6821.2322 1418.089 21663.812 -30334.208 301.25246 -235.62062 1.0000081 0.035 + 75000 -5431.4667 1233.6963 -6665.163 1385.2972 21867.508 -30337.413 295.83957 605.68584 1.015264 0.0375 + 80000 -5560.6719 1236.9415 -6797.6134 1374.1241 21748.636 -30335.156 296.61776 -202.53528 1.015924 0.04 + 85000 -5636.8905 1233.835 -6870.7255 1480.1666 21576.608 -30340.174 295.87281 827.4631 1.0212177 0.0425 + 90000 -5551.2917 1222.5755 -6773.8672 1452.5674 21638.206 -30335.595 293.1728 661.99097 1.0090475 0.045 + 95000 -5543.8224 1249.9355 -6793.758 1396.082 21724.933 -30339.764 299.73372 201.87719 1.0163116 0.0475 + 100000 -5558.5664 1227.1814 -6785.7479 1463.1907 21666.038 -30337.879 294.2773 955.6758 1.0158894 0.05 + 105000 -5507.0698 1233.0098 -6740.0796 1356.1635 21774.574 -30334.594 295.67493 -359.01022 1.0056685 0.0525 + 110000 -5561.0676 1221.0774 -6782.145 1403.5966 21692.913 -30337.463 292.81355 -87.113696 1.0133037 0.055 + 115000 -5526.6141 1243.9541 -6770.5682 1475.7194 21626.703 -30337.179 298.29937 855.85038 1.0118327 0.0575 + 120000 -5555.6741 1253.3796 -6809.0538 1346.5604 21755.315 -30340.743 300.55961 -1079.5856 0.98312027 0.06 + 125000 -5620.4084 1221.0146 -6841.423 1406.8142 21677.116 -30335.053 292.7985 -61.600379 1.0173627 0.0625 + 130000 -5586.4001 1204.2423 -6790.6425 1352.9098 21770.892 -30339.505 288.77651 -460.92375 1.0164837 0.065 + 135000 -5568.5186 1239.2748 -6807.7934 1401.8615 21748.687 -30340.555 297.17728 371.66677 1.0241473 0.0675 + 140000 -5526.4808 1249.0145 -6775.4953 1424.2185 21664.576 -30340.16 299.51285 520.63161 1.0238118 0.07 + 145000 -5532.8733 1254.9515 -6787.8248 1379.0629 21737.241 -30337.358 300.93654 -64.517937 1.0105756 0.0725 + 150000 -5549.4332 1228.3832 -6777.8163 1428.5036 21702.196 -30337.055 294.56547 363.42307 1.0052127 0.075 + 155000 -5547.9284 1256.6973 -6804.6257 1379.9059 21727.03 -30338.382 301.35519 35.503942 1.0222903 0.0775 + 160000 -5481.1383 1320.4344 -6801.5727 1390.3369 21729.299 -30337.062 316.63929 50.667563 1.0171266 0.08 + 165000 -5560.7321 1247.5004 -6808.2325 1422.2771 21662.917 -30341.024 299.14978 56.116137 1.0020068 0.0825 + 170000 -5541.3469 1257.9624 -6799.3094 1381.0133 21739.612 -30336.303 301.65856 -176.83515 1.0084433 0.085 + 175000 -5481.784 1239.9656 -6721.7496 1366.9952 21834.266 -30335.454 297.34293 377.28019 1.0297034 0.0875 + 180000 -5609.1447 1180.414 -6789.5587 1410.9273 21683.391 -30338.821 283.06249 203.46781 1.013427 0.09 + 185000 -5508.6637 1237.4229 -6746.0866 1401.5929 21736.318 -30334.806 296.7332 287.44715 1.0114427 0.0925 + 190000 -5524.666 1249.3421 -6774.008 1414.6887 21711.574 -30338.223 299.5914 108.63857 0.99681381 0.095 + 195000 -5613.4475 1179.1603 -6792.6078 1415.5702 21704.669 -30335.058 282.76187 -4.252137 1.0025742 0.0975 + 200000 -5577.1744 1219.3392 -6796.5136 1358.774 21688.932 -30339.219 292.39674 -339.31655 1.0272643 0.1 + 205000 -5473.5241 1291.8332 -6765.3573 1364.0148 21747.958 -30335.578 309.78075 -140.98482 1.0134706 0.1025 + 210000 -5412.6987 1304.0334 -6716.7321 1399.175 21790.687 -30338.388 312.70635 475.62089 1.0077929 0.105 + 215000 -5498.5445 1272.4319 -6770.9765 1305.2038 21853.899 -30334.099 305.12834 -964.41064 1.0117303 0.1075 + 220000 -5552.46 1236.8433 -6789.3033 1413.5383 21633.766 -30337.007 296.59421 126.59413 1.0135386 0.11 + 225000 -5463.5199 1281.9539 -6745.4738 1391.2426 21760.978 -30337.489 307.41171 372.98508 1.0154691 0.1125 + 230000 -5556.2415 1213.9742 -6770.2157 1373.9439 21746.355 -30331.29 291.11021 310.03784 1.0411894 0.115 + 235000 -5468.6139 1256.2727 -6724.8866 1419.9068 21755.903 -30337.057 301.25335 446.80106 1.008653 0.1175 + 240000 -5505.2272 1297.8543 -6803.0815 1389.9299 21721.555 -30336.374 311.22461 -216.33356 1.0007317 0.12 + 245000 -5556.4175 1231.9791 -6788.3966 1385.1734 21697.589 -30334.804 295.42778 -115.65689 1.0127289 0.1225 + 250000 -5570.5583 1261.1376 -6831.6959 1404.3069 21667.366 -30337.205 302.41997 -90.154201 1.0161797 0.125 + 255000 -5581.0101 1222.6213 -6803.6314 1393.6905 21687.538 -30336.542 293.18377 -58.781363 1.013542 0.1275 + 260000 -5552.6506 1225.5794 -6778.2299 1446.9969 21648.822 -30336.275 293.89312 749.70391 1.0136121 0.13 + 265000 -5527.9133 1245.5123 -6773.4255 1328.166 21792.912 -30336.854 298.67302 -825.99884 1.0063806 0.1325 + 270000 -5565.2798 1266.7326 -6832.0124 1488.6605 21582.46 -30339.347 303.76165 1592.7435 1.0374567 0.135 + 275000 -5567.4599 1211.9673 -6779.4272 1306.1895 21846.2 -30334.296 290.62895 -1062.6911 1.0107451 0.1375 + 280000 -5456.1965 1291.476 -6747.6725 1324.4174 21839.645 -30339.854 309.69509 -531.26163 1.0140474 0.14 + 285000 -5561.638 1229.3427 -6790.9808 1353.7161 21794.932 -30334.258 294.79557 -269.97414 1.0110394 0.1425 + 290000 -5486.1623 1276.1413 -6762.3036 1380.4775 21777.115 -30336.678 306.01784 -56.691362 1.0105051 0.145 + 295000 -5531.2556 1253.1859 -6784.4415 1354.9857 21750.76 -30338.549 300.51314 -555.4993 1.0159961 0.1475 + 300000 -5583.1864 1250.0209 -6833.2073 1431.4702 21654.547 -30337.557 299.75419 360.48799 1.0226237 0.15 + 305000 -5492.9399 1263.2527 -6756.1925 1385.9115 21749.132 -30337.333 302.92716 -94.633279 1.0008411 0.1525 + 310000 -5583.9951 1217.2631 -6801.2582 1439.2175 21660.614 -30332.833 291.89889 575.48041 1.0264848 0.155 + 315000 -5554.3025 1247.1517 -6801.4542 1305.5379 21807.382 -30337.478 299.06616 -1206.257 1.0085908 0.1575 + 320000 -5596.1914 1233.0393 -6829.2307 1431.9073 21667.612 -30337.859 295.682 745.35002 1.0291 0.16 + 325000 -5532.0063 1245.6006 -6777.6069 1479.6102 21640.94 -30338.346 298.69419 1390.0859 1.0311996 0.1625 + 330000 -5511.0183 1236.8356 -6747.854 1332.4766 21826.148 -30335.853 296.59237 -346.80349 1.020578 0.165 + 335000 -5512.3188 1238.1769 -6750.4957 1324.5201 21836.682 -30338.607 296.91401 -457.67242 1.0274241 0.1675 + 340000 -5504.0924 1242.6354 -6746.7278 1432.7958 21708.299 -30333.659 297.98314 674.26615 1.0055018 0.17 + 345000 -5522.5796 1265.0266 -6787.6062 1382.0078 21743.218 -30338.398 303.35254 -151.81029 1.0067371 0.1725 + 350000 -5545.7535 1267.9089 -6813.6624 1404.8847 21674.34 -30337.099 304.04372 128.71982 1.0135501 0.175 + 355000 -5499.0073 1275.2358 -6774.2431 1484.721 21658.719 -30337.688 305.80071 1468.7411 1.0346991 0.1775 + 360000 -5540.4144 1242.034 -6782.4484 1440.0683 21684.985 -30338.578 297.83892 662.99982 1.0085045 0.18 + 365000 -5472.9692 1267.5044 -6740.4736 1350.7945 21806.742 -30338.576 303.94672 -303.53857 1.0149794 0.1825 + 370000 -5563.7998 1257.4972 -6821.297 1363.9578 21745.681 -30339.039 301.54699 -616.39894 1.0015708 0.185 + 375000 -5494.3434 1204.4931 -6698.8365 1308.4989 21883.359 -30336.609 288.83665 -1009.8181 0.99179087 0.1875 + 380000 -5516.3392 1223.7518 -6740.0911 1355.9449 21816.149 -30337.588 293.45488 36.407556 1.02042 0.19 + 385000 -5534.8879 1226.8136 -6761.7015 1433.131 21698.233 -30336.201 294.18909 1224.3283 1.0416014 0.1925 + 390000 -5506.0676 1262.1264 -6768.194 1449.4667 21692.815 -30334.182 302.65707 932.23514 1.0216439 0.195 + 395000 -5601.9693 1234.2373 -6836.2066 1425.5787 21658.64 -30337.816 295.96929 254.00155 1.0148905 0.1975 + 400000 -5523.9324 1254.811 -6778.7434 1371.5302 21763.333 -30334.914 300.90286 -41.512594 1.0129399 0.2 + 405000 -5615.7822 1209.5514 -6825.3336 1431.7105 21604.804 -30336.544 290.04963 385.86176 1.02069 0.2025 + 410000 -5564.9317 1238.9308 -6803.8625 1334.6011 21725.649 -30342.03 297.09479 -668.14712 1.0114204 0.205 + 415000 -5565.723 1201.4165 -6767.1395 1407.6153 21731.714 -30339.794 288.09888 284.39352 1.0181526 0.2075 + 420000 -5514.1574 1259.6967 -6773.8542 1397.8555 21765.77 -30335.098 302.07445 -93.583513 1.003494 0.21 + 425000 -5566.4826 1233.6609 -6800.1435 1354.6757 21745.391 -30337.658 295.83106 -543.91774 1.0113019 0.2125 + 430000 -5544.9786 1227.5367 -6772.5153 1391.971 21756.332 -30337.075 294.36248 -52.853646 1.0029339 0.215 + 435000 -5457.9703 1243.8289 -6701.7992 1355.8144 21842.63 -30336.263 298.26936 96.07031 1.0162599 0.2175 + 440000 -5444.1352 1261.5679 -6705.7031 1327.5589 21849.174 -30337.667 302.52315 -159.33457 1.0201548 0.22 + 445000 -5569.3089 1253.1592 -6822.4681 1450.3256 21615.072 -30333.867 300.50675 497.07257 1.0162108 0.2225 + 450000 -5499.4632 1276.3744 -6775.8376 1436.3419 21681.852 -30337.613 306.07374 416.13585 1.0087874 0.225 + 455000 -5527.7917 1199.0123 -6726.804 1371.2866 21773.376 -30335.146 287.52235 -330.60298 0.99153512 0.2275 + 460000 -5634.9316 1214.1147 -6849.0463 1471.6124 21618.634 -30339.723 291.14391 831.79551 1.0154836 0.23 + 465000 -5492.5994 1247.2074 -6739.8067 1425.1188 21720.998 -30333.086 299.0795 782.63379 1.0210767 0.2325 + 470000 -5528.6598 1242.3825 -6771.0422 1413.2305 21674.806 -30339.41 297.9225 371.75935 1.018354 0.235 + 475000 -5570.6679 1274.1035 -6844.7714 1423.8596 21624.648 -30335.904 305.52919 243.67178 1.0157084 0.2375 + 480000 -5487.1119 1241.0548 -6728.1667 1421.7563 21732.588 -30338.933 297.60413 814.07568 1.0255732 0.24 + 485000 -5575.4172 1242.9613 -6818.3785 1402.7921 21677.417 -30338.336 298.0613 20.597793 1.0229831 0.2425 + 490000 -5578.303 1221.4158 -6799.7188 1430.5395 21694.761 -30336.572 292.89469 430.02647 1.0131845 0.245 + 495000 -5573.1773 1222.1238 -6795.3011 1502.7203 21609.264 -30338.892 293.06448 1494.9905 1.0226527 0.2475 + 500000 -5470.7153 1208.6593 -6679.3745 1401.9799 21819.612 -30335.747 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21701.959 -30338.233 294.13177 150.06013 1.0325882 0.985 + 1975000 -5564.1305 1237.5805 -6801.711 1398.2423 21736.76 -30338.459 296.77099 278.42773 1.0180523 0.9875 + 1980000 -5482.7493 1267.38 -6750.1292 1354.4265 21816.978 -30337.136 303.91688 -264.92549 1.0116111 0.99 + 1985000 -5486.0145 1244.3436 -6730.358 1338.1288 21844.074 -30336.86 298.39277 76.865939 1.0287137 0.9925 + 1990000 -5518.5592 1251.3748 -6769.9341 1251.2427 21885.87 -30337.966 300.07886 -1536.5189 1.0130877 0.995 + 1995000 -5487.626 1271.8163 -6759.4423 1356.5853 21769.656 -30337.831 304.9807 -374.70018 1.0071102 0.9975 + 2000000 -5510.6051 1219.5403 -6730.1454 1414.2091 21757.343 -30335.348 292.44495 576.54022 1.0102751 1 +Loop time of 13908.6 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.424 ns/day, 1.932 hours/ns, 143.796 timesteps/s +95.4% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7652.9 | 8199.2 | 8886.6 | 354.2 | 58.95 +Bond | 25.21 | 26.012 | 27.096 | 14.0 | 0.19 +Kspace | 2159 | 2762 | 3232.9 | 533.0 | 19.86 +Neigh | 571.65 | 572.66 | 573.54 | 2.5 | 4.12 +Comm | 806.99 | 869.79 | 940.86 | 190.9 | 6.25 +Output | 0.032536 | 0.034245 | 0.041095 | 1.2 | 0.00 +Modify | 959.22 | 1140.3 | 1306.8 | 448.8 | 8.20 +Other | | 338.6 | | | 2.43 + +Nlocal: 150.000 ave 159 max 140 min +Histogram: 1 0 2 2 0 2 2 1 0 2 +Nghost: 6121.33 ave 6236 max 6003 min +Histogram: 2 0 0 3 0 2 2 2 0 1 +Neighs: 87038.7 ave 96826 max 77686 min +Histogram: 2 0 1 3 0 1 2 1 1 1 + +Total # of neighbors = 1044464 +Ave neighs/atom = 580.25778 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89191 +Dangerous builds = 0 +Total wall time: 4:02:50 diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-q.fep b/examples/USER/fep/SPCEhyd/fep01/fep01-q.fep new file mode 100644 index 0000000000..553c231860 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-q.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 -0.00130466 18193.2 17742.3 +200000 -0.027526 18951.4 17742.7 +300000 -0.0459414 19629.2 17752.3 +400000 -0.0857092 21019.8 17772.6 +500000 -0.0982497 21457.5 17731.3 +600000 -0.137334 23057.4 17808.5 +700000 -0.170804 24395.7 17801 +800000 -0.223064 26797.3 17738.8 +900000 -0.261826 28800 17791.7 +1000000 -0.286374 30143.5 17783.4 +1100000 -0.349306 33728.2 17757.7 +1200000 -0.408164 37435.9 17787.7 +1300000 -0.496871 43896.5 17766.2 +1400000 -0.602917 53115.7 17749.9 +1500000 -0.72768 65474.3 17765 +1600000 -0.793802 73873.7 17785.7 +1700000 -0.912421 92487.7 17754.8 +1800000 -1.02249 109518 17762.7 +1900000 -1.12599 130115 17752.5 +2000000 -1.2899 174891 17768.3 diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-q.out b/examples/USER/fep/SPCEhyd/fep01/fep01-q.out new file mode 100644 index 0000000000..4d597f88b3 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-q.out @@ -0,0 +1,561 @@ +LAMMPS (29 Oct 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.019 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +Setting atom values ... + 3 settings made for charge +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25066829 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030719151 + estimated relative force accuracy = 9.250981e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.214 | 8.226 | 8.244 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1344.0739 1251.046 93.027896 53.823145 30049.554 -30010.349 300 10284.878 24908.667 0.72058313 + 5000 26.813 -5450.5713 1282.0681 -6732.6394 1325.6489 21834.91 -30297.994 307.43909 -699.90679 18234.717 0.98431826 + 10000 55.604067 -5588.263 1217.9162 -6806.1792 1414.4085 21633.044 -30301.477 292.05551 23.383255 17964.154 0.99914336 + 15000 85.625894 -5502.4932 1306.1963 -6808.6896 1448.9698 21589.863 -30300.506 313.22502 674.44388 17764.828 1.010354 + 20000 119.30994 -5551.8753 1255.7906 -6807.6659 1438.0508 21600.534 -30296.631 301.13775 626.57778 17521.241 1.0244003 + 25000 153.36332 -5513.3214 1262.2974 -6775.6188 1448.1692 21624.738 -30300.649 302.69809 1082.1686 17539.064 1.0233594 + 30000 185.73754 -5517.07 1232.0851 -6749.1552 1351.1278 21743.778 -30297.746 295.45321 -345.74832 17641.782 1.0174009 + 35000 219.88466 -5461.9885 1261.1109 -6723.0993 1320.5321 21811.17 -30298.154 302.41356 -633.99545 17793.771 1.0087106 + 40000 250.59178 -5478.4688 1259.9078 -6738.3767 1361.0965 21772.195 -30298.632 302.12507 251.40827 17555.015 1.0224295 + 45000 284.497 -5586.9018 1253.0148 -6839.9166 1368.2811 21661.619 -30296.221 300.47212 -485.67054 17692.537 1.0144823 + 50000 318.07759 -5566.6473 1284.4686 -6851.116 1421.3632 21574.213 -30298.299 308.01473 123.81461 17666.827 1.0159586 + 55000 342.2475 -5571.8668 1241.516 -6813.3827 1320.1575 21745.617 -30297.514 297.71471 -757.9971 17553.891 1.0224949 + 60000 369.92714 -5405.9904 1244.2976 -6650.288 1321.6833 21864.494 -30297.613 298.38174 -252.7118 17729.038 1.0123936 + 65000 400.90471 -5536.8199 1222.3639 -6759.1838 1335.2142 21756.337 -30299.402 293.12205 -425.71516 17495.348 1.0259165 + 70000 421.35603 -5552.3284 1260.2509 -6812.5793 1340.624 21697.664 -30296.839 302.20732 -845.04229 17882.237 1.0037204 + 75000 441.98615 -5494.066 1286.3299 -6780.3959 1404.289 21683.326 -30293.835 308.46107 382.75947 17905.291 1.002428 + 80000 462.4957 -5550.6324 1269.8456 -6820.4779 1356.8274 21698.112 -30298.489 304.50813 -534.46185 17874.446 1.0041579 + 85000 483.079 -5656.6158 1200.4648 -6857.0807 1457.2846 21562.254 -30300.6 287.87068 686.28181 17521.518 1.0243841 + 90000 510.58296 -5480.2188 1242.2417 -6722.4605 1325.1999 21772.005 -30296.2 297.88874 -353.59603 17662.908 1.016184 + 95000 531.29699 -5537.8929 1265.7042 -6803.5971 1376.1449 21683.369 -30297.657 303.51504 -263.8525 17673.753 1.0155605 + 100000 563.33023 -5538.2683 1254.8684 -6793.1367 1343.4731 21751.843 -30299.503 300.91662 -623.47098 17857.853 1.0050909 +Loop time of 563.33 on 12 procs for 100000 steps with 1800 atoms + +Performance: 15.337 ns/day, 1.565 hours/ns, 177.516 timesteps/s +94.5% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 284.09 | 305.4 | 330.52 | 90.7 | 54.21 +Bond | 1.0744 | 1.1159 | 1.1633 | 3.1 | 0.20 +Kspace | 101.59 | 125.93 | 147.73 | 141.3 | 22.35 +Neigh | 22.44 | 22.466 | 22.486 | 0.3 | 3.99 +Comm | 39.278 | 41.789 | 46.639 | 43.5 | 7.42 +Output | 0.0012299 | 0.0012852 | 0.0017706 | 0.4 | 0.00 +Modify | 42.543 | 55.366 | 62.194 | 102.3 | 9.83 +Other | | 11.26 | | | 2.00 + +Nlocal: 150.000 ave 163 max 133 min +Histogram: 1 1 0 0 1 3 3 0 1 2 +Nghost: 6108.25 ave 6187 max 6048 min +Histogram: 3 0 2 1 1 1 1 1 1 1 +Neighs: 86944.1 ave 96258 max 75267 min +Histogram: 2 0 1 0 1 0 3 3 1 1 + +Total # of neighbors = 1043329 +Ave neighs/atom = 579.62722 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4470 +Dangerous builds = 9 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25102555 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0035374557 + estimated relative force accuracy = 1.0652943e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + 1-1 charge + 2-2 charge +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.592 | 8.613 | 8.629 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_qO v_qH + 0 -5538.2733 1254.8684 -6793.1417 1343.4731 21794.974 -30342.64 300.91662 -475.71492 1.0050909 0 -0 0 + 5000 -5579.9374 1246.75 -6826.6874 1443.8973 21614.133 -30343.039 298.96983 785.16037 1.0322471 0.0025 -0.002119 0.0010595 + 10000 -5528.9995 1276.273 -6805.2725 1375.6345 21734.24 -30343.779 306.04943 -41.209531 1.0207823 0.005 -0.004238 0.002119 + 15000 -5506.4227 1270.5724 -6776.9951 1356.298 21760.893 -30339.74 304.68242 -483.58254 1.0055775 0.0075 -0.006357 0.0031785 + 20000 -5520.1985 1271.766 -6791.9645 1413.5454 21705.741 -30340.672 304.96864 -25.849632 0.9997261 0.01 -0.008476 0.004238 + 25000 -5538.0793 1260.547 -6798.6264 1362.2032 21772.012 -30341.973 302.27834 -32.008776 1.0238659 0.0125 -0.010595 0.0052975 + 30000 -5519.1594 1267.066 -6786.2254 1327.6996 21784.187 -30341.191 303.84159 -919.77668 0.99978921 0.015 -0.012714 0.006357 + 35000 -5565.8849 1244.6201 -6810.505 1384.6297 21700.099 -30337.317 298.45908 -41.645325 1.0154185 0.0175 -0.014833 0.0074165 + 40000 -5610.4882 1225.8647 -6836.3529 1416.9133 21661.893 -30343.456 293.96154 86.229199 1.0091158 0.02 -0.016952 0.008476 + 45000 -5609.3562 1208.1008 -6817.457 1387.4135 21711.193 -30343.791 289.70178 -101.30213 1.0155204 0.0225 -0.019071 0.0095355 + 50000 -5512.9435 1272.9818 -6785.9253 1379.4084 21746.829 -30342.184 305.2602 -12.658236 1.0143328 0.025 -0.02119 0.010595 + 55000 -5568.845 1249.4227 -6818.2677 1397.4685 21704.581 -30340.419 299.61074 -409.12372 0.99849506 0.0275 -0.023309 0.0116545 + 60000 -5519.3972 1216.5292 -6735.9264 1369.8115 21830.467 -30342.642 291.72291 117.70437 1.0138535 0.03 -0.025428 0.012714 + 65000 -5525.0539 1229.5034 -6754.5573 1354.6275 21755.174 -30340.101 294.8341 -462.0909 1.0102225 0.0325 -0.027547 0.0137735 + 70000 -5472.0836 1237.9936 -6710.0772 1352.7747 21872.795 -30340.246 296.87006 -5.9707079 1.010185 0.035 -0.029666 0.014833 + 75000 -5514.8966 1241.7822 -6756.6788 1369.2902 21788.901 -30344.123 297.77855 -36.505421 1.0055449 0.0375 -0.031785 0.0158925 + 80000 -5501.5809 1244.4839 -6746.0648 1406.1414 21762.858 -30338.116 298.42642 356.6391 1.0044866 0.04 -0.033904 0.016952 + 85000 -5522.8846 1243.4435 -6766.3281 1277.631 21834.13 -30341.071 298.17693 -1501.0557 1.0030405 0.0425 -0.036023 0.0180115 + 90000 -5521.2512 1226.9606 -6748.2118 1426.6301 21707.584 -30342.842 294.22434 431.61937 1.0037325 0.045 -0.038142 0.019071 + 95000 -5606.4261 1239.7565 -6846.1826 1458.2919 21603.577 -30341.265 297.2928 452.3491 1.0064454 0.0475 -0.040261 0.0201305 + 100000 -5526.6029 1244.4811 -6771.084 1442.7891 21665.95 -30338.28 298.42575 499.20413 1.0045851 0.05 -0.04238 0.02119 + 105000 -5589.4951 1234.4407 -6823.9358 1418.2214 21663.025 -30341.483 296.01807 101.88725 1.0139383 0.0525 -0.044499 0.0222495 + 110000 -5511.859 1262.1425 -6774.0015 1353.5279 21783.245 -30339.283 302.66093 -199.18931 1.0257755 0.055 -0.046618 0.023309 + 115000 -5647.3449 1229.413 -6876.758 1408.5179 21641.362 -30341.598 294.81243 -298.02921 1.0020969 0.0575 -0.048737 0.0243685 + 120000 -5449.7674 1281.3875 -6731.155 1304.5518 21888.494 -30341.641 307.27589 -694.089 1.0046108 0.06 -0.050856 0.025428 + 125000 -5430.3553 1247.5854 -6677.9407 1342.5284 21899.097 -30343.376 299.17016 125.17161 1.0091105 0.0625 -0.052975 0.0264875 + 130000 -5604.2229 1198.864 -6803.0869 1343.9437 21741.913 -30342.105 287.4868 -1029.1103 0.99252488 0.065 -0.055094 0.027547 + 135000 -5550.2149 1233.8869 -6784.1018 1298.4466 21844.496 -30341.697 295.88527 -1083.9932 1.0128891 0.0675 -0.057213 0.0286065 + 140000 -5526.9114 1246.4353 -6773.3466 1346.6874 21790.011 -30343.164 298.89435 -384.65885 1.0089922 0.07 -0.059332 0.029666 + 145000 -5594.7954 1213.2963 -6808.0917 1391.4251 21671.653 -30341.641 290.94766 -59.474002 1.0195886 0.0725 -0.061451 0.0307255 + 150000 -5580.5229 1259.8574 -6840.3803 1384.5548 21703.974 -30342.483 302.11297 -91.974674 1.0257584 0.075 -0.06357 0.031785 + 155000 -5566.2712 1230.138 -6796.4093 1366.5696 21707.576 -30336.313 294.98629 -482.01244 1.0070735 0.0775 -0.065689 0.0328445 + 160000 -5491.8647 1293.2326 -6785.0974 1386.5259 21718.735 -30343.487 310.11633 -89.376893 1.0093767 0.08 -0.067808 0.033904 + 165000 -5531.3681 1279.7729 -6811.1409 1354.4198 21753.203 -30342.651 306.88869 -392.95774 1.0134907 0.0825 -0.069927 0.0349635 + 170000 -5594.2308 1213.4715 -6807.7023 1482.6412 21600.249 -30341.895 290.98966 928.50126 1.0132201 0.085 -0.072046 0.036023 + 175000 -5519.3482 1257.2925 -6776.6407 1420.4909 21726.753 -30340.213 301.49792 254.94623 0.98901793 0.0875 -0.074165 0.0370825 + 180000 -5426.929 1250.4297 -6677.3587 1356.866 21886.349 -30343.3 299.85221 -245.8457 0.98302571 0.09 -0.076284 0.038142 + 185000 -5512.2746 1245.7072 -6757.9817 1380.9844 21794.2 -30342.884 298.71976 149.05128 1.0150091 0.0925 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1905000 -5486.4216 1290.1083 -6776.5299 1344.556 21824.3 -30385.345 309.36712 -170.76911 1.0220988 0.9525 -0.807339 0.4036695 + 1910000 -5612.2769 1206.579 -6818.8559 1361.0857 21798.985 -30389.316 289.33686 -679.6889 1.0021422 0.955 -0.809458 0.404729 + 1915000 -5587.0108 1277.8116 -6864.8224 1390.9876 21720.193 -30387.546 306.41838 -88.421087 1.026429 0.9575 -0.811577 0.4057885 + 1920000 -5536.6115 1211.5465 -6748.1579 1346.0005 21869.713 -30386.249 290.52804 -614.6848 0.99432544 0.96 -0.813696 0.406848 + 1925000 -5475.7378 1270.4733 -6746.2111 1363.7746 21799.571 -30386.112 304.65867 263.14406 1.0338166 0.9625 -0.815815 0.4079075 + 1930000 -5509.1127 1248.2489 -6757.3616 1334.6571 21873.781 -30385.968 299.32926 -529.83539 1.0071671 0.965 -0.817934 0.408967 + 1935000 -5548.4157 1253.3639 -6801.7796 1361.0982 21797.539 -30389.563 300.55583 -390.63414 1.0119705 0.9675 -0.820053 0.4100265 + 1940000 -5585.3752 1257.0833 -6842.4584 1341.862 21777.004 -30390.791 301.44773 -588.69504 1.0234228 0.97 -0.822172 0.411086 + 1945000 -5553.1361 1239.7945 -6792.9307 1392.65 21775.612 -30388.808 297.30191 401.98554 1.0324973 0.9725 -0.824291 0.4121455 + 1950000 -5608.302 1257.6453 -6865.9473 1385.8155 21666.265 -30389.484 301.58252 -258.45732 1.0221941 0.975 -0.82641 0.413205 + 1955000 -5597.8019 1196.2504 -6794.0523 1368.6962 21798.614 -30384.841 286.86006 -187.46622 1.015951 0.9775 -0.828529 0.4142645 + 1960000 -5558.9543 1259.8231 -6818.7774 1402.0765 21687.027 -30386.699 302.10476 -130.60372 1.0087181 0.98 -0.830648 0.415324 + 1965000 -5522.1401 1225.1335 -6747.2736 1385.1221 21794.241 -30386.219 293.78621 59.455921 1.0156338 0.9825 -0.832767 0.4163835 + 1970000 -5460.8469 1294.812 -6755.6589 1403.377 21789.971 -30387.038 310.49507 67.767671 0.99695881 0.985 -0.834886 0.417443 + 1975000 -5562.7016 1276.5904 -6839.292 1381.4683 21781.499 -30385.8 306.12554 -104.19545 1.0255706 0.9875 -0.837005 0.4185025 + 1980000 -5519.6646 1253.4527 -6773.1173 1464.4023 21698.419 -30387.375 300.57712 1035.4507 1.0129337 0.99 -0.839124 0.419562 + 1985000 -5465.34 1288.7347 -6754.0747 1312.8409 21917.192 -30385.618 309.03772 -632.51392 1.0142034 0.9925 -0.841243 0.4206215 + 1990000 -5579.8472 1232.0079 -6811.8551 1325.3706 21848.546 -30387.507 295.43468 -736.79929 1.0087938 0.995 -0.843362 0.421681 + 1995000 -5474.4313 1277.8474 -6752.2787 1377.0964 21856.577 -30388.53 306.42697 -223.13166 0.99592342 0.9975 -0.845481 0.4227405 + 2000000 -5530.4657 1243.1127 -6773.5784 1448.1254 21758.477 -30388.792 298.09761 750.74861 1.0102049 1 -0.8476 0.4238 +Loop time of 13807.9 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.515 ns/day, 1.918 hours/ns, 144.845 timesteps/s +95.3% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7308.6 | 8043.1 | 8855.3 | 457.7 | 58.25 +Bond | 24.229 | 25.717 | 27.246 | 21.9 | 0.19 +Kspace | 2227.1 | 3047.3 | 3772.6 | 744.0 | 22.07 +Neigh | 525.14 | 526.08 | 527.05 | 2.6 | 3.81 +Comm | 809.43 | 867.32 | 940.11 | 181.0 | 6.28 +Output | 0.033333 | 0.034507 | 0.043203 | 1.4 | 0.00 +Modify | 880.49 | 1047.6 | 1183.6 | 402.0 | 7.59 +Other | | 250.7 | | | 1.82 + +Nlocal: 150.000 ave 167 max 140 min +Histogram: 2 3 2 0 2 0 0 1 1 1 +Nghost: 6112.58 ave 6193 max 6037 min +Histogram: 3 0 2 0 0 3 1 1 0 2 +Neighs: 87266.4 ave 94192 max 79682 min +Histogram: 2 0 1 0 1 4 2 0 0 2 + +Total # of neighbors = 1047197 +Ave neighs/atom = 581.77611 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89139 +Dangerous builds = 0 +Total wall time: 3:59:31 diff --git a/examples/USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp b/examples/USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp new file mode 100644 index 0000000000..2f9bdbb7c5 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp @@ -0,0 +1,72 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style hybrid lj/cut/coul/long 12.0 12.0 lj/cut/soft 2 0.5 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Hwh +pair_coeff 1 2 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Owh +pair_coeff 1 3 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Hw +pair_coeff 1 4 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Ow +pair_coeff 2 2 lj/cut/soft 0.155425 3.165500 0.0 # Owh Owh +pair_coeff 2 3 lj/cut/soft 0.000000 1.000000 0.0 # Owh Hw +pair_coeff 2 4 lj/cut/soft 0.155425 3.165500 0.0 # Owh Ow +pair_coeff 3 3 lj/cut/coul/long 0.000000 0.000000 # Hw Hw +pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # Hw Ow +pair_coeff 4 4 lj/cut/coul/long 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +set type 1*2 charge 0.0 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(0.0,1.0) + +fix ADAPT all adapt/fep 100000 & + pair lj/cut/soft lambda 1*2 3*4 v_lambda & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda + +variable dlambda equal 0.05 + +compute FEP all fep ${TK} & + pair lj/cut/soft lambda 1*2 3*4 v_dlambda & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01-lj.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/fep01/in-fep01-q.lmp b/examples/USER/fep/SPCEhyd/fep01/in-fep01-q.lmp new file mode 100644 index 0000000000..19efe3a9b1 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/in-fep01-q.lmp @@ -0,0 +1,78 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style lj/cut/coul/long 12.0 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 0.000000 1.000000 # Hwh Hwh +pair_coeff 1 2 0.000000 1.000000 # Hwh Owh +pair_coeff 1 3 0.000000 1.000000 # Hwh Hw +pair_coeff 1 4 0.000000 1.000000 # Hwh Ow +pair_coeff 2 2 0.155425 3.165500 # Owh Owh +pair_coeff 2 3 0.000000 1.000000 # Owh Hw +pair_coeff 2 4 0.155425 3.165500 # Owh Ow +pair_coeff 3 3 0.000000 1.000000 # Hw Hw +pair_coeff 3 4 0.000000 1.000000 # Hw Ow +pair_coeff 4 4 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +set type 1*2 charge 0.0 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(0.0,1.0) +variable qH equal 0.4238*v_lambda +variable qO equal -0.8476*v_lambda + +fix ADAPT all adapt/fep 100000 & + atom charge 1 v_qH & + atom charge 2 v_qO & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_qO v_qH + +variable dlambda equal 0.05 +variable dqH equal 0.4238*v_dlambda +variable dqO equal -0.8476*v_dlambda + +compute FEP all fep ${TK} & + atom charge 1 v_dqH & + atom charge 2 v_dqO & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01-q.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep new file mode 100644 index 0000000000..e08c143542 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 0.164332 13580.8 17770.4 +200000 0.129134 14470.4 17769.5 +300000 0.113694 14856.5 17741.9 +400000 0.0945078 15445.3 17780.8 +500000 0.0562545 16508.6 17735.1 +600000 0.0490523 16733.2 17757.8 +700000 -0.0236465 19372.6 17801.7 +800000 -0.0387399 19901 17785.3 +900000 -0.0718098 21703.2 17802.6 +1000000 -0.118193 24005.7 17774.1 +1100000 -0.170254 26527.3 17789.9 +1200000 -0.297445 41864.5 17773.6 +1300000 -0.431516 50576.8 17744 +1400000 -0.467669 44025.5 17719.1 +1500000 -0.317884 31440.4 17731.3 +1600000 -0.218939 25792.6 17718.6 +1700000 -0.107798 21322.2 17753.1 +1800000 -0.0458874 19135.5 17706.5 +1900000 -0.015392 18211.1 17744.9 +2000000 -0.00224303 17811.3 17744.3 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-lj.out b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.out new file mode 100644 index 0000000000..bc93b1637e --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.out @@ -0,0 +1,592 @@ +LAMMPS (29 Oct 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.033 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +Setting atom values ... + 3 settings made for charge +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25066829 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030719151 + estimated relative force accuracy = 9.250981e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.477 | 9.489 | 9.507 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1344.0739 1251.046 93.027896 53.823145 30049.554 -30010.349 300 10284.878 24908.667 0.72058313 + 5000 26.829054 -5531.3966 1246.7673 -6778.164 1430.5662 21645.326 -30297.767 298.97398 343.00879 17939.671 1.0005069 + 10000 60.375331 -5491.2737 1280.0525 -6771.3262 1384.6297 21688.032 -30298.393 306.95574 -300.16806 18083.581 0.99254483 + 15000 94.076576 -5632.0108 1185.0761 -6817.0868 1373.1572 21657.834 -30299.165 284.18046 -509.30462 17853.507 1.0053356 + 20000 126.53271 -5557.9837 1273.3985 -6831.3822 1276.3348 21807.204 -30296.619 305.36012 -1423.8804 17810.87 1.0077422 + 25000 159.26926 -5561.3614 1271.5975 -6832.9588 1454.6816 21523.277 -30299.954 304.92823 245.53675 17839.133 1.0061456 + 30000 191.17362 -5569.1628 1224.4664 -6793.6292 1459.7735 21613.44 -30298.475 293.62623 1166.8411 17466.628 1.0276033 + 35000 225.54672 -5505.5765 1289.9333 -6795.5098 1374.8138 21675.444 -30297.568 309.32515 -277.00241 17845.641 1.0057787 + 40000 259.24748 -5529.8329 1222.5071 -6752.34 1368.482 21714.343 -30299.714 293.15639 -48.777351 17595.097 1.0201004 + 45000 292.69855 -5541.3772 1261.5499 -6802.9272 1371.5857 21681.912 -30295.814 302.51884 -335.65528 17817.714 1.0073551 + 50000 326.91392 -5573.7012 1222.2121 -6795.9133 1327.6979 21746.391 -30299.712 293.08565 -955.31142 17840.793 1.006052 + 55000 361.16613 -5449.164 1267.4384 -6716.6024 1412.1093 21720 -30299.63 303.9309 428.04385 18036.511 0.99513513 + 60000 393.91884 -5546.8912 1190.623 -6737.5143 1330.3252 21806.541 -30300.582 285.51061 -430.37809 17636.451 1.0177085 + 65000 428.22428 -5622.5584 1259.3301 -6881.8885 1509.1614 21478.163 -30299.496 301.98652 975.06072 17605.779 1.0194815 + 70000 462.45487 -5570.183 1218.0018 -6788.1847 1354.4694 21727.024 -30300.976 292.07602 -258.76822 17759.422 1.0106616 + 75000 496.90314 -5627.876 1230.7285 -6858.6045 1476.5693 21530.846 -30297.953 295.12788 553.50896 17749.215 1.0112428 + 80000 531.33879 -5494.2101 1259.607 -6753.8171 1380.283 21711.161 -30298.881 302.05292 211.62464 17627.074 1.0182499 + 85000 564.97941 -5519.5052 1245.7068 -6765.212 1413.8079 21662.496 -30297.084 298.71966 464.57065 17574.97 1.0212686 + 90000 597.70815 -5541.7394 1221.3799 -6763.1193 1438.245 21673.718 -30296.608 292.8861 594.92053 17785.328 1.0091894 + 95000 630.00979 -5506.2477 1292.8624 -6799.1101 1435.7457 21640.887 -30297.759 310.02754 746.74628 17535.628 1.0235599 + 100000 664.4401 -5517.294 1249.4101 -6766.7041 1435.9513 21681.832 -30299.249 299.60772 863.4493 17594.707 1.020123 +Loop time of 664.44 on 12 procs for 100000 steps with 1800 atoms + +Performance: 13.003 ns/day, 1.846 hours/ns, 150.503 timesteps/s +95.1% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 354.67 | 370.51 | 389.45 | 60.8 | 55.76 +Bond | 1.2832 | 1.3258 | 1.3684 | 2.3 | 0.20 +Kspace | 122.53 | 141.54 | 156.98 | 99.1 | 21.30 +Neigh | 28.973 | 29.038 | 29.092 | 0.6 | 4.37 +Comm | 42.452 | 45.845 | 51.532 | 54.0 | 6.90 +Output | 0.0013313 | 0.0013703 | 0.0017405 | 0.3 | 0.00 +Modify | 48.441 | 63.192 | 71.445 | 115.5 | 9.51 +Other | | 12.99 | | | 1.95 + +Nlocal: 150.000 ave 163 max 141 min +Histogram: 2 3 2 0 1 0 1 0 2 1 +Nghost: 6146.42 ave 6218 max 6094 min +Histogram: 3 3 0 0 0 0 4 0 1 1 +Neighs: 87791.7 ave 98973 max 80440 min +Histogram: 2 0 3 3 0 2 0 1 0 1 + +Total # of neighbors = 1053500 +Ave neighs/atom = 585.27778 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4499 +Dangerous builds = 9 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.2513327 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0034853969 + estimated relative force accuracy = 1.0496169e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + lj/cut/soft lambda 1-2 3-4 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.472 | 9.556 | 10.27 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda + 0 -5517.3031 1249.4101 -6766.7132 1435.9513 21762.036 -30379.462 299.60772 824.0149 1.020123 1 + 5000 -5558.3835 1278.7173 -6837.1007 1334.2641 21745.448 -30378.941 306.63556 -767.88312 1.0259151 0.9975 + 10000 -5536.0094 1281.998 -6818.0074 1400.7848 21722.638 -30382.662 307.42228 286.89597 1.0190965 0.995 + 15000 -5481.3474 1257.9731 -6739.3206 1399.5036 21761.099 -30377.92 301.66113 181.6173 1.0045157 0.9925 + 20000 -5576.3444 1286.5841 -6862.9285 1415.5303 21648.92 -30380.138 308.52201 -153.48635 1.0085717 0.99 + 25000 -5514.2625 1300.4887 -6814.7513 1407.9812 21728.21 -30379.084 311.85634 425.39113 1.018525 0.9875 + 30000 -5547.7134 1261.8317 -6809.5451 1380.2714 21733.843 -30375.593 302.58642 -17.777892 1.0150161 0.985 + 35000 -5477.5978 1281.4333 -6759.0311 1368.0059 21793.139 -30378.187 307.28686 -71.109919 1.0111779 0.9825 + 40000 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1334.4733 21816.614 -30381.683 306.71945 -1149.2916 0.98751404 0.175 + 1655000 -5501.82 1268.5575 -6770.3775 1377.245 21798.047 -30376.936 304.19926 1.7461216 1.0198116 0.1725 + 1660000 -5574.8853 1242.4084 -6817.2937 1402.801 21721.393 -30374.675 297.9287 -368.176 0.98829371 0.17 + 1665000 -5573.5235 1222.8083 -6796.3318 1398.8053 21724.515 -30373.998 293.22863 -34.053733 1.0103876 0.1675 + 1670000 -5465.9501 1315.885 -6781.8351 1342.4906 21789.764 -30380.929 315.54835 -711.01584 1.0050507 0.165 + 1675000 -5587.4957 1204.8035 -6792.2993 1411.9342 21755.712 -30382.222 288.91109 512.51181 1.0285941 0.1625 + 1680000 -5505.6492 1268.1162 -6773.7654 1373.3072 21795.716 -30381.924 304.09344 -65.28487 1.0177793 0.16 + 1685000 -5570.1242 1234.0295 -6804.1537 1333.3621 21779.517 -30377.13 295.91945 -832.3622 1.0233325 0.1575 + 1690000 -5491.4354 1286.9136 -6778.349 1302.901 21867.464 -30379.461 308.60103 -1091.2681 1.0076038 0.155 + 1695000 -5557.2902 1233.4916 -6790.7818 1475.5133 21645.505 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304.39806 -41.211787 1.0184863 0.13 + 1745000 -5601.6102 1211.6668 -6813.2769 1457.856 21646.431 -30379.268 290.55689 321.57165 1.0044935 0.1275 + 1750000 -5464.07 1262.7335 -6726.8035 1388.3238 21807.797 -30381.51 302.80266 347.94977 1.0199363 0.125 + 1755000 -5609.8158 1220.0117 -6829.8275 1449.8857 21660.858 -30381.398 292.55801 423.13734 1.0091913 0.1225 + 1760000 -5403.3906 1295.0506 -6698.4412 1376.6218 21890.749 -30379.696 310.55227 307.40852 1.0147058 0.12 + 1765000 -5516.242 1249.2409 -6765.4828 1382.647 21758.198 -30377.246 299.56714 167.93234 1.0231885 0.1175 + 1770000 -5582.0367 1264.8589 -6846.8955 1451.9857 21613.33 -30377.524 303.31232 595.73197 1.0185845 0.115 + 1775000 -5537.7575 1229.4186 -6767.1761 1369.0153 21805.496 -30381.159 294.81376 13.517698 1.0260482 0.1125 + 1780000 -5494.5434 1303.1737 -6797.7171 1436.2813 21746.59 -30380.854 312.50019 737.63948 1.019697 0.11 + 1785000 -5506.8968 1245.4135 -6752.3103 1381.9664 21814.635 -30377.185 298.64934 53.072035 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1835000 -5455.3051 1261.9795 -6717.2846 1352.0659 21888.34 -30378.24 302.62186 -278.9793 1.0005135 0.0825 + 1840000 -5550.1255 1264.0761 -6814.2015 1457.0559 21643.406 -30381.124 303.12461 732.70062 1.0158677 0.08 + 1845000 -5534.0588 1215.4174 -6749.4762 1393.3056 21800.212 -30376.843 291.45629 318.75691 1.0144019 0.0775 + 1850000 -5470.5935 1240.7072 -6711.3007 1398.1611 21825.075 -30377.387 297.52076 246.47011 0.99682722 0.075 + 1855000 -5562.2126 1269.9488 -6832.1614 1405.7155 21717.318 -30382.767 304.5329 158.21904 1.0206821 0.0725 + 1860000 -5593.1478 1212.5719 -6805.7197 1431.8435 21688.522 -30377.259 290.77394 490.69887 1.0155469 0.07 + 1865000 -5547.7314 1230.6551 -6778.3865 1415.4128 21748.348 -30378.118 295.11029 184.13907 0.99833163 0.0675 + 1870000 -5530.8677 1219.9933 -6750.861 1379.1571 21831.652 -30375.929 292.55359 34.766398 1.0094217 0.065 + 1875000 -5568.1541 1254.3638 -6822.5179 1355.1579 21740.634 -30379.983 300.7956 -705.50446 1.0143892 0.0625 + 1880000 -5653.4584 1235.3915 -6888.8499 1430.7173 21633.442 -30379.735 296.24606 102.70794 1.0154835 0.06 + 1885000 -5465.2275 1218.1694 -6683.3969 1239.8122 21974.299 -30378.879 292.11621 -1526.9501 1.00297 0.0575 + 1890000 -5596.8191 1179.0514 -6775.8705 1375.6822 21763.894 -30376.484 282.73574 -135.80694 1.0180663 0.055 + 1895000 -5465.5228 1216.5423 -6682.0651 1399.7408 21824.803 -30381.567 291.72604 189.86203 0.9918745 0.0525 + 1900000 -5525.4584 1268.983 -6794.4415 1386.5598 21763.346 -30379.48 304.30129 -147.74084 1.0101088 0.05 + 1905000 -5629.8529 1254.2275 -6884.0804 1455.3465 21571.828 -30380.574 300.76293 536.16177 1.0309795 0.0475 + 1910000 -5498.7043 1240.937 -6739.6413 1343.971 21867.501 -30378.531 297.57587 -307.05181 1.00532 0.045 + 1915000 -5489.6666 1266.2052 -6755.8718 1356.677 21815.921 -30373.873 303.63517 41.753289 1.0289101 0.0425 + 1920000 -5534.4011 1264.7423 -6799.1433 1414.4972 21675.646 -30381.358 303.28436 307.25885 1.030805 0.04 + 1925000 -5504.0398 1249.1105 -6753.1503 1407.4242 21780.765 -30377.439 299.53588 416.81022 1.0112989 0.0375 + 1930000 -5486.5931 1291.1596 -6777.7527 1380.6453 21793.976 -30378.396 309.61922 -167.68264 1.0083434 0.035 + 1935000 -5482.2055 1242.0698 -6724.2753 1296.2668 21881.772 -30378.102 297.84751 -1240.512 1.0083689 0.0325 + 1940000 -5413.7616 1287.0265 -6700.788 1300.618 21943.573 -30379.549 308.6281 -822.10018 0.9947525 0.03 + 1945000 -5618.7196 1214.3524 -6833.072 1410.8621 21689.242 -30381.323 291.2009 177.78285 1.0261522 0.0275 + 1950000 -5559.1869 1277.5888 -6836.7757 1384.1924 21715.907 -30380.281 306.36495 -269.07872 1.01053 0.025 + 1955000 -5556.8805 1290.1761 -6847.0566 1420.3306 21702.458 -30379.354 309.38338 63.181765 1.0037638 0.0225 + 1960000 -5536.3473 1288.352 -6824.6993 1333.2341 21766.427 -30380.118 308.94596 -956.94729 1.0098248 0.02 + 1965000 -5560.7629 1271.8239 -6832.5868 1394.6008 21745.026 -30375.628 304.98253 27.022116 1.014722 0.0175 + 1970000 -5571.8348 1246.9662 -6818.801 1368.7901 21728.521 -30376.246 299.02167 -642.85981 1.0038267 0.015 + 1975000 -5448.1873 1277.5391 -6725.7263 1376.1799 21855.417 -30379.445 306.35302 158.55616 1.010898 0.0125 + 1980000 -5569.4362 1227.1456 -6796.5818 1384.1163 21747.316 -30379.52 294.26871 -224.4952 1.0128917 0.01 + 1985000 -5490.1779 1256.3196 -6746.4975 1376.0987 21800.479 -30378.853 301.26461 -23.927186 1.0117616 0.0075 + 1990000 -5568.4743 1216.0821 -6784.5564 1365.6444 21804.572 -30380.078 291.61568 -40.531986 1.024747 0.005 + 1995000 -5623.9072 1244.7555 -6868.6627 1444.7105 21613.58 -30377.599 298.49155 401.54781 1.0221617 0.0025 + 2000000 -5564.5636 1253.8102 -6818.3738 1394.5734 21742.16 -30376.703 300.66286 -89.748646 1.0114229 0 +Loop time of 13852.8 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.474 ns/day, 1.924 hours/ns, 144.375 timesteps/s +95.5% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7431.1 | 8143.6 | 8773.3 | 379.5 | 58.79 +Bond | 24.35 | 26.055 | 27.801 | 23.2 | 0.19 +Kspace | 2212.7 | 2764.8 | 3391.2 | 573.6 | 19.96 +Neigh | 568.42 | 569.87 | 570.75 | 2.7 | 4.11 +Comm | 806.14 | 866.5 | 930.63 | 180.1 | 6.26 +Output | 0.032719 | 0.034078 | 0.041882 | 1.3 | 0.00 +Modify | 964.98 | 1144.9 | 1300.5 | 428.3 | 8.26 +Other | | 337 | | | 2.43 + +Nlocal: 150.000 ave 166 max 139 min +Histogram: 3 0 2 0 2 3 0 0 1 1 +Nghost: 6125.92 ave 6158 max 6091 min +Histogram: 1 1 0 2 1 2 2 1 1 1 +Neighs: 87012.7 ave 102741 max 79216 min +Histogram: 2 1 2 3 3 0 0 0 0 1 + +Total # of neighbors = 1044152 +Ave neighs/atom = 580.08444 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89145 +Dangerous builds = 0 +Total wall time: 4:01:57 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-q.fep b/examples/USER/fep/SPCEhyd/fep10/fep10-q.fep new file mode 100644 index 0000000000..fd49769ec2 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-q.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 1.45025 1741.09 17759.6 +200000 1.34275 2079.09 17751.2 +300000 1.11463 3077.67 17744.5 +400000 1.05072 3418.61 17752.1 +500000 0.861524 4545.87 17736.9 +600000 0.752417 5411.55 17755.8 +700000 0.677848 6201.52 17715.7 +800000 0.594413 7014.15 17718.2 +900000 0.482601 8441.94 17738.8 +1000000 0.44748 8942.75 17761.6 +1100000 0.374076 9984.65 17731.4 +1200000 0.310756 11050 17774.3 +1300000 0.246639 12186.7 17783.6 +1400000 0.201753 13117.8 17825.2 +1500000 0.166052 13843.8 17784.7 +1600000 0.136584 14486.5 17742.2 +1700000 0.102778 15331.6 17778.7 +1800000 0.0716746 16103 17743.1 +1900000 0.0513218 16698.6 17801.1 +2000000 0.0250996 17424.1 17780.5 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-q.out b/examples/USER/fep/SPCEhyd/fep10/fep10-q.out new file mode 100644 index 0000000000..36fc89e567 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-q.out @@ -0,0 +1,559 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.020 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.2506685 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030770287 + estimated relative force accuracy = 9.2663804e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.214 | 8.226 | 8.244 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1343.8082 1251.046 92.762256 53.823145 30098.377 -30059.438 300 10285.006 24908.667 0.72058313 + 5000 27.484029 -5481.5313 1291.2507 -6772.7821 1417.9265 21710.404 -30351.578 309.64107 573.94807 17792.658 1.0087737 + 10000 51.222479 -5557.9174 1247.8414 -6805.7588 1463.5652 21652.169 -30349.483 299.23155 1155.9001 17391.932 1.0320167 + 15000 81.534825 -5547.6429 1255.8047 -6803.4476 1434.9211 21679.801 -30351.564 301.14114 414.89266 17774.479 1.0098054 + 20000 108.19472 -5520.4365 1226.2567 -6746.6933 1363.6958 21763.102 -30350.115 294.05555 -159.5117 17640.377 1.017482 + 25000 139.47439 -5523.2547 1214.4617 -6737.7163 1403.2241 21727.256 -30347.421 291.2271 682.49951 17446.971 1.0287611 + 30000 173.52324 -5633.4887 1209.4695 -6842.9582 1384.9611 21696.903 -30350.921 290.02999 -439.40705 17870.41 1.0043846 + 35000 207.46148 -5609.1629 1202.7623 -6811.9252 1459.4041 21642.871 -30348.683 288.4216 870.04629 17620.845 1.0186098 + 40000 240.785 -5613.2727 1218.043 -6831.3157 1458.2338 21629.898 -30351.078 292.08591 578.74278 17728.011 1.0124523 + 45000 274.86574 -5567.9001 1234.3625 -6802.2626 1499.8464 21612.157 -30349.505 295.9993 1143.6708 17911.841 1.0020614 + 50000 308.33717 -5534.5804 1253.1529 -6787.7333 1383.4124 21740.111 -30349.237 300.50525 -236.43099 17808.85 1.0078565 + 55000 340.35767 -5558.5567 1237.2613 -6795.818 1472.1262 21640.69 -30349.9 296.69444 1169.6084 17518.859 1.0245396 + 60000 371.42788 -5620.3085 1217.3007 -6837.6091 1335.6617 21764.982 -30350.897 291.9079 -730.47206 17652.428 1.0167873 + 65000 400.4258 -5523.4332 1219.0927 -6742.5258 1377.9207 21790.846 -30351.438 292.33762 -67.377992 18008.535 0.99668103 + 70000 433.12056 -5549.9652 1278.9899 -6828.9551 1405.3901 21680.053 -30344.054 306.70094 -24.208971 17740.923 1.0117154 + 75000 465.43309 -5468.4134 1328.8758 -6797.2892 1404.3997 21721.55 -30346.155 318.66353 422.45424 17600.531 1.0197854 + 80000 498.33654 -5561.5506 1262.2191 -6823.7698 1375.8895 21728.477 -30350.941 302.67932 -480.08789 17936.63 1.0006765 + 85000 531.18843 -5561.7498 1243.7135 -6805.4633 1411.6336 21707.72 -30349.917 298.24169 31.756571 17844.951 1.0058176 + 90000 565.37172 -5548.2883 1305.5336 -6853.8219 1376.838 21698.95 -30345.634 313.06609 -580.39211 18032.442 0.99535964 + 95000 599.1335 -5491.6607 1249.0766 -6740.7373 1327.508 21805.341 -30346.173 299.52775 -747.34141 17928.72 1.001118 + 100000 632.97763 -5504.9781 1270.9776 -6775.9557 1348.4638 21759.337 -30349.51 304.7796 -112.23793 17469.352 1.0274431 +Loop time of 632.978 on 12 procs for 100000 steps with 1800 atoms + +Performance: 13.650 ns/day, 1.758 hours/ns, 157.983 timesteps/s +95.0% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 307.42 | 344.2 | 378.91 | 110.2 | 54.38 +Bond | 1.1476 | 1.2339 | 1.3345 | 6.3 | 0.19 +Kspace | 109.33 | 144.47 | 180.71 | 170.1 | 22.82 +Neigh | 25.619 | 25.671 | 25.708 | 0.6 | 4.06 +Comm | 41.234 | 45.135 | 50.464 | 52.8 | 7.13 +Output | 0.0012664 | 0.001324 | 0.0018066 | 0.4 | 0.00 +Modify | 46.059 | 59.064 | 69.016 | 114.7 | 9.33 +Other | | 13.2 | | | 2.09 + +Nlocal: 150.000 ave 160 max 138 min +Histogram: 2 0 0 2 1 1 3 0 0 3 +Nghost: 6169.08 ave 6215 max 6126 min +Histogram: 1 1 2 2 0 1 3 0 1 1 +Neighs: 88745.0 ave 98807 max 82382 min +Histogram: 3 0 1 3 0 3 1 0 0 1 + +Total # of neighbors = 1064940 +Ave neighs/atom = 591.63333 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4480 +Dangerous builds = 8 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25148052 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0034663752 + estimated relative force accuracy = 1.0438886e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + 1-1 charge + 2-2 charge +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.210 | 8.549 | 8.629 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_qO v_qH + 0 -5504.9889 1270.9776 -6775.9665 1348.4638 21857.535 -30447.719 304.7796 -83.574867 1.0274431 1 -0.8476 0.4238 + 5000 -5524.9498 1270.0815 -6795.0313 1351.1305 21827.149 -30444.933 304.5647 -593.70775 1.005159 0.9975 -0.845481 0.4227405 + 10000 -5540.3394 1230.4582 -6770.7976 1419.9827 21833.217 -30447.512 295.06306 390.92433 1.0060179 0.995 -0.843362 0.421681 + 15000 -5552.7887 1238.4753 -6791.264 1335.4158 21841.316 -30448.525 296.98555 -977.57176 1.0018216 0.9925 -0.841243 0.4206215 + 20000 -5571.4362 1242.7492 -6814.1854 1430.7811 21758.542 -30446.37 298.01044 389.91739 1.0176182 0.99 -0.839124 0.419562 + 25000 -5460.6807 1271.7643 -6732.445 1445.8579 21824.91 -30444.435 304.96824 662.28347 0.99362968 0.9875 -0.837005 0.4185025 + 30000 -5454.6572 1289.2653 -6743.9226 1383.6837 21875.483 -30446.254 309.16498 76.696731 1.0117008 0.985 -0.834886 0.417443 + 35000 -5460.3689 1262.5044 -6722.8733 1424.7799 21854.486 -30444.887 302.74772 469.28759 0.99223648 0.9825 -0.832767 0.4163835 + 40000 -5617.7692 1259.5855 -6877.3547 1466.8238 21653.475 -30448.558 302.04777 518.56945 1.0149626 0.98 -0.830648 0.415324 + 45000 -5498.7892 1260.7599 -6759.5491 1354.8241 21911.823 -30445.433 302.32939 36.724958 1.0199193 0.9775 -0.828529 0.4142645 + 50000 -5556.2521 1276.3605 -6832.6126 1408.5453 21757.203 -30447.43 306.0704 38.976819 1.012915 0.975 -0.82641 0.413205 + 55000 -5513.8511 1239.4864 -6753.3375 1378.8961 21910.688 -30446.837 297.22802 -155.09229 0.99684598 0.9725 -0.824291 0.4121455 + 60000 -5482.86 1287.2484 -6770.1084 1383.4644 21876.85 -30446.035 308.68131 -23.984269 1.002056 0.97 -0.822172 0.411086 + 65000 -5556.4674 1243.4649 -6799.9323 1374.1364 21841.845 -30449.652 298.18207 13.80546 1.0185986 0.9675 -0.820053 0.4100265 + 70000 -5509.3689 1255.8787 -6765.2476 1342.6439 21905.378 -30448.437 301.15889 -636.57169 1.0013923 0.965 -0.817934 0.408967 + 75000 -5599.5463 1235.6343 -6835.1807 1391.5344 21779.525 -30444.409 296.3043 -272.25195 1.0096277 0.9625 -0.815815 0.4079075 + 80000 -5505.7102 1228.1399 -6733.8502 1402.1931 21862.826 -30444.663 294.50714 287.56695 1.007265 0.96 -0.813696 0.406848 + 85000 -5615.9836 1228.8806 -6844.8643 1412.2136 21728.301 -30447.357 294.68477 88.808898 1.0201101 0.9575 -0.811577 0.4057885 + 90000 -5445.8525 1286.0493 -6731.9017 1365.0964 21944.508 -30446.123 308.39376 -159.5813 0.99818678 0.955 -0.809458 0.404729 + 95000 -5555.6599 1255.1923 -6810.8522 1487.4112 21697.426 -30446.382 300.99428 1056.7026 1.0047794 0.9525 -0.807339 0.4036695 + 100000 -5423.2205 1299.4514 -6722.6719 1340.3931 21969.252 -30445.58 311.60759 -104.22862 1.0205672 0.95 -0.80522 0.40261 + 105000 -5510.0668 1219.7044 -6729.7712 1422.1714 21857.811 -30444.935 292.48431 965.21304 1.0267571 0.9475 -0.803101 0.4015505 + 110000 -5487.6062 1264.3775 -6751.9838 1383.7805 21872.105 -30438.176 303.19689 5.0812841 1.0038721 0.945 -0.800982 0.400491 + 115000 -5584.4825 1223.5314 -6808.0139 1305.413 21904.363 -30442.927 293.40202 -578.05444 1.0328242 0.9425 -0.798863 0.3994315 + 120000 -5523.0074 1287.4784 -6810.4858 1458.6493 21678.215 -30441.67 308.73646 671.54744 1.0055922 0.94 -0.796744 0.398372 + 125000 -5523.9631 1261.6061 -6785.5692 1451.4065 21774.541 -30440.463 302.5323 943.71106 1.023251 0.9375 -0.794625 0.3973125 + 130000 -5480.6587 1228.3138 -6708.9725 1318.5357 22013.43 -30444.357 294.54883 -484.16808 1.0024483 0.935 -0.792506 0.396253 + 135000 -5515.4922 1236.63 -6752.1222 1405.2286 21838.239 -30444.636 296.54306 -33.044871 0.99099073 0.9325 -0.790387 0.3951935 + 140000 -5636.9585 1190.5857 -6827.5442 1401.0211 21837.041 -30443.664 285.50167 -131.26918 1.0073498 0.93 -0.788268 0.394134 + 145000 -5520.4299 1242.8162 -6763.246 1425.5354 21801.806 -30441.82 298.02649 375.70839 1.0055963 0.9275 -0.786149 0.3930745 + 150000 -5466.2108 1221.5587 -6687.7695 1315.243 22002.492 -30445.561 292.92898 -458.87734 1.0111682 0.925 -0.78403 0.392015 + 155000 -5461.822 1239.1272 -6700.9492 1371.2953 21931.804 -30440.608 297.14189 404.63471 1.02125 0.9225 -0.781911 0.3909555 + 160000 -5581.5531 1235.5332 -6817.0862 1387.24 21799.458 -30439.508 296.28004 -313.78406 1.005984 0.92 -0.779792 0.389896 + 165000 -5518.8078 1273.6502 -6792.4581 1375.9673 21862.55 -30442.152 305.42049 -35.844433 1.0122448 0.9175 -0.777673 0.3888365 + 170000 -5515.2831 1285.6763 -6800.9594 1404.6207 21813.634 -30442.455 308.30433 -58.986086 1.010512 0.915 -0.775554 0.387777 + 175000 -5547.8632 1237.0346 -6784.8979 1371.988 21866.075 -30441.096 296.64009 8.7538748 1.0204871 0.9125 -0.773435 0.3867175 + 180000 -5550.9154 1284.8683 -6835.7837 1386.3915 21803.513 -30444.858 308.11056 107.40069 1.0274352 0.91 -0.771316 0.385658 + 185000 -5536.9233 1270.2304 -6807.1538 1398.1504 21809.601 -30443.002 304.60042 -174.16652 0.99755738 0.9075 -0.769197 0.3845985 + 190000 -5518.9253 1280.5079 -6799.4332 1373.9909 21862.478 -30442.723 307.06496 9.6282943 1.0156746 0.905 -0.767078 0.383539 + 195000 -5574.7502 1214.359 -6789.1092 1411.3746 21807.743 -30442.797 291.20249 459.43071 1.0173851 0.9025 -0.764959 0.3824795 + 200000 -5586.1746 1230.4227 -6816.5973 1532.8087 21640.232 -30440.345 295.05456 1663.9344 1.0127589 0.9 -0.76284 0.38142 + 205000 -5530.762 1262.3017 -6793.0637 1421.2001 21765.141 -30437.136 302.69912 362.504 1.0112973 0.8975 -0.760721 0.3803605 + 210000 -5482.179 1264.6727 -6746.8517 1332.5039 21878.405 -30436.424 303.26767 -518.59319 1.0144674 0.895 -0.758602 0.379301 + 215000 -5548.4664 1254.2078 -6802.6742 1439.71 21751.539 -30437.604 300.7582 936.14316 1.0295052 0.8925 -0.756483 0.3782415 + 220000 -5566.4852 1224.3179 -6790.8031 1366.173 21833.016 -30437.139 293.59062 -368.10245 1.0080289 0.89 -0.754364 0.377182 + 225000 -5607.3792 1195.1042 -6802.4834 1434.8209 21716.922 -30436.88 286.58521 313.99343 1.0126994 0.8875 -0.752245 0.3761225 + 230000 -5685.3593 1214.5576 -6899.9169 1452.8971 21628.537 -30433.937 291.2501 -34.04353 1.0037164 0.885 -0.750126 0.375063 + 235000 -5458.1208 1277.1379 -6735.2588 1388.7878 21861.855 -30438.247 306.25684 26.373018 1.0027032 0.8825 -0.748007 0.3740035 + 240000 -5471.8252 1281.8041 -6753.6293 1442.5812 21792.96 -30437.921 307.37578 706.48275 1.0008045 0.88 -0.745888 0.372944 + 245000 -5459.3621 1258.1055 -6717.4676 1394.4965 21879.415 -30435.773 301.69286 446.21806 1.0155238 0.8775 -0.743769 0.3718845 + 250000 -5614.6519 1198.1053 -6812.7572 1397.7454 21767.081 -30436.857 287.30486 146.62072 1.0273533 0.875 -0.74165 0.370825 + 255000 -5573.1837 1250.4489 -6823.6325 1354.8074 21829.39 -30434.368 299.85681 -608.07208 1.0009113 0.8725 -0.739531 0.3697655 + 260000 -5630.451 1202.8398 -6833.2907 1380.657 21778.541 -30440.821 288.44019 -195.24451 1.019413 0.87 -0.737412 0.368706 + 265000 -5533.5948 1273.5591 -6807.1539 1419.8611 21794.887 -30438.706 305.39863 339.13963 1.0138164 0.8675 -0.735293 0.3676465 + 270000 -5640.803 1204.5526 -6845.3556 1495.5078 21652.609 -30438.707 288.85092 1463.7932 1.0356466 0.865 -0.733174 0.366587 + 275000 -5514.7021 1283.4057 -6798.1078 1340.6427 21864.301 -30436.815 307.75984 -449.32236 1.0128657 0.8625 -0.731055 0.3655275 + 280000 -5610.2442 1259.5217 -6869.7659 1411.1009 21686.723 -30440.226 302.03248 -123.59673 1.0128803 0.86 -0.728936 0.364468 + 285000 -5550.4897 1281.3066 -6831.7963 1373.2421 21810.977 -30438.399 307.25647 -248.99043 1.0185983 0.8575 -0.726817 0.3634085 + 290000 -5553.4882 1240.2591 -6793.7473 1391.9459 21802.734 -30437.51 297.4133 -158.86961 1.0031364 0.855 -0.724698 0.362349 + 295000 -5524.2791 1255.0193 -6779.2984 1449.4799 21776.57 -30434.687 300.95281 952.9175 1.0131377 0.8525 -0.722579 0.3612895 + 300000 -5476.0212 1284.8796 -6760.9008 1324.2729 21929.73 -30436.686 308.11327 -465.3353 1.0043923 0.85 -0.72046 0.36023 + 305000 -5438.0362 1298.3446 -6736.3809 1407.4391 21826.292 -30430.432 311.34219 517.43655 1.0077139 0.8475 -0.718341 0.3591705 + 310000 -5535.7453 1264.3612 -6800.1065 1343.2269 21832.58 -30432.621 303.19298 -745.84969 1.0074616 0.845 -0.716222 0.358111 + 315000 -5502.0889 1225.373 -6727.4619 1408.6878 21868.726 -30430.42 293.84363 391.97607 1.0057154 0.8425 -0.714103 0.3570515 + 320000 -5551.1885 1247.6582 -6798.8467 1441.5698 21745.518 -30434.212 299.18761 602.66464 1.0106275 0.84 -0.711984 0.355992 + 325000 -5472.7566 1268.0116 -6740.7682 1396.6033 21874.12 -30434.532 304.06836 68.811265 0.9970358 0.8375 -0.709865 0.3549325 + 330000 -5572.2981 1246.5687 -6818.8668 1407.6183 21773.909 -30431.719 298.92634 224.12439 1.0246504 0.835 -0.707746 0.353873 + 335000 -5499.3422 1205.6434 -6704.9856 1285.2624 21998.798 -30434.913 289.11249 -817.85014 1.0147781 0.8325 -0.705627 0.3528135 + 340000 -5562.2169 1219.1939 -6781.4108 1417.0604 21795.894 -30433.607 292.36189 174.41821 1.0058188 0.83 -0.703508 0.351754 + 345000 -5520.3776 1219.9601 -6740.3377 1367.4757 21877.315 -30431.491 292.54563 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302.36813 -161.29785 0.99503244 0.0675 -0.057213 0.0286065 + 1870000 -5623.139 1216.967 -6840.1059 1413.5807 21703.495 -30397.576 291.82788 76.112007 1.0246491 0.065 -0.055094 0.027547 + 1875000 -5450.2615 1268.385 -6718.6465 1405.9759 21866.321 -30398.11 304.15789 307.93878 0.99773745 0.0625 -0.052975 0.0264875 + 1880000 -5539.8922 1245.1416 -6785.0337 1409.1823 21774.294 -30395.574 298.58413 82.127006 1.0058947 0.06 -0.050856 0.025428 + 1885000 -5514.3045 1240.5608 -6754.8653 1443.7995 21752.107 -30397.218 297.48566 611.17045 1.0085937 0.0575 -0.048737 0.0243685 + 1890000 -5438.3073 1258.3645 -6696.6718 1361.8049 21892.331 -30397.348 301.75497 -267.35927 0.9953092 0.055 -0.046618 0.023309 + 1895000 -5596.2731 1226.9718 -6823.2449 1402.9241 21732.185 -30395.165 294.22702 44.339776 1.0153331 0.0525 -0.044499 0.0222495 + 1900000 -5497.1413 1266.3676 -6763.5089 1373.9826 21832.991 -30399.356 303.67411 -27.290874 1.0132323 0.05 -0.04238 0.02119 + 1905000 -5517.4875 1236.6892 -6754.1767 1367.726 21857.698 -30393.874 296.55726 -499.76394 0.99284077 0.0475 -0.040261 0.0201305 + 1910000 -5552.0873 1269.7208 -6821.8081 1378.8021 21718.781 -30396.478 304.4782 -369.12045 1.0171861 0.045 -0.038142 0.019071 + 1915000 -5499.6451 1278.5051 -6778.1502 1430.6032 21725.761 -30396.795 306.58468 577.53122 1.01326 0.0425 -0.036023 0.0180115 + 1920000 -5487.2658 1251.9078 -6739.1736 1381.7635 21779.483 -30396.642 300.20666 -47.157489 1.0090288 0.04 -0.033904 0.016952 + 1925000 -5538.2174 1250.4348 -6788.6522 1378.1601 21776.002 -30397.01 299.85343 -635.20274 0.98963246 0.0375 -0.031785 0.0158925 + 1930000 -5539.4427 1260.8629 -6800.3057 1358.8021 21770.968 -30400.271 302.3541 -702.50699 0.99578271 0.035 -0.029666 0.014833 + 1935000 -5559.5408 1246.2889 -6805.8297 1426.6663 21737.226 -30396.429 298.85926 214.01347 1.0055051 0.0325 -0.027547 0.0137735 + 1940000 -5527.5821 1225.3364 -6752.9184 1378.8724 21850.255 -30395.169 293.83485 14.506752 1.0028753 0.03 -0.025428 0.012714 + 1945000 -5473.5551 1280.9318 -6754.4869 1425.106 21803.831 -30396.584 307.16659 506.19708 1.0032233 0.0275 -0.023309 0.0116545 + 1950000 -5567.2517 1222.2431 -6789.4948 1305.8232 21889.919 -30396.867 293.09308 -1294.1142 0.99788741 0.025 -0.02119 0.010595 + 1955000 -5484.5853 1260.6694 -6745.2547 1384.597 21831.404 -30392.929 302.30769 156.43697 1.0117059 0.0225 -0.019071 0.0095355 + 1960000 -5620.4544 1193.7438 -6814.1983 1383.8209 21783.257 -30401.598 286.25899 -66.845911 1.0220849 0.02 -0.016952 0.008476 + 1965000 -5545.5269 1233.4885 -6779.0154 1344.2005 21855.912 -30398.255 295.78973 -628.47314 1.0059777 0.0175 -0.014833 0.0074165 + 1970000 -5513.9042 1266.1527 -6780.057 1392.318 21762.753 -30395.542 303.62259 75.831811 1.0061881 0.015 -0.012714 0.006357 + 1975000 -5544.7648 1274.4083 -6819.1731 1391.4464 21746.624 -30396.103 305.60227 -75.461691 1.0034389 0.0125 -0.010595 0.0052975 + 1980000 -5538.5817 1248.0952 -6786.6769 1364.256 21830.009 -30395.903 299.2924 -83.978588 1.0205031 0.01 -0.008476 0.004238 + 1985000 -5595.8323 1230.885 -6826.7174 1357.6211 21780.506 -30393.427 295.16542 -709.11924 1.0035546 0.0075 -0.006357 0.0031785 + 1990000 -5482.4794 1286.6658 -6769.1452 1336.3899 21858.921 -30393.729 308.54161 -827.89365 1.0005728 0.005 -0.004238 0.002119 + 1995000 -5501.4886 1239.738 -6741.2266 1409.7478 21799.031 -30400.217 297.28836 653.89683 1.0202266 0.0025 -0.002119 0.0010595 + 2000000 -5611.4713 1229.0661 -6840.5373 1478.3644 21615.338 -30394.928 294.72923 480.97836 1.00402 0 -0 0 +Loop time of 13776.2 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.543 ns/day, 1.913 hours/ns, 145.178 timesteps/s +95.3% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7579.8 | 8070.7 | 8564.2 | 287.6 | 58.58 +Bond | 24.942 | 25.514 | 26.056 | 6.9 | 0.19 +Kspace | 2484.3 | 2979.3 | 3459.7 | 467.2 | 21.63 +Neigh | 523.25 | 524.15 | 525.06 | 2.5 | 3.80 +Comm | 806.39 | 872.63 | 948.24 | 194.3 | 6.33 +Output | 0.033634 | 0.034536 | 0.042227 | 1.2 | 0.00 +Modify | 864.36 | 1044.2 | 1191.5 | 438.5 | 7.58 +Other | | 259.6 | | | 1.88 + +Nlocal: 150.000 ave 158 max 141 min +Histogram: 1 0 0 2 2 3 2 1 0 1 +Nghost: 6106.00 ave 6170 max 6046 min +Histogram: 2 1 1 1 0 1 2 2 1 1 +Neighs: 86710.6 ave 92374 max 78975 min +Histogram: 1 0 0 3 0 3 1 0 2 2 + +Total # of neighbors = 1040527 +Ave neighs/atom = 578.07056 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89189 +Dangerous builds = 0 +Total wall time: 4:00:09 diff --git a/examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp b/examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp new file mode 100644 index 0000000000..56d2994ec2 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp @@ -0,0 +1,72 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style hybrid lj/cut/coul/long 12.0 12.0 lj/cut/soft 2 0.5 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Hwh +pair_coeff 1 2 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Owh +pair_coeff 1 3 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Hw +pair_coeff 1 4 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Ow +pair_coeff 2 2 lj/cut/soft 0.155425 3.165500 1.0 # Owh Owh +pair_coeff 2 3 lj/cut/soft 0.000000 1.000000 1.0 # Owh Hw +pair_coeff 2 4 lj/cut/soft 0.155425 3.165500 1.0 # Owh Ow +pair_coeff 3 3 lj/cut/coul/long 0.000000 0.000000 # Hw Hw +pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # Hw Ow +pair_coeff 4 4 lj/cut/coul/long 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +set type 1*2 charge 0.0 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(1.0,0.0) + +fix ADAPT all adapt/fep 100000 & + pair lj/cut/soft lambda 1*2 3*4 v_lambda & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda + +variable dlambda equal -0.05 + +compute FEP all fep ${TK} & + pair lj/cut/soft lambda 1*2 3*4 v_dlambda & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10-lj.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/fep10/in-fep10-q.lmp b/examples/USER/fep/SPCEhyd/fep10/in-fep10-q.lmp new file mode 100644 index 0000000000..d9183f7f15 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/in-fep10-q.lmp @@ -0,0 +1,76 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style lj/cut/coul/long 12.0 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 0.000000 1.000000 # Hwh Hwh +pair_coeff 1 2 0.000000 1.000000 # Hwh Owh +pair_coeff 1 3 0.000000 1.000000 # Hwh Hw +pair_coeff 1 4 0.000000 1.000000 # Hwh Ow +pair_coeff 2 2 0.155425 3.165500 # Owh Owh +pair_coeff 2 3 0.000000 1.000000 # Owh Hw +pair_coeff 2 4 0.155425 3.165500 # Owh Ow +pair_coeff 3 3 0.000000 1.000000 # Hw Hw +pair_coeff 3 4 0.000000 1.000000 # Hw Ow +pair_coeff 4 4 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(1.0,0.0) +variable qH equal 0.4238*v_lambda +variable qO equal -0.8476*v_lambda + +fix ADAPT all adapt/fep 100000 & + atom charge 1 v_qH & + atom charge 2 v_qO & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_qO v_qH + +variable dlambda equal -0.05 +variable dqH equal 0.4238*v_dlambda +variable dqO equal -0.8476*v_dlambda + +compute FEP all fep ${TK} & + atom charge 1 v_dqH & + atom charge 2 v_dqO & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10-q.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/mols/data.lmp b/examples/USER/fep/SPCEhyd/mols/data.lmp new file mode 100644 index 0000000000..b6ead1d442 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/data.lmp @@ -0,0 +1,3635 @@ +created by fftool + +1800 atoms +1200 bonds +600 angles +4 atom types +1 bond types +1 angle types +0.000000 29.204526 xlo xhi +0.000000 29.204526 ylo yhi +0.000000 29.204526 zlo zhi + +Masses + + 1 1.008 # Hwh + 2 15.999 # Owh + 3 1.008 # Hw + 4 15.999 # Ow + +Bond Coeffs + + 1 517.630258 1.000000 # Ow-Hw + +Angle Coeffs + + 1 37.950526 109.470000 # Hw-Ow-Hw + +Atoms + + 1 1 1 0.423800 1.469233e+00 2.148142e+00 1.702038e+00 # Hwh SPCE + 2 1 2 -0.847600 1.979799e+00 1.409877e+00 2.142818e+00 # Owh SPCE + 3 1 1 0.423800 2.730865e+00 1.797090e+00 2.677576e+00 # Hwh SPCE + 4 2 3 0.423800 1.499900e+00 3.238303e+00 2.442531e+01 # Hw SPCE + 5 2 4 -0.847600 2.395752e+00 3.669948e+00 2.431980e+01 # Ow SPCE + 6 2 3 0.423800 2.296129e+00 4.663242e+00 2.437847e+01 # Hw SPCE + 7 3 3 0.423800 1.403661e+01 4.588770e+00 2.450878e+01 # Hw SPCE + 8 3 4 -0.847600 1.379951e+01 5.545591e+00 2.467695e+01 # Ow SPCE + 9 3 3 0.423800 1.402354e+01 6.091366e+00 2.386952e+01 # Hw SPCE + 10 4 3 0.423800 2.336049e+01 1.499786e+00 3.153124e+00 # Hw SPCE + 11 4 4 -0.847600 2.409385e+01 2.065977e+00 3.529439e+00 # Ow SPCE + 12 4 3 0.423800 2.490226e+01 1.500034e+00 3.691241e+00 # Hw SPCE + 13 5 3 0.423800 1.644196e+01 1.748367e+00 2.705436e+01 # Hw SPCE + 14 5 4 -0.847600 1.736546e+01 1.496062e+00 2.734329e+01 # Ow SPCE + 15 5 3 0.423800 1.783282e+01 2.301936e+00 2.770680e+01 # Hw SPCE + 16 6 3 0.423800 2.088933e+01 1.895579e+01 2.275309e+01 # Hw SPCE + 17 6 4 -0.847600 2.057929e+01 1.824793e+01 2.211841e+01 # Ow SPCE + 18 6 3 0.423800 1.984085e+01 1.772204e+01 2.254049e+01 # Hw SPCE + 19 7 3 0.423800 1.766189e+01 8.017800e+00 2.498964e+01 # Hw SPCE + 20 7 4 -0.847600 1.725196e+01 8.916174e+00 2.483189e+01 # Ow SPCE + 21 7 3 0.423800 1.625542e+01 8.836819e+00 2.485666e+01 # Hw SPCE + 22 8 3 0.423800 2.770687e+01 2.171554e+01 1.528009e+01 # Hw SPCE + 23 8 4 -0.847600 2.716811e+01 2.251048e+01 1.555905e+01 # Ow SPCE + 24 8 3 0.423800 2.770528e+01 2.307342e+01 1.618718e+01 # Hw SPCE + 25 9 3 0.423800 1.495385e+00 2.572800e+01 2.467279e+01 # Hw SPCE + 26 9 4 -0.847600 1.580382e+00 2.672428e+01 2.468743e+01 # Ow SPCE + 27 9 3 0.423800 1.767742e+00 2.702913e+01 2.562122e+01 # Hw SPCE + 28 10 3 0.423800 8.923646e+00 2.303176e+01 7.542360e+00 # Hw SPCE + 29 10 4 -0.847600 8.109007e+00 2.312152e+01 6.969379e+00 # Ow SPCE + 30 10 3 0.423800 7.298201e+00 2.288018e+01 7.502626e+00 # Hw SPCE + 31 11 3 0.423800 1.123659e+01 2.107791e+01 4.662100e+00 # Hw SPCE + 32 11 4 -0.847600 1.223538e+01 2.105512e+01 4.618509e+00 # Ow SPCE + 33 11 3 0.423800 1.259832e+01 2.069338e+01 5.477241e+00 # Hw SPCE + 34 12 3 0.423800 1.225298e+01 2.161218e+01 1.146502e+01 # Hw SPCE + 35 12 4 -0.847600 1.278626e+01 2.077538e+01 1.134100e+01 # Ow SPCE + 36 12 3 0.423800 1.216660e+01 1.999649e+01 1.124435e+01 # Hw SPCE + 37 13 3 0.423800 2.178085e+01 2.141393e+01 1.947311e+01 # Hw SPCE + 38 13 4 -0.847600 2.200950e+01 2.051108e+01 1.910897e+01 # Ow SPCE + 39 13 3 0.423800 2.190716e+01 1.982534e+01 1.982958e+01 # Hw SPCE + 40 14 3 0.423800 2.603847e+01 7.816317e+00 1.661274e+01 # Hw SPCE + 41 14 4 -0.847600 2.671903e+01 7.539282e+00 1.729103e+01 # Ow SPCE + 42 14 3 0.423800 2.712614e+01 6.667675e+00 1.701797e+01 # Hw SPCE + 43 15 3 0.423800 2.662104e+01 1.315276e+01 2.415551e+01 # Hw SPCE + 44 15 4 -0.847600 2.749092e+01 1.325361e+01 2.463837e+01 # Ow SPCE + 45 15 3 0.423800 2.770488e+01 1.422511e+01 2.474029e+01 # Hw SPCE + 46 16 3 0.423800 2.343696e+01 2.012869e+01 2.434140e+01 # Hw SPCE + 47 16 4 -0.847600 2.284311e+01 1.938463e+01 2.464753e+01 # Ow SPCE + 48 16 3 0.423800 2.328036e+01 1.889915e+01 2.540458e+01 # Hw SPCE + 49 17 3 0.423800 7.794521e+00 2.000989e+01 2.199182e+01 # Hw SPCE + 50 17 4 -0.847600 7.929378e+00 2.033080e+01 2.292928e+01 # Ow SPCE + 51 17 3 0.423800 8.857758e+00 2.010876e+01 2.322729e+01 # Hw SPCE + 52 18 3 0.423800 6.830410e+00 2.518010e+01 2.209866e+01 # Hw SPCE + 53 18 4 -0.847600 6.177519e+00 2.451264e+01 2.174056e+01 # Ow SPCE + 54 18 3 0.423800 6.309669e+00 2.363590e+01 2.220301e+01 # Hw SPCE + 55 19 3 0.423800 1.596377e+01 2.092461e+01 2.446023e+01 # Hw SPCE + 56 19 4 -0.847600 1.590738e+01 1.999342e+01 2.482037e+01 # Ow SPCE + 57 19 3 0.423800 1.681118e+01 1.956697e+01 2.478476e+01 # Hw SPCE + 58 20 3 0.423800 1.911326e+01 2.770546e+01 4.844631e+00 # Hw SPCE + 59 20 4 -0.847600 1.985915e+01 2.703939e+01 4.843586e+00 # Ow SPCE + 60 20 3 0.423800 2.073574e+01 2.752062e+01 4.840568e+00 # Hw SPCE + 61 21 3 0.423800 7.957677e+00 2.769262e+01 2.125162e+01 # Hw SPCE + 62 21 4 -0.847600 7.905132e+00 2.770650e+01 2.225015e+01 # Ow SPCE + 63 21 3 0.423800 8.829127e+00 2.770890e+01 2.263254e+01 # Hw SPCE + 64 22 3 0.423800 2.070265e+01 9.528473e+00 1.663276e+01 # Hw SPCE + 65 22 4 -0.847600 1.973165e+01 9.696078e+00 1.680328e+01 # Ow SPCE + 66 22 3 0.423800 1.934110e+01 8.919385e+00 1.729746e+01 # Hw SPCE + 67 23 3 0.423800 7.809959e+00 8.565464e+00 2.274346e+01 # Hw SPCE + 68 23 4 -0.847600 8.612896e+00 9.122442e+00 2.295575e+01 # Ow SPCE + 69 23 3 0.423800 9.372009e+00 8.852272e+00 2.236351e+01 # Hw SPCE + 70 24 3 0.423800 2.498899e+01 2.308095e+01 1.903531e+01 # Hw SPCE + 71 24 4 -0.847600 2.436019e+01 2.235497e+01 1.931382e+01 # Ow SPCE + 72 24 3 0.423800 2.484014e+01 2.170706e+01 1.990531e+01 # Hw SPCE + 73 25 3 0.423800 1.506895e+00 5.662694e+00 6.920599e+00 # Hw SPCE + 74 25 4 -0.847600 1.784503e+00 6.309796e+00 7.630665e+00 # Ow SPCE + 75 25 3 0.423800 2.707518e+00 6.641971e+00 7.436495e+00 # Hw SPCE + 76 26 3 0.423800 2.153403e+01 1.348159e+01 2.085837e+01 # Hw SPCE + 77 26 4 -0.847600 2.086248e+01 1.274077e+01 2.087218e+01 # Ow SPCE + 78 26 3 0.423800 2.067461e+01 1.247880e+01 2.181880e+01 # Hw SPCE + 79 27 3 0.423800 6.800685e+00 2.203104e+01 2.620499e+01 # Hw SPCE + 80 27 4 -0.847600 6.856841e+00 2.274258e+01 2.550459e+01 # Ow SPCE + 81 27 3 0.423800 6.369339e+00 2.244243e+01 2.468469e+01 # Hw SPCE + 82 28 3 0.423800 2.330650e+01 7.514481e+00 5.018724e+00 # Hw SPCE + 83 28 4 -0.847600 2.253073e+01 6.885276e+00 4.970822e+00 # Ow SPCE + 84 28 3 0.423800 2.286694e+01 5.944773e+00 4.921621e+00 # Hw SPCE + 85 29 3 0.423800 1.465322e+01 1.590735e+01 2.422856e+01 # Hw SPCE + 86 29 4 -0.847600 1.477140e+01 1.663018e+01 2.354771e+01 # Ow SPCE + 87 29 3 0.423800 1.453616e+01 1.751291e+01 2.395449e+01 # Hw SPCE + 88 30 3 0.423800 1.040291e+01 5.254847e+00 1.370622e+01 # Hw SPCE + 89 30 4 -0.847600 1.105724e+01 4.607844e+00 1.409768e+01 # Ow SPCE + 90 30 3 0.423800 1.077812e+01 3.674305e+00 1.387274e+01 # Hw SPCE + 91 31 3 0.423800 2.276938e+01 1.512055e+01 9.190561e+00 # Hw SPCE + 92 31 4 -0.847600 2.301556e+01 1.453653e+01 9.964062e+00 # Ow SPCE + 93 31 3 0.423800 2.340966e+01 1.368242e+01 9.624659e+00 # Hw SPCE + 94 32 3 0.423800 5.188719e+00 2.026958e+01 2.114125e+01 # Hw SPCE + 95 32 4 -0.847600 5.223057e+00 2.126505e+01 2.105256e+01 # Ow SPCE + 96 32 3 0.423800 4.292242e+00 2.162905e+01 2.101958e+01 # Hw SPCE + 97 33 3 0.423800 1.776246e+01 1.332125e+01 2.630655e+01 # Hw SPCE + 98 33 4 -0.847600 1.826497e+01 1.415453e+01 2.653702e+01 # Ow SPCE + 99 33 3 0.423800 1.924234e+01 1.400708e+01 2.638536e+01 # Hw SPCE + 100 34 3 0.423800 2.606566e+00 1.054762e+01 6.428992e+00 # Hw SPCE + 101 34 4 -0.847600 1.625220e+00 1.071787e+01 6.339693e+00 # Ow SPCE + 102 34 3 0.423800 1.425906e+00 1.104165e+01 5.414793e+00 # Hw SPCE + 103 35 3 0.423800 2.588493e+01 4.071742e+00 4.105367e+00 # Hw SPCE + 104 35 4 -0.847600 2.671121e+01 4.617835e+00 4.243387e+00 # Ow SPCE + 105 35 3 0.423800 2.741817e+01 4.051459e+00 4.666975e+00 # Hw SPCE + 106 36 3 0.423800 7.373843e+00 6.669901e+00 1.394201e+01 # Hw SPCE + 107 36 4 -0.847600 7.563042e+00 6.090000e+00 1.473442e+01 # Ow SPCE + 108 36 3 0.423800 7.053521e+00 6.429426e+00 1.552510e+01 # Hw SPCE + 109 37 3 0.423800 4.172482e+00 1.303888e+01 1.710824e+01 # Hw SPCE + 110 37 4 -0.847600 4.702018e+00 1.220690e+01 1.727375e+01 # Ow SPCE + 111 37 3 0.423800 4.203212e+00 1.141758e+01 1.691575e+01 # Hw SPCE + 112 38 3 0.423800 1.949787e+01 5.529973e+00 1.254239e+01 # Hw SPCE + 113 38 4 -0.847600 2.035077e+01 5.090120e+00 1.282362e+01 # Ow SPCE + 114 38 3 0.423800 2.089205e+01 4.864082e+00 1.201373e+01 # Hw SPCE + 115 39 3 0.423800 2.451616e+01 8.924670e+00 1.865568e+01 # Hw SPCE + 116 39 4 -0.847600 2.381451e+01 8.652982e+00 1.799699e+01 # Ow SPCE + 117 39 3 0.423800 2.311781e+01 9.367935e+00 1.793821e+01 # Hw SPCE + 118 40 3 0.423800 1.500065e+00 2.219167e+01 2.760505e+00 # Hw SPCE + 119 40 4 -0.847600 2.224501e+00 2.150236e+01 2.767217e+00 # Ow SPCE + 120 40 3 0.423800 1.817068e+00 2.059122e+01 2.829029e+00 # Hw SPCE + 121 41 3 0.423800 2.640554e+01 1.928714e+01 4.290644e+00 # Hw SPCE + 122 41 4 -0.847600 2.740415e+01 1.931798e+01 4.247967e+00 # Ow SPCE + 123 41 3 0.423800 2.770519e+01 2.026827e+01 4.168519e+00 # Hw SPCE + 124 42 3 0.423800 1.388747e+01 7.977813e+00 2.595555e+01 # Hw SPCE + 125 42 4 -0.847600 1.290644e+01 7.828209e+00 2.607882e+01 # Ow SPCE + 126 42 3 0.423800 1.244102e+01 8.710473e+00 2.614947e+01 # Hw SPCE + 127 43 3 0.423800 2.444541e+01 1.183745e+01 2.520365e+01 # Hw SPCE + 128 43 4 -0.847600 2.466934e+01 1.086365e+01 2.516413e+01 # Ow SPCE + 129 43 3 0.423800 2.566048e+01 1.075222e+01 2.509189e+01 # Hw SPCE + 130 44 3 0.423800 2.483417e+01 1.651695e+01 2.163120e+01 # Hw SPCE + 131 44 4 -0.847600 2.410271e+01 1.585943e+01 2.145058e+01 # Ow SPCE + 132 44 3 0.423800 2.445847e+01 1.492995e+01 2.154809e+01 # Hw SPCE + 133 45 3 0.423800 1.730263e+01 2.595540e+01 3.740298e+00 # Hw SPCE + 134 45 4 -0.847600 1.773679e+01 2.510003e+01 4.022883e+00 # Ow SPCE + 135 45 3 0.423800 1.770998e+01 2.444677e+01 3.266223e+00 # Hw SPCE + 136 46 3 0.423800 1.064666e+01 1.544703e+00 2.342635e+01 # Hw SPCE + 137 46 4 -0.847600 9.658303e+00 1.485990e+00 2.356670e+01 # Ow SPCE + 138 46 3 0.423800 9.290506e+00 2.400694e+00 2.373415e+01 # Hw SPCE + 139 47 3 0.423800 6.958351e+00 1.058272e+01 2.770522e+01 # Hw SPCE + 140 47 4 -0.847600 7.092574e+00 1.157367e+01 2.770263e+01 # Ow SPCE + 141 47 3 0.423800 6.203030e+00 1.203050e+01 2.769941e+01 # Hw SPCE + 142 48 3 0.423800 3.958262e+00 4.358392e+00 8.337038e+00 # Hw SPCE + 143 48 4 -0.847600 3.059091e+00 3.923448e+00 8.385147e+00 # Ow SPCE + 144 48 3 0.423800 3.110013e+00 3.117001e+00 8.974257e+00 # Hw SPCE + 145 49 3 0.423800 2.527221e+01 1.981465e+01 9.871580e+00 # Hw SPCE + 146 49 4 -0.847600 2.589272e+01 1.903608e+01 9.965427e+00 # Ow SPCE + 147 49 3 0.423800 2.675477e+01 1.934357e+01 1.036832e+01 # Hw SPCE + 148 50 3 0.423800 2.513678e+01 1.655111e+01 8.455263e+00 # Hw SPCE + 149 50 4 -0.847600 2.439311e+01 1.719386e+01 8.271354e+00 # Ow SPCE + 150 50 3 0.423800 2.390732e+01 1.691348e+01 7.443466e+00 # Hw SPCE + 151 51 3 0.423800 9.547080e+00 5.818685e+00 7.837619e+00 # Hw SPCE + 152 51 4 -0.847600 9.188230e+00 4.885428e+00 7.821533e+00 # Ow SPCE + 153 51 3 0.423800 9.947239e+00 4.237539e+00 7.757147e+00 # Hw SPCE + 154 52 3 0.423800 1.913212e+01 1.999545e+01 1.375657e+01 # Hw SPCE + 155 52 4 -0.847600 1.977845e+01 1.954444e+01 1.437208e+01 # Ow SPCE + 156 52 3 0.423800 2.009170e+01 1.868964e+01 1.395831e+01 # Hw SPCE + 157 53 3 0.423800 2.488521e+00 4.298268e+00 1.662022e+01 # Hw SPCE + 158 53 4 -0.847600 3.439105e+00 4.019650e+00 1.675720e+01 # Ow SPCE + 159 53 3 0.423800 3.840963e+00 4.558416e+00 1.749763e+01 # Hw SPCE + 160 54 3 0.423800 8.720856e+00 1.200478e+01 2.905857e+00 # Hw SPCE + 161 54 4 -0.847600 8.109727e+00 1.255626e+01 2.338060e+00 # Ow SPCE + 162 54 3 0.423800 7.159796e+00 1.233215e+01 2.555793e+00 # Hw SPCE + 163 55 3 0.423800 1.270857e+01 1.035303e+01 5.382569e+00 # Hw SPCE + 164 55 4 -0.847600 1.322488e+01 9.496640e+00 5.388255e+00 # Ow SPCE + 165 55 3 0.423800 1.305339e+01 9.009733e+00 6.244710e+00 # Hw SPCE + 166 56 3 0.423800 1.684898e+01 2.523462e+01 1.822162e+01 # Hw SPCE + 167 56 4 -0.847600 1.664347e+01 2.603725e+01 1.878158e+01 # Ow SPCE + 168 56 3 0.423800 1.648466e+01 2.575236e+01 1.972689e+01 # Hw SPCE + 169 57 3 0.423800 1.020796e+01 2.594114e+01 7.868994e+00 # Hw SPCE + 170 57 4 -0.847600 1.048594e+01 2.681088e+01 8.276773e+00 # Ow SPCE + 171 57 3 0.423800 1.003609e+01 2.692243e+01 9.162888e+00 # Hw SPCE + 172 58 3 0.423800 2.300209e+01 1.144525e+01 1.973611e+01 # Hw SPCE + 173 58 4 -0.847600 2.326720e+01 1.069841e+01 2.034599e+01 # Ow SPCE + 174 58 3 0.423800 2.274079e+01 1.075787e+01 2.119414e+01 # Hw SPCE + 175 59 3 0.423800 1.609161e+01 1.214359e+01 1.492237e+00 # Hw SPCE + 176 59 4 -0.847600 1.690824e+01 1.157531e+01 1.593113e+00 # Ow SPCE + 177 59 3 0.423800 1.664177e+01 1.065885e+01 1.891605e+00 # Hw SPCE + 178 60 3 0.423800 2.419902e+01 2.411706e+01 6.611761e+00 # Hw SPCE + 179 60 4 -0.847600 2.467864e+01 2.498895e+01 6.710596e+00 # Ow SPCE + 180 60 3 0.423800 2.544873e+01 2.487644e+01 7.338537e+00 # Hw SPCE + 181 61 3 0.423800 1.196568e+01 5.594696e+00 6.473038e+00 # Hw SPCE + 182 61 4 -0.847600 1.199305e+01 6.536579e+00 6.807864e+00 # Ow SPCE + 183 61 3 0.423800 1.267510e+01 6.612062e+00 7.535263e+00 # Hw SPCE + 184 62 3 0.423800 1.669021e+01 8.472310e+00 7.036663e+00 # Hw SPCE + 185 62 4 -0.847600 1.572284e+01 8.690729e+00 6.908251e+00 # Ow SPCE + 186 62 3 0.423800 1.554585e+01 9.621300e+00 7.228737e+00 # Hw SPCE + 187 63 3 0.423800 1.821528e+01 1.487703e+01 1.756524e+01 # Hw SPCE + 188 63 4 -0.847600 1.872911e+01 1.551055e+01 1.814370e+01 # Ow SPCE + 189 63 3 0.423800 1.854708e+01 1.644985e+01 1.785290e+01 # Hw SPCE + 190 64 3 0.423800 7.984302e+00 1.799893e+01 1.529353e+00 # Hw SPCE + 191 64 4 -0.847600 8.826448e+00 1.746123e+01 1.488465e+00 # Ow SPCE + 192 64 3 0.423800 9.462122e+00 1.778360e+01 2.189889e+00 # Hw SPCE + 193 65 3 0.423800 2.562243e+01 6.741416e+00 1.403530e+01 # Hw SPCE + 194 65 4 -0.847600 2.622983e+01 6.086036e+00 1.448423e+01 # Ow SPCE + 195 65 3 0.423800 2.717413e+01 6.262256e+00 1.420632e+01 # Hw SPCE + 196 66 3 0.423800 2.512713e+01 2.094793e+00 1.358574e+01 # Hw SPCE + 197 66 4 -0.847600 2.434949e+01 1.495442e+00 1.339585e+01 # Ow SPCE + 198 66 3 0.423800 2.355565e+01 1.803117e+00 1.392040e+01 # Hw SPCE + 199 67 3 0.423800 9.301908e+00 1.331503e+01 2.358584e+01 # Hw SPCE + 200 67 4 -0.847600 8.584183e+00 1.395669e+01 2.331540e+01 # Ow SPCE + 201 67 3 0.423800 8.271122e+00 1.373659e+01 2.239153e+01 # Hw SPCE + 202 68 3 0.423800 9.955846e+00 1.273829e+01 6.296276e+00 # Hw SPCE + 203 68 4 -0.847600 1.056341e+01 1.199023e+01 6.029323e+00 # Ow SPCE + 204 68 3 0.423800 1.029850e+01 1.165171e+01 5.126425e+00 # Hw SPCE + 205 69 3 0.423800 1.595831e+01 4.015404e+00 2.177868e+01 # Hw SPCE + 206 69 4 -0.847600 1.665439e+01 3.881186e+00 2.248398e+01 # Ow SPCE + 207 69 3 0.423800 1.647833e+01 4.501446e+00 2.324836e+01 # Hw SPCE + 208 70 3 0.423800 1.191249e+01 1.053961e+01 1.614692e+01 # Hw SPCE + 209 70 4 -0.847600 1.285965e+01 1.031522e+01 1.591770e+01 # Ow SPCE + 210 70 3 0.423800 1.326240e+01 1.106545e+01 1.539335e+01 # Hw SPCE + 211 71 3 0.423800 2.756106e+01 7.219592e+00 3.733621e+00 # Hw SPCE + 212 71 4 -0.847600 2.673030e+01 7.191784e+00 3.177694e+00 # Ow SPCE + 213 71 3 0.423800 2.592863e+01 7.212180e+00 3.775112e+00 # Hw SPCE + 214 72 3 0.423800 1.619051e+01 4.555961e+00 1.375257e+01 # Hw SPCE + 215 72 4 -0.847600 1.693660e+01 4.702954e+00 1.310315e+01 # Ow SPCE + 216 72 3 0.423800 1.692272e+01 3.981627e+00 1.241069e+01 # Hw SPCE + 217 73 3 0.423800 2.233085e+01 2.254376e+01 2.509491e+01 # Hw SPCE + 218 73 4 -0.847600 2.137546e+01 2.283349e+01 2.503760e+01 # Ow SPCE + 219 73 3 0.423800 2.132827e+01 2.383218e+01 2.505737e+01 # Hw SPCE + 220 74 3 0.423800 4.614385e+00 2.266996e+01 1.754496e+01 # Hw SPCE + 221 74 4 -0.847600 5.529231e+00 2.271822e+01 1.794587e+01 # Ow SPCE + 222 74 3 0.423800 6.044304e+00 2.345795e+01 1.751287e+01 # Hw SPCE + 223 75 3 0.423800 2.221903e+01 7.556525e+00 1.516871e+01 # Hw SPCE + 224 75 4 -0.847600 2.250349e+01 7.635346e+00 1.421326e+01 # Ow SPCE + 225 75 3 0.423800 2.176672e+01 7.313720e+00 1.361852e+01 # Hw SPCE + 226 76 3 0.423800 2.629759e+01 1.920638e+01 2.353714e+01 # Hw SPCE + 227 76 4 -0.847600 2.715395e+01 1.902228e+01 2.401958e+01 # Ow SPCE + 228 76 3 0.423800 2.770506e+01 1.837985e+01 2.348707e+01 # Hw SPCE + 229 77 3 0.423800 4.143809e+00 1.561555e+01 8.018737e+00 # Hw SPCE + 230 77 4 -0.847600 4.614959e+00 1.553180e+01 8.896805e+00 # Ow SPCE + 231 77 3 0.423800 4.199222e+00 1.615528e+01 9.558946e+00 # Hw SPCE + 232 78 3 0.423800 9.954198e+00 1.261788e+01 1.237010e+01 # Hw SPCE + 233 78 4 -0.847600 9.562880e+00 1.353598e+01 1.243307e+01 # Ow SPCE + 234 78 3 0.423800 8.569485e+00 1.346921e+01 1.252638e+01 # Hw SPCE + 235 79 3 0.423800 2.332846e+01 2.323923e+01 3.781581e+00 # Hw SPCE + 236 79 4 -0.847600 2.276687e+01 2.256928e+01 3.296002e+00 # Ow SPCE + 237 79 3 0.423800 2.333089e+01 2.178393e+01 3.040806e+00 # Hw SPCE + 238 80 3 0.423800 1.563376e+01 9.681389e+00 1.524542e+01 # Hw SPCE + 239 80 4 -0.847600 1.641808e+01 9.172361e+00 1.559999e+01 # Ow SPCE + 240 80 3 0.423800 1.655877e+01 9.404722e+00 1.656239e+01 # Hw SPCE + 241 81 3 0.423800 3.016047e+00 1.608090e+01 2.770691e+01 # Hw SPCE + 242 81 4 -0.847600 3.873141e+00 1.658768e+01 2.761432e+01 # Ow SPCE + 243 81 3 0.423800 4.041570e+00 1.678405e+01 2.664837e+01 # Hw SPCE + 244 82 3 0.423800 2.553862e+01 1.927894e+01 1.283389e+01 # Hw SPCE + 245 82 4 -0.847600 2.595825e+01 2.010455e+01 1.321108e+01 # Ow SPCE + 246 82 3 0.423800 2.694466e+01 1.996635e+01 1.329986e+01 # Hw SPCE + 247 83 3 0.423800 1.446078e+01 5.122478e+00 1.975466e+01 # Hw SPCE + 248 83 4 -0.847600 1.399157e+01 5.719286e+00 1.910377e+01 # Ow SPCE + 249 83 3 0.423800 1.387428e+01 6.626403e+00 1.950797e+01 # Hw SPCE + 250 84 3 0.423800 4.975267e+00 1.195188e+01 1.361200e+01 # Hw SPCE + 251 84 4 -0.847600 5.863360e+00 1.223599e+01 1.397335e+01 # Ow SPCE + 252 84 3 0.423800 6.001585e+00 1.182880e+01 1.487617e+01 # Hw SPCE + 253 85 3 0.423800 1.729394e+01 2.690297e+01 2.489413e+01 # Hw SPCE + 254 85 4 -0.847600 1.798622e+01 2.618717e+01 2.498570e+01 # Ow SPCE + 255 85 3 0.423800 1.753851e+01 2.531197e+01 2.516899e+01 # Hw SPCE + 256 86 3 0.423800 1.443295e+01 1.369845e+01 9.542794e+00 # Hw SPCE + 257 86 4 -0.847600 1.453225e+01 1.337010e+01 1.048212e+01 # Ow SPCE + 258 86 3 0.423800 1.407152e+01 1.248767e+01 1.057721e+01 # Hw SPCE + 259 87 3 0.423800 1.481041e+01 9.892914e+00 2.769929e+01 # Hw SPCE + 260 87 4 -0.847600 1.474545e+01 1.089078e+01 2.770556e+01 # Ow SPCE + 261 87 3 0.423800 1.566461e+01 1.128460e+01 2.771213e+01 # Hw SPCE + 262 88 3 0.423800 2.711944e+01 2.239741e+00 7.551846e+00 # Hw SPCE + 263 88 4 -0.847600 2.613715e+01 2.417616e+00 7.610794e+00 # Ow SPCE + 264 88 3 0.423800 2.588056e+01 2.557524e+00 8.567132e+00 # Hw SPCE + 265 89 3 0.423800 1.579109e+01 5.900382e+00 6.668995e+00 # Hw SPCE + 266 89 4 -0.847600 1.499190e+01 6.158630e+00 6.126217e+00 # Ow SPCE + 267 89 3 0.423800 1.487648e+01 5.510338e+00 5.373624e+00 # Hw SPCE + 268 90 3 0.423800 2.133610e+01 1.746297e+01 9.335501e+00 # Hw SPCE + 269 90 4 -0.847600 2.057506e+01 1.754198e+01 8.691632e+00 # Ow SPCE + 270 90 3 0.423800 2.092169e+01 1.747499e+01 7.756026e+00 # Hw SPCE + 271 91 3 0.423800 5.764508e+00 6.459756e+00 1.799860e+01 # Hw SPCE + 272 91 4 -0.847600 6.332363e+00 5.967190e+00 1.865808e+01 # Ow SPCE + 273 91 3 0.423800 6.766765e+00 6.620913e+00 1.927772e+01 # Hw SPCE + 274 92 3 0.423800 1.519730e+01 1.983322e+01 1.921450e+01 # Hw SPCE + 275 92 4 -0.847600 1.593017e+01 1.916543e+01 1.908429e+01 # Ow SPCE + 276 92 3 0.423800 1.663520e+01 1.955553e+01 1.849204e+01 # Hw SPCE + 277 93 3 0.423800 2.313253e+00 7.250692e+00 1.329362e+01 # Hw SPCE + 278 93 4 -0.847600 1.488319e+00 7.811762e+00 1.322518e+01 # Ow SPCE + 279 93 3 0.423800 1.540991e+00 8.563456e+00 1.388259e+01 # Hw SPCE + 280 94 3 0.423800 2.611731e+01 1.202552e+01 1.053768e+01 # Hw SPCE + 281 94 4 -0.847600 2.710862e+01 1.215596e+01 1.052099e+01 # Ow SPCE + 282 94 3 0.423800 2.756049e+01 1.126726e+01 1.044331e+01 # Hw SPCE + 283 95 3 0.423800 6.603696e+00 2.054040e+01 1.298798e+01 # Hw SPCE + 284 95 4 -0.847600 5.882293e+00 2.028304e+01 1.234506e+01 # Ow SPCE + 285 95 3 0.423800 6.172577e+00 2.050160e+01 1.141341e+01 # Hw SPCE + 286 96 3 0.423800 2.098737e+01 6.874062e+00 1.013861e+01 # Hw SPCE + 287 96 4 -0.847600 2.156028e+01 7.451122e+00 1.072066e+01 # Ow SPCE + 288 96 3 0.423800 2.195352e+01 8.190100e+00 1.017360e+01 # Hw SPCE + 289 97 3 0.423800 5.786826e+00 1.087307e+01 1.086502e+01 # Hw SPCE + 290 97 4 -0.847600 6.324427e+00 1.163284e+01 1.123071e+01 # Ow SPCE + 291 97 3 0.423800 7.142246e+00 1.127568e+01 1.168194e+01 # Hw SPCE + 292 98 3 0.423800 1.143842e+01 2.119323e+01 8.871945e+00 # Hw SPCE + 293 98 4 -0.847600 1.139221e+01 2.127877e+01 7.876682e+00 # Ow SPCE + 294 98 3 0.423800 1.071119e+01 2.064007e+01 7.518516e+00 # Hw SPCE + 295 99 3 0.423800 5.459585e+00 2.383383e+01 5.598160e+00 # Hw SPCE + 296 99 4 -0.847600 5.520099e+00 2.482379e+01 5.470403e+00 # Ow SPCE + 297 99 3 0.423800 5.586370e+00 2.503046e+01 4.494238e+00 # Hw SPCE + 298 100 3 0.423800 2.264458e+00 7.960990e+00 2.770952e+01 # Hw SPCE + 299 100 4 -0.847600 2.090525e+00 8.160734e+00 2.674523e+01 # Ow SPCE + 300 100 3 0.423800 1.495909e+00 7.454707e+00 2.636058e+01 # Hw SPCE + 301 101 3 0.423800 7.095393e+00 1.940453e+01 2.544132e+01 # Hw SPCE + 302 101 4 -0.847600 6.237306e+00 1.963392e+01 2.498190e+01 # Ow SPCE + 303 101 3 0.423800 5.644089e+00 1.882911e+01 2.496253e+01 # Hw SPCE + 304 102 3 0.423800 1.499078e+00 3.404424e+00 2.770580e+01 # Hw SPCE + 305 102 4 -0.847600 2.042815e+00 3.910224e+00 2.703609e+01 # Ow SPCE + 306 102 3 0.423800 1.977853e+00 4.889953e+00 2.722559e+01 # Hw SPCE + 307 103 3 0.423800 5.115452e+00 2.292057e+01 1.247440e+01 # Hw SPCE + 308 103 4 -0.847600 5.773141e+00 2.354653e+01 1.205533e+01 # Ow SPCE + 309 103 3 0.423800 6.680714e+00 2.312664e+01 1.205713e+01 # Hw SPCE + 310 104 3 0.423800 1.944181e+01 2.324594e+01 1.499570e+00 # Hw SPCE + 311 104 4 -0.847600 2.043993e+01 2.318469e+01 1.499022e+00 # Ow SPCE + 312 104 3 0.423800 2.071487e+01 2.222323e+01 1.498289e+00 # Hw SPCE + 313 105 3 0.423800 1.030626e+01 8.957281e+00 6.373247e+00 # Hw SPCE + 314 105 4 -0.847600 9.786014e+00 8.104555e+00 6.326252e+00 # Ow SPCE + 315 105 3 0.423800 8.880748e+00 8.243851e+00 6.727613e+00 # Hw SPCE + 316 106 3 0.423800 1.864859e+01 1.763094e+00 1.290621e+01 # Hw SPCE + 317 106 4 -0.847600 1.923656e+01 2.571543e+00 1.287976e+01 # Ow SPCE + 318 106 3 0.423800 2.017824e+01 2.292795e+00 1.269123e+01 # Hw SPCE + 319 107 3 0.423800 2.129031e+00 5.623946e+00 1.104896e+01 # Hw SPCE + 320 107 4 -0.847600 1.506474e+00 5.035776e+00 1.053275e+01 # Ow SPCE + 321 107 3 0.423800 1.486177e+00 4.126233e+00 1.094786e+01 # Hw SPCE + 322 108 3 0.423800 2.212734e+01 1.355457e+01 3.475366e+00 # Hw SPCE + 323 108 4 -0.847600 2.189942e+01 1.348653e+01 4.446665e+00 # Ow SPCE + 324 108 3 0.423800 2.141982e+01 1.431518e+01 4.735327e+00 # Hw SPCE + 325 109 3 0.423800 2.714041e+01 9.226233e+00 1.942138e+01 # Hw SPCE + 326 109 4 -0.847600 2.695029e+01 1.019981e+01 1.954785e+01 # Ow SPCE + 327 109 3 0.423800 2.770446e+01 1.073827e+01 1.917198e+01 # Hw SPCE + 328 110 3 0.423800 1.145913e+01 1.921390e+01 1.496917e+01 # Hw SPCE + 329 110 4 -0.847600 1.131470e+01 2.018773e+01 1.479367e+01 # Ow SPCE + 330 110 3 0.423800 1.033642e+01 2.036578e+01 1.468754e+01 # Hw SPCE + 331 111 3 0.423800 4.274133e+00 2.306189e+00 2.713568e+01 # Hw SPCE + 332 111 4 -0.847600 4.237246e+00 1.500039e+00 2.654512e+01 # Ow SPCE + 333 111 3 0.423800 3.652688e+00 1.690998e+00 2.575656e+01 # Hw SPCE + 334 112 3 0.423800 2.374365e+01 4.285483e+00 2.548838e+01 # Hw SPCE + 335 112 4 -0.847600 2.363447e+01 3.410101e+00 2.501744e+01 # Ow SPCE + 336 112 3 0.423800 2.453520e+01 3.022399e+00 2.482154e+01 # Hw SPCE + 337 113 3 0.423800 2.147633e+01 2.400029e+01 6.981339e+00 # Hw SPCE + 338 113 4 -0.847600 2.070482e+01 2.460854e+01 6.794782e+00 # Ow SPCE + 339 113 3 0.423800 2.100757e+01 2.555958e+01 6.856910e+00 # Hw SPCE + 340 114 3 0.423800 2.475952e+01 2.542350e+01 2.655084e+01 # Hw SPCE + 341 114 4 -0.847600 2.490466e+01 2.505812e+01 2.563137e+01 # Ow SPCE + 342 114 3 0.423800 2.404295e+01 2.469469e+01 2.527727e+01 # Hw SPCE + 343 115 3 0.423800 2.160335e+01 2.393199e+01 1.009846e+01 # Hw SPCE + 344 115 4 -0.847600 2.078275e+01 2.449002e+01 1.022179e+01 # Ow SPCE + 345 115 3 0.423800 2.003750e+01 2.411294e+01 9.671860e+00 # Hw SPCE + 346 116 3 0.423800 1.865506e+01 2.117845e+01 1.756982e+01 # Hw SPCE + 347 116 4 -0.847600 1.807847e+01 2.183151e+01 1.707884e+01 # Ow SPCE + 348 116 3 0.423800 1.837699e+01 2.276271e+01 1.728801e+01 # Hw SPCE + 349 117 3 0.423800 2.061645e+00 6.549304e+00 1.814025e+01 # Hw SPCE + 350 117 4 -0.847600 1.475173e+00 6.253958e+00 1.889446e+01 # Ow SPCE + 351 117 3 0.423800 1.571483e+00 5.267187e+00 1.902487e+01 # Hw SPCE + 352 118 3 0.423800 1.643494e+01 1.386321e+01 1.572937e+01 # Hw SPCE + 353 118 4 -0.847600 1.600041e+01 1.308756e+01 1.527161e+01 # Ow SPCE + 354 118 3 0.423800 1.500654e+01 1.318983e+01 1.531362e+01 # Hw SPCE + 355 119 3 0.423800 1.886154e+01 1.359977e+01 1.388201e+01 # Hw SPCE + 356 119 4 -0.847600 1.985547e+01 1.361236e+01 1.399129e+01 # Ow SPCE + 357 119 3 0.423800 2.020182e+01 1.267429e+01 1.399938e+01 # Hw SPCE + 358 120 3 0.423800 2.640146e+01 4.249195e+00 1.244508e+01 # Hw SPCE + 359 120 4 -0.847600 2.716791e+01 3.811578e+00 1.291523e+01 # Ow SPCE + 360 120 3 0.423800 2.770629e+01 3.285544e+00 1.225687e+01 # Hw SPCE + 361 121 3 0.423800 1.496812e+00 1.814687e+00 1.782668e+01 # Hw SPCE + 362 121 4 -0.847600 1.815569e+00 1.693357e+00 1.876672e+01 # Ow SPCE + 363 121 3 0.423800 1.625725e+00 2.522412e+00 1.929267e+01 # Hw SPCE + 364 122 3 0.423800 2.680988e+01 1.869516e+01 7.392907e+00 # Hw SPCE + 365 122 4 -0.847600 2.739577e+01 1.944655e+01 7.696489e+00 # Ow SPCE + 366 122 3 0.423800 2.770460e+01 1.997015e+01 6.902469e+00 # Hw SPCE + 367 123 3 0.423800 6.657051e+00 1.748551e+01 3.900748e+00 # Hw SPCE + 368 123 4 -0.847600 7.611764e+00 1.740782e+01 4.187954e+00 # Ow SPCE + 369 123 3 0.423800 7.719232e+00 1.780597e+01 5.098957e+00 # Hw SPCE + 370 124 3 0.423800 1.712795e+01 2.364901e+01 2.137752e+01 # Hw SPCE + 371 124 4 -0.847600 1.651270e+01 2.309626e+01 2.193960e+01 # Ow SPCE + 372 124 3 0.423800 1.702767e+01 2.235135e+01 2.236376e+01 # Hw SPCE + 373 125 3 0.423800 2.465960e+01 9.111990e+00 1.552092e+00 # Hw SPCE + 374 125 4 -0.847600 2.368347e+01 9.328956e+00 1.542385e+00 # Ow SPCE + 375 125 3 0.423800 2.356287e+01 1.032079e+01 1.500818e+00 # Hw SPCE + 376 126 3 0.423800 1.541633e+01 2.513037e+01 2.342964e+01 # Hw SPCE + 377 126 4 -0.847600 1.496712e+01 2.563480e+01 2.416705e+01 # Ow SPCE + 378 126 3 0.423800 1.407826e+01 2.521990e+01 2.436140e+01 # Hw SPCE + 379 127 3 0.423800 2.198927e+01 2.296037e+01 1.264179e+01 # Hw SPCE + 380 127 4 -0.847600 2.135361e+01 2.220618e+01 1.280650e+01 # Ow SPCE + 381 127 3 0.423800 2.142262e+01 2.154325e+01 1.206101e+01 # Hw SPCE + 382 128 3 0.423800 5.808379e+00 1.479597e+00 1.729754e+01 # Hw SPCE + 383 128 4 -0.847600 5.311955e+00 2.244876e+00 1.770731e+01 # Ow SPCE + 384 128 3 0.423800 4.490271e+00 1.903163e+00 1.816345e+01 # Hw SPCE + 385 129 3 0.423800 4.410407e+00 9.586919e+00 1.489573e+01 # Hw SPCE + 386 129 4 -0.847600 4.330005e+00 8.939478e+00 1.413786e+01 # Ow SPCE + 387 129 3 0.423800 5.226071e+00 8.810656e+00 1.371305e+01 # Hw SPCE + 388 130 3 0.423800 8.119198e+00 3.621439e+00 1.317752e+01 # Hw SPCE + 389 130 4 -0.847600 8.167483e+00 2.832111e+00 1.256545e+01 # Ow SPCE + 390 130 3 0.423800 7.317941e+00 2.308454e+00 1.262918e+01 # Hw SPCE + 391 131 3 0.423800 1.605369e+01 6.725170e+00 2.132125e+01 # Hw SPCE + 392 131 4 -0.847600 1.601692e+01 7.081523e+00 2.225488e+01 # Ow SPCE + 393 131 3 0.423800 1.677297e+01 7.720235e+00 2.239787e+01 # Hw SPCE + 394 132 3 0.423800 2.587812e+01 2.770384e+01 6.790070e+00 # Hw SPCE + 395 132 4 -0.847600 2.495789e+01 2.770683e+01 6.398688e+00 # Ow SPCE + 396 132 3 0.423800 2.428216e+01 2.770348e+01 7.135826e+00 # Hw SPCE + 397 133 3 0.423800 3.242275e+00 2.430164e+01 3.033818e+00 # Hw SPCE + 398 133 4 -0.847600 3.385077e+00 2.527679e+01 2.864385e+00 # Ow SPCE + 399 133 3 0.423800 4.115488e+00 2.539474e+01 2.191640e+00 # Hw SPCE + 400 134 3 0.423800 1.391872e+01 1.853150e+01 1.389147e+01 # Hw SPCE + 401 134 4 -0.847600 1.350915e+01 1.835748e+01 1.299594e+01 # Ow SPCE + 402 134 3 0.423800 1.277157e+01 1.768895e+01 1.309098e+01 # Hw SPCE + 403 135 3 0.423800 1.883256e+00 1.950562e+01 6.097187e+00 # Hw SPCE + 404 135 4 -0.847600 2.108048e+00 1.853214e+01 6.139671e+00 # Ow SPCE + 405 135 3 0.423800 1.664096e+00 1.805416e+01 5.381755e+00 # Hw SPCE + 406 136 3 0.423800 1.772073e+01 1.904358e+01 6.835467e+00 # Hw SPCE + 407 136 4 -0.847600 1.848360e+01 1.839868e+01 6.881595e+00 # Ow SPCE + 408 136 3 0.423800 1.815821e+01 1.748070e+01 6.654789e+00 # Hw SPCE + 409 137 3 0.423800 1.668142e+01 1.746799e+01 2.770692e+01 # Hw SPCE + 410 137 4 -0.847600 1.690378e+01 1.739205e+01 2.673492e+01 # Ow SPCE + 411 137 3 0.423800 1.607886e+01 1.715496e+01 2.622181e+01 # Hw SPCE + 412 138 3 0.423800 6.510214e+00 5.350768e+00 8.615350e+00 # Hw SPCE + 413 138 4 -0.847600 6.301757e+00 6.322395e+00 8.727089e+00 # Ow SPCE + 414 138 3 0.423800 7.064288e+00 6.868862e+00 8.380795e+00 # Hw SPCE + 415 139 3 0.423800 1.123604e+01 1.437475e+01 2.577805e+01 # Hw SPCE + 416 139 4 -0.847600 1.147623e+01 1.512029e+01 2.639973e+01 # Ow SPCE + 417 139 3 0.423800 1.064787e+01 1.561484e+01 2.666285e+01 # Hw SPCE + 418 140 3 0.423800 1.018251e+01 2.301900e+01 2.071248e+01 # Hw SPCE + 419 140 4 -0.847600 1.073103e+01 2.232837e+01 2.118382e+01 # Ow SPCE + 420 140 3 0.423800 1.020516e+01 2.148141e+01 2.126196e+01 # Hw SPCE + 421 141 3 0.423800 5.434060e+00 2.503928e+00 1.462372e+01 # Hw SPCE + 422 141 4 -0.847600 6.195222e+00 3.000981e+00 1.504034e+01 # Ow SPCE + 423 141 3 0.423800 5.916457e+00 3.943344e+00 1.522539e+01 # Hw SPCE + 424 142 3 0.423800 2.396703e+01 1.692595e+01 1.892427e+01 # Hw SPCE + 425 142 4 -0.847600 2.487591e+01 1.651107e+01 1.888188e+01 # Ow SPCE + 426 142 3 0.423800 2.528573e+01 1.669671e+01 1.798880e+01 # Hw SPCE + 427 143 3 0.423800 1.739023e+01 2.770535e+01 2.756282e+01 # Hw SPCE + 428 143 4 -0.847600 1.824208e+01 2.718404e+01 2.761360e+01 # Ow SPCE + 429 143 3 0.423800 1.803237e+01 2.621369e+01 2.773377e+01 # Hw SPCE + 430 144 3 0.423800 1.002054e+01 2.068443e+00 2.080057e+01 # Hw SPCE + 431 144 4 -0.847600 1.037196e+01 1.499358e+00 2.005717e+01 # Ow SPCE + 432 144 3 0.423800 1.137167e+01 1.499631e+00 2.008118e+01 # Hw SPCE + 433 145 3 0.423800 5.474756e+00 6.597903e+00 2.212606e+01 # Hw SPCE + 434 145 4 -0.847600 6.060290e+00 6.454103e+00 2.292385e+01 # Ow SPCE + 435 145 3 0.423800 5.607820e+00 5.830491e+00 2.356133e+01 # Hw SPCE + 436 146 3 0.423800 9.616079e+00 2.770577e+01 1.272301e+01 # Hw SPCE + 437 146 4 -0.847600 1.005389e+01 2.758118e+01 1.183261e+01 # Ow SPCE + 438 146 3 0.423800 1.104172e+01 2.770510e+01 1.192665e+01 # Hw SPCE + 439 147 3 0.423800 7.556371e+00 8.751423e+00 1.067315e+01 # Hw SPCE + 440 147 4 -0.847600 6.677067e+00 8.276682e+00 1.071118e+01 # Ow SPCE + 441 147 3 0.423800 6.692592e+00 7.605177e+00 1.145202e+01 # Hw SPCE + 442 148 3 0.423800 1.048902e+01 9.944021e+00 1.499856e+00 # Hw SPCE + 443 148 4 -0.847600 1.107788e+01 9.135791e+00 1.497048e+00 # Ow SPCE + 444 148 3 0.423800 1.051214e+01 8.311210e+00 1.495741e+00 # Hw SPCE + 445 149 3 0.423800 2.225224e+01 1.699334e+01 1.388572e+01 # Hw SPCE + 446 149 4 -0.847600 2.247601e+01 1.610910e+01 1.347578e+01 # Ow SPCE + 447 149 3 0.423800 2.332230e+01 1.619040e+01 1.294930e+01 # Hw SPCE + 448 150 3 0.423800 1.629210e+01 2.770573e+01 8.693261e+00 # Hw SPCE + 449 150 4 -0.847600 1.560110e+01 2.709673e+01 8.303856e+00 # Ow SPCE + 450 150 3 0.423800 1.580582e+01 2.615242e+01 8.561464e+00 # Hw SPCE + 451 151 3 0.423800 2.423080e+01 1.358698e+01 1.852585e+01 # Hw SPCE + 452 151 4 -0.847600 2.350560e+01 1.411138e+01 1.897204e+01 # Ow SPCE + 453 151 3 0.423800 2.267128e+01 1.406026e+01 1.842312e+01 # Hw SPCE + 454 152 3 0.423800 2.207406e+01 4.433705e+00 2.065867e+01 # Hw SPCE + 455 152 4 -0.847600 2.276959e+01 3.724600e+00 2.054287e+01 # Ow SPCE + 456 152 3 0.423800 2.359197e+01 4.126886e+00 2.014056e+01 # Hw SPCE + 457 153 3 0.423800 2.395702e+01 6.074153e+00 1.705293e+01 # Hw SPCE + 458 153 4 -0.847600 2.358426e+01 5.192507e+00 1.734233e+01 # Ow SPCE + 459 153 3 0.423800 2.433467e+01 4.558278e+00 1.752846e+01 # Hw SPCE + 460 154 3 0.423800 1.155557e+01 2.807646e+00 1.636444e+01 # Hw SPCE + 461 154 4 -0.847600 1.146110e+01 1.812305e+00 1.638374e+01 # Ow SPCE + 462 154 3 0.423800 1.138045e+01 1.503463e+00 1.733143e+01 # Hw SPCE + 463 155 3 0.423800 4.135912e+00 2.531900e+01 1.818837e+01 # Hw SPCE + 464 155 4 -0.847600 3.741676e+00 2.521934e+01 1.910196e+01 # Ow SPCE + 465 155 3 0.423800 4.213837e+00 2.448559e+01 1.959050e+01 # Hw SPCE + 466 156 3 0.423800 1.499258e+00 1.198985e+01 2.578979e+01 # Hw SPCE + 467 156 4 -0.847600 2.062832e+00 1.128002e+01 2.536727e+01 # Ow SPCE + 468 156 3 0.423800 1.537875e+00 1.043123e+01 2.530414e+01 # Hw SPCE + 469 157 3 0.423800 6.788951e+00 2.673524e+01 2.771333e+01 # Hw SPCE + 470 157 4 -0.847600 6.736475e+00 2.763375e+01 2.727752e+01 # Ow SPCE + 471 157 3 0.423800 5.853127e+00 2.773069e+01 2.681893e+01 # Hw SPCE + 472 158 3 0.423800 4.823100e+00 1.350860e+01 6.387855e+00 # Hw SPCE + 473 158 4 -0.847600 4.369663e+00 1.263897e+01 6.583146e+00 # Ow SPCE + 474 158 3 0.423800 4.571234e+00 1.236153e+01 7.522508e+00 # Hw SPCE + 475 159 3 0.423800 2.652742e+01 8.643512e+00 1.208390e+01 # Hw SPCE + 476 159 4 -0.847600 2.750728e+01 8.461636e+00 1.216639e+01 # Ow SPCE + 477 159 3 0.423800 2.770441e+01 7.539751e+00 1.183282e+01 # Hw SPCE + 478 160 3 0.423800 1.562548e+01 7.342341e+00 1.368183e+01 # Hw SPCE + 479 160 4 -0.847600 1.644892e+01 7.724632e+00 1.326255e+01 # Ow SPCE + 480 160 3 0.423800 1.657765e+01 7.324209e+00 1.235531e+01 # Hw SPCE + 481 161 3 0.423800 1.832876e+01 3.664241e+00 1.523424e+01 # Hw SPCE + 482 161 4 -0.847600 1.757342e+01 3.228540e+00 1.572376e+01 # Ow SPCE + 483 161 3 0.423800 1.723220e+01 2.455027e+00 1.518968e+01 # Hw SPCE + 484 162 3 0.423800 1.163979e+01 2.726442e+01 5.638394e+00 # Hw SPCE + 485 162 4 -0.847600 1.203117e+01 2.637033e+01 5.856191e+00 # Ow SPCE + 486 162 3 0.423800 1.265936e+01 2.646077e+01 6.628973e+00 # Hw SPCE + 487 163 3 0.423800 3.712836e+00 1.795600e+01 2.104265e+01 # Hw SPCE + 488 163 4 -0.847600 3.729339e+00 1.776723e+01 2.202453e+01 # Ow SPCE + 489 163 3 0.423800 2.793088e+00 1.774262e+01 2.237500e+01 # Hw SPCE + 490 164 3 0.423800 1.215495e+01 1.501989e+00 9.660698e+00 # Hw SPCE + 491 164 4 -0.847600 1.306022e+01 1.479590e+00 9.236442e+00 # Ow SPCE + 492 164 3 0.423800 1.376231e+01 1.546750e+00 9.945354e+00 # Hw SPCE + 493 165 3 0.423800 1.382068e+01 2.627313e+01 1.928618e+01 # Hw SPCE + 494 165 4 -0.847600 1.369118e+01 2.724037e+01 1.950452e+01 # Ow SPCE + 495 165 3 0.423800 1.457266e+01 2.771119e+01 1.946813e+01 # Hw SPCE + 496 166 3 0.423800 1.936570e+01 1.864386e+01 2.521456e+01 # Hw SPCE + 497 166 4 -0.847600 2.026756e+01 1.895792e+01 2.551126e+01 # Ow SPCE + 498 166 3 0.423800 2.023242e+01 1.993867e+01 2.570334e+01 # Hw SPCE + 499 167 3 0.423800 1.169885e+01 2.172581e+00 2.751632e+01 # Hw SPCE + 500 167 4 -0.847600 1.090011e+01 1.573456e+00 2.746098e+01 # Ow SPCE + 501 167 3 0.423800 1.061137e+01 1.490153e+00 2.650720e+01 # Hw SPCE + 502 168 3 0.423800 1.911213e+01 2.158443e+01 1.022983e+01 # Hw SPCE + 503 168 4 -0.847600 1.926141e+01 2.060202e+01 1.011766e+01 # Ow SPCE + 504 168 3 0.423800 1.928483e+01 2.016370e+01 1.101617e+01 # Hw SPCE + 505 169 3 0.423800 1.629210e+00 1.550801e+01 1.095958e+01 # Hw SPCE + 506 169 4 -0.847600 1.493041e+00 1.635194e+01 1.147846e+01 # Ow SPCE + 507 169 3 0.423800 2.168035e+00 1.703190e+01 1.119204e+01 # Hw SPCE + 508 170 3 0.423800 1.102279e+01 4.173853e+00 1.869068e+01 # Hw SPCE + 509 170 4 -0.847600 1.109242e+01 4.502781e+00 1.963246e+01 # Ow SPCE + 510 170 3 0.423800 1.122948e+01 5.493340e+00 1.963029e+01 # Hw SPCE + 511 171 3 0.423800 8.600246e+00 2.481675e+01 1.935975e+01 # Hw SPCE + 512 171 4 -0.847600 8.003650e+00 2.561907e+01 1.934092e+01 # Ow SPCE + 513 171 3 0.423800 7.051209e+00 2.532446e+01 1.926308e+01 # Hw SPCE + 514 172 3 0.423800 7.877713e+00 1.822785e+01 1.950056e+01 # Hw SPCE + 515 172 4 -0.847600 6.923133e+00 1.800620e+01 1.930144e+01 # Ow SPCE + 516 172 3 0.423800 6.847202e+00 1.767403e+01 1.836128e+01 # Hw SPCE + 517 173 3 0.423800 2.715931e+01 1.264839e+01 1.341405e+01 # Hw SPCE + 518 173 4 -0.847600 2.734880e+01 1.167554e+01 1.328112e+01 # Ow SPCE + 519 173 3 0.423800 2.648989e+01 1.118630e+01 1.312977e+01 # Hw SPCE + 520 174 3 0.423800 1.482572e+01 8.447714e+00 1.055548e+01 # Hw SPCE + 521 174 4 -0.847600 1.531227e+01 7.960482e+00 9.830314e+00 # Ow SPCE + 522 174 3 0.423800 1.465158e+01 7.577469e+00 9.184724e+00 # Hw SPCE + 523 175 3 0.423800 6.350160e+00 1.781671e+00 2.021119e+01 # Hw SPCE + 524 175 4 -0.847600 5.554766e+00 1.449580e+00 2.071820e+01 # Ow SPCE + 525 175 3 0.423800 4.990992e+00 2.226040e+00 2.099974e+01 # Hw SPCE + 526 176 3 0.423800 2.360588e+01 2.124534e+01 1.405838e+01 # Hw SPCE + 527 176 4 -0.847600 2.343533e+01 2.028764e+01 1.429017e+01 # Ow SPCE + 528 176 3 0.423800 2.247062e+01 2.007410e+01 1.413605e+01 # Hw SPCE + 529 177 3 0.423800 2.476177e+01 9.495265e+00 2.278084e+01 # Hw SPCE + 530 177 4 -0.847600 2.490594e+01 9.103976e+00 2.187194e+01 # Ow SPCE + 531 177 3 0.423800 2.584301e+01 8.762128e+00 2.180102e+01 # Hw SPCE + 532 178 3 0.423800 2.124801e+01 1.026202e+01 1.226324e+01 # Hw SPCE + 533 178 4 -0.847600 2.175978e+01 1.061858e+01 1.304488e+01 # Ow SPCE + 534 178 3 0.423800 2.143033e+01 1.018622e+01 1.388424e+01 # Hw SPCE + 535 179 3 0.423800 2.770461e+01 2.265303e+01 1.897481e+01 # Hw SPCE + 536 179 4 -0.847600 2.771622e+01 2.165817e+01 1.887413e+01 # Ow SPCE + 537 179 3 0.423800 2.699937e+01 2.137944e+01 1.823504e+01 # Hw SPCE + 538 180 3 0.423800 1.752412e+00 1.211560e+01 2.448378e+00 # Hw SPCE + 539 180 4 -0.847600 2.192876e+00 1.124630e+01 2.672646e+00 # Ow SPCE + 540 180 3 0.423800 1.502189e+00 1.052455e+01 2.717762e+00 # Hw SPCE + 541 181 3 0.423800 2.066796e+01 9.492666e+00 1.990433e+01 # Hw SPCE + 542 181 4 -0.847600 1.987345e+01 1.007578e+01 1.973481e+01 # Ow SPCE + 543 181 3 0.423800 1.945518e+01 1.033091e+01 2.060657e+01 # Hw SPCE + 544 182 3 0.423800 7.526139e+00 1.353553e+01 1.705107e+01 # Hw SPCE + 545 182 4 -0.847600 7.411920e+00 1.404119e+01 1.619593e+01 # Ow SPCE + 546 182 3 0.423800 7.814322e+00 1.495172e+01 1.629081e+01 # Hw SPCE + 547 183 3 0.423800 5.320834e+00 2.489018e+01 2.627333e+01 # Hw SPCE + 548 183 4 -0.847600 4.512268e+00 2.533586e+01 2.665751e+01 # Ow SPCE + 549 183 3 0.423800 3.697906e+00 2.503309e+01 2.616239e+01 # Hw SPCE + 550 184 3 0.423800 2.555518e+01 2.496555e+01 1.499745e+00 # Hw SPCE + 551 184 4 -0.847600 2.580931e+01 2.400607e+01 1.621410e+00 # Ow SPCE + 552 184 3 0.423800 2.498688e+01 2.343773e+01 1.596790e+00 # Hw SPCE + 553 185 3 0.423800 4.020936e+00 8.516876e+00 4.121746e+00 # Hw SPCE + 554 185 4 -0.847600 3.704058e+00 9.464727e+00 4.155894e+00 # Ow SPCE + 555 185 3 0.423800 4.491592e+00 1.008053e+01 4.131828e+00 # Hw SPCE + 556 186 3 0.423800 1.411577e+01 1.487915e+00 1.833251e+01 # Hw SPCE + 557 186 4 -0.847600 1.431943e+01 2.462252e+00 1.842837e+01 # Ow SPCE + 558 186 3 0.423800 1.347701e+01 2.990756e+00 1.832346e+01 # Hw SPCE + 559 187 3 0.423800 3.071401e+00 9.241825e+00 1.816214e+01 # Hw SPCE + 560 187 4 -0.847600 3.300129e+00 8.845865e+00 1.727282e+01 # Ow SPCE + 561 187 3 0.423800 2.487941e+00 8.845219e+00 1.668942e+01 # Hw SPCE + 562 188 3 0.423800 1.493937e+00 2.324979e+01 2.604098e+01 # Hw SPCE + 563 188 4 -0.847600 1.544148e+00 2.354108e+01 2.699630e+01 # Ow SPCE + 564 188 3 0.423800 1.493692e+00 2.273962e+01 2.759223e+01 # Hw SPCE + 565 189 3 0.423800 2.402950e+01 7.504644e+00 1.192867e+01 # Hw SPCE + 566 189 4 -0.847600 2.413727e+01 6.710938e+00 1.132999e+01 # Ow SPCE + 567 189 3 0.423800 2.508872e+01 6.403895e+00 1.135159e+01 # Hw SPCE + 568 190 3 0.423800 8.545646e+00 3.156383e+00 9.861230e+00 # Hw SPCE + 569 190 4 -0.847600 9.351073e+00 2.611171e+00 1.009367e+01 # Ow SPCE + 570 190 3 0.423800 1.011166e+01 3.219788e+00 1.031971e+01 # Hw SPCE + 571 191 3 0.423800 1.499645e+00 2.645193e+01 1.809386e+01 # Hw SPCE + 572 191 4 -0.847600 1.941124e+00 2.732475e+01 1.788582e+01 # Ow SPCE + 573 191 3 0.423800 2.336801e+00 2.770568e+01 1.872148e+01 # Hw SPCE + 574 192 3 0.423800 1.070874e+01 1.082303e+01 1.860632e+01 # Hw SPCE + 575 192 4 -0.847600 1.140325e+01 1.152845e+01 1.874785e+01 # Ow SPCE + 576 192 3 0.423800 1.230497e+01 1.110065e+01 1.881024e+01 # Hw SPCE + 577 193 3 0.423800 1.341290e+01 1.795517e+01 2.013626e+01 # Hw SPCE + 578 193 4 -0.847600 1.307952e+01 1.701238e+01 2.013931e+01 # Ow SPCE + 579 193 3 0.423800 1.309126e+01 1.665771e+01 2.107422e+01 # Hw SPCE + 580 194 3 0.423800 4.807785e+00 9.950438e+00 2.034530e+01 # Hw SPCE + 581 194 4 -0.847600 5.368387e+00 9.471078e+00 2.102053e+01 # Ow SPCE + 582 194 3 0.423800 6.091190e+00 8.962304e+00 2.055288e+01 # Hw SPCE + 583 195 3 0.423800 4.581666e+00 2.365989e+01 9.523923e+00 # Hw SPCE + 584 195 4 -0.847600 4.035775e+00 2.430184e+01 1.006236e+01 # Ow SPCE + 585 195 3 0.423800 3.083838e+00 2.426678e+01 9.758078e+00 # Hw SPCE + 586 196 3 0.423800 1.996454e+01 2.420988e+01 1.557209e+01 # Hw SPCE + 587 196 4 -0.847600 2.025724e+01 2.408856e+01 1.462361e+01 # Ow SPCE + 588 196 3 0.423800 2.091875e+01 2.479965e+01 1.438538e+01 # Hw SPCE + 589 197 3 0.423800 3.003372e+00 1.643713e+01 1.704879e+01 # Hw SPCE + 590 197 4 -0.847600 2.577322e+00 1.558424e+01 1.735056e+01 # Ow SPCE + 591 197 3 0.423800 1.583596e+00 1.569510e+01 1.736541e+01 # Hw SPCE + 592 198 3 0.423800 8.582183e+00 2.224273e+01 1.027837e+01 # Hw SPCE + 593 198 4 -0.847600 8.111157e+00 2.153125e+01 9.756897e+00 # Ow SPCE + 594 198 3 0.423800 8.773035e+00 2.084403e+01 9.457494e+00 # Hw SPCE + 595 199 3 0.423800 9.338267e+00 1.004752e+01 1.312920e+01 # Hw SPCE + 596 199 4 -0.847600 8.797900e+00 9.207329e+00 1.308363e+01 # Ow SPCE + 597 199 3 0.423800 7.916778e+00 9.352906e+00 1.353355e+01 # Hw SPCE + 598 200 3 0.423800 2.194779e+01 1.497417e+00 2.193037e+01 # Hw SPCE + 599 200 4 -0.847600 2.223387e+01 1.544058e+00 2.288744e+01 # Ow SPCE + 600 200 3 0.423800 2.323149e+01 1.499141e+00 2.293970e+01 # Hw SPCE + 601 201 3 0.423800 6.357928e+00 6.228009e+00 5.806627e+00 # Hw SPCE + 602 201 4 -0.847600 6.047437e+00 7.177648e+00 5.848827e+00 # Ow SPCE + 603 201 3 0.423800 6.617086e+00 7.741462e+00 5.250820e+00 # Hw SPCE + 604 202 3 0.423800 1.593029e+01 1.490608e+01 1.881990e+00 # Hw SPCE + 605 202 4 -0.847600 1.499401e+01 1.512044e+01 1.603720e+00 # Ow SPCE + 606 202 3 0.423800 1.441686e+01 1.431299e+01 1.725826e+00 # Hw SPCE + 607 203 3 0.423800 2.152874e+01 7.128493e+00 1.779600e+01 # Hw SPCE + 608 203 4 -0.847600 2.073272e+01 6.564299e+00 1.757685e+01 # Ow SPCE + 609 203 3 0.423800 2.013013e+01 6.514325e+00 1.837333e+01 # Hw SPCE + 610 204 3 0.423800 1.867722e+01 1.499875e+00 1.016897e+01 # Hw SPCE + 611 204 4 -0.847600 1.948249e+01 2.057017e+00 9.966143e+00 # Ow SPCE + 612 204 3 0.423800 2.030669e+01 1.498892e+00 1.006198e+01 # Hw SPCE + 613 205 3 0.423800 2.316922e+01 1.367353e+01 6.885430e+00 # Hw SPCE + 614 205 4 -0.847600 2.260716e+01 1.285895e+01 7.028829e+00 # Ow SPCE + 615 205 3 0.423800 2.319607e+01 1.205233e+01 7.079429e+00 # Hw SPCE + 616 206 3 0.423800 1.724802e+01 2.452784e+01 1.522277e+01 # Hw SPCE + 617 206 4 -0.847600 1.695269e+01 2.377047e+01 1.464039e+01 # Ow SPCE + 618 206 3 0.423800 1.764677e+01 2.305066e+01 1.465218e+01 # Hw SPCE + 619 207 3 0.423800 2.411268e+01 4.355955e+00 1.477705e+01 # Hw SPCE + 620 207 4 -0.847600 2.346927e+01 5.080864e+00 1.453102e+01 # Ow SPCE + 621 207 3 0.423800 2.313742e+01 4.930075e+00 1.359982e+01 # Hw SPCE + 622 208 3 0.423800 4.859519e+00 1.208976e+01 2.528815e+01 # Hw SPCE + 623 208 4 -0.847600 4.768744e+00 1.304357e+01 2.557451e+01 # Ow SPCE + 624 208 3 0.423800 3.968809e+00 1.313902e+01 2.616696e+01 # Hw SPCE + 625 209 3 0.423800 1.172825e+01 2.418010e+01 2.667409e+01 # Hw SPCE + 626 209 4 -0.847600 1.132283e+01 2.504940e+01 2.639133e+01 # Ow SPCE + 627 209 3 0.423800 1.154586e+01 2.522495e+01 2.543246e+01 # Hw SPCE + 628 210 3 0.423800 1.341122e+01 2.770513e+01 2.770549e+01 # Hw SPCE + 629 210 4 -0.847600 1.245960e+01 2.739875e+01 2.768238e+01 # Ow SPCE + 630 210 3 0.423800 1.204322e+01 2.766958e+01 2.681446e+01 # Hw SPCE + 631 211 3 0.423800 1.145241e+01 8.302455e+00 1.779676e+01 # Hw SPCE + 632 211 4 -0.847600 1.125478e+01 7.343016e+00 1.759571e+01 # Ow SPCE + 633 211 3 0.423800 1.210977e+01 6.857989e+00 1.741202e+01 # Hw SPCE + 634 212 3 0.423800 1.287925e+01 1.297774e+01 2.765935e+01 # Hw SPCE + 635 212 4 -0.847600 1.230585e+01 1.215930e+01 2.769630e+01 # Ow SPCE + 636 212 3 0.423800 1.134277e+01 1.242772e+01 2.771694e+01 # Hw SPCE + 637 213 3 0.423800 1.353894e+01 1.030050e+01 8.981176e+00 # Hw SPCE + 638 213 4 -0.847600 1.336051e+01 1.105021e+01 8.343917e+00 # Ow SPCE + 639 213 3 0.423800 1.239877e+01 1.103348e+01 8.070479e+00 # Hw SPCE + 640 214 3 0.423800 1.379608e+01 1.561648e+01 4.066143e+00 # Hw SPCE + 641 214 4 -0.847600 1.425485e+01 1.494262e+01 4.645317e+00 # Ow SPCE + 642 214 3 0.423800 1.500310e+01 1.538348e+01 5.141055e+00 # Hw SPCE + 643 215 3 0.423800 1.743267e+01 1.012996e+01 9.164174e+00 # Hw SPCE + 644 215 4 -0.847600 1.689952e+01 1.019764e+01 1.000748e+01 # Ow SPCE + 645 215 3 0.423800 1.610254e+01 1.078129e+01 9.852029e+00 # Hw SPCE + 646 216 3 0.423800 2.449752e+01 2.458848e+01 1.376845e+01 # Hw SPCE + 647 216 4 -0.847600 2.528553e+01 2.495639e+01 1.426210e+01 # Ow SPCE + 648 216 3 0.423800 2.534289e+01 2.452894e+01 1.516431e+01 # Hw SPCE + 649 217 3 0.423800 1.840558e+01 3.099439e+00 2.461987e+01 # Hw SPCE + 650 217 4 -0.847600 1.888190e+01 2.411523e+00 2.516749e+01 # Ow SPCE + 651 217 3 0.423800 1.859125e+01 1.498335e+00 2.488182e+01 # Hw SPCE + 652 218 3 0.423800 2.313333e+01 2.163166e+01 2.205864e+01 # Hw SPCE + 653 218 4 -0.847600 2.219594e+01 2.130927e+01 2.219041e+01 # Ow SPCE + 654 218 3 0.423800 2.158294e+01 2.209428e+01 2.227978e+01 # Hw SPCE + 655 219 3 0.423800 1.229832e+01 6.995752e+00 1.467363e+01 # Hw SPCE + 656 219 4 -0.847600 1.306529e+01 6.454869e+00 1.432837e+01 # Ow SPCE + 657 219 3 0.423800 1.350970e+01 5.982810e+00 1.508972e+01 # Hw SPCE + 658 220 3 0.423800 1.406803e+01 2.706445e+00 1.555541e+00 # Hw SPCE + 659 220 4 -0.847600 1.438807e+01 3.652120e+00 1.498299e+00 # Ow SPCE + 660 220 3 0.423800 1.360529e+01 4.272470e+00 1.547574e+00 # Hw SPCE + 661 221 3 0.423800 1.346094e+01 1.584618e+01 1.101422e+01 # Hw SPCE + 662 221 4 -0.847600 1.417123e+01 1.647755e+01 1.070299e+01 # Ow SPCE + 663 221 3 0.423800 1.506879e+01 1.605138e+01 1.081592e+01 # Hw SPCE + 664 222 3 0.423800 6.578749e+00 2.770463e+01 1.007095e+01 # Hw SPCE + 665 222 4 -0.847600 5.578913e+00 2.770497e+01 1.008903e+01 # Ow SPCE + 666 222 3 0.423800 5.245578e+00 2.676237e+01 1.010848e+01 # Hw SPCE + 667 223 3 0.423800 2.346524e+01 1.409205e+01 2.397168e+01 # Hw SPCE + 668 223 4 -0.847600 2.273539e+01 1.354071e+01 2.356753e+01 # Ow SPCE + 669 223 3 0.423800 2.313609e+01 1.282550e+01 2.299489e+01 # Hw SPCE + 670 224 3 0.423800 9.455855e+00 2.740531e+01 2.770496e+01 # Hw SPCE + 671 224 4 -0.847600 9.370999e+00 2.698567e+01 2.680125e+01 # Ow SPCE + 672 224 3 0.423800 9.379656e+00 2.769893e+01 2.610040e+01 # Hw SPCE + 673 225 3 0.423800 1.739219e+01 2.174463e+01 3.666550e+00 # Hw SPCE + 674 225 4 -0.847600 1.786402e+01 2.143690e+01 2.840303e+00 # Ow SPCE + 675 225 3 0.423800 1.877157e+01 2.109408e+01 3.082833e+00 # Hw SPCE + 676 226 3 0.423800 2.616571e+01 6.000875e+00 7.270531e+00 # Hw SPCE + 677 226 4 -0.847600 2.581662e+01 5.090419e+00 7.048703e+00 # Ow SPCE + 678 226 3 0.423800 2.500801e+01 5.176179e+00 6.466644e+00 # Hw SPCE + 679 227 3 0.423800 2.463564e+01 9.703885e+00 1.039308e+01 # Hw SPCE + 680 227 4 -0.847600 2.383949e+01 1.018568e+01 1.002699e+01 # Ow SPCE + 681 227 3 0.423800 2.359408e+01 1.093724e+01 1.063930e+01 # Hw SPCE + 682 228 3 0.423800 2.177044e+01 1.687390e+01 2.431866e+01 # Hw SPCE + 683 228 4 -0.847600 2.133664e+01 1.645723e+01 2.511753e+01 # Ow SPCE + 684 228 3 0.423800 2.195993e+01 1.578987e+01 2.552514e+01 # Hw SPCE + 685 229 3 0.423800 7.726348e+00 3.560323e+00 2.179374e+01 # Hw SPCE + 686 229 4 -0.847600 6.861868e+00 4.061639e+00 2.183058e+01 # Ow SPCE + 687 229 3 0.423800 6.645800e+00 4.420653e+00 2.092261e+01 # Hw SPCE + 688 230 3 0.423800 1.884037e+01 1.499599e+00 6.252581e+00 # Hw SPCE + 689 230 4 -0.847600 1.965401e+01 2.001138e+00 6.546590e+00 # Ow SPCE + 690 230 3 0.423800 2.008019e+01 1.523837e+00 7.315065e+00 # Hw SPCE + 691 231 3 0.423800 6.715548e+00 3.056808e+00 2.444232e+01 # Hw SPCE + 692 231 4 -0.847600 6.554914e+00 2.209760e+00 2.393566e+01 # Ow SPCE + 693 231 3 0.423800 6.112326e+00 1.542117e+00 2.453429e+01 # Hw SPCE + 694 232 3 0.423800 1.335233e+01 8.701900e+00 2.332491e+01 # Hw SPCE + 695 232 4 -0.847600 1.284324e+01 9.531573e+00 2.355397e+01 # Ow SPCE + 696 232 3 0.423800 1.192981e+01 9.484446e+00 2.314971e+01 # Hw SPCE + 697 233 3 0.423800 1.642811e+01 5.397368e+00 2.093058e+00 # Hw SPCE + 698 233 4 -0.847600 1.732324e+01 5.692575e+00 1.759011e+00 # Ow SPCE + 699 233 3 0.423800 1.732664e+01 6.686459e+00 1.648636e+00 # Hw SPCE + 700 234 3 0.423800 8.746384e+00 1.194555e+01 1.502826e+01 # Hw SPCE + 701 234 4 -0.847600 8.569902e+00 1.110875e+01 1.554655e+01 # Ow SPCE + 702 234 3 0.423800 9.214489e+00 1.104644e+01 1.630854e+01 # Hw SPCE + 703 235 3 0.423800 2.671040e+01 2.277390e+01 2.443136e+01 # Hw SPCE + 704 235 4 -0.847600 2.634248e+01 2.188483e+01 2.415900e+01 # Ow SPCE + 705 235 3 0.423800 2.540832e+01 2.199999e+01 2.382124e+01 # Hw SPCE + 706 236 3 0.423800 4.314700e+00 6.656624e+00 1.567087e+01 # Hw SPCE + 707 236 4 -0.847600 4.101082e+00 5.989344e+00 1.495735e+01 # Ow SPCE + 708 236 3 0.423800 4.681834e+00 6.155976e+00 1.416051e+01 # Hw SPCE + 709 237 3 0.423800 2.585970e+01 5.937546e+00 1.935423e+01 # Hw SPCE + 710 237 4 -0.847600 2.680819e+01 5.995046e+00 1.966578e+01 # Ow SPCE + 711 237 3 0.423800 2.685723e+01 6.574317e+00 2.047944e+01 # Hw SPCE + 712 238 3 0.423800 2.668626e+01 2.541072e+01 4.880638e+00 # Hw SPCE + 713 238 4 -0.847600 2.764667e+01 2.568864e+01 4.899778e+00 # Ow SPCE + 714 238 3 0.423800 2.770442e+01 2.668068e+01 5.011688e+00 # Hw SPCE + 715 239 3 0.423800 3.799348e+00 1.733873e+01 1.665944e+00 # Hw SPCE + 716 239 4 -0.847600 3.166531e+00 1.811195e+01 1.625052e+00 # Ow SPCE + 717 239 3 0.423800 2.227096e+00 1.777190e+01 1.582255e+00 # Hw SPCE + 718 240 3 0.423800 6.922100e+00 1.626292e+01 2.727964e+01 # Hw SPCE + 719 240 4 -0.847600 6.522882e+00 1.559908e+01 2.664724e+01 # Ow SPCE + 720 240 3 0.423800 6.008322e+00 1.491453e+01 2.716360e+01 # Hw SPCE + 721 241 3 0.423800 3.812524e+00 1.917142e+01 4.078941e+00 # Hw SPCE + 722 241 4 -0.847600 4.650408e+00 1.921783e+01 4.622812e+00 # Ow SPCE + 723 241 3 0.423800 5.291688e+00 1.985376e+01 4.193446e+00 # Hw SPCE + 724 242 3 0.423800 2.392996e+01 9.703159e+00 1.533263e+01 # Hw SPCE + 725 242 4 -0.847600 2.418034e+01 1.027088e+01 1.454841e+01 # Ow SPCE + 726 242 3 0.423800 2.425829e+01 9.697253e+00 1.373301e+01 # Hw SPCE + 727 243 3 0.423800 1.160740e+01 4.289690e+00 2.576183e+01 # Hw SPCE + 728 243 4 -0.847600 1.136615e+01 3.672164e+00 2.501319e+01 # Ow SPCE + 729 243 3 0.423800 1.134214e+01 4.183341e+00 2.415404e+01 # Hw SPCE + 730 244 3 0.423800 3.062271e+00 1.498880e+00 1.558829e+01 # Hw SPCE + 731 244 4 -0.847600 2.459085e+00 1.579929e+00 1.479482e+01 # Ow SPCE + 732 244 3 0.423800 1.507109e+00 1.499362e+00 1.509020e+01 # Hw SPCE + 733 245 3 0.423800 9.267839e+00 2.530564e+01 2.389467e+01 # Hw SPCE + 734 245 4 -0.847600 8.983831e+00 2.446671e+01 2.435894e+01 # Ow SPCE + 735 245 3 0.423800 8.616254e+00 2.382260e+01 2.368811e+01 # Hw SPCE + 736 246 3 0.423800 2.233187e+01 2.661754e+01 9.034738e+00 # Hw SPCE + 737 246 4 -0.847600 2.297202e+01 2.590388e+01 8.750298e+00 # Ow SPCE + 738 246 3 0.423800 2.361025e+01 2.571216e+01 9.495883e+00 # Hw SPCE + 739 247 3 0.423800 6.152311e+00 1.591896e+01 1.583244e+00 # Hw SPCE + 740 247 4 -0.847600 6.458131e+00 1.516173e+01 2.160380e+00 # Ow SPCE + 741 247 3 0.423800 7.447061e+00 1.522371e+01 2.295199e+00 # Hw SPCE + 742 248 3 0.423800 6.249483e+00 8.441998e+00 2.500313e+01 # Hw SPCE + 743 248 4 -0.847600 6.658605e+00 7.854146e+00 2.570102e+01 # Ow SPCE + 744 248 3 0.423800 7.286041e+00 7.207979e+00 2.526652e+01 # Hw SPCE + 745 249 3 0.423800 1.155584e+01 7.485508e+00 4.265325e+00 # Hw SPCE + 746 249 4 -0.847600 1.222371e+01 7.709122e+00 3.555440e+00 # Ow SPCE + 747 249 3 0.423800 1.307003e+01 7.203441e+00 3.722858e+00 # Hw SPCE + 748 250 3 0.423800 6.411808e+00 2.543586e+01 7.998512e+00 # Hw SPCE + 749 250 4 -0.847600 7.212358e+00 2.569130e+01 7.456414e+00 # Ow SPCE + 750 250 3 0.423800 7.538848e+00 2.659058e+01 7.747451e+00 # Hw SPCE + 751 251 3 0.423800 2.686488e+01 1.595570e+01 1.586290e+01 # Hw SPCE + 752 251 4 -0.847600 2.770669e+01 1.542553e+01 1.576147e+01 # Ow SPCE + 753 251 3 0.423800 2.766723e+01 1.489635e+01 1.491388e+01 # Hw SPCE + 754 252 3 0.423800 4.730891e+00 1.312809e+01 1.497769e+00 # Hw SPCE + 755 252 4 -0.847600 4.158177e+00 1.342867e+01 2.260428e+00 # Ow SPCE + 756 252 3 0.423800 3.624401e+00 1.422713e+01 1.981941e+00 # Hw SPCE + 757 253 3 0.423800 2.195203e+01 2.665489e+01 1.887230e+01 # Hw SPCE + 758 253 4 -0.847600 2.258974e+01 2.742501e+01 1.888802e+01 # Ow SPCE + 759 253 3 0.423800 2.352836e+01 2.708031e+01 1.890123e+01 # Hw SPCE + 760 254 3 0.423800 1.253712e+01 3.129762e+00 1.183063e+01 # Hw SPCE + 761 254 4 -0.847600 1.292118e+01 3.990106e+00 1.216575e+01 # Ow SPCE + 762 254 3 0.423800 1.383968e+01 3.827163e+00 1.252605e+01 # Hw SPCE + 763 255 3 0.423800 3.863000e+00 2.523218e+01 2.336537e+01 # Hw SPCE + 764 255 4 -0.847600 3.779878e+00 2.428180e+01 2.306556e+01 # Ow SPCE + 765 255 3 0.423800 4.073781e+00 2.367294e+01 2.380238e+01 # Hw SPCE + 766 256 3 0.423800 1.033123e+01 2.732718e+01 1.991221e+01 # Hw SPCE + 767 256 4 -0.847600 1.083128e+01 2.694936e+01 2.069145e+01 # Ow SPCE + 768 256 3 0.423800 1.037561e+01 2.611750e+01 2.100827e+01 # Hw SPCE + 769 257 3 0.423800 6.606032e+00 3.553686e+00 6.537013e+00 # Hw SPCE + 770 257 4 -0.847600 7.445947e+00 3.035012e+00 6.696762e+00 # Ow SPCE + 771 257 3 0.423800 7.233172e+00 2.208190e+00 7.217426e+00 # Hw SPCE + 772 258 3 0.423800 1.306905e+01 1.800714e+01 6.041763e+00 # Hw SPCE + 773 258 4 -0.847600 1.404572e+01 1.784783e+01 5.897769e+00 # Ow SPCE + 774 258 3 0.423800 1.446986e+01 1.867958e+01 5.539574e+00 # Hw SPCE + 775 259 3 0.423800 6.591547e+00 2.039778e+01 6.554188e+00 # Hw SPCE + 776 259 4 -0.847600 6.892178e+00 1.965746e+01 7.155484e+00 # Ow SPCE + 777 259 3 0.423800 7.891350e+00 1.961712e+01 7.160583e+00 # Hw SPCE + 778 260 3 0.423800 2.102357e+01 1.285810e+01 1.138197e+01 # Hw SPCE + 779 260 4 -0.847600 2.063601e+01 1.330654e+01 1.057655e+01 # Ow SPCE + 780 260 3 0.423800 2.040906e+01 1.425453e+01 1.079974e+01 # Hw SPCE + 781 261 3 0.423800 1.668139e+01 1.365676e+01 7.959222e+00 # Hw SPCE + 782 261 4 -0.847600 1.609109e+01 1.302602e+01 7.455519e+00 # Ow SPCE + 783 261 3 0.423800 1.657944e+01 1.216812e+01 7.295759e+00 # Hw SPCE + 784 262 3 0.423800 1.564369e+01 1.907066e+01 2.197727e+01 # Hw SPCE + 785 262 4 -0.847600 1.642857e+01 1.968608e+01 2.204959e+01 # Ow SPCE + 786 262 3 0.423800 1.726974e+01 1.914825e+01 2.210604e+01 # Hw SPCE + 787 263 3 0.423800 7.519411e+00 1.610097e+01 2.120584e+01 # Hw SPCE + 788 263 4 -0.847600 6.640364e+00 1.562428e+01 2.121221e+01 # Ow SPCE + 789 263 3 0.423800 5.897912e+00 1.629395e+01 2.119468e+01 # Hw SPCE + 790 264 3 0.423800 8.688944e+00 1.522738e+01 1.887923e+01 # Hw SPCE + 791 264 4 -0.847600 9.135790e+00 1.601512e+01 1.845520e+01 # Ow SPCE + 792 264 3 0.423800 1.009324e+01 1.579478e+01 1.826879e+01 # Hw SPCE + 793 265 3 0.423800 2.187599e+01 2.614658e+01 2.179133e+01 # Hw SPCE + 794 265 4 -0.847600 2.260916e+01 2.678722e+01 2.156320e+01 # Ow SPCE + 795 265 3 0.423800 2.235434e+01 2.770623e+01 2.186401e+01 # Hw SPCE + 796 266 3 0.423800 8.584848e+00 1.412426e+01 2.770388e+01 # Hw SPCE + 797 266 4 -0.847600 8.917922e+00 1.350413e+01 2.699360e+01 # Ow SPCE + 798 266 3 0.423800 8.385750e+00 1.363828e+01 2.615766e+01 # Hw SPCE + 799 267 3 0.423800 1.498403e+00 1.136667e+01 1.740482e+01 # Hw SPCE + 800 267 4 -0.847600 1.496704e+00 1.228079e+01 1.699937e+01 # Ow SPCE + 801 267 3 0.423800 1.493879e+00 1.296773e+01 1.772607e+01 # Hw SPCE + 802 268 3 0.423800 2.051142e+01 1.532290e+00 2.720074e+01 # Hw SPCE + 803 268 4 -0.847600 2.144152e+01 1.677620e+00 2.686340e+01 # Ow SPCE + 804 268 3 0.423800 2.143787e+01 1.673320e+00 2.586342e+01 # Hw SPCE + 805 269 3 0.423800 1.074975e+01 1.582297e+01 1.147179e+01 # Hw SPCE + 806 269 4 -0.847600 9.843024e+00 1.620321e+01 1.128940e+01 # Ow SPCE + 807 269 3 0.423800 9.486971e+00 1.582159e+01 1.043641e+01 # Hw SPCE + 808 270 3 0.423800 2.158512e+01 4.175374e+00 2.335242e+01 # Hw SPCE + 809 270 4 -0.847600 2.102097e+01 3.724302e+00 2.404399e+01 # Ow SPCE + 810 270 3 0.423800 2.100196e+01 4.281705e+00 2.487402e+01 # Hw SPCE + 811 271 3 0.423800 1.499420e+00 2.109325e+01 1.083546e+01 # Hw SPCE + 812 271 4 -0.847600 2.014482e+00 2.180659e+01 1.036021e+01 # Ow SPCE + 813 271 3 0.423800 2.990936e+00 2.159428e+01 1.039845e+01 # Hw SPCE + 814 272 3 0.423800 1.593017e+00 7.902730e+00 5.258905e+00 # Hw SPCE + 815 272 4 -0.847600 1.689156e+00 7.147133e+00 4.610962e+00 # Ow SPCE + 816 272 3 0.423800 1.505645e+00 7.476802e+00 3.684873e+00 # Hw SPCE + 817 273 3 0.423800 2.022395e+01 1.561529e+01 1.583840e+01 # Hw SPCE + 818 273 4 -0.847600 1.973203e+01 1.634844e+01 1.536883e+01 # Ow SPCE + 819 273 3 0.423800 1.880786e+01 1.603928e+01 1.514447e+01 # Hw SPCE + 820 274 3 0.423800 1.785576e+00 2.595467e+01 1.540470e+01 # Hw SPCE + 821 274 4 -0.847600 1.929174e+00 2.595737e+01 1.441507e+01 # Ow SPCE + 822 274 3 0.423800 1.499516e+00 2.676845e+01 1.401813e+01 # Hw SPCE + 823 275 3 0.423800 2.471608e+00 1.511177e+01 1.372759e+01 # Hw SPCE + 824 275 4 -0.847600 2.173815e+00 1.544011e+01 1.462398e+01 # Ow SPCE + 825 275 3 0.423800 1.499970e+00 1.616932e+01 1.450486e+01 # Hw SPCE + 826 276 3 0.423800 2.490164e+00 2.322823e+01 1.586321e+01 # Hw SPCE + 827 276 4 -0.847600 2.972830e+00 2.348324e+01 1.502535e+01 # Ow SPCE + 828 276 3 0.423800 3.763314e+00 2.405078e+01 1.525565e+01 # Hw SPCE + 829 277 3 0.423800 1.257057e+01 3.159471e+00 2.191679e+01 # Hw SPCE + 830 277 4 -0.847600 1.321241e+01 3.925963e+00 2.189377e+01 # Ow SPCE + 831 277 3 0.423800 1.270362e+01 4.785319e+00 2.184237e+01 # Hw SPCE + 832 278 3 0.423800 1.172696e+01 1.108398e+01 1.089481e+01 # Hw SPCE + 833 278 4 -0.847600 1.108144e+01 1.033095e+01 1.102229e+01 # Ow SPCE + 834 278 3 0.423800 1.021737e+01 1.055252e+01 1.057030e+01 # Hw SPCE + 835 279 3 0.423800 3.357999e+00 1.799692e+01 1.347523e+01 # Hw SPCE + 836 279 4 -0.847600 4.070804e+00 1.735174e+01 1.375027e+01 # Ow SPCE + 837 279 3 0.423800 4.175658e+00 1.737479e+01 1.474449e+01 # Hw SPCE + 838 280 3 0.423800 2.630102e+01 1.903409e+01 1.695517e+01 # Hw SPCE + 839 280 4 -0.847600 2.716892e+01 1.924741e+01 1.650657e+01 # Ow SPCE + 840 280 3 0.423800 2.727889e+01 1.866650e+01 1.570007e+01 # Hw SPCE + 841 281 3 0.423800 2.251004e+01 6.535603e+00 2.441833e+01 # Hw SPCE + 842 281 4 -0.847600 2.185183e+01 7.272694e+00 2.426517e+01 # Ow SPCE + 843 281 3 0.423800 2.104279e+01 7.120398e+00 2.483285e+01 # Hw SPCE + 844 282 3 0.423800 1.499087e+00 1.589499e+01 2.542090e+01 # Hw SPCE + 845 282 4 -0.847600 1.815620e+00 1.616034e+01 2.451019e+01 # Ow SPCE + 846 282 3 0.423800 2.765466e+00 1.587157e+01 2.439019e+01 # Hw SPCE + 847 283 3 0.423800 7.740973e+00 9.861514e+00 1.493066e+00 # Hw SPCE + 848 283 4 -0.847600 6.754170e+00 9.775212e+00 1.630077e+00 # Ow SPCE + 849 283 3 0.423800 6.577520e+00 9.309741e+00 2.497332e+00 # Hw SPCE + 850 284 3 0.423800 1.061617e+01 1.285220e+01 9.107683e+00 # Hw SPCE + 851 284 4 -0.847600 1.078537e+01 1.346180e+01 9.882119e+00 # Ow SPCE + 852 284 3 0.423800 1.170080e+01 1.385624e+01 9.802028e+00 # Hw SPCE + 853 285 3 0.423800 1.252982e+01 2.440492e+01 2.107781e+01 # Hw SPCE + 854 285 4 -0.847600 1.328350e+01 2.483431e+01 2.157539e+01 # Ow SPCE + 855 285 3 0.423800 1.301279e+01 2.575321e+01 2.186234e+01 # Hw SPCE + 856 286 3 0.423800 1.711392e+01 3.831843e+00 7.910876e+00 # Hw SPCE + 857 286 4 -0.847600 1.745648e+01 2.924441e+00 8.154342e+00 # Ow SPCE + 858 286 3 0.423800 1.668530e+01 2.317735e+00 8.347214e+00 # Hw SPCE + 859 287 3 0.423800 1.418372e+01 2.506933e+01 2.753477e+01 # Hw SPCE + 860 287 4 -0.847600 1.506448e+01 2.551120e+01 2.770510e+01 # Ow SPCE + 861 287 3 0.423800 1.537636e+01 2.596552e+01 2.687064e+01 # Hw SPCE + 862 288 3 0.423800 1.415443e+01 8.808654e+00 1.783263e+01 # Hw SPCE + 863 288 4 -0.847600 1.474094e+01 9.071980e+00 1.859858e+01 # Ow SPCE + 864 288 3 0.423800 1.484475e+01 1.006648e+01 1.861235e+01 # Hw SPCE + 865 289 3 0.423800 4.677556e+00 9.152557e+00 2.714451e+01 # Hw SPCE + 866 289 4 -0.847600 4.161429e+00 9.973113e+00 2.689895e+01 # Ow SPCE + 867 289 3 0.423800 3.680550e+00 1.031808e+01 2.770502e+01 # Hw SPCE + 868 290 3 0.423800 1.681375e+01 5.844343e+00 1.610055e+01 # Hw SPCE + 869 290 4 -0.847600 1.659584e+01 6.638638e+00 1.666766e+01 # Ow SPCE + 870 290 3 0.423800 1.560520e+01 6.774046e+00 1.668509e+01 # Hw SPCE + 871 291 3 0.423800 2.156748e+01 3.556166e+00 8.743084e+00 # Hw SPCE + 872 291 4 -0.847600 2.099885e+01 4.371413e+00 8.633380e+00 # Ow SPCE + 873 291 3 0.423800 2.011280e+01 4.110671e+00 8.250059e+00 # Hw SPCE + 874 292 3 0.423800 2.407964e+00 3.416603e+00 4.875553e+00 # Hw SPCE + 875 292 4 -0.847600 2.941172e+00 4.243659e+00 5.053503e+00 # Ow SPCE + 876 292 3 0.423800 3.734200e+00 4.013998e+00 5.617739e+00 # Hw SPCE + 877 293 3 0.423800 5.101947e+00 1.984796e+01 1.813229e+01 # Hw SPCE + 878 293 4 -0.847600 4.344155e+00 1.945528e+01 1.865340e+01 # Ow SPCE + 879 293 3 0.423800 4.223615e+00 1.849669e+01 1.839539e+01 # Hw SPCE + 880 294 3 0.423800 2.200936e+01 1.060534e+01 3.752114e+00 # Hw SPCE + 881 294 4 -0.847600 2.189049e+01 9.647989e+00 4.015453e+00 # Ow SPCE + 882 294 3 0.423800 2.092346e+01 9.401882e+00 3.949942e+00 # Hw SPCE + 883 295 3 0.423800 1.906823e+01 2.481498e+01 1.981312e+01 # Hw SPCE + 884 295 4 -0.847600 2.004704e+01 2.462769e+01 1.973036e+01 # Ow SPCE + 885 295 3 0.423800 2.020559e+01 2.364324e+01 1.980589e+01 # Hw SPCE + 886 296 3 0.423800 8.611320e+00 2.469462e+01 1.622672e+01 # Hw SPCE + 887 296 4 -0.847600 9.439002e+00 2.491431e+01 1.674313e+01 # Ow SPCE + 888 296 3 0.423800 9.564199e+00 2.590618e+01 1.676596e+01 # Hw SPCE + 889 297 3 0.423800 1.450721e+01 2.761357e+00 1.498414e+01 # Hw SPCE + 890 297 4 -0.847600 1.415911e+01 3.378652e+00 1.568967e+01 # Ow SPCE + 891 297 3 0.423800 1.492505e+01 3.846449e+00 1.613071e+01 # Hw SPCE + 892 298 3 0.423800 1.868170e+01 1.216338e+01 2.369258e+01 # Hw SPCE + 893 298 4 -0.847600 1.793724e+01 1.165537e+01 2.412583e+01 # Ow SPCE + 894 298 3 0.423800 1.733910e+01 1.127446e+01 2.342075e+01 # Hw SPCE + 895 299 3 0.423800 1.579916e+01 1.257851e+01 4.190722e+00 # Hw SPCE + 896 299 4 -0.847600 1.647864e+01 1.330728e+01 4.105902e+00 # Ow SPCE + 897 299 3 0.423800 1.738136e+01 1.290518e+01 3.952950e+00 # Hw SPCE + 898 300 3 0.423800 8.783834e+00 4.391999e+00 2.574931e+01 # Hw SPCE + 899 300 4 -0.847600 8.834362e+00 3.580977e+00 2.633214e+01 # Ow SPCE + 900 300 3 0.423800 9.303500e+00 3.811808e+00 2.718456e+01 # Hw SPCE + 901 301 3 0.423800 6.011865e+00 9.555313e+00 7.226940e+00 # Hw SPCE + 902 301 4 -0.847600 5.112292e+00 9.315952e+00 7.592283e+00 # Ow SPCE + 903 301 3 0.423800 5.076259e+00 9.543963e+00 8.565274e+00 # Hw SPCE + 904 302 3 0.423800 2.627737e+01 1.835769e+01 1.705721e+00 # Hw SPCE + 905 302 4 -0.847600 2.714217e+01 1.785579e+01 1.720783e+00 # Ow SPCE + 906 302 3 0.423800 2.696433e+01 1.689110e+01 1.915100e+00 # Hw SPCE + 907 303 3 0.423800 3.574592e+00 1.061416e+01 2.280540e+01 # Hw SPCE + 908 303 4 -0.847600 3.055829e+00 9.761396e+00 2.274473e+01 # Ow SPCE + 909 303 3 0.423800 2.083376e+00 9.969569e+00 2.263986e+01 # Hw SPCE + 910 304 3 0.423800 6.296561e+00 4.609936e+00 3.590033e+00 # Hw SPCE + 911 304 4 -0.847600 5.307980e+00 4.579235e+00 3.442501e+00 # Ow SPCE + 912 304 3 0.423800 4.921826e+00 5.491212e+00 3.581000e+00 # Hw SPCE + 913 305 3 0.423800 2.206674e+01 2.595682e+01 2.671382e+01 # Hw SPCE + 914 305 4 -0.847600 2.135678e+01 2.658763e+01 2.702694e+01 # Ow SPCE + 915 305 3 0.423800 2.078094e+01 2.613123e+01 2.770524e+01 # Hw SPCE + 916 306 3 0.423800 1.817609e+01 2.098444e+01 2.027086e+01 # Hw SPCE + 917 306 4 -0.847600 1.916371e+01 2.114133e+01 2.027198e+01 # Ow SPCE + 918 306 3 0.423800 1.957493e+01 2.067163e+01 2.105318e+01 # Hw SPCE + 919 307 3 0.423800 1.508206e+01 2.274541e+01 1.655332e+01 # Hw SPCE + 920 307 4 -0.847600 1.463912e+01 2.352206e+01 1.610542e+01 # Ow SPCE + 921 307 3 0.423800 1.476799e+01 2.434437e+01 1.665968e+01 # Hw SPCE + 922 308 3 0.423800 1.860141e+01 7.614679e+00 1.499272e+01 # Hw SPCE + 923 308 4 -0.847600 1.949309e+01 7.194380e+00 1.516084e+01 # Ow SPCE + 924 308 3 0.423800 1.938985e+01 6.200796e+00 1.520703e+01 # Hw SPCE + 925 309 3 0.423800 2.555072e+01 1.158947e+01 2.770860e+01 # Hw SPCE + 926 309 4 -0.847600 2.643932e+01 1.113079e+01 2.770565e+01 # Ow SPCE + 927 309 3 0.423800 2.716796e+01 1.181567e+01 2.770996e+01 # Hw SPCE + 928 310 3 0.423800 1.722971e+01 1.047192e+01 5.228288e+00 # Hw SPCE + 929 310 4 -0.847600 1.777259e+01 9.727661e+00 4.839246e+00 # Ow SPCE + 930 310 3 0.423800 1.859163e+01 9.586550e+00 5.395364e+00 # Hw SPCE + 931 311 3 0.423800 2.587903e+01 2.770480e+01 1.071070e+01 # Hw SPCE + 932 311 4 -0.847600 2.587408e+01 2.767484e+01 9.711163e+00 # Ow SPCE + 933 311 3 0.423800 2.681437e+01 2.762443e+01 9.374545e+00 # Hw SPCE + 934 312 3 0.423800 2.683452e+01 2.499904e+00 1.613606e+01 # Hw SPCE + 935 312 4 -0.847600 2.653269e+01 3.436233e+00 1.631547e+01 # Ow SPCE + 936 312 3 0.423800 2.724944e+01 3.928654e+00 1.680922e+01 # Hw SPCE + 937 313 3 0.423800 1.949268e+01 1.128367e+01 2.484942e+00 # Hw SPCE + 938 313 4 -0.847600 2.013505e+01 1.203650e+01 2.341412e+00 # Ow SPCE + 939 313 3 0.423800 1.964783e+01 1.290736e+01 2.406347e+00 # Hw SPCE + 940 314 3 0.423800 7.709374e+00 2.414404e+01 2.771162e+01 # Hw SPCE + 941 314 4 -0.847600 8.447079e+00 2.438436e+01 2.708072e+01 # Ow SPCE + 942 314 3 0.423800 9.057350e+00 2.360032e+01 2.696734e+01 # Hw SPCE + 943 315 3 0.423800 2.770494e+01 2.154717e+00 2.400702e+01 # Hw SPCE + 944 315 4 -0.847600 2.722867e+01 2.468793e+00 2.482831e+01 # Ow SPCE + 945 315 3 0.423800 2.767391e+01 2.087109e+00 2.563830e+01 # Hw SPCE + 946 316 3 0.423800 2.312652e+01 2.631054e+01 1.499737e+00 # Hw SPCE + 947 316 4 -0.847600 2.283269e+01 2.535561e+01 1.541925e+00 # Ow SPCE + 948 316 3 0.423800 2.209421e+01 2.526330e+01 2.209853e+00 # Hw SPCE + 949 317 3 0.423800 3.512223e+00 1.506331e+01 2.059379e+01 # Hw SPCE + 950 317 4 -0.847600 2.579657e+00 1.521266e+01 2.026513e+01 # Ow SPCE + 951 317 3 0.423800 1.995243e+00 1.548068e+01 2.103105e+01 # Hw SPCE + 952 318 3 0.423800 2.429693e+01 7.441439e+00 8.683691e+00 # Hw SPCE + 953 318 4 -0.847600 2.381138e+01 6.574628e+00 8.570202e+00 # Ow SPCE + 954 318 3 0.423800 2.314115e+01 6.662026e+00 7.833213e+00 # Hw SPCE + 955 319 3 0.423800 7.522703e+00 2.737277e+01 3.043788e+00 # Hw SPCE + 956 319 4 -0.847600 8.363778e+00 2.691935e+01 3.338753e+00 # Ow SPCE + 957 319 3 0.423800 9.106122e+00 2.758810e+01 3.380004e+00 # Hw SPCE + 958 320 3 0.423800 1.882098e+01 5.571858e+00 2.228557e+01 # Hw SPCE + 959 320 4 -0.847600 1.938648e+01 5.803385e+00 2.307715e+01 # Ow SPCE + 960 320 3 0.423800 1.882965e+01 5.766062e+00 2.390694e+01 # Hw SPCE + 961 321 3 0.423800 2.349594e+01 1.890656e+01 2.187820e+01 # Hw SPCE + 962 321 4 -0.847600 2.438719e+01 1.922899e+01 2.155931e+01 # Ow SPCE + 963 321 3 0.423800 2.446815e+01 1.906638e+01 2.057594e+01 # Hw SPCE + 964 322 3 0.423800 9.536260e+00 5.620589e+00 4.385983e+00 # Hw SPCE + 965 322 4 -0.847600 9.017970e+00 4.765629e+00 4.365479e+00 # Ow SPCE + 966 322 3 0.423800 9.365801e+00 4.147994e+00 5.070843e+00 # Hw SPCE + 967 323 3 0.423800 6.563604e+00 1.144852e+01 5.310816e+00 # Hw SPCE + 968 323 4 -0.847600 7.395750e+00 1.159137e+01 5.846659e+00 # Ow SPCE + 969 323 3 0.423800 7.176574e+00 1.211622e+01 6.669152e+00 # Hw SPCE + 970 324 3 0.423800 1.966990e+01 1.748868e+01 1.152281e+01 # Hw SPCE + 971 324 4 -0.847600 2.032778e+01 1.685289e+01 1.192649e+01 # Ow SPCE + 972 324 3 0.423800 1.986999e+01 1.629389e+01 1.261783e+01 # Hw SPCE + 973 325 3 0.423800 1.747869e+01 1.936643e+01 1.586861e+01 # Hw SPCE + 974 325 4 -0.847600 1.772310e+01 1.843509e+01 1.613854e+01 # Ow SPCE + 975 325 3 0.423800 1.692776e+01 1.783807e+01 1.603358e+01 # Hw SPCE + 976 326 3 0.423800 7.512513e+00 6.837798e+00 1.561602e+00 # Hw SPCE + 977 326 4 -0.847600 7.975365e+00 5.953103e+00 1.506077e+00 # Ow SPCE + 978 326 3 0.423800 8.941306e+00 6.067128e+00 1.738364e+00 # Hw SPCE + 979 327 3 0.423800 1.576153e+01 1.524842e+00 5.104682e+00 # Hw SPCE + 980 327 4 -0.847600 1.648750e+01 2.206265e+00 5.011799e+00 # Ow SPCE + 981 327 3 0.423800 1.619187e+01 3.066886e+00 5.426446e+00 # Hw SPCE + 982 328 3 0.423800 1.041282e+01 1.861899e+01 5.679153e+00 # Hw SPCE + 983 328 4 -0.847600 1.039014e+01 1.838326e+01 4.707600e+00 # Ow SPCE + 984 328 3 0.423800 1.080342e+01 1.748259e+01 4.573414e+00 # Hw SPCE + 985 329 3 0.423800 1.662912e+01 1.960472e+01 1.057467e+01 # Hw SPCE + 986 329 4 -0.847600 1.568158e+01 1.987224e+01 1.074964e+01 # Ow SPCE + 987 329 3 0.423800 1.512288e+01 1.905336e+01 1.088108e+01 # Hw SPCE + 988 330 3 0.423800 2.562112e+01 2.330374e+00 2.186263e+01 # Hw SPCE + 989 330 4 -0.847600 2.639694e+01 2.945170e+00 2.172070e+01 # Ow SPCE + 990 330 3 0.423800 2.613489e+01 3.671241e+00 2.108498e+01 # Hw SPCE + 991 331 3 0.423800 2.448963e+01 1.656753e+01 2.459110e+01 # Hw SPCE + 992 331 4 -0.847600 2.532168e+01 1.702758e+01 2.490103e+01 # Ow SPCE + 993 331 3 0.423800 2.611790e+01 1.646961e+01 2.466717e+01 # Hw SPCE + 994 332 3 0.423800 6.417758e+00 2.435520e+01 1.460340e+01 # Hw SPCE + 995 332 4 -0.847600 6.300358e+00 2.524145e+01 1.415532e+01 # Ow SPCE + 996 332 3 0.423800 7.192182e+00 2.558969e+01 1.386657e+01 # Hw SPCE + 997 333 3 0.423800 2.759772e+01 1.733045e+00 3.198930e+00 # Hw SPCE + 998 333 4 -0.847600 2.733255e+01 1.589050e+00 2.245541e+00 # Ow SPCE + 999 333 3 0.423800 2.681386e+01 2.379914e+00 1.920750e+00 # Hw SPCE + 1000 334 3 0.423800 2.588019e+01 1.500059e+00 1.857574e+01 # Hw SPCE + 1001 334 4 -0.847600 2.521085e+01 2.077152e+00 1.904366e+01 # Ow SPCE + 1002 334 3 0.423800 2.452203e+01 1.500061e+00 1.948240e+01 # Hw SPCE + 1003 335 3 0.423800 2.129430e+01 2.706783e+01 2.431980e+01 # Hw SPCE + 1004 335 4 -0.847600 2.048933e+01 2.761599e+01 2.454682e+01 # Ow SPCE + 1005 335 3 0.423800 1.990824e+01 2.770571e+01 2.373794e+01 # Hw SPCE + 1006 336 3 0.423800 7.846173e+00 1.094805e+01 9.044554e+00 # Hw SPCE + 1007 336 4 -0.847600 8.350386e+00 1.031715e+01 8.454855e+00 # Ow SPCE + 1008 336 3 0.423800 9.135128e+00 1.079028e+01 8.054438e+00 # Hw SPCE + 1009 337 3 0.423800 1.813806e+01 1.135820e+01 1.530019e+01 # Hw SPCE + 1010 337 4 -0.847600 1.803468e+01 1.102175e+01 1.436418e+01 # Ow SPCE + 1011 337 3 0.423800 1.870041e+01 1.029479e+01 1.419585e+01 # Hw SPCE + 1012 338 3 0.423800 1.930193e+01 1.912951e+00 3.422805e+00 # Hw SPCE + 1013 338 4 -0.847600 2.017995e+01 1.724286e+00 3.862672e+00 # Ow SPCE + 1014 338 3 0.423800 2.082751e+01 2.453171e+00 3.640448e+00 # Hw SPCE + 1015 339 3 0.423800 4.001940e+00 8.178245e+00 1.133370e+01 # Hw SPCE + 1016 339 4 -0.847600 3.264545e+00 8.098159e+00 1.066300e+01 # Ow SPCE + 1017 339 3 0.423800 3.600575e+00 7.615500e+00 9.854222e+00 # Hw SPCE + 1018 340 3 0.423800 1.659027e+01 2.182766e+01 6.306849e+00 # Hw SPCE + 1019 340 4 -0.847600 1.573368e+01 2.131770e+01 6.228114e+00 # Ow SPCE + 1020 340 3 0.423800 1.525717e+01 2.159339e+01 5.393290e+00 # Hw SPCE + 1021 341 3 0.423800 1.307614e+01 1.247914e+01 2.352415e+01 # Hw SPCE + 1022 341 4 -0.847600 1.282345e+01 1.342121e+01 2.374472e+01 # Ow SPCE + 1023 341 3 0.423800 1.200319e+01 1.367502e+01 2.323212e+01 # Hw SPCE + 1024 342 3 0.423800 1.497260e+00 1.394711e+01 5.663732e+00 # Hw SPCE + 1025 342 4 -0.847600 1.700412e+00 1.368341e+01 4.720762e+00 # Ow SPCE + 1026 342 3 0.423800 2.683724e+00 1.376262e+01 4.556984e+00 # Hw SPCE + 1027 343 3 0.423800 1.331392e+01 4.053633e+00 8.310192e+00 # Hw SPCE + 1028 343 4 -0.847600 1.396490e+01 4.044457e+00 7.551157e+00 # Ow SPCE + 1029 343 3 0.423800 1.422587e+01 3.100890e+00 7.347255e+00 # Hw SPCE + 1030 344 3 0.423800 1.981757e+01 1.143084e+01 8.740400e+00 # Hw SPCE + 1031 344 4 -0.847600 2.013820e+01 1.062139e+01 9.232317e+00 # Ow SPCE + 1032 344 3 0.423800 2.106600e+01 1.078181e+01 9.569139e+00 # Hw SPCE + 1033 345 3 0.423800 1.322045e+01 1.551728e+01 1.471662e+01 # Hw SPCE + 1034 345 4 -0.847600 1.356744e+01 1.622003e+01 1.533770e+01 # Ow SPCE + 1035 345 3 0.423800 1.280432e+01 1.676712e+01 1.568170e+01 # Hw SPCE + 1036 346 3 0.423800 2.397971e+01 1.596693e+01 4.479312e+00 # Hw SPCE + 1037 346 4 -0.847600 2.394370e+01 1.692386e+01 4.191220e+00 # Ow SPCE + 1038 346 3 0.423800 2.474897e+01 1.713577e+01 3.637489e+00 # Hw SPCE + 1039 347 3 0.423800 2.621039e+01 2.495880e+01 9.979554e+00 # Hw SPCE + 1040 347 4 -0.847600 2.717528e+01 2.491488e+01 9.720619e+00 # Ow SPCE + 1041 347 3 0.423800 2.770734e+01 2.453968e+01 1.047966e+01 # Hw SPCE + 1042 348 3 0.423800 1.496218e+01 1.063514e+01 2.219722e+01 # Hw SPCE + 1043 348 4 -0.847600 1.527717e+01 9.890283e+00 2.160902e+01 # Ow SPCE + 1044 348 3 0.423800 1.616433e+01 1.012956e+01 2.121444e+01 # Hw SPCE + 1045 349 3 0.423800 5.054437e+00 2.163300e+01 1.503551e+01 # Hw SPCE + 1046 349 4 -0.847600 4.322602e+00 2.106058e+01 1.466572e+01 # Ow SPCE + 1047 349 3 0.423800 4.564201e+00 2.009674e+01 1.477821e+01 # Hw SPCE + 1048 350 3 0.423800 1.707807e+01 2.164478e+01 1.236295e+01 # Hw SPCE + 1049 350 4 -0.847600 1.667106e+01 2.225955e+01 1.168739e+01 # Ow SPCE + 1050 350 3 0.423800 1.611709e+01 2.294854e+01 1.215474e+01 # Hw SPCE + 1051 351 3 0.423800 6.976035e+00 1.779520e+01 1.276337e+01 # Hw SPCE + 1052 351 4 -0.847600 6.523152e+00 1.699626e+01 1.236766e+01 # Ow SPCE + 1053 351 3 0.423800 7.208840e+00 1.630862e+01 1.212892e+01 # Hw SPCE + 1054 352 3 0.423800 2.164730e+01 2.694246e+01 1.255154e+01 # Hw SPCE + 1055 352 4 -0.847600 2.229751e+01 2.618901e+01 1.245390e+01 # Ow SPCE + 1056 352 3 0.423800 2.315706e+01 2.653692e+01 1.207954e+01 # Hw SPCE + 1057 353 3 0.423800 6.833277e+00 2.770802e+01 1.645841e+01 # Hw SPCE + 1058 353 4 -0.847600 7.004922e+00 2.688481e+01 1.699957e+01 # Ow SPCE + 1059 353 3 0.423800 6.350781e+00 2.617384e+01 1.674145e+01 # Hw SPCE + 1060 354 3 0.423800 1.839299e+01 2.770356e+01 2.009264e+01 # Hw SPCE + 1061 354 4 -0.847600 1.905118e+01 2.770991e+01 2.084546e+01 # Ow SPCE + 1062 354 3 0.423800 1.998036e+01 2.770478e+01 2.047586e+01 # Hw SPCE + 1063 355 3 0.423800 2.064587e+01 1.196502e+01 2.770409e+01 # Hw SPCE + 1064 355 4 -0.847600 2.115792e+01 1.209057e+01 2.685436e+01 # Ow SPCE + 1065 355 3 0.423800 2.178395e+01 1.286403e+01 2.695363e+01 # Hw SPCE + 1066 356 3 0.423800 2.679484e+01 2.239034e+01 1.193203e+01 # Hw SPCE + 1067 356 4 -0.847600 2.667630e+01 2.273676e+01 1.286259e+01 # Ow SPCE + 1068 356 3 0.423800 2.726684e+01 2.353199e+01 1.299996e+01 # Hw SPCE + 1069 357 3 0.423800 2.770507e+01 1.752615e+01 1.228536e+01 # Hw SPCE + 1070 357 4 -0.847600 2.749083e+01 1.721084e+01 1.320985e+01 # Ow SPCE + 1071 357 3 0.423800 2.659323e+01 1.677004e+01 1.321203e+01 # Hw SPCE + 1072 358 3 0.423800 7.054104e+00 1.410756e+01 4.776771e+00 # Hw SPCE + 1073 358 4 -0.847600 8.051952e+00 1.404602e+01 4.799402e+00 # Ow SPCE + 1074 358 3 0.423800 8.434858e+00 1.493321e+01 5.056846e+00 # Hw SPCE + 1075 359 3 0.423800 7.117855e+00 1.158648e+01 2.086169e+01 # Hw SPCE + 1076 359 4 -0.847600 7.039453e+00 1.242040e+01 2.031541e+01 # Ow SPCE + 1077 359 3 0.423800 7.832717e+00 1.249916e+01 1.971165e+01 # Hw SPCE + 1078 360 3 0.423800 2.261313e+01 1.962782e+01 4.727741e+00 # Hw SPCE + 1079 360 4 -0.847600 2.305377e+01 1.917276e+01 5.501535e+00 # Ow SPCE + 1080 360 3 0.423800 2.246091e+01 1.923188e+01 6.304662e+00 # Hw SPCE + 1081 361 3 0.423800 2.644084e+00 2.634256e+01 1.150517e+01 # Hw SPCE + 1082 361 4 -0.847600 2.636942e+00 2.733967e+01 1.158078e+01 # Ow SPCE + 1083 361 3 0.423800 1.836409e+00 2.770428e+01 1.110516e+01 # Hw SPCE + 1084 362 3 0.423800 8.040783e+00 1.358334e+01 9.796191e+00 # Hw SPCE + 1085 362 4 -0.847600 7.086989e+00 1.388373e+01 9.802364e+00 # Ow SPCE + 1086 362 3 0.423800 6.576055e+00 1.338543e+01 9.101906e+00 # Hw SPCE + 1087 363 3 0.423800 2.619651e+00 1.319647e+01 2.242900e+01 # Hw SPCE + 1088 363 4 -0.847600 1.972508e+00 1.282938e+01 2.309717e+01 # Ow SPCE + 1089 363 3 0.423800 1.494472e+00 1.358356e+01 2.354737e+01 # Hw SPCE + 1090 364 3 0.423800 4.287560e+00 6.326031e+00 2.681750e+01 # Hw SPCE + 1091 364 4 -0.847600 4.221751e+00 5.858179e+00 2.593615e+01 # Ow SPCE + 1092 364 3 0.423800 4.606223e+00 4.938624e+00 2.601739e+01 # Hw SPCE + 1093 365 3 0.423800 2.134184e+01 1.704290e+01 5.072956e+00 # Hw SPCE + 1094 365 4 -0.847600 2.040579e+01 1.710436e+01 4.726504e+00 # Ow SPCE + 1095 365 3 0.423800 2.037017e+01 1.673983e+01 3.795993e+00 # Hw SPCE + 1096 366 3 0.423800 1.898318e+01 2.671834e+01 1.475007e+01 # Hw SPCE + 1097 366 4 -0.847600 1.928304e+01 2.767034e+01 1.481164e+01 # Ow SPCE + 1098 366 3 0.423800 2.028241e+01 2.770555e+01 1.481376e+01 # Hw SPCE + 1099 367 3 0.423800 2.348205e+01 1.705352e+01 2.743345e+01 # Hw SPCE + 1100 367 4 -0.847600 2.446126e+01 1.722463e+01 2.754240e+01 # Ow SPCE + 1101 367 3 0.423800 2.461312e+01 1.819940e+01 2.770595e+01 # Hw SPCE + 1102 368 3 0.423800 2.430373e+01 1.513396e+01 1.529098e+01 # Hw SPCE + 1103 368 4 -0.847600 2.387002e+01 1.513478e+01 1.619203e+01 # Ow SPCE + 1104 368 3 0.423800 2.295803e+01 1.553908e+01 1.612260e+01 # Hw SPCE + 1105 369 3 0.423800 1.140164e+01 2.512691e+01 1.865711e+01 # Hw SPCE + 1106 369 4 -0.847600 1.159315e+01 2.415737e+01 1.850437e+01 # Ow SPCE + 1107 369 3 0.423800 1.256364e+01 2.403832e+01 1.829465e+01 # Hw SPCE + 1108 370 3 0.423800 1.903749e+01 1.236107e+01 6.079139e+00 # Hw SPCE + 1109 370 4 -0.847600 2.003143e+01 1.240506e+01 6.179850e+00 # Ow SPCE + 1110 370 3 0.423800 2.044270e+01 1.158083e+01 5.790615e+00 # Hw SPCE + 1111 371 3 0.423800 1.282548e+01 1.241244e+01 1.303471e+01 # Hw SPCE + 1112 371 4 -0.847600 1.310760e+01 1.337123e+01 1.300088e+01 # Ow SPCE + 1113 371 3 0.423800 1.235662e+01 1.392727e+01 1.264472e+01 # Hw SPCE + 1114 372 3 0.423800 1.455246e+01 1.713196e+01 1.777281e+01 # Hw SPCE + 1115 372 4 -0.847600 1.483389e+01 1.618051e+01 1.789743e+01 # Ow SPCE + 1116 372 3 0.423800 1.582185e+01 1.614204e+01 1.804727e+01 # Hw SPCE + 1117 373 3 0.423800 2.660254e+01 1.154715e+01 7.873309e+00 # Hw SPCE + 1118 373 4 -0.847600 2.566434e+01 1.120992e+01 7.951077e+00 # Ow SPCE + 1119 373 3 0.423800 2.566312e+01 1.021159e+01 7.893201e+00 # Hw SPCE + 1120 374 3 0.423800 8.706708e+00 9.237566e+00 1.972409e+01 # Hw SPCE + 1121 374 4 -0.847600 8.843305e+00 8.419627e+00 1.916524e+01 # Ow SPCE + 1122 374 3 0.423800 9.468501e+00 7.795949e+00 1.963445e+01 # Hw SPCE + 1123 375 3 0.423800 1.904385e+01 2.517573e+01 1.240879e+01 # Hw SPCE + 1124 375 4 -0.847600 1.846922e+01 2.435960e+01 1.234762e+01 # Ow SPCE + 1125 375 3 0.423800 1.904403e+01 2.355925e+01 1.217725e+01 # Hw SPCE + 1126 376 3 0.423800 1.112677e+01 1.997104e+01 2.147548e+00 # Hw SPCE + 1127 376 4 -0.847600 1.122781e+01 2.093546e+01 1.903215e+00 # Ow SPCE + 1128 376 3 0.423800 1.219941e+01 2.116740e+01 1.856343e+00 # Hw SPCE + 1129 377 3 0.423800 2.578920e+01 1.183896e+01 1.708350e+01 # Hw SPCE + 1130 377 4 -0.847600 2.566789e+01 1.208960e+01 1.612305e+01 # Ow SPCE + 1131 377 3 0.423800 2.594628e+01 1.304067e+01 1.598904e+01 # Hw SPCE + 1132 378 3 0.423800 1.394495e+01 2.009220e+01 8.623841e+00 # Hw SPCE + 1133 378 4 -0.847600 1.430818e+01 1.923404e+01 8.261025e+00 # Ow SPCE + 1134 378 3 0.423800 1.528668e+01 1.933569e+01 8.081558e+00 # Hw SPCE + 1135 379 3 0.423800 5.844676e+00 2.770452e+01 2.407135e+01 # Hw SPCE + 1136 379 4 -0.847600 6.002067e+00 2.672754e+01 2.421532e+01 # Ow SPCE + 1137 379 3 0.423800 6.928604e+00 2.658707e+01 2.456432e+01 # Hw SPCE + 1138 380 3 0.423800 1.960711e+01 1.884907e+01 1.867877e+01 # Hw SPCE + 1139 380 4 -0.847600 1.959153e+01 1.836640e+01 1.955444e+01 # Ow SPCE + 1140 380 3 0.423800 1.864928e+01 1.830285e+01 1.988328e+01 # Hw SPCE + 1141 381 3 0.423800 1.937001e+01 2.231144e+01 7.504950e+00 # Hw SPCE + 1142 381 4 -0.847600 1.903775e+01 2.136844e+01 7.486339e+00 # Ow SPCE + 1143 381 3 0.423800 1.981507e+01 2.074229e+01 7.425510e+00 # Hw SPCE + 1144 382 3 0.423800 1.186903e+01 7.804165e+00 2.097534e+01 # Hw SPCE + 1145 382 4 -0.847600 1.191707e+01 8.691479e+00 2.051668e+01 # Ow SPCE + 1146 382 3 0.423800 1.284539e+01 9.055616e+00 2.059166e+01 # Hw SPCE + 1147 383 3 0.423800 1.254816e+01 1.752163e+01 2.720322e+01 # Hw SPCE + 1148 383 4 -0.847600 1.171866e+01 1.807176e+01 2.729959e+01 # Ow SPCE + 1149 383 3 0.423800 1.195006e+01 1.895518e+01 2.770705e+01 # Hw SPCE + 1150 384 3 0.423800 2.457569e+01 2.221691e+01 1.644026e+01 # Hw SPCE + 1151 384 4 -0.847600 2.471053e+01 2.126493e+01 1.671514e+01 # Ow SPCE + 1152 384 3 0.423800 2.384588e+01 2.088835e+01 1.704767e+01 # Hw SPCE + 1153 385 3 0.423800 1.283404e+01 2.766561e+01 2.418101e+01 # Hw SPCE + 1154 385 4 -0.847600 1.206202e+01 2.770764e+01 2.354681e+01 # Ow SPCE + 1155 385 3 0.423800 1.120852e+01 2.757858e+01 2.405168e+01 # Hw SPCE + 1156 386 3 0.423800 1.749501e+01 9.243189e+00 2.770432e+01 # Hw SPCE + 1157 386 4 -0.847600 1.707406e+01 8.336104e+00 2.770498e+01 # Ow SPCE + 1158 386 3 0.423800 1.778896e+01 7.636892e+00 2.770954e+01 # Hw SPCE + 1159 387 3 0.423800 3.764698e+00 4.444911e+00 2.206397e+01 # Hw SPCE + 1160 387 4 -0.847600 3.228879e+00 4.580528e+00 2.123060e+01 # Ow SPCE + 1161 387 3 0.423800 3.845459e+00 4.663162e+00 2.044766e+01 # Hw SPCE + 1162 388 3 0.423800 1.825404e+01 5.005912e+00 1.014694e+01 # Hw SPCE + 1163 388 4 -0.847600 1.843498e+01 5.919465e+00 9.782683e+00 # Ow SPCE + 1164 388 3 0.423800 1.764323e+01 6.507321e+00 9.948697e+00 # Hw SPCE + 1165 389 3 0.423800 1.376578e+01 2.484946e+01 1.386117e+01 # Hw SPCE + 1166 389 4 -0.847600 1.385130e+01 2.411884e+01 1.318378e+01 # Ow SPCE + 1167 389 3 0.423800 1.295121e+01 2.391359e+01 1.279947e+01 # Hw SPCE + 1168 390 3 0.423800 6.083757e+00 4.915302e+00 1.185692e+01 # Hw SPCE + 1169 390 4 -0.847600 5.091254e+00 4.926633e+00 1.173522e+01 # Ow SPCE + 1170 390 3 0.423800 4.865042e+00 5.402990e+00 1.088557e+01 # Hw SPCE + 1171 391 3 0.423800 1.088455e+01 2.264855e+01 1.611957e+01 # Hw SPCE + 1172 391 4 -0.847600 1.184680e+01 2.283963e+01 1.592573e+01 # Ow SPCE + 1173 391 3 0.423800 1.194451e+01 2.378898e+01 1.562707e+01 # Hw SPCE + 1174 392 3 0.423800 2.206544e+01 9.962865e+00 2.373843e+01 # Hw SPCE + 1175 392 4 -0.847600 2.203099e+01 1.070683e+01 2.440575e+01 # Ow SPCE + 1176 392 3 0.423800 2.122829e+01 1.127638e+01 2.422883e+01 # Hw SPCE + 1177 393 3 0.423800 2.149681e+00 4.701448e+00 2.459932e+00 # Hw SPCE + 1178 393 4 -0.847600 2.971895e+00 4.426184e+00 1.961740e+00 # Ow SPCE + 1179 393 3 0.423800 3.296291e+00 5.191193e+00 1.405388e+00 # Hw SPCE + 1180 394 3 0.423800 2.234775e+01 2.162751e+01 2.770458e+01 # Hw SPCE + 1181 394 4 -0.847600 2.136405e+01 2.144770e+01 2.770458e+01 # Ow SPCE + 1182 394 3 0.423800 2.086664e+01 2.231522e+01 2.770463e+01 # Hw SPCE + 1183 395 3 0.423800 1.025105e+01 1.356885e+01 1.665922e+01 # Hw SPCE + 1184 395 4 -0.847600 1.035969e+01 1.403984e+01 1.578379e+01 # Ow SPCE + 1185 395 3 0.423800 1.099242e+01 1.352554e+01 1.520487e+01 # Hw SPCE + 1186 396 3 0.423800 1.072202e+01 2.377633e+01 9.484681e+00 # Hw SPCE + 1187 396 4 -0.847600 1.155152e+01 2.385537e+01 1.003758e+01 # Ow SPCE + 1188 396 3 0.423800 1.158705e+01 2.476225e+01 1.045747e+01 # Hw SPCE + 1189 397 3 0.423800 2.341205e+01 1.813661e+01 1.100851e+01 # Hw SPCE + 1190 397 4 -0.847600 2.312469e+01 1.893695e+01 1.153470e+01 # Ow SPCE + 1191 397 3 0.423800 2.213380e+01 1.891079e+01 1.166681e+01 # Hw SPCE + 1192 398 3 0.423800 1.500790e+01 2.394339e+01 3.351174e+00 # Hw SPCE + 1193 398 4 -0.847600 1.452101e+01 2.480831e+01 3.229359e+00 # Ow SPCE + 1194 398 3 0.423800 1.385157e+01 2.492026e+01 3.963743e+00 # Hw SPCE + 1195 399 3 0.423800 1.479502e+01 1.286237e+01 2.563621e+01 # Hw SPCE + 1196 399 4 -0.847600 1.547417e+01 1.230040e+01 2.516403e+01 # Ow SPCE + 1197 399 3 0.423800 1.510530e+01 1.138206e+01 2.502053e+01 # Hw SPCE + 1198 400 3 0.423800 8.068136e+00 1.885540e+01 1.505299e+01 # Hw SPCE + 1199 400 4 -0.847600 7.813925e+00 1.834922e+01 1.587711e+01 # Ow SPCE + 1200 400 3 0.423800 8.632664e+00 1.794760e+01 1.628743e+01 # Hw SPCE + 1201 401 3 0.423800 4.063418e+00 2.228502e+01 2.617453e+01 # Hw SPCE + 1202 401 4 -0.847600 4.103168e+00 2.200493e+01 2.713369e+01 # Ow SPCE + 1203 401 3 0.423800 4.240658e+00 2.281008e+01 2.771061e+01 # Hw SPCE + 1204 402 3 0.423800 1.495103e+00 1.280834e+01 9.475737e+00 # Hw SPCE + 1205 402 4 -0.847600 1.505699e+00 1.300445e+01 8.495213e+00 # Ow SPCE + 1206 402 3 0.423800 2.251321e+00 1.363848e+01 8.290148e+00 # Hw SPCE + 1207 403 3 0.423800 2.465760e+01 6.451081e+00 2.270306e+01 # Hw SPCE + 1208 403 4 -0.847600 2.409442e+01 5.715878e+00 2.232582e+01 # Ow SPCE + 1209 403 3 0.423800 2.432171e+01 4.854913e+00 2.278088e+01 # Hw SPCE + 1210 404 3 0.423800 1.999267e+01 7.260978e+00 2.497131e+00 # Hw SPCE + 1211 404 4 -0.847600 2.085928e+01 6.772162e+00 2.396875e+00 # Ow SPCE + 1212 404 3 0.423800 2.067784e+01 5.804151e+00 2.223575e+00 # Hw SPCE + 1213 405 3 0.423800 9.804016e+00 1.166498e+01 2.144260e+01 # Hw SPCE + 1214 405 4 -0.847600 1.060905e+01 1.108039e+01 2.134174e+01 # Ow SPCE + 1215 405 3 0.423800 1.143569e+01 1.162260e+01 2.149231e+01 # Hw SPCE + 1216 406 3 0.423800 3.092468e+00 1.075047e+01 1.184205e+01 # Hw SPCE + 1217 406 4 -0.847600 2.172613e+00 1.036170e+01 1.189426e+01 # Ow SPCE + 1218 406 3 0.423800 1.497139e+00 1.108044e+01 1.172948e+01 # Hw SPCE + 1219 407 3 0.423800 8.342000e+00 1.946949e+00 1.825736e+01 # Hw SPCE + 1220 407 4 -0.847600 7.967584e+00 2.874061e+00 1.827399e+01 # Ow SPCE + 1221 407 3 0.423800 8.362019e+00 3.379098e+00 1.904168e+01 # Hw SPCE + 1222 408 3 0.423800 1.182612e+01 2.367595e+01 5.346337e+00 # Hw SPCE + 1223 408 4 -0.847600 1.218656e+01 2.331296e+01 6.205591e+00 # Ow SPCE + 1224 408 3 0.423800 1.183999e+01 2.385789e+01 6.969091e+00 # Hw SPCE + 1225 409 3 0.423800 2.018572e+01 8.334075e+00 2.235069e+01 # Hw SPCE + 1226 409 4 -0.847600 1.935425e+01 8.544535e+00 2.286486e+01 # Ow SPCE + 1227 409 3 0.423800 1.940926e+01 9.477685e+00 2.322011e+01 # Hw SPCE + 1228 410 3 0.423800 1.150389e+01 1.904731e+01 2.337866e+01 # Hw SPCE + 1229 410 4 -0.847600 1.246144e+01 1.912402e+01 2.310078e+01 # Ow SPCE + 1230 410 3 0.423800 1.251260e+01 1.953763e+01 2.219177e+01 # Hw SPCE + 1231 411 3 0.423800 1.847815e+01 4.974998e+00 2.770084e+01 # Hw SPCE + 1232 411 4 -0.847600 1.940796e+01 5.342993e+00 2.770581e+01 # Ow SPCE + 1233 411 3 0.423800 2.006473e+01 4.589757e+00 2.767000e+01 # Hw SPCE + 1234 412 3 0.423800 1.580751e+01 1.573107e+01 1.381081e+01 # Hw SPCE + 1235 412 4 -0.847600 1.558902e+01 1.492275e+01 1.326411e+01 # Ow SPCE + 1236 412 3 0.423800 1.643597e+01 1.449518e+01 1.294811e+01 # Hw SPCE + 1237 413 3 0.423800 2.552671e+01 2.186200e+01 4.694186e+00 # Hw SPCE + 1238 413 4 -0.847600 2.590407e+01 2.278594e+01 4.631422e+00 # Ow SPCE + 1239 413 3 0.423800 2.664316e+01 2.279908e+01 3.957950e+00 # Hw SPCE + 1240 414 3 0.423800 1.035260e+01 1.601592e+01 2.375608e+01 # Hw SPCE + 1241 414 4 -0.847600 1.119407e+01 1.631619e+01 2.330691e+01 # Ow SPCE + 1242 414 3 0.423800 1.194221e+01 1.632219e+01 2.397043e+01 # Hw SPCE + 1243 415 3 0.423800 1.366476e+01 2.199974e+01 2.177637e+01 # Hw SPCE + 1244 415 4 -0.847600 1.412014e+01 2.188301e+01 2.265898e+01 # Ow SPCE + 1245 415 3 0.423800 1.408048e+01 2.274131e+01 2.317060e+01 # Hw SPCE + 1246 416 3 0.423800 2.364272e+01 2.771622e+01 1.585868e+01 # Hw SPCE + 1247 416 4 -0.847600 2.381273e+01 2.673639e+01 1.575366e+01 # Ow SPCE + 1248 416 3 0.423800 2.301817e+01 2.630404e+01 1.532735e+01 # Hw SPCE + 1249 417 3 0.423800 9.899911e+00 1.878785e+01 1.222479e+01 # Hw SPCE + 1250 417 4 -0.847600 9.152062e+00 1.943110e+01 1.238898e+01 # Ow SPCE + 1251 417 3 0.423800 9.422298e+00 2.034259e+01 1.207890e+01 # Hw SPCE + 1252 418 3 0.423800 1.878242e+01 4.765640e+00 5.930390e+00 # Hw SPCE + 1253 418 4 -0.847600 1.891751e+01 4.352003e+00 5.030026e+00 # Ow SPCE + 1254 418 3 0.423800 1.970449e+01 4.776921e+00 4.582694e+00 # Hw SPCE + 1255 419 3 0.423800 2.569329e+00 2.015592e+01 1.667337e+01 # Hw SPCE + 1256 419 4 -0.847600 1.639651e+00 1.989432e+01 1.641401e+01 # Ow SPCE + 1257 419 3 0.423800 1.669728e+00 1.906197e+01 1.586059e+01 # Hw SPCE + 1258 420 3 0.423800 1.419487e+01 1.526132e+01 2.687487e+01 # Hw SPCE + 1259 420 4 -0.847600 1.473359e+01 1.511839e+01 2.770514e+01 # Ow SPCE + 1260 420 3 0.423800 1.562750e+01 1.474196e+01 2.746177e+01 # Hw SPCE + 1261 421 3 0.423800 1.225934e+01 4.584227e+00 3.933375e+00 # Hw SPCE + 1262 421 4 -0.847600 1.246279e+01 3.746427e+00 4.440028e+00 # Ow SPCE + 1263 421 3 0.423800 1.333976e+01 3.376246e+00 4.133605e+00 # Hw SPCE + 1264 422 3 0.423800 1.620747e+01 1.499403e+00 1.137835e+01 # Hw SPCE + 1265 422 4 -0.847600 1.549499e+01 1.586802e+00 1.207458e+01 # Ow SPCE + 1266 422 3 0.423800 1.590320e+01 1.493891e+00 1.298273e+01 # Hw SPCE + 1267 423 3 0.423800 9.040061e+00 1.791814e+01 2.669513e+01 # Hw SPCE + 1268 423 4 -0.847600 9.361578e+00 1.786689e+01 2.574961e+01 # Ow SPCE + 1269 423 3 0.423800 9.763981e+00 1.874370e+01 2.548640e+01 # Hw SPCE + 1270 424 3 0.423800 4.419758e+00 1.589273e+01 4.038818e+00 # Hw SPCE + 1271 424 4 -0.847600 3.943488e+00 1.618125e+01 4.869433e+00 # Ow SPCE + 1272 424 3 0.423800 4.594864e+00 1.661046e+01 5.495121e+00 # Hw SPCE + 1273 425 3 0.423800 1.842571e+01 1.489983e+00 1.787524e+01 # Hw SPCE + 1274 425 4 -0.847600 1.758392e+01 1.950976e+00 1.815609e+01 # Ow SPCE + 1275 425 3 0.423800 1.679908e+01 1.499453e+00 1.773164e+01 # Hw SPCE + 1276 426 3 0.423800 9.617069e+00 1.503555e+01 7.768316e+00 # Hw SPCE + 1277 426 4 -0.847600 9.908997e+00 1.580937e+01 7.206183e+00 # Ow SPCE + 1278 426 3 0.423800 1.087713e+01 1.599609e+01 7.373049e+00 # Hw SPCE + 1279 427 3 0.423800 1.761915e+01 1.824001e+01 1.495841e+00 # Hw SPCE + 1280 427 4 -0.847600 1.707860e+01 1.740503e+01 1.598843e+00 # Ow SPCE + 1281 427 3 0.423800 1.610784e+01 1.764023e+01 1.646897e+00 # Hw SPCE + 1282 428 3 0.423800 2.926508e+00 1.529462e+00 2.267458e+01 # Hw SPCE + 1283 428 4 -0.847600 2.327395e+00 2.065396e+00 2.207974e+01 # Ow SPCE + 1284 428 3 0.423800 1.514758e+00 1.528181e+00 2.185386e+01 # Hw SPCE + 1285 429 3 0.423800 1.553029e+01 1.331892e+01 2.261128e+01 # Hw SPCE + 1286 429 4 -0.847600 1.550843e+01 1.423794e+01 2.221768e+01 # Ow SPCE + 1287 429 3 0.423800 1.458388e+01 1.444035e+01 2.189481e+01 # Hw SPCE + 1288 430 3 0.423800 4.535770e+00 7.778783e+00 1.481895e+00 # Hw SPCE + 1289 430 4 -0.847600 3.543503e+00 7.902817e+00 1.486495e+00 # Ow SPCE + 1290 430 3 0.423800 3.329718e+00 8.879692e+00 1.489737e+00 # Hw SPCE + 1291 431 3 0.423800 2.525719e+01 1.568518e+01 1.106507e+01 # Hw SPCE + 1292 431 4 -0.847600 2.557432e+01 1.474391e+01 1.094918e+01 # Ow SPCE + 1293 431 3 0.423800 2.628269e+01 1.454508e+01 1.162645e+01 # Hw SPCE + 1294 432 3 0.423800 1.664803e+01 1.910926e+01 3.917316e+00 # Hw SPCE + 1295 432 4 -0.847600 1.723132e+01 1.835477e+01 4.218178e+00 # Ow SPCE + 1296 432 3 0.423800 1.819067e+01 1.863032e+01 4.157108e+00 # Hw SPCE + 1297 433 3 0.423800 1.358310e+01 2.662050e+01 1.011150e+01 # Hw SPCE + 1298 433 4 -0.847600 1.300630e+01 2.743245e+01 1.002187e+01 # Ow SPCE + 1299 433 3 0.423800 1.296445e+01 2.770719e+01 9.061266e+00 # Hw SPCE + 1300 434 3 0.423800 1.435488e+01 2.080827e+01 2.772371e+01 # Hw SPCE + 1301 434 4 -0.847600 1.506496e+01 2.013414e+01 2.752040e+01 # Ow SPCE + 1302 434 3 0.423800 1.464175e+01 1.930210e+01 2.716177e+01 # Hw SPCE + 1303 435 3 0.423800 2.167525e+01 2.207461e+01 1.584656e+01 # Hw SPCE + 1304 435 4 -0.847600 2.087644e+01 2.148761e+01 1.597828e+01 # Ow SPCE + 1305 435 3 0.423800 2.114010e+01 2.067901e+01 1.650425e+01 # Hw SPCE + 1306 436 3 0.423800 1.336152e+01 8.766368e+00 1.286048e+01 # Hw SPCE + 1307 436 4 -0.847600 1.290502e+01 9.628651e+00 1.307975e+01 # Ow SPCE + 1308 436 3 0.423800 1.199822e+01 9.439351e+00 1.345642e+01 # Hw SPCE + 1309 437 3 0.423800 2.687223e+01 1.379076e+01 4.532287e+00 # Hw SPCE + 1310 437 4 -0.847600 2.610111e+01 1.321002e+01 4.793266e+00 # Ow SPCE + 1311 437 3 0.423800 2.541665e+01 1.376000e+01 5.271855e+00 # Hw SPCE + 1312 438 3 0.423800 2.387246e+01 1.507034e+00 1.669725e+01 # Hw SPCE + 1313 438 4 -0.847600 2.319211e+01 2.086236e+00 1.714629e+01 # Ow SPCE + 1314 438 3 0.423800 2.251393e+01 1.510750e+00 1.760333e+01 # Hw SPCE + 1315 439 3 0.423800 2.653441e+01 1.338040e+01 1.698890e+00 # Hw SPCE + 1316 439 4 -0.847600 2.568911e+01 1.287185e+01 1.862766e+00 # Ow SPCE + 1317 439 3 0.423800 2.578217e+01 1.194475e+01 1.499689e+00 # Hw SPCE + 1318 440 3 0.423800 1.654650e+01 7.351076e+00 4.198674e+00 # Hw SPCE + 1319 440 4 -0.847600 1.720204e+01 6.630419e+00 4.424346e+00 # Ow SPCE + 1320 440 3 0.423800 1.811991e+01 7.022369e+00 4.486733e+00 # Hw SPCE + 1321 441 3 0.423800 1.561748e+01 2.344616e+01 2.579500e+01 # Hw SPCE + 1322 441 4 -0.847600 1.584177e+01 2.276826e+01 2.649512e+01 # Ow SPCE + 1323 441 3 0.423800 1.643484e+01 2.318456e+01 2.718429e+01 # Hw SPCE + 1324 442 3 0.423800 6.712087e+00 1.647363e+01 2.402889e+01 # Hw SPCE + 1325 442 4 -0.847600 7.684457e+00 1.666294e+01 2.389230e+01 # Ow SPCE + 1326 442 3 0.423800 7.794810e+00 1.757954e+01 2.350803e+01 # Hw SPCE + 1327 443 3 0.423800 5.195124e+00 1.484833e+01 1.345621e+01 # Hw SPCE + 1328 443 4 -0.847600 5.562996e+00 1.495140e+01 1.438035e+01 # Ow SPCE + 1329 443 3 0.423800 4.853276e+00 1.472796e+01 1.504847e+01 # Hw SPCE + 1330 444 3 0.423800 8.810832e+00 8.170650e+00 3.650788e+00 # Hw SPCE + 1331 444 4 -0.847600 9.231504e+00 9.063820e+00 3.809800e+00 # Ow SPCE + 1332 444 3 0.423800 8.600516e+00 9.642123e+00 4.326925e+00 # Hw SPCE + 1333 445 3 0.423800 1.481433e+01 2.127865e+01 2.698847e+00 # Hw SPCE + 1334 445 4 -0.847600 1.527661e+01 2.130491e+01 1.812501e+00 # Ow SPCE + 1335 445 3 0.423800 1.564077e+01 2.039825e+01 1.599517e+00 # Hw SPCE + 1336 446 3 0.423800 2.770585e+01 9.745885e+00 6.112819e+00 # Hw SPCE + 1337 446 4 -0.847600 2.769138e+01 8.749499e+00 6.196517e+00 # Ow SPCE + 1338 446 3 0.423800 2.675145e+01 8.420868e+00 6.104123e+00 # Hw SPCE + 1339 447 3 0.423800 1.995729e+01 2.430246e+01 2.248412e+01 # Hw SPCE + 1340 447 4 -0.847600 1.958412e+01 2.507755e+01 2.299401e+01 # Ow SPCE + 1341 447 3 0.423800 1.884602e+01 2.549888e+01 2.246704e+01 # Hw SPCE + 1342 448 3 0.423800 1.497281e+00 1.817499e+01 1.855576e+01 # Hw SPCE + 1343 448 4 -0.847600 1.565131e+00 1.860877e+01 1.945422e+01 # Ow SPCE + 1344 448 3 0.423800 1.511007e+00 1.960184e+01 1.934984e+01 # Hw SPCE + 1345 449 3 0.423800 1.522308e+01 5.358237e+00 1.071042e+01 # Hw SPCE + 1346 449 4 -0.847600 1.552152e+01 4.758830e+00 9.967693e+00 # Ow SPCE + 1347 449 3 0.423800 1.530075e+01 3.810494e+00 1.019556e+01 # Hw SPCE + 1348 450 3 0.423800 2.551853e+01 2.712094e+01 2.391955e+01 # Hw SPCE + 1349 450 4 -0.847600 2.545744e+01 2.641384e+01 2.321508e+01 # Ow SPCE + 1350 450 3 0.423800 2.636236e+01 2.625938e+01 2.281851e+01 # Hw SPCE + 1351 451 3 0.423800 2.385946e+01 4.277050e+00 1.008061e+01 # Hw SPCE + 1352 451 4 -0.847600 2.334099e+01 3.853916e+00 1.082367e+01 # Ow SPCE + 1353 451 3 0.423800 2.397243e+01 3.414585e+00 1.146264e+01 # Hw SPCE + 1354 452 3 0.423800 1.024842e+01 2.543775e+01 1.414465e+01 # Hw SPCE + 1355 452 4 -0.847600 1.115630e+01 2.571591e+01 1.383099e+01 # Ow SPCE + 1356 452 3 0.423800 1.146598e+01 2.650375e+01 1.436336e+01 # Hw SPCE + 1357 453 3 0.423800 1.117636e+01 1.477962e+01 4.921439e+00 # Hw SPCE + 1358 453 4 -0.847600 1.106953e+01 1.411588e+01 4.181144e+00 # Ow SPCE + 1359 453 3 0.423800 1.192150e+01 1.360514e+01 4.065876e+00 # Hw SPCE + 1360 454 3 0.423800 1.155263e+01 2.419941e+01 2.638042e+00 # Hw SPCE + 1361 454 4 -0.847600 1.124181e+01 2.513186e+01 2.453834e+00 # Ow SPCE + 1362 454 3 0.423800 1.199737e+01 2.566636e+01 2.075120e+00 # Hw SPCE + 1363 455 3 0.423800 1.904382e+01 8.719465e+00 1.089114e+01 # Hw SPCE + 1364 455 4 -0.847600 1.879769e+01 8.867065e+00 1.184908e+01 # Ow SPCE + 1365 455 3 0.423800 1.935399e+01 8.274179e+00 1.243132e+01 # Hw SPCE + 1366 456 3 0.423800 2.055866e+01 2.186209e+01 5.026626e+00 # Hw SPCE + 1367 456 4 -0.847600 2.043424e+01 2.280967e+01 4.732347e+00 # Ow SPCE + 1368 456 3 0.423800 1.947974e+01 2.307708e+01 4.864316e+00 # Hw SPCE + 1369 457 3 0.423800 9.488490e+00 2.282360e+01 1.375688e+01 # Hw SPCE + 1370 457 4 -0.847600 1.031447e+01 2.268450e+01 1.321061e+01 # Ow SPCE + 1371 457 3 0.423800 1.029828e+01 2.329670e+01 1.242008e+01 # Hw SPCE + 1372 458 3 0.423800 2.759400e+01 1.561429e+01 1.901357e+01 # Hw SPCE + 1373 458 4 -0.847600 2.771901e+01 1.477632e+01 1.848237e+01 # Ow SPCE + 1374 458 3 0.423800 2.682701e+01 1.442853e+01 1.819361e+01 # Hw SPCE + 1375 459 3 0.423800 9.097112e+00 5.763777e+00 1.055170e+01 # Hw SPCE + 1376 459 4 -0.847600 8.930312e+00 6.009500e+00 1.150658e+01 # Ow SPCE + 1377 459 3 0.423800 9.350086e+00 6.896101e+00 1.170082e+01 # Hw SPCE + 1378 460 3 0.423800 5.431310e+00 2.264163e+01 3.120189e+00 # Hw SPCE + 1379 460 4 -0.847600 5.550080e+00 2.304881e+01 2.214596e+00 # Ow SPCE + 1380 460 3 0.423800 6.336473e+00 2.366641e+01 2.227360e+00 # Hw SPCE + 1381 461 3 0.423800 1.793842e+01 1.486923e+01 5.835118e+00 # Hw SPCE + 1382 461 4 -0.847600 1.846091e+01 1.518650e+01 5.043692e+00 # Ow SPCE + 1383 461 3 0.423800 1.785140e+01 1.566604e+01 4.412394e+00 # Hw SPCE + 1384 462 3 0.423800 2.184585e+00 1.115490e+01 1.453262e+01 # Hw SPCE + 1385 462 4 -0.847600 2.343389e+00 1.213111e+01 1.438500e+01 # Ow SPCE + 1386 462 3 0.423800 1.503737e+00 1.255845e+01 1.404979e+01 # Hw SPCE + 1387 463 3 0.423800 1.441481e+01 3.522791e+00 2.760204e+01 # Hw SPCE + 1388 463 4 -0.847600 1.362346e+01 4.133742e+00 2.762456e+01 # Ow SPCE + 1389 463 3 0.423800 1.393539e+01 5.080332e+00 2.770621e+01 # Hw SPCE + 1390 464 3 0.423800 1.499700e+00 2.188838e+01 2.362087e+01 # Hw SPCE + 1391 464 4 -0.847600 1.945099e+00 2.224829e+01 2.280106e+01 # Ow SPCE + 1392 464 3 0.423800 1.720463e+00 2.166848e+01 2.201789e+01 # Hw SPCE + 1393 465 3 0.423800 2.708400e+01 2.218371e+01 9.205305e+00 # Hw SPCE + 1394 465 4 -0.847600 2.770480e+01 2.226015e+01 8.425070e+00 # Ow SPCE + 1395 465 3 0.423800 2.735466e+01 2.294536e+01 7.786410e+00 # Hw SPCE + 1396 466 3 0.423800 1.333326e+01 1.012770e+01 2.714313e+00 # Hw SPCE + 1397 466 4 -0.847600 1.396010e+01 1.090684e+01 2.710577e+00 # Ow SPCE + 1398 466 3 0.423800 1.343444e+01 1.175750e+01 2.703131e+00 # Hw SPCE + 1399 467 3 0.423800 1.830816e+01 1.219159e+01 1.158591e+01 # Hw SPCE + 1400 467 4 -0.847600 1.755544e+01 1.270612e+01 1.117519e+01 # Ow SPCE + 1401 467 3 0.423800 1.789433e+01 1.322125e+01 1.038792e+01 # Hw SPCE + 1402 468 3 0.423800 2.172042e+01 6.831038e+00 2.770644e+01 # Hw SPCE + 1403 468 4 -0.847600 2.223302e+01 6.193086e+00 2.713176e+01 # Ow SPCE + 1404 468 3 0.423800 2.267323e+01 5.504849e+00 2.770842e+01 # Hw SPCE + 1405 469 3 0.423800 6.268257e+00 1.075389e+01 2.334065e+01 # Hw SPCE + 1406 469 4 -0.847600 7.056234e+00 1.126624e+01 2.368211e+01 # Ow SPCE + 1407 469 3 0.423800 7.274106e+00 1.096339e+01 2.460991e+01 # Hw SPCE + 1408 470 3 0.423800 3.714354e+00 2.000821e+00 1.146332e+01 # Hw SPCE + 1409 470 4 -0.847600 2.897249e+00 1.502381e+00 1.175297e+01 # Ow SPCE + 1410 470 3 0.423800 2.235593e+00 1.482765e+00 1.100342e+01 # Hw SPCE + 1411 471 3 0.423800 2.322907e+01 2.917361e+00 5.997148e+00 # Hw SPCE + 1412 471 4 -0.847600 2.223897e+01 2.777046e+00 5.995080e+00 # Ow SPCE + 1413 471 3 0.423800 2.177665e+01 3.663721e+00 6.003295e+00 # Hw SPCE + 1414 472 3 0.423800 1.763400e+01 1.243773e+01 2.094696e+01 # Hw SPCE + 1415 472 4 -0.847600 1.752266e+01 1.335506e+01 2.056472e+01 # Ow SPCE + 1416 472 3 0.423800 1.837391e+01 1.363744e+01 2.012242e+01 # Hw SPCE + 1417 473 3 0.423800 2.155614e+01 1.654986e+01 2.018860e+01 # Hw SPCE + 1418 473 4 -0.847600 2.107547e+01 1.603549e+01 1.947841e+01 # Ow SPCE + 1419 473 3 0.423800 2.128393e+01 1.642895e+01 1.858301e+01 # Hw SPCE + 1420 474 3 0.423800 1.728050e+01 2.423683e+01 9.871601e+00 # Hw SPCE + 1421 474 4 -0.847600 1.738375e+01 2.347556e+01 9.231428e+00 # Ow SPCE + 1422 474 3 0.423800 1.719527e+01 2.379354e+01 8.302252e+00 # Hw SPCE + 1423 475 3 0.423800 1.650810e+00 6.990915e+00 2.295043e+01 # Hw SPCE + 1424 475 4 -0.847600 2.208121e+00 7.329955e+00 2.370836e+01 # Ow SPCE + 1425 475 3 0.423800 3.171215e+00 7.128177e+00 2.353022e+01 # Hw SPCE + 1426 476 3 0.423800 1.499730e+00 8.992460e+00 8.752017e+00 # Hw SPCE + 1427 476 4 -0.847600 1.510449e+00 9.936633e+00 9.081292e+00 # Ow SPCE + 1428 476 3 0.423800 2.456253e+00 1.025222e+01 9.157852e+00 # Hw SPCE + 1429 477 3 0.423800 1.524357e+00 1.612612e+01 7.337394e+00 # Hw SPCE + 1430 477 4 -0.847600 1.499367e+00 1.628416e+01 8.324511e+00 # Ow SPCE + 1431 477 3 0.423800 1.500368e+00 1.726779e+01 8.504717e+00 # Hw SPCE + 1432 478 3 0.423800 4.508742e+00 2.060049e+01 1.519230e+00 # Hw SPCE + 1433 478 4 -0.847600 5.486779e+00 2.039253e+01 1.505170e+00 # Ow SPCE + 1434 478 3 0.423800 5.616682e+00 1.940102e+01 1.500039e+00 # Hw SPCE + 1435 479 3 0.423800 1.922274e+01 8.093379e+00 8.219502e+00 # Hw SPCE + 1436 479 4 -0.847600 1.916411e+01 7.383197e+00 7.517929e+00 # Ow SPCE + 1437 479 3 0.423800 1.995519e+01 6.775915e+00 7.591466e+00 # Hw SPCE + 1438 480 3 0.423800 1.943784e+01 1.013386e+01 2.597417e+01 # Hw SPCE + 1439 480 4 -0.847600 2.017081e+01 9.453976e+00 2.599674e+01 # Ow SPCE + 1440 480 3 0.423800 2.007103e+01 8.883198e+00 2.681176e+01 # Hw SPCE + 1441 481 3 0.423800 4.192983e+00 2.092863e+01 2.367681e+01 # Hw SPCE + 1442 481 4 -0.847600 3.622627e+00 2.015436e+01 2.340257e+01 # Ow SPCE + 1443 481 3 0.423800 3.162762e+00 1.977780e+01 2.420677e+01 # Hw SPCE + 1444 482 3 0.423800 2.075118e+01 1.717508e+01 2.770677e+01 # Hw SPCE + 1445 482 4 -0.847600 1.976142e+01 1.731709e+01 2.769234e+01 # Ow SPCE + 1446 482 3 0.423800 1.929769e+01 1.643117e+01 2.768228e+01 # Hw SPCE + 1447 483 3 0.423800 6.778056e+00 1.536002e+01 7.209241e+00 # Hw SPCE + 1448 483 4 -0.847600 7.198296e+00 1.626143e+01 7.313492e+00 # Ow SPCE + 1449 483 3 0.423800 6.485256e+00 1.694623e+01 7.463902e+00 # Hw SPCE + 1450 484 3 0.423800 2.425409e+01 5.401110e+00 1.659432e+00 # Hw SPCE + 1451 484 4 -0.847600 2.351087e+01 5.727686e+00 2.243365e+00 # Ow SPCE + 1452 484 3 0.423800 2.360826e+01 6.712456e+00 2.387383e+00 # Hw SPCE + 1453 485 3 0.423800 1.686252e+01 4.577775e+00 1.853409e+01 # Hw SPCE + 1454 485 4 -0.847600 1.717109e+01 5.331094e+00 1.911486e+01 # Ow SPCE + 1455 485 3 0.423800 1.782031e+01 4.985329e+00 1.979233e+01 # Hw SPCE + 1456 486 3 0.423800 2.559447e+01 6.830529e+00 2.554992e+01 # Hw SPCE + 1457 486 4 -0.847600 2.476010e+01 7.328675e+00 2.578589e+01 # Ow SPCE + 1458 486 3 0.423800 2.465753e+01 8.114730e+00 2.517630e+01 # Hw SPCE + 1459 487 3 0.423800 2.618329e+01 1.274776e+01 2.027220e+01 # Hw SPCE + 1460 487 4 -0.847600 2.536296e+01 1.243771e+01 2.075274e+01 # Ow SPCE + 1461 487 3 0.423800 2.554309e+01 1.241004e+01 2.173600e+01 # Hw SPCE + 1462 488 3 0.423800 1.919981e+01 2.661638e+00 2.030213e+01 # Hw SPCE + 1463 488 4 -0.847600 1.973061e+01 2.904574e+00 2.111406e+01 # Ow SPCE + 1464 488 3 0.423800 1.914388e+01 2.856844e+00 2.192244e+01 # Hw SPCE + 1465 489 3 0.423800 2.266744e+01 1.984307e+01 8.978618e+00 # Hw SPCE + 1466 489 4 -0.847600 2.185883e+01 2.037567e+01 9.228600e+00 # Ow SPCE + 1467 489 3 0.423800 2.212644e+01 2.132149e+01 9.412457e+00 # Hw SPCE + 1468 490 3 0.423800 4.817158e+00 1.523570e+00 6.050418e+00 # Hw SPCE + 1469 490 4 -0.847600 4.254228e+00 1.621274e+00 6.871127e+00 # Ow SPCE + 1470 490 3 0.423800 3.291277e+00 1.497598e+00 6.631484e+00 # Hw SPCE + 1471 491 3 0.423800 1.079473e+01 2.139909e+01 1.857674e+01 # Hw SPCE + 1472 491 4 -0.847600 1.177944e+01 2.140440e+01 1.840264e+01 # Ow SPCE + 1473 491 3 0.423800 1.226661e+01 2.114195e+01 1.923559e+01 # Hw SPCE + 1474 492 3 0.423800 2.471848e+01 2.047547e+01 7.260132e+00 # Hw SPCE + 1475 492 4 -0.847600 2.453164e+01 2.145726e+01 7.225866e+00 # Ow SPCE + 1476 492 3 0.423800 2.451936e+01 2.182685e+01 8.154981e+00 # Hw SPCE + 1477 493 3 0.423800 1.868210e+01 2.290815e+01 2.448807e+01 # Hw SPCE + 1478 493 4 -0.847600 1.872346e+01 2.190901e+01 2.448402e+01 # Ow SPCE + 1479 493 3 0.423800 1.929678e+01 2.160222e+01 2.372430e+01 # Hw SPCE + 1480 494 3 0.423800 9.843500e+00 1.140046e+01 2.548708e+01 # Hw SPCE + 1481 494 4 -0.847600 1.054880e+01 1.070283e+01 2.536110e+01 # Ow SPCE + 1482 494 3 0.423800 1.144375e+01 1.114300e+01 2.528825e+01 # Hw SPCE + 1483 495 3 0.423800 6.422993e+00 1.821276e+01 9.903863e+00 # Hw SPCE + 1484 495 4 -0.847600 7.333960e+00 1.850491e+01 9.612681e+00 # Ow SPCE + 1485 495 3 0.423800 8.018713e+00 1.813856e+01 1.024268e+01 # Hw SPCE + 1486 496 3 0.423800 2.471333e+01 2.384780e+01 2.166757e+01 # Hw SPCE + 1487 496 4 -0.847600 2.416185e+01 2.454566e+01 2.121055e+01 # Ow SPCE + 1488 496 3 0.423800 2.476291e+01 2.524546e+01 2.082453e+01 # Hw SPCE + 1489 497 3 0.423800 2.590620e+00 8.091003e+00 2.061080e+01 # Hw SPCE + 1490 497 4 -0.847600 3.231566e+00 7.330610e+00 2.071564e+01 # Ow SPCE + 1491 497 3 0.423800 3.920110e+00 7.372830e+00 1.999168e+01 # Hw SPCE + 1492 498 3 0.423800 8.949464e+00 2.425655e+01 3.695045e+00 # Hw SPCE + 1493 498 4 -0.847600 9.202844e+00 2.412128e+01 4.652907e+00 # Ow SPCE + 1494 498 3 0.423800 9.142579e+00 2.499262e+01 5.139877e+00 # Hw SPCE + 1495 499 3 0.423800 1.764683e+01 2.974023e+00 1.499949e+00 # Hw SPCE + 1496 499 4 -0.847600 1.685020e+01 2.477365e+00 1.844498e+00 # Ow SPCE + 1497 499 3 0.423800 1.705690e+01 1.499622e+00 1.880419e+00 # Hw SPCE + 1498 500 3 0.423800 2.126518e+01 3.913868e+00 1.808240e+01 # Hw SPCE + 1499 500 4 -0.847600 2.045368e+01 3.344904e+00 1.794915e+01 # Ow SPCE + 1500 500 3 0.423800 1.970398e+01 3.909289e+00 1.760359e+01 # Hw SPCE + 1501 501 3 0.423800 1.495876e+00 2.614890e+01 2.082634e+01 # Hw SPCE + 1502 501 4 -0.847600 2.060720e+00 2.545025e+01 2.126548e+01 # Ow SPCE + 1503 501 3 0.423800 1.496549e+00 2.465376e+01 2.148298e+01 # Hw SPCE + 1504 502 3 0.423800 2.279048e+01 9.290222e+00 2.681803e+01 # Hw SPCE + 1505 502 4 -0.847600 2.327017e+01 9.655579e+00 2.761579e+01 # Ow SPCE + 1506 502 3 0.423800 2.416046e+01 9.208611e+00 2.770297e+01 # Hw SPCE + 1507 503 3 0.423800 1.498663e+00 4.051791e+00 1.406843e+01 # Hw SPCE + 1508 503 4 -0.847600 2.227842e+00 4.516378e+00 1.356598e+01 # Ow SPCE + 1509 503 3 0.423800 2.947213e+00 3.859735e+00 1.333943e+01 # Hw SPCE + 1510 504 3 0.423800 4.121509e+00 1.297824e+01 1.026964e+01 # Hw SPCE + 1511 504 4 -0.847600 3.726321e+00 1.373934e+01 1.078398e+01 # Ow SPCE + 1512 504 3 0.423800 3.570218e+00 1.345664e+01 1.173040e+01 # Hw SPCE + 1513 505 3 0.423800 1.938062e+01 1.410367e+01 8.241157e+00 # Hw SPCE + 1514 505 4 -0.847600 1.995758e+01 1.491592e+01 8.155362e+00 # Ow SPCE + 1515 505 3 0.423800 2.066193e+01 1.475299e+01 7.464465e+00 # Hw SPCE + 1516 506 3 0.423800 1.635093e+01 4.629187e+00 2.599280e+01 # Hw SPCE + 1517 506 4 -0.847600 1.660343e+01 5.572751e+00 2.577847e+01 # Ow SPCE + 1518 506 3 0.423800 1.597027e+01 6.198813e+00 2.623361e+01 # Hw SPCE + 1519 507 3 0.423800 2.572095e+01 1.411800e+01 2.664163e+01 # Hw SPCE + 1520 507 4 -0.847600 2.489025e+01 1.466440e+01 2.653495e+01 # Ow SPCE + 1521 507 3 0.423800 2.417927e+01 1.431235e+01 2.714369e+01 # Hw SPCE + 1522 508 3 0.423800 2.106512e+01 3.934685e+00 1.521472e+01 # Hw SPCE + 1523 508 4 -0.847600 2.145982e+01 3.015920e+00 1.522367e+01 # Ow SPCE + 1524 508 3 0.423800 2.073659e+01 2.343985e+00 1.538314e+01 # Hw SPCE + 1525 509 3 0.423800 1.747101e+01 1.089516e+01 1.867742e+01 # Hw SPCE + 1526 509 4 -0.847600 1.750084e+01 1.180616e+01 1.826610e+01 # Ow SPCE + 1527 509 3 0.423800 1.671577e+01 1.192311e+01 1.765784e+01 # Hw SPCE + 1528 510 3 0.423800 2.149389e+01 8.833650e+00 6.611416e+00 # Hw SPCE + 1529 510 4 -0.847600 2.177394e+01 9.611791e+00 7.173615e+00 # Ow SPCE + 1530 510 3 0.423800 2.254669e+01 9.345700e+00 7.749852e+00 # Hw SPCE + 1531 511 3 0.423800 3.791408e+00 1.897825e+01 1.012530e+01 # Hw SPCE + 1532 511 4 -0.847600 3.851687e+00 1.885137e+01 9.135211e+00 # Ow SPCE + 1533 511 3 0.423800 3.179880e+00 1.943767e+01 8.682525e+00 # Hw SPCE + 1534 512 3 0.423800 1.252372e+01 2.047991e+01 2.549174e+01 # Hw SPCE + 1535 512 4 -0.847600 1.324747e+01 2.111712e+01 2.522688e+01 # Ow SPCE + 1536 512 3 0.423800 1.305955e+01 2.201712e+01 2.562020e+01 # Hw SPCE + 1537 513 3 0.423800 9.857980e+00 8.140566e+00 9.299584e+00 # Hw SPCE + 1538 513 4 -0.847600 1.080806e+01 7.847241e+00 9.193255e+00 # Ow SPCE + 1539 513 3 0.423800 1.136372e+01 8.620982e+00 8.889004e+00 # Hw SPCE + 1540 514 3 0.423800 2.468682e+01 1.540730e+01 1.499507e+00 # Hw SPCE + 1541 514 4 -0.847600 2.388089e+01 1.498355e+01 1.912937e+00 # Ow SPCE + 1542 514 3 0.423800 2.305466e+01 1.541498e+01 1.550717e+00 # Hw SPCE + 1543 515 3 0.423800 1.464646e+01 2.252692e+01 1.926250e+01 # Hw SPCE + 1544 515 4 -0.847600 1.547386e+01 2.308846e+01 1.925340e+01 # Ow SPCE + 1545 515 3 0.423800 1.626223e+01 2.251673e+01 1.902626e+01 # Hw SPCE + 1546 516 3 0.423800 2.767962e+01 2.118986e+01 2.645961e+01 # Hw SPCE + 1547 516 4 -0.847600 2.770572e+01 2.108694e+01 2.745396e+01 # Ow SPCE + 1548 516 3 0.423800 2.734198e+01 2.019016e+01 2.770589e+01 # Hw SPCE + 1549 517 3 0.423800 5.473025e+00 1.539565e+01 1.766372e+01 # Hw SPCE + 1550 517 4 -0.847600 5.457163e+00 1.532146e+01 1.866084e+01 # Ow SPCE + 1551 517 3 0.423800 5.719911e+00 1.439500e+01 1.893036e+01 # Hw SPCE + 1552 518 3 0.423800 1.355721e+01 1.609064e+01 7.981517e+00 # Hw SPCE + 1553 518 4 -0.847600 1.451195e+01 1.585086e+01 7.805517e+00 # Ow SPCE + 1554 518 3 0.423800 1.510515e+01 1.659197e+01 8.119965e+00 # Hw SPCE + 1555 519 3 0.423800 1.185686e+01 2.756045e+01 1.746044e+01 # Hw SPCE + 1556 519 4 -0.847600 1.271387e+01 2.750488e+01 1.694815e+01 # Ow SPCE + 1557 519 3 0.423800 1.289860e+01 2.655139e+01 1.670998e+01 # Hw SPCE + 1558 520 3 0.423800 2.770610e+01 1.433506e+01 2.192258e+01 # Hw SPCE + 1559 520 4 -0.847600 2.713948e+01 1.511976e+01 2.217392e+01 # Ow SPCE + 1560 520 3 0.423800 2.770524e+01 1.594383e+01 2.220271e+01 # Hw SPCE + 1561 521 3 0.423800 1.499493e+01 1.238797e+01 2.007948e+01 # Hw SPCE + 1562 521 4 -0.847600 1.464506e+01 1.280227e+01 1.923927e+01 # Ow SPCE + 1563 521 3 0.423800 1.485236e+01 1.378055e+01 1.923864e+01 # Hw SPCE + 1564 522 3 0.423800 1.136191e+01 6.926399e+00 2.399031e+01 # Hw SPCE + 1565 522 4 -0.847600 1.054592e+01 7.370139e+00 2.436079e+01 # Ow SPCE + 1566 522 3 0.423800 9.932311e+00 6.677061e+00 2.473911e+01 # Hw SPCE + 1567 523 3 0.423800 7.548290e+00 2.174968e+00 3.349358e+00 # Hw SPCE + 1568 523 4 -0.847600 6.864919e+00 1.475454e+00 3.558363e+00 # Ow SPCE + 1569 523 3 0.423800 5.952602e+00 1.884488e+00 3.539162e+00 # Hw SPCE + 1570 524 3 0.423800 2.257539e+01 7.886933e+00 2.106609e+01 # Hw SPCE + 1571 524 4 -0.847600 2.236455e+01 7.157236e+00 2.041564e+01 # Ow SPCE + 1572 524 3 0.423800 2.320865e+01 6.845285e+00 1.997954e+01 # Hw SPCE + 1573 525 3 0.423800 1.931716e+01 2.614213e+01 1.741829e+01 # Hw SPCE + 1574 525 4 -0.847600 1.896046e+01 2.707452e+01 1.747657e+01 # Ow SPCE + 1575 525 3 0.423800 1.970938e+01 2.770594e+01 1.767766e+01 # Hw SPCE + 1576 526 3 0.423800 1.293280e+01 1.317757e+01 1.712150e+01 # Hw SPCE + 1577 526 4 -0.847600 1.315759e+01 1.415177e+01 1.710169e+01 # Ow SPCE + 1578 526 3 0.423800 1.254740e+01 1.464728e+01 1.771987e+01 # Hw SPCE + 1579 527 3 0.423800 7.790007e+00 6.046852e+00 2.770758e+01 # Hw SPCE + 1580 527 4 -0.847600 6.829260e+00 5.769427e+00 2.770728e+01 # Ow SPCE + 1581 527 3 0.423800 6.770591e+00 4.771151e+00 2.770535e+01 # Hw SPCE + 1582 528 3 0.423800 1.123375e+01 2.298556e+01 2.380651e+01 # Hw SPCE + 1583 528 4 -0.847600 1.075845e+01 2.212317e+01 2.398080e+01 # Ow SPCE + 1584 528 3 0.423800 1.039779e+01 2.212396e+01 2.491350e+01 # Hw SPCE + 1585 529 3 0.423800 4.200882e+00 1.931622e+01 2.770757e+01 # Hw SPCE + 1586 529 4 -0.847600 5.175713e+00 1.953916e+01 2.770789e+01 # Ow SPCE + 1587 529 3 0.423800 5.710832e+00 1.869439e+01 2.770832e+01 # Hw SPCE + 1588 530 3 0.423800 2.770456e+01 1.697514e+01 9.342626e+00 # Hw SPCE + 1589 530 4 -0.847600 2.770706e+01 1.614854e+01 9.905419e+00 # Ow SPCE + 1590 530 3 0.423800 2.770253e+01 1.534242e+01 9.313697e+00 # Hw SPCE + 1591 531 3 0.423800 1.832884e+01 7.670320e+00 2.009972e+01 # Hw SPCE + 1592 531 4 -0.847600 1.770977e+01 8.379274e+00 1.976188e+01 # Ow SPCE + 1593 531 3 0.423800 1.728273e+01 8.071375e+00 1.891168e+01 # Hw SPCE + 1594 532 3 0.423800 1.164885e+01 2.369859e+00 6.675939e+00 # Hw SPCE + 1595 532 4 -0.847600 1.119973e+01 1.488536e+00 6.822766e+00 # Ow SPCE + 1596 532 3 0.423800 1.021557e+01 1.629733e+00 6.930003e+00 # Hw SPCE + 1597 533 3 0.423800 1.736192e+01 1.608261e+01 2.086977e+01 # Hw SPCE + 1598 533 4 -0.847600 1.663485e+01 1.658639e+01 2.133622e+01 # Ow SPCE + 1599 533 3 0.423800 1.582226e+01 1.661428e+01 2.075406e+01 # Hw SPCE + 1600 534 3 0.423800 2.770538e+01 1.618975e+01 6.697811e+00 # Hw SPCE + 1601 534 4 -0.847600 2.683077e+01 1.586285e+01 6.339763e+00 # Ow SPCE + 1602 534 3 0.423800 2.644970e+01 1.654559e+01 5.716346e+00 # Hw SPCE + 1603 535 3 0.423800 1.073071e+01 3.382764e+00 1.994761e+00 # Hw SPCE + 1604 535 4 -0.847600 1.068786e+01 2.506336e+00 2.474384e+00 # Ow SPCE + 1605 535 3 0.423800 1.061173e+01 1.764903e+00 1.807690e+00 # Hw SPCE + 1606 536 3 0.423800 5.975184e+00 9.418923e+00 1.756302e+01 # Hw SPCE + 1607 536 4 -0.847600 6.920951e+00 9.718084e+00 1.768962e+01 # Ow SPCE + 1608 536 3 0.423800 6.942337e+00 1.070925e+01 1.782049e+01 # Hw SPCE + 1609 537 3 0.423800 1.360924e+01 2.146817e+01 1.387145e+01 # Hw SPCE + 1610 537 4 -0.847600 1.450822e+01 2.119277e+01 1.353090e+01 # Ow SPCE + 1611 537 3 0.423800 1.516476e+01 2.119288e+01 1.428519e+01 # Hw SPCE + 1612 538 3 0.423800 8.874645e+00 2.735638e+00 1.567786e+01 # Hw SPCE + 1613 538 4 -0.847600 8.841213e+00 1.743745e+00 1.555526e+01 # Ow SPCE + 1614 538 3 0.423800 9.281324e+00 1.499682e+00 1.469112e+01 # Hw SPCE + 1615 539 3 0.423800 2.677837e+01 2.727822e+01 1.521683e+01 # Hw SPCE + 1616 539 4 -0.847600 2.716773e+01 2.651889e+01 1.573819e+01 # Ow SPCE + 1617 539 3 0.423800 2.770480e+01 2.593640e+01 1.512805e+01 # Hw SPCE + 1618 540 3 0.423800 1.348931e+01 2.050695e+01 1.644491e+01 # Hw SPCE + 1619 540 4 -0.847600 1.379303e+01 1.955419e+01 1.644174e+01 # Ow SPCE + 1620 540 3 0.423800 1.479253e+01 1.952299e+01 1.643578e+01 # Hw SPCE + 1621 541 3 0.423800 2.712765e+01 2.770458e+01 1.499784e+00 # Hw SPCE + 1622 541 4 -0.847600 2.710752e+01 2.724363e+01 2.386980e+00 # Ow SPCE + 1623 541 3 0.423800 2.619044e+01 2.731545e+01 2.779174e+00 # Hw SPCE + 1624 542 3 0.423800 9.946949e+00 2.110450e+01 2.770454e+01 # Hw SPCE + 1625 542 4 -0.847600 9.160696e+00 2.085784e+01 2.713800e+01 # Ow SPCE + 1626 542 3 0.423800 8.468408e+00 2.041129e+01 2.770486e+01 # Hw SPCE + 1627 543 3 0.423800 1.504399e+00 1.083302e+01 2.009960e+01 # Hw SPCE + 1628 543 4 -0.847600 1.816408e+00 1.177936e+01 2.018384e+01 # Ow SPCE + 1629 543 3 0.423800 2.807855e+00 1.181584e+01 2.005853e+01 # Hw SPCE + 1630 544 3 0.423800 2.543910e+01 2.947611e+00 2.768656e+01 # Hw SPCE + 1631 544 4 -0.847600 2.451490e+01 2.595735e+00 2.753807e+01 # Ow SPCE + 1632 544 3 0.423800 2.455905e+01 1.616936e+00 2.733806e+01 # Hw SPCE + 1633 545 3 0.423800 2.361457e+01 1.312219e+01 1.230861e+01 # Hw SPCE + 1634 545 4 -0.847600 2.413492e+01 1.356531e+01 1.303860e+01 # Ow SPCE + 1635 545 3 0.423800 2.440618e+01 1.288209e+01 1.371657e+01 # Hw SPCE + 1636 546 3 0.423800 1.870442e+01 2.642254e+01 9.001379e+00 # Hw SPCE + 1637 546 4 -0.847600 1.888946e+01 2.680197e+01 8.094851e+00 # Ow SPCE + 1638 546 3 0.423800 1.831281e+01 2.634447e+01 7.417974e+00 # Hw SPCE + 1639 547 3 0.423800 1.955187e+01 2.669861e+01 1.982066e+00 # Hw SPCE + 1640 547 4 -0.847600 1.983701e+01 2.765621e+01 2.023180e+00 # Ow SPCE + 1641 547 3 0.423800 2.083300e+01 2.770447e+01 2.098561e+00 # Hw SPCE + 1642 548 3 0.423800 5.421499e+00 2.757790e+01 1.294457e+01 # Hw SPCE + 1643 548 4 -0.847600 5.110506e+00 2.770464e+01 1.388649e+01 # Ow SPCE + 1644 548 3 0.423800 4.115657e+00 2.761068e+01 1.392453e+01 # Hw SPCE + 1645 549 3 0.423800 1.667681e+01 2.723516e+01 2.218951e+01 # Hw SPCE + 1646 549 4 -0.847600 1.593196e+01 2.771570e+01 2.265241e+01 # Ow SPCE + 1647 549 3 0.423800 1.507418e+01 2.754768e+01 2.216664e+01 # Hw SPCE + 1648 550 3 0.423800 2.433245e+01 2.342839e+01 1.128065e+01 # Hw SPCE + 1649 550 4 -0.847600 2.415467e+01 2.258524e+01 1.077321e+01 # Ow SPCE + 1650 550 3 0.423800 2.415864e+01 2.180938e+01 1.140410e+01 # Hw SPCE + 1651 551 3 0.423800 1.837587e+01 2.123822e+01 2.725995e+01 # Hw SPCE + 1652 551 4 -0.847600 1.779349e+01 2.043021e+01 2.734918e+01 # Ow SPCE + 1653 551 3 0.423800 1.833384e+01 1.966748e+01 2.770453e+01 # Hw SPCE + 1654 552 3 0.423800 1.592706e+01 1.936515e+00 2.435957e+01 # Hw SPCE + 1655 552 4 -0.847600 1.505896e+01 1.499035e+00 2.412505e+01 # Ow SPCE + 1656 552 3 0.423800 1.454993e+01 2.085140e+00 2.349467e+01 # Hw SPCE + 1657 553 3 0.423800 1.747565e+01 1.731294e+01 9.312832e+00 # Hw SPCE + 1658 553 4 -0.847600 1.766196e+01 1.635124e+01 9.111737e+00 # Ow SPCE + 1659 553 3 0.423800 1.809084e+01 1.592158e+01 9.906376e+00 # Hw SPCE + 1660 554 3 0.423800 8.312156e+00 2.203891e+01 1.687596e+01 # Hw SPCE + 1661 554 4 -0.847600 8.145446e+00 2.107334e+01 1.667629e+01 # Ow SPCE + 1662 554 3 0.423800 7.160271e+00 2.090436e+01 1.664666e+01 # Hw SPCE + 1663 555 3 0.423800 1.452310e+01 2.241336e+01 9.977204e+00 # Hw SPCE + 1664 555 4 -0.847600 1.467835e+01 2.336383e+01 9.707951e+00 # Ow SPCE + 1665 555 3 0.423800 1.427486e+01 2.397365e+01 1.039009e+01 # Hw SPCE + 1666 556 3 0.423800 2.770573e+01 9.991646e+00 1.639356e+01 # Hw SPCE + 1667 556 4 -0.847600 2.733485e+01 1.000499e+01 1.546498e+01 # Ow SPCE + 1668 556 3 0.423800 2.770500e+01 9.233753e+00 1.494711e+01 # Hw SPCE + 1669 557 3 0.423800 2.255789e+01 1.833507e+01 1.626641e+01 # Hw SPCE + 1670 557 4 -0.847600 2.351546e+01 1.820880e+01 1.652545e+01 # Ow SPCE + 1671 557 3 0.423800 2.406042e+01 1.802400e+01 1.570760e+01 # Hw SPCE + 1672 558 3 0.423800 1.525572e+01 2.770743e+01 1.200379e+01 # Hw SPCE + 1673 558 4 -0.847600 1.484040e+01 2.707735e+01 1.265992e+01 # Ow SPCE + 1674 558 3 0.423800 1.406834e+01 2.752601e+01 1.311006e+01 # Hw SPCE + 1675 559 3 0.423800 1.658932e+01 1.906188e+01 1.328318e+01 # Hw SPCE + 1676 559 4 -0.847600 1.675201e+01 1.815055e+01 1.290501e+01 # Ow SPCE + 1677 559 3 0.423800 1.758478e+01 1.776758e+01 1.330480e+01 # Hw SPCE + 1678 560 3 0.423800 1.004229e+01 1.712720e+01 2.079854e+01 # Hw SPCE + 1679 560 4 -0.847600 1.063564e+01 1.789587e+01 2.103746e+01 # Ow SPCE + 1680 560 3 0.423800 1.010311e+01 1.874227e+01 2.103197e+01 # Hw SPCE + 1681 561 3 0.423800 2.500505e+01 1.070351e+01 4.512067e+00 # Hw SPCE + 1682 561 4 -0.847600 2.573603e+01 1.010670e+01 4.181178e+00 # Ow SPCE + 1683 561 3 0.423800 2.648741e+01 1.066421e+01 3.828189e+00 # Hw SPCE + 1684 562 3 0.423800 1.210303e+01 1.800383e+01 9.349879e+00 # Hw SPCE + 1685 562 4 -0.847600 1.113080e+01 1.778888e+01 9.442458e+00 # Ow SPCE + 1686 562 3 0.423800 1.060025e+01 1.863653e+01 9.439283e+00 # Hw SPCE + 1687 563 3 0.423800 1.030762e+01 7.414060e+00 2.769564e+01 # Hw SPCE + 1688 563 4 -0.847600 1.049207e+01 6.470196e+00 2.742160e+01 # Ow SPCE + 1689 563 3 0.423800 1.141031e+01 6.209855e+00 2.772004e+01 # Hw SPCE + 1690 564 3 0.423800 4.398211e+00 2.689864e+01 2.124419e+01 # Hw SPCE + 1691 564 4 -0.847600 4.266022e+00 2.770576e+01 2.181959e+01 # Ow SPCE + 1692 564 3 0.423800 3.351717e+00 2.768078e+01 2.222384e+01 # Hw SPCE + 1693 565 3 0.423800 8.283521e+00 2.495708e+01 9.955134e+00 # Hw SPCE + 1694 565 4 -0.847600 7.965370e+00 2.543617e+01 1.077322e+01 # Ow SPCE + 1695 565 3 0.423800 8.600427e+00 2.526670e+01 1.152686e+01 # Hw SPCE + 1696 566 3 0.423800 2.718771e+01 5.401651e+00 2.294482e+01 # Hw SPCE + 1697 566 4 -0.847600 2.770619e+01 6.078594e+00 2.346725e+01 # Ow SPCE + 1698 566 3 0.423800 2.727173e+01 6.974594e+00 2.337542e+01 # Hw SPCE + 1699 567 3 0.423800 1.344671e+01 1.859690e+01 1.608430e+00 # Hw SPCE + 1700 567 4 -0.847600 1.362491e+01 1.880297e+01 2.570605e+00 # Ow SPCE + 1701 567 3 0.423800 1.316244e+01 1.812923e+01 3.146969e+00 # Hw SPCE + 1702 568 3 0.423800 1.583162e+01 2.444348e+01 5.926474e+00 # Hw SPCE + 1703 568 4 -0.847600 1.499075e+01 2.459672e+01 6.445563e+00 # Ow SPCE + 1704 568 3 0.423800 1.478045e+01 2.378288e+01 6.987262e+00 # Hw SPCE + 1705 569 3 0.423800 9.922789e+00 5.193782e+00 2.202243e+01 # Hw SPCE + 1706 569 4 -0.847600 9.563582e+00 6.125784e+00 2.207083e+01 # Ow SPCE + 1707 569 3 0.423800 8.644820e+00 6.149777e+00 2.167675e+01 # Hw SPCE + 1708 570 3 0.423800 8.914720e+00 8.315418e+00 1.641874e+01 # Hw SPCE + 1709 570 4 -0.847600 9.302874e+00 8.063947e+00 1.553212e+01 # Ow SPCE + 1710 570 3 0.423800 1.015658e+01 8.564357e+00 1.538800e+01 # Hw SPCE + 1711 571 3 0.423800 1.175235e+01 1.796050e+01 1.792472e+01 # Hw SPCE + 1712 571 4 -0.847600 1.132726e+01 1.866461e+01 1.849353e+01 # Ow SPCE + 1713 571 3 0.423800 1.034732e+01 1.870417e+01 1.829820e+01 # Hw SPCE + 1714 572 3 0.423800 2.334407e+01 2.469584e+01 1.753610e+01 # Hw SPCE + 1715 572 4 -0.847600 2.274051e+01 2.390140e+01 1.760386e+01 # Ow SPCE + 1716 572 3 0.423800 2.178874e+01 2.420714e+01 1.762968e+01 # Hw SPCE + 1717 573 3 0.423800 1.560477e+01 2.702754e+01 1.716266e+00 # Hw SPCE + 1718 573 4 -0.847600 1.525408e+01 2.737955e+01 2.584082e+00 # Ow SPCE + 1719 573 3 0.423800 1.428469e+01 2.760432e+01 2.485249e+00 # Hw SPCE + 1720 574 3 0.423800 7.381621e+00 2.092978e+01 1.938298e+01 # Hw SPCE + 1721 574 4 -0.847600 8.033211e+00 2.166093e+01 1.958511e+01 # Ow SPCE + 1722 574 3 0.423800 7.576710e+00 2.237804e+01 2.011176e+01 # Hw SPCE + 1723 575 3 0.423800 1.345344e+01 1.285413e+01 6.248165e+00 # Hw SPCE + 1724 575 4 -0.847600 1.335825e+01 1.348350e+01 7.019426e+00 # Ow SPCE + 1725 575 3 0.423800 1.239316e+01 1.371343e+01 7.144852e+00 # Hw SPCE + 1726 576 3 0.423800 1.684996e+01 1.496546e+00 2.112863e+01 # Hw SPCE + 1727 576 4 -0.847600 1.612315e+01 1.500121e+00 2.044180e+01 # Ow SPCE + 1728 576 3 0.423800 1.523334e+01 1.502605e+00 2.089813e+01 # Hw SPCE + 1729 577 3 0.423800 1.259795e+01 6.059961e+00 1.028903e+01 # Hw SPCE + 1730 577 4 -0.847600 1.265203e+01 6.809136e+00 1.094919e+01 # Ow SPCE + 1731 577 3 0.423800 1.210535e+01 6.583051e+00 1.175544e+01 # Hw SPCE + 1732 578 3 0.423800 1.175266e+01 1.642499e+01 1.504706e+00 # Hw SPCE + 1733 578 4 -0.847600 1.124046e+01 1.563939e+01 1.851816e+00 # Ow SPCE + 1734 578 3 0.423800 1.171187e+01 1.479512e+01 1.596895e+00 # Hw SPCE + 1735 579 3 0.423800 1.964008e+01 1.500636e+01 2.214316e+01 # Hw SPCE + 1736 579 4 -0.847600 2.038415e+01 1.503982e+01 2.281043e+01 # Ow SPCE + 1737 579 3 0.423800 2.013831e+01 1.449401e+01 2.361146e+01 # Hw SPCE + 1738 580 3 0.423800 6.359780e+00 1.494462e+00 9.725939e+00 # Hw SPCE + 1739 580 4 -0.847600 5.623160e+00 2.122431e+00 9.474851e+00 # Ow SPCE + 1740 580 3 0.423800 5.796855e+00 3.019459e+00 9.881263e+00 # Hw SPCE + 1741 581 3 0.423800 2.339449e+01 2.716322e+01 4.184562e+00 # Hw SPCE + 1742 581 4 -0.847600 2.365407e+01 2.624102e+01 4.471228e+00 # Ow SPCE + 1743 581 3 0.423800 2.284652e+01 2.575711e+01 4.808419e+00 # Hw SPCE + 1744 582 3 0.423800 2.817273e+00 2.461806e+01 5.932450e+00 # Hw SPCE + 1745 582 4 -0.847600 2.010189e+00 2.426140e+01 6.402994e+00 # Ow SPCE + 1746 582 3 0.423800 1.499435e+00 2.366530e+01 5.783477e+00 # Hw SPCE + 1747 583 3 0.423800 1.234255e+01 1.396176e+01 2.037507e+01 # Hw SPCE + 1748 583 4 -0.847600 1.153188e+01 1.453863e+01 2.027487e+01 # Ow SPCE + 1749 583 3 0.423800 1.071536e+01 1.396252e+01 2.023761e+01 # Hw SPCE + 1750 584 3 0.423800 2.810909e+00 2.179238e+01 7.310922e+00 # Hw SPCE + 1751 584 4 -0.847600 3.683406e+00 2.228090e+01 7.320812e+00 # Ow SPCE + 1752 584 3 0.423800 4.405822e+00 2.166653e+01 7.638090e+00 # Hw SPCE + 1753 585 3 0.423800 8.448996e+00 2.068506e+01 1.886024e+00 # Hw SPCE + 1754 585 4 -0.847600 8.120115e+00 2.158805e+01 1.609529e+00 # Ow SPCE + 1755 585 3 0.423800 8.825993e+00 2.227138e+01 1.796065e+00 # Hw SPCE + 1756 586 3 0.423800 1.552035e+01 1.189869e+01 1.283899e+01 # Hw SPCE + 1757 586 4 -0.847600 1.524184e+01 1.098045e+01 1.255745e+01 # Ow SPCE + 1758 586 3 0.423800 1.602690e+01 1.036326e+01 1.260993e+01 # Hw SPCE + 1759 587 3 0.423800 1.037404e+01 1.680250e+01 1.410571e+01 # Hw SPCE + 1760 587 4 -0.847600 9.390321e+00 1.671053e+01 1.395132e+01 # Ow SPCE + 1761 587 3 0.423800 9.132024e+00 1.574640e+01 1.401253e+01 # Hw SPCE + 1762 588 3 0.423800 1.925143e+01 2.771036e+01 1.136823e+01 # Hw SPCE + 1763 588 4 -0.847600 1.825753e+01 2.762221e+01 1.143454e+01 # Ow SPCE + 1764 588 3 0.423800 1.797827e+01 2.770904e+01 1.239082e+01 # Hw SPCE + 1765 589 3 0.423800 5.368954e+00 1.319885e+01 2.246010e+01 # Hw SPCE + 1766 589 4 -0.847600 5.623630e+00 1.391457e+01 2.311039e+01 # Ow SPCE + 1767 589 3 0.423800 4.872485e+00 1.456903e+01 2.319682e+01 # Hw SPCE + 1768 590 3 0.423800 2.502067e+01 2.248026e+01 2.658176e+01 # Hw SPCE + 1769 590 4 -0.847600 2.503552e+01 2.164180e+01 2.712652e+01 # Ow SPCE + 1770 590 3 0.423800 2.494862e+01 2.084997e+01 2.652199e+01 # Hw SPCE + 1771 591 3 0.423800 2.771210e+01 9.857496e+00 2.349471e+01 # Hw SPCE + 1772 591 4 -0.847600 2.758172e+01 1.077731e+01 2.312465e+01 # Ow SPCE + 1773 591 3 0.423800 2.770545e+01 1.075806e+01 2.213252e+01 # Hw SPCE + 1774 592 3 0.423800 2.236208e+01 1.289022e+01 1.568659e+01 # Hw SPCE + 1775 592 4 -0.847600 2.242230e+01 1.193201e+01 1.596625e+01 # Ow SPCE + 1776 592 3 0.423800 2.300802e+01 1.185651e+01 1.677324e+01 # Hw SPCE + 1777 593 3 0.423800 1.988201e+01 1.279194e+01 1.687017e+01 # Hw SPCE + 1778 593 4 -0.847600 2.021378e+01 1.300179e+01 1.778990e+01 # Ow SPCE + 1779 593 3 0.423800 2.066551e+01 1.219616e+01 1.817317e+01 # Hw SPCE + 1780 594 3 0.423800 1.468952e+01 2.770673e+01 5.255360e+00 # Hw SPCE + 1781 594 4 -0.847600 1.548366e+01 2.712680e+01 5.437112e+00 # Ow SPCE + 1782 594 3 0.423800 1.628119e+01 2.770158e+01 5.620343e+00 # Hw SPCE + 1783 595 3 0.423800 8.562539e+00 2.043599e+01 4.622579e+00 # Hw SPCE + 1784 595 4 -0.847600 8.510816e+00 2.140691e+01 4.856324e+00 # Ow SPCE + 1785 595 3 0.423800 7.721353e+00 2.181791e+01 4.400437e+00 # Hw SPCE + 1786 596 3 0.423800 2.770600e+01 1.600690e+01 2.686389e+01 # Hw SPCE + 1787 596 4 -0.847600 2.714850e+01 1.666860e+01 2.736525e+01 # Ow SPCE + 1788 596 3 0.423800 2.770517e+01 1.746675e+01 2.759565e+01 # Hw SPCE + 1789 597 3 0.423800 1.659849e+01 2.708928e+01 1.606821e+01 # Hw SPCE + 1790 597 4 -0.847600 1.561098e+01 2.693173e+01 1.606789e+01 # Ow SPCE + 1791 597 3 0.423800 1.515025e+01 2.770484e+01 1.563196e+01 # Hw SPCE + 1792 598 3 0.423800 2.769724e+01 2.030543e+01 2.142814e+01 # Hw SPCE + 1793 598 4 -0.847600 2.694008e+01 2.095316e+01 2.151277e+01 # Ow SPCE + 1794 598 3 0.423800 2.730269e+01 2.188246e+01 2.158290e+01 # Hw SPCE + 1795 599 3 0.423800 8.916687e+00 5.895426e+00 1.772221e+01 # Hw SPCE + 1796 599 4 -0.847600 9.042735e+00 5.158155e+00 1.705847e+01 # Ow SPCE + 1797 599 3 0.423800 9.690399e+00 5.450297e+00 1.635478e+01 # Hw SPCE + 1798 600 3 0.423800 1.753578e+01 1.707234e+01 2.389138e+01 # Hw SPCE + 1799 600 4 -0.847600 1.803190e+01 1.621348e+01 2.401877e+01 # Ow SPCE + 1800 600 3 0.423800 1.745017e+01 1.544840e+01 2.374267e+01 # Hw SPCE + +Bonds + + 1 1 2 1 # Ow-Hw + 2 1 3 2 # Ow-Hw + 3 1 5 4 # Ow-Hw + 4 1 6 5 # Ow-Hw + 5 1 8 7 # Ow-Hw + 6 1 9 8 # Ow-Hw + 7 1 11 10 # Ow-Hw + 8 1 12 11 # Ow-Hw + 9 1 14 13 # Ow-Hw + 10 1 15 14 # Ow-Hw + 11 1 17 16 # Ow-Hw + 12 1 18 17 # Ow-Hw + 13 1 20 19 # Ow-Hw + 14 1 21 20 # Ow-Hw + 15 1 23 22 # Ow-Hw + 16 1 24 23 # Ow-Hw + 17 1 26 25 # Ow-Hw + 18 1 27 26 # Ow-Hw + 19 1 29 28 # Ow-Hw + 20 1 30 29 # Ow-Hw + 21 1 32 31 # Ow-Hw + 22 1 33 32 # Ow-Hw + 23 1 35 34 # Ow-Hw + 24 1 36 35 # Ow-Hw + 25 1 38 37 # Ow-Hw + 26 1 39 38 # Ow-Hw + 27 1 41 40 # Ow-Hw + 28 1 42 41 # Ow-Hw + 29 1 44 43 # Ow-Hw + 30 1 45 44 # Ow-Hw + 31 1 47 46 # Ow-Hw + 32 1 48 47 # Ow-Hw + 33 1 50 49 # Ow-Hw + 34 1 51 50 # Ow-Hw + 35 1 53 52 # Ow-Hw + 36 1 54 53 # Ow-Hw + 37 1 56 55 # Ow-Hw + 38 1 57 56 # Ow-Hw + 39 1 59 58 # Ow-Hw + 40 1 60 59 # Ow-Hw + 41 1 62 61 # Ow-Hw + 42 1 63 62 # Ow-Hw + 43 1 65 64 # Ow-Hw + 44 1 66 65 # Ow-Hw + 45 1 68 67 # Ow-Hw + 46 1 69 68 # Ow-Hw + 47 1 71 70 # Ow-Hw + 48 1 72 71 # Ow-Hw + 49 1 74 73 # Ow-Hw + 50 1 75 74 # Ow-Hw + 51 1 77 76 # Ow-Hw + 52 1 78 77 # Ow-Hw + 53 1 80 79 # Ow-Hw + 54 1 81 80 # Ow-Hw + 55 1 83 82 # Ow-Hw + 56 1 84 83 # Ow-Hw + 57 1 86 85 # Ow-Hw + 58 1 87 86 # Ow-Hw + 59 1 89 88 # Ow-Hw + 60 1 90 89 # Ow-Hw + 61 1 92 91 # Ow-Hw + 62 1 93 92 # Ow-Hw + 63 1 95 94 # Ow-Hw + 64 1 96 95 # Ow-Hw + 65 1 98 97 # Ow-Hw + 66 1 99 98 # Ow-Hw + 67 1 101 100 # Ow-Hw + 68 1 102 101 # Ow-Hw + 69 1 104 103 # Ow-Hw + 70 1 105 104 # Ow-Hw + 71 1 107 106 # Ow-Hw + 72 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1 1399 1400 1401 # Hw-Ow-Hw + 468 1 1402 1403 1404 # Hw-Ow-Hw + 469 1 1405 1406 1407 # Hw-Ow-Hw + 470 1 1408 1409 1410 # Hw-Ow-Hw + 471 1 1411 1412 1413 # Hw-Ow-Hw + 472 1 1414 1415 1416 # Hw-Ow-Hw + 473 1 1417 1418 1419 # Hw-Ow-Hw + 474 1 1420 1421 1422 # Hw-Ow-Hw + 475 1 1423 1424 1425 # Hw-Ow-Hw + 476 1 1426 1427 1428 # Hw-Ow-Hw + 477 1 1429 1430 1431 # Hw-Ow-Hw + 478 1 1432 1433 1434 # Hw-Ow-Hw + 479 1 1435 1436 1437 # Hw-Ow-Hw + 480 1 1438 1439 1440 # Hw-Ow-Hw + 481 1 1441 1442 1443 # Hw-Ow-Hw + 482 1 1444 1445 1446 # Hw-Ow-Hw + 483 1 1447 1448 1449 # Hw-Ow-Hw + 484 1 1450 1451 1452 # Hw-Ow-Hw + 485 1 1453 1454 1455 # Hw-Ow-Hw + 486 1 1456 1457 1458 # Hw-Ow-Hw + 487 1 1459 1460 1461 # Hw-Ow-Hw + 488 1 1462 1463 1464 # Hw-Ow-Hw + 489 1 1465 1466 1467 # Hw-Ow-Hw + 490 1 1468 1469 1470 # Hw-Ow-Hw + 491 1 1471 1472 1473 # Hw-Ow-Hw + 492 1 1474 1475 1476 # Hw-Ow-Hw + 493 1 1477 1478 1479 # Hw-Ow-Hw + 494 1 1480 1481 1482 # Hw-Ow-Hw + 495 1 1483 1484 1485 # Hw-Ow-Hw + 496 1 1486 1487 1488 # Hw-Ow-Hw + 497 1 1489 1490 1491 # Hw-Ow-Hw + 498 1 1492 1493 1494 # Hw-Ow-Hw + 499 1 1495 1496 1497 # Hw-Ow-Hw + 500 1 1498 1499 1500 # Hw-Ow-Hw + 501 1 1501 1502 1503 # Hw-Ow-Hw + 502 1 1504 1505 1506 # Hw-Ow-Hw + 503 1 1507 1508 1509 # Hw-Ow-Hw + 504 1 1510 1511 1512 # Hw-Ow-Hw + 505 1 1513 1514 1515 # Hw-Ow-Hw + 506 1 1516 1517 1518 # Hw-Ow-Hw + 507 1 1519 1520 1521 # Hw-Ow-Hw + 508 1 1522 1523 1524 # Hw-Ow-Hw + 509 1 1525 1526 1527 # Hw-Ow-Hw + 510 1 1528 1529 1530 # Hw-Ow-Hw + 511 1 1531 1532 1533 # Hw-Ow-Hw + 512 1 1534 1535 1536 # Hw-Ow-Hw + 513 1 1537 1538 1539 # Hw-Ow-Hw + 514 1 1540 1541 1542 # Hw-Ow-Hw + 515 1 1543 1544 1545 # Hw-Ow-Hw + 516 1 1546 1547 1548 # Hw-Ow-Hw + 517 1 1549 1550 1551 # Hw-Ow-Hw + 518 1 1552 1553 1554 # Hw-Ow-Hw + 519 1 1555 1556 1557 # Hw-Ow-Hw + 520 1 1558 1559 1560 # Hw-Ow-Hw + 521 1 1561 1562 1563 # Hw-Ow-Hw + 522 1 1564 1565 1566 # Hw-Ow-Hw + 523 1 1567 1568 1569 # Hw-Ow-Hw + 524 1 1570 1571 1572 # Hw-Ow-Hw + 525 1 1573 1574 1575 # Hw-Ow-Hw + 526 1 1576 1577 1578 # Hw-Ow-Hw + 527 1 1579 1580 1581 # Hw-Ow-Hw + 528 1 1582 1583 1584 # Hw-Ow-Hw + 529 1 1585 1586 1587 # Hw-Ow-Hw + 530 1 1588 1589 1590 # Hw-Ow-Hw + 531 1 1591 1592 1593 # Hw-Ow-Hw + 532 1 1594 1595 1596 # Hw-Ow-Hw + 533 1 1597 1598 1599 # Hw-Ow-Hw + 534 1 1600 1601 1602 # Hw-Ow-Hw + 535 1 1603 1604 1605 # Hw-Ow-Hw + 536 1 1606 1607 1608 # Hw-Ow-Hw + 537 1 1609 1610 1611 # Hw-Ow-Hw + 538 1 1612 1613 1614 # Hw-Ow-Hw + 539 1 1615 1616 1617 # Hw-Ow-Hw + 540 1 1618 1619 1620 # Hw-Ow-Hw + 541 1 1621 1622 1623 # Hw-Ow-Hw + 542 1 1624 1625 1626 # Hw-Ow-Hw + 543 1 1627 1628 1629 # Hw-Ow-Hw + 544 1 1630 1631 1632 # Hw-Ow-Hw + 545 1 1633 1634 1635 # Hw-Ow-Hw + 546 1 1636 1637 1638 # Hw-Ow-Hw + 547 1 1639 1640 1641 # Hw-Ow-Hw + 548 1 1642 1643 1644 # Hw-Ow-Hw + 549 1 1645 1646 1647 # Hw-Ow-Hw + 550 1 1648 1649 1650 # Hw-Ow-Hw + 551 1 1651 1652 1653 # Hw-Ow-Hw + 552 1 1654 1655 1656 # Hw-Ow-Hw + 553 1 1657 1658 1659 # Hw-Ow-Hw + 554 1 1660 1661 1662 # Hw-Ow-Hw + 555 1 1663 1664 1665 # Hw-Ow-Hw + 556 1 1666 1667 1668 # Hw-Ow-Hw + 557 1 1669 1670 1671 # Hw-Ow-Hw + 558 1 1672 1673 1674 # Hw-Ow-Hw + 559 1 1675 1676 1677 # Hw-Ow-Hw + 560 1 1678 1679 1680 # Hw-Ow-Hw + 561 1 1681 1682 1683 # Hw-Ow-Hw + 562 1 1684 1685 1686 # Hw-Ow-Hw + 563 1 1687 1688 1689 # Hw-Ow-Hw + 564 1 1690 1691 1692 # Hw-Ow-Hw + 565 1 1693 1694 1695 # Hw-Ow-Hw + 566 1 1696 1697 1698 # Hw-Ow-Hw + 567 1 1699 1700 1701 # Hw-Ow-Hw + 568 1 1702 1703 1704 # Hw-Ow-Hw + 569 1 1705 1706 1707 # Hw-Ow-Hw + 570 1 1708 1709 1710 # Hw-Ow-Hw + 571 1 1711 1712 1713 # Hw-Ow-Hw + 572 1 1714 1715 1716 # Hw-Ow-Hw + 573 1 1717 1718 1719 # Hw-Ow-Hw + 574 1 1720 1721 1722 # Hw-Ow-Hw + 575 1 1723 1724 1725 # Hw-Ow-Hw + 576 1 1726 1727 1728 # Hw-Ow-Hw + 577 1 1729 1730 1731 # Hw-Ow-Hw + 578 1 1732 1733 1734 # Hw-Ow-Hw + 579 1 1735 1736 1737 # Hw-Ow-Hw + 580 1 1738 1739 1740 # Hw-Ow-Hw + 581 1 1741 1742 1743 # Hw-Ow-Hw + 582 1 1744 1745 1746 # Hw-Ow-Hw + 583 1 1747 1748 1749 # Hw-Ow-Hw + 584 1 1750 1751 1752 # Hw-Ow-Hw + 585 1 1753 1754 1755 # Hw-Ow-Hw + 586 1 1756 1757 1758 # Hw-Ow-Hw + 587 1 1759 1760 1761 # Hw-Ow-Hw + 588 1 1762 1763 1764 # Hw-Ow-Hw + 589 1 1765 1766 1767 # Hw-Ow-Hw + 590 1 1768 1769 1770 # Hw-Ow-Hw + 591 1 1771 1772 1773 # Hw-Ow-Hw + 592 1 1774 1775 1776 # Hw-Ow-Hw + 593 1 1777 1778 1779 # Hw-Ow-Hw + 594 1 1780 1781 1782 # Hw-Ow-Hw + 595 1 1783 1784 1785 # Hw-Ow-Hw + 596 1 1786 1787 1788 # Hw-Ow-Hw + 597 1 1789 1790 1791 # Hw-Ow-Hw + 598 1 1792 1793 1794 # Hw-Ow-Hw + 599 1 1795 1796 1797 # Hw-Ow-Hw + 600 1 1798 1799 1800 # Hw-Ow-Hw diff --git a/examples/USER/fep/SPCEhyd/mols/spce.ff b/examples/USER/fep/SPCEhyd/mols/spce.ff new file mode 100644 index 0000000000..b9fd69f4fd --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce.ff @@ -0,0 +1,14 @@ +# SPC/E water (kJ/mol, A, deg) + +ATOMS +# type m/uma q/e pot pars +Ow Ow 15.999 -0.8476 lj 3.1655 0.6503 +Hw Hw 1.008 0.4238 lj 0.0000 0.0000 + +BONDS +# i j pot re/A ka/kJmol-1 +Ow Hw cons 1.000 4331.53 + +ANGLES +# i j k pot th/deg ka/kjmol-1 +Hw Ow Hw harm 109.47 317.57 diff --git a/examples/USER/fep/SPCEhyd/mols/spce.zmat b/examples/USER/fep/SPCEhyd/mols/spce.zmat new file mode 100644 index 0000000000..e5e60c4f1b --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce.zmat @@ -0,0 +1,7 @@ +SPCE + +Hw +Ow 1 1.000 +Hw 2 1.000 1 109.47 + +spce.ff diff --git a/examples/USER/fep/SPCEhyd/mols/spce_h.ff b/examples/USER/fep/SPCEhyd/mols/spce_h.ff new file mode 100644 index 0000000000..a1c6933404 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce_h.ff @@ -0,0 +1,14 @@ +# SPC/E water (kJ/mol, A, deg) + +ATOMS +# type m/uma q/e pot pars +Owh Ow 15.999 -0.8476 lj 3.1655 0.6503 +Hwh Hw 1.008 0.4238 lj 0.0000 0.0000 + +BONDS +# i j pot re/A ka/kJmol-1 +Ow Hw cons 1.000 4331.53 + +ANGLES +# i j k pot th/deg ka/kjmol-1 +Hw Ow Hw harm 109.47 317.57 diff --git a/examples/USER/fep/SPCEhyd/mols/spce_h.zmat b/examples/USER/fep/SPCEhyd/mols/spce_h.zmat new file mode 100644 index 0000000000..54c4cf9107 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce_h.zmat @@ -0,0 +1,7 @@ +SPCE + +Hwh +Owh 1 1.000 +Hwh 2 1.000 1 109.47 + +spce_h.ff diff --git a/examples/USER/hdnnp/data.H2O-360mol b/examples/USER/hdnnp/data.H2O-360mol new file mode 100644 index 0000000000..3791f07585 --- /dev/null +++ b/examples/USER/hdnnp/data.H2O-360mol @@ -0,0 +1,1096 @@ +LAMMPS data file, 360 water molecules + +1080 atoms +2 atom types + +0.0 2.2695686722465727E+01 xlo xhi +0.0 2.3586033624598713E+01 ylo yhi +0.0 2.2237130028217017E+01 zlo zhi + +Masses + +1 1.00794 +2 15.9994 + +Atoms # atomic + +1 2 1.7548118361224624E+01 7.3699168122955889E+00 5.5591101411055377E-01 +2 1 1.7052018361224619E+01 7.5604368122955892E+00 1.3882600141105546E+00 +3 1 1.8473918361224619E+01 7.4162968122955890E+00 8.4111101411055411E-01 +4 2 9.1706683612246138E+00 1.2915816812295594E+01 2.5107200141105555E+00 +5 1 9.7830883612246140E+00 1.2151816812295593E+01 2.3347500141105550E+00 +6 1 9.1892283612246164E+00 1.3443216812295594E+01 1.6591000141105545E+00 +7 2 1.8399218361224623E+01 1.7424016812295601E+01 6.5473300141105586E+00 +8 1 1.8345918361224623E+01 1.8268716812295594E+01 7.0339200141105591E+00 +9 1 1.9026818361224624E+01 1.6834816812295600E+01 7.0045500141105599E+00 +10 2 5.7216883612246123E+00 1.6305516812295600E+01 1.0104620014110562E+01 +11 1 6.2668083612246122E+00 1.5517116812295598E+01 9.8182400141105628E+00 +12 1 6.2385083612246124E+00 1.6937316812295599E+01 1.0608050014110562E+01 +13 2 1.1317118361224615E+01 1.1227616812295592E+01 1.5996300141105546E+00 +14 1 1.1296018361224618E+01 1.0203716812295591E+01 1.7394500141105549E+00 +15 1 1.1304118361224615E+01 1.1323916812295593E+01 6.1680301411055383E-01 +16 2 7.8280183612246139E+00 2.2671316812295601E+01 4.2759600141105567E+00 +17 1 7.1177183612246129E+00 2.2216116812295603E+01 3.7208400141105566E+00 +18 1 8.3989583612246133E+00 2.2791416812295601E+01 3.4672900141105565E+00 +19 2 4.3278983612246105E+00 8.5704868122955897E+00 1.9742050014110571E+01 +20 1 5.3082183612246112E+00 8.2615268122955889E+00 1.9662550014110568E+01 +21 1 4.0620583612246106E+00 8.0321368122955903E+00 2.0571250014110571E+01 +22 2 1.7732618361224624E+01 1.5933416812295597E+01 1.9881550014110569E+01 +23 1 1.8279418361224621E+01 1.5600716812295596E+01 2.0596350014110573E+01 +24 1 1.6762718361224621E+01 1.5919016812295597E+01 2.0129250014110571E+01 +25 2 8.8204883612246157E+00 2.0042116812295600E+01 1.5762450014110566E+01 +26 1 7.9101683612246143E+00 1.9947516812295600E+01 1.6194150014110569E+01 +27 1 9.2758283612246135E+00 1.9487716812295599E+01 1.6447350014110569E+01 +28 2 1.1361918361224616E+01 1.2958816812295595E+01 1.5721550014110568E+01 +29 1 1.0710518361224615E+01 1.3138916812295594E+01 1.6487150014110568E+01 +30 1 1.1182418361224618E+01 1.2046616812295593E+01 1.5544250014110565E+01 +31 2 9.0853583612246158E+00 1.8028316812295600E+01 1.3540150014110566E+01 +32 1 9.0982483612246146E+00 1.8864216812295595E+01 1.4036250014110564E+01 +33 1 9.8956783612246166E+00 1.8073516812295594E+01 1.3050750014110566E+01 +34 2 3.3490983612246099E+00 1.3145316812295595E+01 2.1514250014110569E+01 +35 1 3.9414483612246105E+00 1.3751716812295594E+01 2.2021150014110574E+01 +36 1 3.6130383612246102E+00 1.3223816812295594E+01 2.0535850014110569E+01 +37 2 6.4411883612246124E+00 7.5546068122955887E+00 1.2406250014110563E+01 +38 1 6.4110583612246135E+00 7.3084268122955889E+00 1.1455550014110564E+01 +39 1 5.9502783612246120E+00 6.8079868122955887E+00 1.2882150014110564E+01 +40 2 3.1816283612246097E+00 1.3743768122955837E+00 1.8410650014110569E+01 +41 1 2.7456683612246096E+00 1.9753168122955844E+00 1.7761550014110568E+01 +42 1 3.3321183612246101E+00 6.4900681229558332E-01 1.7765450014110570E+01 +43 2 1.1615018361224617E+01 8.3421868122955907E+00 9.3717400141105607E+00 +44 1 1.1505118361224616E+01 9.2703268122955897E+00 8.9617500141105602E+00 +45 1 1.1720018361224618E+01 8.5827868122955895E+00 1.0287050014110562E+01 +46 2 1.6212718361224624E+01 1.6780668122955840E+00 1.1987450014110564E+01 +47 1 1.6817418361224618E+01 9.2842081229558349E-01 1.2089350014110565E+01 +48 1 1.6302618361224624E+01 1.6888668122955843E+00 1.0949350014110564E+01 +49 2 5.7806183612246125E+00 2.3120416812295598E+01 5.7535201411055370E-01 +50 1 6.0597183612246122E+00 2.2879416812295602E+01 2.1923350014110571E+01 +51 1 6.1737883612246121E+00 3.7587181229558303E-01 7.5628401411055390E-01 +52 2 6.9870736122460764E-01 4.4018468122955863E+00 2.0745450014110574E+01 +53 1 1.0849233612246079E+00 5.0078768122955868E+00 2.1326650014110573E+01 +54 1 1.1343483612246081E+00 3.5552568122955859E+00 2.0739850014110569E+01 +55 2 1.2474018361224617E+01 1.8462716812295600E+01 4.2626300141105569E+00 +56 1 1.2631218361224617E+01 1.9451616812295601E+01 4.1598600141105573E+00 +57 1 1.1535518361224616E+01 1.8339216812295600E+01 3.8941600141105570E+00 +58 2 1.4727518361224622E+01 1.1649916812295594E+01 1.2720850014110564E+01 +59 1 1.4211718361224619E+01 1.2472216812295594E+01 1.2857350014110564E+01 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4.0591700141105562E+00 +1036 2 1.7009718361224621E+01 1.1077816812295593E+01 1.3982750014110566E+01 +1037 1 1.7416618361224621E+01 1.1915716812295594E+01 1.4114250014110565E+01 +1038 1 1.6152518361224622E+01 1.1296216812295594E+01 1.3498650014110565E+01 +1039 2 1.5292118361224619E+01 2.2286916812295601E+01 2.0549250014110573E+01 +1040 1 1.5719918361224620E+01 2.1812016812295600E+01 2.1274150014110575E+01 +1041 1 1.5371618361224622E+01 2.3218716812295604E+01 2.0712450014110569E+01 +1042 2 7.0554283612246129E+00 1.6077516812295599E+01 1.7628950014110565E+01 +1043 1 6.9981783612246131E+00 1.6403416812295596E+01 1.6704450014110570E+01 +1044 1 7.7722083612246129E+00 1.5403516812295596E+01 1.7707550014110570E+01 +1045 2 9.1948983612246149E+00 1.0623516812295591E+01 9.8707000141105627E+00 +1046 1 8.5664583612246137E+00 1.0414716812295591E+01 9.1563400141105618E+00 +1047 1 8.9125783612246146E+00 1.1463416812295593E+01 1.0255350014110562E+01 +1048 2 3.4275083612246098E+00 1.4718216812295594E+01 1.7487000141105546E+00 +1049 1 2.7882983612246091E+00 1.5297516812295596E+01 1.3626300141105543E+00 +1050 1 3.7876783612246099E+00 1.5291116812295597E+01 2.4465400141105555E+00 +1051 2 1.3184418361224617E+01 1.6254416812295595E+01 1.6217400141105547E+00 +1052 1 1.2358318361224617E+01 1.5655016812295598E+01 1.4601300141105547E+00 +1053 1 1.3636118361224620E+01 1.6118716812295595E+01 7.4275201411055392E-01 +1054 2 2.1478318361224627E+01 9.3499668122955910E+00 1.3041450014110564E+01 +1055 1 2.0571518361224623E+01 9.4989368122955913E+00 1.3473650014110564E+01 +1056 1 2.1367718361224625E+01 9.0415068122955891E+00 1.2126950014110564E+01 +1057 2 1.3240818361224617E+01 2.1513516812295602E+01 7.6613400141105599E+00 +1058 1 1.3173218361224619E+01 2.0794016812295602E+01 8.3871300141105607E+00 +1059 1 1.2721018361224617E+01 2.1148516812295600E+01 6.8687800141105599E+00 +1060 2 1.0706218361224616E+01 9.0730668122955915E+00 1.2194050014110564E+01 +1061 1 1.0209918361224616E+01 9.5840168122955909E+00 1.1511850014110562E+01 +1062 1 1.0127718361224616E+01 8.2990868122955899E+00 1.2386250014110566E+01 +1063 2 9.8246936122460771E-01 9.5211468122955907E+00 1.0116250014110562E+01 +1064 1 1.2453883612246077E+00 1.0440616812295591E+01 1.0422250014110562E+01 +1065 1 1.6324283612246082E+00 8.8711068122955901E+00 1.0428050014110564E+01 +1066 2 2.1805418361224621E+01 1.8063116812295597E+01 1.9102050014110567E+01 +1067 1 2.1618318361224627E+01 1.8993216812295604E+01 1.8788850014110569E+01 +1068 1 8.4032061224607005E-02 1.8152616812295598E+01 1.9376750014110570E+01 +1069 2 4.9490783612246112E+00 4.5899568122955863E+00 4.0229100141105567E+00 +1070 1 4.9939883612246110E+00 5.4655868122955873E+00 4.4890400141105573E+00 +1071 1 4.2701383612246104E+00 4.0452668122955862E+00 4.5228100141105569E+00 +1072 2 1.8242218361224626E+01 2.9008968122955854E+00 1.5903950014110567E+01 +1073 1 1.8887118361224626E+01 2.5084568122955848E+00 1.5204150014110565E+01 +1074 1 1.8162418361224624E+01 2.1789868122955851E+00 1.6617050014110568E+01 +1075 2 3.9899383612246102E+00 1.9364416812295598E+01 1.3871050014110565E+01 +1076 1 4.3833283612246108E+00 2.0252516812295600E+01 1.3695350014110566E+01 +1077 1 3.1540783612246095E+00 1.9562116812295599E+01 1.4347050014110566E+01 +1078 2 7.0537683612246127E+00 1.4620616812295594E+01 6.4024900141105583E+00 +1079 1 7.6585583612246131E+00 1.3942216812295593E+01 6.0279100141105584E+00 +1080 1 6.2108683612246125E+00 1.4238816812295596E+01 6.6619400141105594E+00 diff --git a/examples/USER/hdnnp/hdnnp-data/input.nn b/examples/USER/hdnnp/hdnnp-data/input.nn new file mode 100644 index 0000000000..885ec0ec70 --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/input.nn @@ -0,0 +1,120 @@ +############################################################################### +# HDNNP for water H2O +############################################################################### +# Length unit : Bohr +# Energy unit : Ha +# Reference method: RPBE-D3 +############################################################################### + +############################################################################### +# DATA SET NORMALIZATION +############################################################################### +# This section was automatically added by nnp-norm. +mean_energy -2.5521343547039809E+01 +conv_energy 2.4265748255366972E+02 +conv_length 5.8038448995319847E+00 +############################################################################### + +############################################################################### +# GENERAL NNP SETTINGS +############################################################################### +# These keywords are (almost) always required. +number_of_elements 2 # Number of elements. +elements H O # Specification of elements. +#atom_energy H -0.45890771 # Free atom reference energy (H). +#atom_energy O -74.94518524 # Free atom reference energy (O). +cutoff_type 2 # Cutoff type. +scale_symmetry_functions # Scale all symmetry functions with min/max values. +#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. +scale_min_short 0.0 # Minimum value for scaling. +scale_max_short 1.0 # Maximum value for scaling. +center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. +global_hidden_layers_short 2 # Number of hidden layers. +global_nodes_short 25 25 # Number of nodes in each hidden layer. +global_activation_short t t l # Activation function for each hidden layer and output layer. +#normalize_nodes # Normalize input of nodes. + +############################################################################### +# SYMMETRY FUNCTIONS +############################################################################### + +# Radial symmetry function (type 2): +#symfunction_short 2 + +# Narrow Angular symmetry function (type 3): +#symfunction_short 3 + +# Wide Angular symmetry function (type 9): +#symfunction_short 9 + +# radial H H +symfunction_short H 2 H 0.001 0.0 12.00 +symfunction_short H 2 H 0.01 0.0 12.00 +symfunction_short H 2 H 0.03 0.0 12.00 +symfunction_short H 2 H 0.06 0.0 12.00 +symfunction_short H 2 H 0.15 1.9 12.00 +symfunction_short H 2 H 0.30 1.9 12.00 +symfunction_short H 2 H 0.60 1.9 12.00 +symfunction_short H 2 H 1.50 1.9 12.00 + +# radial H O / O H +symfunction_short H 2 O 0.001 0.0 12.00 +symfunction_short H 2 O 0.01 0.0 12.00 +symfunction_short H 2 O 0.03 0.0 12.00 +symfunction_short H 2 O 0.06 0.0 12.00 +symfunction_short H 2 O 0.15 0.9 12.00 +symfunction_short H 2 O 0.30 0.9 12.00 +symfunction_short H 2 O 0.60 0.9 12.00 +symfunction_short H 2 O 1.50 0.9 12.00 + +symfunction_short O 2 H 0.001 0.0 12.00 +symfunction_short O 2 H 0.01 0.0 12.00 +symfunction_short O 2 H 0.03 0.0 12.00 +symfunction_short O 2 H 0.06 0.0 12.00 +symfunction_short O 2 H 0.15 0.9 12.00 +symfunction_short O 2 H 0.30 0.9 12.00 +symfunction_short O 2 H 0.60 0.9 12.00 +symfunction_short O 2 H 1.50 0.9 12.00 + +# radial O O +symfunction_short O 2 O 0.001 0.0 12.00 +symfunction_short O 2 O 0.01 0.0 12.00 +symfunction_short O 2 O 0.03 0.0 12.00 +symfunction_short O 2 O 0.06 0.0 12.00 +symfunction_short O 2 O 0.15 4.0 12.00 +symfunction_short O 2 O 0.30 4.0 12.00 +symfunction_short O 2 O 0.60 4.0 12.00 +symfunction_short O 2 O 1.50 4.0 12.00 + +# angular +symfunction_short H 3 O H 0.2 1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.07 1.0 1.0 12.00000 +symfunction_short H 3 O H 0.07 1.0 1.0 12.00000 +symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000 +symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.03 1.0 1.0 12.00000 +symfunction_short H 3 O H 0.03 1.0 1.0 12.00000 +symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000 +symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.01 1.0 4.0 12.00000 +symfunction_short H 3 O H 0.01 1.0 4.0 12.00000 +symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000 +symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000 + +symfunction_short O 3 O H 0.03 1.0 1.0 12.00000 +symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000 +symfunction_short O 3 O H 0.001 1.0 4.0 12.00000 +symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000 + +symfunction_short H 3 O O 0.03 1.0 1.0 12.00000 +symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000 +symfunction_short H 3 O O 0.001 1.0 4.0 12.00000 +symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000 + +symfunction_short O 3 O O 0.03 1.0 1.0 12.00000 +symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000 +symfunction_short O 3 O O 0.001 1.0 4.0 12.00000 +symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000 diff --git a/examples/USER/hdnnp/hdnnp-data/scaling.data b/examples/USER/hdnnp/hdnnp-data/scaling.data new file mode 100644 index 0000000000..2a9e0ad7a6 --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/scaling.data @@ -0,0 +1,72 @@ +################################################################################ +# Symmetry function scaling data. +################################################################################ +# Col Name Description +################################################################################ +# 1 e_index Element index. +# 2 sf_index Symmetry function index. +# 3 sf_min Symmetry function minimum. +# 4 sf_max Symmetry function maximum. +# 5 sf_mean Symmetry function mean. +# 6 sf_sigma Symmetry function sigma. +######################################################################################################################### +# 1 2 3 4 5 6 +# e_index sf_index sf_min sf_max sf_mean sf_sigma +######################################################################################################################### + 1 1 1.0882016636170764E+00 9.6166419119419064E+00 2.2691752247542194E+00 6.7883526611658462E-01 + 1 2 7.3274438904180561E-01 5.0028559321574191E+00 1.3272332317543580E+00 3.3936750181780473E-01 + 1 3 7.6010783783215696E-01 7.1427942966219815E+00 1.6470726712825305E+00 5.0771115927383836E-01 + 1 4 5.4842285884800812E-01 3.7661771168267726E+00 1.0163698211361718E+00 2.5362958053787776E-01 + 1 5 4.0080665126604625E-01 4.1469832401668629E+00 9.0925040981537897E-01 2.9758019277508319E-01 + 1 6 3.6209352253798227E-01 2.2678239402766054E+00 6.4931154122889623E-01 1.4835420345383032E-01 + 1 7 1.8919103878435897E-01 2.2292652677252804E+00 4.5693857051003817E-01 1.5976079618578123E-01 + 1 8 2.6704178695764313E-01 1.3208742362468955E+00 4.2395636902644862E-01 8.0492394978461931E-02 + 1 9 2.4513099752055156E-01 9.4751160662053002E-01 3.6244199023263673E-01 5.2993540556109331E-02 + 1 10 2.2248910067848982E-01 2.7596216013647377E+00 5.3891576898130766E-01 2.0137334230483950E-01 + 1 11 1.4743601726548086E-01 5.5599270746969276E-01 2.6773972195910817E-01 2.6188094566404998E-02 + 1 12 9.9110926426029380E-02 1.7265405335201480E+00 2.9553976311554875E-01 1.1619768775752932E-01 + 1 13 6.5093699123904267E-02 3.4521757733971170E-01 1.8521249136783141E-01 1.9741155185936318E-02 + 1 14 3.1653527247865069E-02 9.1293170125596168E-01 1.5025164684953513E-01 5.3480187368038674E-02 + 1 15 2.9202821602466694E-03 2.6453981776124141E-01 7.6525296616004684E-02 1.8780956137549487E-02 + 1 16 3.2145385719803329E-04 2.8696425565429240E-01 4.5792284631233672E-02 2.3263495133568998E-02 + 1 17 2.4693757528509622E-04 1.3848731138266304E-01 1.7693289653297604E-02 9.7460303038080908E-03 + 1 18 5.0992836797990751E-03 5.8319173651547385E-01 2.3851656540978389E-02 3.7790771891778152E-02 + 1 19 3.2282960174310170E-04 2.1613962298381925E-01 1.7072560754702336E-02 1.4026518665786077E-02 + 1 20 4.9647513277769700E-02 1.6851617426880194E+00 1.4541325969622534E-01 1.0954306125703028E-01 + 1 21 3.4073471604482227E-03 3.1637071808861689E-01 1.8422597685566724E-02 2.0125274191649719E-02 + 1 22 1.3121382132811807E-04 1.0258348935693713E-01 6.3684016949344113E-03 6.6071626858835051E-03 + 1 23 3.3813162813665906E-02 9.1618560879938926E-01 8.1266384503339575E-02 5.7918502576695730E-02 + 1 24 4.1708500446352870E-04 1.5785966980407021E-01 4.6646981268568697E-03 9.8630700614506465E-03 + 1 25 7.3528900917695290E-04 5.9225627251013026E-02 3.7042174075139758E-03 3.3118079036492621E-03 + 1 26 8.9828333062972592E-03 1.9426085555380754E-01 2.4093377110646338E-02 1.0980657457661532E-02 + 1 27 2.1228022180417653E-04 8.7777813240869640E-03 2.0550705761547970E-03 5.8802103858137246E-04 + 2 1 1.5142595331454245E+00 1.0005711988559998E+01 2.6544664635087183E+00 6.7806617585688911E-01 + 2 2 4.4366445360926199E-01 4.6195409357987076E+00 9.6587051599896101E-01 3.3688559575009042E-01 + 2 3 1.1907810568758714E+00 7.5323544094345003E+00 2.0327396422723472E+00 5.0607867531004169E-01 + 2 4 2.7576036468694687E-01 3.3862131032504492E+00 6.5929732667024776E-01 2.5004687333979903E-01 + 2 5 8.0580777590695674E-01 4.5356481255168557E+00 1.2986230824577940E+00 2.9449908325462404E-01 + 2 6 1.0517053799863604E-01 1.8909877539194515E+00 3.0673921331641835E-01 1.4198497108573313E-01 + 2 7 5.6949141690859706E-01 2.6154328621607852E+00 8.4791273805289546E-01 1.5714071578589769E-01 + 2 8 2.3251646720171416E-02 9.3641034200657891E-01 1.1140979781150941E-01 6.9796654369842781E-02 + 2 9 5.1354161698115419E-01 1.8545341781448565E+00 7.2488398046527269E-01 9.8011511620611044E-02 + 2 10 1.1057465545812291E-01 2.9121456897811342E+00 4.7474421797982730E-01 2.3441807910092233E-01 + 2 11 3.5269317308496489E-01 1.0714592032613128E+00 5.3547944391821678E-01 4.5179661104166338E-02 + 2 12 3.0424313539726355E-02 2.5277642768509305E+00 3.1652845366685045E-01 2.1026891409654727E-01 + 2 13 1.5980022688828247E-01 6.6348817066386512E-01 3.7042498273566293E-01 3.0753700953611234E-02 + 2 14 2.7781847150922931E-03 2.3030057819082539E+00 1.7737800292869690E-01 1.8600239464755819E-01 + 2 15 9.5641036809349829E-03 3.9085233064570807E-01 1.5305059323200970E-01 2.7862233984302390E-02 + 2 16 3.7500170432292374E-06 2.0367068825281995E+00 5.4144316535640342E-02 1.4305857218443538E-01 + 2 17 2.4726232100491033E-03 3.4335400617385042E-01 1.6684597803376652E-02 2.1902951351570905E-02 + 2 18 1.7405672406959600E-05 5.6319316766205302E-02 9.5478184601751693E-04 3.3588039002222358E-03 + 2 19 5.4785372164647961E-02 3.0182597583971442E+00 2.0392031625072374E-01 2.0088721011517138E-01 + 2 20 1.3795234987637416E-03 4.9878800454061323E-01 1.2788265359933434E-02 3.1829452602194934E-02 + 2 21 6.6852772684814245E-03 2.6739582842775905E-01 3.0851859894574358E-02 1.7089886758420030E-02 + 2 22 1.7021399438214336E-02 1.4167796508898451E+00 7.6274174813506748E-02 9.2852504206357669E-02 + 2 23 1.9759831791959857E-02 4.0756378297923890E-01 4.8843503112397949E-02 2.5474332458885439E-02 + 2 24 5.2768632746659245E-04 2.3324050667069166E-01 7.2057238727819412E-03 1.4495435261027742E-02 + 2 25 1.1144879740881719E-05 3.5285772934088612E-02 4.2545240948261025E-04 2.0471375111485984E-03 + 2 26 1.6013752685265073E-02 8.2245409953473059E-01 5.0845479076508403E-02 5.2802834522172923E-02 + 2 27 3.9898424495541764E-03 7.8557031440100300E-01 3.6926675414383096E-02 5.0474458307624794E-02 + 2 28 4.0523818189746699E-05 9.8448068666705968E-02 1.2119235889230262E-03 5.7945700128174639E-03 + 2 29 6.0374649986214514E-03 9.9251766407842473E-02 1.6156539248049700E-02 5.5245068674135743E-03 + 2 30 2.9595491075765732E-03 1.5478537567691833E-01 1.1641055270110553E-02 8.9415193910804703E-03 diff --git a/examples/USER/hdnnp/hdnnp-data/weights.001.data b/examples/USER/hdnnp/hdnnp-data/weights.001.data new file mode 100644 index 0000000000..deb5012acb --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/weights.001.data @@ -0,0 +1,1392 @@ +################################################################################ +# Neural network connection values (weights and biases). +################################################################################ +# Col Name Description +################################################################################ +# 1 connection Neural network connection value. +# 2 t Connection type (a = weight, b = bias). +# 3 index Index enumerating weights. +# 4 l_s Starting point layer (end point layer for biases). +# 5 n_s Starting point neuron in starting layer (end point neuron for biases). +# 6 l_e End point layer. +# 7 n_e End point neuron in end layer. +################################################################################ +# 1 2 3 4 5 6 7 +# connection t index l_s n_s l_e n_e +############################################################ + 1.2539155865352127E+00 a 1 0 1 1 1 + 2.2490365890661286E+00 a 2 0 1 1 2 + 4.9361851928374572E+00 a 3 0 1 1 3 + -2.3971991574908125E+00 a 4 0 1 1 4 + -1.8596992303156465E+00 a 5 0 1 1 5 + 3.8287764168815897E+00 a 6 0 1 1 6 + 7.4523181738636106E+00 a 7 0 1 1 7 + 6.0971861116881998E+00 a 8 0 1 1 8 + -8.7239359226117639E+00 a 9 0 1 1 9 + -1.8255232070184267E+01 a 10 0 1 1 10 + -7.8065643887610179E+00 a 11 0 1 1 11 + 1.4247237398130265E+01 a 12 0 1 1 12 + 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1205 1 21 2 5 + 4.8026156110006928E-02 a 1206 1 21 2 6 + -1.2317220364565722E+00 a 1207 1 21 2 7 + -9.2171220979112878E-01 a 1208 1 21 2 8 + -8.3293051813215280E-01 a 1209 1 21 2 9 + 3.7826002267822101E-01 a 1210 1 21 2 10 + -1.2566916573054130E+00 a 1211 1 21 2 11 + -1.4542331491456711E-01 a 1212 1 21 2 12 + -1.0890378021893508E+00 a 1213 1 21 2 13 + -5.8298836953764355E-01 a 1214 1 21 2 14 + -1.9020824106971643E+00 a 1215 1 21 2 15 + 4.4353810152599149E-01 a 1216 1 21 2 16 + -2.9928311527046703E-01 a 1217 1 21 2 17 + -7.7527928990984052E-01 a 1218 1 21 2 18 + 2.6159175407438195E-01 a 1219 1 21 2 19 + -2.6604337400489050E-02 a 1220 1 21 2 20 + -4.6552795168897604E-01 a 1221 1 21 2 21 + 1.1611386377657384E+00 a 1222 1 21 2 22 + -1.2972265245341139E+00 a 1223 1 21 2 23 + 1.8117173751313085E+00 a 1224 1 21 2 24 + 1.0433495561237927E+00 a 1225 1 21 2 25 + 1.5410314634266913E+00 a 1226 1 22 2 1 + 6.6201420998527072E-01 a 1227 1 22 2 2 + 1.1189293597068475E+00 a 1228 1 22 2 3 + 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1 23 2 2 + -2.3555430378419923E-01 a 1253 1 23 2 3 + -1.3434989779696097E-01 a 1254 1 23 2 4 + 3.7852663531566189E-01 a 1255 1 23 2 5 + 9.8266847359694973E-02 a 1256 1 23 2 6 + 3.2721968443206462E-01 a 1257 1 23 2 7 + -3.7061171550241617E-01 a 1258 1 23 2 8 + 2.2862436245090851E+00 a 1259 1 23 2 9 + 1.7674065728047832E+00 a 1260 1 23 2 10 + -5.2627257197444939E-02 a 1261 1 23 2 11 + 9.4094481148145870E-01 a 1262 1 23 2 12 + 1.0616552648143298E+00 a 1263 1 23 2 13 + -1.6065739188681796E-01 a 1264 1 23 2 14 + 1.6833160475834315E+00 a 1265 1 23 2 15 + -5.5679530352182072E-01 a 1266 1 23 2 16 + 4.2170082515325280E-01 a 1267 1 23 2 17 + 1.8142946234467967E+00 a 1268 1 23 2 18 + -6.0004075552166369E-01 a 1269 1 23 2 19 + 8.6767695096505049E-01 a 1270 1 23 2 20 + 1.7471709925670367E-01 a 1271 1 23 2 21 + 6.3494817986861019E-01 a 1272 1 23 2 22 + 7.9839233743975266E-02 a 1273 1 23 2 23 + -8.7497499907984810E-01 a 1274 1 23 2 24 + -2.1279336414401262E-01 a 1275 1 23 2 25 + 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1 24 2 24 + -1.6060924344568878E-02 a 1300 1 24 2 25 + -1.1558703878945702E+00 a 1301 1 25 2 1 + 5.5859771317693908E-02 a 1302 1 25 2 2 + -1.9275021348316721E+00 a 1303 1 25 2 3 + 4.2881321046205173E-01 a 1304 1 25 2 4 + 6.6308764508018558E-01 a 1305 1 25 2 5 + -2.5357661809360188E-01 a 1306 1 25 2 6 + 7.7965409617466697E-01 a 1307 1 25 2 7 + -1.9470416731652336E+00 a 1308 1 25 2 8 + 2.0923659915641873E-01 a 1309 1 25 2 9 + 8.9211452410465542E-01 a 1310 1 25 2 10 + -1.9807939822570442E-01 a 1311 1 25 2 11 + -5.0922943173038127E-01 a 1312 1 25 2 12 + 1.3378430979044107E+00 a 1313 1 25 2 13 + -6.8964614083753073E-01 a 1314 1 25 2 14 + 7.6939619343191556E-01 a 1315 1 25 2 15 + -1.5783243312480257E+00 a 1316 1 25 2 16 + 2.3586020281744577E+00 a 1317 1 25 2 17 + -5.1641666185758928E-01 a 1318 1 25 2 18 + 1.0291540870545792E+00 a 1319 1 25 2 19 + 1.5269830348487650E+00 a 1320 1 25 2 20 + -2.8987700591417855E+00 a 1321 1 25 2 21 + 9.0207337792476916E-01 a 1322 1 25 2 22 + 1.9890049402284911E+00 a 1323 1 25 2 23 + 3.9387622927433424E-01 a 1324 1 25 2 24 + 9.9397126232482103E-01 a 1325 1 25 2 25 + 2.5306467041996967E+00 b 1326 2 1 + 3.1633393474977245E+00 b 1327 2 2 + -1.1644295509710691E+00 b 1328 2 3 + -5.7686722641223600E+00 b 1329 2 4 + 2.0065022303893989E+00 b 1330 2 5 + -5.9106057000795840E+00 b 1331 2 6 + -1.1326093285804056E+01 b 1332 2 7 + -3.9025063397327071E+00 b 1333 2 8 + 4.4520505166676267E+00 b 1334 2 9 + -1.7352681951318241E+00 b 1335 2 10 + -2.1518912430432668E+00 b 1336 2 11 + 5.0463376560082969E+00 b 1337 2 12 + -2.2614514173852837E-01 b 1338 2 13 + -4.1454590614747211E+00 b 1339 2 14 + 1.6688417293495756E+00 b 1340 2 15 + -5.8649976938793378E+00 b 1341 2 16 + -3.8350084459541849E+00 b 1342 2 17 + 1.3730477223722950E+00 b 1343 2 18 + 1.8506935712854127E+00 b 1344 2 19 + 5.7362757779153428E+00 b 1345 2 20 + 7.2901484895568780E+00 b 1346 2 21 + 3.9773783666446022E-01 b 1347 2 22 + -6.1298011242151409E+00 b 1348 2 23 + 9.9698755072742991E+00 b 1349 2 24 + 1.1801564149295556E+00 b 1350 2 25 + 1.2704098997067026E+01 a 1351 2 1 3 1 + 1.5947733940307620E+00 a 1352 2 2 3 1 + -1.6022927057878529E+00 a 1353 2 3 3 1 + -1.5507258540777733E+00 a 1354 2 4 3 1 + 1.8696884022727636E+00 a 1355 2 5 3 1 + -8.2051908880071633E-01 a 1356 2 6 3 1 + 9.4325719092522542E-01 a 1357 2 7 3 1 + 2.4098435369626174E+00 a 1358 2 8 3 1 + 1.4100759633042474E+00 a 1359 2 9 3 1 + -1.4613034838529613E+00 a 1360 2 10 3 1 + 1.0296574685193380E+00 a 1361 2 11 3 1 + 1.2413851904356363E+00 a 1362 2 12 3 1 + -6.3168181712211169E-01 a 1363 2 13 3 1 + 7.6424175125347729E+00 a 1364 2 14 3 1 + -1.3477038299214714E+00 a 1365 2 15 3 1 + -1.6064659765754943E+00 a 1366 2 16 3 1 + -8.9624380518145874E-01 a 1367 2 17 3 1 + -1.0509865792522375E+00 a 1368 2 18 3 1 + 8.1847872933853638E-01 a 1369 2 19 3 1 + 1.2845504810303034E+00 a 1370 2 20 3 1 + -5.1879822944368881E-01 a 1371 2 21 3 1 + -7.2018714033119180E-01 a 1372 2 22 3 1 + 5.9870832883780798E+00 a 1373 2 23 3 1 + -6.0589155387470683E-01 a 1374 2 24 3 1 + 5.0177609140285355E+00 a 1375 2 25 3 1 + 9.7386086372975722E+00 b 1376 3 1 diff --git a/examples/USER/hdnnp/hdnnp-data/weights.008.data b/examples/USER/hdnnp/hdnnp-data/weights.008.data new file mode 100644 index 0000000000..fbdbaa1411 --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/weights.008.data @@ -0,0 +1,1467 @@ +################################################################################ +# Neural network connection values (weights and biases). +################################################################################ +# Col Name Description +################################################################################ +# 1 connection Neural network connection value. +# 2 t Connection type (a = weight, b = bias). +# 3 index Index enumerating weights. +# 4 l_s Starting point layer (end point layer for biases). +# 5 n_s Starting point neuron in starting layer (end point neuron for biases). +# 6 l_e End point layer. +# 7 n_e End point neuron in end layer. +################################################################################ +# 1 2 3 4 5 6 7 +# connection t index l_s n_s l_e n_e +############################################################ + -4.2252995889643252E-01 a 1 0 1 1 1 + -6.0555645962054347E+00 a 2 0 1 1 2 + 1.4040722027928377E+01 a 3 0 1 1 3 + -2.7041370011942618E+00 a 4 0 1 1 4 + -3.8202743208058858E+00 a 5 0 1 1 5 + -3.3612643261393358E+00 a 6 0 1 1 6 + -2.0418101025905258E+00 a 7 0 1 1 7 + 7.5707237340996727E+00 a 8 0 1 1 8 + -5.8098755815926548E+00 a 9 0 1 1 9 + -6.0966886893925210E-01 a 10 0 1 1 10 + 5.8061564015115206E+00 a 11 0 1 1 11 + -1.5509339733099867E+00 a 12 0 1 1 12 + 1.9747395485200818E+00 a 13 0 1 1 13 + 4.5260782279680539E-01 a 14 0 1 1 14 + 9.9210415760283279E+00 a 15 0 1 1 15 + -6.5078831481547121E+00 a 16 0 1 1 16 + -3.4768832871318085E+00 a 17 0 1 1 17 + -1.9463994340943838E+00 a 18 0 1 1 18 + -3.4186058699290269E+00 a 19 0 1 1 19 + 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6.5654373849726466E-01 a 1235 1 19 2 10 + -9.0407721196091848E-02 a 1236 1 19 2 11 + 1.5566506128138184E+00 a 1237 1 19 2 12 + -9.4986537106149321E-02 a 1238 1 19 2 13 + -2.3530503270088396E-01 a 1239 1 19 2 14 + 3.6439425212581661E-01 a 1240 1 19 2 15 + 1.2871636736138770E+00 a 1241 1 19 2 16 + -8.4712787652121069E-01 a 1242 1 19 2 17 + -1.0234220464653516E+00 a 1243 1 19 2 18 + -1.3802013894870373E+00 a 1244 1 19 2 19 + 4.6238544527464259E-01 a 1245 1 19 2 20 + -3.1736140472371468E+00 a 1246 1 19 2 21 + 1.7897235482645921E+00 a 1247 1 19 2 22 + -1.2075712900497950E+00 a 1248 1 19 2 23 + -3.1032297572767770E-01 a 1249 1 19 2 24 + 2.1706205401676661E+00 a 1250 1 19 2 25 + 6.9973782486580109E+00 a 1251 1 20 2 1 + 2.9325190821916197E-01 a 1252 1 20 2 2 + -1.2648655109330131E+00 a 1253 1 20 2 3 + -4.3905910522706337E-01 a 1254 1 20 2 4 + 4.2887555555714030E-01 a 1255 1 20 2 5 + 1.3300944280643934E+00 a 1256 1 20 2 6 + 1.0988390404457922E+00 a 1257 1 20 2 7 + 2.3801051936039075E+00 a 1258 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-8.9797316703694119E-02 a 1282 1 21 2 7 + -7.9615421262219899E-01 a 1283 1 21 2 8 + -2.5074736863647562E-01 a 1284 1 21 2 9 + -3.2383137185187805E-01 a 1285 1 21 2 10 + -7.7486670060442631E-01 a 1286 1 21 2 11 + -1.7378145875987788E-01 a 1287 1 21 2 12 + 1.7001762592878558E+00 a 1288 1 21 2 13 + -1.7033999809142997E+00 a 1289 1 21 2 14 + 3.7961258225336264E-01 a 1290 1 21 2 15 + 6.0929689839357426E-01 a 1291 1 21 2 16 + -1.9171250145280534E+00 a 1292 1 21 2 17 + -1.6594854242769004E+00 a 1293 1 21 2 18 + -2.8219229087100910E+00 a 1294 1 21 2 19 + -4.3902463688638738E-01 a 1295 1 21 2 20 + -1.1744026035352828E+00 a 1296 1 21 2 21 + 3.9648025457334164E+00 a 1297 1 21 2 22 + -1.3587513635268793E+00 a 1298 1 21 2 23 + 3.9463311556495906E-02 a 1299 1 21 2 24 + -4.6280624473662763E-01 a 1300 1 21 2 25 + 8.3725910272757709E+00 a 1301 1 22 2 1 + 1.2030400911595496E+00 a 1302 1 22 2 2 + 5.2723639396495003E-01 a 1303 1 22 2 3 + 2.4863416823271995E+00 a 1304 1 22 2 4 + 5.0656775645932173E-01 a 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1352 1 24 2 2 + 2.4714648764760871E-01 a 1353 1 24 2 3 + -4.2700090187223255E-01 a 1354 1 24 2 4 + 1.9684439924637190E-01 a 1355 1 24 2 5 + -1.6150658390090172E-01 a 1356 1 24 2 6 + -8.4941771549071021E-01 a 1357 1 24 2 7 + 3.2616941337700417E-01 a 1358 1 24 2 8 + -6.0235251095177200E-01 a 1359 1 24 2 9 + 2.0073315297316108E+00 a 1360 1 24 2 10 + 6.8678637919958119E-01 a 1361 1 24 2 11 + -1.4709309602563259E+00 a 1362 1 24 2 12 + -7.3119546383323997E-01 a 1363 1 24 2 13 + 5.9624465461749732E-01 a 1364 1 24 2 14 + 1.1965703107989687E+00 a 1365 1 24 2 15 + -4.8078015734066326E-01 a 1366 1 24 2 16 + 2.8731897539798784E-01 a 1367 1 24 2 17 + 2.8943049077679879E+00 a 1368 1 24 2 18 + 4.4309374097560666E-01 a 1369 1 24 2 19 + -5.2571668466848664E-01 a 1370 1 24 2 20 + 2.6293009755349539E+00 a 1371 1 24 2 21 + 1.1166360248787797E+00 a 1372 1 24 2 22 + 1.4367909042068954E+00 a 1373 1 24 2 23 + 1.2263949730702137E+00 a 1374 1 24 2 24 + -1.5658327417588482E+00 a 1375 1 24 2 25 + 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1 25 2 24 + 3.7575240210802421E+00 a 1400 1 25 2 25 + -1.0787018434494783E+01 b 1401 2 1 + -8.4067078142086771E-01 b 1402 2 2 + 9.3201271110229211E-01 b 1403 2 3 + -1.8318272256547821E+00 b 1404 2 4 + -2.1732436845179119E+00 b 1405 2 5 + -2.6390929073478930E+00 b 1406 2 6 + 3.7489748853957300E-01 b 1407 2 7 + -2.3789675524866163E+00 b 1408 2 8 + 2.7252644932624959E+00 b 1409 2 9 + 2.5100559841854970E+00 b 1410 2 10 + -2.4897033671113025E-01 b 1411 2 11 + 2.6913296692082476E+00 b 1412 2 12 + 5.8162695990329221E+00 b 1413 2 13 + -1.5170700889568940E+00 b 1414 2 14 + 4.2121259244130220E+00 b 1415 2 15 + 2.2987725066596130E+00 b 1416 2 16 + -7.1493650128731911E-01 b 1417 2 17 + -3.9961443472349811E-01 b 1418 2 18 + 7.8083705485664430E+00 b 1419 2 19 + -4.0462773256448170E-01 b 1420 2 20 + -1.4333029489891109E+00 b 1421 2 21 + -4.9517224038431467E+00 b 1422 2 22 + 1.0702867307710989E+01 b 1423 2 23 + -9.7535853921453985E-01 b 1424 2 24 + 5.3161969295054172E+00 b 1425 2 25 + -5.1941647295982207E-01 a 1426 2 1 3 1 + -7.7346657642095373E-01 a 1427 2 2 3 1 + 1.4003893583106508E+00 a 1428 2 3 3 1 + 8.9188080044914464E-01 a 1429 2 4 3 1 + -2.0147808233792022E+00 a 1430 2 5 3 1 + -1.8131831735812174E+00 a 1431 2 6 3 1 + 3.3217884596641700E+00 a 1432 2 7 3 1 + -1.2675289031787327E+00 a 1433 2 8 3 1 + -1.2791140359120716E+00 a 1434 2 9 3 1 + 1.9731828075446340E+00 a 1435 2 10 3 1 + -2.3928332883234411E+00 a 1436 2 11 3 1 + -1.1755085043375486E+00 a 1437 2 12 3 1 + 2.6525670286472951E+00 a 1438 2 13 3 1 + -2.4861988521743901E+00 a 1439 2 14 3 1 + 1.2534500349238071E+00 a 1440 2 15 3 1 + 2.8804282010183990E+00 a 1441 2 16 3 1 + -2.0327745898215275E+00 a 1442 2 17 3 1 + -1.1760164122204946E+00 a 1443 2 18 3 1 + -9.9841804355412322E-01 a 1444 2 19 3 1 + -1.8663330516323837E+00 a 1445 2 20 3 1 + 6.3266049836286531E-01 a 1446 2 21 3 1 + 1.2025500357718348E+00 a 1447 2 22 3 1 + 1.1367820678861495E-01 a 1448 2 23 3 1 + -2.6481374255863193E+00 a 1449 2 24 3 1 + 5.2166795947347921E-01 a 1450 2 25 3 1 + 4.8693043186011655E+00 b 1451 3 1 diff --git a/examples/USER/hdnnp/in.hdnnp b/examples/USER/hdnnp/in.hdnnp new file mode 100644 index 0000000000..79edc605be --- /dev/null +++ b/examples/USER/hdnnp/in.hdnnp @@ -0,0 +1,47 @@ +############################################################################### +# MD simulation for HDNNP water +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "data.H2O-360mol" +# Timesteps +variable numSteps equal 10 +variable dt equal 0.0005 +# HDNNP +variable hdnnpCutoff equal 6.36 +variable hdnnpDir string "hdnnp-data" + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary p p p +atom_style atomic +read_data ${cfgFile} +timestep ${dt} +thermo 1 + +############################################################################### +# HDNNP +############################################################################### +pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 +pair_coeff * * H O + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve + +############################################################################### +# OUTPUT +############################################################################### +dump 1 all atom 1 dump.hdnnp + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/USER/mdi/README b/examples/USER/mdi/README new file mode 100644 index 0000000000..086341f785 --- /dev/null +++ b/examples/USER/mdi/README @@ -0,0 +1,24 @@ +This dir contains scripts that demonstrate how to use LAMMPS as an +MDI engine. LAMMPS as an engine performs the MD timestepping. +The driver is a simple Python script. Every timestep the driver +sends one or more commands to LAMMPS. + +-------------- + +The Script.sh file has comands to perform some very simple example +runs. + +-------------- + +More complex calculations using LAMMPS as an MDI engine will +typically require the use of an MDI driver. Several MDI drivers +support calculations with LAMMPS, and include: + +Ab Initio Molecular Dynamics (AIMD) Driver: +https://github.com/MolSSI-MDI/MDI_AIMD_Driver + +Nudged Elastic Band (NEB) Driver: +https://github.com/MolSSI-MDI/MDI_NEB_Driver + +Metadynamics Driver: +https://github.com/MolSSI-MDI/MDI_Metadynamics diff --git a/examples/USER/mdi/Script.sh b/examples/USER/mdi/Script.sh new file mode 100644 index 0000000000..9e3f6e5f62 --- /dev/null +++ b/examples/USER/mdi/Script.sh @@ -0,0 +1,16 @@ +#!/bin/bash +# sample launch scripts + + +# TCP, running LAMMPS on one proc + +python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" & +../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out & +wait + + +# TCP, running LAMMPS on two procs + +python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" & +mpiexec -n 2 ../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out & +wait diff --git a/examples/USER/mdi/driver.py b/examples/USER/mdi/driver.py new file mode 100644 index 0000000000..934f6f7be1 --- /dev/null +++ b/examples/USER/mdi/driver.py @@ -0,0 +1,24 @@ +import sys +import mdi + +use_mpi4py = False +try: + from mpi4py import MPI + use_mpi4py = True +except: + pass + +# Initialize the MDI Library +mdi.MDI_Init(sys.argv[2]) + +# Connect to the engine +comm = mdi.MDI_Accept_communicator() + +# Determine the name of the engine +mdi.MDI_Send_Command("1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 2.1827873e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 -2.910383e-11 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 2.910383e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 0 + 70 74.623347 -938.5575 -936.09782 55565.237 0 4.3655746e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.910383e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 0 + 100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11 +Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms + +Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.468 | 11.468 | 11.468 | 0.0 | 99.96 +Neigh | 0.001181 | 0.001181 | 0.001181 | 0.0 | 0.01 +Comm | 0.001207 | 0.001207 | 0.001207 | 0.0 | 0.01 +Output | 0.000876 | 0.000876 | 0.000876 | 0.0 | 0.01 +Modify | 0.000455 | 0.000455 | 0.000455 | 0.0 | 0.00 +Other | | 0.000397 | | | 0.00 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2201.00 ave 2201 max 2201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 43118.0 ave 43118 max 43118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:11 diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.4 b/examples/USER/pace/log.03Feb2021.pace.product.g++.4 new file mode 100644 index 0000000000..052becb7d6 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.product.g++.4 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE product + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace product +ACE version: 2021.2.3 +Product evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 -1.4551915e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 0 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 -1.4551915e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 7.2759576e-12 + 70 74.623347 -938.5575 -936.09782 55565.237 0 0 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 -1.4551915e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11 +Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms + +Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.1375 | 3.3058 | 3.469 | 6.5 | 93.30 +Neigh | 0.000284 | 0.00031975 | 0.000352 | 0.0 | 0.01 +Comm | 0.071607 | 0.23492 | 0.40336 | 24.6 | 6.63 +Output | 0.001189 | 0.0012315 | 0.001347 | 0.2 | 0.03 +Modify | 0.000311 | 0.00032725 | 0.000351 | 0.0 | 0.01 +Other | | 0.0005298 | | | 0.01 + +Nlocal: 64.0000 ave 71 max 57 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 1373.00 ave 1380 max 1366 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 10779.5 ave 11978 max 9604 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 new file mode 100644 index 0000000000..e6de3bd5c6 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace recursive +ACE version: 2021.2.3 +Recursive evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 0 + 10 280.68558 -945.35055 -936.09878 46326.919 0 5.8207661e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 1.4551915e-11 + 30 160.53661 -941.38948 -936.09798 52222.083 0 7.2759576e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 -5.8207661e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 0 + 60 53.124678 -937.84857 -936.09751 56878.948 0 8.7311491e-11 + 70 74.623347 -938.5575 -936.09782 55565.237 0 -1.4551915e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 2.910383e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 0 +Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms + +Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.3103 | 9.3103 | 9.3103 | 0.0 | 99.96 +Neigh | 0.001214 | 0.001214 | 0.001214 | 0.0 | 0.01 +Comm | 0.001176 | 0.001176 | 0.001176 | 0.0 | 0.01 +Output | 0.000827 | 0.000827 | 0.000827 | 0.0 | 0.01 +Modify | 0.000479 | 0.000479 | 0.000479 | 0.0 | 0.01 +Other | | 0.000363 | | | 0.00 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2201.00 ave 2201 max 2201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 43118.0 ave 43118 max 43118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:09 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 new file mode 100644 index 0000000000..b816f8e570 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace recursive +ACE version: 2021.2.3 +Recursive evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 -5.0931703e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 1.4551915e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 0 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 0 + 50 59.165961 -938.04759 -936.0974 56850.103 0 -2.910383e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 1.4551915e-11 + 70 74.623347 -938.5575 -936.09782 55565.237 0 3.6379788e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 -7.2759576e-12 + 90 142.02657 -940.77975 -936.09837 52001.1 0 -2.910383e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 7.2759576e-12 +Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms + +Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5753 | 2.723 | 2.8656 | 6.3 | 93.46 +Neigh | 0.000308 | 0.000365 | 0.00046 | 0.0 | 0.01 +Comm | 0.045106 | 0.18792 | 0.33552 | 24.1 | 6.45 +Output | 0.001213 | 0.001259 | 0.001388 | 0.2 | 0.04 +Modify | 0.000304 | 0.00033 | 0.00037 | 0.0 | 0.01 +Other | | 0.0005595 | | | 0.02 + +Nlocal: 64.0000 ave 71 max 57 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 1373.00 ave 1380 max 1366 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 10779.5 ave 11978 max 9604 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/USER/rann/in.rann b/examples/USER/rann/in.rann new file mode 100644 index 0000000000..32f79bb257 --- /dev/null +++ b/examples/USER/rann/in.rann @@ -0,0 +1,34 @@ +units metal +dimension 3 +boundary p p p +atom_style atomic + +lattice hcp 2.995 origin 0.5 0.5 0.5 +region whole block 0 4 0 2 0 1.94 units lattice +create_box 2 whole +create_atoms 2 box +timestep 0.001 +set group all type 1 +set group all type/fraction 2 0.10 486 + +pair_style rann +pair_coeff * * TiZr_2.rann Ti Zr +velocity all create 300 12345 mom yes rot no loop geom + +compute peratom all pe/atom +#dump 1 all custom 10 rann.dump id type x y z c_peratom +#dump_modify 1 element Ti Zr + +thermo 25 +thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp + +fix 1 all box/relax aniso 0.0 +min_style cg +minimize 1.0e-10 1.0e-10 250 1000 +unfix 1 +#write_restart TiZr.min +#-------------------------EQUILIBRATION-------------------------------- + +fix 1 all npt temp 300 300 0.1 aniso 0 0 1 +run 250 +unfix 1 diff --git a/examples/USER/rann/log.22Jun21.rann.g++.1 b/examples/USER/rann/log.22Jun21.rann.g++.1 new file mode 100644 index 0000000000..40309e5d0a --- /dev/null +++ b/examples/USER/rann/log.22Jun21.rann.g++.1 @@ -0,0 +1,149 @@ +LAMMPS (27 May 2021) + using 1 OpenMP thread(s) per MPI task +units metal +dimension 3 +boundary p p p +atom_style atomic + +lattice hcp 2.995 origin 0.5 0.5 0.5 +Lattice spacing in x,y,z = 2.9950000 5.1874922 4.8908145 +region whole block 0 4 0 2 0 1.94 units lattice +create_box 2 whole +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (11.980000 10.374984 9.4881802) + 1 by 1 by 1 MPI processor grid +create_atoms 2 box +Created 64 atoms + create_atoms CPU = 0.001 seconds +timestep 0.001 +set group all type 1 +Setting atom values ... + 64 settings made for type +set group all type/fraction 2 0.10 486 +Setting atom values ... + 3 settings made for type/fraction + +pair_style rann +pair_coeff * * TiZr_2.rann Ti Zr +velocity all create 300 12345 mom yes rot no loop geom + +compute peratom all pe/atom +#dump 1 all custom 10 rann.dump id type x y z c_peratom +#dump_modify 1 element Ti Zr + +thermo 25 +thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp + +fix 1 all box/relax aniso 0.0 +min_style cg +minimize 1.0e-10 1.0e-10 250 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 3 3 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair rann, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.731 | 4.731 | 4.731 Mbytes +Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp + 0 11.98 10.374984 9.4881802 -29375.303 -28706.895 -32525.995 -26893.017 -405.95229 150.93453 -694.91972 -103433.05 300 + 25 11.950182 10.349549 9.4684279 -21452.379 -23337.292 -22794.542 -18225.304 -134.67238 18.687575 99.672896 -103433.82 300 + 50 11.920232 10.32424 9.4496837 -14826.163 -16604.987 -16114.802 -11758.699 -137.29961 19.192625 98.496407 -103433.93 300 + 75 11.890282 10.299105 9.4325798 -8241.3799 -9829.5396 -9413.8421 -5480.758 -139.61723 19.753871 96.739255 -103434.01 300 + 100 11.860332 10.274334 9.4188725 -1918.2777 -3140.1632 -2843.6796 229.00961 -141.67556 20.337591 93.803319 -103434.06 300 + 125 11.833362 10.25385 9.4174816 2267.7814 2244.5712 2225.4032 2333.3697 -145.79432 20.426911 85.921454 -103434.27 300 + 150 11.845047 10.264313 9.3943614 2154.2266 2077.795 2064.0012 2320.8837 -166.59541 20.457485 86.593349 -103434.98 300 + 175 11.851749 10.270526 9.3807742 2356.6765 2258.3767 2245.2877 2566.3649 -198.93901 21.826088 87.211907 -103435.42 300 + 200 11.85791 10.276284 9.3740248 2116.088 2014.9253 2000.9373 2332.4013 -239.79555 23.069264 88.211395 -103435.71 300 + 225 11.86067 10.279084 9.3688089 2380.6783 2266.3876 2253.624 2622.0232 -284.70218 23.782436 89.32664 -103435.9 300 + 250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300 +Loop time of 5.54687 on 1 procs for 250 steps with 64 atoms + +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -103433.047620681 -103436.028362733 -103436.034678926 + Force two-norm initial, final = 40.834083 2.1923162 + Force max component initial, final = 25.471215 0.42479025 + Final line search alpha, max atom move = 0.0013092641 0.00055616263 + Iterations, force evaluations = 250 250 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.535 | 5.535 | 5.535 | 0.0 | 99.79 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0021643 | 0.0021643 | 0.0021643 | 0.0 | 0.04 +Output | 0.00040175 | 0.00040175 | 0.00040175 | 0.0 | 0.01 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.009261 | | | 0.17 + +Nlocal: 64.0000 ave 64 max 64 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1508.00 ave 1508 max 1508 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15136.0 ave 15136 max 15136 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15136 +Ave neighs/atom = 236.50000 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix 1 +#write_restart TiZr.min +#-------------------------EQUILIBRATION-------------------------------- + +fix 1 all npt temp 300 300 0.1 aniso 0 0 1 +run 250 +Per MPI rank memory allocation (min/avg/max) = 3.606 | 3.606 | 3.606 Mbytes +Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp + 250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300 + 275 11.868972 10.287532 9.3712492 5459.6466 3913.9919 6041.4929 6423.455 1860.057 -169.89698 -163.71384 -103435.08 182.98209 + 300 11.883725 10.306821 9.3893899 821.53461 -1023.4738 2711.5668 776.51078 2816.8806 446.29412 -732.33785 -103434.5 116.94541 + 325 11.894878 10.332706 9.4085094 -7099.8438 -7329.3175 -4694.3612 -9275.8528 2957.9222 1086.6737 -1549.5101 -103434.96 192.09731 + 350 11.885259 10.347441 9.4071117 -6402.0644 -5181.1103 -5986.8957 -8038.1873 3057.1547 867.09919 -1625.3988 -103434.62 168.81926 + 375 11.860011 10.346166 9.3858556 -2508.1672 766.71963 -4549.8268 -3741.3944 1666.1095 224.37185 -926.42628 -103434.73 195.28196 + 400 11.837235 10.332927 9.3557562 3324.0157 7044.0305 -512.01476 3440.0314 -1246.2047 -108.13943 -18.443174 -103434.99 245.22981 + 425 11.835641 10.318434 9.3346884 8707.7341 9660.2158 4055.4863 12407.5 -2772.2282 -243.25933 619.5127 -103434.58 215.25674 + 450 11.862626 10.313654 9.3420741 6651.6061 5159.117 3236.6007 11559.101 -2538.4591 -179.54384 998.92807 -103434.53 225.2827 + 475 11.905198 10.317019 9.3767687 -823.32707 -3847.0367 -1183.0257 2560.0812 -2415.4604 -135.15481 1006.8549 -103434.64 259.05599 + 500 11.936602 10.317134 9.4184969 -7923.5224 -11138.312 -5701.3928 -6930.8623 -2175.4452 878.30934 737.79497 -103434.28 240.16605 +Loop time of 5.28008 on 1 procs for 250 steps with 64 atoms + +Performance: 4.091 ns/day, 5.867 hours/ns, 47.348 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.2728 | 5.2728 | 5.2728 | 0.0 | 99.86 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0021591 | 0.0021591 | 0.0021591 | 0.0 | 0.04 +Output | 0.00040452 | 0.00040452 | 0.00040452 | 0.0 | 0.01 +Modify | 0.0040597 | 0.0040597 | 0.0040597 | 0.0 | 0.08 +Other | | 0.0006859 | | | 0.01 + +Nlocal: 64.0000 ave 64 max 64 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1508.00 ave 1508 max 1508 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15320.0 ave 15320 max 15320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15320 +Ave neighs/atom = 239.37500 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix 1 +Total wall time: 0:00:10 diff --git a/examples/USER/rann/log.22Jun21.rann.g++.4 b/examples/USER/rann/log.22Jun21.rann.g++.4 new file mode 100644 index 0000000000..4f31af6ce2 --- /dev/null +++ b/examples/USER/rann/log.22Jun21.rann.g++.4 @@ -0,0 +1,149 @@ +LAMMPS (27 May 2021) + using 1 OpenMP thread(s) per MPI task +units metal +dimension 3 +boundary p p p +atom_style atomic + +lattice hcp 2.995 origin 0.5 0.5 0.5 +Lattice spacing in x,y,z = 2.9950000 5.1874922 4.8908145 +region whole block 0 4 0 2 0 1.94 units lattice +create_box 2 whole +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (11.980000 10.374984 9.4881802) + 2 by 2 by 1 MPI processor grid +create_atoms 2 box +Created 64 atoms + create_atoms CPU = 0.000 seconds +timestep 0.001 +set group all type 1 +Setting atom values ... + 64 settings made for type +set group all type/fraction 2 0.10 486 +Setting atom values ... + 3 settings made for type/fraction + +pair_style rann +pair_coeff * * TiZr_2.rann Ti Zr +velocity all create 300 12345 mom yes rot no loop geom + +compute peratom all pe/atom +#dump 1 all custom 10 rann.dump id type x y z c_peratom +#dump_modify 1 element Ti Zr + +thermo 25 +thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp + +fix 1 all box/relax aniso 0.0 +min_style cg +minimize 1.0e-10 1.0e-10 250 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 3 3 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair rann, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes +Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp + 0 11.98 10.374984 9.4881802 -29375.303 -28706.895 -32525.995 -26893.017 -405.95229 150.93453 -694.91972 -103433.05 300 + 25 11.950182 10.349549 9.4684279 -21452.379 -23337.292 -22794.542 -18225.304 -134.67238 18.687575 99.672896 -103433.82 300 + 50 11.920232 10.32424 9.4496837 -14826.163 -16604.987 -16114.802 -11758.699 -137.29961 19.192625 98.496407 -103433.93 300 + 75 11.890282 10.299105 9.4325798 -8241.3799 -9829.5396 -9413.8421 -5480.758 -139.61723 19.753871 96.739255 -103434.01 300 + 100 11.860332 10.274334 9.4188725 -1918.2777 -3140.1632 -2843.6796 229.00961 -141.67556 20.337591 93.803319 -103434.06 300 + 125 11.833362 10.25385 9.4174816 2267.7814 2244.5712 2225.4032 2333.3697 -145.79432 20.426911 85.921454 -103434.27 300 + 150 11.845047 10.264313 9.3943614 2154.2266 2077.795 2064.0012 2320.8837 -166.59541 20.457485 86.593349 -103434.98 300 + 175 11.851749 10.270526 9.3807742 2356.6765 2258.3767 2245.2877 2566.3649 -198.93901 21.826088 87.211907 -103435.42 300 + 200 11.85791 10.276284 9.3740248 2116.088 2014.9253 2000.9373 2332.4013 -239.79555 23.069264 88.211395 -103435.71 300 + 225 11.86067 10.279084 9.3688089 2380.6783 2266.3876 2253.624 2622.0232 -284.70218 23.782436 89.32664 -103435.9 300 + 250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300 +Loop time of 2.4811 on 4 procs for 250 steps with 64 atoms + +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -103433.047620681 -103436.028362733 -103436.034678926 + Force two-norm initial, final = 40.834083 2.1923162 + Force max component initial, final = 25.471215 0.42479025 + Final line search alpha, max atom move = 0.0013092641 0.00055616263 + Iterations, force evaluations = 250 250 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3295 | 2.3474 | 2.3627 | 0.9 | 94.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.089974 | 0.10466 | 0.12186 | 4.0 | 4.22 +Output | 0.00048351 | 0.0010692 | 0.0028254 | 3.1 | 0.04 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.02802 | | | 1.13 + +Nlocal: 16.0000 ave 16 max 16 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1035.00 ave 1035 max 1035 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 3784.00 ave 3784 max 3784 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15136 +Ave neighs/atom = 236.50000 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix 1 +#write_restart TiZr.min +#-------------------------EQUILIBRATION-------------------------------- + +fix 1 all npt temp 300 300 0.1 aniso 0 0 1 +run 250 +Per MPI rank memory allocation (min/avg/max) = 3.353 | 3.353 | 3.353 Mbytes +Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp + 250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300 + 275 11.868972 10.287532 9.3712492 5459.6466 3913.9919 6041.4929 6423.455 1860.057 -169.89698 -163.71384 -103435.08 182.98209 + 300 11.883725 10.306821 9.3893899 821.53461 -1023.4738 2711.5668 776.51078 2816.8806 446.29412 -732.33785 -103434.5 116.94541 + 325 11.894878 10.332706 9.4085094 -7099.8438 -7329.3175 -4694.3612 -9275.8528 2957.9222 1086.6737 -1549.5101 -103434.96 192.09731 + 350 11.885259 10.347441 9.4071117 -6402.0644 -5181.1103 -5986.8957 -8038.1873 3057.1547 867.09919 -1625.3988 -103434.62 168.81926 + 375 11.860011 10.346166 9.3858556 -2508.1672 766.71963 -4549.8268 -3741.3944 1666.1095 224.37185 -926.42628 -103434.73 195.28196 + 400 11.837235 10.332927 9.3557562 3324.0157 7044.0305 -512.01476 3440.0314 -1246.2047 -108.13943 -18.443174 -103434.99 245.22981 + 425 11.835641 10.318434 9.3346884 8707.7341 9660.2158 4055.4863 12407.5 -2772.2282 -243.25933 619.5127 -103434.58 215.25674 + 450 11.862626 10.313654 9.3420741 6651.6061 5159.117 3236.6007 11559.101 -2538.4591 -179.54384 998.92807 -103434.53 225.2827 + 475 11.905198 10.317019 9.3767687 -823.32707 -3847.0367 -1183.0257 2560.0812 -2415.4604 -135.15481 1006.8549 -103434.64 259.05599 + 500 11.936602 10.317134 9.4184969 -7923.5224 -11138.312 -5701.3928 -6930.8623 -2175.4452 878.30934 737.79497 -103434.28 240.16605 +Loop time of 2.55414 on 4 procs for 250 steps with 64 atoms + +Performance: 8.457 ns/day, 2.838 hours/ns, 97.880 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5174 | 2.1911 | 2.5037 | 26.7 | 85.79 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.035032 | 0.34713 | 1.0204 | 67.1 | 13.59 +Output | 0.00048485 | 0.0010827 | 0.0028745 | 3.1 | 0.04 +Modify | 0.01054 | 0.012633 | 0.013719 | 1.1 | 0.49 +Other | | 0.002167 | | | 0.08 + +Nlocal: 16.0000 ave 18 max 11 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Nghost: 1035.00 ave 1040 max 1033 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 3830.00 ave 4316 max 2636 min +Histogram: 1 0 0 0 0 0 0 0 1 2 + +Total # of neighbors = 15320 +Ave neighs/atom = 239.37500 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix 1 +Total wall time: 0:00:05 diff --git a/examples/VISCOSITY/README b/examples/VISCOSITY/README index 8235fa1f77..b56b54340c 100644 --- a/examples/VISCOSITY/README +++ b/examples/VISCOSITY/README @@ -28,7 +28,7 @@ minute or so and produce the accompanying log files and profile files (for velocity or momentum flux). See the Movies page of the LAMMPS web site -(http://lammps.sandia.gov/movies.html), for animations of the NEMD +(https://www.lammps.org/movies.html), for animations of the NEMD scripts, created using the dump image command. The state point of the LJ fluid is rho* = 0.6, T* = 1.0, and Rcut = diff --git a/examples/deposit/in.deposit.molecule.rigid-nve-small b/examples/deposit/in.deposit.molecule.rigid-nve-small new file mode 100644 index 0000000000..b2af77ac00 --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-nve-small @@ -0,0 +1,56 @@ +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nve/small molecule mol dimer +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 & + mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 diff --git a/examples/deposit/in.deposit.molecule.rigid-nvt-small b/examples/deposit/in.deposit.molecule.rigid-nvt-small new file mode 100644 index 0000000000..9ceb1b3984 --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-nvt-small @@ -0,0 +1,56 @@ +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 & + mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 diff --git a/examples/deposit/in.deposit.molecule.rigid-small b/examples/deposit/in.deposit.molecule.rigid-small new file mode 100644 index 0000000000..2e6a84e54b --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-small @@ -0,0 +1,56 @@ +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/small molecule mol dimer +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 & + mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 diff --git a/examples/deposit/in.deposit.molecule.shake b/examples/deposit/in.deposit.molecule.shake index 7bd701c924..30c6bd7a53 100644 --- a/examples/deposit/in.deposit.molecule.shake +++ b/examples/deposit/in.deposit.molecule.shake @@ -21,11 +21,11 @@ bond_coeff 1 5.0 1.0 neigh_modify delay 0 -group addatoms type 2 +group addatoms empty region mobile block 0 5 0 5 2 INF group mobile region mobile -compute add addatoms temp +compute add addatoms temp compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 new file mode 100644 index 0000000000..792d3954c1 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nve/small molecule mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615 + 900 368 1.1250034 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655 + 1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041 + 1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272 + 1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641 + 1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595 + 1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503 + 1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922 + 1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709 + 1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665 + 1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025 + 2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647 + 2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526 + 2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284 + 2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436 + 2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839 + 2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448 + 2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222 + 2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856 + 2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872 + 2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283 + 3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953 + 3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935 + 3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713 + 3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674 + 3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626 + 3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941 + 3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484 + 3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147 + 3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799 + 3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878 + 4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433 + 4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822 + 4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778 + 4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913 + 4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275 + 4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051 + 4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572 + 4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509 + 4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049 + 4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429 + 5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531 + 5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403 + 5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239 + 5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702 + 5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883 + 5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171 + 5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419 + 5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563 + 5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625 + 5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757 + 6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047 + 6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913 + 6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083 + 6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967 + 6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489 + 6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516 + 6600 482 0.354106 -6.6890268 -6.567808 -0.81897158 + 6700 484 0.3504816 -6.681739 -6.5604463 -0.811609 + 6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296 + 6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651 + 7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078 + 7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001 + 7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767 + 7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121 + 7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584 + 7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602 + 7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497 + 7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548 + 7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084 + 7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684 + 8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575 + 8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457 + 8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287 + 8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937 + 8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496 + 8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738 + 8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327 + 8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016 + 8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456 + 8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919 + 9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061 + 9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298 + 9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671 + 9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602 + 9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131 + 9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326 + 9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105 + 9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932 + 9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759 + 9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312 + 10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213 +Loop time of 16.7275 on 1 procs for 10000 steps with 550 atoms + +Performance: 258256.688 tau/day, 597.816 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.2508 | 9.2508 | 9.2508 | 0.0 | 55.30 +Bond | 0.021603 | 0.021603 | 0.021603 | 0.0 | 0.13 +Neigh | 4.5325 | 4.5325 | 4.5325 | 0.0 | 27.10 +Comm | 0.62777 | 0.62777 | 0.62777 | 0.0 | 3.75 +Output | 0.006916 | 0.006916 | 0.006916 | 0.0 | 0.04 +Modify | 2.218 | 2.218 | 2.218 | 0.0 | 13.26 +Other | | 0.07002 | | | 0.42 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2344.00 ave 2344 max 2344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36607.0 ave 36607 max 36607 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36607 +Ave neighs/atom = 66.558182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 847 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 new file mode 100644 index 0000000000..e9158cd7ec --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 4 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.002 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nve/small molecule mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 + 200 354 1.0081552 -6.8645575 -6.850318 -0.69629729 + 300 356 1.0085803 -6.821677 -6.8004288 -0.69532657 + 400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568 + 500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641 + 600 362 1.026146 -6.7129201 -6.6704003 -0.67063836 + 700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472 + 800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282 + 900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928 + 1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047 + 1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289 + 1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821 + 1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688 + 1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401 + 1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986 + 1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779 + 1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111 + 1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786 + 1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098 + 2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072 + 2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411 + 2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854 + 2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918 + 2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214 + 2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183 + 2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893 + 2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506 + 2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082 + 2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652 + 3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355 + 3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541 + 3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248 + 3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819 + 3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309 + 3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397 + 3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391 + 3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397 + 3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111 + 3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465 + 4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933 + 4100 432 0.44820466 -6.640222 -6.5338771 -0.805972 + 4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414 + 4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484 + 4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062 + 4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194 + 4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114 + 4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577 + 4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746 + 4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416 + 5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399 + 5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755 + 5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092 + 5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134 + 5400 458 0.37764326 -6.661431 -6.550117 -0.72187808 + 5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745 + 5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454 + 5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312 + 5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125 + 5900 468 0.346812 -6.681215 -6.57191 -0.81184233 + 6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821 + 6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598 + 6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526 + 6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174 + 6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407 + 6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289 + 6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442 + 6700 484 0.37615026 -6.722917 -6.592741 -0.76534055 + 6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211 + 6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458 + 7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555 + 7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708 + 7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153 + 7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931 + 7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391 + 7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083 + 7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572 + 7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335 + 7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197 + 7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073 + 8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575 + 8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257 + 8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132 + 8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415 + 8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921 + 8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077 + 8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137 + 8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836 + 8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107 + 8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959 + 9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529 + 9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692 + 9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911 + 9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935 + 9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598 + 9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851 + 9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104 + 9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581 + 9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905 + 9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157 + 10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157 +Loop time of 16.2553 on 4 procs for 10000 steps with 550 atoms + +Performance: 265759.101 tau/day, 615.183 timesteps/s +97.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0034051 | 2.6646 | 8.0317 | 200.7 | 16.39 +Bond | 0.0022626 | 0.0072971 | 0.019437 | 8.3 | 0.04 +Neigh | 0.018657 | 1.218 | 3.7621 | 137.5 | 7.49 +Comm | 1.1497 | 6.7957 | 12.192 | 164.2 | 41.81 +Output | 0.010692 | 0.01431 | 0.019901 | 3.2 | 0.09 +Modify | 3.1502 | 5.3779 | 11.342 | 149.0 | 33.08 +Other | | 0.1775 | | | 1.09 + +Nlocal: 137.500 ave 299 max 2 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1903.75 ave 2686 max 529 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Neighs: 9209.75 ave 23206 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 36839 +Ave neighs/atom = 66.980000 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 829 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 new file mode 100644 index 0000000000..5abc557d8b --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615 + 900 368 1.1250034 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655 + 1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041 + 1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272 + 1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641 + 1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595 + 1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503 + 1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922 + 1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709 + 1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665 + 1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025 + 2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647 + 2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526 + 2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284 + 2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436 + 2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839 + 2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448 + 2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222 + 2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856 + 2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872 + 2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283 + 3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953 + 3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935 + 3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713 + 3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674 + 3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626 + 3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941 + 3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484 + 3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147 + 3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799 + 3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878 + 4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433 + 4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822 + 4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778 + 4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913 + 4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275 + 4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051 + 4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572 + 4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509 + 4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049 + 4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429 + 5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531 + 5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403 + 5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239 + 5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702 + 5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883 + 5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171 + 5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419 + 5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563 + 5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625 + 5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757 + 6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047 + 6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913 + 6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083 + 6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967 + 6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489 + 6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516 + 6600 482 0.354106 -6.6890268 -6.567808 -0.81897158 + 6700 484 0.3504816 -6.681739 -6.5604463 -0.811609 + 6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296 + 6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651 + 7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078 + 7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001 + 7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767 + 7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121 + 7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584 + 7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602 + 7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497 + 7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548 + 7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084 + 7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684 + 8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575 + 8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457 + 8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287 + 8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937 + 8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496 + 8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738 + 8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327 + 8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016 + 8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456 + 8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919 + 9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061 + 9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298 + 9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671 + 9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602 + 9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131 + 9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326 + 9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105 + 9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932 + 9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759 + 9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312 + 10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213 +Loop time of 16.6615 on 1 procs for 10000 steps with 550 atoms + +Performance: 259279.806 tau/day, 600.185 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.2639 | 9.2639 | 9.2639 | 0.0 | 55.60 +Bond | 0.021559 | 0.021559 | 0.021559 | 0.0 | 0.13 +Neigh | 4.544 | 4.544 | 4.544 | 0.0 | 27.27 +Comm | 0.62792 | 0.62792 | 0.62792 | 0.0 | 3.77 +Output | 0.0069666 | 0.0069666 | 0.0069666 | 0.0 | 0.04 +Modify | 2.1282 | 2.1282 | 2.1282 | 0.0 | 12.77 +Other | | 0.06897 | | | 0.41 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2344.00 ave 2344 max 2344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36607.0 ave 36607 max 36607 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36607 +Ave neighs/atom = 66.558182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 847 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 new file mode 100644 index 0000000000..7239fc9bb9 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 4 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.002 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 + 200 354 1.0081552 -6.8645575 -6.850318 -0.69629729 + 300 356 1.0085803 -6.821677 -6.8004288 -0.69532657 + 400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568 + 500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641 + 600 362 1.026146 -6.7129201 -6.6704003 -0.67063836 + 700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472 + 800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282 + 900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928 + 1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047 + 1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289 + 1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821 + 1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688 + 1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401 + 1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986 + 1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779 + 1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111 + 1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786 + 1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098 + 2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072 + 2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411 + 2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854 + 2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918 + 2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214 + 2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183 + 2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893 + 2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506 + 2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082 + 2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652 + 3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355 + 3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541 + 3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248 + 3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819 + 3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309 + 3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397 + 3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391 + 3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397 + 3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111 + 3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465 + 4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933 + 4100 432 0.44820466 -6.640222 -6.5338771 -0.805972 + 4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414 + 4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484 + 4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062 + 4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194 + 4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114 + 4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577 + 4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746 + 4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416 + 5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399 + 5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755 + 5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092 + 5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134 + 5400 458 0.37764326 -6.661431 -6.550117 -0.72187808 + 5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745 + 5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454 + 5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312 + 5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125 + 5900 468 0.346812 -6.681215 -6.57191 -0.81184233 + 6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821 + 6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598 + 6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526 + 6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174 + 6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407 + 6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289 + 6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442 + 6700 484 0.37615026 -6.722917 -6.592741 -0.76534055 + 6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211 + 6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458 + 7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555 + 7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708 + 7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153 + 7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931 + 7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391 + 7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083 + 7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572 + 7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335 + 7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197 + 7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073 + 8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575 + 8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257 + 8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132 + 8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415 + 8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921 + 8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077 + 8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137 + 8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836 + 8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107 + 8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959 + 9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529 + 9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692 + 9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911 + 9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935 + 9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598 + 9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851 + 9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104 + 9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581 + 9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905 + 9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157 + 10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157 +Loop time of 16.1559 on 4 procs for 10000 steps with 550 atoms + +Performance: 267395.139 tau/day, 618.970 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0035574 | 2.5467 | 7.5373 | 192.6 | 15.76 +Bond | 0.0022929 | 0.0073138 | 0.019471 | 8.3 | 0.05 +Neigh | 0.018645 | 1.2357 | 3.8167 | 138.4 | 7.65 +Comm | 1.1946 | 6.6335 | 11.87 | 158.8 | 41.06 +Output | 0.010714 | 0.014391 | 0.020006 | 3.2 | 0.09 +Modify | 3.4474 | 5.6081 | 11.47 | 143.2 | 34.71 +Other | | 0.1102 | | | 0.68 + +Nlocal: 137.500 ave 299 max 2 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1903.75 ave 2686 max 529 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Neighs: 9209.75 ave 23206 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 36839 +Ave neighs/atom = 66.980000 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 829 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 new file mode 100644 index 0000000000..0f5a1afcfa --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/small molecule mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958952 -6.6412275 -6.5813425 -0.68789614 + 900 368 1.1250033 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326373 -6.5993719 -6.5160856 -0.6968868 + 1100 372 1.1397426 -6.5912861 -6.5070309 -0.63330356 + 1200 374 1.0514292 -6.5905747 -6.5062354 -0.71020362 + 1300 376 1.003296 -6.5747765 -6.4880555 -0.65459732 + 1400 378 0.82999289 -6.5681797 -6.4913285 -0.60438126 + 1500 380 0.90239175 -6.575298 -6.4862461 -0.66528725 + 1600 382 0.86399799 -6.5692206 -6.4787496 -0.65027781 + 1700 384 0.64747231 -6.5644237 -6.4927634 -0.6304614 + 1800 386 0.74288971 -6.5515735 -6.4649672 -0.67772325 + 1900 388 0.7257202 -6.5565091 -6.4676644 -0.66173549 + 2000 390 0.73381036 -6.5631515 -6.4690733 -0.64685916 + 2100 392 0.76476562 -6.5574124 -6.4549885 -0.68866192 + 2200 394 0.65932468 -6.5511557 -6.459118 -0.71728829 + 2300 396 0.70269509 -6.5728146 -6.4707819 -0.64362081 + 2400 398 0.60528919 -6.5845991 -6.4933494 -0.63956327 + 2500 400 0.51025744 -6.5812452 -6.5015175 -0.68706961 + 2600 402 0.5245131 -6.6003894 -6.5155801 -0.68972215 + 2700 404 0.46330251 -6.5659175 -6.4885092 -0.72870942 + 2800 406 0.48039778 -6.5715192 -6.488692 -0.753758 + 2900 408 0.53698616 -6.5813154 -6.4858951 -0.67117541 + 3000 410 0.50231419 -6.5886963 -6.4968096 -0.71905351 + 3100 412 0.49420225 -6.596733 -6.5037702 -0.65947518 + 3200 414 0.42703699 -6.5879338 -6.5054146 -0.80033546 + 3300 416 0.44306009 -6.580249 -6.4923825 -0.76503083 + 3400 418 0.55620672 -6.5923388 -6.4792346 -0.69367877 + 3500 420 0.39815033 -6.5911154 -6.5081674 -0.65569211 + 3600 422 0.44197847 -6.6026382 -6.5083774 -0.73299102 + 3700 424 0.45049389 -6.6060616 -6.5077817 -0.7552914 + 3800 426 0.43047295 -6.6079275 -6.51193 -0.71501328 + 3900 428 0.43779129 -6.6099306 -6.5102001 -0.71539515 + 4000 430 0.41113503 -6.6123009 -6.5166881 -0.74177096 + 4100 432 0.32800011 -6.5983566 -6.5205325 -0.71688103 + 4200 434 0.39168203 -6.6110342 -6.5162724 -0.78927697 + 4300 436 0.48151013 -6.6183315 -6.4996106 -0.70523035 + 4400 438 0.45391027 -6.6331732 -6.5191775 -0.7270855 + 4500 440 0.349126 -6.6091657 -6.5199006 -0.76974115 + 4600 442 0.43375023 -6.6219188 -6.5090653 -0.74576212 + 4700 444 0.40071749 -6.6184164 -6.5123707 -0.71919052 + 4800 446 0.414292 -6.6298132 -6.5183445 -0.76237313 + 4900 448 0.44210681 -6.6364174 -6.5155288 -0.78753121 + 5000 450 0.36101771 -6.6232703 -6.5229876 -0.73927083 + 5100 452 0.41481171 -6.6442404 -6.5272305 -0.76316209 + 5200 454 0.40283527 -6.6512252 -6.5358759 -0.79645689 + 5300 456 0.3642061 -6.6530346 -6.5472072 -0.77458364 + 5400 458 0.38449826 -6.6514864 -6.5381518 -0.73083784 + 5500 460 0.42559408 -6.6769326 -6.5497169 -0.78932279 + 5600 462 0.38905756 -6.6698705 -6.5519743 -0.77118812 + 5700 464 0.38354955 -6.6706904 -6.5528977 -0.75067129 + 5800 466 0.36760943 -6.6942519 -6.5798669 -0.685487 + 5900 468 0.30783118 -6.6838159 -6.5867965 -0.79233808 + 6000 470 0.33145368 -6.6733504 -6.5675673 -0.84390449 + 6100 472 0.39252324 -6.6912189 -6.5643973 -0.83342022 + 6200 474 0.32342144 -6.6906083 -6.5848481 -0.71262158 + 6300 476 0.34445238 -6.7008453 -6.5868721 -0.76650756 + 6400 478 0.38152782 -6.7017838 -6.5740758 -0.77113022 + 6500 480 0.37540166 -6.7119996 -6.5849105 -0.79907635 + 6600 482 0.3579419 -6.7034721 -6.5809401 -0.8141269 + 6700 484 0.33538235 -6.6916682 -6.575601 -0.83265486 + 6800 486 0.34081871 -6.6931924 -6.573976 -0.80582583 + 6900 488 0.3555283 -6.6939997 -6.5683263 -0.74771423 + 7000 490 0.3543769 -6.7093364 -6.5827732 -0.77643516 + 7100 492 0.31263107 -6.698361 -6.5855723 -0.73108333 + 7200 494 0.32107 -6.6959056 -6.5789166 -0.7575478 + 7300 496 0.32908165 -6.7137605 -6.592677 -0.86538023 + 7400 498 0.32539571 -6.7030353 -6.5821554 -0.79337428 + 7500 500 0.33902577 -6.7078178 -6.5806832 -0.85408988 + 7600 502 0.35530921 -6.707507 -6.5730274 -0.79914613 + 7700 504 0.32391812 -6.6978823 -6.5741635 -0.78603595 + 7800 506 0.36390015 -6.7151325 -6.5748943 -0.83164222 + 7900 508 0.3372561 -6.7086718 -6.5775535 -0.7949992 + 8000 510 0.36612946 -6.7225238 -6.5789437 -0.80322866 + 8100 512 0.34622305 -6.7229825 -6.5860486 -0.70478659 + 8200 514 0.3212233 -6.7202524 -6.5921381 -0.91836713 + 8300 516 0.3402461 -6.721488 -6.5846642 -0.88273592 + 8400 518 0.34070258 -6.7268378 -6.5887152 -0.76057264 + 8500 520 0.36267747 -6.744602 -6.5963924 -0.81051317 + 8600 522 0.3439948 -6.7376267 -6.595943 -0.84600203 + 8700 524 0.30960289 -6.7276471 -6.5991382 -0.90965986 + 8800 526 0.28868972 -6.7159628 -6.595218 -0.876093 + 8900 528 0.31020216 -6.7162903 -6.5855707 -0.83193125 + 9000 530 0.31836275 -6.7171479 -6.5819939 -0.82093897 + 9100 532 0.32543293 -6.724167 -6.5850016 -0.7690143 + 9200 534 0.32644265 -6.7139575 -6.5733549 -0.86903096 + 9300 536 0.33050759 -6.7254715 -6.5821077 -0.94504522 + 9400 538 0.30372582 -6.7139931 -6.5813247 -0.91128612 + 9500 540 0.32943659 -6.7206223 -6.5757312 -0.87818439 + 9600 542 0.30911968 -6.708091 -6.5712114 -0.79092372 + 9700 544 0.33909826 -6.7222948 -6.5711342 -0.80266151 + 9800 546 0.29015141 -6.7086869 -6.5784908 -0.87763769 + 9900 548 0.33838474 -6.7384955 -6.5856667 -0.85630604 + 10000 550 0.30213198 -6.7338924 -6.5965597 -0.75738882 +Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms + +Performance: 249924.414 tau/day, 578.529 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.637 | 9.637 | 9.637 | 0.0 | 55.75 +Bond | 0.025444 | 0.025444 | 0.025444 | 0.0 | 0.15 +Neigh | 4.6852 | 4.6852 | 4.6852 | 0.0 | 27.11 +Comm | 0.65556 | 0.65556 | 0.65556 | 0.0 | 3.79 +Output | 0.0099883 | 0.0099883 | 0.0099883 | 0.0 | 0.06 +Modify | 2.1895 | 2.1895 | 2.1895 | 0.0 | 12.67 +Other | | 0.08248 | | | 0.48 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2367.00 ave 2367 max 2367 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36781.0 ave 36781 max 36781 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36781 +Ave neighs/atom = 66.874545 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 840 +Dangerous builds = 0 +Total wall time: 0:00:17 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 new file mode 100644 index 0000000000..0dcae43ba2 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 4 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.139 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/small molecule mol dimer + create bodies CPU = 0.006 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 + 200 354 1.0081552 -6.8645575 -6.850318 -0.69629729 + 300 356 1.0085803 -6.821677 -6.8004288 -0.69532657 + 400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568 + 500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641 + 600 362 1.026146 -6.7129201 -6.6704003 -0.67063836 + 700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472 + 800 366 1.0958893 -6.6402029 -6.5803182 -0.66307281 + 900 368 1.1231768 -6.6050912 -6.5364187 -0.64076928 + 1000 370 1.1976283 -6.5942507 -6.5133299 -0.69249019 + 1100 372 1.0506263 -6.5772313 -6.499564 -0.63072939 + 1200 374 0.93724351 -6.5732957 -6.4981157 -0.64963897 + 1300 376 0.93899686 -6.5578406 -6.4766773 -0.65096289 + 1400 378 0.8704974 -6.5468498 -6.4662482 -0.67613931 + 1500 380 0.84490693 -6.5401094 -6.4567304 -0.64385968 + 1600 382 0.9243154 -6.5611604 -6.4643734 -0.62096869 + 1700 384 0.67202953 -6.5590557 -6.4846775 -0.67807465 + 1800 386 0.8712464 -6.5654953 -6.4639251 -0.65860236 + 1900 388 0.70011668 -6.5808612 -6.495151 -0.65146463 + 2000 390 0.64019295 -6.5652168 -6.4831408 -0.70291888 + 2100 392 0.67578277 -6.5596196 -6.469113 -0.63315981 + 2200 394 0.60785287 -6.558941 -6.4740885 -0.7133822 + 2300 396 0.8155086 -6.5756022 -6.4571887 -0.69176417 + 2400 398 0.69028748 -6.5875474 -6.483484 -0.63743938 + 2500 400 0.5013913 -6.5871851 -6.5088427 -0.65872179 + 2600 402 0.51268385 -6.5782356 -6.495339 -0.74289067 + 2700 404 0.57745388 -6.5815718 -6.4850912 -0.67922914 + 2800 406 0.47317895 -6.5974978 -6.5159152 -0.64657562 + 2900 408 0.50593124 -6.6019054 -6.5120034 -0.64211427 + 3000 410 0.44423233 -6.5956684 -6.5144064 -0.66526127 + 3100 412 0.40808865 -6.5949863 -6.5182221 -0.62722445 + 3200 414 0.40692632 -6.5866689 -6.5080358 -0.76440608 + 3300 416 0.43908529 -6.5851721 -6.4980939 -0.69345883 + 3400 418 0.53825907 -6.5880076 -6.478553 -0.69726204 + 3500 420 0.46363057 -6.6135193 -6.5169296 -0.58015901 + 3600 422 0.39262699 -6.621857 -6.5381213 -0.74921264 + 3700 424 0.42679205 -6.6146579 -6.5215488 -0.69040431 + 3800 426 0.38997492 -6.6139725 -6.5270063 -0.78237667 + 3900 428 0.5222531 -6.6403886 -6.5214174 -0.78298122 + 4000 430 0.47841128 -6.6502681 -6.5390097 -0.68125967 + 4100 432 0.44609186 -6.6610827 -6.5552392 -0.81157037 + 4200 434 0.4591431 -6.6858064 -6.5747234 -0.79000753 + 4300 436 0.40690573 -6.6800195 -6.579693 -0.6781696 + 4400 438 0.43023944 -6.6849804 -6.5769294 -0.7620548 + 4500 440 0.40889421 -6.6783124 -6.5737656 -0.8577593 + 4600 442 0.41452051 -6.6968565 -6.5890061 -0.70427746 + 4700 444 0.36740394 -6.6920933 -6.5948636 -0.69303162 + 4800 446 0.40112316 -6.6869413 -6.5790158 -0.84792822 + 4900 448 0.42437165 -6.6789835 -6.5629444 -0.82278531 + 5000 450 0.41822898 -6.6770254 -6.5608507 -0.72224472 + 5100 452 0.38445688 -6.6738997 -6.5654522 -0.7022418 + 5200 454 0.39998238 -6.6670536 -6.5525212 -0.73639959 + 5300 456 0.39471029 -6.6728592 -6.5581681 -0.70419927 + 5400 458 0.35817807 -6.6702423 -6.5646658 -0.81657219 + 5500 460 0.37151428 -6.6690855 -6.558035 -0.78076653 + 5600 462 0.32642513 -6.6622352 -6.5633185 -0.69118644 + 5700 464 0.43665879 -6.6811227 -6.5470195 -0.77500043 + 5800 466 0.40704721 -6.6858874 -6.5592311 -0.72683597 + 5900 468 0.3861903 -6.6896953 -6.5679794 -0.78001958 + 6000 470 0.34073346 -6.6833717 -6.574627 -0.78170837 + 6100 472 0.39953874 -6.7083668 -6.5792785 -0.81791744 + 6200 474 0.36685189 -6.7114648 -6.5915027 -0.80545451 + 6300 476 0.35851799 -6.7261023 -6.607475 -0.77350495 + 6400 478 0.41771823 -6.7427425 -6.6029205 -0.85319003 + 6500 480 0.36519478 -6.732662 -6.6090284 -0.78712805 + 6600 482 0.30669571 -6.7269784 -6.6219892 -0.76698134 + 6700 484 0.3384344 -6.7261448 -6.6090213 -0.79935239 + 6800 486 0.36420902 -6.7320259 -6.6046277 -0.84650552 + 6900 488 0.40181215 -6.7490619 -6.6070279 -0.75753238 + 7000 490 0.30536068 -6.7398924 -6.6308351 -0.73210162 + 7100 492 0.28813004 -6.7257287 -6.6217794 -0.92178435 + 7200 494 0.30956277 -6.7342688 -6.6214727 -0.77532949 + 7300 496 0.36625115 -6.7528159 -6.6180561 -0.76247835 + 7400 498 0.30935271 -6.7401433 -6.6252231 -0.82809158 + 7500 500 0.33222282 -6.7410421 -6.6164585 -0.81948236 + 7600 502 0.33318693 -6.7488106 -6.622704 -0.82395904 + 7700 504 0.34570598 -6.7547394 -6.6226989 -0.85644369 + 7800 506 0.34587242 -6.7446006 -6.6113099 -0.82476511 + 7900 508 0.2969166 -6.7305429 -6.6151078 -0.8210214 + 8000 510 0.32355758 -6.7437629 -6.6168776 -0.81719054 + 8100 512 0.33784479 -6.7545537 -6.6209335 -0.78082067 + 8200 514 0.32351289 -6.7525032 -6.6234757 -0.87093587 + 8300 516 0.31900134 -6.7550972 -6.6268166 -0.79928704 + 8400 518 0.3338521 -6.7588757 -6.6235302 -0.81699503 + 8500 520 0.33115184 -6.7614854 -6.6261589 -0.79958489 + 8600 522 0.29478929 -6.7490188 -6.6276018 -0.81954456 + 8700 524 0.267993 -6.7467764 -6.6355389 -0.76642994 + 8800 526 0.28792085 -6.7527118 -6.6322887 -0.86911619 + 8900 528 0.32430992 -6.75901 -6.6223453 -0.87087898 + 9000 530 0.33151321 -6.7534845 -6.6127478 -0.79309499 + 9100 532 0.32760982 -6.7599992 -6.6199028 -0.7506309 + 9200 534 0.32579101 -6.7671489 -6.6268269 -0.94238755 + 9300 536 0.35144354 -6.7782581 -6.625813 -0.77952234 + 9400 538 0.33689976 -6.7804455 -6.6332867 -0.75768501 + 9500 540 0.3052486 -6.7745436 -6.6402908 -0.89621525 + 9600 542 0.30617581 -6.7648172 -6.6292412 -0.90623541 + 9700 544 0.30097715 -6.7714379 -6.6372707 -0.85534149 + 9800 546 0.31297479 -6.7814978 -6.6410604 -0.88651064 + 9900 548 0.31832347 -6.790661 -6.6468926 -1.006 + 10000 550 0.29239559 -6.7823137 -6.6494066 -1.0337518 +Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms + +Performance: 124259.065 tau/day, 287.637 timesteps/s +73.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0076709 | 3.1286 | 9.1834 | 211.7 | 9.00 +Bond | 0.0040276 | 0.010416 | 0.022169 | 7.0 | 0.03 +Neigh | 0.052413 | 1.5948 | 4.885 | 155.3 | 4.59 +Comm | 4.9736 | 12.242 | 20.073 | 166.2 | 35.21 +Output | 0.053549 | 0.10104 | 0.21642 | 21.0 | 0.29 +Modify | 13.435 | 16.191 | 23.851 | 110.0 | 46.57 +Other | | 1.499 | | | 4.31 + +Nlocal: 137.500 ave 299 max 2 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1898.75 ave 2679 max 524 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Neighs: 9204.00 ave 23014 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 36816 +Ave neighs/atom = 66.938182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 832 +Dangerous builds = 0 +Total wall time: 0:00:34 diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2 index b5e11d212d..1da9020a64 100644 --- a/examples/gcmc/in.gcmc.co2 +++ b/examples/gcmc/in.gcmc.co2 @@ -1,4 +1,4 @@ -# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics +# GCMC for CO2 molecular fluid, rigid/small dynamics # Rigid CO2 TraPPE model # [Potoff and J.I. Siepmann, Vapor-liquid equilibria of # mixtures containing alkanes, carbon dioxide and @@ -7,7 +7,7 @@ # variables available on command line variable mu index -8.1 -variable disp index 0.5 +variable disp index 0.5 variable temp index 338.0 variable lbox index 10.0 variable spacing index 5.0 @@ -17,7 +17,7 @@ variable spacing index 5.0 units real atom_style full boundary p p p -pair_style lj/cut/coul/long 14 +pair_style lj/cut/coul/long 14 pair_modify mix arithmetic tail yes kspace_style ewald 0.0001 bond_style harmonic @@ -25,7 +25,7 @@ angle_style harmonic # box, start molecules on simple cubic lattice -lattice sc ${spacing} +lattice sc ${spacing} region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box create_box 2 box & bond/types 1 & @@ -34,56 +34,56 @@ create_box 2 box & extra/angle/per/atom 1 & extra/special/per/atom 2 molecule co2mol CO2.txt -create_atoms 0 box mol co2mol 464563 units box - -# rigid CO2 TraPPE model +create_atoms 0 box mol co2mol 464563 units box + +# rigid CO2 TraPPE model pair_coeff 1 1 0.053649 2.8 -pair_coeff 2 2 0.156973 3.05 -bond_coeff 1 0 1.16 -angle_coeff 1 0 180 +pair_coeff 2 2 0.156973 3.05 +bond_coeff 1 0 1.16 +angle_coeff 1 0 180 # masses -mass 1 12.0107 -mass 2 15.9994 +mass 1 12.0107 +mass 2 15.9994 # MD settings group co2 type 1 2 neighbor 2.0 bin neigh_modify every 1 delay 10 check yes -velocity all create ${temp} 54654 +velocity all create ${temp} 54654 timestep 1.0 -# rigid constraints with thermostat +# rigid constraints with thermostat -fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol +fix myrigid co2 rigid/small molecule mol co2mol # dynamically update fix rigid/nvt/small temperature ndof -fix_modify myrigidnvt dynamic/dof yes +fix_modify myrigid dynamic/dof yes # gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & - co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt + co2mol tfac_insert ${tfac} group co2 rigid myrigid # atom counts -variable carbon atom "type==1" +variable carbon atom "type==1" variable oxygen atom "type==2" -group carbon dynamic co2 var carbon -group oxygen dynamic co2 var oxygen +group carbon dynamic co2 var carbon +group oxygen dynamic co2 var oxygen variable nC equal count(carbon) variable nO equal count(oxygen) # output -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) +variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) +variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) +variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) +variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) # dynamically update default temperature ndof compute_modify thermo_temp dynamic/dof yes diff --git a/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 b/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 deleted file mode 100644 index 4ed9056d04..0000000000 --- a/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 +++ /dev/null @@ -1,196 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics -# Rigid CO2 TraPPE model -# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of -# mixtures containing alkanes, carbon dioxide and -# nitrogen AIChE J., 47,1676-1682 (2001)]. - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 1 MPI processor grid -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with max type 2 - 2 bonds with max type 1 - 1 angles with max type 1 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -create_atoms 0 box mol co2mol 464563 units box -Created 24 atoms - Time spent = 0.00134993 secs - -# rigid CO2 TraPPE model - -pair_coeff 1 1 0.053649 2.8 -pair_coeff 2 2 0.156973 3.05 -bond_coeff 1 0 1.16 -angle_coeff 1 0 180 - -# masses - -mass 1 12.0107 -mass 2 15.9994 - -# MD settings - -group co2 type 1 2 -24 atoms in group co2 -neighbor 2.0 bin -neigh_modify every 1 delay 10 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -# rigid constraints with thermostat - -fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol -8 rigid bodies with 24 atoms - 1.16 = max distance from body owner to body atom - -# dynamically update fix rigid/nvt/small temperature ndof -fix_modify myrigidnvt dynamic/dof yes - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt - -# atom counts - -variable carbon atom "type==1" -variable oxygen atom "type==2" -group carbon dynamic co2 var carbon -dynamic group carbon defined -group oxygen dynamic co2 var oxygen -dynamic group oxygen defined -variable nC equal count(carbon) -variable nO equal count(oxygen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) - -# dynamically update default temperature ndof -compute_modify thermo_temp dynamic/dof yes - -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO -thermo 1000 - -# run - -run 20000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - G vector (1/distance) = 0.164636 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 2 2 2 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO - 0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16 - 1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10 - 2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12 - 3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24 - 4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24 - 5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18 - 6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12 - 7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4 - 8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16 - 9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14 - 10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16 - 11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20 - 12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28 - 13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10 - 14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10 - 15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22 - 16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2 - 17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18 - 18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6 - 19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10 - 20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18 -Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms - -Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s -98.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63 -Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11 -Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80 -Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54 -Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28 -Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01 -Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45 -Other | | 0.03692 | | | 0.18 - -Nlocal: 27 ave 27 max 27 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2081 ave 2081 max 2081 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 6264 ave 6264 max 6264 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 6264 -Ave neighs/atom = 232 -Ave special neighs/atom = 2 -Neighbor list builds = 20177 -Dangerous builds = 0 - -Total wall time: 0:00:21 diff --git a/examples/gcmc/log.31Mar21.gcmc.co2.g++.1 b/examples/gcmc/log.31Mar21.gcmc.co2.g++.1 new file mode 100644 index 0000000000..80de6554e4 --- /dev/null +++ b/examples/gcmc/log.31Mar21.gcmc.co2.g++.1 @@ -0,0 +1,196 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# GCMC for CO2 molecular fluid, rigid/small dynamics +# Rigid CO2 TraPPE model +# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of +# mixtures containing alkanes, carbon dioxide and +# nitrogen AIChE J., 47,1676-1682 (2001)]. + +# variables available on command line + +variable mu index -8.1 +variable disp index 0.5 +variable temp index 338.0 +variable lbox index 10.0 +variable spacing index 5.0 + +# global model settings + +units real +atom_style full +boundary p p p +pair_style lj/cut/coul/long 14 +pair_modify mix arithmetic tail yes +kspace_style ewald 0.0001 +bond_style harmonic +angle_style harmonic + +# box, start molecules on simple cubic lattice + +lattice sc ${spacing} +lattice sc 5.0 +Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000 +region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 10.0 units box +create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000) + 1 by 1 by 1 MPI processor grid +molecule co2mol CO2.txt +Read molecule template co2mol: + 1 molecules + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +create_atoms 0 box mol co2mol 464563 units box +Created 24 atoms + create_atoms CPU = 0.002 seconds + +# rigid CO2 TraPPE model + +pair_coeff 1 1 0.053649 2.8 +pair_coeff 2 2 0.156973 3.05 +bond_coeff 1 0 1.16 +angle_coeff 1 0 180 + +# masses + +mass 1 12.0107 +mass 2 15.9994 + +# MD settings + +group co2 type 1 2 +24 atoms in group co2 +neighbor 2.0 bin +neigh_modify every 1 delay 10 check yes +velocity all create ${temp} 54654 +velocity all create 338.0 54654 +timestep 1.0 + +# rigid constraints with thermostat + +fix myrigid co2 rigid/small molecule mol co2mol + create bodies CPU = 0.000 seconds + 8 rigid bodies with 24 atoms + 1.1600000 = max distance from body owner to body atom + +# dynamically update fix rigid/nvt/small temperature ndof +fix_modify myrigid dynamic/dof yes + +# gcmc + +variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) +fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid + +# atom counts + +variable carbon atom "type==1" +variable oxygen atom "type==2" +group carbon dynamic co2 var carbon +dynamic group carbon defined +group oxygen dynamic co2 var oxygen +dynamic group oxygen defined +variable nC equal count(carbon) +variable nO equal count(oxygen) + +# output + +variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) +variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) +variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) +variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) + +# dynamically update default temperature ndof +compute_modify thermo_temp dynamic/dof yes + +thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO +thermo 1000 + +# run + +run 20000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.16463644 + estimated absolute RMS force accuracy = 0.033206372 + estimated relative force accuracy = 0.0001 + KSpace vectors: actual max1d max3d = 16 2 62 + kxmax kymax kzmax = 2 2 2 +WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:482) +0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc +0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes +Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO + 0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16 + 1000 261.50949 -204.60974 -9.6459249 8.3147747 0.51155641 21 0.096366192 0.097590121 0 0 7 14 + 2000 479.39697 231.28436 -7.0089345 10.47927 0.36539744 15 0.085531005 0.085453295 0 0 5 10 + 3000 318.31766 -433.17133 -7.3680951 8.5396005 0.43847693 18 0.078556687 0.080101462 0 0 6 12 + 4000 357.40776 -186.78 -16.453111 14.915105 0.65771539 27 0.082003877 0.08249082 0 0 9 18 + 5000 399.94731 1524.2909 -16.624678 18.677282 0.73079488 30 0.071285101 0.072731705 0 0 10 20 + 6000 354.71736 60.134827 -18.988979 16.565073 0.73079488 30 0.071615663 0.071713414 0 0 10 20 + 7000 483.32057 966.32174 -5.7393251 10.565037 0.36539744 15 0.087027775 0.089855826 0 0 5 10 + 8000 547.68562 494.96891 -4.125626 11.97201 0.36539744 15 0.11738082 0.11937373 0 0 5 10 + 9000 433.76488 390.91467 -0.85312985 5.1718828 0.21923846 9 0.13265238 0.13513212 0 0 3 6 + 10000 330.01685 -862.07457 -26.494645 18.690633 0.87695385 36 0.13775034 0.13905403 0 0 12 24 + 11000 334.26318 -578.48274 -13.236965 12.288625 0.5846359 24 0.13713936 0.13960485 0 0 8 16 + 12000 243.68657 -1244.7156 -25.757644 12.590645 0.80387436 33 0.1339588 0.13588739 0 0 11 22 + 13000 307.66758 -429.66928 -17.864639 14.367878 0.73079488 30 0.12604721 0.1278094 0 0 10 20 + 14000 330.91434 495.97112 -15.374248 13.809499 0.65771539 27 0.12011756 0.12145865 0 0 9 18 + 15000 564.87966 982.72332 -14.810525 26.379517 0.73079488 30 0.12164324 0.12343521 0 0 10 20 + 16000 342.63867 -54.776299 -2.2580523 5.7875978 0.29231795 12 0.13535812 0.13790758 0 0 4 8 + 17000 461.07005 -2.4317694 -1.145154 3.2068452 0.14615898 6 0.1444739 0.14730804 0 0 2 4 + 18000 197.21207 -40.124433 -7.0857418 5.2906654 0.43847693 18 0.14403997 0.14574329 0 0 6 12 + 19000 393.36395 -420.49802 -11.172739 14.461366 0.5846359 24 0.15005606 0.15142063 0 0 8 16 + 20000 356.48539 56.071962 -1.7861789 4.2504609 0.21923846 9 0.15422732 0.15627984 0 0 3 6 +Loop time of 19.5982 on 1 procs for 20000 steps with 9 atoms + +Performance: 88.171 ns/day, 0.272 hours/ns, 1020.502 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3404 | 2.3404 | 2.3404 | 0.0 | 11.94 +Bond | 0.033919 | 0.033919 | 0.033919 | 0.0 | 0.17 +Kspace | 0.19974 | 0.19974 | 0.19974 | 0.0 | 1.02 +Neigh | 0.11478 | 0.11478 | 0.11478 | 0.0 | 0.59 +Comm | 0.22538 | 0.22538 | 0.22538 | 0.0 | 1.15 +Output | 0.00096536 | 0.00096536 | 0.00096536 | 0.0 | 0.00 +Modify | 16.627 | 16.627 | 16.627 | 0.0 | 84.84 +Other | | 0.05594 | | | 0.29 + +Nlocal: 9.00000 ave 9 max 9 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 703.000 ave 703 max 703 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 719.000 ave 719 max 719 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 719 +Ave neighs/atom = 79.888889 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 20196 +Dangerous builds = 0 + +Total wall time: 0:00:19 diff --git a/examples/granregion/in.granregion.funnel b/examples/granregion/in.granregion.funnel index 63e79a7114..ef74ce5109 100644 --- a/examples/granregion/in.granregion.funnel +++ b/examples/granregion/in.granregion.funnel @@ -86,7 +86,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/granregion/in.granregion.mixer b/examples/granregion/in.granregion.mixer index f9a9d04cbe..383f51f074 100644 --- a/examples/granregion/in.granregion.mixer +++ b/examples/granregion/in.granregion.mixer @@ -49,7 +49,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/kim/in.kim-pm-property b/examples/kim/in.kim-pm-property index d69879c728..8beae19b68 100644 --- a/examples/kim/in.kim-pm-property +++ b/examples/kim/in.kim-pm-property @@ -11,18 +11,18 @@ # argon. The material properties computed in LAMMPS are represented as a # standard KIM property instance format. (See # `https://openkim.org/doc/schema/properties-framework/` and -# `https://lammps.sandia.gov/doc/kim_commands.html` for further details). +# `https://docs.lammps.org/kim_commands.html` for further details). # Then the created property instance is written to a file named `results.edn` # using the `kim property dump` command. # # Requirement: # # This example requires LAMMPS built with the Python 3.6 or later package -# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for +# installed. See the `https://docs.lammps.org/python.html` doc page for # more info on building LAMMPS with the version of Python on your system. # After successfully building LAMMPS with Python, you need to install the # kim-property Python package, See the -# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for +# `https://docs.lammps.org/Build_extras.html#kim` doc page for # further details. # # This example requires that the KIM Portable Model (PM) diff --git a/examples/kim/in.kim-query b/examples/kim/in.kim-query index a0d1379372..483641bd8b 100644 --- a/examples/kim/in.kim-query +++ b/examples/kim/in.kim-query @@ -6,7 +6,7 @@ # the KIM package, is the KIM API library that must be downloaded from the # OpenKIM website and installed before LAMMPS is compiled. The 'kim query' # command requires the libcurl library to be installed. See the -# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further +# `https://docs.lammps.org/Build_extras.html#kim` doc page for further # details # # This example requires that the KIM Models diff --git a/examples/kim/log.10Feb21.in.kim-pm-property.clang.1 b/examples/kim/log.10Feb21.in.kim-pm-property.clang.1 index 6cd2f12ac1..94076af1ac 100644 --- a/examples/kim/log.10Feb21.in.kim-pm-property.clang.1 +++ b/examples/kim/log.10Feb21.in.kim-pm-property.clang.1 @@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021) # argon. The material properties computed in LAMMPS are represented as a # standard KIM property instance format. (See # `https://openkim.org/doc/schema/properties-framework/` and -# `https://lammps.sandia.gov/doc/kim_commands.html` for further details). +# `https://docs.lammps.org/kim_commands.html` for further details). # Then the created property instance is written to a file named `results.edn` # using the `kim property dump` command. # # Requirement: # # This example requires LAMMPS built with the Python 3.6 or later package -# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for +# installed. See the `https://docs.lammps.org/python.html` doc page for # more info on building LAMMPS with the version of Python on your system. # After successfully building LAMMPS with Python, you need to install the # kim-property Python package, See the -# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for +# `https://docs.lammps.org/Build_extras.html#kim` doc page for # further details. # # This example requires that the KIM Portable Model (PM) diff --git a/examples/kim/log.10Feb21.in.kim-pm-property.clang.4 b/examples/kim/log.10Feb21.in.kim-pm-property.clang.4 index 0270896de1..9c88cb87c9 100644 --- a/examples/kim/log.10Feb21.in.kim-pm-property.clang.4 +++ b/examples/kim/log.10Feb21.in.kim-pm-property.clang.4 @@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021) # argon. The material properties computed in LAMMPS are represented as a # standard KIM property instance format. (See # `https://openkim.org/doc/schema/properties-framework/` and -# `https://lammps.sandia.gov/doc/kim_commands.html` for further details). +# `https://docs.lammps.org/kim_commands.html` for further details). # Then the created property instance is written to a file named `results.edn` # using the `kim property dump` command. # # Requirement: # # This example requires LAMMPS built with the Python 3.6 or later package -# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for +# installed. See the `https://docs.lammps.org/python.html` doc page for # more info on building LAMMPS with the version of Python on your system. # After successfully building LAMMPS with Python, you need to install the # kim-property Python package, See the -# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for +# `https://docs.lammps.org/Build_extras.html#kim` doc page for # further details. # # This example requires that the KIM Portable Model (PM) diff --git a/examples/kim/log.10Feb21.in.kim-query.clang.1 b/examples/kim/log.10Feb21.in.kim-query.clang.1 index 42f216dfc0..4aac964710 100644 --- a/examples/kim/log.10Feb21.in.kim-query.clang.1 +++ b/examples/kim/log.10Feb21.in.kim-query.clang.1 @@ -7,7 +7,7 @@ LAMMPS (10 Feb 2021) # the KIM package, is the KIM API library that must be downloaded from the # OpenKIM website and installed before LAMMPS is compiled. The 'kim query' # command requires the libcurl library to be installed. See the -# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further +# `https://docs.lammps.org/Build_extras.html#kim` doc page for further # details # # This example requires that the KIM Models diff --git a/examples/melt/in.melt b/examples/melt/in.melt index 8431a4344e..f169dc2ffc 100644 --- a/examples/melt/in.melt +++ b/examples/melt/in.melt @@ -9,7 +9,7 @@ create_box 1 box create_atoms 1 box mass 1 1.0 -velocity all create 3.0 87287 +velocity all create 3.0 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 diff --git a/examples/melt/log.27Nov18.melt.g++.4 b/examples/melt/log.27Nov18.melt.g++.4 deleted file mode 100644 index 927895b1cd..0000000000 --- a/examples/melt/log.27Nov18.melt.g++.4 +++ /dev/null @@ -1,85 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 3d Lennard-Jones melt - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 -region box block 0 10 0 10 0 10 -create_box 1 box -Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 4000 atoms - Time spent = 0.00041604 secs -mass 1 1.0 - -velocity all create 3.0 87287 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify every 20 delay 0 check no - -fix 1 all nve - -#dump id all atom 50 dump.melt - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -thermo 50 -run 250 -Neighbor list info ... - update every 20 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 12 12 12 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 3 -6.7733681 0 -2.2744931 -3.7033504 - 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 - 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 - 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 - 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 - 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 -Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms - -Performance: 483592.231 tau/day, 1119.426 timesteps/s -97.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05 -Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29 -Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47 -Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09 -Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72 -Other | | 0.00085 | | | 0.38 - -Nlocal: 1000 ave 1010 max 982 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 2703.75 ave 2713 max 2689 min -Histogram: 1 0 0 0 0 0 0 2 0 1 -Neighs: 37915.5 ave 39239 max 36193 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 151662 -Ave neighs/atom = 37.9155 -Neighbor list builds = 12 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/melt/log.27Nov18.melt.g++.1 b/examples/melt/log.8Apr21.melt.g++.1 similarity index 51% rename from examples/melt/log.27Nov18.melt.g++.1 rename to examples/melt/log.8Apr21.melt.g++.1 index 69b39e6011..a3b6d003db 100644 --- a/examples/melt/log.27Nov18.melt.g++.1 +++ b/examples/melt/log.8Apr21.melt.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (27 Nov 2018) +LAMMPS (8 Apr 2021) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt @@ -6,17 +6,17 @@ units lj atom_style atomic lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 region box block 0 10 0 10 0 10 create_box 1 box -Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms - Time spent = 0.000645638 secs + create_atoms CPU = 0.002 seconds mass 1 1.0 -velocity all create 3.0 87287 +velocity all create 3.0 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 @@ -48,38 +48,38 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.222 | 3.222 | 3.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 - 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 - 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 - 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 - 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 - 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 -Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms + 50 1.6842865 -4.8082494 0 -2.2824513 5.5666131 + 100 1.6712577 -4.7875609 0 -2.281301 5.6613913 + 150 1.6444751 -4.7471034 0 -2.2810074 5.8614211 + 200 1.6471542 -4.7509053 0 -2.2807916 5.8805431 + 250 1.6645597 -4.7774327 0 -2.2812174 5.7526089 +Loop time of 1.61045 on 1 procs for 250 steps with 4000 atoms -Performance: 147983.915 tau/day, 342.555 timesteps/s +Performance: 67062.020 tau/day, 155.236 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12 -Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63 -Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86 -Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02 -Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97 -Other | | 0.002878 | | | 0.39 +Pair | 1.3961 | 1.3961 | 1.3961 | 0.0 | 86.69 +Neigh | 0.13555 | 0.13555 | 0.13555 | 0.0 | 8.42 +Comm | 0.037732 | 0.037732 | 0.037732 | 0.0 | 2.34 +Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02 +Modify | 0.038016 | 0.038016 | 0.038016 | 0.0 | 2.36 +Other | | 0.002731 | | | 0.17 -Nlocal: 4000 ave 4000 max 4000 min +Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5499 ave 5499 max 5499 min +Nghost: 5506.00 ave 5506 max 5506 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 151513 ave 151513 max 151513 min +Neighs: 151788.0 ave 151788 max 151788 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 151513 -Ave neighs/atom = 37.8783 +Total # of neighbors = 151788 +Ave neighs/atom = 37.947000 Neighbor list builds = 12 Dangerous builds not checked -Total wall time: 0:00:00 +Total wall time: 0:00:01 diff --git a/examples/melt/log.8Apr21.melt.g++.4 b/examples/melt/log.8Apr21.melt.g++.4 new file mode 100644 index 0000000000..1edbeac7aa --- /dev/null +++ b/examples/melt/log.8Apr21.melt.g++.4 @@ -0,0 +1,85 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 3.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.706 | 2.706 | 2.706 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6842865 -4.8082494 0 -2.2824513 5.5666131 + 100 1.6712577 -4.7875609 0 -2.281301 5.6613913 + 150 1.6444751 -4.7471034 0 -2.2810074 5.8614211 + 200 1.6471542 -4.7509053 0 -2.2807916 5.8805431 + 250 1.6645597 -4.7774327 0 -2.2812174 5.7526089 +Loop time of 0.490832 on 4 procs for 250 steps with 4000 atoms + +Performance: 220034.754 tau/day, 509.340 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.35932 | 0.37256 | 0.38746 | 1.9 | 75.90 +Neigh | 0.035928 | 0.038449 | 0.042344 | 1.3 | 7.83 +Comm | 0.053452 | 0.068917 | 0.08485 | 5.3 | 14.04 +Output | 0.00015545 | 0.00023746 | 0.00047684 | 0.0 | 0.05 +Modify | 0.0096958 | 0.0097951 | 0.0098989 | 0.1 | 2.00 +Other | | 0.0008721 | | | 0.18 + +Nlocal: 1000.00 ave 1008 max 987 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 2711.25 ave 2728 max 2693 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 37947.0 ave 38966 max 37338 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 151788 +Ave neighs/atom = 37.947000 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/mliap/Ni_Mo.data b/examples/mliap/Ni_Mo.data new file mode 100644 index 0000000000..9711e3832b --- /dev/null +++ b/examples/mliap/Ni_Mo.data @@ -0,0 +1,26 @@ +NiMo.data (written by ASE) + +10 atoms +2 atom types +0.0 5.7209004999999999 xlo xhi +0.0 5.7209004999999999 ylo yhi +0.0 3.5556619999999999 zlo zhi + +Masses + +1 95.96 +2 58.6934 + + +Atoms + + 1 1 0 0 0 + 2 1 2.86045025 2.86045025 1.7778309999999999 + 3 2 2.2921502965812497 4.5858137713447498 0 + 4 2 3.4287502034187498 1.13508672865525 0 + 5 2 1.72536352134475 0.56829995341874995 1.7778309999999999 + 6 2 3.9955369786552501 5.1526005465812501 1.7778309999999999 + 7 2 5.1526005465812501 1.72536352134475 1.7778309999999999 + 8 2 0.56829995341874995 3.9955369786552501 1.7778309999999999 + 9 2 4.5858137713447498 3.4287502034187498 0 + 10 2 1.13508672865525 2.2921502965812497 0 diff --git a/examples/mliap/Ni_Mo.mliap.descriptor b/examples/mliap/Ni_Mo.mliap.descriptor new file mode 120000 index 0000000000..aef91dff49 --- /dev/null +++ b/examples/mliap/Ni_Mo.mliap.descriptor @@ -0,0 +1 @@ +../../potentials/Ni_Mo.mliap.descriptor \ No newline at end of file diff --git a/examples/mliap/Ni_Mo.mliap.model b/examples/mliap/Ni_Mo.mliap.model new file mode 120000 index 0000000000..5d95a4b76e --- /dev/null +++ b/examples/mliap/Ni_Mo.mliap.model @@ -0,0 +1 @@ +../../potentials/Ni_Mo.mliap.model \ No newline at end of file diff --git a/examples/mliap/Si.nn.mliap.descriptor b/examples/mliap/Si.nn.mliap.descriptor new file mode 120000 index 0000000000..919e3e58d8 --- /dev/null +++ b/examples/mliap/Si.nn.mliap.descriptor @@ -0,0 +1 @@ +../../potentials/Si.nn.mliap.descriptor \ No newline at end of file diff --git a/examples/mliap/Si.nn.mliap.model b/examples/mliap/Si.nn.mliap.model new file mode 120000 index 0000000000..940fade2fc --- /dev/null +++ b/examples/mliap/Si.nn.mliap.model @@ -0,0 +1 @@ +../../potentials/Si.nn.mliap.model \ No newline at end of file diff --git a/examples/mliap/compute.quadratic.gg0.dat b/examples/mliap/compute.quadratic.gg0.dat new file mode 100644 index 0000000000..0a6695c1ab --- /dev/null +++ b/examples/mliap/compute.quadratic.gg0.dat @@ -0,0 +1,17 @@ +# Time-averaged data for fix snap +# TimeStep Number-of-rows +# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] c_snap[14] c_snap[15] c_snap[16] c_snap[17] c_snap[18] c_snap[19] c_snap[20] c_snap[21] c_snap[22] c_snap[23] c_snap[24] c_snap[25] c_snap[26] c_snap[27] c_snap[28] c_snap[29] c_snap[30] c_snap[31] c_snap[32] c_snap[33] c_snap[34] c_snap[35] c_snap[36] c_snap[37] c_snap[38] c_snap[39] c_snap[40] c_snap[41] c_snap[42] c_snap[43] +0 13 +1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 3.31573e+10 3.88807e+10 1.95617e+10 2.23819e+10 7.50718e+09 1.1398e+10 1.14692e+10 1.31227e+10 4.40152e+09 2.88519e+09 6.60228e+09 2.21449e+09 3.77706e+09 2.53375e+09 4.24928e+08 322.87 +2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 0 -3.76889e+07 -5.33719e+07 -7.9033e+07 -3.95849e+07 -2.20973e+07 -4.24099e+07 -5.9058e+07 -2.74755e+07 -1.57438e+07 -4.1327e+07 -1.77189e+07 -2.66745e+07 -2.23073e+07 -4.48124e+06 -20.7188 +3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 0 -2.3255e+08 -3.35235e+08 -5.0113e+08 -2.51613e+08 -1.36345e+08 -2.65149e+08 -3.72304e+08 -1.73849e+08 -9.88886e+07 -2.6097e+08 -1.12172e+08 -1.69137e+08 -1.41653e+08 -2.8484e+07 -106.829 +4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 0 1.46568e+08 2.08973e+08 3.10574e+08 1.55696e+08 8.59341e+07 1.65757e+08 2.3156e+08 1.07878e+08 6.16434e+07 1.62145e+08 6.95847e+07 1.04822e+08 8.77079e+07 1.76257e+07 74.8128 +5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 0 3.76889e+07 5.33719e+07 7.9033e+07 3.95849e+07 2.20973e+07 4.24099e+07 5.9058e+07 2.74755e+07 1.57438e+07 4.1327e+07 1.77189e+07 2.66745e+07 2.23073e+07 4.48124e+06 20.7188 +6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 0 2.3255e+08 3.35235e+08 5.0113e+08 2.51613e+08 1.36345e+08 2.65149e+08 3.72304e+08 1.73849e+08 9.88886e+07 2.6097e+08 1.12172e+08 1.69137e+08 1.41653e+08 2.8484e+07 106.829 +7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 0 -1.46568e+08 -2.08973e+08 -3.10574e+08 -1.55696e+08 -8.59341e+07 -1.65757e+08 -2.3156e+08 -1.07878e+08 -6.16434e+07 -1.62145e+08 -6.95847e+07 -1.04822e+08 -8.77079e+07 -1.76257e+07 -74.8128 +8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 0 -6.70623e+10 -7.41396e+10 -9.24395e+10 -4.65087e+10 -3.93191e+10 -6.32509e+10 -7.68322e+10 -3.48602e+10 -2.18699e+10 -5.2291e+10 -2.21123e+10 -3.11993e+10 -2.61618e+10 -5.26504e+09 1.3152e+08 +9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 0 -6.68105e+10 -7.36261e+10 -9.1545e+10 -4.60582e+10 -3.91714e+10 -6.28755e+10 -7.62227e+10 -3.45676e+10 -2.17185e+10 -5.18538e+10 -2.19213e+10 -3.08974e+10 -2.59085e+10 -5.21405e+09 1.2154e+08 +10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 0 -6.69666e+10 -7.39444e+10 -9.20993e+10 -4.63376e+10 -3.9263e+10 -6.31081e+10 -7.66004e+10 -3.47491e+10 -2.18124e+10 -5.21248e+10 -2.20397e+10 -3.10845e+10 -2.60656e+10 -5.24568e+09 1.27407e+08 +11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 0 -2.06474e+08 -3.3576e+08 -5.32545e+08 -2.70086e+08 -1.21057e+08 -2.57765e+08 -3.81922e+08 -1.81728e+08 -9.90436e+07 -2.70414e+08 -1.17681e+08 -1.7974e+08 -1.51444e+08 -3.05753e+07 -5.32884e+06 +12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 0 -3.33961e+07 -5.43839e+07 -8.63107e+07 -4.37476e+07 -1.95804e+07 -4.17369e+07 -6.18761e+07 -2.94301e+07 -1.60423e+07 -4.38153e+07 -1.90614e+07 -2.91308e+07 -2.45361e+07 -4.95247e+06 -1.08912e+06 +13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 0 5.30528e+07 8.63186e+07 1.36941e+08 6.94355e+07 3.11053e+07 6.62589e+07 9.81954e+07 4.67164e+07 2.54626e+07 6.95288e+07 3.02541e+07 4.6219e+07 3.89377e+07 7.86049e+06 1.50556e+06 diff --git a/examples/mliap/compute.quadratic.gg1.dat b/examples/mliap/compute.quadratic.gg1.dat new file mode 100644 index 0000000000..0a6695c1ab --- /dev/null +++ b/examples/mliap/compute.quadratic.gg1.dat @@ -0,0 +1,17 @@ +# Time-averaged data for fix snap +# TimeStep Number-of-rows +# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] c_snap[14] c_snap[15] c_snap[16] c_snap[17] c_snap[18] c_snap[19] c_snap[20] c_snap[21] c_snap[22] c_snap[23] c_snap[24] c_snap[25] c_snap[26] c_snap[27] c_snap[28] c_snap[29] c_snap[30] c_snap[31] c_snap[32] c_snap[33] c_snap[34] c_snap[35] c_snap[36] c_snap[37] c_snap[38] c_snap[39] c_snap[40] c_snap[41] c_snap[42] c_snap[43] +0 13 +1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 3.31573e+10 3.88807e+10 1.95617e+10 2.23819e+10 7.50718e+09 1.1398e+10 1.14692e+10 1.31227e+10 4.40152e+09 2.88519e+09 6.60228e+09 2.21449e+09 3.77706e+09 2.53375e+09 4.24928e+08 322.87 +2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 0 -3.76889e+07 -5.33719e+07 -7.9033e+07 -3.95849e+07 -2.20973e+07 -4.24099e+07 -5.9058e+07 -2.74755e+07 -1.57438e+07 -4.1327e+07 -1.77189e+07 -2.66745e+07 -2.23073e+07 -4.48124e+06 -20.7188 +3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 0 -2.3255e+08 -3.35235e+08 -5.0113e+08 -2.51613e+08 -1.36345e+08 -2.65149e+08 -3.72304e+08 -1.73849e+08 -9.88886e+07 -2.6097e+08 -1.12172e+08 -1.69137e+08 -1.41653e+08 -2.8484e+07 -106.829 +4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 0 1.46568e+08 2.08973e+08 3.10574e+08 1.55696e+08 8.59341e+07 1.65757e+08 2.3156e+08 1.07878e+08 6.16434e+07 1.62145e+08 6.95847e+07 1.04822e+08 8.77079e+07 1.76257e+07 74.8128 +5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 0 3.76889e+07 5.33719e+07 7.9033e+07 3.95849e+07 2.20973e+07 4.24099e+07 5.9058e+07 2.74755e+07 1.57438e+07 4.1327e+07 1.77189e+07 2.66745e+07 2.23073e+07 4.48124e+06 20.7188 +6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 0 2.3255e+08 3.35235e+08 5.0113e+08 2.51613e+08 1.36345e+08 2.65149e+08 3.72304e+08 1.73849e+08 9.88886e+07 2.6097e+08 1.12172e+08 1.69137e+08 1.41653e+08 2.8484e+07 106.829 +7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 0 -1.46568e+08 -2.08973e+08 -3.10574e+08 -1.55696e+08 -8.59341e+07 -1.65757e+08 -2.3156e+08 -1.07878e+08 -6.16434e+07 -1.62145e+08 -6.95847e+07 -1.04822e+08 -8.77079e+07 -1.76257e+07 -74.8128 +8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 0 -6.70623e+10 -7.41396e+10 -9.24395e+10 -4.65087e+10 -3.93191e+10 -6.32509e+10 -7.68322e+10 -3.48602e+10 -2.18699e+10 -5.2291e+10 -2.21123e+10 -3.11993e+10 -2.61618e+10 -5.26504e+09 1.3152e+08 +9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 0 -6.68105e+10 -7.36261e+10 -9.1545e+10 -4.60582e+10 -3.91714e+10 -6.28755e+10 -7.62227e+10 -3.45676e+10 -2.17185e+10 -5.18538e+10 -2.19213e+10 -3.08974e+10 -2.59085e+10 -5.21405e+09 1.2154e+08 +10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 0 -6.69666e+10 -7.39444e+10 -9.20993e+10 -4.63376e+10 -3.9263e+10 -6.31081e+10 -7.66004e+10 -3.47491e+10 -2.18124e+10 -5.21248e+10 -2.20397e+10 -3.10845e+10 -2.60656e+10 -5.24568e+09 1.27407e+08 +11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 0 -2.06474e+08 -3.3576e+08 -5.32545e+08 -2.70086e+08 -1.21057e+08 -2.57765e+08 -3.81922e+08 -1.81728e+08 -9.90436e+07 -2.70414e+08 -1.17681e+08 -1.7974e+08 -1.51444e+08 -3.05753e+07 -5.32884e+06 +12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 0 -3.33961e+07 -5.43839e+07 -8.63107e+07 -4.37476e+07 -1.95804e+07 -4.17369e+07 -6.18761e+07 -2.94301e+07 -1.60423e+07 -4.38153e+07 -1.90614e+07 -2.91308e+07 -2.45361e+07 -4.95247e+06 -1.08912e+06 +13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 0 5.30528e+07 8.63186e+07 1.36941e+08 6.94355e+07 3.11053e+07 6.62589e+07 9.81954e+07 4.67164e+07 2.54626e+07 6.95288e+07 3.02541e+07 4.6219e+07 3.89377e+07 7.86049e+06 1.50556e+06 diff --git a/examples/mliap/compute.snap.gg0.dat b/examples/mliap/compute.snap.gg0.dat new file mode 100644 index 0000000000..4351b21103 --- /dev/null +++ b/examples/mliap/compute.snap.gg0.dat @@ -0,0 +1,17 @@ +# Time-averaged data for fix snap +# TimeStep Number-of-rows +# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] +0 13 +1 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 322.87 +2 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 -20.7188 +3 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 -106.829 +4 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 74.8128 +5 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 20.7188 +6 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 106.829 +7 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 -74.8128 +8 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 1.3152e+08 +9 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 1.2154e+08 +10 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 1.27407e+08 +11 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 -5.32884e+06 +12 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 -1.08912e+06 +13 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 1.50556e+06 diff --git a/examples/mliap/compute.snap.gg1.dat b/examples/mliap/compute.snap.gg1.dat new file mode 100644 index 0000000000..4351b21103 --- /dev/null +++ b/examples/mliap/compute.snap.gg1.dat @@ -0,0 +1,17 @@ +# Time-averaged data for fix snap +# TimeStep Number-of-rows +# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] +0 13 +1 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 322.87 +2 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 -20.7188 +3 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 -106.829 +4 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 74.8128 +5 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 20.7188 +6 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 106.829 +7 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 -74.8128 +8 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 1.3152e+08 +9 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 1.2154e+08 +10 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 1.27407e+08 +11 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 -5.32884e+06 +12 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 -1.08912e+06 +13 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 1.50556e+06 diff --git a/examples/mliap/in.mliap.so3.Ni_Mo b/examples/mliap/in.mliap.so3.Ni_Mo new file mode 100644 index 0000000000..34c900a972 --- /dev/null +++ b/examples/mliap/in.mliap.so3.Ni_Mo @@ -0,0 +1,25 @@ +# ---------- Initialize Simulation --------------------- +clear +units metal +dimension 3 +boundary p p p +atom_style atomic +read_data Ni_Mo.data + +#change_box all x scale 0.9 y scale 0.9 z scale 0.9 + +pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor +pair_coeff * * Mo Ni + +variable e equal pe +variable N equal count(all) + +thermo_style custom pe pxx pyy pzz pxy pxz pyz +thermo 1 + +# dump 1 all custom 1 dump.myforce.* id type fx fy fz + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +run 3 diff --git a/examples/mliap/in.mliap.so3.nn.Si b/examples/mliap/in.mliap.so3.nn.Si new file mode 100644 index 0000000000..675f65f299 --- /dev/null +++ b/examples/mliap/in.mliap.so3.nn.Si @@ -0,0 +1,52 @@ +# Run NPT MD simulation for Si at 500 K. +variable nsteps index 100 #0 + +# NOTE: These are not intended to represent real materials + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +#read_data Si.data +lattice diamond 5.43 +region box block 0 2 0 2 0 2 +create_box 1 box +create_atoms 1 box +mass 1 29.0 + +# temperature +variable t equal 500. + + +# Potential +#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt +pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor +pair_coeff * * Si Si + +# Set-up output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create $t 5287287 loop geom +fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2 +run ${nsteps} diff --git a/examples/mliap/log.03Mar21.mliap.nn.Cu.g++.1 b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.1 similarity index 69% rename from examples/mliap/log.03Mar21.mliap.nn.Cu.g++.1 rename to examples/mliap/log.14Jun21.mliap.nn.Cu.g++.1 index 151972e99a..7e23163086 100644 --- a/examples/mliap/log.03Mar21.mliap.nn.Cu.g++.1 +++ b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (10 Feb 2021) - using 1 OpenMP thread(s) per MPI task +LAMMPS (27 May 2021) # Demonstrate MLIAP interface to SNAP nn Cu potential # Initialize simulation @@ -93,30 +92,30 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 31.17 | 31.17 | 31.17 Mbytes Step Temp E_pair c_energy TotEng Press v_press 0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505 - 10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504 - 20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718 - 30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378 - 40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151 - 50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675 - 60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654 - 70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077 - 80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217 - 90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598 - 100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141 -Loop time of 12.7584 on 1 procs for 100 steps with 256 atoms + 10 294.11049 -4.0927998 -4.0927998 -4.0549315 -2654.7826 2654.7826 + 20 276.89115 -4.0905826 -4.0905826 -4.0549314 -1879.2872 1879.2872 + 30 249.71134 -4.0870829 -4.0870829 -4.0549312 -627.47006 627.47006 + 40 214.92415 -4.0826036 -4.0826036 -4.054931 995.44801 -995.44801 + 50 175.86879 -4.0775747 -4.0775747 -4.0549307 2811.6019 -2811.6019 + 60 136.62706 -4.0725218 -4.0725218 -4.0549303 4640.4144 -4640.4144 + 70 101.48566 -4.0679968 -4.0679968 -4.05493 6313.5871 -6313.5871 + 80 74.248664 -4.0644897 -4.0644897 -4.0549298 7644.1364 -7644.1364 + 90 57.500423 -4.0623332 -4.0623332 -4.0549297 8514.2222 -8514.2222 + 100 52.104609 -4.0616385 -4.0616385 -4.0549298 8870.8923 -8870.8923 +Loop time of 4.77867 on 1 procs for 100 steps with 256 atoms -Performance: 0.339 ns/day, 70.880 hours/ns, 7.838 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.904 ns/day, 26.548 hours/ns, 20.926 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 12.755 | 12.755 | 12.755 | 0.0 | 99.97 +Pair | 4.7771 | 4.7771 | 4.7771 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0014069 | 0.0014069 | 0.0014069 | 0.0 | 0.01 -Output | 0.00085897 | 0.00085897 | 0.00085897 | 0.0 | 0.01 -Modify | 0.00075486 | 0.00075486 | 0.00075486 | 0.0 | 0.01 -Other | | 0.0003242 | | | 0.00 +Comm | 0.00052619 | 0.00052619 | 0.00052619 | 0.0 | 0.01 +Output | 0.00054073 | 0.00054073 | 0.00054073 | 0.0 | 0.01 +Modify | 0.00021744 | 0.00021744 | 0.00021744 | 0.0 | 0.00 +Other | | 0.0002317 | | | 0.00 Nlocal: 256.000 ave 256 max 256 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -131,4 +130,4 @@ Total # of neighbors = 19968 Ave neighs/atom = 78.000000 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:12 +Total wall time: 0:00:04 diff --git a/examples/mliap/log.03Mar21.mliap.nn.Cu.g++.4 b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.4 similarity index 69% rename from examples/mliap/log.03Mar21.mliap.nn.Cu.g++.4 rename to examples/mliap/log.14Jun21.mliap.nn.Cu.g++.4 index a7be3b1415..6738ce3f75 100644 --- a/examples/mliap/log.03Mar21.mliap.nn.Cu.g++.4 +++ b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (10 Feb 2021) - using 1 OpenMP thread(s) per MPI task +LAMMPS (27 May 2021) # Demonstrate MLIAP interface to SNAP nn Cu potential # Initialize simulation @@ -93,30 +92,30 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 30.85 | 30.85 | 30.85 Mbytes Step Temp E_pair c_energy TotEng Press v_press 0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505 - 10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504 - 20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718 - 30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378 - 40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151 - 50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675 - 60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654 - 70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077 - 80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217 - 90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598 - 100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141 -Loop time of 3.22769 on 4 procs for 100 steps with 256 atoms + 10 294.11049 -4.0927998 -4.0927998 -4.0549315 -2654.7826 2654.7826 + 20 276.89115 -4.0905826 -4.0905826 -4.0549314 -1879.2872 1879.2872 + 30 249.71134 -4.0870829 -4.0870829 -4.0549312 -627.47006 627.47006 + 40 214.92415 -4.0826036 -4.0826036 -4.054931 995.44801 -995.44801 + 50 175.86879 -4.0775747 -4.0775747 -4.0549307 2811.6019 -2811.6019 + 60 136.62706 -4.0725218 -4.0725218 -4.0549303 4640.4144 -4640.4144 + 70 101.48566 -4.0679968 -4.0679968 -4.05493 6313.5871 -6313.5871 + 80 74.248664 -4.0644897 -4.0644897 -4.0549298 7644.1364 -7644.1364 + 90 57.500423 -4.0623332 -4.0623332 -4.0549297 8514.2222 -8514.2222 + 100 52.104609 -4.0616385 -4.0616385 -4.0549298 8870.8923 -8870.8923 +Loop time of 1.25021 on 4 procs for 100 steps with 256 atoms -Performance: 1.338 ns/day, 17.932 hours/ns, 30.982 timesteps/s -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 3.455 ns/day, 6.946 hours/ns, 79.987 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.19 | 3.2037 | 3.2196 | 0.7 | 99.26 +Pair | 1.2256 | 1.2347 | 1.2415 | 0.5 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0061415 | 0.022081 | 0.035855 | 8.9 | 0.68 -Output | 0.00093221 | 0.00094824 | 0.00098861 | 0.0 | 0.03 -Modify | 0.0002173 | 0.00022773 | 0.00024477 | 0.0 | 0.01 -Other | | 0.0006805 | | | 0.02 +Comm | 0.0074687 | 0.014311 | 0.023481 | 4.8 | 1.14 +Output | 0.00060678 | 0.00062859 | 0.00066781 | 0.0 | 0.05 +Modify | 8.7976e-05 | 9.7811e-05 | 0.00010943 | 0.0 | 0.01 +Other | | 0.0004484 | | | 0.04 Nlocal: 64.0000 ave 64 max 64 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -131,4 +130,4 @@ Total # of neighbors = 19968 Ave neighs/atom = 78.000000 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:01 diff --git a/examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.1 b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.1 similarity index 89% rename from examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.1 rename to examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.1 index e22afa65f0..088e00fced 100644 --- a/examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.1 +++ b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (10 Feb 2021) - using 1 OpenMP thread(s) per MPI task +LAMMPS (27 May 2021) # Demonstrate MLIAP interface to linear SNAP potential # Initialize simulation @@ -125,20 +124,20 @@ Step Temp E_pair c_energy TotEng Press v_press 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 -Loop time of 3.05207 on 1 procs for 100 steps with 128 atoms +Loop time of 1.46158 on 1 procs for 100 steps with 128 atoms -Performance: 1.415 ns/day, 16.956 hours/ns, 32.765 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 2.956 ns/day, 8.120 hours/ns, 68.419 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.0503 | 3.0503 | 3.0503 | 0.0 | 99.94 +Pair | 1.4607 | 1.4607 | 1.4607 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00072395 | 0.00072395 | 0.00072395 | 0.0 | 0.02 -Output | 0.00050893 | 0.00050893 | 0.00050893 | 0.0 | 0.02 -Modify | 0.00037375 | 0.00037375 | 0.00037375 | 0.0 | 0.01 -Other | | 0.0001878 | | | 0.01 +Comm | 0.00028086 | 0.00028086 | 0.00028086 | 0.0 | 0.02 +Output | 0.00035334 | 0.00035334 | 0.00035334 | 0.0 | 0.02 +Modify | 0.00011992 | 0.00011992 | 0.00011992 | 0.0 | 0.01 +Other | | 0.0001502 | | | 0.01 Nlocal: 128.000 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -154,4 +153,4 @@ Ave neighs/atom = 58.000000 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:01 diff --git a/examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.4 b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.4 similarity index 89% rename from examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.4 rename to examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.4 index b0fdd57ce2..eb03f14da5 100644 --- a/examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.4 +++ b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (10 Feb 2021) - using 1 OpenMP thread(s) per MPI task +LAMMPS (27 May 2021) # Demonstrate MLIAP interface to linear SNAP potential # Initialize simulation @@ -32,7 +31,7 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms - create_atoms CPU = 0.000 seconds + create_atoms CPU = 0.001 seconds mass 1 180.88 @@ -125,20 +124,20 @@ Step Temp E_pair c_energy TotEng Press v_press 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 -Loop time of 0.858301 on 4 procs for 100 steps with 128 atoms +Loop time of 0.466162 on 4 procs for 100 steps with 128 atoms -Performance: 5.033 ns/day, 4.768 hours/ns, 116.509 timesteps/s -100.2% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 9.267 ns/day, 2.590 hours/ns, 214.518 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.75351 | 0.79999 | 0.85429 | 4.2 | 93.21 +Pair | 0.36478 | 0.41101 | 0.45575 | 6.9 | 88.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0026857 | 0.057019 | 0.10354 | 15.8 | 6.64 -Output | 0.00078796 | 0.00080864 | 0.00085671 | 0.0 | 0.09 -Modify | 0.00011437 | 0.00012275 | 0.00013339 | 0.0 | 0.01 -Other | | 0.0003564 | | | 0.04 +Comm | 0.0095217 | 0.054209 | 0.10046 | 19.0 | 11.63 +Output | 0.00042248 | 0.00045168 | 0.00051188 | 0.0 | 0.10 +Modify | 5.4359e-05 | 6.0737e-05 | 6.5088e-05 | 0.0 | 0.01 +Other | | 0.0004352 | | | 0.09 Nlocal: 32.0000 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.1 b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.1 new file mode 100644 index 0000000000..057732ec8c --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.1 @@ -0,0 +1,88 @@ +LAMMPS (27 May 2021) +# ---------- Initialize Simulation --------------------- +clear +units metal +dimension 3 +boundary p p p +atom_style atomic +read_data Ni_Mo.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + read_data CPU = 0.000 seconds + +#change_box all x scale 0.9 y scale 0.9 z scale 0.9 + +pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor +Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05 +SO3 keyword rcutfac 4.1 +SO3 keyword nmax 3 +SO3 keyword lmax 2 +SO3 keyword alpha 2.0 +SO3 keyword nelems 2 +SO3 keyword elems Mo +SO3 keyword radelems 0.5 +SO3 keyword welems 42 +pair_coeff * * Mo Ni + +variable e equal pe +variable N equal count(all) + +thermo_style custom pe pxx pyy pzz pxy pxz pyz +thermo 1 + +# dump 1 all custom 1 dump.myforce.* id type fx fy fz + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +run 3 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 17.22 | 17.22 | 17.22 Mbytes +PotEng Pxx Pyy Pzz Pxy Pxz Pyz + -60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498 + -60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829 + -60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456 + -60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916 +Loop time of 0.00634885 on 1 procs for 3 steps with 10 atoms + +Performance: 40.826 ns/day, 0.588 hours/ns, 472.527 timesteps/s +78.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0063019 | 0.0063019 | 0.0063019 | 0.0 | 99.26 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.12 +Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.54 +Modify | 2.1458e-06 | 2.1458e-06 | 2.1458e-06 | 0.0 | 0.03 +Other | | 3.099e-06 | | | 0.05 + +Nlocal: 10.0000 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 423.000 ave 423 max 423 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 780.000 ave 780 max 780 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 780 +Ave neighs/atom = 78.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.4 b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.4 new file mode 100644 index 0000000000..a7da331482 --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.4 @@ -0,0 +1,88 @@ +LAMMPS (27 May 2021) +# ---------- Initialize Simulation --------------------- +clear +units metal +dimension 3 +boundary p p p +atom_style atomic +read_data Ni_Mo.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 10 atoms + read_data CPU = 0.000 seconds + +#change_box all x scale 0.9 y scale 0.9 z scale 0.9 + +pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor +Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05 +SO3 keyword rcutfac 4.1 +SO3 keyword nmax 3 +SO3 keyword lmax 2 +SO3 keyword alpha 2.0 +SO3 keyword nelems 2 +SO3 keyword elems Mo +SO3 keyword radelems 0.5 +SO3 keyword welems 42 +pair_coeff * * Mo Ni + +variable e equal pe +variable N equal count(all) + +thermo_style custom pe pxx pyy pzz pxy pxz pyz +thermo 1 + +# dump 1 all custom 1 dump.myforce.* id type fx fy fz + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +run 3 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 17.23 | 17.23 | 17.23 Mbytes +PotEng Pxx Pyy Pzz Pxy Pxz Pyz + -60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498 + -60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829 + -60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456 + -60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916 +Loop time of 0.00191921 on 4 procs for 3 steps with 10 atoms + +Performance: 135.056 ns/day, 0.178 hours/ns, 1563.143 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0012183 | 0.0015162 | 0.0018141 | 0.8 | 79.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 5.3883e-05 | 0.00035822 | 0.00065947 | 0.0 | 18.67 +Output | 3.4094e-05 | 3.8326e-05 | 4.6492e-05 | 0.0 | 2.00 +Modify | 9.5367e-07 | 1.1325e-06 | 1.4305e-06 | 0.0 | 0.06 +Other | | 5.305e-06 | | | 0.28 + +Nlocal: 2.50000 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 303.500 ave 304 max 303 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 195.000 ave 234 max 156 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 780 +Ave neighs/atom = 78.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.1 b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.1 new file mode 100644 index 0000000000..0b67712e7e --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.1 @@ -0,0 +1,124 @@ +LAMMPS (27 May 2021) +# Run NPT MD simulation for Si at 500 K. +variable nsteps index 100 #0 + +# NOTE: These are not intended to represent real materials + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +#read_data Si.data +lattice diamond 5.43 +Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000 +region box block 0 2 0 2 0 2 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 64 atoms + create_atoms CPU = 0.000 seconds +mass 1 29.0 + +# temperature +variable t equal 500. + + +# Potential +#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt +pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor +SO3 keyword rcutfac 5.0 +SO3 keyword nmax 3 +SO3 keyword lmax 4 +SO3 keyword alpha 2.0 +SO3 keyword nelems 1 +SO3 keyword elems Si +SO3 keyword radelems 0.5 +SO3 keyword welems 14 +pair_coeff * * Si Si + +# Set-up output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create $t 5287287 loop geom +velocity all create 500 5287287 loop geom +fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2 +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 298.3 | 298.3 | 298.3 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456 + 10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624 + 20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165 + 30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641 + 40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177 + 50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008 + 60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639 + 70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391 + 80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675 + 90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78 + 100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458 +Loop time of 3.39264 on 1 procs for 100 steps with 64 atoms + +Performance: 1.273 ns/day, 18.848 hours/ns, 29.476 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.391 | 3.391 | 3.391 | 0.0 | 99.95 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00029302 | 0.00029302 | 0.00029302 | 0.0 | 0.01 +Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.01 +Modify | 0.00074792 | 0.00074792 | 0.00074792 | 0.0 | 0.02 +Other | | 0.0002153 | | | 0.01 + +Nlocal: 64.0000 ave 64 max 64 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 557.000 ave 557 max 557 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 2944.00 ave 2944 max 2944 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2944 +Ave neighs/atom = 46.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.4 b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.4 new file mode 100644 index 0000000000..7cde39a04e --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.4 @@ -0,0 +1,124 @@ +LAMMPS (27 May 2021) +# Run NPT MD simulation for Si at 500 K. +variable nsteps index 100 #0 + +# NOTE: These are not intended to represent real materials + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +#read_data Si.data +lattice diamond 5.43 +Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000 +region box block 0 2 0 2 0 2 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 64 atoms + create_atoms CPU = 0.000 seconds +mass 1 29.0 + +# temperature +variable t equal 500. + + +# Potential +#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt +pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor +SO3 keyword rcutfac 5.0 +SO3 keyword nmax 3 +SO3 keyword lmax 4 +SO3 keyword alpha 2.0 +SO3 keyword nelems 1 +SO3 keyword elems Si +SO3 keyword radelems 0.5 +SO3 keyword welems 14 +pair_coeff * * Si Si + +# Set-up output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create $t 5287287 loop geom +velocity all create 500 5287287 loop geom +fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2 +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 298.2 | 298.2 | 298.2 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456 + 10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624 + 20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165 + 30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641 + 40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177 + 50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008 + 60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639 + 70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391 + 80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675 + 90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78 + 100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458 +Loop time of 1.06231 on 4 procs for 100 steps with 64 atoms + +Performance: 4.067 ns/day, 5.902 hours/ns, 94.135 timesteps/s +95.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.97395 | 1.0072 | 1.048 | 2.7 | 94.81 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012069 | 0.052803 | 0.086037 | 12.0 | 4.97 +Output | 0.00052595 | 0.0005523 | 0.00062776 | 0.0 | 0.05 +Modify | 0.0014014 | 0.001442 | 0.0014772 | 0.1 | 0.14 +Other | | 0.0003045 | | | 0.03 + +Nlocal: 16.0000 ave 16 max 16 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 349.000 ave 349 max 349 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 736.000 ave 736 max 736 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2944 +Ave neighs/atom = 46.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/multi/data.powerlaw b/examples/multi/data.powerlaw new file mode 100644 index 0000000000..2ce54cf4a6 --- /dev/null +++ b/examples/multi/data.powerlaw @@ -0,0 +1,20015 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000 + +10000 atoms +1 atom types + +9.95143358025075 331.8139610404791 xlo xhi +9.95143358025075 331.8139610404791 ylo yhi +0 1 zlo zhi +0 0 0 xy xz yz + +Atoms # sphere + +16 1 27.0148 1 21.578661820808055 19.894003593559244 0 0 0 0 +6528 1 1.2402 1 40.11018907053191 29.030167715273407 0 0 1 0 +8976 1 1.0539 1 36.97821790225197 19.05186774766389 0 0 0 0 +168 1 7.3782 1 49.35369389791803 25.320840580930078 0 0 0 0 +194 1 6.9422 1 37.8963499906581 24.060540533134542 0 0 0 0 +208 1 6.6527 1 30.20573931579442 36.96891799058152 0 0 0 0 +336 1 5.417 1 42.81946909263247 31.018306090834393 0 0 0 0 +346 1 5.3618 1 17.904145680770682 40.365474113094464 0 0 0 0 +364 1 5.1987 1 45.47784864569917 20.574121185710485 0 0 0 0 +412 1 4.8776 1 22.52913680808026 42.40500703613544 0 0 0 0 +439 1 4.6882 1 35.32921707623989 30.55316138336846 0 0 0 0 +511 1 4.3207 1 43.71579096264905 26.313752950912164 0 0 0 0 +527 1 4.2767 1 40.53481826871412 15.977906579131261 0 0 0 0 +529 1 4.2701 1 14.88365052239063 45.532953698817934 0 0 0 0 +543 1 4.2317 1 22.663739581205114 36.42482542930276 0 0 0 0 +5300 1 1.3759 1 11.61412862355682 32.093048107213875 0 1 0 0 +569 1 4.1329 1 11.928958139921995 34.823339484175335 0 0 0 0 +4350 1 1.5228 1 15.212423557099871 48.57106966637227 0 1 0 0 +629 1 3.9339 1 45.09696092099179 35.7722795000036 0 0 0 0 +3990 1 1.5888 1 58.92019192272275 14.95895467917481 0 0 0 0 +675 1 3.8345 1 40.15765471413111 36.06383064621343 0 0 0 0 +9041 1 1.0504 1 55.77699479392789 9.970907140369798 0 0 0 0 +816 1 3.5492 1 16.452908912680222 36.21565336475413 0 0 0 0 +818 1 3.5444 1 36.541570162495695 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-7.725564834869343e-06 +6337 -0.0010501585618178401 3.1637071442245886e-05 0 0 0 0.0005189063800513128 +7189 -0.0010027915591139453 0.00023723368847990806 0 0 0 -2.1267115444176427e-05 +2680 -0.00030891216853277394 -0.00020457606529057616 0 0 0 -4.82731205087499e-05 +6160 -0.0007557869392639718 -0.00015627695707974944 0 0 0 -2.465884924693401e-05 +535 -0.0008767474296707425 0.00012151744175138143 0 0 0 1.245320689560073e-05 +8425 -0.0007512233785204506 0.0005405466387555643 0 0 0 -0.0001045579395697344 diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid new file mode 100644 index 0000000000..9f9883f61a --- /dev/null +++ b/examples/multi/in.colloid @@ -0,0 +1,67 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +create_atoms 1 box + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +set group all type/fraction 3 0.333 43684 +set group all type/fraction 4 0.250 87811 + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 5 single 60.0 60.0 0.0 units box +create_atoms 5 single 130.0 130.0 0.0 units box + +set type 1 mass 400 +set type 2 mass 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 & + mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 100 + +timestep 0.005 + +run 2000 diff --git a/examples/multi/in.granular b/examples/multi/in.granular new file mode 100644 index 0000000000..468d0dcbf1 --- /dev/null +++ b/examples/multi/in.granular @@ -0,0 +1,50 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +create_atoms 1 box +change_box all triclinic + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 2 single 20.0 20.0 0.0 units box +create_atoms 2 single 60.0 60.0 0.0 units box + +set type 2 mass 400 +set type 1 mass 1 +set type 2 diameter 20 +set type 1 diameter 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old + +# granular potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol +thermo 100 + +timestep 0.005 + +run 2000 diff --git a/examples/multi/in.powerlaw b/examples/multi/in.powerlaw new file mode 100644 index 0000000000..b69e6a56a3 --- /dev/null +++ b/examples/multi/in.powerlaw @@ -0,0 +1,33 @@ +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +change_box all triclinic + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-4 + +# dump 1 all custom 20000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 100 + +timestep 0.005 + +run 1000 diff --git a/examples/multi/log.30Nov20.colloid.intel.1 b/examples/multi/log.30Nov20.colloid.intel.1 new file mode 100644 index 0000000000..5dcb8c3bf1 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 4.385 | 4.385 | 4.385 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702 + 7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386 + 8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372 + 9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764 + 10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941 + 11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993 + 12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363 + 13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226 + 14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372 + 15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715 + 16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607 + 17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6 + 18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856 + 19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867 + 20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666 + 21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277 + 22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593 + 23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968 + 24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941 + 25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154 + 26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774 + 27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521 + 28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093 + 29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945 + 30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305 + 31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392 + 32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609 + 33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572 + 34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49 + 35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819 + 36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608 + 37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772 + 38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511 + 39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647 + 40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198 + 41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649 + 42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804 + 43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893 + 44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262 + 45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842 + 46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151 + 47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334 + 48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246 + 49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093 + 50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715 +Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms + +Performance: 1093493.133 tau/day, 2531.234 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.789 | 10.789 | 10.789 | 0.0 | 54.62 +Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59 +Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70 +Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01 +Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11 +Other | | 0.7856 | | | 3.98 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 584.000 ave 584 max 584 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25892.0 ave 25892 max 25892 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25892 +Ave neighs/atom = 8.5565102 +Neighbor list builds = 4330 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:19 diff --git a/examples/multi/log.30Nov20.colloid.intel.4 b/examples/multi/log.30Nov20.colloid.intel.4 new file mode 100644 index 0000000000..906400df66 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 4.327 | 4.329 | 4.330 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289 + 4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708 + 5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295 + 6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648 + 7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448 + 8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484 + 9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609 + 10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542 + 11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927 + 12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009 + 13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654 + 14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89 + 15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786 + 16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792 + 17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809 + 18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172 + 19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244 + 20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884 + 21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487 + 22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812 + 23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427 + 24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79 + 25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756 + 26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645 + 27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657 + 28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079 + 29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99 + 30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355 + 31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196 + 32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934 + 33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442 + 34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628 + 35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725 + 36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049 + 37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825 + 38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497 + 39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469 + 40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846 + 41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515 + 42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657 + 43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024 + 44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224 + 45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959 + 46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822 + 47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892 + 48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453 + 49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918 + 50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268 +Loop time of 6.98615 on 4 procs for 50000 steps with 3026 atoms + +Performance: 3091831.080 tau/day, 7157.016 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01 +Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04 +Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39 +Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01 +Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41 +Other | | 0.4281 | | | 6.13 + +Nlocal: 756.500 ave 839 max 673 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 292.500 ave 307 max 282 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 6435.25 ave 7367 max 5493 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 25741 +Ave neighs/atom = 8.5066094 +Neighbor list builds = 4335 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:07 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.1 b/examples/multi/log.30Nov20.colloid.old.intel.1 new file mode 100644 index 0000000000..70c7db2afd --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old #multi +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi/old #multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702 + 7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387 + 8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802 + 9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722 + 10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135 + 11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116 + 12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208 + 13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901 + 14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344 + 15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963 + 16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043 + 17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977 + 18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99 + 19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325 + 20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745 + 21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298 + 22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199 + 23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71 + 24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334 + 25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577 + 26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041 + 27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392 + 28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419 + 29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642 + 30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15 + 31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091 + 32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726 + 33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866 + 34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869 + 35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285 + 36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264 + 37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274 + 38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252 + 39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857 + 40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905 + 41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981 + 42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931 + 43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82 + 44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18 + 45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013 + 46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611 + 47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083 + 48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933 + 49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165 + 50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069 +Loop time of 28.5339 on 1 procs for 50000 steps with 3026 atoms + +Performance: 756994.490 tau/day, 1752.302 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.918 | 10.918 | 10.918 | 0.0 | 38.26 +Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36 +Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51 +Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00 +Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57 +Other | | 0.9412 | | | 3.30 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2292.00 ave 2292 max 2292 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25767.0 ave 25767 max 25767 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25767 +Ave neighs/atom = 8.5152016 +Neighbor list builds = 4332 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:28 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.4 b/examples/multi/log.30Nov20.colloid.old.intel.4 new file mode 100644 index 0000000000..6d159d9405 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old #multi +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi/old #multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.406 | 4.410 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814168 1.8042332 0.075557943 77825.289 + 4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521 + 5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581 + 6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994 + 7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068 + 8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899 + 9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69 + 10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271 + 11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223 + 12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869 + 13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441 + 14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432 + 15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491 + 16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633 + 17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582 + 18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933 + 19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945 + 20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271 + 21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934 + 22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03 + 23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999 + 24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323 + 25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848 + 26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597 + 27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24 + 28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441 + 29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266 + 30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051 + 31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903 + 32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077 + 33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987 + 34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964 + 35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433 + 36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246 + 37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664 + 38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421 + 39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293 + 40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176 + 41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599 + 42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922 + 43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928 + 44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954 + 45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662 + 46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162 + 47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453 + 48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543 + 49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823 + 50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277 +Loop time of 10.7578 on 4 procs for 50000 steps with 3026 atoms + +Performance: 2007847.166 tau/day, 4647.794 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98 +Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74 +Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79 +Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01 +Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19 +Other | | 0.5686 | | | 5.29 + +Nlocal: 756.500 ave 838 max 693 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1282.50 ave 1333 max 1216 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 6426.25 ave 7350 max 5786 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 25705 +Ave neighs/atom = 8.4947125 +Neighbor list builds = 4326 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/multi/log.30Nov20.granular.intel.1 b/examples/multi/log.30Nov20.granular.intel.1 new file mode 100644 index 0000000000..06d02b8531 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32604952 0 0.32595042 0.17341597 7862.5013 + 2000 0.12631038 0 0.12627198 0.069126477 8216.6956 + 3000 0.069351715 0 0.069330635 0.040799593 8344.1931 + 4000 0.045023755 0 0.04501007 0.029184795 8239.1832 + 5000 0.032735149 0 0.0327252 0.025640841 7943.5691 + 6000 0.026205227 0 0.026197262 0.021206924 7617.6672 + 7000 0.02165475 0 0.021648168 0.018789365 7255.2897 + 8000 0.018299317 0 0.018293755 0.019272158 6887.3386 + 9000 0.016283763 0 0.016278813 0.020434892 6524.0274 + 10000 0.015148918 0 0.015144313 0.021650465 6168.4941 + 11000 0.014180465 0 0.014176155 0.022320009 5823.98 + 12000 0.013505744 0 0.013501639 0.023978674 5492.4853 + 13000 0.013009585 0 0.01300563 0.024391329 5175.7455 + 14000 0.012494373 0 0.012490576 0.027331543 4874.3212 + 15000 0.012057669 0 0.012054004 0.030561239 4589.518 + 16000 0.011510988 0 0.01150749 0.034613772 4321.1694 + 17000 0.011198594 0 0.01119519 0.042263536 4070.0115 + 18000 0.010978603 0 0.010975266 0.053637275 3836.0304 + 19000 0.010768789 0 0.010765516 0.069472547 3619.75 + 20000 0.0102256 0 0.010222492 0.085332898 3420.2738 + 21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821 + 22000 0.006565581 0 0.0065635854 0.14807426 3071.3012 + 23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162 + 24000 0.0040345997 0 0.0040333734 0.237983 2792.2658 + 25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475 + 26000 0.0024157863 0 0.002415052 0.33851944 2578.4972 + 27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264 + 28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871 + 29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208 + 30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452 + 31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456 + 32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224 + 33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345 + 34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045 + 35000 0.00075804791 0 0.0007578175 0.6359631 2072.525 + 36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907 + 37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831 + 38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441 + 39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127 + 40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006 + 41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939 + 42000 0.00025394755 0 0.00025387036 0.80529272 1893.064 + 43000 0.00021067821 0 0.00021061418 0.82962095 1872.365 + 44000 0.00017927684 0 0.00017922235 0.85522899 1853.531 + 45000 0.0001464225 0 0.000146378 0.87925998 1837.2423 + 46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227 + 47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605 + 48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227 + 49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811 + 50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507 +Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms + +Performance: 393345.914 tau/day, 910.523 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 44.691 | 44.691 | 44.691 | 0.0 | 81.38 +Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39 +Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37 +Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00 +Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43 +Other | | 0.7794 | | | 1.42 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 525.000 ave 525 max 525 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 26732.0 ave 26732 max 26732 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 26732 +Ave neighs/atom = 8.1252280 +Neighbor list builds = 342 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:54 diff --git a/examples/multi/log.30Nov20.granular.intel.4 b/examples/multi/log.30Nov20.granular.intel.4 new file mode 100644 index 0000000000..3aa05d79c7 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32605303 0 0.32595393 0.17341558 7862.5037 + 2000 0.12631567 0 0.12627728 0.069188881 8216.7174 + 3000 0.069373812 0 0.069352726 0.040740832 8344.2982 + 4000 0.045084633 0 0.045070929 0.029328609 8239.3656 + 5000 0.032681746 0 0.032671813 0.025416741 7943.7831 + 6000 0.026301239 0 0.026293245 0.021418793 7617.8426 + 7000 0.021666723 0 0.021660138 0.018961011 7255.9338 + 8000 0.018141337 0 0.018135823 0.019306113 6887.4963 + 9000 0.015922309 0 0.015917469 0.020033398 6524.016 + 10000 0.014744547 0 0.014740066 0.020959503 6168.1945 + 11000 0.013872852 0 0.013868636 0.021708943 5823.3153 + 12000 0.013321594 0 0.013317545 0.02332141 5491.4979 + 13000 0.01269964 0 0.012695779 0.024796428 5174.6263 + 14000 0.01227055 0 0.012266821 0.027785072 4873.4516 + 15000 0.012120508 0 0.012116824 0.029656636 4588.8603 + 16000 0.011612027 0 0.011608498 0.034695109 4320.4674 + 17000 0.011216697 0 0.011213288 0.042746966 4069.4275 + 18000 0.010950166 0 0.010946838 0.053528994 3835.5439 + 19000 0.010887635 0 0.010884325 0.069684492 3619.562 + 20000 0.010563449 0 0.010560238 0.08654561 3420.2636 + 21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408 + 22000 0.006929086 0 0.0069269799 0.15018917 3072.0438 + 23000 0.0052239156 0 0.0052223277 0.19067193 2924.441 + 24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426 + 25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912 + 26000 0.002549072 0 0.0025482972 0.33567824 2579.3738 + 27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502 + 28000 0.001772982 0 0.0017724431 0.41079958 2411.9111 + 29000 0.001127719 0 0.0011273762 0.44752241 2341.1888 + 30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611 + 31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328 + 32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674 + 33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696 + 34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504 + 35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077 + 36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251 + 37000 0.0003540723 0 0.00035396468 0.68803919 2005.497 + 38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345 + 39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979 + 40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695 + 41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326 + 42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474 + 43000 0.00021545017 0 0.00021538468 0.82803644 1872.073 + 44000 0.00017293257 0 0.00017288 0.85436769 1852.6548 + 45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087 + 46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977 + 47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913 + 48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082 + 49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875 + 50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247 +Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms + +Performance: 1217551.996 tau/day, 2818.407 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21 +Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31 +Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10 +Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01 +Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32 +Other | | 0.5419 | | | 3.05 + +Nlocal: 822.500 ave 897 max 779 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 190.500 ave 211 max 179 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 6665.75 ave 7329 max 6104 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 26663 +Ave neighs/atom = 8.1042553 +Neighbor list builds = 342 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:17 diff --git a/examples/multi/log.30Nov20.granular.old.intel.1 b/examples/multi/log.30Nov20.granular.old.intel.1 new file mode 100644 index 0000000000..f928621824 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 + 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 + 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 + 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 + 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 + 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 + 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 + 18000 0.01100067 0 0.010997326 0.04899206 3825.155 + 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 + 20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658 + 21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002 + 22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986 + 23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014 + 24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113 + 25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604 + 26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564 + 27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379 + 28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461 + 29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308 + 30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316 + 31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683 + 32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093 + 33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574 + 34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254 + 35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217 + 36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654 + 37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901 + 38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136 + 39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531 + 40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834 + 41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027 + 42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714 + 43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408 + 44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677 + 45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144 + 46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355 + 47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285 + 48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043 + 49000 0.00018879338 0 0.000188736 0.95775166 1780.0323 + 50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442 +Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms + +Performance: 289297.713 tau/day, 669.671 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 56.696 | 56.696 | 56.696 | 0.0 | 75.93 +Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98 +Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29 +Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00 +Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29 +Other | | 1.125 | | | 1.51 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6295.00 ave 6295 max 6295 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 53729.0 ave 53729 max 53729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 53729 +Ave neighs/atom = 16.331003 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:14 diff --git a/examples/multi/log.30Nov20.granular.old.intel.4 b/examples/multi/log.30Nov20.granular.old.intel.4 new file mode 100644 index 0000000000..507de22119 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.063 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.20 | 10.20 | 10.20 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 + 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 + 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 + 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 + 15000 0.01184269 0 0.01183909 0.028504106 4577.901 + 16000 0.01143291 0 0.011429435 0.033564204 4309.88 + 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 + 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 + 19000 0.010225905 0 0.010222797 0.063669588 3607.6622 + 20000 0.0091390255 0 0.0091362477 0.088165402 3408.567 + 21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936 + 22000 0.00601731 0 0.0060154811 0.15261994 3064.3873 + 23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782 + 24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897 + 25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164 + 26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312 + 27000 0.001700508 0 0.0016999912 0.37665013 2487.1626 + 28000 0.0014434246 0 0.0014429859 0.41572163 2409.327 + 29000 0.00089885063 0 0.00089857742 0.453431 2340.2313 + 30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155 + 31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349 + 32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738 + 33000 0.00044719326 0 0.00044705733 0.59696179 2142.571 + 34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282 + 35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008 + 36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242 + 37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235 + 38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706 + 39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838 + 40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034 + 41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108 + 42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649 + 43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672 + 44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284 + 45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755 + 46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989 + 47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606 + 48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258 + 49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032 + 50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534 +Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms + +Performance: 716540.413 tau/day, 1658.658 timesteps/s +90.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14 +Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87 +Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09 +Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00 +Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27 +Other | | 0.7918 | | | 2.63 + +Nlocal: 822.500 ave 859 max 785 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 3049.75 ave 3089 max 2999 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 13440.5 ave 14459 max 11964 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 53762 +Ave neighs/atom = 16.341033 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:30 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.1 b/examples/multi/log.30Nov20.powerlaw.intel.1 new file mode 100644 index 0000000000..d0ed6e2685 --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.1 @@ -0,0 +1,291 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.027 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-4 + +# dump 1 all custom 20000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 200000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 14.77 | 14.77 | 14.77 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917 + 1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806 + 2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933 + 3000 0.00022105227 0 0.00022103017 0.58295464 103595.49 -0.011327442 + 4000 0.00020888366 0 0.00020886277 0.5826542 103595.49 -0.014147424 + 5000 0.00019912663 0 0.00019910672 0.58175837 103595.49 -0.015685634 + 6000 0.0001989441 0 0.00019892421 0.58170841 103595.49 -0.017379973 + 7000 0.00019307783 0 0.00019305852 0.58133913 103595.49 -0.019556709 + 8000 0.00018132444 0 0.00018130631 0.58134077 103595.49 -0.021609399 + 9000 0.00017909088 0 0.00017907297 0.58117179 103595.49 -0.023603514 + 10000 0.00018391928 0 0.00018390089 0.58070675 103595.49 -0.026026784 + 11000 0.00018985439 0 0.00018983541 0.58006086 103595.49 -0.028574238 + 12000 0.00018903569 0 0.00018901678 0.5794232 103595.49 -0.031151884 + 13000 0.00019070382 0 0.00019068475 0.57890243 103595.49 -0.033469404 + 14000 0.00019371625 0 0.00019369688 0.5787389 103595.49 -0.035646526 + 15000 0.00019833475 0 0.00019831492 0.57883166 103595.49 -0.037709788 + 16000 0.0002011729 0 0.00020115278 0.57875606 103595.49 -0.039452453 + 17000 0.00020285197 0 0.00020283169 0.5786311 103595.49 -0.040960671 + 18000 0.00020319174 0 0.00020317142 0.57842387 103595.49 -0.042257072 + 19000 0.00020290253 0 0.00020288224 0.57795042 103595.49 -0.043364149 + 20000 0.00020509848 0 0.00020507797 0.5771478 103595.49 -0.044392259 + 21000 0.00021803258 0 0.00021801078 0.57569003 103595.49 -0.044749043 + 22000 0.00020751217 0 0.00020749141 0.57477071 103595.49 -0.045719593 + 23000 0.00022053275 0 0.0002205107 0.57409228 103595.49 -0.047332146 + 24000 0.00022689646 0 0.00022687377 0.57325004 103595.49 -0.04871759 + 25000 0.00025224804 0 0.00025222282 0.57283712 103595.49 -0.050254871 + 26000 0.00025343198 0 0.00025340664 0.57238659 103595.49 -0.051604284 + 27000 0.00026689801 0 0.00026687132 0.57221042 103595.49 -0.052915257 + 28000 0.00027867954 0 0.00027865167 0.57197974 103595.49 -0.053832129 + 29000 0.00028697929 0 0.00028695059 0.57177264 103595.49 -0.054693121 + 30000 0.00028857612 0 0.00028854727 0.57145453 103595.49 -0.055559611 + 31000 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0.00080250542 0 0.00080242517 0.5519122 103595.49 -0.091897169 + 184000 0.00081235214 0 0.00081227091 0.55172769 103595.49 -0.091906209 + 185000 0.00078879443 0 0.00078871555 0.55145488 103595.49 -0.091198506 + 186000 0.00078497746 0 0.00078489896 0.55202944 103595.49 -0.091674987 + 187000 0.00079483049 0 0.000794751 0.55278073 103595.49 -0.092508295 + 188000 0.00079056756 0 0.0007904885 0.55362903 103595.49 -0.092801369 + 189000 0.00079162262 0 0.00079154346 0.55429061 103595.49 -0.092964781 + 190000 0.00078121133 0 0.00078113321 0.55386716 103595.49 -0.092689851 + 191000 0.00076574893 0 0.00076567235 0.5546533 103595.49 -0.093414672 + 192000 0.00076215201 0 0.0007620758 0.55503049 103595.49 -0.093986391 + 193000 0.00075652635 0 0.0007564507 0.55477696 103595.49 -0.094417347 + 194000 0.00075725781 0 0.00075718208 0.55457687 103595.49 -0.094241721 + 195000 0.0007434693 0 0.00074339496 0.55471575 103595.49 -0.094102015 + 196000 0.00073792493 0 0.00073785114 0.55463671 103595.49 -0.094452279 + 197000 0.00074673445 0 0.00074665978 0.55459327 103595.49 -0.09463863 + 198000 0.00072734835 0 0.00072727561 0.55514628 103595.49 -0.094622434 + 199000 0.00071846919 0 0.00071839734 0.55501969 103595.49 -0.094414887 + 200000 0.00072384651 0 0.00072377412 0.55533335 103595.49 -0.094159469 +Loop time of 443.321 on 1 procs for 200000 steps with 10000 atoms + +Performance: 194892.839 tau/day, 451.141 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 362.28 | 362.28 | 362.28 | 0.0 | 81.72 +Neigh | 1.737 | 1.737 | 1.737 | 0.0 | 0.39 +Comm | 5.0082 | 5.0082 | 5.0082 | 0.0 | 1.13 +Output | 0.01774 | 0.01774 | 0.01774 | 0.0 | 0.00 +Modify | 64.992 | 64.992 | 64.992 | 0.0 | 14.66 +Other | | 9.286 | | | 2.09 + +Nlocal: 10000.0 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 487.000 ave 487 max 487 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 34427.0 ave 34427 max 34427 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 34427 +Ave neighs/atom = 3.4427000 +Neighbor list builds = 244 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:07:23 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.4 b/examples/multi/log.30Nov20.powerlaw.intel.4 new file mode 100644 index 0000000000..109b4582db --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.4 @@ -0,0 +1,291 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.114 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-4 + +# dump 1 all custom 20000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 200000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917 + 1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806 + 2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933 + 3000 0.00022105227 0 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0.5526242 103595.49 -0.092013313 + 184000 0.00072460909 0 0.00072453663 0.55230817 103595.49 -0.092211243 + 185000 0.00072499917 0 0.00072492667 0.55273387 103595.49 -0.092920761 + 186000 0.00072852698 0 0.00072845413 0.55358929 103595.49 -0.093428623 + 187000 0.00072515668 0 0.00072508417 0.55336733 103595.49 -0.093440126 + 188000 0.00071355728 0 0.00071348593 0.55408468 103595.49 -0.094819333 + 189000 0.00071703212 0 0.00071696042 0.55424355 103595.49 -0.096198144 + 190000 0.00071808849 0 0.00071801668 0.55504118 103595.49 -0.097199842 + 191000 0.00072458142 0 0.00072450896 0.55493515 103595.49 -0.097564772 + 192000 0.00071472504 0 0.00071465357 0.55572657 103595.49 -0.097663072 + 193000 0.00070803966 0 0.00070796886 0.55546116 103595.49 -0.097306162 + 194000 0.00068236077 0 0.00068229254 0.55581155 103595.49 -0.097141594 + 195000 0.00067304613 0 0.00067297882 0.55559507 103595.49 -0.096646489 + 196000 0.00066680808 0 0.0006667414 0.55512029 103595.49 -0.096241456 + 197000 0.00065829161 0 0.00065822578 0.55545375 103595.49 -0.095808778 + 198000 0.0006617611 0 0.00066169492 0.55551074 103595.49 -0.095423531 + 199000 0.00066805655 0 0.00066798975 0.55581298 103595.49 -0.095287337 + 200000 0.00067263902 0 0.00067257175 0.55601669 103595.49 -0.095551006 +Loop time of 145.127 on 4 procs for 200000 steps with 10000 atoms + +Performance: 595339.507 tau/day, 1378.101 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 57.89 | 91.946 | 113.82 | 229.7 | 63.36 +Neigh | 0.34276 | 0.48607 | 0.56708 | 13.1 | 0.33 +Comm | 6.569 | 28.916 | 63.505 | 417.0 | 19.92 +Output | 0.0087178 | 0.011935 | 0.01563 | 2.3 | 0.01 +Modify | 10.432 | 16.495 | 20.378 | 97.7 | 11.37 +Other | | 7.272 | | | 5.01 + +Nlocal: 2500.00 ave 2990 max 1652 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 228.000 ave 254 max 198 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 8611.25 ave 10364 max 5676 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 34445 +Ave neighs/atom = 3.4445000 +Neighbor list builds = 241 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:25 diff --git a/examples/plugins/.clang-format b/examples/plugins/.clang-format new file mode 100644 index 0000000000..d5bb8c37a3 --- /dev/null +++ b/examples/plugins/.clang-format @@ -0,0 +1,32 @@ +--- +Language: Cpp +BasedOnStyle: LLVM +AccessModifierOffset: -1 +AlignConsecutiveAssignments: false +AlignConsecutiveDeclarations: false +AlignEscapedNewlines: Left +AlignOperands: false +AllowShortBlocksOnASingleLine: true +AllowShortFunctionsOnASingleLine: Inline +AllowShortIfStatementsOnASingleLine: WithoutElse +AllowShortLambdasOnASingleLine: None +AllowShortLoopsOnASingleLine: true +BraceWrapping: + AfterFunction: true +BreakBeforeBraces: Custom +BreakConstructorInitializers: AfterColon +BreakInheritanceList: AfterColon +ColumnLimit: 100 +IndentCaseLabels: true +IndentWidth: 2 +NamespaceIndentation: Inner +ObjCBlockIndentWidth: 2 +PenaltyBreakAssignment: 4 +ReflowComments: false +SpaceAfterCStyleCast: true +SpacesBeforeTrailingComments: 4 +SpacesInContainerLiterals: false +Standard: Cpp11 +TabWidth: 2 +UseTab: Never +... diff --git a/examples/plugins/.gitignore b/examples/plugins/.gitignore new file mode 100644 index 0000000000..0ec9e7f982 --- /dev/null +++ b/examples/plugins/.gitignore @@ -0,0 +1 @@ +/build* diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt new file mode 100644 index 0000000000..6e29676530 --- /dev/null +++ b/examples/plugins/CMakeLists.txt @@ -0,0 +1,68 @@ +########################################## +# CMake build system for plugin examples. +# The is meant to be used as a template for plugins that are +# distributed independent from the LAMMPS package. +########################################## + +cmake_minimum_required(VERSION 3.10) + +# enforce out-of-source build +if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) + message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. " + "Please remove CMakeCache.txt and CMakeFiles first.") +endif() + +project(plugins VERSION 1.0 LANGUAGES CXX) + +# NOTE: the next line should be commented out when used outside of the LAMMPS package +get_filename_component(LAMMPS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../../src ABSOLUTE) +set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR} CACHE PATH "Location of LAMMPS headers") +if(NOT LAMMPS_HEADER_DIR) + message(FATAL_ERROR "Must set LAMMPS_HEADER_DIR") +endif() + +# by default, install into $HOME/.local (not /usr/local), +# so that no root access (and sudo) is needed +if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE) +endif() + +# C++11 is required +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED ON) + +# bail out on windows +if(CMAKE_SYSTEM_NAME STREQUAL Windows) + message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows") +endif() + +set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}) +include(CheckIncludeFileCXX) +include(LAMMPSInterfaceCXX) + +########################## +# building the plugins + +add_library(morse2plugin MODULE morse2plugin.cpp pair_morse2.cpp pair_morse2_omp.cpp) +target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/USER-OMP") +target_link_libraries(morse2plugin PRIVATE lammps) + +add_library(nve2plugin MODULE nve2plugin.cpp fix_nve2.cpp) +target_link_libraries(nve2plugin PRIVATE lammps) + +add_library(helloplugin MODULE helloplugin.cpp) +target_link_libraries(helloplugin PRIVATE lammps) + +add_library(zero2plugin MODULE zero2plugin.cpp pair_zero2.cpp bond_zero2.cpp + angle_zero2.cpp dihedral_zero2.cpp improper_zero2.cpp) +target_link_libraries(zero2plugin PRIVATE lammps) + +set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES + PREFIX "" + LINK_FLAGS "-rdynamic") + +# MacOS seems to need this +if(CMAKE_SYSTEM_NAME STREQUAL Darwin) + set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES + LINK_FLAGS "-Wl,-undefined,dynamic_lookup") +endif() diff --git a/examples/plugins/LAMMPSInterfaceCXX.cmake b/examples/plugins/LAMMPSInterfaceCXX.cmake new file mode 100644 index 0000000000..02f9159319 --- /dev/null +++ b/examples/plugins/LAMMPSInterfaceCXX.cmake @@ -0,0 +1,86 @@ +# Cmake script code to define the LAMMPS C++ interface +# settings required for building LAMMPS plugins + +################################################################################ +# helper function +function(validate_option name values) + string(TOLOWER ${${name}} needle_lower) + string(TOUPPER ${${name}} needle_upper) + list(FIND ${values} ${needle_lower} IDX_LOWER) + list(FIND ${values} ${needle_upper} IDX_UPPER) + if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0) + list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}}) + message(FATAL_ERROR "\n########################################################################\n" + "Invalid value '${${name}}' for option ${name}\n" + "\n" + "Possible values are:\n" + "${POSSIBLE_VALUE_LIST}" + "########################################################################") + endif() +endfunction(validate_option) + +################################################################################# +# LAMMPS C++ interface. We only need the header related parts. +add_library(lammps INTERFACE) +target_include_directories(lammps INTERFACE ${LAMMPS_HEADER_DIR}) + +################################################################################ +# MPI configuration +if(NOT CMAKE_CROSSCOMPILING) + set(MPI_CXX_SKIP_MPICXX TRUE) + find_package(MPI QUIET) + option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) +else() + option(BUILD_MPI "Build MPI version" OFF) +endif() + +if(BUILD_MPI) + find_package(MPI REQUIRED) + option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) + if(LAMMPS_LONGLONG_TO_LONG) + target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG) + endif() + target_link_libraries(lammps INTERFACE MPI::MPI_CXX) +else() + target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS") +endif() + +set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") +set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) +set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) +validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) +string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) +target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES}) + +################################################################################ +# detect if we may enable OpenMP support by default +set(BUILD_OMP_DEFAULT OFF) +find_package(OpenMP QUIET) +if(OpenMP_FOUND) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(HAVE_OMP_H_INCLUDE) + set(BUILD_OMP_DEFAULT ON) + endif() +endif() + +option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT}) + +if(BUILD_OMP) + find_package(OpenMP REQUIRED) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(NOT HAVE_OMP_H_INCLUDE) + message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") + endif() + + if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR + (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) + # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. + # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe. + target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4) + else() + target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3) + endif() + target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX) +endif() diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile new file mode 100644 index 0000000000..f4d8b41086 --- /dev/null +++ b/examples/plugins/Makefile @@ -0,0 +1,6 @@ +CXX=mpicxx +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp +LD=$(CXX) -shared -rdynamic -fopenmp +DSOEXT=.so + +include Makefile.common diff --git a/examples/plugins/Makefile.common b/examples/plugins/Makefile.common new file mode 100644 index 0000000000..e78fa13feb --- /dev/null +++ b/examples/plugins/Makefile.common @@ -0,0 +1,36 @@ +default: morse2plugin$(DSOEXT) nve2plugin$(DSOEXT) helloplugin$(DSOEXT) zero2plugin$(DSOEXT) + +helloplugin$(DSOEXT): helloplugin.o + $(LD) -o $@ $^ + +morse2plugin$(DSOEXT): morse2plugin.o pair_morse2.o pair_morse2_omp.o + $(LD) -o $@ $^ + +nve2plugin$(DSOEXT): nve2plugin.o fix_nve2.o + $(LD) -o $@ $^ + +zero2plugin$(DSOEXT): zero2plugin.o pair_zero2.o bond_zero2.o angle_zero2.o dihedral_zero2.o improper_zero2.o + $(LD) -o $@ $^ + +.cpp.o: + $(CXX) -o $@ $(CXXFLAGS) -c $< + +helloplugin.o: helloplugin.cpp + +pair_morse2.o: pair_morse2.cpp pair_morse2.h +pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h +morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h + +fix_nve2.o: fix_nve2.cpp fix_nve2.h +nve2plugin.o: nve2plugin.cpp fix_nve2.h + +pair_zero2.o: pair_zero2.cpp pair_zero2.h +bond_zero2.o: bond_zero2.cpp bond_zero2.h +angle_zero2.o: angle_zero2.cpp angle_zero2.h +dihedral_zero2.o: dihedral_zero2.cpp dihedral_zero2.h +improper_zero2.o: improper_zero2.cpp improper_zero2.h +zero2plugin.o: zero2plugin.cpp pair_zero2.h bond_zero2.h angle_zero2.h dihedral_zero2.h + +clean: + rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles + diff --git a/examples/plugins/Makefile.macos b/examples/plugins/Makefile.macos new file mode 100644 index 0000000000..a7c20ff90f --- /dev/null +++ b/examples/plugins/Makefile.macos @@ -0,0 +1,6 @@ +CXX=mpicxx +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP +LD=$(CXX) -bundle -rdynamic -Wl,-undefined,dynamic_lookup +DSOEXT=.dylib + +include Makefile.common diff --git a/examples/plugins/Makefile.serial b/examples/plugins/Makefile.serial new file mode 100644 index 0000000000..ecc7631a05 --- /dev/null +++ b/examples/plugins/Makefile.serial @@ -0,0 +1,6 @@ +CXX=g++ +CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp +LD=$(CXX) -shared -rdynamic -fopenmp +DSOEXT=.so + +include Makefile.common diff --git a/examples/plugins/angle_zero2.cpp b/examples/plugins/angle_zero2.cpp new file mode 100644 index 0000000000..bc2f6869dc --- /dev/null +++ b/examples/plugins/angle_zero2.cpp @@ -0,0 +1,152 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "angle_zero2.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +AngleZero2::AngleZero2(LAMMPS *lmp) : Angle(lmp), coeffflag(1) {} + +/* ---------------------------------------------------------------------- */ + +AngleZero2::~AngleZero2() +{ + if (allocated && !copymode) { + memory->destroy(setflag); + memory->destroy(theta0); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleZero2::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); +} + +/* ---------------------------------------------------------------------- */ + +void AngleZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) error->all(FLERR, "Illegal angle_style command"); + + if (narg == 1) { + if (strcmp("nocoeff", arg[0]) == 0) + coeffflag = 0; + else + error->all(FLERR, "Illegal angle_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleZero2::allocate() +{ + allocated = 1; + int n = atom->nangletypes; + + memory->create(theta0, n + 1, "angle:theta0"); + memory->create(setflag, n + 1, "angle:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void AngleZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 2)) + error->all(FLERR, "Incorrect args for angle coefficients"); + + if (!allocated) allocate(); + + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error); + + double theta0_one = 0.0; + if (coeffflag && (narg == 2)) theta0_one = utils::numeric(FLERR, arg[1], false, lmp); + + // convert theta0 from degrees to radians + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + theta0[i] = theta0_one / 180.0 * MY_PI; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); +} + +/* ---------------------------------------------------------------------- */ + +double AngleZero2::equilibrium_angle(int i) +{ + return theta0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void AngleZero2::write_restart(FILE *fp) +{ + fwrite(&theta0[1], sizeof(double), atom->nangletypes, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void AngleZero2::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + utils::sfread(FLERR, &theta0[1], sizeof(double), atom->nangletypes, fp, nullptr, error); + } + MPI_Bcast(&theta0[1], atom->nangletypes, MPI_DOUBLE, 0, world); + + for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; +} +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void AngleZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp, "%d %g\n", i, theta0[i] / MY_PI * 180.0); +} + +/* ---------------------------------------------------------------------- */ + +double AngleZero2::single(int /*type*/, int /*i1*/, int /*i2*/, int /*i3*/) +{ + return 0.0; +} diff --git a/examples/plugins/angle_zero2.h b/examples/plugins/angle_zero2.h new file mode 100644 index 0000000000..4c9e6e9b24 --- /dev/null +++ b/examples/plugins/angle_zero2.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_ANGLE_ZERO2_H +#define LMP_ANGLE_ZERO2_H + +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleZero2 : public Angle { + public: + AngleZero2(class LAMMPS *); + virtual ~AngleZero2(); + virtual void compute(int, int); + virtual void coeff(int, char **); + virtual void settings(int, char **); + + double equilibrium_angle(int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + double single(int, int, int, int); + + protected: + double *theta0; + int coeffflag; + + void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for angle coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/examples/plugins/bond_zero2.cpp b/examples/plugins/bond_zero2.cpp new file mode 100644 index 0000000000..768f176c63 --- /dev/null +++ b/examples/plugins/bond_zero2.cpp @@ -0,0 +1,160 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "bond_zero2.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondZero2::BondZero2(LAMMPS *lmp) : Bond(lmp), coeffflag(1) {} + +/* ---------------------------------------------------------------------- */ + +BondZero2::~BondZero2() +{ + if (allocated && !copymode) { + memory->destroy(setflag); + memory->destroy(r0); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondZero2::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); +} + +/* ---------------------------------------------------------------------- */ + +void BondZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) error->all(FLERR, "Illegal bond_style command"); + + if (narg == 1) { + if (strcmp("nocoeff", arg[0]) == 0) + coeffflag = 0; + else + error->all(FLERR, "Illegal bond_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondZero2::allocate() +{ + allocated = 1; + int n = atom->nbondtypes; + + memory->create(r0, n + 1, "bond:r0"); + memory->create(setflag, n + 1, "bond:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void BondZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 2)) + error->all(FLERR, "Incorrect args for bond coefficients"); + + if (!allocated) allocate(); + + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); + + double r0_one = 0.0; + if (coeffflag && (narg == 2)) r0_one = utils::numeric(FLERR, arg[1], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + r0[i] = r0_one; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); +} + +/* ---------------------------------------------------------------------- + return an equilbrium bond length +------------------------------------------------------------------------- */ + +double BondZero2::equilibrium_distance(int i) +{ + return r0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void BondZero2::write_restart(FILE *fp) +{ + fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void BondZero2::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); + } + MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world); + + for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void BondZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nbondtypes; i++) fprintf(fp, "%d %g\n", i, r0[i]); +} + +/* ---------------------------------------------------------------------- */ + +double BondZero2::single(int /*type*/, double /*rsq*/, int /*i*/, int /*j*/, double & /*fforce*/) +{ + return 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void *BondZero2::extract(const char *str, int &dim) +{ + dim = 1; + if (strcmp(str, "r0") == 0) return (void *) r0; + return nullptr; +} diff --git a/examples/plugins/bond_zero2.h b/examples/plugins/bond_zero2.h new file mode 100644 index 0000000000..247d3e2f63 --- /dev/null +++ b/examples/plugins/bond_zero2.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_BOND_ZERO2_H +#define LMP_BOND_ZERO2_H + +#include "bond.h" + +namespace LAMMPS_NS { + +class BondZero2 : public Bond { + public: + BondZero2(class LAMMPS *); + virtual ~BondZero2(); + virtual void compute(int, int); + virtual void settings(int, char **); + + void coeff(int, char **); + double equilibrium_distance(int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + double single(int, double, int, int, double &); + virtual void *extract(const char *, int &); + + protected: + double *r0; + int coeffflag; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for bond coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/examples/plugins/dihedral_zero2.cpp b/examples/plugins/dihedral_zero2.cpp new file mode 100644 index 0000000000..a597d7a48e --- /dev/null +++ b/examples/plugins/dihedral_zero2.cpp @@ -0,0 +1,120 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "dihedral_zero2.h" + +#include "atom.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +DihedralZero2::DihedralZero2(LAMMPS *lmp) : Dihedral(lmp), coeffflag(1) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +DihedralZero2::~DihedralZero2() +{ + if (allocated && !copymode) { memory->destroy(setflag); } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralZero2::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); +} + +/* ---------------------------------------------------------------------- */ + +void DihedralZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) error->all(FLERR, "Illegal dihedral_style command"); + + if (narg == 1) { + if (strcmp("nocoeff", arg[0]) == 0) + coeffflag = 0; + else + error->all(FLERR, "Illegal dihedral_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralZero2::allocate() +{ + allocated = 1; + int n = atom->ndihedraltypes; + + memory->create(setflag, n + 1, "dihedral:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void DihedralZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 1)) + error->all(FLERR, "Incorrect args for dihedral coefficients"); + + if (!allocated) allocate(); + + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void DihedralZero2::write_restart(FILE * /*fp*/) {} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void DihedralZero2::read_restart(FILE * /*fp*/) +{ + allocate(); + for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) fprintf(fp, "%d\n", i); +} diff --git a/examples/plugins/dihedral_zero2.h b/examples/plugins/dihedral_zero2.h new file mode 100644 index 0000000000..c343849f7d --- /dev/null +++ b/examples/plugins/dihedral_zero2.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + + Identical to dihedral harmonic, except if all k's are zero the + force loop is skipped. + +------------------------------------------------------------------------- */ + +#ifndef LMP_DIHEDRAL_ZERO2_H +#define LMP_DIHEDRAL_ZERO2_H + +#include "dihedral.h" + +namespace LAMMPS_NS { + +class DihedralZero2 : public Dihedral { + public: + DihedralZero2(class LAMMPS *); + virtual ~DihedralZero2(); + virtual void compute(int, int); + virtual void coeff(int, char **); + virtual void settings(int, char **); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + protected: + int coeffflag; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for dihedral coefficients + +UNDOCUMENTED + +*/ diff --git a/examples/plugins/fix_nve2.cpp b/examples/plugins/fix_nve2.cpp new file mode 100644 index 0000000000..498cb40d21 --- /dev/null +++ b/examples/plugins/fix_nve2.cpp @@ -0,0 +1,170 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_nve2.h" +#include "atom.h" +#include "error.h" +#include "force.h" +#include "respa.h" +#include "update.h" +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixNVE2::FixNVE2(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) +{ + if (strcmp(style, "nve/sphere") != 0 && narg < 3) error->all(FLERR, "Illegal fix nve command"); + + dynamic_group_allow = 1; + time_integrate = 1; +} + +/* ---------------------------------------------------------------------- */ + +int FixNVE2::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= INITIAL_INTEGRATE_RESPA; + mask |= FINAL_INTEGRATE_RESPA; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::init() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + + if (strstr(update->integrate_style, "respa")) step_respa = ((Respa *) update->integrate)->step; +} + +/* ---------------------------------------------------------------------- + allow for both per-type and per-atom mass +------------------------------------------------------------------------- */ + +void FixNVE2::initial_integrate(int /*vflag*/) +{ + double dtfm; + + // update v and x of atoms in group + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::final_integrate() +{ + double dtfm; + + // update v of atoms in group + + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) +{ + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + + // innermost level - NVE update of v and x + // all other levels - NVE update of v + + if (ilevel == 0) + initial_integrate(vflag); + else + final_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::final_integrate_respa(int ilevel, int /*iloop*/) +{ + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + final_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::reset_dt() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} diff --git a/src/USER-MISC/fix_propel_self.h b/examples/plugins/fix_nve2.h similarity index 50% rename from src/USER-MISC/fix_propel_self.h rename to examples/plugins/fix_nve2.h index 47d1e1255b..423946f8c0 100644 --- a/src/USER-MISC/fix_propel_self.h +++ b/examples/plugins/fix_nve2.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -13,54 +13,41 @@ #ifdef FIX_CLASS -FixStyle(propel/self,FixPropelSelf) +FixStyle(nve2, FixNVE2) #else -#ifndef LMP_FIX_PROPEL_SELF_H -#define LMP_FIX_PROPEL_SELF_H +#ifndef LMP_FIX_NVE2_H +#define LMP_FIX_NVE2_H #include "fix.h" namespace LAMMPS_NS { -class FixPropelSelf : public Fix { +class FixNVE2 : public Fix { public: - - FixPropelSelf(class LAMMPS *, int, char **); - virtual ~FixPropelSelf(); - virtual int setmask(); - virtual void post_force(int); - - double memory_usage(); + FixNVE2(class LAMMPS *, int, char **); + virtual ~FixNVE2() {} + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + virtual void initial_integrate_respa(int, int, int); + virtual void final_integrate_respa(int, int); + virtual void reset_dt(); protected: - enum operation_modes { - VELOCITY = 0, - QUATERNION = 1 - }; - -private: - double magnitude; - int mode; - - // If 0, apply fix to everything in group. If > 0, apply only to those - // types i for which i <= n_types_filter _and_ apply_to_type[i] == 1: - int n_types_filter; - int *apply_to_type; //< Specifies, per type, if the fix applies to it or not. - - - int atoms_have_quaternion(); - - template void post_force_velocity(int); - template void post_force_quaternion(int); + double dtv, dtf; + double *step_respa; + int mass_require; }; -} + +} // namespace LAMMPS_NS #endif #endif -/* ERROR/WARNING messages: + /* ERROR/WARNING messages: E: Illegal ... command diff --git a/examples/plugins/helloplugin.cpp b/examples/plugins/helloplugin.cpp new file mode 100644 index 0000000000..9f3406a282 --- /dev/null +++ b/examples/plugins/helloplugin.cpp @@ -0,0 +1,45 @@ + +#include "lammpsplugin.h" + +#include "comm.h" +#include "command.h" +#include "error.h" +#include "version.h" + +#include + +namespace LAMMPS_NS { +class Hello : public Command { + public: + Hello(class LAMMPS *lmp) : Command(lmp){}; + void command(int, char **); +}; +} // namespace LAMMPS_NS + +using namespace LAMMPS_NS; + +void Hello::command(int argc, char **argv) +{ + if (argc != 1) error->all(FLERR, "Illegal hello command"); + if (comm->me == 0) utils::logmesg(lmp, fmt::format("Hello, {}!\n", argv[0])); +} + +static Command *hellocreator(LAMMPS *lmp) +{ + return new Hello(lmp); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + plugin.version = LAMMPS_VERSION; + plugin.style = "command"; + plugin.name = "hello"; + plugin.info = "Hello world command v1.1"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); +} diff --git a/examples/plugins/improper_zero2.cpp b/examples/plugins/improper_zero2.cpp new file mode 100644 index 0000000000..9b0335df8b --- /dev/null +++ b/examples/plugins/improper_zero2.cpp @@ -0,0 +1,120 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "improper_zero2.h" + +#include "atom.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ImproperZero2::ImproperZero2(LAMMPS *lmp) : Improper(lmp), coeffflag(1) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +ImproperZero2::~ImproperZero2() +{ + if (allocated && !copymode) { memory->destroy(setflag); } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperZero2::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); +} + +/* ---------------------------------------------------------------------- */ + +void ImproperZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) error->all(FLERR, "Illegal improper_style command"); + + if (narg == 1) { + if (strcmp("nocoeff", arg[0]) == 0) + coeffflag = 0; + else + error->all(FLERR, "Illegal improper_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperZero2::allocate() +{ + allocated = 1; + int n = atom->nimpropertypes; + + memory->create(setflag, n + 1, "improper:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void ImproperZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 1)) + error->all(FLERR, "Incorrect args for improper coefficients"); + + if (!allocated) allocate(); + + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nimpropertypes, ilo, ihi, error); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void ImproperZero2::write_restart(FILE * /*fp*/) {} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void ImproperZero2::read_restart(FILE * /*fp*/) +{ + allocate(); + for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) fprintf(fp, "%d\n", i); +} diff --git a/examples/plugins/improper_zero2.h b/examples/plugins/improper_zero2.h new file mode 100644 index 0000000000..21cbd87c03 --- /dev/null +++ b/examples/plugins/improper_zero2.h @@ -0,0 +1,53 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_IMPROPER_ZERO2_H +#define LMP_IMPROPER_ZERO2_H + +#include "improper.h" + +namespace LAMMPS_NS { + +class ImproperZero2 : public Improper { + public: + ImproperZero2(class LAMMPS *); + virtual ~ImproperZero2(); + virtual void compute(int, int); + virtual void coeff(int, char **); + virtual void settings(int, char **); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + protected: + int coeffflag; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for improper coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp new file mode 100644 index 0000000000..13dc3507f1 --- /dev/null +++ b/examples/plugins/morse2plugin.cpp @@ -0,0 +1,43 @@ + +#include "lammpsplugin.h" + +#include "version.h" + +#include + +#include "pair_morse2.h" +#include "pair_morse2_omp.h" + +using namespace LAMMPS_NS; + +static Pair *morse2creator(LAMMPS *lmp) +{ + return new PairMorse2(lmp); +} + +static Pair *morse2ompcreator(LAMMPS *lmp) +{ + return new PairMorse2OMP(lmp); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + // register plain morse2 pair style + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "morse2"; + plugin.info = "Morse2 variant pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); + + // also register morse2/omp pair style. only need to update changed fields + plugin.name = "morse2/omp"; + plugin.info = "Morse2 variant pair style for OpenMP v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2ompcreator; + (*register_plugin)(&plugin, lmp); +} diff --git a/examples/plugins/nve2plugin.cpp b/examples/plugins/nve2plugin.cpp new file mode 100644 index 0000000000..3c622f925c --- /dev/null +++ b/examples/plugins/nve2plugin.cpp @@ -0,0 +1,30 @@ + +#include "lammpsplugin.h" + +#include "version.h" + +#include + +#include "fix_nve2.h" + +using namespace LAMMPS_NS; + +static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv) +{ + return new FixNVE2(lmp, argc, argv); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + plugin.version = LAMMPS_VERSION; + plugin.style = "fix"; + plugin.name = "nve2"; + plugin.info = "NVE2 variant fix style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); +} diff --git a/examples/plugins/pair_morse2.cpp b/examples/plugins/pair_morse2.cpp new file mode 100644 index 0000000000..738fd53e87 --- /dev/null +++ b/examples/plugins/pair_morse2.cpp @@ -0,0 +1,353 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_morse2.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairMorse2::PairMorse2(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairMorse2::~PairMorse2() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(d0); + memory->destroy(alpha); + memory->destroy(r0); + memory->destroy(morse1); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairMorse2::compute(int eflag, int vflag) +{ + int i, j, ii, jj, inum, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; + double rsq, r, dr, dexp, factor_lj; + int *ilist, *jlist, *numneigh, **firstneigh; + + evdwl = 0.0; + ev_init(eflag, vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = factor_lj * morse1[itype][jtype] * (dexp * dexp - dexp) / r; + + f[i][0] += delx * fpair; + f[i][1] += dely * fpair; + f[i][2] += delz * fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx * fpair; + f[j][1] -= dely * fpair; + f[j][2] -= delz * fpair; + } + + if (eflag) { + evdwl = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) - offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairMorse2::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) setflag[i][j] = 0; + + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + + memory->create(cut, n + 1, n + 1, "pair:cut"); + memory->create(d0, n + 1, n + 1, "pair:d0"); + memory->create(alpha, n + 1, n + 1, "pair:alpha"); + memory->create(r0, n + 1, n + 1, "pair:r0"); + memory->create(morse1, n + 1, n + 1, "pair:morse1"); + memory->create(offset, n + 1, n + 1, "pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairMorse2::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); + + cut_global = utils::numeric(FLERR, arg[0], false, lmp); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairMorse2::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); + + double d0_one = utils::numeric(FLERR, arg[2], false, lmp); + double alpha_one = utils::numeric(FLERR, arg[3], false, lmp); + double r0_one = utils::numeric(FLERR, arg[4], false, lmp); + + double cut_one = cut_global; + if (narg == 6) cut_one = utils::numeric(FLERR, arg[5], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { + d0[i][j] = d0_one; + alpha[i][j] = alpha_one; + r0[i][j] = r0_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairMorse2::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + + morse1[i][j] = 2.0 * d0[i][j] * alpha[i][j]; + + if (offset_flag) { + double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); + offset[i][j] = d0[i][j] * (exp(2.0 * alpha_dr) - 2.0 * exp(alpha_dr)); + } else + offset[i][j] = 0.0; + + d0[j][i] = d0[i][j]; + alpha[j][i] = alpha[i][j]; + r0[j][i] = r0[i][j]; + morse1[j][i] = morse1[i][j]; + offset[j][i] = offset[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMorse2::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1, fp); + if (setflag[i][j]) { + fwrite(&d0[i][j], sizeof(double), 1, fp); + fwrite(&alpha[i][j], sizeof(double), 1, fp); + fwrite(&r0[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMorse2::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i, j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR, &d0[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &alpha[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &r0[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); + } + MPI_Bcast(&d0[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&alpha[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMorse2::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&offset_flag, sizeof(int), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMorse2::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error); + utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); + } + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairMorse2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp, "%d %g %g %g\n", i, d0[i][i], alpha[i][i], r0[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairMorse2::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp, "%d %d %g %g %g %g\n", i, j, d0[i][j], alpha[i][j], r0[i][j], cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) +{ + double r, dr, dexp, phi; + + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fforce = factor_lj * morse1[itype][jtype] * (dexp * dexp - dexp) / r; + + phi = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) - offset[itype][jtype]; + return factor_lj * phi; +} + +/* ---------------------------------------------------------------------- */ + +void *PairMorse2::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str, "d0") == 0) return (void *) d0; + if (strcmp(str, "r0") == 0) return (void *) r0; + if (strcmp(str, "alpha") == 0) return (void *) alpha; + return nullptr; +} diff --git a/examples/plugins/pair_morse2.h b/examples/plugins/pair_morse2.h new file mode 100644 index 0000000000..753743fc4e --- /dev/null +++ b/examples/plugins/pair_morse2.h @@ -0,0 +1,70 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_PAIR_MORSE2_H +#define LMP_PAIR_MORSE2_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairMorse2 : public Pair { + public: + PairMorse2(class LAMMPS *); + virtual ~PairMorse2(); + virtual void compute(int, int); + + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_global; + double **cut; + double **d0, **alpha, **r0; + double **morse1; + double **offset; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/examples/plugins/pair_morse2_omp.cpp b/examples/plugins/pair_morse2_omp.cpp new file mode 100644 index 0000000000..9c81bad970 --- /dev/null +++ b/examples/plugins/pair_morse2_omp.cpp @@ -0,0 +1,164 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_morse2_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairMorse2OMP::PairMorse2OMP(LAMMPS *lmp) : PairMorse2(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairMorse2OMP::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + const int inum = list->inum; + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + if (evflag) { + if (eflag) { + if (force->newton_pair) + eval<1, 1, 1>(ifrom, ito, thr); + else + eval<1, 1, 0>(ifrom, ito, thr); + } else { + if (force->newton_pair) + eval<1, 0, 1>(ifrom, ito, thr); + else + eval<1, 0, 0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) + eval<0, 0, 1>(ifrom, ito, thr); + else + eval<0, 0, 0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairMorse2OMP::eval(int iifrom, int iito, ThrData *const thr) +{ + int i, j, ii, jj, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; + double rsq, r, dr, dexp, factor_lj; + int *ilist, *jlist, *numneigh, **firstneigh; + + evdwl = 0.0; + + const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0]; + dbl3_t *_noalias const f = (dbl3_t *) thr->get_f()[0]; + const int *_noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double *_noalias const special_lj = force->special_lj; + double fxtmp, fytmp, fztmp; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp = fytmp = fztmp = 0.0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx * delx + dely * dely + delz * delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = factor_lj * morse1[itype][jtype] * (dexp * dexp - dexp) / r; + + fxtmp += delx * fpair; + fytmp += dely * fpair; + fztmp += delz * fpair; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= delx * fpair; + f[j].y -= dely * fpair; + f[j].z -= delz * fpair; + } + + if (EFLAG) { + evdwl = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) - offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (EVFLAG) + ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, 0.0, fpair, delx, dely, delz, thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairMorse2OMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairMorse2::memory_usage(); + + return bytes; +} diff --git a/examples/plugins/pair_morse2_omp.h b/examples/plugins/pair_morse2_omp.h new file mode 100644 index 0000000000..6c27f42125 --- /dev/null +++ b/examples/plugins/pair_morse2_omp.h @@ -0,0 +1,41 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifndef LMP_PAIR_MORSE2_OMP_H +#define LMP_PAIR_MORSE2_OMP_H + +#include "pair_morse2.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairMorse2OMP : public PairMorse2, public ThrOMP { + + public: + PairMorse2OMP(class LAMMPS *); + + virtual void compute(int, int); + virtual double memory_usage(); + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/examples/plugins/pair_zero2.cpp b/examples/plugins/pair_zero2.cpp new file mode 100644 index 0000000000..c5197a67a6 --- /dev/null +++ b/examples/plugins/pair_zero2.cpp @@ -0,0 +1,237 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "pair_zero2.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairZero2::PairZero2(LAMMPS *lmp) : Pair(lmp) +{ + coeffflag = 1; + writedata = 1; + single_enable = 1; + respa_enable = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairZero2::~PairZero2() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairZero2::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairZero2::compute_outer(int eflag, int vflag) +{ + ev_init(eflag, vflag); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairZero2::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) setflag[i][j] = 0; + + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + memory->create(cut, n + 1, n + 1, "pair:cut"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairZero2::settings(int narg, char **arg) +{ + if ((narg != 1) && (narg != 2)) error->all(FLERR, "Illegal pair_style command"); + + cut_global = utils::numeric(FLERR, arg[0], false, lmp); + if (narg == 2) { + if (strcmp("nocoeff", arg[1]) == 0) + coeffflag = 0; + else + error->all(FLERR, "Illegal pair_style command"); + } + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i + 1; j <= atom->ntypes; j++) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairZero2::coeff(int narg, char **arg) +{ + if ((narg < 2) || (coeffflag && narg > 3)) + error->all(FLERR, "Incorrect args for pair coefficients"); + + if (!allocated) allocate(); + + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); + + double cut_one = cut_global; + if (coeffflag && (narg == 3)) cut_one = utils::numeric(FLERR, arg[2], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairZero2::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { cut[i][j] = mix_distance(cut[i][i], cut[j][j]); } + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairZero2::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1, fp); + if (setflag[i][j]) { fwrite(&cut[i][j], sizeof(double), 1, fp); } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairZero2::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i, j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); + if (setflag[i][j]) { + if (me == 0) { utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); } + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairZero2::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&coeffflag, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairZero2::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &coeffflag, sizeof(int), 1, fp, nullptr, error); + } + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&coeffflag, 1, MPI_INT, 0, world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d\n", i); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairZero2::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) fprintf(fp, "%d %d %g\n", i, j, cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairZero2::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */, double /* rsq */, + double /*factor_coul*/, double /* factor_lj */, double &fforce) +{ + fforce = 0.0; + return 0.0; +} diff --git a/examples/plugins/pair_zero2.h b/examples/plugins/pair_zero2.h new file mode 100644 index 0000000000..9f96b7757c --- /dev/null +++ b/examples/plugins/pair_zero2.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + + Pair zero is a dummy pair interaction useful for requiring a + force cutoff distance in the absence of pair-interactions or + with hybrid/overlay if a larger force cutoff distance is required. + + This can be used in conjunction with bond/create to create bonds + that are longer than the cutoff of a given force field, or to + calculate radial distribution functions for models without + pair interactions. + +------------------------------------------------------------------------- */ + +#ifndef LMP_PAIR_ZERO2_H +#define LMP_PAIR_ZERO2_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairZero2 : public Pair { + public: + PairZero2(class LAMMPS *); + virtual ~PairZero2(); + virtual void compute(int, int); + virtual void compute_outer(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global; + double **cut; + int coeffflag; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +U: Pair cutoff < Respa interior cutoff + +One or more pairwise cutoffs are too short to use with the specified +rRESPA cutoffs. + +*/ diff --git a/examples/plugins/zero2plugin.cpp b/examples/plugins/zero2plugin.cpp new file mode 100644 index 0000000000..cd3c024219 --- /dev/null +++ b/examples/plugins/zero2plugin.cpp @@ -0,0 +1,78 @@ + +#include "lammpsplugin.h" +#include "version.h" + +#include + +#include "angle_zero2.h" +#include "bond_zero2.h" +#include "dihedral_zero2.h" +#include "improper_zero2.h" +#include "pair_zero2.h" + +using namespace LAMMPS_NS; + +static Pair *pairzerocreator(LAMMPS *lmp) +{ + return new PairZero2(lmp); +} + +static Bond *bondzerocreator(LAMMPS *lmp) +{ + return new BondZero2(lmp); +} + +static Angle *anglezerocreator(LAMMPS *lmp) +{ + return new AngleZero2(lmp); +} + +static Dihedral *dihedralzerocreator(LAMMPS *lmp) +{ + return new DihedralZero2(lmp); +} + +static Improper *improperzerocreator(LAMMPS *lmp) +{ + return new ImproperZero2(lmp); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + // register zero2 pair style + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "zero2"; + plugin.info = "Zero2 variant pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &pairzerocreator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); + + // register zero2 bond style + plugin.style = "bond"; + plugin.info = "Zero2 variant bond style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &bondzerocreator; + (*register_plugin)(&plugin, lmp); + + // register zero2 angle style + plugin.style = "angle"; + plugin.info = "Zero2 variant angle style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &anglezerocreator; + (*register_plugin)(&plugin, lmp); + + // register zero2 dihedral style + plugin.style = "dihedral"; + plugin.info = "Zero2 variant dihedral style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &dihedralzerocreator; + (*register_plugin)(&plugin, lmp); + + // register zero2 improper style + plugin.style = "improper"; + plugin.info = "Zero2 variant improper style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &improperzerocreator; + (*register_plugin)(&plugin, lmp); +} diff --git a/examples/python/in.fix_python_invoke_neighlist b/examples/python/in.fix_python_invoke_neighlist index af0399ae1f..f45a92c510 100644 --- a/examples/python/in.fix_python_invoke_neighlist +++ b/examples/python/in.fix_python_invoke_neighlist @@ -33,7 +33,7 @@ def post_force_callback(lmp, v): print(pid_prefix, "### POST_FORCE ###", t) #mylist = L.numpy.get_neighlist(0) - idx = L.find_pair_neighlist("lj/cut", request=0) + idx = L.find_pair_neighlist("lj/cut", reqid=0) mylist = L.numpy.get_neighlist(idx) print(pid_prefix, mylist) nlocal = L.extract_global("nlocal") diff --git a/examples/python/py_nve.py b/examples/python/py_nve.py index 9ff7c0978b..740668b850 100644 --- a/examples/python/py_nve.py +++ b/examples/python/py_nve.py @@ -1,7 +1,5 @@ from __future__ import print_function -from lammps import lammps, LAMMPS_INT, LAMMPS_DOUBLE -import ctypes -import traceback +from lammps import lammps import numpy as np class LAMMPSFix(object): @@ -80,36 +78,30 @@ class NVE_Opt(LAMMPSFixMove): self.ntypes = self.lmp.extract_global("ntypes") self.dtv = dt self.dtf = 0.5 * dt * ftm2v - self.mass = self.lmp.numpy.extract_atom("mass") def initial_integrate(self, vflag): - nlocal = self.lmp.extract_global("nlocal") + mass = self.lmp.numpy.extract_atom("mass") atype = self.lmp.numpy.extract_atom("type") x = self.lmp.numpy.extract_atom("x") v = self.lmp.numpy.extract_atom("v") f = self.lmp.numpy.extract_atom("f") dtf = self.dtf dtv = self.dtv - mass = self.mass dtfm = dtf / np.take(mass, atype) - dtfm.reshape((nlocal, 1)) for d in range(x.shape[1]): - v[:,d] += dtfm[:,0] * f[:,d] + v[:,d] += dtfm * f[:,d] x[:,d] += dtv * v[:,d] def final_integrate(self): - nlocal = self.lmp.extract_global("nlocal") mass = self.lmp.numpy.extract_atom("mass") atype = self.lmp.numpy.extract_atom("type") v = self.lmp.numpy.extract_atom("v") f = self.lmp.numpy.extract_atom("f") dtf = self.dtf - mass = self.mass dtfm = dtf / np.take(mass, atype) - dtfm.reshape((nlocal, 1)) for d in range(v.shape[1]): - v[:,d] += dtfm[:,0] * f[:,d] + v[:,d] += dtfm * f[:,d] diff --git a/examples/reax/HNS/README.txt b/examples/reax/HNS/README.txt index 95ffbb0ebb..2af416442c 100644 --- a/examples/reax/HNS/README.txt +++ b/examples/reax/HNS/README.txt @@ -15,7 +15,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov The file is read line by line looking for keywords to set up this run. It will read in the configuration given by the argument of the read_data command, which is supplied in this distribution. The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here. - More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section. + More information about each of the individual commands can be found online at www.lammps.org in the user manual section. *There are four free variables in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken. *The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z. @@ -27,7 +27,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov lmp_serial -in in.reaxc.hns -v x 2 -v y 2 -v z 2 -v t 100 2) LAMMPS Data file for crystalline HNS - This file matches the LAMMPS data format, more information about this data structure can be found at lammps.sandia.gov + This file matches the LAMMPS data format, more information about this data structure can be found at www.lammps.org This particular data file is of the energetic material Hexanitrostilbene (HNS) with atom_style charge (id type q x y z). The file contains eight molecules (2 unit cells). diff --git a/examples/srd/in.srd.mixture b/examples/srd/in.srd.mixture index ff6e6f5b72..6a0100d800 100644 --- a/examples/srd/in.srd.mixture +++ b/examples/srd/in.srd.mixture @@ -62,7 +62,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/fortran/lammps.f90 b/fortran/lammps.f90 index 9e6ca22d5a..21909e1288 100644 --- a/fortran/lammps.f90 +++ b/fortran/lammps.f90 @@ -1,6 +1,6 @@ ! ------------------------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator -! http://lammps.sandia.gov, Sandia National Laboratories +! https://www.lammps.org/ Sandia National Laboratories ! Steve Plimpton, sjplimp@sandia.gov ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/lib/README b/lib/README index d89490e202..2b7a38f5db 100644 --- a/lib/README +++ b/lib/README @@ -19,39 +19,43 @@ atc atomistic-to-continuum methods, USER-ATC package from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia) awpmd antisymmetrized wave packet molecular dynamics, AWPMD package from Ilya Valuev (JIHT RAS) -colvars collective variable module (Metadynamics, ABF and more) +colvars collective variable module (Metadynamics, ABF and more) from Giacomo Fiorin and Jerome Henin (ICMS, Temple U) compress hook to system lib for performing I/O compression, COMPRESS pkg - from Axel Kohlmeyer (Temple U) -gpu general GPU routines, GPU package - from Mike Brown (ORNL) + from Axel Kohlmeyer (Temple U) +gpu general GPU routines, GPU package + from Mike Brown (ORNL) h5md ch5md library for output of MD data in HDF5 format from Pierre de Buyl (KU Leuven) +hdnnp hooks to n2p2, neural network potential package, used by USER-HDNNP + from Andreas Singraber kim hooks to the KIM library, used by KIM package from Ryan Elliott and Ellad Tadmor (U Minn) kokkos Kokkos package for GPU and many-core acceleration from Kokkos development team (Sandia) linalg set of BLAS and LAPACK routines needed by USER-ATC package - from Axel Kohlmeyer (Temple U) + from Axel Kohlmeyer (Temple U) message client/server communication library via MPI, sockets, files - from Steve Plimpton (Sandia) + from Steve Plimpton (Sandia) molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package from Axel Kohlmeyer (Temple U) and the VMD development team mscg hooks to the MSCG library, used by fix_mscg command from Jacob Wagner and Greg Voth group (U Chicago) netcdf hooks to a NetCDF library installed on your system from Lars Pastewka (Karlsruhe Institute of Technology) -poems POEMS rigid-body integration package, POEMS package +plugin settings to load styles into LAMMPS from plugins + from Axel Kohlmeyer (Temple U) +poems POEMS rigid-body integration package, POEMS package from Rudranarayan Mukherjee (RPI) python hooks to the system Python library, used by the PYTHON package from the LAMMPS development team -qmmm quantum mechanics/molecular mechanics coupling interface +qmmm quantum mechanics/molecular mechanics coupling interface from Axel Kohlmeyer (Temple U) quip interface to QUIP/libAtoms framework, USER-QUIP package from Albert Bartok-Partay and Gabor Csanyi (U Cambridge) smd hooks to Eigen library, used by USER-SMD package from Georg Ganzenmueller (Ernst Mach Institute, Germany) voronoi hooks to the Voro++ library, used by compute voronoi/atom command - from Daniel Schwen (LANL) + from Daniel Schwen (LANL) vtk hooks to the VTK library, used by dump custom/vtk command from Richard Berger (JKU) diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp index 5727af1904..b123331ee7 100644 --- a/lib/atc/LammpsInterface.cpp +++ b/lib/atc/LammpsInterface.cpp @@ -26,6 +26,7 @@ #include "bond.h" // bond potentials #include "comm.h" // #include "fix.h" +#include "utils.h" // ATC includes #include "ATC_Error.h" @@ -47,6 +48,7 @@ using std::pair; using std::string; using std::set; using LAMMPS_NS::bigint; +using LAMMPS_NS::utils::read_lines_from_file; namespace ATC { @@ -236,7 +238,7 @@ std::string LammpsInterface::read_file(std::string filename) const std::stringstream s; bool eof = false; while ( ! eof) { - eof = lammps_->comm->read_lines_from_file(fp,1,MAXLINE,buffer); + eof = read_lines_from_file(fp,1,MAXLINE,buffer,comm_rank(),lammps_->world); s << buffer; } fclose(fp); diff --git a/lib/gpu/Makefile.cuda b/lib/gpu/Makefile.cuda index 7020f18cf3..e02501d080 100644 --- a/lib/gpu/Makefile.cuda +++ b/lib/gpu/Makefile.cuda @@ -45,7 +45,7 @@ CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC CUDA_LINK = $(CUDA_LIB) -lcudart -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) BIN2C = $(CUDA_HOME)/bin/bin2c @@ -103,7 +103,6 @@ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation diff --git a/lib/gpu/Makefile.cuda_mps b/lib/gpu/Makefile.cuda_mps index 21aac89151..f52bd07fcf 100644 --- a/lib/gpu/Makefile.cuda_mps +++ b/lib/gpu/Makefile.cuda_mps @@ -44,7 +44,7 @@ CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC CUDA_LINK = $(CUDA_LIB) -lcudart -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) BIN2C = $(CUDA_HOME)/bin/bin2c @@ -102,7 +102,6 @@ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation diff --git a/lib/gpu/Makefile.hip b/lib/gpu/Makefile.hip index dbdef433ec..a736988596 100644 --- a/lib/gpu/Makefile.hip +++ b/lib/gpu/Makefile.hip @@ -1,6 +1,6 @@ # /* ---------------------------------------------------------------------- # Generic Linux Makefile for HIP -# - export HIP_PLATFORM=hcc (or nvcc) before execution +# - export HIP_PLATFORM=amd (or nvcc) before execution # - change HIP_ARCH for your GPU # ------------------------------------------------------------------------- */ @@ -42,6 +42,10 @@ ifeq (hcc,$(HIP_PLATFORM)) HIP_OPTS += -ffast-math # possible values: gfx803,gfx900,gfx906 HIP_ARCH = gfx906 +else ifeq (amd,$(HIP_PLATFORM)) + HIP_OPTS += -ffast-math + # possible values: gfx803,gfx900,gfx906 + HIP_ARCH = gfx906 else ifeq (nvcc,$(HIP_PLATFORM)) HIP_OPTS += --use_fast_math HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \ diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index d3275b890f..56942d3f3c 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -30,7 +30,7 @@ $(OBJ_DIR): # Compilers and linkers -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ $(CUDPP_OPT) @@ -46,7 +46,6 @@ $(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \ $(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin $(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h - rm $(OBJ_DIR)/pppm_f.cubin $(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \ lal_pre_cuda_hip.h @@ -54,12 +53,10 @@ $(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h - rm $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation diff --git a/lib/gpu/Nvidia.makefile_multi b/lib/gpu/Nvidia.makefile_multi index 6716388562..ddbee4f2a1 100644 --- a/lib/gpu/Nvidia.makefile_multi +++ b/lib/gpu/Nvidia.makefile_multi @@ -29,7 +29,7 @@ $(OBJ_DIR): # Compilers and linkers -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ $(CUDPP_OPT) @@ -54,7 +54,6 @@ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation diff --git a/lib/gpu/README b/lib/gpu/README index dfffe11b81..3185db3af6 100644 --- a/lib/gpu/README +++ b/lib/gpu/README @@ -29,7 +29,7 @@ LAMMPS styles and neighbor list builds using CUDA, OpenCL, or ROCm HIP. Pair styles supported by this library are marked in the list of Pair style potentials with a "g". See the online version at: -https://lammps.sandia.gov/doc/Commands_pair.html +https://docs.lammps.org/Commands_pair.html In addition the (plain) pppm kspace style is supported as well. @@ -212,8 +212,8 @@ additionally requires cub (https://nvlabs.github.io/cub). Download and extract the cub directory to lammps/lib/gpu/ or specify an appropriate path in lammps/lib/gpu/Makefile.hip. 2. In Makefile.hip it is possible to specify the target platform via -export HIP_PLATFORM=hcc or HIP_PLATFORM=nvcc as well as the target -architecture (gfx803, gfx900, gfx906 etc.) +export HIP_PLATFORM=amd (ROCm >= 4.1), HIP_PLATFORM=hcc (ROCm <= 4.0) +or HIP_PLATFORM=nvcc as well as the target architecture (gfx803, gfx900, gfx906 etc.) 3. If your MPI implementation does not support `mpicxx --showme` command, it is required to specify the corresponding MPI compiler and linker flags in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip. @@ -278,4 +278,3 @@ and Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High Performance Computers - Three-Body Potentials. Computer Physics Communications. 2013. 184: p. 2785–2793. - diff --git a/lib/gpu/geryon/hip_device.h b/lib/gpu/geryon/hip_device.h index d3917ed0cf..11100cbea1 100644 --- a/lib/gpu/geryon/hip_device.h +++ b/lib/gpu/geryon/hip_device.h @@ -8,10 +8,6 @@ #ifndef HIP_DEVICE #define HIP_DEVICE -// workaround after GPU package Feb2021 update -// todo: make new neighbor code work with HIP -#define LAL_USE_OLD_NEIGHBOR - #include #include #include diff --git a/lib/gpu/geryon/hip_texture.h b/lib/gpu/geryon/hip_texture.h index 9117adc879..8738f6e2ea 100644 --- a/lib/gpu/geryon/hip_texture.h +++ b/lib/gpu/geryon/hip_texture.h @@ -128,12 +128,12 @@ class UCL_Const { _cq)); } /// Get device ptr associated with object - inline const void* begin() const { return &_global; } + inline const hipDeviceptr_t * begin() const { return &_global; } inline void clear() {} private: hipStream_t _cq; - void* _global; + hipDeviceptr_t _global; size_t _global_bytes; friend class UCL_Kernel; }; diff --git a/lib/gpu/geryon/nvd_device.h b/lib/gpu/geryon/nvd_device.h index 87d5faaf48..52b2ed478e 100644 --- a/lib/gpu/geryon/nvd_device.h +++ b/lib/gpu/geryon/nvd_device.h @@ -24,10 +24,6 @@ #ifndef NVD_DEVICE #define NVD_DEVICE -// workaround after GPU package Feb2021 update -// todo: make new neighbor code work with CUDA -#define LAL_USE_OLD_NEIGHBOR - #include #include #include diff --git a/lib/gpu/geryon/nvd_kernel.h b/lib/gpu/geryon/nvd_kernel.h index c31b8cdf9b..798b12e53c 100644 --- a/lib/gpu/geryon/nvd_kernel.h +++ b/lib/gpu/geryon/nvd_kernel.h @@ -108,17 +108,14 @@ class UCL_Program { std::cerr << log << std::endl << "----------------------------------------------------------\n\n"; #endif - if (foutput != NULL) { - fprintf(foutput,"\n\n"); - fprintf(foutput, - "----------------------------------------------------------\n"); - fprintf(foutput," UCL Error: Error compiling PTX Program...\n"); - fprintf(foutput, - "----------------------------------------------------------\n"); - fprintf(foutput,"%s\n",log); - fprintf(foutput, - "----------------------------------------------------------\n"); - fprintf(foutput,"\n\n"); + if (foutput != nullptr) { + fprintf(foutput,"\n\n"); + fprintf(foutput, "----------------------------------------------------------\n"); + fprintf(foutput, " UCL Error: Error compiling PTX Program...\n"); + fprintf(foutput, "----------------------------------------------------------\n"); + fprintf(foutput, "%s\n",log->c_str()); + fprintf(foutput, "----------------------------------------------------------\n"); + fprintf(foutput,"\n\n"); } return UCL_COMPILE_ERROR; } diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h index 435ee24dd3..a8e5020f00 100644 --- a/lib/gpu/geryon/ocl_device.h +++ b/lib/gpu/geryon/ocl_device.h @@ -29,7 +29,7 @@ #include #ifndef CL_TARGET_OPENCL_VERSION -#define CL_TARGET_OPENCL_VERSION 210 +#define CL_TARGET_OPENCL_VERSION 300 #endif #ifdef __APPLE__ @@ -728,6 +728,9 @@ void UCL_Device::print_all(std::ostream &out) { out << "\nDevice " << i << ": \"" << name(i).c_str() << "\"\n"; out << " Type of device: " << device_type_name(i).c_str() << std::endl; + out << " Supported OpenCL Version: " + << _properties[i].cl_device_version / 100 << "." + << _properties[i].cl_device_version % 100 << std::endl; out << " Is a subdevice: "; if (is_subdevice(i)) out << "Yes\n"; @@ -796,6 +799,16 @@ void UCL_Device::print_all(std::ostream &out) { out << "Yes\n"; else out << "No\n"; + out << " Subgroup support: "; + if (_properties[i].has_subgroup_support) + out << "Yes\n"; + else + out << "No\n"; + out << " Shuffle support: "; + if (_properties[i].has_shuffle_support) + out << "Yes\n"; + else + out << "No\n"; } } } diff --git a/lib/gpu/geryon/ocl_macros.h b/lib/gpu/geryon/ocl_macros.h index 0e9ce78389..5e5a190ede 100644 --- a/lib/gpu/geryon/ocl_macros.h +++ b/lib/gpu/geryon/ocl_macros.h @@ -5,7 +5,7 @@ #include #ifndef CL_TARGET_OPENCL_VERSION -#define CL_TARGET_OPENCL_VERSION 210 +#define CL_TARGET_OPENCL_VERSION 300 #endif #ifdef __APPLE__ diff --git a/lib/gpu/lal_base_atomic.cpp b/lib/gpu/lal_base_atomic.cpp index d35919105d..6aad138aa1 100644 --- a/lib/gpu/lal_base_atomic.cpp +++ b/lib/gpu/lal_base_atomic.cpp @@ -335,7 +335,7 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_charge.cpp b/lib/gpu/lal_base_charge.cpp index b0d08e4df7..9045420425 100644 --- a/lib/gpu/lal_base_charge.cpp +++ b/lib/gpu/lal_base_charge.cpp @@ -348,7 +348,7 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_dipole.cpp b/lib/gpu/lal_base_dipole.cpp index 9781065b13..439637cbde 100644 --- a/lib/gpu/lal_base_dipole.cpp +++ b/lib/gpu/lal_base_dipole.cpp @@ -356,7 +356,7 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp index 4b6a964bfb..d3c3353415 100644 --- a/lib/gpu/lal_base_dpd.cpp +++ b/lib/gpu/lal_base_dpd.cpp @@ -356,7 +356,7 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_ellipsoid.cpp b/lib/gpu/lal_base_ellipsoid.cpp index 98411a8033..2e22b2f602 100644 --- a/lib/gpu/lal_base_ellipsoid.cpp +++ b/lib/gpu/lal_base_ellipsoid.cpp @@ -554,7 +554,7 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_lj_fast.max_subgroup_size(_block_size); mx_subgroup_sz = std::min(mx_subgroup_sz, k_ellipsoid.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_sphere_ellipsoid.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_three.cpp b/lib/gpu/lal_base_three.cpp index 660385eb56..15ef20230d 100644 --- a/lib/gpu/lal_base_three.cpp +++ b/lib/gpu/lal_base_three.cpp @@ -461,7 +461,7 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair.max_subgroup_size(_block_size); mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_center.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_end.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_charmm.cpp b/lib/gpu/lal_charmm.cpp index 811a431cc7..a78043af40 100644 --- a/lib/gpu/lal_charmm.cpp +++ b/lib/gpu/lal_charmm.cpp @@ -150,7 +150,7 @@ int CHARMMT::loop(const int eflag, const int vflag) { &_cut_coul_innersq, &this->_threads_per_atom); } else { this->k_pair.set_size(GX,BX); - this->k_pair.run(&this->atom->x, &ljd, &sp_lj, + this->k_pair.run(&this->atom->x, &lj1, &_lj_types, &sp_lj, &this->nbor->dev_nbor, this->_nbor_data, &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->atom->q, diff --git a/lib/gpu/lal_charmm.cu b/lib/gpu/lal_charmm.cu index 304dc34e8b..589d9adc91 100644 --- a/lib/gpu/lal_charmm.cu +++ b/lib/gpu/lal_charmm.cu @@ -29,7 +29,8 @@ _texture(q_tex, int2); #endif __kernel void k_charmm(const __global numtyp4 *restrict x_, - const __global numtyp2 *restrict ljd, + const __global numtyp4 *restrict lj1, + const int lj_types, const __global numtyp *restrict sp_lj, const __global int *dev_nbor, const __global int *dev_packed, @@ -88,20 +89,14 @@ __kernel void k_charmm(const __global numtyp4 *restrict x_, numtyp delz = ix.z-jx.z; numtyp rsq = delx*delx+dely*dely+delz*delz; + int mtype=itype*lj_types+jtype; if (rsq cut_lj_innersq) { switch1 = (cut_ljsq-rsq); numtyp switch2 = (numtyp)12.0*rsq*switch1*(rsq-cut_lj_innersq)* @@ -109,7 +104,7 @@ __kernel void k_charmm(const __global numtyp4 *restrict x_, switch1 *= switch1; switch1 *= (cut_ljsq+(numtyp)2.0*rsq-(numtyp)3.0*cut_lj_innersq)* denom_lj; - switch2 *= lj3-lj4; + switch2 *= r6inv*(lj1[mtype].z*r6inv-lj1[mtype].w); force_lj = force_lj*switch1+switch2; } } else @@ -137,7 +132,7 @@ __kernel void k_charmm(const __global numtyp4 *restrict x_, if (EVFLAG && eflag) { e_coul += forcecoul; if (rsq < cut_ljsq) { - numtyp e=lj3-lj4; + numtyp e=r6inv*(lj1[mtype].z*r6inv-lj1[mtype].w); if (rsq > cut_lj_innersq) e *= switch1; energy+=factor_lj*e; diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index a65c3d8810..e2b5b9cdb5 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -18,6 +18,7 @@ #include #include #include +#include #if (LAL_USE_OMP == 1) #include #endif @@ -777,6 +778,7 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer &ans, #ifdef USE_OPENCL // Workaround for timing issue on Intel OpenCL if (times[3] > 80e6) times[3]=0.0; + if (times[5] > 80e6) times[5]=0.0; #endif if (replica_me()==0) @@ -1025,6 +1027,22 @@ Device global_device; } using namespace LAMMPS_AL; + +bool lmp_has_gpu_device() +{ + UCL_Device gpu; + return (gpu.num_platforms() > 0); +} + +std::string lmp_gpu_device_info() +{ + std::ostringstream out; + UCL_Device gpu; + if (gpu.num_platforms() > 0) + gpu.print_all(out); + return out.str(); +} + int lmp_init_device(MPI_Comm world, MPI_Comm replica, const int ngpu, const int first_gpu_id, const int gpu_mode, const double particle_split, const int t_per_atom, @@ -1061,7 +1079,7 @@ bool lmp_gpu_config(const std::string &category, const std::string &setting) return setting == "opencl"; #elif defined(USE_HIP) return setting == "hip"; -#elif defined(USE_CUDA) +#elif defined(USE_CUDA) || defined(USE_CUDART) return setting == "cuda"; #endif return false; diff --git a/lib/gpu/lal_eam.cpp b/lib/gpu/lal_eam.cpp index cdafe72898..2c0d63f7bf 100644 --- a/lib/gpu/lal_eam.cpp +++ b/lib/gpu/lal_eam.cpp @@ -46,7 +46,7 @@ template int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, double rdr, double rdrho, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, @@ -243,6 +243,12 @@ int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor, z2r_spline2_tex.get_texture(*(this->pair_program),"z2r_sp2_tex"); z2r_spline2_tex.bind_float(z2r_spline2,4); + UCL_H_Vec host_write(lj_types*lj_types,*(this->ucl_device), + UCL_WRITE_ONLY); + host_write.zero(); + cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq); + _allocated=true; this->_max_bytes=type2rhor_z2r.row_bytes() + type2frho.row_bytes() @@ -252,6 +258,7 @@ int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor, + frho_spline2.row_bytes() + z2r_spline1.row_bytes() + z2r_spline2.row_bytes() + + cutsq.row_bytes() + _fp.device.row_bytes(); return 0; } @@ -270,6 +277,7 @@ void EAMT::clear() { frho_spline2.clear(); z2r_spline1.clear(); z2r_spline2.clear(); + cutsq.clear(); _fp.clear(); @@ -477,7 +485,7 @@ void EAMT::compute2(int *ilist, const bool eflag, const bool vflag, } // --------------------------------------------------------------------------- -// Calculate per-atom energies and forces +// Calculate per-atom fp // --------------------------------------------------------------------------- template int EAMT::loop(const int eflag, const int vflag) { @@ -498,7 +506,7 @@ int EAMT::loop(const int eflag, const int vflag) { k_energy_sel->set_size(GX,BX); k_energy_sel->run(&this->atom->x, &type2rhor_z2r, &type2frho, - &rhor_spline2, &frho_spline1,&frho_spline2, + &rhor_spline2, &frho_spline1, &frho_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &_fp, &this->ans->engv, &eflag, &ainum, &nbor_pitch, &_ntypes, &_cutforcesq, &_rdr, &_rdrho, @@ -506,7 +514,7 @@ int EAMT::loop(const int eflag, const int vflag) { } else { this->k_energy.set_size(GX,BX); this->k_energy.run(&this->atom->x, &type2rhor_z2r, &type2frho, - &rhor_spline2, &frho_spline1, &frho_spline2, + &rhor_spline2, &frho_spline1, &frho_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &_fp, &this->ans->engv,&eflag, &ainum, &nbor_pitch, &_ntypes, &_cutforcesq, &_rdr, &_rdrho, &_rhomax, &_nrho, @@ -545,7 +553,7 @@ void EAMT::loop2(const bool _eflag, const bool _vflag) { if (shared_types) { this->k_pair_sel->set_size(GX,BX); this->k_pair_sel->run(&this->atom->x, &_fp, &type2rhor_z2r, - &rhor_spline1, &z2r_spline1, &z2r_spline2, + &rhor_spline1, &z2r_spline1, &z2r_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &_cutforcesq, &_rdr, @@ -553,7 +561,7 @@ void EAMT::loop2(const bool _eflag, const bool _vflag) { } else { this->k_pair.set_size(GX,BX); this->k_pair.run(&this->atom->x, &_fp, &type2rhor_z2r, &rhor_spline1, - &z2r_spline1, &z2r_spline2, &this->nbor->dev_nbor, + &z2r_spline1, &z2r_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &_ntypes, &_cutforcesq, &_rdr, &_nr, diff --git a/lib/gpu/lal_eam.cu b/lib/gpu/lal_eam.cu index 3955f3cc8a..dc518fb550 100644 --- a/lib/gpu/lal_eam.cu +++ b/lib/gpu/lal_eam.cu @@ -216,6 +216,7 @@ __kernel void k_energy(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict rhor_spline2, const __global numtyp4 *restrict frho_spline1, const __global numtyp4 *restrict frho_spline2, + const __global numtyp *restrict cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global numtyp *restrict fp_, @@ -225,7 +226,7 @@ __kernel void k_energy(const __global numtyp4 *restrict x_, const numtyp rdr, const numtyp rdrho, const numtyp rhomax, const int nrho, const int nr, const int t_per_atom) { - int tid, ii, offset, i, itype; + int tid, ii, offset, i, itype, tfrho; atom_info(t_per_atom,ii,tid,offset); int n_stride; @@ -242,6 +243,7 @@ __kernel void k_energy(const __global numtyp4 *restrict x_, numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i]; itype=ix.w; + tfrho=type2frho[itype]; for ( ; nbor(numtyp)0) { numtyp p = ucl_sqrt(rsq)*rdr + (numtyp)1.0; int m=p; m = MIN(m,nr-1); @@ -270,7 +273,6 @@ __kernel void k_energy(const __global numtyp4 *restrict x_, } } // for nbor } // if ii - const numtyp tfrho=type2frho[itype]; store_energy_fp(rho,energy,ii,inum,tid,t_per_atom,offset, eflag,vflag,engv,rdrho,nrho,i,rhomax,tfrho); } @@ -281,6 +283,7 @@ __kernel void k_energy_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict rhor_spline2, const __global numtyp4 *restrict frho_spline1, const __global numtyp4 *restrict frho_spline2, + const __global numtyp *restrict cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global numtyp *restrict fp_, @@ -291,7 +294,7 @@ __kernel void k_energy_fast(const __global numtyp4 *restrict x_, const numtyp rdrho, const numtyp rhomax, const int nrho, const int nr, const int t_per_atom) { - int tid, ii, offset, i, itype; + int tid, ii, offset, i, itype, tfrho; atom_info(t_per_atom,ii,tid,offset); #ifndef ONETYPE @@ -305,9 +308,9 @@ __kernel void k_energy_fast(const __global numtyp4 *restrict x_, } __syncthreads(); #else - const numtyp type2rhor_z2rx= + const int type2rhor_z2rx= type2rhor_z2r_in[ONETYPE*MAX_SHARED_TYPES+ONETYPE].x; - const numtyp tfrho=type2frho_in[ONETYPE]; + tfrho=type2frho_in[ONETYPE]; #endif int n_stride; @@ -325,6 +328,7 @@ __kernel void k_energy_fast(const __global numtyp4 *restrict x_, numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i]; #ifndef ONETYPE itype=ix.w; + tfrho=type2frho[itype]; #endif for ( ; nbor(numtyp)0) { numtyp p = ucl_sqrt(rsq)*rdr + (numtyp)1.0; int m=p; m = MIN(m,nr-1); @@ -347,7 +352,7 @@ __kernel void k_energy_fast(const __global numtyp4 *restrict x_, p = MIN(p,(numtyp)1.0); #ifndef ONETYPE - int jtype=fast_mul((int)MAX_SHARED_TYPES,jx.w); + int jtype = fast_mul((int)MAX_SHARED_TYPES,jx.w); int mtype = jtype+itype; int index = type2rhor_z2r[mtype].x*(nr+1)+m; #else @@ -358,9 +363,6 @@ __kernel void k_energy_fast(const __global numtyp4 *restrict x_, } } // for nbor } // if ii - #ifndef ONETYPE - const numtyp tfrho=type2frho[itype]; - #endif store_energy_fp(rho,energy,ii,inum,tid,t_per_atom,offset, eflag,vflag,engv,rdrho,nrho,i,rhomax,tfrho); } @@ -371,6 +373,7 @@ __kernel void k_eam(const __global numtyp4 *restrict x_, const __global numtyp4 *rhor_spline1, const __global numtyp4 *z2r_spline1, const __global numtyp4 *z2r_spline2, + const __global numtyp *cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global acctyp4 *ans, @@ -416,7 +419,8 @@ __kernel void k_eam(const __global numtyp4 *restrict x_, numtyp delz = ix.z-jx.z; numtyp rsq = delx*delx+dely*dely+delz*delz; - if (rsq(numtyp)0) { numtyp r = ucl_sqrt(rsq); numtyp p = r*rdr + (numtyp)1.0; int m=p; @@ -480,6 +484,7 @@ __kernel void k_eam_fast(const __global numtyp4 *x_, const __global numtyp4 *rhor_spline1, const __global numtyp4 *z2r_spline1, const __global numtyp4 *z2r_spline2, + const __global numtyp *cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global acctyp4 *ans, @@ -498,8 +503,8 @@ __kernel void k_eam_fast(const __global numtyp4 *x_, __syncthreads(); #else const int oi=ONETYPE*MAX_SHARED_TYPES+ONETYPE; - const numtyp type2rhor_z2rx=type2rhor_z2r_in[oi].x; - const numtyp type2rhor_z2ry=type2rhor_z2r_in[oi].y; + const int type2rhor_z2rx=type2rhor_z2r_in[oi].x; + const int type2rhor_z2ry=type2rhor_z2r_in[oi].y; #endif int n_stride; @@ -542,7 +547,8 @@ __kernel void k_eam_fast(const __global numtyp4 *x_, numtyp delz = ix.z-jx.z; numtyp rsq = delx*delx+dely*dely+delz*delz; - if (rsq(numtyp)0) { numtyp r = ucl_sqrt(rsq); numtyp p = r*rdr + (numtyp)1.0; int m=p; diff --git a/lib/gpu/lal_eam.h b/lib/gpu/lal_eam.h index 3cbaeac0b8..efc38537d6 100644 --- a/lib/gpu/lal_eam.h +++ b/lib/gpu/lal_eam.h @@ -40,8 +40,8 @@ class EAM : public BaseAtomic { * - -5 Double precision is not supported on card **/ int init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, - double ***host_z2r_spline, double ***host_frho_spline, double rdr, - double rdrho, double rhomax, int nrhor, int nrho, int nz2r, + double ***host_z2r_spline, double ***host_frho_spline, double** host_cutsq, + double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, const double gpu_split, FILE *_screen); @@ -112,6 +112,8 @@ class EAM : public BaseAtomic { UCL_D_Vec frho_spline1, frho_spline2; UCL_D_Vec rhor_spline1, rhor_spline2; + UCL_D_Vec cutsq; + numtyp _cutforcesq,_rdr,_rdrho, _rhomax; int _nfrho,_nrhor,_nrho,_nz2r,_nr; diff --git a/lib/gpu/lal_eam_alloy_ext.cpp b/lib/gpu/lal_eam_alloy_ext.cpp index f7c4986e68..5a3dfb9d6d 100644 --- a/lib/gpu/lal_eam_alloy_ext.cpp +++ b/lib/gpu/lal_eam_alloy_ext.cpp @@ -30,7 +30,7 @@ static EAM EAMALMF; int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, @@ -66,7 +66,7 @@ int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq, if (world_me==0) init_ok=EAMALMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, nz2r, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); @@ -86,7 +86,7 @@ int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq, if (gpu_rank==i && world_me!=0) init_ok=EAMALMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); diff --git a/lib/gpu/lal_eam_ext.cpp b/lib/gpu/lal_eam_ext.cpp index 3010e0ea7f..a884335bd9 100644 --- a/lib/gpu/lal_eam_ext.cpp +++ b/lib/gpu/lal_eam_ext.cpp @@ -30,7 +30,7 @@ static EAM EAMMF; int eam_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, @@ -66,7 +66,7 @@ int eam_gpu_init(const int ntypes, double host_cutforcesq, if (world_me==0) init_ok=EAMMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, nz2r, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); @@ -86,7 +86,7 @@ int eam_gpu_init(const int ntypes, double host_cutforcesq, if (gpu_rank==i && world_me!=0) init_ok=EAMMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); diff --git a/lib/gpu/lal_eam_fs_ext.cpp b/lib/gpu/lal_eam_fs_ext.cpp index 205b601562..5aad871237 100644 --- a/lib/gpu/lal_eam_fs_ext.cpp +++ b/lib/gpu/lal_eam_fs_ext.cpp @@ -30,7 +30,7 @@ static EAM EAMFSMF; int eam_fs_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, @@ -66,7 +66,7 @@ int eam_fs_gpu_init(const int ntypes, double host_cutforcesq, if (world_me==0) init_ok=EAMFSMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, nz2r, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); @@ -86,7 +86,7 @@ int eam_fs_gpu_init(const int ntypes, double host_cutforcesq, if (gpu_rank==i && world_me!=0) init_ok=EAMFSMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); diff --git a/lib/gpu/lal_lj_cubic.cu b/lib/gpu/lal_lj_cubic.cu index a91326d521..df3398afd7 100644 --- a/lib/gpu/lal_lj_cubic.cu +++ b/lib/gpu/lal_lj_cubic.cu @@ -26,10 +26,10 @@ _texture_2d( pos_tex,int4); // LJ quantities scaled by epsilon and rmin = sigma*2^1/6 (see src/pair_lj_cubic.h) -#define _RT6TWO (numtyp)1.1224621 -#define _PHIS (numtyp)-0.7869823 /* energy at s */ -#define _DPHIDS (numtyp)2.6899009 /* gradient at s */ -#define _A3 (numtyp)27.93357 /* cubic coefficient */ +#define _RT6TWO (numtyp)1.1224620483093730 /* 2^1/6 */ +#define _PHIS (numtyp)-0.7869822485207097 /* energy at s */ +#define _DPHIDS (numtyp)2.6899008972047196 /* gradient at s */ +#define _A3 (numtyp)27.9335700460986445 /* cubic coefficient */ __kernel void k_lj_cubic(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, diff --git a/lib/gpu/lal_lj_smooth.cpp b/lib/gpu/lal_lj_smooth.cpp new file mode 100644 index 0000000000..42ffdabcf2 --- /dev/null +++ b/lib/gpu/lal_lj_smooth.cpp @@ -0,0 +1,192 @@ +/*************************************************************************** + lj_smooth.cpp + ------------------- + Gurgen Melikyan (HSE University) + Class for acceleration of the lj/smooth pair style. + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + begin : + email : gkmeliyan@edu.hse.ru + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "lj_smooth_cl.h" +#elif defined(USE_CUDART) +const char *lj_smooth=0; +#else +#include "lj_smooth_cubin.h" +#endif + +#include "lal_lj_smooth.h" +#include +namespace LAMMPS_AL { +#define LJSMOOTHT LJSMOOTH + +extern Device device; + +template +LJSMOOTHT::LJSMOOTH() : BaseAtomic(), _allocated(false) { +} + +template +LJSMOOTHT::~LJSMOOTH() { + clear(); +} + +template +int LJSMOOTHT::bytes_per_atom(const int max_nbors) const { + return this->bytes_per_atom_atomic(max_nbors); +} + +template +int LJSMOOTHT::init(const int ntypes, + double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_inner_sq) { + const int max_shared_types=this->device->max_shared_types(); + + int onetype=0; + #ifdef USE_OPENCL + if (maxspecial==0) + for (int i=1; i0) { + if (onetype>0) + onetype=-1; + else if (onetype==0) + onetype=i*max_shared_types+j; + } + if (onetype<0) onetype=0; + #endif + + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,lj_smooth,"k_lj_smooth",onetype); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + shared_types=false; + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + shared_types=true; + } + _lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2, + host_cutsq, cut_inner_sq); + + lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4, + host_offset); + + ljsw.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, + host_ljsw3,host_ljsw4); + + ljsw0.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack2(ntypes,lj_types,ljsw0,host_write,host_ljsw0,cut_inner); + + UCL_H_Vec dview; + sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY); + dview.view(host_special_lj,4,*(this->ucl_device)); + ucl_copy(sp_lj,dview,false); + + _allocated=true; + this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+ljsw.row_bytes()+ljsw0.row_bytes()+sp_lj.row_bytes(); + return 0; +} + +template +void LJSMOOTHT::reinit(const int ntypes, double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_inner_sq) { + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(_lj_types*_lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; i<_lj_types*_lj_types; i++) + host_write[i]=0.0; + + this->atom->type_pack4(ntypes,_lj_types,lj1,host_write,host_lj1,host_lj2, + host_cutsq,cut_inner_sq); + this->atom->type_pack4(ntypes,_lj_types,lj3,host_write,host_lj3,host_lj4, + host_offset); + this->atom->type_pack4(ntypes,_lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, + host_ljsw3,host_ljsw4); + this->atom->type_pack2(ntypes,_lj_types,ljsw0,host_write,host_ljsw0,cut_inner); +} + +template +void LJSMOOTHT::clear() { + if (!_allocated) + return; + _allocated=false; + + lj1.clear(); + lj3.clear(); + ljsw.clear(); + ljsw0.clear(); + sp_lj.clear(); + this->clear_atomic(); +} + +template +double LJSMOOTHT::host_memory_usage() const { + return this->host_memory_usage_atomic()+sizeof(LJSMOOTH); +} + +// --------------------------------------------------------------------------- +// Calculate energies, forces, and torques +// --------------------------------------------------------------------------- +template +int LJSMOOTHT::loop(const int eflag, const int vflag) { + // Compute the block size and grid size to keep all cores busy + const int BX=this->block_size(); + + int GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/this->_threads_per_atom))); + + int ainum=this->ans->inum(); + int nbor_pitch=this->nbor->nbor_pitch(); + this->time_pair.start(); + if (shared_types) { + this->k_pair_sel->set_size(GX,BX); + this->k_pair_sel->run(&this->atom->x, &lj1, &lj3, &ljsw, &ljsw0, &sp_lj, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, + &vflag, &ainum, &nbor_pitch, + &this->_threads_per_atom); + } else { + this->k_pair.set_size(GX,BX); + this->k_pair.run(&this->atom->x, &lj1, &lj3, &ljsw, &ljsw0, &_lj_types, &sp_lj, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, &vflag, + &ainum, &nbor_pitch, &this->_threads_per_atom); + } + this->time_pair.stop(); + return GX; +} + +template class LJSMOOTH; +} diff --git a/lib/gpu/lal_lj_smooth.cu b/lib/gpu/lal_lj_smooth.cu new file mode 100644 index 0000000000..d4a99ed3a7 --- /dev/null +++ b/lib/gpu/lal_lj_smooth.cu @@ -0,0 +1,259 @@ +// ************************************************************************** +// lj_smooth.cu +// ------------------- +// Gurgen Melikyan (HSE University) +// +// Device code for acceleration of the lj/smooth pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : +// email : gkmeliyan@edu.hse.ru +// *************************************************************************** + +#if defined(NV_KERNEL) || defined(USE_HIP) +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +_texture( pos_tex,float4); +#else +_texture_2d( pos_tex,int4); +#endif +#else +#define pos_tex x_ +#endif + +__kernel void k_lj_smooth(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict lj1, + const __global numtyp4 *restrict lj3, + const __global numtyp4 *restrict ljsw, + const __global numtyp2 *restrict ljsw0, + const int lj_types, + const __global numtyp *restrict sp_lj, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + int n_stride; + local_allocate_store_pair(); + + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp energy, virial[6]; + if (EVFLAG) { + energy=(acctyp)0; + for (int i=0; i<6; i++) virial[i]=(acctyp)0; + } + + if (ii +class LJSMOOTH : public BaseAtomic { + public: + LJSMOOTH(); + ~LJSMOOTH(); + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successful + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, + double **host_lj1, double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, + double **host_ljsw3, double **host_ljsw4, + double **cut_inner, double **cut_inner_sq); + + /// Send updated coeffs from host to device (to be compatible with fix adapt) + void reinit(const int ntypes, double **host_cutsq, + double **host_lj1, double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, + double **host_ljsw3, double **host_ljsw4, + double **cut_inner, double **cut_inner_sq); + + /// Clear all host and device data + /** \note This is called at the beginning of the init() routine **/ + void clear(); + + /// Returns memory usage on device per atom + int bytes_per_atom(const int max_nbors) const; + + /// Total host memory used by library for pair style + double host_memory_usage() const; + + // --------------------------- TYPE DATA -------------------------- + + /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = cut_inner_sq + UCL_D_Vec lj1; + /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset + UCL_D_Vec lj3; + /// ljsw.x = ljsw1, ljsw.y = ljsw2, ljsw.z = ljsw3, ljsw.w = ljsw4 + UCL_D_Vec ljsw; + /// ljsw0.x = ljsw0 ljsw0.y = cut_inner + UCL_D_Vec ljsw0; + /// Special LJ values + UCL_D_Vec sp_lj; + + /// If atom type constants fit in shared memory, use fast kernels + bool shared_types; + + /// Number of atom types + int _lj_types; + + private: + bool _allocated; + int loop(const int _eflag, const int _vflag); +}; + +} + +#endif diff --git a/lib/gpu/lal_lj_smooth_ext.cpp b/lib/gpu/lal_lj_smooth_ext.cpp new file mode 100644 index 0000000000..48dad74071 --- /dev/null +++ b/lib/gpu/lal_lj_smooth_ext.cpp @@ -0,0 +1,144 @@ +/*************************************************************************** + lj_smooth_ext.cpp + ------------------- + Gurgen Melikyan (HSE University) + + Functions for LAMMPS access to lj/smooth acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : gkmeliyan@edu.hse.ru + ***************************************************************************/ + +#include +#include +#include + +#include "lal_lj_smooth.h" + +using namespace std; +using namespace LAMMPS_AL; + +static LJSMOOTH LJSMTMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double *special_lj, const int inum, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { + LJSMTMF.clear(); + gpu_mode=LJSMTMF.device->gpu_mode(); + double gpu_split=LJSMTMF.device->particle_split(); + int first_gpu=LJSMTMF.device->first_device(); + int last_gpu=LJSMTMF.device->last_device(); + int world_me=LJSMTMF.device->world_me(); + int gpu_rank=LJSMTMF.device->gpu_rank(); + int procs_per_gpu=LJSMTMF.device->procs_per_gpu(); + + LJSMTMF.device->init_message(screen,"lj/smooth",first_gpu,last_gpu); + + bool message=false; + if (LJSMTMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=LJSMTMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, + host_lj4, offset, special_lj, inum, nall, max_nbors, + maxspecial, cell_size, gpu_split, screen, + host_ljsw0, host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); + + LJSMTMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + LJSMTMF.estimate_gpu_overhead(); + return init_ok; +} + +// --------------------------------------------------------------------------- +// Copy updated coeffs from host to device +// --------------------------------------------------------------------------- +void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { + int world_me=LJSMTMF.device->world_me(); + int gpu_rank=LJSMTMF.device->gpu_rank(); + int procs_per_gpu=LJSMTMF.device->procs_per_gpu(); + + if (world_me==0) + LJSMTMF.reinit(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, offset, host_ljsw0, host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); + LJSMTMF.device->world_barrier(); + + for (int i=0; igpu_barrier(); + } +} + +void ljsmt_gpu_clear() { + LJSMTMF.clear(); +} + +int ** ljsmt_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success) { + return LJSMTMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success); +} + +void ljsmt_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success) { + LJSMTMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success); +} + +double ljsmt_gpu_bytes() { + return LJSMTMF.host_memory_usage(); +} diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu index bd900d9244..f9dadb9651 100644 --- a/lib/gpu/lal_lj_tip4p_long.cu +++ b/lib/gpu/lal_lj_tip4p_long.cu @@ -35,6 +35,16 @@ _texture( q_tex,int2); #endif #else +#ifdef LAMMPS_SMALLBIG +#define tagint int +#endif +#ifdef LAMMPS_BIGBIG +#include "inttypes.h" +#define tagint int64_t +#endif +#ifdef LAMMPS_SMALLSMALL +#define tagint int +#endif #define pos_tex x_ #define q_tex q_ #endif diff --git a/lib/gpu/lal_neighbor.cpp b/lib/gpu/lal_neighbor.cpp index aabba49575..a0d2eaa8c3 100644 --- a/lib/gpu/lal_neighbor.cpp +++ b/lib/gpu/lal_neighbor.cpp @@ -740,6 +740,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum, // If binning on GPU, do this now if (_gpu_nbor==1) { + mn = _max_nbors; const numtyp i_cell_size=static_cast(1.0/_cell_size); const int neigh_block=_block_cell_id; const int GX=(int)ceil((float)nall/neigh_block); diff --git a/lib/gpu/lal_neighbor.h b/lib/gpu/lal_neighbor.h index 5939567a41..c1e1a87ef4 100644 --- a/lib/gpu/lal_neighbor.h +++ b/lib/gpu/lal_neighbor.h @@ -26,13 +26,17 @@ #if !defined(USE_OPENCL) && !defined(USE_HIP) #ifndef LAL_USE_OLD_NEIGHBOR -// Issue with incorrect results with CUDA 11.2 -#if (CUDA_VERSION > 11019) && (CUDA_VERSION < 11030) +// Issue with incorrect results with CUDA >= 11.2 +#if (CUDA_VERSION > 11019) #define LAL_USE_OLD_NEIGHBOR #endif #endif #endif +#if defined(USE_HIP) +#define LAL_USE_OLD_NEIGHBOR +#endif + namespace LAMMPS_AL { class Neighbor { diff --git a/lib/gpu/lal_neighbor_gpu.cu b/lib/gpu/lal_neighbor_gpu.cu index 2aca505396..6fd724b494 100644 --- a/lib/gpu/lal_neighbor_gpu.cu +++ b/lib/gpu/lal_neighbor_gpu.cu @@ -34,12 +34,16 @@ _texture_2d( pos_tex,int4); #endif #ifdef NV_KERNEL -#if (__CUDACC_VER_MAJOR__ == 11) && (__CUDACC_VER_MINOR__ == 2) -// Issue with incorrect results in CUDA 11.2 +#if (__CUDACC_VER_MAJOR__ == 11) && (__CUDACC_VER_MINOR__ >= 2) +// Issue with incorrect results in CUDA >= 11.2 #define LAL_USE_OLD_NEIGHBOR #endif #endif +#ifdef USE_HIP +#define LAL_USE_OLD_NEIGHBOR +#endif + __kernel void calc_cell_id(const numtyp4 *restrict x_, unsigned *restrict cell_id, int *restrict particle_id, @@ -115,7 +119,7 @@ __kernel void kernel_calc_cell_counts(const unsigned *restrict cell_id, #define tagint int #endif #ifdef LAMMPS_BIGBIG -#define tagint long long int +#define tagint long #endif #ifdef LAMMPS_SMALLSMALL #define tagint int diff --git a/lib/gpu/lal_pre_cuda_hip.h b/lib/gpu/lal_pre_cuda_hip.h index d37b4a94c2..dfb6229bed 100644 --- a/lib/gpu/lal_pre_cuda_hip.h +++ b/lib/gpu/lal_pre_cuda_hip.h @@ -30,7 +30,7 @@ // ------------------------------------------------------------------------- -#ifdef __HIP_PLATFORM_HCC__ +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #define CONFIG_ID 303 #define SIMD_SIZE 64 #else @@ -161,7 +161,7 @@ // KERNEL MACROS - TEXTURES // ------------------------------------------------------------------------- -#ifdef __HIP_PLATFORM_HCC__ +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #define _texture(name, type) __device__ type* name #define _texture_2d(name, type) __device__ type* name #else @@ -201,7 +201,7 @@ #define mu_tex mu_ #endif -#ifdef __HIP_PLATFORM_HCC__ +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #undef fetch4 #undef fetch @@ -266,7 +266,7 @@ typedef struct _double4 double4; #endif #endif -#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) +#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #ifdef _SINGLE_SINGLE #define shfl_down __shfl_down diff --git a/lib/gpu/lal_tersoff.cpp b/lib/gpu/lal_tersoff.cpp index e0e87d9148..ac5e5bc600 100644 --- a/lib/gpu/lal_tersoff.cpp +++ b/lib/gpu/lal_tersoff.cpp @@ -108,10 +108,7 @@ int TersoffT::init(const int ntypes, const int nlocal, const int nall, const int _nparams = nparams; _nelements = nelements; - UCL_H_Vec host_write(ntypes*ntypes,*(this->ucl_device), - UCL_READ_WRITE); - host_write.zero(); - cutsq_pair.alloc(ntypes*ntypes,*(this->ucl_device),UCL_READ_ONLY); + _cutsq_max=0.0; for (int ii=1; iihost_write[ii*ntypes+jj]) - host_write[ii*ntypes+jj]=host_cutsq[ijkparam]; + if (host_cutsq[ijkparam]>_cutsq_max) _cutsq_max=host_cutsq[ijkparam]; } } } - ucl_copy(cutsq_pair,host_write,ntypes*ntypes); // -------------------------------------------------------------------- UCL_H_Vec dview(nparams,*(this->ucl_device), @@ -235,7 +230,6 @@ void TersoffT::clear() { ts3.clear(); ts4.clear(); ts5.clear(); - cutsq_pair.clear(); map.clear(); elem2param.clear(); _zetaij.clear(); @@ -286,7 +280,7 @@ int TersoffT::loop(const int eflag, const int vflag, const int evatom, int BX=this->block_pair(); int GX=static_cast(ceil(static_cast(ainum)/BX)); this->k_short_nbor.set_size(GX,BX); - this->k_short_nbor.run(&this->atom->x, &cutsq_pair, &_ntypes, + this->k_short_nbor.run(&this->atom->x, &_cutsq_max, &_ntypes, &this->nbor->dev_nbor, &this->nbor->dev_packed, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_tersoff.cu b/lib/gpu/lal_tersoff.cu index 03ce68be77..8baa5ce12a 100644 --- a/lib/gpu/lal_tersoff.cu +++ b/lib/gpu/lal_tersoff.cu @@ -226,17 +226,13 @@ _texture_2d( pos_tex,int4); #endif __kernel void k_tersoff_short_nbor(const __global numtyp4 *restrict x_, - const __global numtyp *restrict cutsq_pair, - const int ntypes, __global int * dev_nbor, + const numtyp cutsq, const int ntypes, + __global int * dev_nbor, const __global int * dev_packed, const int inum, const int nbor_pitch, const int t_per_atom_in) { const int ii=GLOBAL_ID_X; - #ifdef ONETYPE - const numtyp cutsq=cutsq_pair[ONETYPE]; - #endif - if (ii { /// ts5.x = beta, ts5.y = powern, ts5.z = lam2, ts5.w = bigb UCL_D_Vec ts5; - UCL_D_Vec cutsq_pair; + numtyp _cutsq_max; UCL_D_Vec elem2param; UCL_D_Vec map; diff --git a/lib/gpu/lal_tersoff_extra.h b/lib/gpu/lal_tersoff_extra.h index da2568aa1b..9fe2c63176 100644 --- a/lib/gpu/lal_tersoff_extra.h +++ b/lib/gpu/lal_tersoff_extra.h @@ -142,7 +142,10 @@ ucl_inline numtyp ters_fa_d(const numtyp r, numtyp *ans_d) { #ifndef ONETYPE - if (r > param_bigr + param_bigd) return (numtyp)0.0; + if (r > param_bigr + param_bigd) { + *ans_d = (numtyp)0.0; + return (numtyp)0.0; + } #endif numtyp dfc; const numtyp fc=ters_fc_d(r,param_bigr,param_bigd,&dfc); diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp index b7b0fff1b9..347feab06f 100644 --- a/lib/gpu/lal_tersoff_mod.cpp +++ b/lib/gpu/lal_tersoff_mod.cpp @@ -105,10 +105,7 @@ int TersoffMT::init(const int ntypes, const int nlocal, const int nall, const in _nparams = nparams; _nelements = nelements; - UCL_H_Vec host_write(ntypes*ntypes,*(this->ucl_device), - UCL_READ_WRITE); - host_write.zero(); - cutsq_pair.alloc(ntypes*ntypes,*(this->ucl_device),UCL_READ_ONLY); + _cutsq_max=0.0; for (int ii=1; iihost_write[ii*ntypes+jj]) - host_write[ii*ntypes+jj]=host_cutsq[ijkparam]; + if (host_cutsq[ijkparam]>_cutsq_max) _cutsq_max=host_cutsq[ijkparam]; } } } - ucl_copy(cutsq_pair,host_write,ntypes*ntypes); UCL_H_Vec dview(nparams,*(this->ucl_device), UCL_WRITE_ONLY); @@ -229,7 +224,6 @@ void TersoffMT::clear() { ts3.clear(); ts4.clear(); ts5.clear(); - cutsq_pair.clear(); map.clear(); elem2param.clear(); _zetaij.clear(); @@ -275,7 +269,7 @@ int TersoffMT::loop(const int eflag, const int vflag, const int evatom, int BX=this->block_pair(); int GX=static_cast(ceil(static_cast(ainum)/BX)); this->k_short_nbor.set_size(GX,BX); - this->k_short_nbor.run(&this->atom->x, &cutsq_pair, &_ntypes, + this->k_short_nbor.run(&this->atom->x, &_cutsq_max, &_ntypes, &this->nbor->dev_nbor, &this->nbor->dev_packed, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_tersoff_mod.cu b/lib/gpu/lal_tersoff_mod.cu index 44b04c6933..1eb57683d5 100644 --- a/lib/gpu/lal_tersoff_mod.cu +++ b/lib/gpu/lal_tersoff_mod.cu @@ -220,17 +220,13 @@ _texture_2d( pos_tex,int4); #endif __kernel void k_tersoff_mod_short_nbor(const __global numtyp4 *restrict x_, - const __global numtyp *restrict cutsq_pair, - const int ntypes, __global int * dev_nbor, - const __global int * dev_packed, - const int inum, const int nbor_pitch, - const int t_per_atom) { + const numtyp cutsq, const int ntypes, + __global int * dev_nbor, + const __global int * dev_packed, + const int inum, const int nbor_pitch, + const int t_per_atom) { const int ii=GLOBAL_ID_X; - #ifdef ONETYPE - const numtyp cutsq=cutsq_pair[ONETYPE]; - #endif - if (ii { /// ts5.x = c5, ts5.y = h UCL_D_Vec ts5; - UCL_D_Vec cutsq_pair; + numtyp _cutsq_max; UCL_D_Vec elem2param; UCL_D_Vec map; diff --git a/lib/gpu/lal_tersoff_zbl.cpp b/lib/gpu/lal_tersoff_zbl.cpp index 4456712b0a..4fba97606c 100644 --- a/lib/gpu/lal_tersoff_zbl.cpp +++ b/lib/gpu/lal_tersoff_zbl.cpp @@ -112,10 +112,7 @@ int TersoffZT::init(const int ntypes, const int nlocal, const int nall, _nparams = nparams; _nelements = nelements; - UCL_H_Vec host_write(ntypes*ntypes,*(this->ucl_device), - UCL_READ_WRITE); - host_write.zero(); - cutsq_pair.alloc(ntypes*ntypes,*(this->ucl_device),UCL_READ_ONLY); + _cutsq_max=0.0; for (int ii=1; iihost_write[ii*ntypes+jj]) - host_write[ii*ntypes+jj]=host_cutsq[ijkparam]; + if (host_cutsq[ijkparam]>_cutsq_max) _cutsq_max=host_cutsq[ijkparam]; } } } - ucl_copy(cutsq_pair,host_write,ntypes*ntypes); UCL_H_Vec dview(nparams,*(this->ucl_device), UCL_WRITE_ONLY); @@ -253,7 +248,6 @@ void TersoffZT::clear() { ts4.clear(); ts5.clear(); ts6.clear(); - cutsq_pair.clear(); map.clear(); elem2param.clear(); _zetaij.clear(); @@ -299,7 +293,7 @@ int TersoffZT::loop(const int eflag, const int vflag, const int evatom, int BX=this->block_pair(); int GX=static_cast(ceil(static_cast(ainum)/BX)); this->k_short_nbor.set_size(GX,BX); - this->k_short_nbor.run(&this->atom->x, &cutsq_pair, &_ntypes, + this->k_short_nbor.run(&this->atom->x, &_cutsq_max, &_ntypes, &this->nbor->dev_nbor, &this->nbor->dev_packed, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_tersoff_zbl.cu b/lib/gpu/lal_tersoff_zbl.cu index fce1ccc406..6250fa55de 100644 --- a/lib/gpu/lal_tersoff_zbl.cu +++ b/lib/gpu/lal_tersoff_zbl.cu @@ -238,17 +238,13 @@ _texture( ts6_tex,int4); #endif __kernel void k_tersoff_zbl_short_nbor(const __global numtyp4 *restrict x_, - const __global numtyp *restrict cutsq_pair, - const int ntypes, __global int * dev_nbor, - const __global int * dev_packed, - const int inum, const int nbor_pitch, - const int t_per_atom) { + const numtyp cutsq, const int ntypes, + __global int * dev_nbor, + const __global int * dev_packed, + const int inum, const int nbor_pitch, + const int t_per_atom) { const int ii=GLOBAL_ID_X; - #ifdef ONETYPE - const numtyp cutsq=cutsq_pair[ONETYPE]; - #endif - if (ii { /// ts6.x = Z_i, ts6.y = Z_j, ts6.z = ZBLcut, ts6.w = ZBLexpscale UCL_D_Vec ts6; - UCL_D_Vec cutsq_pair; + numtyp _cutsq_max; UCL_D_Vec elem2param; UCL_D_Vec map; diff --git a/lib/hdnnp/Install.py b/lib/hdnnp/Install.py new file mode 100644 index 0000000000..3b232f400b --- /dev/null +++ b/lib/hdnnp/Install.py @@ -0,0 +1,122 @@ +#!/usr/bin/env python + +""" +Install.py tool to download, unpack, build, and link to the n2p2 library +used to automate the steps described in the README file in this dir +""" + +from __future__ import print_function +import sys, os, platform, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import get_cpus, fullpath, geturl, checkmd5sum + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = "2.1.4" + +# help message + +HELP = """ +Syntax from src dir: make lib-hdnnp args="-b" + or: make lib-hdnnp args="-b -v 2.1.4" + or: make lib-hdnnp args="-p /usr/local/n2p2" + +Syntax from lib dir: python Install.py -b -v 2.1.4 + or: python Install.py -b + or: python Install.py -p /usr/local/n2p2 + +Example: + +make lib-hdnnp args="-b" # download/build in lib/hdnnp/n2p2 +make lib-hdnnp args="-p $HOME/n2p2" # use existing n2p2 installation in $HOME/n2p2 +""" + +# known checksums for different n2p2 versions. used to validate the download. +checksums = { \ + '2.1.4' : '9595b066636cd6b90b0fef93398297a5', \ + } + +# parse and process arguments + +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the n2p2 library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing n2p2 installation") +parser.add_argument("-v", "--version", default=version, choices=checksums.keys(), + help="set version of n2p2 to download and build (default: %s)" % version) + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) + +buildflag = args.build +pathflag = args.path is not None +n2p2path = args.path + +homepath = fullpath('.') +homedir = "%s/n2p2" % (homepath) + +if pathflag: + if not os.path.isdir(n2p2path): + sys.exit("n2p2 path %s does not exist" % n2p2path) + homedir = fullpath(n2p2path) + if not os.path.isfile(os.path.join(homedir, 'include', 'InterfaceLammps.h')): + sys.exit("No n2p2 installation found at %s" % n2p2path) + +# download and unpack n2p2 tarball + +if buildflag: + url = "https://github.com/CompPhysVienna/n2p2/archive/v%s.tar.gz" % (version) + filename = "n2p2-%s.tar.gz" %version + print("Downloading n2p2 ...") + geturl(url, filename) + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], filename): + sys.exit("Checksum for n2p2 library does not match") + + print("Unpacking n2p2 source tarball ...") + if os.path.exists("%s/n2p2-%s" % (homepath, version)): + shutil.rmtree("%s/n2p2-%s" % (homepath, version)) + if os.path.exists(homedir): + shutil.rmtree(homedir) + cmd = 'cd "%s"; tar -xzvf %s' % (homepath, filename) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + os.remove(os.path.join(homepath, filename)) + + # build n2p2 + print("Building n2p2 ...") + n_cpus = get_cpus() + cmd = 'unset MAKEFLAGS MAKELEVEL MAKEOVERRIDES MFLAGS && cd %s/n2p2-%s/src && make -j%d libnnpif' % (homepath, version, n_cpus) + try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + + # set correct homedir for linking step + homedir = "%s/n2p2-%s" % (homepath, version) + +# create 2 links in lib/hdnnp to n2p2 installation dir + +print("Creating links to n2p2 include and lib files") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") +if os.path.isfile("Makefile.lammps") or os.path.islink("Makefile.lammps"): + os.remove("Makefile.lammps") +os.symlink(os.path.join(homedir, 'include'), 'includelink') +os.symlink(os.path.join(homedir, 'lib'), 'liblink') +os.symlink(os.path.join(homedir, 'lib', 'Makefile.lammps-extra'), 'Makefile.lammps') diff --git a/lib/hdnnp/README b/lib/hdnnp/README new file mode 100644 index 0000000000..ed61f211ea --- /dev/null +++ b/lib/hdnnp/README @@ -0,0 +1,75 @@ +The USER-HDNNP package requires access to pre-compiled libraries of the n2p2 +package (https://github.com/CompPhysVienna/n2p2). More precisely, the n2p2 core +library ("libnnp"), the interface library ("libnnpif"), some headers and extra +build helper files are needed. These files will be created automatically during +the n2p2 build process. + +This file gives some basic instructions on how to compile n2p2 manually. How to +integrate it then in the LAMMPS build process or how to use the automatic +download and build option is described in detail on the USER-HDNNP build +instructions page of the LAMMPS documentation. + +IMPORTANT: The n2p2 version must be "v2.1.4" or higher. + +Basic build instructions for n2p2 +================================= + +The n2p2 software package comes with lots of useful tools for creating and +applying high-dimensional neural network potentials (HDNNPs). In order to use +n2p2 together with LAMMPS only some parts of the n2p2 code need to be compiled. +As an example, everything related to HDNNP training is not required and would +only add unwanted library dependencies. Hence, the build infrastructure of n2p2 +is designed to allow a separate build of the LAMMPS interface. + +After downloading n2p2, change to the "src" directory and simply execute + + make libnnpif + +which should create the following files needed by the USER-HDNNP package: + + * "n2p2/lib/libnnp.a" + * "n2p2/lib/libnnpif.a" + * "n2p2/lib/lammps-extra.cmake" + * "n2p2/lib/Makefile.lammps-extra" + * "n2p2/include/InterfaceLammps.h" and many other header files. + +If you prefer dynamically linked libraries use + + make MODE=shared libnnpif + +instead (by default MODE=static) which will create *.so versions of the +libraries. By default, n2p2 uses the GNU C++ compiler and the corresponding +settings can be found in "n2p2/src/makefile.gnu". Other makefile presets are +also available (e.g. "makefile.intel") and can be activated by supplying the +"COMP" argument: + + make COMP=intel libnnpif + +Please make sure that your compiler settings for n2p2 and LAMMPS are compatible +(avoid mixing different compilers). + +If you want to build a serial version of LAMMPS with USER-HDNNP package n2p2 must +also be built with MPI disabled. This can be achieved with a preprocessor flag +(-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in the +provided compiler-specific settings makefiles. For example, if you use the GNU +compiler simply remove the comment character '#' in front of the corresponding +line (around line 49) in "makefile.gnu". It should then look like this: + + PROJECT_OPTIONS+= -DN2P2_NO_MPI + +After compiling n2p2 with this flag turned on you can build a serial LAMMPS +version with "-D BUILD_MPI=off" (CMake) or "make serial" (traditional). + +For more information about the n2p2 build process please visit +https://compphysvienna.github.io/n2p2/topics/build.html or ask questions on the +Github issue page (https://github.com/CompPhysVienna/n2p2/issues). + +Testing a successful build of LAMMPS with USER-HDNNP +==================================================== + +An example is provided in the LAMMPS directory "examples/USER/hdnnp" which runs +10 timesteps with 360 water molecules. The neural network potential is defined +via files in the "hdnnp-data" subdirectory. Use the "in.hdnnp" LAMMPS script file +to run the simulation. You should see a large output of the n2p2 library when +the pair style "hdnnp" is initialized, followed by the LAMMPS per-timestep +output. diff --git a/lib/kokkos/BUILD.md b/lib/kokkos/BUILD.md index e1f0e3e472..bb1a31f266 100644 --- a/lib/kokkos/BUILD.md +++ b/lib/kokkos/BUILD.md @@ -262,6 +262,9 @@ Architecture-specific optimizations can be enabled by specifying `-DKokkos_ARCH_ * Kokkos_ARCH_ZEN2 * Whether to optimize for the Zen2 architecture * BOOL Default: OFF +* Kokkos_ARCH_ZEN3 + * Whether to optimize for the Zen3 architecture + * BOOL Default: OFF * Kokkos_ARCH_HSW * Whether to optimize for the HSW architecture * BOOL Default: OFF diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index c759181aa2..7bb6de4cd9 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,183 @@ # Change Log +## [3.4.01](https://github.com/kokkos/kokkos/tree/3.4.01) (2021-05-19) +[Full Changelog](https://github.com/kokkos/kokkos/compare/3.4.00...3.4.01) + +**Bug Fixes:** +- Windows: Remove atomic_compare_exchange_strong overload conflicts with Windows [\#4024](https://github.com/kokkos/kokkos/pull/4024) +- OpenMPTarget: Fixup allocation headers with OpenMPTarget backend [\#4020](https://github.com/kokkos/kokkos/pull/4020) +- OpenMPTarget: Add missing specailization for OMPT to Kokkos Random [\#4022](https://github.com/kokkos/kokkos/pull/4022) +- AMD: Add support for AMD Zen3 CPU architecture [\#4021](https://github.com/kokkos/kokkos/pull/4021) +- SYCL: Implement SYCL::print_configuration [\#4012](https://github.com/kokkos/kokkos/pull/4012) +- Containers: staticcsrgraph: use device type instead of execution space to construct views [\#3998](https://github.com/kokkos/kokkos/pull/3998) +- nvcc_wrapper: fix errors in argument handling, suppress duplicates of GPU architecture and RDC flags [\#4006](https://github.com/kokkos/kokkos/pull/4006) +- CI: Add icpx testing to intel container [\#4004](https://github.com/kokkos/kokkos/pull/4004) +- CMake/TRIBITS: Keep quoted compiler flags when passing to Trilinos [\#4007](https://github.com/kokkos/kokkos/pull/4007) +- CMake: Rename IntelClang to IntelLLVM [\#3945](https://github.com/kokkos/kokkos/pull/3945) + +## [3.4.00](https://github.com/kokkos/kokkos/tree/3.4.00) (2021-04-25) +[Full Changelog](https://github.com/kokkos/kokkos/compare/3.3.01...3.4.00) + +**Highlights:** +- SYCL Backend Almost Feature Complete +- OpenMPTarget Backend Almost Feature Complete +- Performance Improvements for HIP backend +- Require CMake 3.16 or newer +- Tool Callback Interface Enhancements +- cmath wrapper functions available now in Kokkos::Experimental + +**Features:** +- Implement parallel_scan with ThreadVectorRange and Reducer [\#3861](https://github.com/kokkos/kokkos/pull/3861) +- Implement SYCL Random [\#3849](https://github.com/kokkos/kokkos/pull/3849) +- OpenMPTarget: Adding Implementation for nested reducers [\#3845](https://github.com/kokkos/kokkos/pull/3845) +- Implement UniqueToken for SYCL [\#3833](https://github.com/kokkos/kokkos/pull/3833) +- OpenMPTarget: UniqueToken::Global implementation [\#3823](https://github.com/kokkos/kokkos/pull/3823) +- DualView sync's on ExecutionSpaces [\#3822](https://github.com/kokkos/kokkos/pull/3822) +- SYCL outer TeamPolicy parallel_reduce [\#3818](https://github.com/kokkos/kokkos/pull/3818) +- SYCL TeamPolicy::team_scan [\#3815](https://github.com/kokkos/kokkos/pull/3815) +- SYCL MDRangePolicy parallel_reduce [\#3801](https://github.com/kokkos/kokkos/pull/3801) +- Enable use of execution space instances in ScatterView [\#3786](https://github.com/kokkos/kokkos/pull/3786) +- SYCL TeamPolicy nested parallel_reduce [\#3783](https://github.com/kokkos/kokkos/pull/3783) +- OpenMPTarget: MDRange with TagType for parallel_for [\#3781](https://github.com/kokkos/kokkos/pull/3781) +- Adding OpenMPTarget parallel_scan [\#3655](https://github.com/kokkos/kokkos/pull/3655) +- SYCL basic TeamPolicy [\#3654](https://github.com/kokkos/kokkos/pull/3654) +- OpenMPTarget: scratch memory implementation [\#3611](https://github.com/kokkos/kokkos/pull/3611) + +**Implemented enhancements Backends and Archs:** +- SYCL choose a specific GPU [\#3918](https://github.com/kokkos/kokkos/pull/3918) +- [HIP] Lock access to scratch memory when using Teams [\#3916](https://github.com/kokkos/kokkos/pull/3916) +- [HIP] fix multithreaded access to get_next_driver [\#3908](https://github.com/kokkos/kokkos/pull/3908) +- Forward declare HIPHostPinnedSpace and SYCLSharedUSMSpace [\#3902](https://github.com/kokkos/kokkos/pull/3902) +- Let SYCL USMObjectMem use SharedAllocationRecord [\#3898](https://github.com/kokkos/kokkos/pull/3898) +- Implement clock_tic for SYCL [\#3893](https://github.com/kokkos/kokkos/pull/3893) +- Don't use a static variable in HIPInternal::scratch_space [\#3866](https://github.com/kokkos/kokkos/pull/3866)(https://github.com/kokkos/kokkos/pull/3866) +- Reuse memory for SYCL parallel_reduce [\#3873](https://github.com/kokkos/kokkos/pull/3873) +- Update SYCL compiler in CI [\#3826](https://github.com/kokkos/kokkos/pull/3826) +- Introduce HostSharedPtr to manage m_space_instance for Cuda/HIP/SYCL [\#3824](https://github.com/kokkos/kokkos/pull/3824) +- [HIP] Use shuffle for range reduction [\#3811](https://github.com/kokkos/kokkos/pull/3811) +- OpenMPTarget: Changes to the hierarchical parallelism [\#3808](https://github.com/kokkos/kokkos/pull/3808) +- Remove ExtendedReferenceWrapper for SYCL parallel_reduce [\#3802](https://github.com/kokkos/kokkos/pull/3802) +- Eliminate sycl_indirect_launch [\#3777](https://github.com/kokkos/kokkos/pull/3777) +- OpenMPTarget: scratch implementation for parallel_reduce [\#3776](https://github.com/kokkos/kokkos/pull/3776) +- Allow initializing SYCL execution space from sycl::queue and SYCL::impl_static_fence [\#3767](https://github.com/kokkos/kokkos/pull/3767) +- SYCL TeamPolicy scratch memory alternative [\#3763](https://github.com/kokkos/kokkos/pull/3763) +- Alternative implementation for SYCL TeamPolicy [\#3759](https://github.com/kokkos/kokkos/pull/3759) +- Unify handling of synchronous errors in SYCL [\#3754](https://github.com/kokkos/kokkos/pull/3754) +- core/Cuda: Half_t updates for cgsolve [\#3746](https://github.com/kokkos/kokkos/pull/3746) +- Unify HIPParallelLaunch structures [\#3733](https://github.com/kokkos/kokkos/pull/3733) +- Improve performance for SYCL parallel_reduce [\#3732](https://github.com/kokkos/kokkos/pull/3732) +- Use consistent types in Kokkos_OpenMPTarget_Parallel.hpp [\#3703](https://github.com/kokkos/kokkos/pull/3703) +- Implement non-blocking kernel launches for HIP backend [\#3697](https://github.com/kokkos/kokkos/pull/3697) +- Change SYCLInternal::m_queue std::unique_ptr -> std::optional [\#3677](https://github.com/kokkos/kokkos/pull/3677) +- Use alternative SYCL parallel_reduce implementation [\#3671](https://github.com/kokkos/kokkos/pull/3671) +- Use runtime values in KokkosExp_MDRangePolicy.hpp [\#3626](https://github.com/kokkos/kokkos/pull/3626) +- Clean up AnalyzePolicy [\#3564](https://github.com/kokkos/kokkos/pull/3564) +- Changes for indirect launch of SYCL parallel reduce [\#3511](https://github.com/kokkos/kokkos/pull/3511) + +**Implemented enhancements BuildSystem:** +- Also require C++14 when building gtest [\#3912](https://github.com/kokkos/kokkos/pull/3912) +- Fix compiling SYCL with OpenMP [\#3874](https://github.com/kokkos/kokkos/pull/3874) +- Require C++17 for SYCL (at configuration time) [\#3869](https://github.com/kokkos/kokkos/pull/3869) +- Add COMPILE_DEFINITIONS argument to kokkos_create_imported_tpl [\#3862](https://github.com/kokkos/kokkos/pull/3862) +- Do not pass arch flags to the linker with no rdc [\#3846](https://github.com/kokkos/kokkos/pull/3846) +- Try compiling C++14 check with C++14 support and print error message [\#3843](https://github.com/kokkos/kokkos/pull/3843) +- Enable HIP with Cray Clang [\#3842](https://github.com/kokkos/kokkos/pull/3842) +- Add an option to disable header self containment tests [\#3834](https://github.com/kokkos/kokkos/pull/3834) +- CMake check for C++14 [\#3809](https://github.com/kokkos/kokkos/pull/3809) +- Prefer -std=* over --std=* [\#3779](https://github.com/kokkos/kokkos/pull/3779) +- Kokkos launch compiler updates [\#3778](https://github.com/kokkos/kokkos/pull/3778) +- Updated comments and enabled no-op for kokkos_launch_compiler [\#3774](https://github.com/kokkos/kokkos/pull/3774) +- Apple's Clang not correctly recognised [\#3772](https://github.com/kokkos/kokkos/pull/3772) +- kokkos_launch_compiler + CUDA auto-detect arch [\#3770](https://github.com/kokkos/kokkos/pull/3770) +- Add Spack test support for Kokkos [\#3753](https://github.com/kokkos/kokkos/pull/3753) +- Split SYCL tests for aot compilation [\#3741](https://github.com/kokkos/kokkos/pull/3741) +- Use consistent OpenMP flag for IntelClang [\#3735](https://github.com/kokkos/kokkos/pull/3735) +- Add support for -Wno-deprecated-gpu-targets [\#3722](https://github.com/kokkos/kokkos/pull/3722) +- Add configuration to target CUDA compute capability 8.6 [\#3713](https://github.com/kokkos/kokkos/pull/3713) +- Added VERSION and SOVERSION to KOKKOS_INTERNAL_ADD_LIBRARY [\#3706](https://github.com/kokkos/kokkos/pull/3706) +- Add fast-math to known NVCC flags [\#3699](https://github.com/kokkos/kokkos/pull/3699) +- Add MI-100 arch string [\#3698](https://github.com/kokkos/kokkos/pull/3698) +- Require CMake >=3.16 [\#3679](https://github.com/kokkos/kokkos/pull/3679) +- KokkosCI.cmake, KokkosCTest.cmake.in, CTestConfig.cmake.in + CI updates [\#2844](https://github.com/kokkos/kokkos/pull/2844) + +**Implemented enhancements Tools:** +- Improve readability of the callback invocation in profiling [\#3860](https://github.com/kokkos/kokkos/pull/3860) +- V1.1 Tools Interface: incremental, action-based [\#3812](https://github.com/kokkos/kokkos/pull/3812) +- Enable launch latency simulations [\#3721](https://github.com/kokkos/kokkos/pull/3721) +- Added metadata callback to tools interface [\#3711](https://github.com/kokkos/kokkos/pull/3711) +- MDRange Tile Size Tuning [\#3688](https://github.com/kokkos/kokkos/pull/3688) +- Added support for command-line args for kokkos-tools [\#3627](https://github.com/kokkos/kokkos/pull/3627) +- Query max tile sizes for an MDRangePolicy, and set tile sizes on an existing policy [\#3481](https://github.com/kokkos/kokkos/pull/3481) + +**Implemented enhancements Other:** +- Try detecting ndevices in get_gpu [\#3921](https://github.com/kokkos/kokkos/pull/3921) +- Use strcmp to compare names() [\#3909](https://github.com/kokkos/kokkos/pull/3909) +- Add execution space arguments for constructor overloads that might allocate a new underlying View [\#3904](https://github.com/kokkos/kokkos/pull/3904) +- Prefix labels in internal use of kokkos_malloc [\#3891](https://github.com/kokkos/kokkos/pull/3891) +- Prefix labels for internal uses of SharedAllocationRecord [\#3890](https://github.com/kokkos/kokkos/pull/3890) +- Add missing hypot math function [\#3880](https://github.com/kokkos/kokkos/pull/3880) +- Unify algorithm unit tests to avoid code duplication [\#3851](https://github.com/kokkos/kokkos/pull/3851) +- DualView.template view() better matches for Devices in UVMSpace cases [\#3857](https://github.com/kokkos/kokkos/pull/3857) +- More extensive disentangling of Policy Traits [\#3829](https://github.com/kokkos/kokkos/pull/3829) +- Replaced nanosleep and sched_yield with STL routines [\#3825](https://github.com/kokkos/kokkos/pull/3825) +- Constructing Atomic Subviews [\#3810](https://github.com/kokkos/kokkos/pull/3810) +- Metadata Declaration in Core [\#3729](https://github.com/kokkos/kokkos/pull/3729) +- Allow using tagged final functor in parallel_reduce [\#3714](https://github.com/kokkos/kokkos/pull/3714) +- Major duplicate code removal in SharedAllocationRecord specializations [\#3658](https://github.com/kokkos/kokkos/pull/3658) + +**Fixed bugs:** +- Provide forward declarations in Kokkos_ViewLayoutTiled.hpp for XL [\#3911](https://github.com/kokkos/kokkos/pull/3911) +- Fixup absolute value of floating points in Kokkos complex [\#3882](https://github.com/kokkos/kokkos/pull/3882) +- Address intel 17 ICE [\#3881](https://github.com/kokkos/kokkos/pull/3881) +- Add missing pow(Kokkos::complex) overloads [\#3868](https://github.com/kokkos/kokkos/pull/3868) +- Fix bug {pow, log}(Kokkos::complex) [\#3866](https://github.com/kokkos/kokkos/pull/3866)(https://github.com/kokkos/kokkos/pull/3866) +- Cleanup writing to output streams in Cuda [\#3859](https://github.com/kokkos/kokkos/pull/3859) +- Fixup cache CUDA fallback execution space instance used by DualView::sync [\#3856](https://github.com/kokkos/kokkos/pull/3856) +- Fix cmake warning with pthread [\#3854](https://github.com/kokkos/kokkos/pull/3854) +- Fix typo FOUND_CUDA_{DRIVVER -> DRIVER} [\#3852](https://github.com/kokkos/kokkos/pull/3852) +- Fix bug in SYCL team_reduce [\#3848](https://github.com/kokkos/kokkos/pull/3848) +- Atrocious bug in MDRange tuning [\#3803](https://github.com/kokkos/kokkos/pull/3803) +- Fix compiling SYCL with Kokkos_ENABLE_TUNING=ON [\#3800](https://github.com/kokkos/kokkos/pull/3800) +- Fixed command line parsing bug [\#3797](https://github.com/kokkos/kokkos/pull/3797) +- Workaround race condition in SYCL parallel_reduce [\#3782](https://github.com/kokkos/kokkos/pull/3782) +- Fix Atomic{Min,Max} for Kepler30 [\#3780](https://github.com/kokkos/kokkos/pull/3780) +- Fix SYCL typo [\#3755](https://github.com/kokkos/kokkos/pull/3755) +- Fixed Kokkos_install_additional_files macro [\#3752](https://github.com/kokkos/kokkos/pull/3752) +- Fix a typo for Kokkos_ARCH_A64FX [\#3751](https://github.com/kokkos/kokkos/pull/3751) +- OpenMPTarget: fixes and workarounds to work with "Release" build type [\#3748](https://github.com/kokkos/kokkos/pull/3748) +- Fix parsing bug for number of devices command line argument [\#3724](https://github.com/kokkos/kokkos/pull/3724) +- Avoid more warnings with clang and C++20 [\#3719](https://github.com/kokkos/kokkos/pull/3719) +- Fix gcc-10.1 C++20 warnings [\#3718](https://github.com/kokkos/kokkos/pull/3718) +- Fix cuda cache config not being set correct [\#3712](https://github.com/kokkos/kokkos/pull/3712) +- Fix dualview deepcopy perftools [\#3701](https://github.com/kokkos/kokkos/pull/3701) +- use drand instead of frand in drand [\#3696](https://github.com/kokkos/kokkos/pull/3696) + +**Incompatibilities:** +- Remove unimplemented member functions of SYCLDevice [\#3919](https://github.com/kokkos/kokkos/pull/3919) +- Replace cl::sycl [\#3896](https://github.com/kokkos/kokkos/pull/3896) +- Get rid of SYCL workaround in Kokkos_Complex.hpp [\#3884](https://github.com/kokkos/kokkos/pull/3884) +- Replace most uses of if_c [\#3883](https://github.com/kokkos/kokkos/pull/3883) +- Remove Impl::enable_if_type [\#3863](https://github.com/kokkos/kokkos/pull/3863) +- Remove HostBarrier test [\#3847](https://github.com/kokkos/kokkos/pull/3847) +- Avoid (void) interface [\#3836](https://github.com/kokkos/kokkos/pull/3836) +- Remove VerifyExecutionCanAccessMemorySpace [\#3813](https://github.com/kokkos/kokkos/pull/3813) +- Avoid duplicated code in ScratchMemorySpace [\#3793](https://github.com/kokkos/kokkos/pull/3793) +- Remove superfluous FunctorFinal specialization [\#3788](https://github.com/kokkos/kokkos/pull/3788) +- Rename cl::sycl -> sycl in Kokkos_MathematicalFunctions.hpp [\#3678](https://github.com/kokkos/kokkos/pull/3678) +- Remove integer_sequence backward compatibility implementation [\#3533](https://github.com/kokkos/kokkos/pull/3533) + +**Enabled tests:** +- Fixup re-enable core performance tests [\#3903](https://github.com/kokkos/kokkos/pull/3903) +- Enable more SYCL tests [\#3900](https://github.com/kokkos/kokkos/pull/3900) +- Restrict MDRange Policy tests for Intel GPUs [\#3853](https://github.com/kokkos/kokkos/pull/3853) +- Disable death tests for rawhide [\#3844](https://github.com/kokkos/kokkos/pull/3844) +- OpenMPTarget: Block unit tests that do not pass with the nvidia compiler [\#3839](https://github.com/kokkos/kokkos/pull/3839) +- Enable Bitset container test for SYCL [\#3830](https://github.com/kokkos/kokkos/pull/3830) +- Enable some more SYCL tests [\#3744](https://github.com/kokkos/kokkos/pull/3744) +- Enable SYCL atomic tests [\#3742](https://github.com/kokkos/kokkos/pull/3742) +- Enable more SYCL perf_tests [\#3692](https://github.com/kokkos/kokkos/pull/3692) +- Enable examples for SYCL [\#3691](https://github.com/kokkos/kokkos/pull/3691) + ## [3.3.01](https://github.com/kokkos/kokkos/tree/3.3.01) (2021-01-06) [Full Changelog](https://github.com/kokkos/kokkos/compare/3.3.00...3.3.01) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index 7bc3c77256..9452027d8e 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -72,7 +72,7 @@ ENDFUNCTION() LIST(APPEND CMAKE_MODULE_PATH cmake/Modules) IF(NOT KOKKOS_HAS_TRILINOS) - cmake_minimum_required(VERSION 3.10 FATAL_ERROR) + cmake_minimum_required(VERSION 3.16 FATAL_ERROR) set(CMAKE_DISABLE_SOURCE_CHANGES ON) set(CMAKE_DISABLE_IN_SOURCE_BUILD ON) IF (Spack_WORKAROUND) @@ -111,27 +111,25 @@ ENDIF() set(Kokkos_VERSION_MAJOR 3) -set(Kokkos_VERSION_MINOR 3) -set(Kokkos_VERSION_PATCH 1) +set(Kokkos_VERSION_MINOR 4) +set(Kokkos_VERSION_PATCH 01) set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}") math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}") -IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.12.0") - MESSAGE(STATUS "Setting policy CMP0074 to use _ROOT variables") - CMAKE_POLICY(SET CMP0074 NEW) -ENDIF() +MESSAGE(STATUS "Setting policy CMP0074 to use _ROOT variables") +CMAKE_POLICY(SET CMP0074 NEW) # Load either the real TriBITS or a TriBITS wrapper # for certain utility functions that are universal (like GLOBAL_SET) INCLUDE(${KOKKOS_SRC_PATH}/cmake/fake_tribits.cmake) -IF (Kokkos_ENABLE_CUDA AND ${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.14.0") - #If we are building CUDA, we have tricked CMake because we declare a CXX project - #If the default C++ standard for a given compiler matches the requested - #standard, then CMake just omits the -std flag in later versions of CMake - #This breaks CUDA compilation (CUDA compiler can have a different default - #-std then the underlying host compiler by itself). Setting this variable - #forces CMake to always add the -std flag even if it thinks it doesn't need it +IF (Kokkos_ENABLE_CUDA) + # If we are building CUDA, we have tricked CMake because we declare a CXX project + # If the default C++ standard for a given compiler matches the requested + # standard, then CMake just omits the -std flag in later versions of CMake + # This breaks CUDA compilation (CUDA compiler can have a different default + # -std then the underlying host compiler by itself). Setting this variable + # forces CMake to always add the -std flag even if it thinks it doesn't need it GLOBAL_SET(CMAKE_CXX_STANDARD_DEFAULT 98) ENDIF() @@ -139,15 +137,19 @@ ENDIF() # I really wish these were regular variables # but scoping issues can make it difficult GLOBAL_SET(KOKKOS_COMPILE_OPTIONS) -GLOBAL_SET(KOKKOS_LINK_OPTIONS -DKOKKOS_DEPENDENCE) +GLOBAL_SET(KOKKOS_LINK_OPTIONS) GLOBAL_SET(KOKKOS_CUDA_OPTIONS) GLOBAL_SET(KOKKOS_CUDAFE_OPTIONS) GLOBAL_SET(KOKKOS_XCOMPILER_OPTIONS) # We need to append text here for making sure TPLs # we import are available for an installed Kokkos GLOBAL_SET(KOKKOS_TPL_EXPORTS) -# this could probably be scoped to project +# KOKKOS_DEPENDENCE is used by kokkos_launch_compiler GLOBAL_SET(KOKKOS_COMPILE_DEFINITIONS KOKKOS_DEPENDENCE) +# MSVC never goes through kokkos_launch_compiler +IF(NOT MSVC) + GLOBAL_APPEND(KOKKOS_LINK_OPTIONS -DKOKKOS_DEPENDENCE) +ENDIF() # Include a set of Kokkos-specific wrapper functions that # will either call raw CMake or TriBITS @@ -204,8 +206,13 @@ ENDIF() IF (KOKKOS_HAS_TRILINOS) # Overwrite the old flags at the top-level # Because Tribits doesn't use lists, it uses spaces for the list of CXX flags - # we have to match the annoying behavior - STRING(REPLACE ";" " " KOKKOSCORE_COMPILE_OPTIONS "${KOKKOS_COMPILE_OPTIONS}") + # we have to match the annoying behavior, also we have to preserve quotes + # which needs another workaround. + SET(KOKKOS_COMPILE_OPTIONS_TMP) + FOREACH(OPTION ${KOKKOS_COMPILE_OPTIONS}) + LIST(APPEND KOKKOS_COMPILE_OPTIONS_TMP \"${OPTION}\") + ENDFOREACH() + STRING(REPLACE ";" " " KOKKOSCORE_COMPILE_OPTIONS "${KOKKOS_COMPILE_OPTIONS_TMP}") LIST(APPEND KOKKOS_ALL_COMPILE_OPTIONS ${KOKKOS_COMPILE_OPTIONS}) IF (KOKKOS_ENABLE_CUDA) LIST(APPEND KOKKOS_ALL_COMPILE_OPTIONS ${KOKKOS_CUDA_OPTIONS}) diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index 061b7a46ee..013d2b3ede 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -11,8 +11,8 @@ CXXFLAGS += $(SHFLAGS) endif KOKKOS_VERSION_MAJOR = 3 -KOKKOS_VERSION_MINOR = 3 -KOKKOS_VERSION_PATCH = 1 +KOKKOS_VERSION_MINOR = 4 +KOKKOS_VERSION_PATCH = 01 KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc) # Options: Cuda,HIP,OpenMP,Pthread,Serial @@ -20,11 +20,11 @@ KOKKOS_DEVICES ?= "OpenMP" #KOKKOS_DEVICES ?= "Pthread" # Options: # Intel: KNC,KNL,SNB,HSW,BDW,SKX -# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80 +# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80,Ampere86 # ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX # IBM: BGQ,Power7,Power8,Power9 # AMD-GPUS: Vega900,Vega906,Vega908 -# AMD-CPUS: AMDAVX,Zen,Zen2 +# AMD-CPUS: AMDAVX,Zen,Zen2,Zen3 KOKKOS_ARCH ?= "" # Options: yes,no KOKKOS_DEBUG ?= "no" @@ -164,17 +164,17 @@ KOKKOS_INTERNAL_OS_DARWIN := $(call kokkos_has_string,$(KOKKOS_OS),Darwin) KOKKOS_CXX_VERSION := $(strip $(shell $(CXX) --version 2>&1)) KOKKOS_INTERNAL_COMPILER_INTEL := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Intel Corporation) KOKKOS_INTERNAL_COMPILER_PGI := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),PGI) -KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2>&1 | grep XL | wc -l)) -KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-" | wc -l)) -KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell echo "$(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep nvcc | wc -l)>0" | bc)) +KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2>&1 | grep -c XL)) +KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep -c "CC-")) +KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell echo "$(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep -c nvcc)>0" | bc)) KOKKOS_INTERNAL_COMPILER_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),clang) -KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Apple LLVM) +KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Apple clang) KOKKOS_INTERNAL_COMPILER_HCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),HCC) KOKKOS_INTERNAL_COMPILER_GCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),GCC) # Check Host Compiler if using NVCC through nvcc_wrapper ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER := $(strip $(shell echo $(CXX) | grep nvcc_wrapper | wc -l)) + KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER := $(strip $(shell echo $(CXX) | grep -c nvcc_wrapper)) ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER), 1) KOKKOS_CXX_HOST_VERSION := $(strip $(shell $(CXX) $(CXXFLAGS) --host-version 2>&1)) @@ -297,11 +297,11 @@ else #KOKKOS_INTERNAL_CXX1Z_FLAG := -hstd=c++1z #KOKKOS_INTERNAL_CXX2A_FLAG := -hstd=c++2a else - KOKKOS_INTERNAL_CXX14_FLAG := --std=c++14 - KOKKOS_INTERNAL_CXX1Y_FLAG := --std=c++1y - KOKKOS_INTERNAL_CXX17_FLAG := --std=c++17 - KOKKOS_INTERNAL_CXX1Z_FLAG := --std=c++1z - KOKKOS_INTERNAL_CXX2A_FLAG := --std=c++2a + KOKKOS_INTERNAL_CXX14_FLAG := -std=c++14 + KOKKOS_INTERNAL_CXX1Y_FLAG := -std=c++1y + KOKKOS_INTERNAL_CXX17_FLAG := -std=c++17 + KOKKOS_INTERNAL_CXX1Z_FLAG := -std=c++1z + KOKKOS_INTERNAL_CXX2A_FLAG := -std=c++2a endif endif endif @@ -332,6 +332,7 @@ KOKKOS_INTERNAL_USE_ARCH_VOLTA70 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volt KOKKOS_INTERNAL_USE_ARCH_VOLTA72 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta72) KOKKOS_INTERNAL_USE_ARCH_TURING75 := $(call kokkos_has_string,$(KOKKOS_ARCH),Turing75) KOKKOS_INTERNAL_USE_ARCH_AMPERE80 := $(call kokkos_has_string,$(KOKKOS_ARCH),Ampere80) +KOKKOS_INTERNAL_USE_ARCH_AMPERE86 := $(call kokkos_has_string,$(KOKKOS_ARCH),Ampere86) KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \ @@ -344,7 +345,8 @@ KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLE + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \ + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \ + $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \ - + $(KOKKOS_INTERNAL_USE_ARCH_AMPERE80)) + + $(KOKKOS_INTERNAL_USE_ARCH_AMPERE80) \ + + $(KOKKOS_INTERNAL_USE_ARCH_AMPERE86)) #SEK: This seems like a bug to me ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) @@ -380,6 +382,7 @@ KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ # AMD based. KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX) +KOKKOS_INTERNAL_USE_ARCH_ZEN3 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen3) KOKKOS_INTERNAL_USE_ARCH_ZEN2 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen2) KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen) KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900) @@ -389,12 +392,12 @@ KOKKOS_INTERNAL_USE_ARCH_VEGA908 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega # Any AVX? KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM)) KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX)) -KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) +KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3)) KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL)) KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SKX)) # Decide what ISA level we are able to support. -KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) +KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3)) KOKKOS_INTERNAL_USE_ISA_KNC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNC)) KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER8) + $(KOKKOS_INTERNAL_USE_ARCH_POWER9)) KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER7)) @@ -585,10 +588,10 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1) endif ifeq ($(KOKKOS_INTERNAL_ENABLE_TUNING), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_TUNING") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_TUNING") endif -tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_LIBDL") +tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_LIBDL") ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) ifneq ($(KOKKOS_CMAKE), yes) @@ -752,6 +755,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_A64FX), 1) KOKKOS_CXXFLAGS += -march=armv8.2-a+sve KOKKOS_LDFLAGS += -march=armv8.2-a+sve + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_CXXFLAGS += -msve-vector-bits=512 + KOKKOS_LDFLAGS += -msve-vector-bits=512 + endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1) + KOKKOS_CXXFLAGS += -msve-vector-bits=512 + KOKKOS_LDFLAGS += -msve-vector-bits=512 + endif endif ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN), 1) @@ -780,6 +791,19 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN2), 1) endif endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN3), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_ZEN3") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_AVX2") + + ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) + KOKKOS_CXXFLAGS += -mavx2 + KOKKOS_LDFLAGS += -mavx2 + else + KOKKOS_CXXFLAGS += -march=znver3 -mtune=znver3 + KOKKOS_LDFLAGS += -march=znver3 -mtune=znver3 + endif +endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV80") tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV8_THUNDERX") @@ -1100,6 +1124,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA_ARCH), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE80") KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_80 endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMPERE86), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE86") + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_86 + endif ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) @@ -1159,14 +1188,13 @@ endif KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h 2>&1) ifeq ($(KOKKOS_INTERNAL_LS_CONFIG), KokkosCore_config.h) - KOKKOS_INTERNAL_NEW_CONFIG := $(strip $(shell diff KokkosCore_config.h KokkosCore_config.tmp | grep define | wc -l)) + KOKKOS_INTERNAL_NEW_CONFIG := $(strip $(shell diff KokkosCore_config.h KokkosCore_config.tmp | grep -c define)) else KOKKOS_INTERNAL_NEW_CONFIG := 1 endif ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0) tmp := $(shell cp KokkosCore_config.tmp KokkosCore_config.h) -endif # Functions for generating config header file kokkos_start_config_header = $(shell sed 's~@INCLUDE_NEXT_FILE@~~g' $(KOKKOS_PATH)/cmake/KokkosCore_Config_HeaderSet.in > $1) @@ -1181,41 +1209,42 @@ tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp") tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp") ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_SetupBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) else endif endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_SetupBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") +endif endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/*.hpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/impl/*.hpp) @@ -1334,7 +1363,7 @@ ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) endif # With Cygwin functions such as fdopen and fileno are not defined -# when strict ansi is enabled. strict ansi gets enabled with --std=c++14 +# when strict ansi is enabled. strict ansi gets enabled with -std=c++14 # though. So we hard undefine it here. Not sure if that has any bad side effects # This is needed for gtest actually, not for Kokkos itself! ifeq ($(KOKKOS_INTERNAL_OS_CYGWIN), 1) diff --git a/lib/kokkos/Makefile.targets b/lib/kokkos/Makefile.targets index 5a03f7d17e..cf9fc24242 100644 --- a/lib/kokkos/Makefile.targets +++ b/lib/kokkos/Makefile.targets @@ -36,6 +36,8 @@ Kokkos_MemorySpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_ $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemorySpace.cpp Kokkos_HostSpace_deepcopy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp +Kokkos_NumericTraits.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_NumericTraits.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_NumericTraits.cpp ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) Kokkos_Cuda_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Instance.cpp diff --git a/lib/kokkos/algorithms/CMakeLists.txt b/lib/kokkos/algorithms/CMakeLists.txt index fd099054ba..4df76a1dbb 100644 --- a/lib/kokkos/algorithms/CMakeLists.txt +++ b/lib/kokkos/algorithms/CMakeLists.txt @@ -5,10 +5,12 @@ KOKKOS_SUBPACKAGE(Algorithms) IF (NOT Kokkos_INSTALL_TESTING) ADD_SUBDIRECTORY(src) ENDIF() - -KOKKOS_ADD_TEST_DIRECTORIES(unit_tests) +IF(NOT (KOKKOS_ENABLE_OPENMPTARGET + AND (KOKKOS_CXX_COMPILER_ID STREQUAL PGI OR + KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC))) + KOKKOS_ADD_TEST_DIRECTORIES(unit_tests) +ENDIF() KOKKOS_SUBPACKAGE_POSTPROCESS() - diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index 69d6cf8f35..55ce19971f 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -668,6 +668,43 @@ struct Random_UniqueIndex { }; #endif +#ifdef KOKKOS_ENABLE_SYCL +template <> +struct Random_UniqueIndex { + using locks_view_type = View; + KOKKOS_FUNCTION + static int get_state_idx(const locks_view_type& locks_) { +#ifdef KOKKOS_ARCH_INTEL_GEN + int i = Kokkos::Impl::clock_tic() % locks_.extent(0); +#else + int i = 0; +#endif + while (Kokkos::atomic_compare_exchange(&locks_(i), 0, 1)) { + i = (i + 1) % static_cast(locks_.extent(0)); + } + return i; + } +}; +#endif + +#ifdef KOKKOS_ENABLE_OPENMPTARGET +template <> +struct Random_UniqueIndex { + using locks_view_type = View; + KOKKOS_FUNCTION + static int get_state_idx(const locks_view_type& locks) { + const int team_size = omp_get_num_threads(); + int i = omp_get_team_num() * team_size + omp_get_thread_num(); + const int lock_size = locks.extent_int(0); + + while (Kokkos::atomic_compare_exchange(&locks(i), 0, 1)) { + i = (i + 1) % lock_size; + } + return i; + } +}; +#endif + } // namespace Impl template @@ -1028,7 +1065,7 @@ class Random_XorShift1024 { KOKKOS_INLINE_FUNCTION double drand(const double& start, const double& end) { - return frand(end - start) + start; + return drand(end - start) + start; } // Marsaglia polar method for drawing a standard normal distributed random diff --git a/lib/kokkos/algorithms/unit_tests/CMakeLists.txt b/lib/kokkos/algorithms/unit_tests/CMakeLists.txt index 819c9e54ba..50f8f0a332 100644 --- a/lib/kokkos/algorithms/unit_tests/CMakeLists.txt +++ b/lib/kokkos/algorithms/unit_tests/CMakeLists.txt @@ -3,6 +3,7 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR}) KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/../src ) +KOKKOS_INCLUDE_DIRECTORIES(${KOKKOS_SOURCE_DIR}/core/unit_test/category_files) SET(GTEST_SOURCE_DIR ${${PARENT_PACKAGE_NAME}_SOURCE_DIR}/tpls/gtest) @@ -25,7 +26,7 @@ KOKKOS_ADD_TEST_LIBRARY( TARGET_COMPILE_DEFINITIONS(kokkosalgorithms_gtest PUBLIC GTEST_HAS_TR1_TUPLE=0 GTEST_HAS_PTHREAD=0) IF((NOT (Kokkos_ENABLE_CUDA AND WIN32)) AND (NOT ("${KOKKOS_CXX_COMPILER_ID}" STREQUAL "Fujitsu"))) -TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_11) + TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_14) ENDIF() # Suppress clang-tidy diagnostics on code that we do not have control over @@ -33,51 +34,42 @@ IF(CMAKE_CXX_CLANG_TIDY) SET_TARGET_PROPERTIES(kokkosalgorithms_gtest PROPERTIES CXX_CLANG_TIDY "") ENDIF() -SET(SOURCES - UnitTestMain.cpp -) +SET(ALGORITHM UnitTestMain.cpp) IF(Kokkos_ENABLE_OPENMP) - LIST( APPEND SOURCES - TestOpenMP.cpp + LIST(APPEND ALGORITHM_SOURCES TestOpenMP_Sort1D.cpp TestOpenMP_Sort3D.cpp TestOpenMP_SortDynamicView.cpp - TestOpenMP_Random.cpp ) ENDIF() -IF(Kokkos_ENABLE_HIP) - LIST( APPEND SOURCES - TestHIP.cpp - ) -ENDIF() +foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL;OpenMPTarget) + # Because there is always an exception to the rule + if(Tag STREQUAL "Threads") + set(DEVICE "PTHREAD") + else() + string(TOUPPER ${Tag} DEVICE) + endif() -IF(Kokkos_ENABLE_CUDA) - LIST( APPEND SOURCES - TestCuda.cpp - ) -ENDIF() - -IF(Kokkos_ENABLE_HPX) - LIST( APPEND SOURCES - TestHPX.cpp - ) -ENDIF() - -IF(Kokkos_ENABLE_SERIAL) - LIST( APPEND SOURCES - TestSerial.cpp - ) -ENDIF() - -IF(Kokkos_ENABLE_PTHREAD) - LIST( APPEND SOURCES - TestThreads.cpp - ) -ENDIF() + if(Kokkos_ENABLE_${DEVICE}) + set(dir ${CMAKE_CURRENT_BINARY_DIR}) + set(file ${dir}/Test${Tag}.cpp) + # Write to a temporary intermediate file and call configure_file to avoid + # updating timestamps triggering unnecessary rebuilds on subsequent cmake runs. + file(WRITE ${dir}/dummy.cpp + "#include \n" + "#include \n" + "#include \n" + ) + configure_file(${dir}/dummy.cpp ${file}) + list(APPEND ALGORITHM_SOURCES ${file}) + endif() +endforeach() KOKKOS_ADD_EXECUTABLE_AND_TEST( UnitTest - SOURCES ${SOURCES} + SOURCES + UnitTestMain.cpp + ${ALGORITHM_SOURCES} ) diff --git a/lib/kokkos/algorithms/unit_tests/Makefile b/lib/kokkos/algorithms/unit_tests/Makefile index c112d7c6fc..dd0aa87de0 100644 --- a/lib/kokkos/algorithms/unit_tests/Makefile +++ b/lib/kokkos/algorithms/unit_tests/Makefile @@ -20,11 +20,19 @@ override LDFLAGS += -lpthread include $(KOKKOS_PATH)/Makefile.kokkos -KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/algorithms/unit_tests +KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/algorithms/unit_tests -I${KOKKOS_PATH}/core/unit_test/category_files TEST_TARGETS = TARGETS = +tmp := $(foreach device, $(KOKKOS_DEVICELIST), \ + $(if $(filter Test$(device).cpp, $(shell ls Test$(device).cpp 2>/dev/null)),,\ + $(shell echo "\#include " > Test$(device).cpp); \ + $(shell echo "\#include " >> Test$(device).cpp); \ + $(shell echo "\#include " >> Test$(device).cpp); \ + ) \ +) + ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA = TestCuda.o UnitTestMain.o gtest-all.o TARGETS += KokkosAlgorithms_UnitTest_Cuda @@ -44,7 +52,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) - OBJ_OPENMP = TestOpenMP.o TestOpenMP_Random.o TestOpenMP_Sort1D.o TestOpenMP_Sort3D.o TestOpenMP_SortDynamicView.o UnitTestMain.o gtest-all.o + OBJ_OPENMP = TestOpenMP.o TestOpenMP_Sort1D.o TestOpenMP_Sort3D.o TestOpenMP_SortDynamicView.o UnitTestMain.o gtest-all.o TARGETS += KokkosAlgorithms_UnitTest_OpenMP TEST_TARGETS += test-openmp endif diff --git a/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp b/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp index a9b2010ad0..4a5839f0c8 100644 --- a/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp @@ -59,6 +59,8 @@ TEST(openmp, SortUnsigned1D) { Impl::test_1D_sort(171); } +TEST(openmp, SortIssue1160) { Impl::test_issue_1160_sort(); } + } // namespace Test #else void KOKKOS_ALGORITHMS_UNITTESTS_TESTOPENMP_PREVENT_LINK_ERROR() {} diff --git a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp index caba92c152..c37e779c99 100644 --- a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp @@ -109,6 +109,16 @@ struct RandomProperties { } }; +// FIXME_OPENMPTARGET: Need this for OpenMPTarget because contra to the standard +// llvm requires the binary operator defined not just the += +KOKKOS_INLINE_FUNCTION +RandomProperties operator+(const RandomProperties& org, + const RandomProperties& add) { + RandomProperties val = org; + val += add; + return val; +} + template struct test_random_functor { using rnd_type = typename GeneratorPool::generator_type; @@ -491,6 +501,34 @@ void test_random(unsigned int num_draws) { } } // namespace Impl +template +void test_random_xorshift64() { +#if defined(KOKKOS_ENABLE_SYCL) || defined(KOKKOS_ENABLE_CUDA) || \ + defined(KOKKOS_ENABLE_HIP) + const int num_draws = 132141141; +#else // SERIAL, HPX, OPENMP + const int num_draws = 10240000; +#endif + Impl::test_random>(num_draws); + Impl::test_random>>( + num_draws); +} + +template +void test_random_xorshift1024() { +#if defined(KOKKOS_ENABLE_SYCL) || defined(KOKKOS_ENABLE_CUDA) || \ + defined(KOKKOS_ENABLE_HIP) + const int num_draws = 52428813; +#else // SERIAL, HPX, OPENMP + const int num_draws = 10130144; +#endif + Impl::test_random>( + num_draws); + Impl::test_random>>( + num_draws); +} } // namespace Test #endif // KOKKOS_TEST_UNORDERED_MAP_HPP diff --git a/lib/kokkos/algorithms/unit_tests/TestRandomCommon.hpp b/lib/kokkos/algorithms/unit_tests/TestRandomCommon.hpp new file mode 100644 index 0000000000..c6d3b59ae1 --- /dev/null +++ b/lib/kokkos/algorithms/unit_tests/TestRandomCommon.hpp @@ -0,0 +1,60 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 3.0 +// Copyright (2020) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#ifndef KOKKOS_ALGORITHMS_UNITTESTS_TESTRANDOM_COMMON_HPP +#define KOKKOS_ALGORITHMS_UNITTESTS_TESTRANDOM_COMMON_HPP + +#include + +namespace Test { + +TEST(TEST_CATEGORY, Random_XorShift64) { + test_random_xorshift64(); +} +TEST(TEST_CATEGORY, Random_XorShift1024_0) { + test_random_xorshift1024(); +} +} // namespace Test + +#endif diff --git a/lib/kokkos/algorithms/unit_tests/TestSort.hpp b/lib/kokkos/algorithms/unit_tests/TestSort.hpp index a3c362ec20..9c6308c843 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSort.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSort.hpp @@ -370,7 +370,10 @@ template void test_sort(unsigned int N) { test_1D_sort(N); test_3D_sort(N); +// FIXME_OPENMPTARGET: OpenMPTarget doesn't support DynamicView yet. +#ifndef KOKKOS_ENABLE_OPENMPTARGET test_dynamic_view_sort(N); +#endif test_issue_1160_sort(); } } // namespace Impl diff --git a/lib/kokkos/containers/unit_tests/TestHPX_Category.hpp b/lib/kokkos/algorithms/unit_tests/TestSortCommon.hpp similarity index 88% rename from lib/kokkos/containers/unit_tests/TestHPX_Category.hpp rename to lib/kokkos/algorithms/unit_tests/TestSortCommon.hpp index 64fc7c0757..56657b6574 100644 --- a/lib/kokkos/containers/unit_tests/TestHPX_Category.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSortCommon.hpp @@ -42,10 +42,14 @@ //@HEADER */ -#ifndef KOKKOS_TEST_HPX_HPP -#define KOKKOS_TEST_HPX_HPP +#ifndef KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_COMMON_HPP +#define KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_COMMON_HPP -#define TEST_CATEGORY hpx -#define TEST_EXECSPACE Kokkos::Experimental::HPX +#include +namespace Test { +TEST(TEST_CATEGORY, SortUnsigned) { + Impl::test_sort(171); +} +} // namespace Test #endif diff --git a/lib/kokkos/appveyor.yml b/lib/kokkos/appveyor.yml index c40bf066b7..e8763c0b66 100644 --- a/lib/kokkos/appveyor.yml +++ b/lib/kokkos/appveyor.yml @@ -3,8 +3,4 @@ image: clone_folder: c:\projects\source build_script: - cmd: >- - mkdir build && - cd build && - cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON && - cmake --build . --target install && - ctest -C Debug -V + cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON -DCMAKE_CXX_FLAGS="/W0 /EHsc /d1reportClassLayoutChanges" -DCTEST_ARGS="-C Debug -V --output-on-failure" -DBUILD_NAME=MSVC-2019 -DBUILD_TYPE=Debug -DSITE=AppVeyor -DTARGET=install -P cmake/KokkosCI.cmake diff --git a/lib/kokkos/bin/kokkos_launch_compiler b/lib/kokkos/bin/kokkos_launch_compiler index 1fbebf648f..d929d24f1d 100755 --- a/lib/kokkos/bin/kokkos_launch_compiler +++ b/lib/kokkos/bin/kokkos_launch_compiler @@ -13,6 +13,17 @@ # $1 are 'ar', 'cmake', etc. during the linking phase # +# emit a message about the underlying command executed +: ${DEBUG:=0} +: ${KOKKOS_DEBUG_LAUNCH_COMPILER:=${DEBUG}} + +debug-message() +{ + if [ "${KOKKOS_DEBUG_LAUNCH_COMPILER}" -ne 0 ]; then + echo -e "##### $(basename ${BASH_SOURCE[0]}) executing: \"$@\"... #####" + fi +} + # check the arguments for the KOKKOS_DEPENDENCE compiler definition KOKKOS_DEPENDENCE=0 for i in ${@} @@ -23,16 +34,30 @@ do fi done -# if C++ is not passed, someone is probably trying to invoke it directly +# if Kokkos compiler is not passed, someone is probably trying to invoke it directly if [ -z "${1}" ]; then - echo -e "\n${BASH_SOURCE[0]} was invoked without the C++ compiler as the first argument." + echo -e "\n${BASH_SOURCE[0]} was invoked without the Kokkos compiler as the first argument." echo "This script is not indended to be directly invoked by any mechanism other" - echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake\n" + echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake.\n" + exit 1 +fi + +# if Kokkos compiler is not passed, someone is probably trying to invoke it directly +if [ -z "${2}" ]; then + echo -e "\n${BASH_SOURCE[0]} was invoked without the C++ compiler as the second argument." + echo "This script is not indended to be directly invoked by any mechanism other" + echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake.\n" exit 1 fi # if there aren't two args, this isn't necessarily invalid, just a bit strange -if [ -z "${2}" ]; then exit 0; fi +if [ -z "${3}" ]; then exit 0; fi + +# store the Kokkos compiler +KOKKOS_COMPILER=${1} + +# remove the Kokkos compiler from the arguments +shift # store the expected C++ compiler CXX_COMPILER=${1} @@ -40,48 +65,57 @@ CXX_COMPILER=${1} # remove the expected C++ compiler from the arguments shift -# after the above shift, $1 is now the exe for the compile or link command, e.g. -# kokkos_launch_compiler g++ gcc -c file.c -o file.o +# NOTE: in below, ${KOKKOS_COMPILER} is usually nvcc_wrapper +# +# after the above shifts, $1 is now the exe for the compile or link command, e.g. +# kokkos_launch_compiler ${KOKKOS_COMPILER} g++ gcc -c file.c -o file.o # becomes: # kokkos_launch_compiler gcc -c file.c -o file.o -# Check to see if the executable is the C++ compiler and if it is not, then +# We check to see if the executable is the C++ compiler and if it is not, then # just execute the command. # # Summary: -# kokkos_launch_compiler g++ gcc -c file.c -o file.o +# kokkos_launch_compiler ${KOKKOS_COMPILER} g++ gcc -c file.c -o file.o # results in this command being executed: # gcc -c file.c -o file.o # and -# kokkos_launch_compiler g++ g++ -c file.cpp -o file.o +# kokkos_launch_compiler ${KOKKOS_COMPILER} g++ g++ -c file.cpp -o file.o # results in this command being executed: -# nvcc_wrapper -c file.cpp -o file.o +# ${KOKKOS_COMPILER} -c file.cpp -o file.o if [[ "${KOKKOS_DEPENDENCE}" -eq "0" || "${CXX_COMPILER}" != "${1}" ]]; then - # the command does not depend on Kokkos so just execute the command w/o re-directing to nvcc_wrapper + debug-message $@ + # the command does not depend on Kokkos so just execute the command w/o re-directing to ${KOKKOS_COMPILER} eval $@ else - # the executable is the C++ compiler, so we need to re-direct to nvcc_wrapper - - # find the nvcc_wrapper from the same build/install - NVCC_WRAPPER="$(dirname ${BASH_SOURCE[0]})/nvcc_wrapper" - - if [ -z "${NVCC_WRAPPER}" ]; then - echo -e "\nError: nvcc_wrapper not found in $(dirname ${BASH_SOURCE[0]}).\n" + # the executable is the C++ compiler, so we need to re-direct to ${KOKKOS_COMPILER} + if [ ! -f "${KOKKOS_COMPILER}" ]; then + echo -e "\nError: the compiler redirect for Kokkos was not found at ${KOKKOS_COMPILER}\n" exit 1 fi - # set default nvcc wrapper compiler if not specified - : ${NVCC_WRAPPER_DEFAULT_COMPILER:=${CXX_COMPILER}} - export NVCC_WRAPPER_DEFAULT_COMPILER + # find the nvcc_wrapper from the same build/install + NVCC_WRAPPER="$(dirname ${BASH_SOURCE[0]})/nvcc_wrapper" + if [ "${KOKKOS_COMPILER}" = "${NVCC_WRAPPER}" ]; then + # this should only be valid in the install tree -- it will be set to CMAKE_CXX_COMPILER used using Kokkos installation + if [ -z $(echo "@NVCC_WRAPPER_DEFAULT_COMPILER@" | grep 'NVCC_WRAPPER_DEFAULT_COMPILER') ]; then + : ${NVCC_WRAPPER_DEFAULT_COMPILER:="@NVCC_WRAPPER_DEFAULT_COMPILER@"} + fi - # calling itself will cause an infinitely long build - if [ "${NVCC_WRAPPER}" = "${NVCC_WRAPPER_DEFAULT_COMPILER}" ]; then - echo -e "\nError: NVCC_WRAPPER == NVCC_WRAPPER_DEFAULT_COMPILER. Terminating to avoid infinite loop!\n" - exit 1 + # set default nvcc wrapper compiler if not specified + : ${NVCC_WRAPPER_DEFAULT_COMPILER:=${CXX_COMPILER}} + export NVCC_WRAPPER_DEFAULT_COMPILER + + # nvcc_wrapper calling itself will cause an infinitely long build + if [ "${NVCC_WRAPPER}" = "${NVCC_WRAPPER_DEFAULT_COMPILER}" ]; then + echo -e "\nError: NVCC_WRAPPER == NVCC_WRAPPER_DEFAULT_COMPILER. Terminating to avoid infinite loop!\n" + exit 1 + fi fi # discard the compiler from the command shift - # execute nvcc_wrapper - ${NVCC_WRAPPER} $@ + debug-message ${KOKKOS_COMPILER} $@ + # execute ${KOKKOS_COMPILER} (again, usually nvcc_wrapper) + ${KOKKOS_COMPILER} $@ fi diff --git a/lib/kokkos/bin/nvcc_wrapper b/lib/kokkos/bin/nvcc_wrapper index 4ecf4c66d5..4e52e4d09f 100755 --- a/lib/kokkos/bin/nvcc_wrapper +++ b/lib/kokkos/bin/nvcc_wrapper @@ -67,6 +67,11 @@ shared_versioned_libraries="" # Does the User set the architecture arch_set=0 +arch_flag="" + +# Does the user set RDC? +rdc_set=0 +rdc_flag="" # Does the user overwrite the host compiler ccbin_set=0 @@ -190,22 +195,48 @@ do host_only_args="$host_only_args $1 $2" shift ;; + # Handle nvcc args controlling whether to generated relocatable device code + --relocatable-device-code=*|-rdc=*) + if [ "$rdc_set" -eq 0 ]; then + rdc_set=1 + rdc_flag="$1" + cuda_args="$cuda_args $rdc_flag" + elif [ "$rdc_flag" != "$1" ]; then + echo "RDC is being set twice with different flags, which is not handled" + echo "$rdc_flag" + echo "$1" + exit 1 + fi + ;; + -rdc) + if [ "$rdc_set" -eq 0 ]; then + rdc_set=1 + rdc_flag="$1 $2" + cuda_args="$cuda_args $rdc_flag" + shift + elif [ "$rdc_flag" != "$1 $2" ]; then + echo "RDC is being set twice with different flags, which is not handled" + echo "$rdc_flag" + echo "$1 $2" + exit 1 + fi + ;; #Handle known nvcc args - --dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|-expt-relaxed-constexpr|--resource-usage|-Xptxas*|--fmad*|--Wext-lambda-captures-this|-Wext-lambda-captures-this) + --dryrun|--verbose|--keep|--keep-dir*|-G|-lineinfo|-expt-extended-lambda|-expt-relaxed-constexpr|--resource-usage|-Xptxas*|--fmad=*|--use_fast_math|--Wext-lambda-captures-this|-Wext-lambda-captures-this) cuda_args="$cuda_args $1" ;; #Handle more known nvcc args - --expt-extended-lambda|--expt-relaxed-constexpr) + --expt-extended-lambda|--expt-relaxed-constexpr|--Wno-deprecated-gpu-targets|-Wno-deprecated-gpu-targets) cuda_args="$cuda_args $1" ;; #Handle known nvcc args that have an argument - -rdc|-maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart|-include) + -maxrregcount=*|--maxrregcount=*) + cuda_args="$cuda_args $1" + ;; + -maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart|-include) cuda_args="$cuda_args $1 $2" shift ;; - -rdc=*|-maxrregcount*|--maxrregcount*) - cuda_args="$cuda_args $1" - ;; #Handle unsupported standard flags --std=c++1y|-std=c++1y|--std=gnu++1y|-std=gnu++1y|--std=c++1z|-std=c++1z|--std=gnu++1z|-std=gnu++1z|--std=c++2a|-std=c++2a) fallback_std_flag="-std=c++14" @@ -323,20 +354,36 @@ do ;; #Handle -arch argument (if its not set use a default) this is the version with = sign - -arch*|-gencode*) - cuda_args="$cuda_args $1" - arch_set=1 + -arch=*|-gencode=*) + if [ "$arch_set" -eq 0 ]; then + arch_set=1 + arch_flag="$1" + cuda_args="$cuda_args $arch_flag" + elif [ "$arch_flag" != "$1" ]; then + echo "ARCH is being set twice with different flags, which is not handled" + echo "$arch_flag" + echo "$1" + exit 1 + fi + ;; + #Handle -arch argument (if its not set use a default) this is the version without = sign + -arch|-gencode) + if [ "$arch_set" -eq 0 ]; then + arch_set=1 + arch_flag="$1 $2" + cuda_args="$cuda_args $arch_flag" + shift + elif [ "$arch_flag" != "$1 $2" ]; then + echo "ARCH is being set twice with different flags, which is not handled" + echo "$arch_flag" + echo "$1 $2" + exit 1 + fi ;; #Handle -code argument (if its not set use a default) this is the version with = sign -code*) cuda_args="$cuda_args $1" ;; - #Handle -arch argument (if its not set use a default) this is the version without = sign - -arch|-gencode) - cuda_args="$cuda_args $1 $2" - arch_set=1 - shift - ;; #Handle -code argument (if its not set use a default) this is the version without = sign -code) cuda_args="$cuda_args $1 $2" diff --git a/lib/kokkos/cmake/CTestConfig.cmake.in b/lib/kokkos/cmake/CTestConfig.cmake.in new file mode 100644 index 0000000000..1f82c0d64d --- /dev/null +++ b/lib/kokkos/cmake/CTestConfig.cmake.in @@ -0,0 +1,91 @@ +#----------------------------------------------------------------------------------------# +# +# CTestConfig.cmake template for Kokkos +# +#----------------------------------------------------------------------------------------# + +# +# dash-board related +# +set(CTEST_PROJECT_NAME "Kokkos") +set(CTEST_NIGHTLY_START_TIME "01:00:00 UTC") +set(CTEST_DROP_METHOD "https") +set(CTEST_DROP_SITE "cdash.nersc.gov") +set(CTEST_DROP_LOCATION "/submit.php?project=${CTEST_PROJECT_NAME}") +set(CTEST_CDASH_VERSION "1.6") +set(CTEST_CDASH_QUERY_VERSION TRUE) +set(CTEST_SUBMIT_RETRY_COUNT "1") +set(CTEST_SUBMIT_RETRY_DELAY "30") + +# +# configure/build related +# +set(CTEST_BUILD_NAME "@BUILD_NAME@") +set(CTEST_MODEL "@MODEL@") +set(CTEST_SITE "@SITE@") +set(CTEST_CONFIGURATION_TYPE "@BUILD_TYPE@") +set(CTEST_SOURCE_DIRECTORY "@SOURCE_REALDIR@") +set(CTEST_BINARY_DIRECTORY "@BINARY_REALDIR@") + +# +# configure/build related +# +set(CTEST_UPDATE_TYPE "git") +set(CTEST_UPDATE_VERSION_ONLY ON) +# set(CTEST_GENERATOR "") +# set(CTEST_GENERATOR_PLATFORM "") + +# +# testing related +# +set(CTEST_TIMEOUT "7200") +set(CTEST_TEST_TIMEOUT "7200") +set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_ERRORS "100") +set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_WARNINGS "100") +set(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE "1048576") + +# +# coverage related +# +set(CTEST_CUSTOM_COVERAGE_EXCLUDE ".*tpls/.*;/usr/.*;.*unit_test/.*;.*unit_tests/.*;.*perf_test/.*") + +# +# commands +# +if(NOT "@CHECKOUT_COMMAND@" STREQUAL "") + set(CTEST_CHECKOUT_COMMAND "@CHECKOUT_COMMAND@") +endif() +set(CTEST_UPDATE_COMMAND "@GIT_EXECUTABLE@") +set(CTEST_CONFIGURE_COMMAND "@CMAKE_COMMAND@ -DCMAKE_BUILD_TYPE=@BUILD_TYPE@ -DKokkos_ENABLE_TESTS=ON @CONFIG_ARGS@ @SOURCE_REALDIR@") +set(CTEST_BUILD_COMMAND "@CMAKE_COMMAND@ --build @BINARY_REALDIR@ --target @TARGET@") +if(NOT WIN32) + set(CTEST_BUILD_COMMAND "${CTEST_BUILD_COMMAND} -- -j@BUILD_JOBS@") +endif() +set(CTEST_COVERAGE_COMMAND "gcov") +set(CTEST_MEMORYCHECK_COMMAND "valgrind") +set(CTEST_GIT_COMMAND "@GIT_EXECUTABLE@") + +# +# various configs +# +set(APPEND_VALUE @APPEND@) +if(APPEND_VALUE) + set(APPEND_CTEST APPEND) +endif() + +macro(SET_TEST_PROP VAR) + if(NOT "${ARGS}" STREQUAL "") + set(${VAR}_CTEST ${VAR} ${ARGN}) + endif() +endmacro() + +set_test_prop(START @START@) +set_test_prop(END @END@) +set_test_prop(STRIDE @STRIDE@) +set_test_prop(INCLUDE @INCLUDE@) +set_test_prop(EXCLUDE @EXCLUDE@) +set_test_prop(INCLUDE_LABEL @INCLUDE_LABEL@) +set_test_prop(EXCLUDE_LABEL @EXCLUDE_LABEL@) +set_test_prop(PARALLEL_LEVEL @PARALLEL_LEVEL@) +set_test_prop(STOP_TIME @STOP_TIME@) +set_test_prop(COVERAGE_LABELS @LABELS@) diff --git a/lib/kokkos/cmake/KokkosCI.cmake b/lib/kokkos/cmake/KokkosCI.cmake new file mode 100644 index 0000000000..e8c9af37ad --- /dev/null +++ b/lib/kokkos/cmake/KokkosCI.cmake @@ -0,0 +1,350 @@ +cmake_minimum_required(VERSION 3.16 FATAL_ERROR) + +message(STATUS "") + +get_cmake_property(_cached_vars CACHE_VARIABLES) +set(KOKKOS_CMAKE_ARGS) +set(EXCLUDED_VARIABLES "CMAKE_COMMAND" "CMAKE_CPACK_COMMAND" "CMAKE_CTEST_COMMAND" "CMAKE_ROOT" + "CTEST_ARGS" "BUILD_NAME" "CMAKE_CXX_FLAGS" "CMAKE_BUILD_TYPE") +list(SORT _cached_vars) +foreach(_var ${_cached_vars}) + if(NOT "${_var}" IN_LIST EXCLUDED_VARIABLES) + list(APPEND KOKKOS_CMAKE_ARGS ${_var}) + if("${_var}" STREQUAL "CMAKE_BUILD_TYPE") + set(BUILD_TYPE "${CMAKE_BUILD_TYPE}") + endif() + endif() +endforeach() + + +#----------------------------------------------------------------------------------------# +# +# Macros and variables +# +#----------------------------------------------------------------------------------------# + +macro(CHECK_REQUIRED VAR) + if(NOT DEFINED ${VAR}) + message(FATAL_ERROR "Error! Variable '${VAR}' must be defined") + endif() +endmacro() + +# require the build name variable +CHECK_REQUIRED(BUILD_NAME) + +# uses all args +macro(SET_DEFAULT VAR) + if(NOT DEFINED ${VAR}) + set(${VAR} ${ARGN}) + endif() + # remove these ctest configuration variables from the defines + # passed to the Kokkos configuration + if("${VAR}" IN_LIST KOKKOS_CMAKE_ARGS) + list(REMOVE_ITEM KOKKOS_CMAKE_ARGS "${VAR}") + endif() +endmacro() + +# uses first arg -- useful for selecting via priority from multiple +# potentially defined variables, e.g.: +# +# set_default_arg1(BUILD_NAME ${TRAVIS_BUILD_NAME} ${BUILD_NAME}) +# +macro(SET_DEFAULT_ARG1 VAR) + if(NOT DEFINED ${VAR}) + foreach(_ARG ${ARGN}) + if(NOT "${_ARG}" STREQUAL "") + set(${VAR} ${_ARG}) + break() + endif() + endforeach() + endif() + # remove these ctest configuration variables from the defines + # passed to the Kokkos configuration + if("${VAR}" IN_LIST KOKKOS_CMAKE_ARGS) + list(REMOVE_ITEM KOKKOS_CMAKE_ARGS "${VAR}") + endif() +endmacro() + +# determine the default working directory +if(NOT "$ENV{WORKSPACE}" STREQUAL "") + set(WORKING_DIR "$ENV{WORKSPACE}") +else() + get_filename_component(WORKING_DIR ${CMAKE_CURRENT_LIST_DIR} DIRECTORY) +endif() + +# determine the hostname +execute_process(COMMAND hostname + OUTPUT_VARIABLE HOSTNAME + OUTPUT_STRIP_TRAILING_WHITESPACE) + +SET_DEFAULT(HOSTNAME "$ENV{HOSTNAME}") + +# get the number of processors +include(ProcessorCount) +ProcessorCount(NUM_PROCESSORS) + +# find git +find_package(Git QUIET) +if(NOT GIT_EXECUTABLE) + unset(GIT_EXECUTABLE CACHE) + unset(GIT_EXECUTABLE) +endif() + +function(EXECUTE_GIT_COMMAND VAR) + set(${VAR} "" PARENT_SCOPE) + execute_process(COMMAND ${GIT_EXECUTABLE} ${ARGN} + OUTPUT_VARIABLE VAL + RESULT_VARIABLE RET + OUTPUT_STRIP_TRAILING_WHITESPACE + WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR} + ERROR_QUIET) + string(REPLACE ";" " " _CMD "${GIT_EXECUTABLE} ${ARGN}") + set(LAST_GIT_COMMAND "${_CMD}" PARENT_SCOPE) + if(RET EQUAL 0) + set(${VAR} "${VAL}" PARENT_SCOPE) + endif() +endfunction() + +# just gets the git branch name if available +function(GET_GIT_BRANCH_NAME VAR) + execute_git_command(GIT_BRANCH branch --show-current) + set(_INVALID "%D" "HEAD") + if(NOT GIT_BRANCH OR "${GIT_BRANCH}" IN_LIST _INVALID) + execute_git_command(GIT_BRANCH show -s --format=%D) + if(NOT GIT_BRANCH OR "${GIT_BRANCH}" IN_LIST _INVALID) + execute_git_command(GIT_BRANCH --describe all) + endif() + endif() + # + if(GIT_BRANCH) + string(REPLACE " " ";" _DESC "${GIT_BRANCH}") + # just set it to last one via loop instead of wonky cmake index manip + foreach(_ITR ${_DESC}) + set(GIT_BRANCH "${_ITR}") + endforeach() + set(${VAR} "${GIT_BRANCH}" PARENT_SCOPE) + message(STATUS "GIT BRANCH via '${LAST_GIT_COMMAND}': ${GIT_BRANCH}") + endif() +endfunction() + +# just gets the git branch name if available +function(GET_GIT_AUTHOR_NAME VAR) + execute_git_command(GIT_AUTHOR show -s --format=%an) + if(GIT_AUTHOR) + string(LENGTH "${GIT_AUTHOR}" STRLEN) + # if the build name gets too long, this can cause submission errors + if(STRLEN GREATER 24) + # remove middle initial + string(REGEX REPLACE " [A-Z]\. " " " GIT_AUTHOR "${GIT_AUTHOR}") + # get first and sur name + string(REGEX REPLACE "([A-Za-z]+) ([A-Za-z]+)" "\\1" F_NAME "${GIT_AUTHOR}") + string(REGEX REPLACE "([A-Za-z]+) ([A-Za-z]+)" "\\2" S_NAME "${GIT_AUTHOR}") + if(S_NAME) + set(GIT_AUTHOR "${S_NAME}") + elseif(F_NAME) + set(GIT_AUTHOR "${F_NAME}") + endif() + endif() + # remove any spaces, quotes, periods, etc. + string(REGEX REPLACE "[ ',;_\.\"]+" "" GIT_AUTHOR "${GIT_AUTHOR}") + set(${VAR} "${GIT_AUTHOR}" PARENT_SCOPE) + message(STATUS "GIT AUTHOR via '${LAST_GIT_COMMAND}': ${GIT_AUTHOR}") + endif() +endfunction() + +# get the name of the branch +GET_GIT_BRANCH_NAME(GIT_BRANCH) +# get the name of the author +GET_GIT_AUTHOR_NAME(GIT_AUTHOR) +# author, prefer git method for consistency +SET_DEFAULT_ARG1(AUTHOR ${GIT_AUTHOR} $ENV{GIT_AUTHOR} $ENV{AUTHOR}) +# SLUG == owner_name/repo_name +SET_DEFAULT_ARG1(SLUG $ENV{TRAVIS_PULL_REQUEST_SLUG} $ENV{TRAVIS_REPO_SLUG} $ENV{APPVEYOR_REPO_NAME} $ENV{PULL_REQUEST_SLUG} $ENV{REPO_SLUG}) +# branch name +SET_DEFAULT_ARG1(BRANCH $ENV{TRAVIS_PULL_REQUEST_BRANCH} $ENV{TRAVIS_BRANCH} $ENV{APPVEYOR_PULL_REQUEST_HEAD_REPO_BRANCH} $ENV{APPVEYOR_REPO_BRANCH} $ENV{GIT_BRANCH} $ENV{BRANCH_NAME} $ENV{BRANCH} ${GIT_BRANCH}) +# pull request number +SET_DEFAULT_ARG1(PULL_REQUEST_NUM $ENV{TRAVIS_PULL_REQUEST} $ENV{CHANGE_ID} $ENV{APPVEYOR_PULL_REQUEST_NUMBER} $ENV{PULL_REQUEST_NUM}) +# get the event type, e.g. push, pull_request, api, cron, etc. +SET_DEFAULT_ARG1(EVENT_TYPE $ENV{TRAVIS_EVENT_TYPE} ${EVENT_TYPE}) + +if("${BRANCH}" STREQUAL "") + message(STATUS "Checked: environment variables for Travis, Appveyor, Jenkins (git plugin), BRANCH_NAME, BRANCH and 'git branch --show-current'") + message(FATAL_ERROR "Error! Git branch could not be determined. Please provide -DBRANCH=") +endif() + +#----------------------------------------------------------------------------------------# +# +# Set default values if not provided on command-line +# +#----------------------------------------------------------------------------------------# + +SET_DEFAULT(SOURCE_DIR "${WORKING_DIR}") # source directory +SET_DEFAULT(BINARY_DIR "${WORKING_DIR}/build") # build directory +SET_DEFAULT(BUILD_TYPE "${CMAKE_BUILD_TYPE}") # Release, Debug, etc. +SET_DEFAULT(MODEL "Continuous") # Continuous, Nightly, or Experimental +SET_DEFAULT(JOBS 1) # number of parallel ctests +SET_DEFAULT(CTEST_COMMAND "${CMAKE_CTEST_COMMAND}") # just in case +SET_DEFAULT(CTEST_ARGS "-V --output-on-failure") # extra arguments when ctest is called +SET_DEFAULT(GIT_EXECUTABLE "git") # ctest_update +SET_DEFAULT(TARGET "all") # build target +SET_DEFAULT_ARG1(SITE "$ENV{SITE}" + "${HOSTNAME}") # update site +SET_DEFAULT_ARG1(BUILD_JOBS "$ENV{BUILD_JOBS}" + "${NUM_PROCESSORS}") # number of parallel compile jobs +# +# The variable below correspond to ctest arguments, i.e. START,END,STRIDE are +# '-I START,END,STRIDE' +# +SET_DEFAULT(START "") +SET_DEFAULT(END "") +SET_DEFAULT(STRIDE "") +SET_DEFAULT(INCLUDE "") +SET_DEFAULT(EXCLUDE "") +SET_DEFAULT(INCLUDE_LABEL "") +SET_DEFAULT(EXCLUDE_LABEL "") +SET_DEFAULT(PARALLEL_LEVEL "") +SET_DEFAULT(STOP_TIME "") +SET_DEFAULT(LABELS "") +SET_DEFAULT(NOTES "") + +# default static build tag for Nightly +set(BUILD_TAG "${BRANCH}") + +if(NOT BUILD_TYPE) + # default for kokkos if not specified + set(BUILD_TYPE "RelWithDebInfo") +endif() + +# generate dynamic name if continuous or experimental model +if(NOT "${MODEL}" STREQUAL "Nightly") + if(EVENT_TYPE AND PULL_REQUEST_NUM) + # e.g. pull_request/123 + if(AUTHOR) + set(BUILD_TAG "${AUTHOR}/${EVENT_TYPE}/${PULL_REQUEST_NUM}") + else() + set(BUILD_TAG "${EVENT_TYPE}/${PULL_REQUEST_NUM}") + endif() + elseif(SLUG) + # e.g. owner_name/repo_name + set(BUILD_TAG "${SLUG}") + elseif(AUTHOR) + set(BUILD_TAG "${AUTHOR}/${BRANCH}") + endif() + if(EVENT_TYPE AND NOT PULL_REQUEST_NUM) + set(BUILD_TAG "${BUILD_TAG}-${EVENT_TYPE}") + endif() +endif() + +# unnecessary +string(REPLACE "/remotes/" "/" BUILD_TAG "${BUILD_TAG}") +string(REPLACE "/origin/" "/" BUILD_TAG "${BUILD_TAG}") + +message(STATUS "BUILD_TAG: ${BUILD_TAG}") + +set(BUILD_NAME "[${BUILD_TAG}] [${BUILD_NAME}-${BUILD_TYPE}]") + +# colons in build name create extra (empty) entries in CDash +string(REPLACE ":" "-" BUILD_NAME "${BUILD_NAME}") +# unnecessary info +string(REPLACE "/merge]" "]" BUILD_NAME "${BUILD_NAME}") +# consistency +string(REPLACE "/pr/" "/pull/" BUILD_NAME "${BUILD_NAME}") +string(REPLACE "pull_request/" "pull/" BUILD_NAME "${BUILD_NAME}") +# miscellaneous from missing fields +string(REPLACE "--" "-" BUILD_NAME "${BUILD_NAME}") +string(REPLACE "-]" "]" BUILD_NAME "${BUILD_NAME}") + +# check binary directory +if(EXISTS ${BINARY_DIR}) + if(NOT IS_DIRECTORY "${BINARY_DIR}") + message(FATAL_ERROR "Error! '${BINARY_DIR}' already exists and is not a directory!") + endif() + file(GLOB BINARY_DIR_FILES "${BINARY_DIR}/*") + if(NOT "${BINARY_DIR_FILES}" STREQUAL "") + message(FATAL_ERROR "Error! '${BINARY_DIR}' already exists and is not empty!") + endif() +endif() + +get_filename_component(SOURCE_REALDIR ${SOURCE_DIR} REALPATH) +get_filename_component(BINARY_REALDIR ${BINARY_DIR} REALPATH) + +#----------------------------------------------------------------------------------------# +# +# Generate the CTestConfig.cmake +# +#----------------------------------------------------------------------------------------# + +set(CONFIG_ARGS) +foreach(_ARG ${KOKKOS_CMAKE_ARGS}) + if(NOT "${${_ARG}}" STREQUAL "") + get_property(_ARG_TYPE CACHE ${_ARG} PROPERTY TYPE) + if("${_ARG_TYPE}" STREQUAL "UNINITIALIZED") + if("${${_ARG}}" STREQUAL "ON" OR "${${_ARG}}" STREQUAL "OFF") + set(_ARG_TYPE "BOOL") + elseif(EXISTS "${${_ARG}}" AND NOT IS_DIRECTORY "${${_ARG}}") + set(_ARG_TYPE "FILEPATH") + elseif(EXISTS "${${_ARG}}" AND IS_DIRECTORY "${${_ARG}}") + set(_ARG_TYPE "PATH") + elseif(NOT "${${_ARG}}" STREQUAL "") + set(_ARG_TYPE "STRING") + endif() + endif() + set(CONFIG_ARGS "${CONFIG_ARGS}set(${_ARG} \"${${_ARG}}\" CACHE ${_ARG_TYPE} \"\")\n") + endif() +endforeach() + +file(WRITE ${BINARY_REALDIR}/initial-cache.cmake +" +set(CMAKE_CXX_FLAGS \"${CMAKE_CXX_FLAGS}\" CACHE STRING \"\") +${CONFIG_ARGS} +") + +file(READ ${BINARY_REALDIR}/initial-cache.cmake _CACHE_INFO) +message(STATUS "Initial cache:\n${_CACHE_INFO}") + +# initialize the cache +set(CONFIG_ARGS "-C ${BINARY_REALDIR}/initial-cache.cmake") + + +# generate the CTestConfig.cmake +configure_file( + ${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake.in + ${BINARY_REALDIR}/CTestConfig.cmake + @ONLY) + +# copy/generate the dashboard script +configure_file( + ${CMAKE_CURRENT_LIST_DIR}/KokkosCTest.cmake.in + ${BINARY_REALDIR}/KokkosCTest.cmake + @ONLY) + +# custom CTest settings go in ${BINARY_DIR}/CTestCustom.cmake +execute_process( + COMMAND ${CMAKE_COMMAND} -E touch CTestCustom.cmake + WORKING_DIRECTORY ${BINARY_REALDIR} + ) + +#----------------------------------------------------------------------------------------# +# +# Execute CTest +# +#----------------------------------------------------------------------------------------# + +message(STATUS "") +message(STATUS "BUILD_NAME: ${BUILD_NAME}") +message(STATUS "Executing '${CTEST_COMMAND} -S KokkosCTest.cmake ${CTEST_ARGS}'...") +message(STATUS "") + +# e.g. -DCTEST_ARGS="--output-on-failure -VV" should really be -DCTEST_ARGS="--output-on-failure;-VV" +string(REPLACE " " ";" CTEST_ARGS "${CTEST_ARGS}") + +execute_process( + COMMAND ${CTEST_COMMAND} -S KokkosCTest.cmake ${CTEST_ARGS} + RESULT_VARIABLE RET + WORKING_DIRECTORY ${BINARY_REALDIR} + ) + +# ensure that any non-zero result variable gets propagated +if(NOT RET EQUAL 0) + message(FATAL_ERROR "CTest return non-zero exit code: ${RET}") +endif() diff --git a/lib/kokkos/cmake/KokkosCTest.cmake.in b/lib/kokkos/cmake/KokkosCTest.cmake.in new file mode 100644 index 0000000000..b6917f3cc1 --- /dev/null +++ b/lib/kokkos/cmake/KokkosCTest.cmake.in @@ -0,0 +1,261 @@ +cmake_minimum_required(VERSION 3.16 FATAL_ERROR) + +if(EXISTS "${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake") + include("${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake") +endif() + +include(ProcessorCount) +ProcessorCount(CTEST_PROCESSOR_COUNT) + +cmake_policy(SET CMP0009 NEW) +cmake_policy(SET CMP0011 NEW) + +# ---------------------------------------------------------------------------- # +# -- Commands +# ---------------------------------------------------------------------------- # +find_program(CTEST_CMAKE_COMMAND NAMES cmake) +find_program(CTEST_UNAME_COMMAND NAMES uname) + +find_program(CTEST_BZR_COMMAND NAMES bzr) +find_program(CTEST_CVS_COMMAND NAMES cvs) +find_program(CTEST_GIT_COMMAND NAMES git) +find_program(CTEST_HG_COMMAND NAMES hg) +find_program(CTEST_P4_COMMAND NAMES p4) +find_program(CTEST_SVN_COMMAND NAMES svn) + +find_program(VALGRIND_COMMAND NAMES valgrind) +find_program(GCOV_COMMAND NAMES gcov) +find_program(LCOV_COMMAND NAMES llvm-cov) +find_program(MEMORYCHECK_COMMAND NAMES valgrind ) + +set(MEMORYCHECK_TYPE Valgrind) +# set(MEMORYCHECK_TYPE Purify) +# set(MEMORYCHECK_TYPE BoundsChecker) +# set(MEMORYCHECK_TYPE ThreadSanitizer) +# set(MEMORYCHECK_TYPE AddressSanitizer) +# set(MEMORYCHECK_TYPE LeakSanitizer) +# set(MEMORYCHECK_TYPE MemorySanitizer) +# set(MEMORYCHECK_TYPE UndefinedBehaviorSanitizer) +set(MEMORYCHECK_COMMAND_OPTIONS "--trace-children=yes --leak-check=full") + +# ---------------------------------------------------------------------------- # +# -- Settings +# ---------------------------------------------------------------------------- # +## -- Process timeout in seconds +set(CTEST_TIMEOUT "7200") +## -- Set output to English +set(ENV{LC_MESSAGES} "en_EN" ) + + +# ---------------------------------------------------------------------------- # +# -- Copy ctest configuration file +# ---------------------------------------------------------------------------- # +macro(COPY_CTEST_CONFIG_FILES) + + foreach(_FILE CTestConfig.cmake CTestCustom.cmake) + + # if current directory is not binary or source directory + if(NOT "${CMAKE_CURRENT_LIST_DIR}" STREQUAL "${CTEST_BINARY_DIRECTORY}" AND + NOT "${CTEST_SOURCE_DIRECTORY}" STREQUAL "${CTEST_BINARY_DIRECTORY}") + + # if file exists in current directory + if(EXISTS ${CMAKE_CURRENT_LIST_DIR}/${_FILE}) + configure_file(${CMAKE_CURRENT_LIST_DIR}/${_FILE} + ${CTEST_BINARY_DIRECTORY}/${_FILE} COPYONLY) + endif() + + # if source and binary differ + elseif(NOT "${CTEST_SOURCE_DIRECTORY}" STREQUAL "${CTEST_BINARY_DIRECTORY}") + + # if file exists in source directory but not in binary directory + if(EXISTS ${CTEST_SOURCE_DIRECTORY}/${_FILE} AND + NOT EXISTS ${CTEST_BINARY_DIRECTORY}/${_FILE}) + configure_file(${CTEST_SOURCE_DIRECTORY}/${_FILE} + ${CTEST_BINARY_DIRECTORY}/${_FILE} COPYONLY) + endif() + + endif() + endforeach() + +endmacro() + +ctest_read_custom_files("${CMAKE_CURRENT_LIST_DIR}") + +message(STATUS "CTEST_MODEL: ${CTEST_MODEL}") + +#-------------------------------------------------------------------------# +# Start +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running START_CTEST stage...") +message(STATUS "") + +ctest_start(${CTEST_MODEL} TRACK ${CTEST_MODEL} ${APPEND_CTEST} + ${CTEST_SOURCE_DIRECTORY} ${CTEST_BINARY_DIRECTORY}) + + +#-------------------------------------------------------------------------# +# Config +# +copy_ctest_config_files() +ctest_read_custom_files("${CTEST_BINARY_DIRECTORY}") + + +#-------------------------------------------------------------------------# +# Update +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_UPDATE stage...") +message(STATUS "") + +ctest_update(SOURCE "${CTEST_SOURCE_DIRECTORY}" + RETURN_VALUE up_ret) + + +#-------------------------------------------------------------------------# +# Configure +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_CONFIGURE stage...") +message(STATUS "") + +ctest_configure(BUILD "${CTEST_BINARY_DIRECTORY}" + SOURCE ${CTEST_SOURCE_DIRECTORY} + ${APPEND_CTEST} + OPTIONS "${CTEST_CONFIGURE_OPTIONS}" + RETURN_VALUE config_ret) + + +#-------------------------------------------------------------------------# +# Echo configure log bc Damien wants to delay merging this PR for eternity +# +file(GLOB _configure_log "${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastConfigure*.log") +# should only have one but loop just for safety +foreach(_LOG ${_configure_log}) + file(READ ${_LOG} _LOG_MESSAGE) + message(STATUS "Configure Log: ${_LOG}") + message(STATUS "\n${_LOG_MESSAGE}\n") +endforeach() + + +#-------------------------------------------------------------------------# +# Build +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_BUILD stage...") +message(STATUS "") + +ctest_build(BUILD "${CTEST_BINARY_DIRECTORY}" + ${APPEND_CTEST} + RETURN_VALUE build_ret) + + +#-------------------------------------------------------------------------# +# Echo build log bc Damien wants to delay merging this PR for eternity +# +file(GLOB _build_log "${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastBuild*.log") +# should only have one but loop just for safety +foreach(_LOG ${_build_log}) + file(READ ${_LOG} _LOG_MESSAGE) + message(STATUS "Build Log: ${_LOG}") + message(STATUS "\n${_LOG_MESSAGE}\n") +endforeach() + + +#-------------------------------------------------------------------------# +# Test +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_TEST stage...") +message(STATUS "") + +ctest_test(RETURN_VALUE test_ret + ${APPEND_CTEST} + ${START_CTEST} + ${END_CTEST} + ${STRIDE_CTEST} + ${INCLUDE_CTEST} + ${EXCLUDE_CTEST} + ${INCLUDE_LABEL_CTEST} + ${EXCLUDE_LABEL_CTEST} + ${PARALLEL_LEVEL_CTEST} + ${STOP_TIME_CTEST} + SCHEDULE_RANDOM OFF) + + +#-------------------------------------------------------------------------# +# Coverage +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_COVERAGE stage...") +message(STATUS "") + +execute_process(COMMAND ${CTEST_COVERAGE_COMMAND} ${CTEST_COVERAGE_EXTRA_FLAGS} + WORKING_DIRECTORY ${CTEST_BINARY_DIRECTORY} + ERROR_QUIET) + +ctest_coverage(${APPEND_CTEST} + ${CTEST_COVERAGE_LABELS} + RETURN_VALUE cov_ret) + + +#-------------------------------------------------------------------------# +# MemCheck +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_MEMCHECK stage...") +message(STATUS "") + +ctest_memcheck(RETURN_VALUE mem_ret + ${APPEND_CTEST} + ${START_CTEST} + ${END_CTEST} + ${STRIDE_CTEST} + ${INCLUDE_CTEST} + ${EXCLUDE_CTEST} + ${INCLUDE_LABEL_CTEST} + ${EXCLUDE_LABEL_CTEST} + ${PARALLEL_LEVEL_CTEST}) + + +#-------------------------------------------------------------------------# +# Submit +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_SUBMIT stage...") +message(STATUS "") + +file(GLOB_RECURSE NOTE_FILES "${CTEST_BINARY_DIRECTORY}/*CTestNotes.cmake") +foreach(_FILE ${NOTE_FILES}) + message(STATUS "Including CTest notes files: \"${_FILE}\"...") + include("${_FILE}") +endforeach() + +# capture submit error so it doesn't fail because of a submission error +ctest_submit(RETURN_VALUE submit_ret + RETRY_COUNT 2 + RETRY_DELAY 10 + CAPTURE_CMAKE_ERROR submit_err) + +#-------------------------------------------------------------------------# +# Submit +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Finished ${CTEST_MODEL} Stages (${STAGES})") +message(STATUS "") + + +#-------------------------------------------------------------------------# +# Non-zero exit codes for important errors +# +if(NOT config_ret EQUAL 0) + message(FATAL_ERROR "Error during configuration! Exit code: ${config_ret}") +endif() + +if(NOT build_ret EQUAL 0) + message(FATAL_ERROR "Error during build! Exit code: ${build_ret}") +endif() + +if(NOT test_ret EQUAL 0) + message(FATAL_ERROR "Error during testing! Exit code: ${test_ret}") +endif() diff --git a/lib/kokkos/cmake/KokkosConfig.cmake.in b/lib/kokkos/cmake/KokkosConfig.cmake.in index 9fbd22ee5c..44a8fcd9c3 100644 --- a/lib/kokkos/cmake/KokkosConfig.cmake.in +++ b/lib/kokkos/cmake/KokkosConfig.cmake.in @@ -19,17 +19,44 @@ INCLUDE("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake") INCLUDE("${Kokkos_CMAKE_DIR}/KokkosConfigCommon.cmake") UNSET(Kokkos_CMAKE_DIR) -# if CUDA was enabled and separable compilation was specified, e.g. -# find_package(Kokkos COMPONENTS separable_compilation) -# then we set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK -IF(@Kokkos_ENABLE_CUDA@ AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) +# check for conflicts +IF("launch_compiler" IN_LIST Kokkos_FIND_COMPONENTS AND + "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) + MESSAGE(STATUS "'launch_compiler' implies global redirection of targets depending on Kokkos to appropriate compiler.") + MESSAGE(STATUS "'separable_compilation' implies explicitly defining where redirection occurs via 'kokkos_compilation(PROJECT|TARGET|SOURCE|DIRECTORY ...)'") + MESSAGE(FATAL_ERROR "Conflicting COMPONENTS: 'launch_compiler' and 'separable_compilation'") +ENDIF() + +IF("launch_compiler" IN_LIST Kokkos_FIND_COMPONENTS) + # + # if find_package(Kokkos COMPONENTS launch_compiler) then rely on the + # RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK to always redirect to the + # appropriate compiler for Kokkos + # + + MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to the appropriate compiler for Kokkos") + kokkos_compilation( + GLOBAL + CHECK_CUDA_COMPILES) + +ELSEIF(@Kokkos_ENABLE_CUDA@ AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) + # + # if CUDA was enabled, separable compilation was not specified, and current compiler + # cannot compile CUDA, then set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK globally and + # kokkos_launch_compiler will re-direct to the compiler used to compile CUDA code during installation. + # kokkos_launch_compiler will re-direct if ${CMAKE_CXX_COMPILER} and -DKOKKOS_DEPENDENCE is present, + # otherwise, the original command will be executed + # + # run test to see if CMAKE_CXX_COMPILER=nvcc_wrapper kokkos_compiler_is_nvcc(IS_NVCC ${CMAKE_CXX_COMPILER}) - # if not nvcc_wrapper, use RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK - IF(NOT IS_NVCC AND NOT CMAKE_CXX_COMPILER_ID STREQUAL Clang AND - (NOT DEFINED Kokkos_LAUNCH_COMPILER OR Kokkos_LAUNCH_COMPILER)) - MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to nvcc_wrapper") + + # if not nvcc_wrapper and Kokkos_LAUNCH_COMPILER was not set to OFF + IF(NOT IS_NVCC AND (NOT DEFINED Kokkos_LAUNCH_COMPILER OR Kokkos_LAUNCH_COMPILER)) + MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to the appropriate compiler for Kokkos") kokkos_compilation(GLOBAL) ENDIF() - UNSET(IS_NVCC) # be mindful of the environment, pollution is bad + + # be mindful of the environment, pollution is bad + UNSET(IS_NVCC) ENDIF() diff --git a/lib/kokkos/cmake/KokkosConfigCommon.cmake.in b/lib/kokkos/cmake/KokkosConfigCommon.cmake.in index 42c755c215..ab93e65afe 100644 --- a/lib/kokkos/cmake/KokkosConfigCommon.cmake.in +++ b/lib/kokkos/cmake/KokkosConfigCommon.cmake.in @@ -3,6 +3,7 @@ SET(Kokkos_OPTIONS @KOKKOS_ENABLED_OPTIONS@) SET(Kokkos_TPLS @KOKKOS_ENABLED_TPLS@) SET(Kokkos_ARCH @KOKKOS_ENABLED_ARCH_LIST@) SET(Kokkos_CXX_COMPILER "@CMAKE_CXX_COMPILER@") +SET(Kokkos_CXX_COMPILER_ID "@KOKKOS_CXX_COMPILER_ID@") # These are needed by KokkosKernels FOREACH(DEV ${Kokkos_DEVICES}) @@ -13,13 +14,13 @@ IF(NOT Kokkos_FIND_QUIETLY) MESSAGE(STATUS "Enabled Kokkos devices: ${Kokkos_DEVICES}") ENDIF() -IF (Kokkos_ENABLE_CUDA AND ${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.14.0") - #If we are building CUDA, we have tricked CMake because we declare a CXX project - #If the default C++ standard for a given compiler matches the requested - #standard, then CMake just omits the -std flag in later versions of CMake - #This breaks CUDA compilation (CUDA compiler can have a different default - #-std then the underlying host compiler by itself). Setting this variable - #forces CMake to always add the -std flag even if it thinks it doesn't need it +IF (Kokkos_ENABLE_CUDA) + # If we are building CUDA, we have tricked CMake because we declare a CXX project + # If the default C++ standard for a given compiler matches the requested + # standard, then CMake just omits the -std flag in later versions of CMake + # This breaks CUDA compilation (CUDA compiler can have a different default + # -std then the underlying host compiler by itself). Setting this variable + # forces CMake to always add the -std flag even if it thinks it doesn't need it SET(CMAKE_CXX_STANDARD_DEFAULT 98 CACHE INTERNAL "" FORCE) ENDIF() @@ -90,52 +91,6 @@ function(kokkos_check) endif() endfunction() -# this function is provided to easily select which files use nvcc_wrapper: -# -# GLOBAL --> all files -# TARGET --> all files in a target -# SOURCE --> specific source files -# DIRECTORY --> all files in directory -# PROJECT --> all files/targets in a project/subproject -# -FUNCTION(kokkos_compilation) - CMAKE_PARSE_ARGUMENTS(COMP "GLOBAL;PROJECT" "" "DIRECTORY;TARGET;SOURCE" ${ARGN}) - - # search relative first and then absolute - SET(_HINTS "${CMAKE_CURRENT_LIST_DIR}/../.." "@CMAKE_INSTALL_PREFIX@") - - # find kokkos_launch_compiler - FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER - NAMES kokkos_launch_compiler - HINTS ${_HINTS} - PATHS ${_HINTS} - PATH_SUFFIXES bin) - - IF(NOT Kokkos_COMPILE_LAUNCHER) - MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'") - ENDIF() - - IF(COMP_GLOBAL) - # if global, don't bother setting others - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - ELSE() - FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE) - # make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...) - IF("${_TYPE}" STREQUAL "PROJECT" AND COMP_${_TYPE}) - LIST(APPEND COMP_DIRECTORY ${PROJECT_SOURCE_DIR}) - UNSET(COMP_${_TYPE}) - ENDIF() - # set the properties if defined - IF(COMP_${_TYPE}) - # MESSAGE(STATUS "Using nvcc_wrapper :: ${_TYPE} :: ${COMP_${_TYPE}}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - ENDIF() - ENDFOREACH() - ENDIF() -ENDFUNCTION() - # A test to check whether a downstream project set the C++ compiler to NVCC or not # this is called only when Kokkos was installed with Kokkos_ENABLE_CUDA=ON FUNCTION(kokkos_compiler_is_nvcc VAR COMPILER) @@ -159,3 +114,161 @@ FUNCTION(kokkos_compiler_is_nvcc VAR COMPILER) ENDIF() ENDFUNCTION() +# this function checks whether the current CXX compiler supports building CUDA +FUNCTION(kokkos_cxx_compiler_cuda_test _VAR _COMPILER) + + FILE(WRITE ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu +" +#include +#include + +__global__ +void kernel(int sz, double* data) +{ + int _beg = blockIdx.x * blockDim.x + threadIdx.x; + for(int i = _beg; i < sz; ++i) + data[i] += static_cast(i); +} + +int main() +{ + double* data = NULL; + int blocks = 64; + int grids = 64; + int ret = cudaMalloc(&data, blocks * grids * sizeof(double)); + if(ret != cudaSuccess) + return EXIT_FAILURE; + kernel<<>>(blocks * grids, data); + cudaDeviceSynchronize(); + return EXIT_SUCCESS; +} +") + + # save the command for debugging + SET(_COMMANDS "${_COMPILER} ${ARGN} -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu") + + # use execute_process instead of try compile because we want to set custom compiler + EXECUTE_PROCESS(COMMAND ${_COMPILER} ${ARGN} -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu + RESULT_VARIABLE _RET + WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/compile_tests + TIMEOUT 15 + OUTPUT_QUIET + ERROR_QUIET) + + IF(NOT _RET EQUAL 0) + # save the command for debugging + SET(_COMMANDS "${_COMMAND}\n${_COMPILER} --cuda-gpu-arch=sm_35 ${ARGN} -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu") + # try the compile test again with clang arguments + EXECUTE_PROCESS(COMMAND ${_COMPILER} --cuda-gpu-arch=sm_35 -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu + RESULT_VARIABLE _RET + WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/compile_tests + TIMEOUT 15 + OUTPUT_QUIET + ERROR_QUIET) + ENDIF() + + SET(${_VAR}_COMMANDS "${_COMMANDS}" PARENT_SCOPE) + SET(${_VAR} ${_RET} PARENT_SCOPE) +ENDFUNCTION() + +# this function is provided to easily select which files use the same compiler as Kokkos +# when it was installed (or nvcc_wrapper): +# +# GLOBAL --> all files +# TARGET --> all files in a target +# SOURCE --> specific source files +# DIRECTORY --> all files in directory +# PROJECT --> all files/targets in a project/subproject +# +# Use the COMPILER argument to specify a compiler, if needed. By default, it will +# set the values to ${Kokkos_CXX_COMPILER} unless Kokkos_ENABLE_CUDA=ON and +# Kokkos_CXX_COMPILER_ID is NVIDIA, then it will set it to nvcc_wrapper +# +# Use CHECK_CUDA_COMPILES to run a check when CUDA is enabled +# +FUNCTION(kokkos_compilation) + CMAKE_PARSE_ARGUMENTS(COMP + "GLOBAL;PROJECT;CHECK_CUDA_COMPILES" + "COMPILER" + "DIRECTORY;TARGET;SOURCE;COMMAND_PREFIX" + ${ARGN}) + + # if built w/o CUDA support, we want to basically make this a no-op + SET(_Kokkos_ENABLE_CUDA @Kokkos_ENABLE_CUDA@) + + # search relative first and then absolute + SET(_HINTS "${CMAKE_CURRENT_LIST_DIR}/../.." "@CMAKE_INSTALL_PREFIX@") + + # find kokkos_launch_compiler + FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER + NAMES kokkos_launch_compiler + HINTS ${_HINTS} + PATHS ${_HINTS} + PATH_SUFFIXES bin) + + IF(NOT Kokkos_COMPILE_LAUNCHER) + MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'") + ENDIF() + + # if COMPILER was not specified, assume Kokkos_CXX_COMPILER + IF(NOT COMP_COMPILER) + SET(COMP_COMPILER ${Kokkos_CXX_COMPILER}) + IF(_Kokkos_ENABLE_CUDA AND Kokkos_CXX_COMPILER_ID STREQUAL NVIDIA) + # find nvcc_wrapper + FIND_PROGRAM(Kokkos_NVCC_WRAPPER + NAMES nvcc_wrapper + HINTS ${_HINTS} + PATHS ${_HINTS} + PATH_SUFFIXES bin) + # fatal if we can't nvcc_wrapper + IF(NOT Kokkos_NVCC_WRAPPER) + MESSAGE(FATAL_ERROR "Kokkos could not find nvcc_wrapper. Please set '-DKokkos_NVCC_WRAPPER=/path/to/nvcc_wrapper'") + ENDIF() + SET(COMP_COMPILER ${Kokkos_NVCC_WRAPPER}) + ENDIF() + ENDIF() + + # check that the original compiler still exists! + IF(NOT EXISTS ${COMP_COMPILER}) + MESSAGE(FATAL_ERROR "Kokkos could not find original compiler: '${COMP_COMPILER}'") + ENDIF() + + # try to ensure that compiling cuda code works! + IF(_Kokkos_ENABLE_CUDA AND COMP_CHECK_CUDA_COMPILES) + + # this may fail if kokkos_compiler launcher was used during install + kokkos_cxx_compiler_cuda_test(_COMPILES_CUDA + ${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}) + + # if above failed, throw an error + IF(NOT _COMPILES_CUDA) + MESSAGE(FATAL_ERROR "kokkos_cxx_compiler_cuda_test failed! Test commands:\n${_COMPILES_CUDA_COMMANDS}") + ENDIF() + ENDIF() + + IF(COMP_COMMAND_PREFIX) + SET(_PREFIX "${COMP_COMMAND_PREFIX}") + STRING(REPLACE ";" " " _PREFIX "${COMP_COMMAND_PREFIX}") + SET(Kokkos_COMPILER_LAUNCHER "${_PREFIX} ${Kokkos_COMPILE_LAUNCHER}") + ENDIF() + + IF(COMP_GLOBAL) + # if global, don't bother setting others + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + ELSE() + FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE) + # make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...) + IF("${_TYPE}" STREQUAL "PROJECT" AND COMP_${_TYPE}) + LIST(APPEND COMP_DIRECTORY ${PROJECT_SOURCE_DIR}) + UNSET(COMP_${_TYPE}) + ENDIF() + # set the properties if defined + IF(COMP_${_TYPE}) + # MESSAGE(STATUS "Using ${COMP_COMPILER} :: ${_TYPE} :: ${COMP_${_TYPE}}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + ENDIF() + ENDFOREACH() + ENDIF() +ENDFUNCTION() diff --git a/lib/kokkos/cmake/KokkosCore_config.h.in b/lib/kokkos/cmake/KokkosCore_config.h.in index 0259fe69d5..3455b0cb42 100644 --- a/lib/kokkos/cmake/KokkosCore_config.h.in +++ b/lib/kokkos/cmake/KokkosCore_config.h.in @@ -78,6 +78,7 @@ #cmakedefine KOKKOS_ARCH_POWER7 #cmakedefine KOKKOS_ARCH_POWER8 #cmakedefine KOKKOS_ARCH_POWER9 +#cmakedefine KOKKOS_ARCH_INTEL_GEN #cmakedefine KOKKOS_ARCH_KEPLER #cmakedefine KOKKOS_ARCH_KEPLER30 #cmakedefine KOKKOS_ARCH_KEPLER32 @@ -95,5 +96,9 @@ #cmakedefine KOKKOS_ARCH_VOLTA72 #cmakedefine KOKKOS_ARCH_TURING75 #cmakedefine KOKKOS_ARCH_AMPERE80 +#cmakedefine KOKKOS_ARCH_AMPERE86 #cmakedefine KOKKOS_ARCH_AMD_ZEN #cmakedefine KOKKOS_ARCH_AMD_ZEN2 +#cmakedefine KOKKOS_ARCH_AMD_ZEN3 + +#cmakedefine KOKKOS_IMPL_DISABLE_SYCL_DEVICE_PRINTF diff --git a/lib/kokkos/cmake/Modules/CudaToolkit.cmake b/lib/kokkos/cmake/Modules/CudaToolkit.cmake index d620a71d36..eda5541f7c 100644 --- a/lib/kokkos/cmake/Modules/CudaToolkit.cmake +++ b/lib/kokkos/cmake/Modules/CudaToolkit.cmake @@ -481,76 +481,6 @@ if(CMAKE_CUDA_COMPILER_LOADED AND NOT CUDAToolkit_BIN_DIR AND CMAKE_CUDA_COMPILE unset(cuda_dir) endif() -IF(CMAKE_VERSION VERSION_LESS "3.12.0") - function(import_target_link_libraries target) - cmake_parse_arguments(HACK - "SYSTEM;INTERFACE;PUBLIC" - "" - "" - ${ARGN} - ) - get_target_property(LIBS ${target} INTERFACE_LINK_LIBRARIES) - if (LIBS) - list(APPEND LIBS ${HACK_UNPARSED_ARGUMENTS}) - else() - set(LIBS ${HACK_UNPARSED_ARGUMENTS}) - endif() - set_target_properties(${target} PROPERTIES - INTERFACE_LINK_LIBRARIES "${LIBS}") - endfunction() -ELSE() - function(import_target_link_libraries) - target_link_libraries(${ARGN}) - endfunction() -ENDIF() - -IF(CMAKE_VERSION VERSION_LESS "3.13.0") - function(import_target_link_directories target) - cmake_parse_arguments(HACK - "SYSTEM;INTERFACE;PUBLIC" - "" - "" - ${ARGN} - ) - get_target_property(LINK_LIBS ${target} INTERFACE_LINK_LIBRARIES) - if (LINK_LIBS) #could be not-found - set(LINK_LIBS_LIST ${LINK_LIBS}) - endif() - foreach(LIB ${HACK_UNPARSED_ARGUMENTS}) - list(APPEND LINK_LIBS_LIST -L${LIB}) - endforeach() - set_target_properties(${target} PROPERTIES - INTERFACE_LINK_LIBRARIES "${LINK_LIBS_LIST}") - endfunction() -ELSE() - function(import_target_link_directories) - target_link_directories(${ARGN}) - endfunction() -ENDIF() - -IF(CMAKE_VERSION VERSION_LESS "3.12.0") - function(import_target_include_directories target) - cmake_parse_arguments(HACK - "SYSTEM;INTERFACE;PUBLIC" - "" - "" - ${ARGN} - ) - get_target_property(INLUDE_DIRS ${target} INTERFACE_INCLUDE_DIRECTORIES) - if (INCLUDE_DIRS) - list(APPEND INCLUDE_DIRS ${HACK_UNPARSED_ARGUMENTS}) - else() - set(INCLUDE_DIRS ${HACK_UNPARSED_ARGUMENTS}) - endif() - set_target_properties(${target} PROPERTIES - INTERFACE_INCLUDE_DIRECTORIES "${INCLUDE_DIRS}") - endfunction() -ELSE() - function(import_target_include_directories) - target_include_directories(${ARGN}) - endfunction() -ENDIF() - # Try language- or user-provided path first. if(CUDAToolkit_BIN_DIR) find_program(CUDAToolkit_NVCC_EXECUTABLE @@ -854,11 +784,11 @@ if(CUDAToolkit_FOUND) if (NOT TARGET CUDA::${lib_name} AND CUDA_${lib_name}_LIBRARY) add_library(CUDA::${lib_name} IMPORTED INTERFACE) - import_target_include_directories(CUDA::${lib_name} SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") - import_target_link_libraries(CUDA::${lib_name} INTERFACE "${CUDA_${lib_name}_LIBRARY}") + target_include_directories(CUDA::${lib_name} SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") + target_link_libraries(CUDA::${lib_name} INTERFACE "${CUDA_${lib_name}_LIBRARY}") foreach(dep ${arg_DEPS}) if(TARGET CUDA::${dep}) - import_target_link_libraries(CUDA::${lib_name} INTERFACE CUDA::${dep}) + target_link_libraries(CUDA::${lib_name} INTERFACE CUDA::${dep}) endif() endforeach() endif() @@ -866,8 +796,8 @@ if(CUDAToolkit_FOUND) if(NOT TARGET CUDA::toolkit) add_library(CUDA::toolkit IMPORTED INTERFACE) - import_target_include_directories(CUDA::toolkit SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") - import_target_link_directories(CUDA::toolkit INTERFACE "${CUDAToolkit_LIBRARY_DIR}") + target_include_directories(CUDA::toolkit SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") + target_link_directories(CUDA::toolkit INTERFACE "${CUDAToolkit_LIBRARY_DIR}") endif() _CUDAToolkit_find_and_add_import_lib(cuda_driver ALT cuda) @@ -882,11 +812,11 @@ if(CUDAToolkit_FOUND) AND TARGET CUDA::cudart_static) add_library(CUDA::cudart_static_deps IMPORTED INTERFACE) - import_target_link_libraries(CUDA::cudart_static INTERFACE CUDA::cudart_static_deps) + target_link_libraries(CUDA::cudart_static INTERFACE CUDA::cudart_static_deps) if(UNIX AND (CMAKE_C_COMPILER OR CMAKE_CXX_COMPILER)) find_package(Threads REQUIRED) - import_target_link_libraries(CUDA::cudart_static_deps INTERFACE Threads::Threads ${CMAKE_DL_LIBS}) + target_link_libraries(CUDA::cudart_static_deps INTERFACE Threads::Threads ${CMAKE_DL_LIBS}) endif() if(UNIX AND NOT APPLE) @@ -896,7 +826,7 @@ if(CUDAToolkit_FOUND) if(NOT CUDAToolkit_rt_LIBRARY) message(WARNING "Could not find librt library, needed by CUDA::cudart_static") else() - import_target_link_libraries(CUDA::cudart_static_deps INTERFACE ${CUDAToolkit_rt_LIBRARY}) + target_link_libraries(CUDA::cudart_static_deps INTERFACE ${CUDAToolkit_rt_LIBRARY}) endif() endif() endif() diff --git a/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake b/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake index a1072a60c6..8d58d96415 100644 --- a/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake +++ b/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake @@ -25,7 +25,7 @@ IF (TARGET CUDA::cuda_driver) SET(FOUND_CUDA_DRIVER TRUE) KOKKOS_EXPORT_IMPORTED_TPL(CUDA::cuda_driver) ELSE() - SET(FOUND_CUDA_DRIVVER FALSE) + SET(FOUND_CUDA_DRIVER FALSE) ENDIF() include(FindPackageHandleStandardArgs) diff --git a/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake b/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake index 1d154e29af..a743fca0e4 100644 --- a/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake +++ b/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake @@ -10,7 +10,7 @@ TRY_COMPILE(KOKKOS_HAS_PTHREAD_ARG # ${CMAKE_CXX${KOKKOS_CXX_STANDARD}_STANDARD_COMPILE_OPTION} INCLUDE(FindPackageHandleStandardArgs) -FIND_PACKAGE_HANDLE_STANDARD_ARGS(PTHREAD DEFAULT_MSG KOKKOS_HAS_PTHREAD_ARG) +FIND_PACKAGE_HANDLE_STANDARD_ARGS(TPLPTHREAD DEFAULT_MSG KOKKOS_HAS_PTHREAD_ARG) #Only create the TPL if we succeed IF (KOKKOS_HAS_PTHREAD_ARG) KOKKOS_CREATE_IMPORTED_TPL(PTHREAD diff --git a/lib/kokkos/cmake/Modules/FindTPLROCM.cmake b/lib/kokkos/cmake/Modules/FindTPLROCM.cmake new file mode 100644 index 0000000000..512ad6ceb2 --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindTPLROCM.cmake @@ -0,0 +1,11 @@ +include(FindPackageHandleStandardArgs) + +FIND_LIBRARY(AMD_HIP_LIBRARY amdhip64 PATHS ENV ROCM_PATH PATH_SUFFIXES lib) +FIND_LIBRARY(HSA_RUNTIME_LIBRARY hsa-runtime64 PATHS ENV ROCM_PATH PATH_SUFFIXES lib) + +find_package_handle_standard_args(TPLROCM DEFAULT_MSG AMD_HIP_LIBRARY HSA_RUNTIME_LIBRARY) + +kokkos_create_imported_tpl(ROCM INTERFACE + LINK_LIBRARIES ${HSA_RUNTIME_LIBRARY} ${AMD_HIP_LIBRARY} + COMPILE_DEFINITIONS __HIP_ROCclr__ +) diff --git a/lib/kokkos/cmake/compile_tests/cplusplus14.cpp b/lib/kokkos/cmake/compile_tests/cplusplus14.cpp new file mode 100644 index 0000000000..52ec9885ec --- /dev/null +++ b/lib/kokkos/cmake/compile_tests/cplusplus14.cpp @@ -0,0 +1,8 @@ +#include + +int main() { + // _t versions of type traits were added in C++14 + std::remove_cv_t i = 0; + + return i; +} diff --git a/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc b/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc index 48c01c070c..a26ac5af4b 100644 --- a/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc +++ b/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc @@ -72,6 +72,7 @@ int main() { case 72: std::cout << "Set -DKokkos_ARCH_VOLTA72=ON ." << std::endl; break; case 75: std::cout << "Set -DKokkos_ARCH_TURING75=ON ." << std::endl; break; case 80: std::cout << "Set -DKokkos_ARCH_AMPERE80=ON ." << std::endl; break; + case 86: std::cout << "Set -DKokkos_ARCH_AMPERE86=ON ." << std::endl; break; default: std::cout << "Compute capability " << compute_capability << " is not supported" << std::endl; diff --git a/lib/kokkos/cmake/compile_tests/pthread.cpp b/lib/kokkos/cmake/compile_tests/pthread.cpp index 92310da029..3f83bf6a5f 100644 --- a/lib/kokkos/cmake/compile_tests/pthread.cpp +++ b/lib/kokkos/cmake/compile_tests/pthread.cpp @@ -2,7 +2,7 @@ void* kokkos_test(void* args) { return args; } -int main(void) { +int main() { pthread_t thread; /* Use NULL to avoid C++11. Some compilers do not have C++11 by default. Forcing C++11 diff --git a/lib/kokkos/cmake/fake_tribits.cmake b/lib/kokkos/cmake/fake_tribits.cmake index 2e82a46235..fbd6745a60 100644 --- a/lib/kokkos/cmake/fake_tribits.cmake +++ b/lib/kokkos/cmake/fake_tribits.cmake @@ -81,10 +81,16 @@ ENDMACRO() FUNCTION(KOKKOS_ADD_TEST) if (KOKKOS_HAS_TRILINOS) CMAKE_PARSE_ARGUMENTS(TEST - "" + "SKIP_TRIBITS" "EXE;NAME;TOOL" "ARGS" ${ARGN}) + + IF(TEST_SKIP_TRIBITS) + MESSAGE(STATUS "Skipping test ${TEST_NAME} in TriBits") + RETURN() + ENDIF() + IF(TEST_EXE) SET(EXE_ROOT ${TEST_EXE}) ELSE() @@ -119,11 +125,10 @@ FUNCTION(KOKKOS_ADD_TEST) endif() else() CMAKE_PARSE_ARGUMENTS(TEST - "WILL_FAIL" + "WILL_FAIL;SKIP_TRIBITS" "FAIL_REGULAR_EXPRESSION;PASS_REGULAR_EXPRESSION;EXE;NAME;TOOL" "CATEGORIES;ARGS" ${ARGN}) - SET(TESTS_ADDED) # To match Tribits, we should always be receiving # the root names of exes/libs IF(TEST_EXE) @@ -135,48 +140,27 @@ FUNCTION(KOKKOS_ADD_TEST) # These should be the full target name SET(TEST_NAME ${PACKAGE_NAME}_${TEST_NAME}) SET(EXE ${PACKAGE_NAME}_${EXE_ROOT}) - IF (TEST_ARGS) - SET(TEST_NUMBER 0) - FOREACH (ARG_STR ${TEST_ARGS}) - # This is passed as a single string blob to match TriBITS behavior - # We need this to be turned into a list - STRING(REPLACE " " ";" ARG_STR_LIST ${ARG_STR}) - IF(WIN32) - ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} - COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${ARG_STR_LIST}) - ELSE() - ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} COMMAND ${EXE} ${ARG_STR_LIST}) - ENDIF() - LIST(APPEND TESTS_ADDED "${TEST_NAME}${TEST_NUMBER}") - MATH(EXPR TEST_NUMBER "${TEST_NUMBER} + 1") - ENDFOREACH() + IF(WIN32) + ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} + COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${TEST_ARGS}) ELSE() - IF(WIN32) - ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} - COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX}) - ELSE() - ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE}) - ENDIF() - LIST(APPEND TESTS_ADDED "${TEST_NAME}") + ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE} ${TEST_ARGS}) + ENDIF() + IF(TEST_WILL_FAIL) + SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES WILL_FAIL ${TEST_WILL_FAIL}) + ENDIF() + IF(TEST_FAIL_REGULAR_EXPRESSION) + SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES FAIL_REGULAR_EXPRESSION ${TEST_FAIL_REGULAR_EXPRESSION}) + ENDIF() + IF(TEST_PASS_REGULAR_EXPRESSION) + SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES PASS_REGULAR_EXPRESSION ${TEST_PASS_REGULAR_EXPRESSION}) + ENDIF() + IF(TEST_TOOL) + ADD_DEPENDENCIES(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool + SET_PROPERTY(TEST ${TEST_NAME} APPEND_STRING PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$") ENDIF() - - FOREACH(TEST_NAME ${TESTS_ADDED}) - IF(TEST_WILL_FAIL) - SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES WILL_FAIL ${TEST_WILL_FAIL}) - ENDIF() - IF(TEST_FAIL_REGULAR_EXPRESSION) - SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES FAIL_REGULAR_EXPRESSION ${TEST_FAIL_REGULAR_EXPRESSION}) - ENDIF() - IF(TEST_PASS_REGULAR_EXPRESSION) - SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES PASS_REGULAR_EXPRESSION ${TEST_PASS_REGULAR_EXPRESSION}) - ENDIF() - if(TEST_TOOL) - add_dependencies(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool - set_property(TEST ${TEST_NAME} APPEND_STRING PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$") - endif() - ENDFOREACH() VERIFY_EMPTY(KOKKOS_ADD_TEST ${TEST_UNPARSED_ARGUMENTS}) - endif() + ENDIF() ENDFUNCTION() FUNCTION(KOKKOS_ADD_ADVANCED_TEST) @@ -326,14 +310,6 @@ ENDIF() ENDFUNCTION() -FUNCTION(KOKKOS_TARGET_COMPILE_DEFINITIONS) - IF (KOKKOS_HAS_TRILINOS) - TARGET_COMPILE_DEFINITIONS(${TARGET} ${ARGN}) - ELSE() - TARGET_COMPILE_DEFINITIONS(${TARGET} ${ARGN}) - ENDIF() -ENDFUNCTION() - FUNCTION(KOKKOS_INCLUDE_DIRECTORIES) IF(KOKKOS_HAS_TRILINOS) TRIBITS_INCLUDE_DIRECTORIES(${ARGN}) @@ -350,10 +326,6 @@ ENDIF() ENDFUNCTION() -MACRO(KOKKOS_ADD_COMPILE_OPTIONS) -ADD_COMPILE_OPTIONS(${ARGN}) -ENDMACRO() - MACRO(PRINTALL match) get_cmake_property(_variableNames VARIABLES) list (SORT _variableNames) @@ -376,4 +348,3 @@ FUNCTION(GLOBAL_APPEND VARNAME) LIST(APPEND TEMP ${ARGN}) GLOBAL_SET(${VARNAME} ${TEMP}) ENDFUNCTION() - diff --git a/lib/kokkos/cmake/kokkos_arch.cmake b/lib/kokkos/cmake/kokkos_arch.cmake index 53aaf7dccf..e8b85542c6 100644 --- a/lib/kokkos/cmake/kokkos_arch.cmake +++ b/lib/kokkos/cmake/kokkos_arch.cmake @@ -35,7 +35,7 @@ KOKKOS_ARCH_OPTION(ARMV80 HOST "ARMv8.0 Compatible CPU") KOKKOS_ARCH_OPTION(ARMV81 HOST "ARMv8.1 Compatible CPU") KOKKOS_ARCH_OPTION(ARMV8_THUNDERX HOST "ARMv8 Cavium ThunderX CPU") KOKKOS_ARCH_OPTION(ARMV8_THUNDERX2 HOST "ARMv8 Cavium ThunderX2 CPU") -KOKKOS_ARCH_OPTION(A64FX HOST "ARMv8.2 with SVE Suport") +KOKKOS_ARCH_OPTION(A64FX HOST "ARMv8.2 with SVE Support") KOKKOS_ARCH_OPTION(WSM HOST "Intel Westmere CPU") KOKKOS_ARCH_OPTION(SNB HOST "Intel Sandy/Ivy Bridge CPUs") KOKKOS_ARCH_OPTION(HSW HOST "Intel Haswell CPUs") @@ -60,11 +60,13 @@ KOKKOS_ARCH_OPTION(VOLTA70 GPU "NVIDIA Volta generation CC 7.0") KOKKOS_ARCH_OPTION(VOLTA72 GPU "NVIDIA Volta generation CC 7.2") KOKKOS_ARCH_OPTION(TURING75 GPU "NVIDIA Turing generation CC 7.5") KOKKOS_ARCH_OPTION(AMPERE80 GPU "NVIDIA Ampere generation CC 8.0") +KOKKOS_ARCH_OPTION(AMPERE86 GPU "NVIDIA Ampere generation CC 8.6") KOKKOS_ARCH_OPTION(ZEN HOST "AMD Zen architecture") KOKKOS_ARCH_OPTION(ZEN2 HOST "AMD Zen2 architecture") +KOKKOS_ARCH_OPTION(ZEN3 HOST "AMD Zen3 architecture") KOKKOS_ARCH_OPTION(VEGA900 GPU "AMD GPU MI25 GFX900") KOKKOS_ARCH_OPTION(VEGA906 GPU "AMD GPU MI50/MI60 GFX906") -KOKKOS_ARCH_OPTION(VEGA908 GPU "AMD GPU") +KOKKOS_ARCH_OPTION(VEGA908 GPU "AMD GPU MI100 GFX908") KOKKOS_ARCH_OPTION(INTEL_GEN GPU "Intel GPUs Gen9+") @@ -141,8 +143,16 @@ ENDIF() #------------------------------- KOKKOS_HIP_OPTIONS --------------------------- #clear anything that might be in the cache GLOBAL_SET(KOKKOS_AMDGPU_OPTIONS) -IF(KOKKOS_CXX_COMPILER_ID STREQUAL HIP) - SET(AMDGPU_ARCH_FLAG "--amdgpu-target") +IF(KOKKOS_ENABLE_HIP) + IF(KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) + SET(AMDGPU_ARCH_FLAG "--amdgpu-target") + ELSE() + SET(AMDGPU_ARCH_FLAG "--offload-arch") + GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS -x hip) + IF(DEFINED ENV{ROCM_PATH}) + GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS --rocm-path=$ENV{ROCM_PATH}) + ENDIF() + ENDIF() ENDIF() @@ -183,6 +193,8 @@ ENDIF() IF (KOKKOS_ARCH_A64FX) COMPILER_SPECIFIC_FLAGS( DEFAULT -march=armv8.2-a+sve + Clang -march=armv8.2-a+sve -msve-vector-bits=512 + GCC -march=armv8.2-a+sve -msve-vector-bits=512 ) ENDIF() @@ -204,6 +216,15 @@ IF (KOKKOS_ARCH_ZEN2) SET(KOKKOS_ARCH_AMD_AVX2 ON) ENDIF() +IF (KOKKOS_ARCH_ZEN3) + COMPILER_SPECIFIC_FLAGS( + Intel -mavx2 + DEFAULT -march=znver3 -mtune=znver3 + ) + SET(KOKKOS_ARCH_AMD_ZEN3 ON) + SET(KOKKOS_ARCH_AMD_AVX2 ON) +ENDIF() + IF (KOKKOS_ARCH_WSM) COMPILER_SPECIFIC_FLAGS( Intel -xSSE4.2 @@ -273,7 +294,7 @@ IF (KOKKOS_ARCH_SKX) ) ENDIF() -IF (KOKKOS_ARCH_WSM OR KOKKOS_ARCH_SNB OR KOKKOS_ARCH_HSW OR KOKKOS_ARCH_BDW OR KOKKOS_ARCH_KNL OR KOKKOS_ARCH_SKX OR KOKKOS_ARCH_ZEN OR KOKKOS_ARCH_ZEN2) +IF (KOKKOS_ARCH_WSM OR KOKKOS_ARCH_SNB OR KOKKOS_ARCH_HSW OR KOKKOS_ARCH_BDW OR KOKKOS_ARCH_KNL OR KOKKOS_ARCH_SKX OR KOKKOS_ARCH_ZEN OR KOKKOS_ARCH_ZEN2 OR KOKKOS_ARCH_ZEN3) SET(KOKKOS_USE_ISA_X86_64 ON) ENDIF() @@ -309,7 +330,7 @@ IF (KOKKOS_ARCH_POWER8 OR KOKKOS_ARCH_POWER9) SET(KOKKOS_USE_ISA_POWERPCLE ON) ENDIF() -IF (Kokkos_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) +IF (KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) COMPILER_SPECIFIC_FLAGS( Clang -fcuda-rdc NVIDIA --relocatable-device-code=true @@ -333,8 +354,8 @@ ENDIF() #Right now we cannot get the compiler ID when cross-compiling, so just check #that HIP is enabled -IF (Kokkos_ENABLE_HIP) - IF (Kokkos_ENABLE_HIP_RELOCATABLE_DEVICE_CODE) +IF (KOKKOS_ENABLE_HIP) + IF (KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE) COMPILER_SPECIFIC_FLAGS( DEFAULT -fgpu-rdc ) @@ -345,8 +366,7 @@ IF (Kokkos_ENABLE_HIP) ENDIF() ENDIF() - -IF (Kokkos_ENABLE_SYCL) +IF (KOKKOS_ENABLE_SYCL) COMPILER_SPECIFIC_FLAGS( DEFAULT -fsycl ) @@ -363,7 +383,7 @@ FUNCTION(CHECK_CUDA_ARCH ARCH FLAG) MESSAGE(FATAL_ERROR "Multiple GPU architectures given! Already have ${CUDA_ARCH_ALREADY_SPECIFIED}, but trying to add ${ARCH}. If you are re-running CMake, try clearing the cache and running again.") ENDIF() SET(CUDA_ARCH_ALREADY_SPECIFIED ${ARCH} PARENT_SCOPE) - IF (NOT KOKKOS_ENABLE_CUDA AND NOT KOKKOS_ENABLE_OPENMPTARGET) + IF (NOT KOKKOS_ENABLE_CUDA AND NOT KOKKOS_ENABLE_OPENMPTARGET AND NOT KOKKOS_ENABLE_SYCL) MESSAGE(WARNING "Given CUDA arch ${ARCH}, but Kokkos_ENABLE_CUDA and Kokkos_ENABLE_OPENMPTARGET are OFF. Option will be ignored.") UNSET(KOKKOS_ARCH_${ARCH} PARENT_SCOPE) ELSE() @@ -396,6 +416,7 @@ CHECK_CUDA_ARCH(VOLTA70 sm_70) CHECK_CUDA_ARCH(VOLTA72 sm_72) CHECK_CUDA_ARCH(TURING75 sm_75) CHECK_CUDA_ARCH(AMPERE80 sm_80) +CHECK_CUDA_ARCH(AMPERE86 sm_86) SET(AMDGPU_ARCH_ALREADY_SPECIFIED "") FUNCTION(CHECK_AMDGPU_ARCH ARCH FLAG) @@ -405,12 +426,12 @@ FUNCTION(CHECK_AMDGPU_ARCH ARCH FLAG) ENDIF() SET(AMDGPU_ARCH_ALREADY_SPECIFIED ${ARCH} PARENT_SCOPE) IF (NOT KOKKOS_ENABLE_HIP AND NOT KOKKOS_ENABLE_OPENMPTARGET) - MESSAGE(WARNING "Given HIP arch ${ARCH}, but Kokkos_ENABLE_AMDGPU and Kokkos_ENABLE_OPENMPTARGET are OFF. Option will be ignored.") + MESSAGE(WARNING "Given AMD GPU architecture ${ARCH}, but Kokkos_ENABLE_HIP and Kokkos_ENABLE_OPENMPTARGET are OFF. Option will be ignored.") UNSET(KOKKOS_ARCH_${ARCH} PARENT_SCOPE) ELSE() SET(KOKKOS_AMDGPU_ARCH_FLAG ${FLAG} PARENT_SCOPE) GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS "${AMDGPU_ARCH_FLAG}=${FLAG}") - IF(KOKKOS_ENABLE_HIP) + IF(KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE) GLOBAL_APPEND(KOKKOS_LINK_OPTIONS "${AMDGPU_ARCH_FLAG}=${FLAG}") ENDIF() ENDIF() @@ -446,7 +467,25 @@ IF (KOKKOS_ENABLE_OPENMPTARGET) ENDIF() IF (KOKKOS_ARCH_INTEL_GEN) COMPILER_SPECIFIC_FLAGS( - IntelClang -fopenmp-targets=spir64 -D__STRICT_ANSI__ + IntelLLVM -fopenmp-targets=spir64 -D__STRICT_ANSI__ + ) + ENDIF() +ENDIF() + +IF (KOKKOS_ENABLE_SYCL) + IF(CUDA_ARCH_ALREADY_SPECIFIED) + IF(KOKKOS_ENABLE_UNSUPPORTED_ARCHS) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=nvptx64-nvidia-cuda-sycldevice + ) + # FIXME_SYCL The CUDA backend doesn't support printf yet. + GLOBAL_SET(KOKKOS_IMPL_DISABLE_SYCL_DEVICE_PRINTF ON) + ELSE() + MESSAGE(SEND_ERROR "Setting a CUDA architecture for SYCL is only allowed with Kokkos_ENABLE_UNSUPPORTED_ARCHS=ON!") + ENDIF() + ELSEIF(KOKKOS_ARCH_INTEL_GEN) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device skl" ) ENDIF() ENDIF() @@ -464,6 +503,43 @@ IF(KOKKOS_ENABLE_CUDA AND NOT CUDA_ARCH_ALREADY_SPECIFIED) ${CMAKE_CURRENT_SOURCE_DIR}/cmake/compile_tests/cuda_compute_capability.cc COMPILE_DEFINITIONS -DSM_ONLY RUN_OUTPUT_VARIABLE _CUDA_COMPUTE_CAPABILITY) + + # if user is using kokkos_compiler_launcher, above will fail. + IF(NOT _COMPILE_RESULT OR NOT _RESULT EQUAL 0) + # check to see if CUDA is not already enabled (may happen when Kokkos is subproject) + GET_PROPERTY(_ENABLED_LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) + # language has to be fully enabled, just checking for CMAKE_CUDA_COMPILER isn't enough + IF(NOT "CUDA" IN_LIST _ENABLED_LANGUAGES) + # make sure the user knows that we aren't using CUDA compiler for anything else + MESSAGE(STATUS "CUDA auto-detection of architecture failed with ${CMAKE_CXX_COMPILER}. Enabling CUDA language ONLY to auto-detect architecture...") + INCLUDE(CheckLanguage) + CHECK_LANGUAGE(CUDA) + IF(CMAKE_CUDA_COMPILER) + ENABLE_LANGUAGE(CUDA) + ELSE() + MESSAGE(STATUS "CUDA language could not be enabled") + ENDIF() + ENDIF() + + # if CUDA was enabled, this will be defined + IF(CMAKE_CUDA_COMPILER) + # copy our test to .cu so cmake compiles as CUDA + CONFIGURE_FILE( + ${PROJECT_SOURCE_DIR}/cmake/compile_tests/cuda_compute_capability.cc + ${PROJECT_BINARY_DIR}/compile_tests/cuda_compute_capability.cu + COPYONLY + ) + # run test again + TRY_RUN( + _RESULT + _COMPILE_RESULT + ${_BINARY_TEST_DIR} + ${PROJECT_BINARY_DIR}/compile_tests/cuda_compute_capability.cu + COMPILE_DEFINITIONS -DSM_ONLY + RUN_OUTPUT_VARIABLE _CUDA_COMPUTE_CAPABILITY) + ENDIF() + ENDIF() + LIST(FIND KOKKOS_CUDA_ARCH_FLAGS sm_${_CUDA_COMPUTE_CAPABILITY} FLAG_INDEX) IF(_COMPILE_RESULT AND _RESULT EQUAL 0 AND NOT FLAG_INDEX EQUAL -1) MESSAGE(STATUS "Detected CUDA Compute Capability ${_CUDA_COMPUTE_CAPABILITY}") @@ -500,7 +576,7 @@ IF (KOKKOS_ENABLE_CUDA) SET(KOKKOS_ARCH_VOLTA ON) ENDIF() - IF (KOKKOS_ARCH_AMPERE80) + IF (KOKKOS_ARCH_AMPERE80 OR KOKKOS_ARCH_AMPERE86) SET(KOKKOS_ARCH_AMPERE ON) ENDIF() ENDIF() diff --git a/lib/kokkos/cmake/kokkos_compiler_id.cmake b/lib/kokkos/cmake/kokkos_compiler_id.cmake index e6600161f9..23847263a9 100644 --- a/lib/kokkos/cmake/kokkos_compiler_id.cmake +++ b/lib/kokkos/cmake/kokkos_compiler_id.cmake @@ -27,6 +27,12 @@ IF(Kokkos_ENABLE_CUDA) PATHS ${PROJECT_SOURCE_DIR} PATH_SUFFIXES bin) + FIND_PROGRAM(Kokkos_NVCC_WRAPPER + NAMES nvcc_wrapper + HINTS ${PROJECT_SOURCE_DIR} + PATHS ${PROJECT_SOURCE_DIR} + PATH_SUFFIXES bin) + # check if compiler was set to nvcc_wrapper kokkos_internal_have_compiler_nvcc(${CMAKE_CXX_COMPILER}) # if launcher was found and nvcc_wrapper was not specified as @@ -37,7 +43,7 @@ IF(Kokkos_ENABLE_CUDA) # if the second argument matches the C++ compiler, it forwards the rest of the # args to nvcc_wrapper kokkos_internal_have_compiler_nvcc( - ${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER} -DKOKKOS_DEPENDENCE) + ${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER} -DKOKKOS_DEPENDENCE) SET(INTERNAL_USE_COMPILER_LAUNCHER true) ENDIF() ENDIF() @@ -55,32 +61,7 @@ IF(INTERNAL_HAVE_COMPILER_NVCC) SET(KOKKOS_CXX_COMPILER_VERSION ${TEMP_CXX_COMPILER_VERSION} CACHE STRING INTERNAL FORCE) MESSAGE(STATUS "Compiler Version: ${KOKKOS_CXX_COMPILER_VERSION}") IF(INTERNAL_USE_COMPILER_LAUNCHER) - IF(Kokkos_LAUNCH_COMPILER_INFO) - GET_FILENAME_COMPONENT(BASE_COMPILER_NAME ${CMAKE_CXX_COMPILER} NAME) - # does not have STATUS intentionally - MESSAGE("") - MESSAGE("Kokkos_LAUNCH_COMPILER_INFO (${Kokkos_COMPILE_LAUNCHER}):") - MESSAGE(" - Kokkos + CUDA backend requires the C++ files to be compiled as CUDA code.") - MESSAGE(" - kokkos_launch_compiler permits CMAKE_CXX_COMPILER to be set to a traditional C++ compiler when Kokkos_ENABLE_CUDA=ON") - MESSAGE(" by prefixing all the compile and link commands with the path to the script + CMAKE_CXX_COMPILER (${CMAKE_CXX_COMPILER}).") - MESSAGE(" - If any of the compile or link commands have CMAKE_CXX_COMPILER as the first argument, it replaces CMAKE_CXX_COMPILER with nvcc_wrapper.") - MESSAGE(" - If the compile or link command is not CMAKE_CXX_COMPILER, it just executes the command.") - MESSAGE(" - If using ccache, set CMAKE_CXX_COMPILER to nvcc_wrapper explicitly.") - MESSAGE(" - kokkos_compiler_launcher is available to downstream projects as well.") - MESSAGE(" - If CMAKE_CXX_COMPILER=nvcc_wrapper, all legacy behavior will be preserved during 'find_package(Kokkos)'") - MESSAGE(" - If CMAKE_CXX_COMPILER is not nvcc_wrapper, 'find_package(Kokkos)' will apply 'kokkos_compilation(GLOBAL)' unless separable compilation is enabled") - MESSAGE(" - This can be disabled via '-DKokkos_LAUNCH_COMPILER=OFF'") - MESSAGE(" - Use 'find_package(Kokkos COMPONENTS separable_compilation)' to enable separable compilation") - MESSAGE(" - Separable compilation allows you to control the scope of where the compiler transformation behavior (${BASE_COMPILER_NAME} -> nvcc_wrapper) is applied") - MESSAGE(" - The compiler transformation can be applied on a per-project, per-directory, per-target, and/or per-source-file basis") - MESSAGE(" - 'kokkos_compilation(PROJECT)' will apply the compiler transformation to all targets in a project/subproject") - MESSAGE(" - 'kokkos_compilation(TARGET [...])' will apply the compiler transformation to the specified target(s)") - MESSAGE(" - 'kokkos_compilation(SOURCE [...])' will apply the compiler transformation to the specified source file(s)") - MESSAGE(" - 'kokkos_compilation(DIRECTORY [...])' will apply the compiler transformation to the specified directories") - MESSAGE("") - ELSE() - MESSAGE(STATUS "kokkos_launch_compiler (${Kokkos_COMPILE_LAUNCHER}) is enabled... Set Kokkos_LAUNCH_COMPILER_INFO=ON for more info.") - ENDIF() + MESSAGE(STATUS "kokkos_launch_compiler (${Kokkos_COMPILE_LAUNCHER}) is enabled...") kokkos_compilation(GLOBAL) ENDIF() ENDIF() @@ -92,7 +73,11 @@ IF(Kokkos_ENABLE_HIP) OUTPUT_STRIP_TRAILING_WHITESPACE) STRING(REPLACE "\n" " - " INTERNAL_COMPILER_VERSION_ONE_LINE ${INTERNAL_COMPILER_VERSION} ) - SET(KOKKOS_CXX_COMPILER_ID HIP CACHE STRING INTERNAL FORCE) + + STRING(FIND ${INTERNAL_COMPILER_VERSION_ONE_LINE} "HIP version" INTERNAL_COMPILER_VERSION_CONTAINS_HIP) + IF(INTERNAL_COMPILER_VERSION_CONTAINS_HIP GREATER -1) + SET(KOKKOS_CXX_COMPILER_ID HIPCC CACHE STRING INTERNAL FORCE) + ENDIF() STRING(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" TEMP_CXX_COMPILER_VERSION ${INTERNAL_COMPILER_VERSION_ONE_LINE}) @@ -103,8 +88,7 @@ ENDIF() IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) # The Cray compiler reports as Clang to most versions of CMake EXECUTE_PROCESS(COMMAND ${CMAKE_CXX_COMPILER} --version - COMMAND grep Cray - COMMAND wc -l + COMMAND grep -c Cray OUTPUT_VARIABLE INTERNAL_HAVE_CRAY_COMPILER OUTPUT_STRIP_TRAILING_WHITESPACE) IF (INTERNAL_HAVE_CRAY_COMPILER) #not actually Clang @@ -112,13 +96,12 @@ IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) ENDIF() # The clang based Intel compiler reports as Clang to most versions of CMake EXECUTE_PROCESS(COMMAND ${CMAKE_CXX_COMPILER} --version - COMMAND grep icpx - COMMAND wc -l + COMMAND grep -c "DPC++\\|icpx" OUTPUT_VARIABLE INTERNAL_HAVE_INTEL_COMPILER OUTPUT_STRIP_TRAILING_WHITESPACE) IF (INTERNAL_HAVE_INTEL_COMPILER) #not actually Clang SET(KOKKOS_CLANG_IS_INTEL TRUE) - SET(KOKKOS_CXX_COMPILER_ID IntelClang CACHE STRING INTERNAL FORCE) + SET(KOKKOS_CXX_COMPILER_ID IntelLLVM CACHE STRING INTERNAL FORCE) ENDIF() ENDIF() @@ -174,7 +157,7 @@ ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") ENDIF() SET(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Kokkos turns off CXX extensions" FORCE) -ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL HIP) +ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 3.8.0) MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") ENDIF() diff --git a/lib/kokkos/cmake/kokkos_corner_cases.cmake b/lib/kokkos/cmake/kokkos_corner_cases.cmake index 3962c4b16e..a84ac2b630 100644 --- a/lib/kokkos/cmake/kokkos_corner_cases.cmake +++ b/lib/kokkos/cmake/kokkos_corner_cases.cmake @@ -49,11 +49,14 @@ ENDIF() IF (KOKKOS_CXX_STANDARD STREQUAL 17) IF (KOKKOS_CXX_COMPILER_ID STREQUAL GNU AND KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 7) - MESSAGE(FATAL_ERROR "You have requested c++17 support for GCC ${KOKKOS_CXX_COMPILER_VERSION}. Although CMake has allowed this and GCC accepts -std=c++1z/c++17, GCC <= 6 does not properly support *this capture. Please reduce the C++ standard to 14 or upgrade the compiler if you do need C++17 support.") + MESSAGE(FATAL_ERROR "You have requested C++17 support for GCC ${KOKKOS_CXX_COMPILER_VERSION}. Although CMake has allowed this and GCC accepts -std=c++1z/c++17, GCC < 7 does not properly support *this capture. Please reduce the C++ standard to 14 or upgrade the compiler if you do need C++17 support.") ENDIF() IF (KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA AND KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 11) - MESSAGE(FATAL_ERROR "You have requested c++17 support for NVCC ${KOKKOS_CXX_COMPILER_VERSION}. NVCC only supports C++17 from version 11 on. Please reduce the C++ standard to 14 or upgrade the compiler if you need C++17 support.") + MESSAGE(FATAL_ERROR "You have requested C++17 support for NVCC ${KOKKOS_CXX_COMPILER_VERSION}. NVCC only supports C++17 from version 11 on. Please reduce the C++ standard to 14 or upgrade the compiler if you need C++17 support.") + ENDIF() + IF (KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA AND KOKKOS_ENABLE_CUDA_CONSTEXPR) + MESSAGE(WARNING "You have requested -DKokkos_ENABLE_CUDA_CONSTEXPR=ON with C++17 support for NVCC ${KOKKOS_CXX_COMPILER_VERSION} which is known to trigger compiler bugs. See https://github.com/kokkos/kokkos/issues/3496") ENDIF() ENDIF() diff --git a/lib/kokkos/cmake/kokkos_enable_devices.cmake b/lib/kokkos/cmake/kokkos_enable_devices.cmake index 41ee10a8a0..d7f83ddbdf 100644 --- a/lib/kokkos/cmake/kokkos_enable_devices.cmake +++ b/lib/kokkos/cmake/kokkos_enable_devices.cmake @@ -48,9 +48,6 @@ IF(KOKKOS_ENABLE_OPENMP) IF(KOKKOS_CLANG_IS_CRAY) SET(ClangOpenMPFlag -fopenmp) ENDIF() - IF(KOKKOS_CLANG_IS_INTEL) - SET(ClangOpenMPFlag -fiopenmp) - ENDIF() IF(KOKKOS_COMPILER_CLANG_MSVC) #for clang-cl expression /openmp yields an error, so directly add the specific Clang flag SET(ClangOpenMPFlag /clang:-fopenmp=libomp) @@ -64,6 +61,7 @@ IF(KOKKOS_ENABLE_OPENMP) COMPILER_SPECIFIC_FLAGS( COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Clang -Xcompiler ${ClangOpenMPFlag} + IntelLLVM -Xcompiler -fiopenmp PGI -Xcompiler -mp Cray NO-VALUE-SPECIFIED XL -Xcompiler -qsmp=omp @@ -72,6 +70,7 @@ IF(KOKKOS_ENABLE_OPENMP) ELSE() COMPILER_SPECIFIC_FLAGS( Clang ${ClangOpenMPFlag} + IntelLLVM -fiopenmp AppleClang -Xpreprocessor -fopenmp PGI -mp Cray NO-VALUE-SPECIFIED @@ -93,7 +92,7 @@ IF (KOKKOS_ENABLE_OPENMPTARGET) COMPILER_SPECIFIC_FLAGS( Clang ${ClangOpenMPFlag} -Wno-openmp-mapping - IntelClang -fiopenmp -Wno-openmp-mapping + IntelLLVM -fiopenmp -Wno-openmp-mapping XL -qsmp=omp -qoffload -qnoeh PGI -mp=gpu DEFAULT -fopenmp @@ -152,3 +151,11 @@ IF (KOKKOS_ENABLE_HIP) ENDIF() KOKKOS_DEVICE_OPTION(SYCL OFF DEVICE "Whether to build SYCL backend") + +## SYCL has extra setup requirements, turn on Kokkos_Setup_SYCL.hpp in macros +IF (KOKKOS_ENABLE_SYCL) + IF(KOKKOS_CXX_STANDARD LESS 17) + MESSAGE(FATAL_ERROR "SYCL backend requires C++17 or newer!") + ENDIF() + LIST(APPEND DEVICE_SETUP_LIST SYCL) +ENDIF() diff --git a/lib/kokkos/cmake/kokkos_enable_options.cmake b/lib/kokkos/cmake/kokkos_enable_options.cmake index 5df498f373..95bce66c7b 100644 --- a/lib/kokkos/cmake/kokkos_enable_options.cmake +++ b/lib/kokkos/cmake/kokkos_enable_options.cmake @@ -48,6 +48,7 @@ KOKKOS_ENABLE_OPTION(COMPILER_WARNINGS OFF "Whether to print all compiler war KOKKOS_ENABLE_OPTION(PROFILING_LOAD_PRINT OFF "Whether to print information about which profiling tools got loaded") KOKKOS_ENABLE_OPTION(TUNING OFF "Whether to create bindings for tuning tools") KOKKOS_ENABLE_OPTION(AGGRESSIVE_VECTORIZATION OFF "Whether to aggressively vectorize loops") +KOKKOS_ENABLE_OPTION(LAUNCH_COMPILER ON "Whether to potentially use the launch compiler") IF (KOKKOS_ENABLE_CUDA) SET(KOKKOS_COMPILER_CUDA_VERSION "${KOKKOS_COMPILER_VERSION_MAJOR}${KOKKOS_COMPILER_VERSION_MINOR}") @@ -68,6 +69,15 @@ ELSE() ENDIF() KOKKOS_ENABLE_OPTION(COMPLEX_ALIGN ${COMPLEX_ALIGN_DEFAULT} "Whether to align Kokkos::complex to 2*alignof(RealType)") +IF (KOKKOS_ENABLE_TESTS) + SET(HEADER_SELF_CONTAINMENT_TESTS_DEFAULT ON) +ELSE() + SET(HEADER_SELF_CONTAINMENT_TESTS_DEFAULT OFF) +ENDIF() +KOKKOS_ENABLE_OPTION(HEADER_SELF_CONTAINMENT_TESTS ${HEADER_SELF_CONTAINMENT_TESTS_DEFAULT} "Enable header self-containment unit tests") +IF (NOT KOKKOS_ENABLE_TESTS AND KOKKOS_ENABLE_HEADER_SELF_CONTAINMENT_TESTS) + MESSAGE(WARNING "Kokkos_ENABLE_HEADER_SELF_CONTAINMENT_TESTS is ON but Kokkos_ENABLE_TESTS is OFF. Option will be ignored.") +ENDIF() IF (KOKKOS_ENABLE_CUDA AND (KOKKOS_CXX_COMPILER_ID STREQUAL Clang)) SET(CUDA_CONSTEXPR_DEFAULT ON) @@ -76,14 +86,14 @@ ELSE() ENDIF() KOKKOS_ENABLE_OPTION(CUDA_CONSTEXPR ${CUDA_CONSTEXPR_DEFAULT} "Whether to activate experimental relaxed constexpr functions") +Kokkos_ENABLE_OPTION(UNSUPPORTED_ARCHS OFF "Whether to allow architectures in backends Kokkos doesn't optimize for") + FUNCTION(check_device_specific_options) CMAKE_PARSE_ARGUMENTS(SOME "" "DEVICE" "OPTIONS" ${ARGN}) IF(NOT KOKKOS_ENABLE_${SOME_DEVICE}) FOREACH(OPTION ${SOME_OPTIONS}) - IF(CMAKE_VERSION VERSION_GREATER_EQUAL 3.14) - IF(NOT DEFINED CACHE{Kokkos_ENABLE_${OPTION}} OR NOT DEFINED CACHE{Kokkos_ENABLE_${SOME_DEVICE}}) - MESSAGE(FATAL_ERROR "Internal logic error: option '${OPTION}' or device '${SOME_DEVICE}' not recognized.") - ENDIF() + IF(NOT DEFINED CACHE{Kokkos_ENABLE_${OPTION}} OR NOT DEFINED CACHE{Kokkos_ENABLE_${SOME_DEVICE}}) + MESSAGE(FATAL_ERROR "Internal logic error: option '${OPTION}' or device '${SOME_DEVICE}' not recognized.") ENDIF() IF(KOKKOS_ENABLE_${OPTION}) MESSAGE(WARNING "Kokkos_ENABLE_${OPTION} is ON but ${SOME_DEVICE} backend is not enabled. Option will be ignored.") diff --git a/lib/kokkos/cmake/kokkos_functions.cmake b/lib/kokkos/cmake/kokkos_functions.cmake index 2b17d648b4..e1a3e5f8bd 100644 --- a/lib/kokkos/cmake/kokkos_functions.cmake +++ b/lib/kokkos/cmake/kokkos_functions.cmake @@ -169,9 +169,7 @@ MACRO(kokkos_export_imported_tpl NAME) ENDIF() SET(TPL_LINK_OPTIONS) - IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13.0") - GET_TARGET_PROPERTY(TPL_LINK_OPTIONS ${NAME} INTERFACE_LINK_OPTIONS) - ENDIF() + GET_TARGET_PROPERTY(TPL_LINK_OPTIONS ${NAME} INTERFACE_LINK_OPTIONS) IF(TPL_LINK_OPTIONS) KOKKOS_APPEND_CONFIG_LINE("INTERFACE_LINK_OPTIONS ${TPL_LINK_OPTIONS}") ENDIF() @@ -230,9 +228,7 @@ MACRO(kokkos_import_tpl NAME) # I have still been getting errors about ROOT variables being ignored # I'm not sure if this is a scope issue - but make sure # the policy is set before we do any find_package calls - IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.12.0") - CMAKE_POLICY(SET CMP0074 NEW) - ENDIF() + CMAKE_POLICY(SET CMP0074 NEW) IF (KOKKOS_ENABLE_${NAME}) #Tack on a TPL here to make sure we avoid using anyone else's find @@ -314,7 +310,7 @@ MACRO(kokkos_create_imported_tpl NAME) CMAKE_PARSE_ARGUMENTS(TPL "INTERFACE" "LIBRARY" - "LINK_LIBRARIES;INCLUDES;COMPILE_OPTIONS;LINK_OPTIONS" + "LINK_LIBRARIES;INCLUDES;COMPILE_DEFINITIONS;COMPILE_OPTIONS;LINK_OPTIONS" ${ARGN}) @@ -334,6 +330,9 @@ MACRO(kokkos_create_imported_tpl NAME) IF(TPL_INCLUDES) TARGET_INCLUDE_DIRECTORIES(${NAME} INTERFACE ${TPL_INCLUDES}) ENDIF() + IF(TPL_COMPILE_DEFINITIONS) + TARGET_COMPILE_DEFINITIONS(${NAME} INTERFACE ${TPL_COMPILE_DEFINITIONS}) + ENDIF() IF(TPL_COMPILE_OPTIONS) TARGET_COMPILE_OPTIONS(${NAME} INTERFACE ${TPL_COMPILE_OPTIONS}) ENDIF() @@ -355,6 +354,10 @@ MACRO(kokkos_create_imported_tpl NAME) SET_TARGET_PROPERTIES(${NAME} PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${TPL_INCLUDES}") ENDIF() + IF(TPL_COMPILE_DEFINITIONS) + SET_TARGET_PROPERTIES(${NAME} PROPERTIES + INTERFACE_COMPILE_DEFINITIONS "${TPL_COMPILE_DEFINITIONS}") + ENDIF() IF(TPL_COMPILE_OPTIONS) SET_TARGET_PROPERTIES(${NAME} PROPERTIES INTERFACE_COMPILE_OPTIONS "${TPL_COMPILE_OPTIONS}") @@ -770,7 +773,7 @@ FUNCTION(kokkos_link_tpl TARGET) ENDFUNCTION() FUNCTION(COMPILER_SPECIFIC_OPTIONS_HELPER) - SET(COMPILERS NVIDIA PGI XL DEFAULT Cray Intel Clang AppleClang IntelClang GNU HIP Fujitsu) + SET(COMPILERS NVIDIA PGI XL DEFAULT Cray Intel Clang AppleClang IntelLLVM GNU HIPCC Fujitsu) CMAKE_PARSE_ARGUMENTS( PARSE "LINK_OPTIONS;COMPILE_OPTIONS;COMPILE_DEFINITIONS;LINK_LIBRARIES" @@ -926,6 +929,9 @@ ENDFUNCTION() # DIRECTORY --> all files in directory # PROJECT --> all files/targets in a project/subproject # +# NOTE: this is VERY DIFFERENT than the version in KokkosConfigCommon.cmake.in. +# This version explicitly uses nvcc_wrapper. +# FUNCTION(kokkos_compilation) # check whether the compiler already supports building CUDA KOKKOS_CXX_COMPILER_CUDA_TEST(Kokkos_CXX_COMPILER_COMPILES_CUDA) @@ -947,10 +953,21 @@ FUNCTION(kokkos_compilation) MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'") ENDIF() + # find nvcc_wrapper + FIND_PROGRAM(Kokkos_NVCC_WRAPPER + NAMES nvcc_wrapper + HINTS ${PROJECT_SOURCE_DIR} + PATHS ${PROJECT_SOURCE_DIR} + PATH_SUFFIXES bin) + + IF(NOT Kokkos_COMPILE_LAUNCHER) + MESSAGE(FATAL_ERROR "Kokkos could not find 'nvcc_wrapper'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/nvcc_wrapper'") + ENDIF() + IF(COMP_GLOBAL) # if global, don't bother setting others - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") ELSE() FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE) # make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...) @@ -961,8 +978,8 @@ FUNCTION(kokkos_compilation) # set the properties if defined IF(COMP_${_TYPE}) # MESSAGE(STATUS "Using nvcc_wrapper :: ${_TYPE} :: ${COMP_${_TYPE}}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") ENDIF() ENDFOREACH() ENDIF() diff --git a/lib/kokkos/cmake/kokkos_test_cxx_std.cmake b/lib/kokkos/cmake/kokkos_test_cxx_std.cmake index 1d7da922eb..707fb000af 100644 --- a/lib/kokkos/cmake/kokkos_test_cxx_std.cmake +++ b/lib/kokkos/cmake/kokkos_test_cxx_std.cmake @@ -86,6 +86,19 @@ ELSE() MESSAGE(FATAL_ERROR "Unknown C++ standard ${KOKKOS_CXX_STANDARD} - must be 14, 17, or 20") ENDIF() +# Enforce that we can compile a simple C++14 program + +TRY_COMPILE(CAN_COMPILE_CPP14 + ${KOKKOS_TOP_BUILD_DIR}/corner_cases + ${KOKKOS_SOURCE_DIR}/cmake/compile_tests/cplusplus14.cpp + OUTPUT_VARIABLE ERROR_MESSAGE + CXX_STANDARD 14 +) +if (NOT CAN_COMPILE_CPP14) + UNSET(CAN_COMPILE_CPP14 CACHE) #make sure CMake always re-runs this + MESSAGE(FATAL_ERROR "C++${KOKKOS_CXX_STANDARD}-compliant compiler detected, but unable to compile C++14 or later program. Verify that ${CMAKE_CXX_COMPILER_ID}:${CMAKE_CXX_COMPILER_VERSION} is set up correctly (e.g., check that correct library headers are being used).\nFailing output:\n ${ERROR_MESSAGE}") +ENDIF() +UNSET(CAN_COMPILE_CPP14 CACHE) #make sure CMake always re-runs this # Enforce that extensions are turned off for nvcc_wrapper. diff --git a/lib/kokkos/cmake/kokkos_tpls.cmake b/lib/kokkos/cmake/kokkos_tpls.cmake index b58d3696ea..d8d044c9d7 100644 --- a/lib/kokkos/cmake/kokkos_tpls.cmake +++ b/lib/kokkos/cmake/kokkos_tpls.cmake @@ -1,5 +1,6 @@ KOKKOS_CFG_DEPENDS(TPLS OPTIONS) KOKKOS_CFG_DEPENDS(TPLS DEVICES) +KOKKOS_CFG_DEPENDS(TPLS COMPILER_ID) FUNCTION(KOKKOS_TPL_OPTION PKG DEFAULT) CMAKE_PARSE_ARGUMENTS(PARSED @@ -38,6 +39,12 @@ IF(KOKKOS_ENABLE_MEMKIND) ENDIF() KOKKOS_TPL_OPTION(CUDA ${Kokkos_ENABLE_CUDA} TRIBITS CUDA) KOKKOS_TPL_OPTION(LIBRT Off) +IF(KOKKOS_ENABLE_HIP AND NOT KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) + SET(ROCM_DEFAULT ON) +ELSE() + SET(ROCM_DEFAULT OFF) +ENDIF() +KOKKOS_TPL_OPTION(ROCM ${ROCM_DEFAULT}) IF (WIN32) SET(LIBDL_DEFAULT Off) @@ -70,6 +77,7 @@ KOKKOS_IMPORT_TPL(LIBRT) KOKKOS_IMPORT_TPL(LIBDL) KOKKOS_IMPORT_TPL(MEMKIND) KOKKOS_IMPORT_TPL(PTHREAD INTERFACE) +KOKKOS_IMPORT_TPL(ROCM INTERFACE) #Convert list to newlines (which CMake doesn't always like in cache variables) STRING(REPLACE ";" "\n" KOKKOS_TPL_EXPORT_TEMP "${KOKKOS_TPL_EXPORTS}") diff --git a/lib/kokkos/cmake/kokkos_tribits.cmake b/lib/kokkos/cmake/kokkos_tribits.cmake index 059fb192f0..afa036066a 100644 --- a/lib/kokkos/cmake/kokkos_tribits.cmake +++ b/lib/kokkos/cmake/kokkos_tribits.cmake @@ -141,39 +141,54 @@ FUNCTION(KOKKOS_ADD_EXECUTABLE ROOT_NAME) ENDFUNCTION() FUNCTION(KOKKOS_ADD_EXECUTABLE_AND_TEST ROOT_NAME) -CMAKE_PARSE_ARGUMENTS(PARSE - "" - "" - "SOURCES;CATEGORIES;ARGS" - ${ARGN}) -VERIFY_EMPTY(KOKKOS_ADD_EXECUTABLE_AND_TEST ${PARSE_UNPARSED_ARGUMENTS}) + CMAKE_PARSE_ARGUMENTS(PARSE + "" + "" + "SOURCES;CATEGORIES;ARGS" + ${ARGN}) + VERIFY_EMPTY(KOKKOS_ADD_EXECUTABLE_AND_TEST ${PARSE_UNPARSED_ARGUMENTS}) -IF (KOKKOS_HAS_TRILINOS) - IF(DEFINED PARSE_ARGS) - STRING(REPLACE ";" " " PARSE_ARGS "${PARSE_ARGS}") - ENDIF() - TRIBITS_ADD_EXECUTABLE_AND_TEST( - ${ROOT_NAME} - SOURCES ${PARSE_SOURCES} - TESTONLYLIBS kokkos_gtest - NUM_MPI_PROCS 1 - COMM serial mpi - ARGS ${PARSE_ARGS} - CATEGORIES ${PARSE_CATEGORIES} - SOURCES ${PARSE_SOURCES} - FAIL_REGULAR_EXPRESSION " FAILED " - ARGS ${PARSE_ARGS} - ) -ELSE() - KOKKOS_ADD_TEST_EXECUTABLE(${ROOT_NAME} - SOURCES ${PARSE_SOURCES} - ) - KOKKOS_ADD_TEST(NAME ${ROOT_NAME} - EXE ${ROOT_NAME} - FAIL_REGULAR_EXPRESSION " FAILED " - ARGS ${PARSE_ARGS} - ) -ENDIF() + IF (KOKKOS_HAS_TRILINOS) + IF(DEFINED PARSE_ARGS) + STRING(REPLACE ";" " " PARSE_ARGS "${PARSE_ARGS}") + ENDIF() + TRIBITS_ADD_EXECUTABLE_AND_TEST( + ${ROOT_NAME} + SOURCES ${PARSE_SOURCES} + TESTONLYLIBS kokkos_gtest + NUM_MPI_PROCS 1 + COMM serial mpi + ARGS ${PARSE_ARGS} + CATEGORIES ${PARSE_CATEGORIES} + SOURCES ${PARSE_SOURCES} + FAIL_REGULAR_EXPRESSION " FAILED " + ARGS ${PARSE_ARGS} + ) + ELSE() + KOKKOS_ADD_TEST_EXECUTABLE(${ROOT_NAME} + SOURCES ${PARSE_SOURCES} + ) + IF (PARSE_ARGS) + SET(TEST_NUMBER 0) + FOREACH (ARG_STR ${PARSE_ARGS}) + # This is passed as a single string blob to match TriBITS behavior + # We need this to be turned into a list + STRING(REPLACE " " ";" ARG_STR_LIST ${ARG_STR}) + LIST(APPEND TEST_NAME "${ROOT_NAME}${TEST_NUMBER}") + MATH(EXPR TEST_NUMBER "${TEST_NUMBER} + 1") + KOKKOS_ADD_TEST(NAME ${TEST_NAME} + EXE ${ROOT_NAME} + FAIL_REGULAR_EXPRESSION " FAILED " + ARGS ${ARG_STR_LIST} + ) + ENDFOREACH() + ELSE() + KOKKOS_ADD_TEST(NAME ${ROOT_NAME} + EXE ${ROOT_NAME} + FAIL_REGULAR_EXPRESSION " FAILED " + ) + ENDIF() + ENDIF() ENDFUNCTION() FUNCTION(KOKKOS_SET_EXE_PROPERTY ROOT_NAME) @@ -301,11 +316,26 @@ ENDMACRO() ## Includes generated header files, scripts such as nvcc_wrapper and hpcbind, ## as well as other files provided through plugins. MACRO(KOKKOS_INSTALL_ADDITIONAL_FILES) - # kokkos_launch_compiler is used by Kokkos to prefix compiler commands so that they forward to nvcc_wrapper + + # kokkos_launch_compiler is used by Kokkos to prefix compiler commands so that they forward to original kokkos compiler + # if nvcc_wrapper was not used as CMAKE_CXX_COMPILER, configure the original compiler into kokkos_launch_compiler + IF(NOT "${CMAKE_CXX_COMPILER}" MATCHES "nvcc_wrapper") + SET(NVCC_WRAPPER_DEFAULT_COMPILER "${CMAKE_CXX_COMPILER}") + ELSE() + IF(NOT "$ENV{NVCC_WRAPPER_DEFAULT_COMPILER}" STREQUAL "") + SET(NVCC_WRAPPER_DEFAULT_COMPILER "$ENV{NVCC_WRAPPER_DEFAULT_COMPILER}") + ENDIF() + ENDIF() + + CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/bin/kokkos_launch_compiler + ${PROJECT_BINARY_DIR}/temp/kokkos_launch_compiler + @ONLY) + INSTALL(PROGRAMS "${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper" "${CMAKE_CURRENT_SOURCE_DIR}/bin/hpcbind" "${CMAKE_CURRENT_SOURCE_DIR}/bin/kokkos_launch_compiler" + "${PROJECT_BINARY_DIR}/temp/kokkos_launch_compiler" DESTINATION ${CMAKE_INSTALL_BINDIR}) INSTALL(FILES "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_config.h" @@ -313,7 +343,7 @@ MACRO(KOKKOS_INSTALL_ADDITIONAL_FILES) "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_SetupBackend.hpp" "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_DeclareBackend.hpp" "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_PostInclude.hpp" - DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) + DESTINATION ${KOKKOS_HEADER_DIR}) ENDMACRO() FUNCTION(KOKKOS_SET_LIBRARY_PROPERTIES LIBRARY_NAME) @@ -330,24 +360,12 @@ FUNCTION(KOKKOS_SET_LIBRARY_PROPERTIES LIBRARY_NAME) ${LIBRARY_NAME} PUBLIC $<$:${KOKKOS_LINK_OPTIONS}> ) - ELSEIF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13") + ELSE() #I can use link options #just assume CXX linkage TARGET_LINK_OPTIONS( ${LIBRARY_NAME} PUBLIC ${KOKKOS_LINK_OPTIONS} ) - ELSE() - #assume CXX linkage, we have no good way to check otherwise - IF (PARSE_PLAIN_STYLE) - TARGET_LINK_LIBRARIES( - ${LIBRARY_NAME} ${KOKKOS_LINK_OPTIONS} - ) - ELSE() - #well, have to do it the wrong way for now - TARGET_LINK_LIBRARIES( - ${LIBRARY_NAME} PUBLIC ${KOKKOS_LINK_OPTIONS} - ) - ENDIF() ENDIF() TARGET_COMPILE_OPTIONS( @@ -448,6 +466,13 @@ FUNCTION(KOKKOS_INTERNAL_ADD_LIBRARY LIBRARY_NAME) ${PARSE_SOURCES} ) + IF(PARSE_SHARED OR BUILD_SHARED_LIBS) + SET_TARGET_PROPERTIES(${LIBRARY_NAME} PROPERTIES + VERSION ${Kokkos_VERSION} + SOVERSION ${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR} + ) + ENDIF() + KOKKOS_INTERNAL_ADD_LIBRARY_INSTALL(${LIBRARY_NAME}) #In case we are building in-tree, add an alias name diff --git a/lib/kokkos/containers/src/CMakeLists.txt b/lib/kokkos/containers/src/CMakeLists.txt index 7000624b6b..98655896d4 100644 --- a/lib/kokkos/containers/src/CMakeLists.txt +++ b/lib/kokkos/containers/src/CMakeLists.txt @@ -26,8 +26,6 @@ KOKKOS_ADD_LIBRARY( HEADERS ${KOKKOS_CONTAINER_HEADERS} ) -SET_TARGET_PROPERTIES(kokkoscontainers PROPERTIES VERSION ${Kokkos_VERSION}) - KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkoscontainers ${KOKKOS_TOP_BUILD_DIR} ${CMAKE_CURRENT_BINARY_DIR} @@ -36,4 +34,3 @@ KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkoscontainers KOKKOS_LINK_INTERNAL_LIBRARY(kokkoscontainers kokkoscore) #----------------------------------------------------------------------------- - diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 689f0eb2ed..45710d1f73 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -91,6 +91,25 @@ namespace Kokkos { * behavior. Please see the documentation of Kokkos::View for * examples. The default suffices for most users. */ + +namespace Impl { + +#ifdef KOKKOS_ENABLE_CUDA + +inline const Kokkos::Cuda& get_cuda_space(const Kokkos::Cuda& in) { return in; } + +inline const Kokkos::Cuda& get_cuda_space() { + return *Kokkos::Impl::cuda_get_deep_copy_space(); +} + +template +inline const Kokkos::Cuda& get_cuda_space(const NonCudaExecSpace&) { + return get_cuda_space(); +} + +#endif // KOKKOS_ENABLE_CUDA + +} // namespace Impl template class DualView : public ViewTraits { @@ -295,6 +314,53 @@ class DualView : public ViewTraits { "DualView constructed with incompatible views"); } } + // does the DualView have only one device + struct impl_dualview_is_single_device { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device match the device of t_dev? + template + struct impl_device_matches_tdev_device { + enum : bool { + value = std::is_same::value + }; + }; + // does the given device match the device of t_host? + template + struct impl_device_matches_thost_device { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device match the execution space of t_host? + template + struct impl_device_matches_thost_exec { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device match the execution space of t_dev? + template + struct impl_device_matches_tdev_exec { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device's memory space match the memory space of t_dev? + template + struct impl_device_matches_tdev_memory_space { + enum : bool { + value = std::is_same::value + }; + }; //@} //! \name Methods for synchronizing, marking as modified, and getting Views. @@ -302,7 +368,7 @@ class DualView : public ViewTraits { /// \brief Return a View on a specific device \c Device. /// - /// Please don't be afraid of the if_c expression in the return + /// Please don't be afraid of the nested if_c expressions in the return /// value's type. That just tells the method what the return type /// should be: t_dev if the \c Device template parameter matches /// this DualView's device type, else t_host. @@ -323,10 +389,17 @@ class DualView : public ViewTraits { /// typename dual_view_type::t_host hostView = DV.view (); /// \endcode template - KOKKOS_INLINE_FUNCTION const typename Impl::if_c< - std::is_same::value, - t_dev, t_host>::type& + KOKKOS_INLINE_FUNCTION const typename std::conditional_t< + impl_device_matches_tdev_device::value, t_dev, + typename std::conditional_t< + impl_device_matches_thost_device::value, t_host, + typename std::conditional_t< + impl_device_matches_thost_exec::value, t_host, + typename std::conditional_t< + impl_device_matches_tdev_exec::value, t_dev, + typename std::conditional_t< + impl_device_matches_tdev_memory_space::value, + t_dev, t_host> > > > > view() const { constexpr bool device_is_memspace = std::is_same::value; @@ -463,6 +536,7 @@ class DualView : public ViewTraits { true); } } + /// \brief Update data on device or host only if data in the other /// space has been marked as modified. /// @@ -480,12 +554,9 @@ class DualView : public ViewTraits { /// the data in either View. You must manually mark modified data /// as modified, by calling the modify() method with the /// appropriate template parameter. - template - void sync(const typename std::enable_if< - (std::is_same::value) || - (std::is_same::value), - int>::type& = 0) { + // deliberately passing args by cref as they're used multiple times + template + void sync_impl(std::true_type, Args const&... args) { if (modified_flags.data() == nullptr) return; int dev = get_device_side(); @@ -497,12 +568,12 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), true); } #endif - deep_copy(d_view, h_view); + deep_copy(args..., d_view, h_view); modified_flags(0) = modified_flags(1) = 0; impl_report_device_sync(); } @@ -514,12 +585,12 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), false); } #endif - deep_copy(h_view, d_view); + deep_copy(args..., h_view, d_view); modified_flags(0) = modified_flags(1) = 0; impl_report_host_sync(); } @@ -533,10 +604,26 @@ class DualView : public ViewTraits { template void sync(const typename std::enable_if< - (!std::is_same::value) || + (std::is_same::value) || (std::is_same::value), int>::type& = 0) { + sync_impl(std::true_type{}); + } + + template + void sync(const ExecutionSpace& exec, + const typename std::enable_if< + (std::is_same::value) || + (std::is_same::value), + int>::type& = 0) { + sync_impl(std::true_type{}, exec); + } + + // deliberately passing args by cref as they're used multiple times + template + void sync_impl(std::false_type, Args const&...) { if (modified_flags.data() == nullptr) return; int dev = get_device_side(); @@ -557,7 +644,27 @@ class DualView : public ViewTraits { } } - void sync_host() { + template + void sync(const typename std::enable_if< + (!std::is_same::value) || + (std::is_same::value), + int>::type& = 0) { + sync_impl(std::false_type{}); + } + template + void sync(const ExecutionSpace& exec, + const typename std::enable_if< + (!std::is_same::value) || + (std::is_same::value), + int>::type& = 0) { + sync_impl(std::false_type{}, exec); + } + + // deliberately passing args by cref as they're used multiple times + template + void sync_host_impl(Args const&... args) { if (!std::is_same::value) Impl::throw_runtime_exception( @@ -569,18 +676,26 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), false); } #endif - deep_copy(h_view, d_view); + deep_copy(args..., h_view, d_view); modified_flags(1) = modified_flags(0) = 0; impl_report_host_sync(); } } - void sync_device() { + template + void sync_host(const ExecSpace& exec) { + sync_host_impl(exec); + } + void sync_host() { sync_host_impl(); } + + // deliberately passing args by cref as they're used multiple times + template + void sync_device_impl(Args const&... args) { if (!std::is_same::value) Impl::throw_runtime_exception( @@ -592,17 +707,23 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), true); } #endif - deep_copy(d_view, h_view); + deep_copy(args..., d_view, h_view); modified_flags(1) = modified_flags(0) = 0; impl_report_device_sync(); } } + template + void sync_device(const ExecSpace& exec) { + sync_device_impl(exec); + } + void sync_device() { sync_device_impl(); } + template bool need_sync() const { if (modified_flags.data() == nullptr) return false; @@ -658,6 +779,7 @@ class DualView : public ViewTraits { template void modify() { if (modified_flags.data() == nullptr) return; + if (impl_dualview_is_single_device::value) return; int dev = get_device_side(); if (dev == 1) { // if Device is the same as DualView's device type @@ -690,6 +812,7 @@ class DualView : public ViewTraits { } inline void modify_host() { + if (impl_dualview_is_single_device::value) return; if (modified_flags.data() != nullptr) { modified_flags(0) = (modified_flags(1) > modified_flags(0) ? modified_flags(1) @@ -710,6 +833,7 @@ class DualView : public ViewTraits { } inline void modify_device() { + if (impl_dualview_is_single_device::value) return; if (modified_flags.data() != nullptr) { modified_flags(1) = (modified_flags(1) > modified_flags(0) ? modified_flags(1) diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index c66d7a5f36..c6323fef93 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -245,13 +245,10 @@ KOKKOS_INLINE_FUNCTION bool dyn_rank_view_verify_operator_bounds( return (size_t(i) < map.extent(R)) && dyn_rank_view_verify_operator_bounds(rank, map, args...); } else if (i != 0) { - // FIXME_SYCL SYCL doesn't allow printf in kernels -#ifndef KOKKOS_ENABLE_SYCL - printf( + KOKKOS_IMPL_DO_NOT_USE_PRINTF( "DynRankView Debug Bounds Checking Error: at rank %u\n Extra " "arguments beyond the rank must be zero \n", R); -#endif return (false) && dyn_rank_view_verify_operator_bounds(rank, map, args...); } else { @@ -575,37 +572,22 @@ class DynRankView : public ViewTraits { (is_layout_left || is_layout_right || is_layout_stride) }; - template ::accessible> - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() {} - }; - - template - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() { - Kokkos::abort( - "Kokkos::DynRankView ERROR: attempt to access inaccessible memory " - "space"); - }; - }; - // Bounds checking macros #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) // rank of the calling operator - included as first argument in ARG -#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ - DynRankView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); \ - Kokkos::Impl::dyn_rank_view_verify_operator_bounds< \ - typename traits::memory_space> \ +#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); \ + Kokkos::Impl::dyn_rank_view_verify_operator_bounds< \ + typename traits::memory_space> \ ARG; #else -#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ - DynRankView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); +#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); #endif diff --git a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp index 06bd556661..cc949d4c55 100644 --- a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp @@ -76,6 +76,12 @@ struct ChunkArraySpace { using memory_space = typename Kokkos::Experimental::HIPHostPinnedSpace; }; #endif +#ifdef KOKKOS_ENABLE_SYCL +template <> +struct ChunkArraySpace { + using memory_space = typename Kokkos::Experimental::SYCLSharedUSMSpace; +}; +#endif } // end namespace Impl /** \brief Dynamic views are restricted to rank-one and no layout. diff --git a/lib/kokkos/containers/src/Kokkos_OffsetView.hpp b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp index 4fd084338e..0f21a08ba3 100644 --- a/lib/kokkos/containers/src/Kokkos_OffsetView.hpp +++ b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp @@ -377,34 +377,20 @@ class OffsetView : public ViewTraits { std::is_same::value && (is_layout_left || is_layout_right || is_layout_stride); - template ::accessible> - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() {} - }; - - template - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() { - Kokkos::abort( - "Kokkos::View ERROR: attempt to access inaccessible memory space"); - }; - }; - #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) -#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ - OffsetView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); \ - Kokkos::Experimental::Impl::offsetview_verify_operator_bounds< \ - typename traits::memory_space> \ +#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); \ + Kokkos::Experimental::Impl::offsetview_verify_operator_bounds< \ + typename traits::memory_space> \ ARG; #else -#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ - OffsetView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); +#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); #endif public: diff --git a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp index 5e18f5a80e..dcd4cf73e5 100644 --- a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp +++ b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp @@ -649,13 +649,13 @@ struct ReduceDuplicatesBase { size_t stride; size_t start; size_t n; - ReduceDuplicatesBase(ValueType const* src_in, ValueType* dest_in, - size_t stride_in, size_t start_in, size_t n_in, - std::string const& name) + ReduceDuplicatesBase(ExecSpace const& exec_space, ValueType const* src_in, + ValueType* dest_in, size_t stride_in, size_t start_in, + size_t n_in, std::string const& name) : src(src_in), dst(dest_in), stride(stride_in), start(start_in), n(n_in) { parallel_for( std::string("Kokkos::ScatterView::ReduceDuplicates [") + name + "]", - RangePolicy(0, stride), + RangePolicy(exec_space, 0, stride), static_cast(*this)); } }; @@ -667,9 +667,10 @@ template struct ReduceDuplicates : public ReduceDuplicatesBase { using Base = ReduceDuplicatesBase; - ReduceDuplicates(ValueType const* src_in, ValueType* dst_in, size_t stride_in, - size_t start_in, size_t n_in, std::string const& name) - : Base(src_in, dst_in, stride_in, start_in, n_in, name) {} + ReduceDuplicates(ExecSpace const& exec_space, ValueType const* src_in, + ValueType* dst_in, size_t stride_in, size_t start_in, + size_t n_in, std::string const& name) + : Base(exec_space, src_in, dst_in, stride_in, start_in, n_in, name) {} KOKKOS_FORCEINLINE_FUNCTION void operator()(size_t i) const { for (size_t j = Base::start; j < Base::n; ++j) { ScatterValue struct ResetDuplicatesBase { using Derived = ResetDuplicates; ValueType* data; - ResetDuplicatesBase(ValueType* data_in, size_t size_in, - std::string const& name) + ResetDuplicatesBase(ExecSpace const& exec_space, ValueType* data_in, + size_t size_in, std::string const& name) : data(data_in) { parallel_for( std::string("Kokkos::ScatterView::ResetDuplicates [") + name + "]", - RangePolicy(0, size_in), + RangePolicy(exec_space, 0, size_in), static_cast(*this)); } }; @@ -703,8 +704,9 @@ struct ResetDuplicatesBase { template struct ResetDuplicates : public ResetDuplicatesBase { using Base = ResetDuplicatesBase; - ResetDuplicates(ValueType* data_in, size_t size_in, std::string const& name) - : Base(data_in, size_in, name) {} + ResetDuplicates(ExecSpace const& exec_space, ValueType* data_in, + size_t size_in, std::string const& name) + : Base(exec_space, data_in, size_in, name) {} KOKKOS_FORCEINLINE_FUNCTION void operator()(size_t i) const { ScatterValue @@ -713,6 +715,16 @@ struct ResetDuplicates : public ResetDuplicatesBase { } }; +template +void check_scatter_view_allocation_properties_argument( + ViewCtorProp const&) { + static_assert(ViewCtorProp::has_execution_space && + ViewCtorProp::has_label && + ViewCtorProp::initialize, + "Allocation property must have an execution name as well as a " + "label, and must perform the view initialization"); +} + } // namespace Experimental } // namespace Impl } // namespace Kokkos @@ -762,10 +774,26 @@ class ScatterView const& original_view) : internal_view(original_view) {} + template + ScatterView(execution_space const& /* exec_space */, + View const& original_view) + : internal_view(original_view) {} + template ScatterView(std::string const& name, Dims... dims) : internal_view(name, dims...) {} + // This overload allows specifying an execution space instance to be + // used by passing, e.g., Kokkos::view_alloc(exec_space, "label") as + // first argument. + template + ScatterView(::Kokkos::Impl::ViewCtorProp const& arg_prop, Dims... dims) + : internal_view(arg_prop, dims...) { + using ::Kokkos::Impl::Experimental:: + check_scatter_view_allocation_properties_argument; + check_scatter_view_allocation_properties_argument(arg_prop); + } + template KOKKOS_FUNCTION ScatterView( const ScatterView void contribute_into(View const& dest) const { + contribute_into(execution_space(), dest); + } + + template + void contribute_into(execution_space const& exec_space, + View const& dest) const { using dest_type = View; static_assert(std::is_same::value, "ScatterView contribute destination has different layout"); static_assert( - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< - memory_space, typename dest_type::memory_space>::value, + Kokkos::Impl::SpaceAccessibility< + execution_space, typename dest_type::memory_space>::accessible, "ScatterView contribute destination memory space not accessible"); if (dest.data() == internal_view.data()) return; Kokkos::Impl::Experimental::ReduceDuplicates( - internal_view.data(), dest.data(), 0, 0, 1, internal_view.label()); + exec_space, internal_view.data(), dest.data(), 0, 0, 1, + internal_view.label()); } - void reset() { + void reset(execution_space const& exec_space = execution_space()) { Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data(), internal_view.size(), internal_view.label()); + exec_space, internal_view.data(), internal_view.size(), + internal_view.label()); } template void reset_except(View const& view) { - if (view.data() != internal_view.data()) reset(); + reset_except(execution_space(), view); + } + + template + void reset_except(const execution_space& exec_space, + View const& view) { + if (view.data() != internal_view.data()) reset(exec_space); } void resize(const size_t n0 = 0, const size_t n1 = 0, const size_t n2 = 0, @@ -928,10 +970,16 @@ class ScatterView ScatterView(View const& original_view) + : ScatterView(execution_space(), original_view) {} + + template + ScatterView(execution_space const& exec_space, + View const& original_view) : unique_token(), internal_view( view_alloc(WithoutInitializing, - std::string("duplicated_") + original_view.label()), + std::string("duplicated_") + original_view.label(), + exec_space), unique_token.size(), original_view.rank_dynamic > 0 ? original_view.extent(0) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, @@ -949,14 +997,32 @@ class ScatterView ScatterView(std::string const& name, Dims... dims) - : internal_view(view_alloc(WithoutInitializing, name), + : ScatterView(view_alloc(execution_space(), name), dims...) {} + + // This overload allows specifying an execution space instance to be + // used by passing, e.g., Kokkos::view_alloc(exec_space, "label") as + // first argument. + template + ScatterView(::Kokkos::Impl::ViewCtorProp const& arg_prop, Dims... dims) + : internal_view(view_alloc(WithoutInitializing, + static_cast<::Kokkos::Impl::ViewCtorProp< + void, std::string> const&>(arg_prop) + .value), unique_token.size(), dims...) { - reset(); + using ::Kokkos::Impl::Experimental:: + check_scatter_view_allocation_properties_argument; + check_scatter_view_allocation_properties_argument(arg_prop); + + auto const exec_space = + static_cast<::Kokkos::Impl::ViewCtorProp const&>( + arg_prop) + .value; + reset(exec_space); } template @@ -984,37 +1050,51 @@ class ScatterView void contribute_into(View const& dest) const { + contribute_into(execution_space(), dest); + } + + template + void contribute_into(execution_space const& exec_space, + View const& dest) const { using dest_type = View; static_assert(std::is_same::value, "ScatterView deep_copy destination has different layout"); static_assert( - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< - memory_space, typename dest_type::memory_space>::value, + Kokkos::Impl::SpaceAccessibility< + execution_space, typename dest_type::memory_space>::accessible, "ScatterView deep_copy destination memory space not accessible"); bool is_equal = (dest.data() == internal_view.data()); size_t start = is_equal ? 1 : 0; Kokkos::Impl::Experimental::ReduceDuplicates( - internal_view.data(), dest.data(), internal_view.stride(0), start, - internal_view.extent(0), internal_view.label()); + exec_space, internal_view.data(), dest.data(), internal_view.stride(0), + start, internal_view.extent(0), internal_view.label()); } - void reset() { + void reset(execution_space const& exec_space = execution_space()) { Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data(), internal_view.size(), internal_view.label()); + exec_space, internal_view.data(), internal_view.size(), + internal_view.label()); } + template void reset_except(View const& view) { + reset_except(execution_space(), view); + } + + template + void reset_except(execution_space const& exec_space, + View const& view) { if (view.data() != internal_view.data()) { - reset(); + reset(exec_space); return; } Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data() + view.size(), internal_view.size() - view.size(), - internal_view.label()); + exec_space, internal_view.data() + view.size(), + internal_view.size() - view.size(), internal_view.label()); } void resize(const size_t n0 = 0, const size_t n1 = 0, const size_t n2 = 0, @@ -1075,7 +1155,13 @@ class ScatterView - ScatterView(View const& original_view) : unique_token() { + ScatterView(View const& original_view) + : ScatterView(execution_space(), original_view) {} + + template + ScatterView(execution_space const& exec_space, + View const& original_view) + : unique_token() { size_t arg_N[8] = {original_view.rank > 0 ? original_view.extent(0) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, original_view.rank > 1 ? original_view.extent(1) @@ -1094,14 +1180,27 @@ class ScatterView - ScatterView(std::string const& name, Dims... dims) { + ScatterView(std::string const& name, Dims... dims) + : ScatterView(view_alloc(execution_space(), name), dims...) {} + + // This overload allows specifying an execution space instance to be + // used by passing, e.g., Kokkos::view_alloc(exec_space, "label") as + // first argument. + template + ScatterView(::Kokkos::Impl::ViewCtorProp const& arg_prop, + Dims... dims) { + using ::Kokkos::Impl::Experimental:: + check_scatter_view_allocation_properties_argument; + check_scatter_view_allocation_properties_argument(arg_prop); + original_view_type original_view; size_t arg_N[8] = {original_view.rank > 0 ? original_view.static_extent(0) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, @@ -1120,10 +1219,20 @@ class ScatterView const&>( + arg_prop) + .value; internal_view = internal_view_type(view_alloc(WithoutInitializing, name), arg_N[0], arg_N[1], arg_N[2], arg_N[3], arg_N[4], arg_N[5], arg_N[6], arg_N[7]); - reset(); + + auto const exec_space = + static_cast<::Kokkos::Impl::ViewCtorProp const&>( + arg_prop) + .value; + reset(exec_space); } template @@ -1166,6 +1275,12 @@ class ScatterView void contribute_into(View const& dest) const { + contribute_into(execution_space(), dest); + } + + template + void contribute_into(execution_space const& exec_space, + View const& dest) const { using dest_type = View; static_assert( std::is_same::value, "ScatterView deep_copy destination has different layout"); static_assert( - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< - memory_space, typename dest_type::memory_space>::value, + Kokkos::Impl::SpaceAccessibility< + execution_space, typename dest_type::memory_space>::accessible, "ScatterView deep_copy destination memory space not accessible"); auto extent = internal_view.extent(internal_view_type::rank - 1); bool is_equal = (dest.data() == internal_view.data()); size_t start = is_equal ? 1 : 0; Kokkos::Impl::Experimental::ReduceDuplicates( - internal_view.data(), dest.data(), + exec_space, internal_view.data(), dest.data(), internal_view.stride(internal_view_type::rank - 1), start, extent, internal_view.label()); } - void reset() { + void reset(execution_space const& exec_space = execution_space()) { Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data(), internal_view.size(), internal_view.label()); + exec_space, internal_view.data(), internal_view.size(), + internal_view.label()); } + template void reset_except(View const& view) { + reset_except(execution_space(), view); + } + + template + void reset_except(execution_space const& exec_space, + View const& view) { if (view.data() != internal_view.data()) { - reset(); + reset(exec_space); return; } Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data() + view.size(), internal_view.size() - view.size(), - internal_view.label()); + exec_space, internal_view.data() + view.size(), + internal_view.size() - view.size(), internal_view.label()); } void resize(const size_t n0 = 0, const size_t n1 = 0, const size_t n2 = 0, @@ -1316,21 +1439,21 @@ template ::array_layout, typename ViewTraits::device_type, Op, - typename Kokkos::Impl::if_c< + std::conditional_t< std::is_same::value, typename Kokkos::Impl::Experimental::DefaultDuplication< typename ViewTraits::execution_space>::type, - Duplication>::type, - typename Kokkos::Impl::if_c< + Duplication>, + std::conditional_t< std::is_same::value, typename Kokkos::Impl::Experimental::DefaultContribution< typename ViewTraits::execution_space, - typename Kokkos::Impl::if_c< + typename std::conditional_t< std::is_same::value, typename Kokkos::Impl::Experimental::DefaultDuplication< typename ViewTraits::execution_space>::type, - Duplication>::type>::type, - Contribution>::type> + Duplication>>::type, + Contribution>> create_scatter_view(View const& original_view) { return original_view; // implicit ScatterView constructor call } @@ -1365,12 +1488,21 @@ create_scatter_view(Op, Duplication, Contribution, namespace Kokkos { namespace Experimental { +template +void contribute( + typename ES::execution_space const& exec_space, View& dest, + Kokkos::Experimental::ScatterView const& src) { + src.contribute_into(exec_space, dest); +} + template void contribute( View& dest, Kokkos::Experimental::ScatterView const& src) { - src.contribute_into(dest); + using execution_space = typename ES::execution_space; + contribute(execution_space{}, dest, src); } } // namespace Experimental diff --git a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp index d2affda93a..edb0e7261d 100644 --- a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp +++ b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp @@ -264,26 +264,24 @@ class UnorderedMap { private: enum : size_type { invalid_index = ~static_cast(0) }; - using impl_value_type = - typename Impl::if_c::type; + using impl_value_type = std::conditional_t; - using key_type_view = typename Impl::if_c< + using key_type_view = std::conditional_t< is_insertable_map, View, - View > >::type; + View > >; - using value_type_view = - typename Impl::if_c, - View > >::type; + using value_type_view = std::conditional_t< + is_insertable_map || is_modifiable_map, + View, + View > >; - using size_type_view = typename Impl::if_c< + using size_type_view = std::conditional_t< is_insertable_map, View, - View > >::type; + View > >; using bitset_type = - typename Impl::if_c, - ConstBitset >::type; + std::conditional_t, + ConstBitset >; enum { modified_idx = 0, erasable_idx = 1, failed_insert_idx = 2 }; enum { num_scalars = 3 }; @@ -540,10 +538,7 @@ class UnorderedMap { // Previously claimed an unused entry that was not inserted. // Release this unused entry immediately. if (!m_available_indexes.reset(new_index)) { - // FIXME_SYCL SYCL doesn't allow printf in kernels -#ifndef KOKKOS_ENABLE_SYCL - printf("Unable to free existing\n"); -#endif + KOKKOS_IMPL_DO_NOT_USE_PRINTF("Unable to free existing\n"); } } @@ -659,8 +654,8 @@ class UnorderedMap { /// /// 'const value_type' via Cuda texture fetch must return by value. KOKKOS_FORCEINLINE_FUNCTION - typename Impl::if_c<(is_set || has_const_value), impl_value_type, - impl_value_type &>::type + std::conditional_t<(is_set || has_const_value), impl_value_type, + impl_value_type &> value_at(size_type i) const { return m_values[is_set ? 0 : (i < capacity() ? i : capacity())]; } diff --git a/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp b/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp index 6e450598d1..6047e60f3d 100644 --- a/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp +++ b/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp @@ -57,10 +57,22 @@ namespace Kokkos { namespace Impl { +KOKKOS_FORCEINLINE_FUNCTION +unsigned rotate_left(unsigned i, int r) { + constexpr int size = static_cast(sizeof(unsigned) * CHAR_BIT); + return r ? ((i << r) | (i >> (size - r))) : i; +} + KOKKOS_FORCEINLINE_FUNCTION unsigned rotate_right(unsigned i, int r) { - enum { size = static_cast(sizeof(unsigned) * CHAR_BIT) }; + constexpr int size = static_cast(sizeof(unsigned) * CHAR_BIT); + // FIXME_SYCL llvm.fshr.i32 missing + // (https://github.com/intel/llvm/issues/3308) +#ifdef __SYCL_DEVICE_ONLY__ + return rotate_left(i, size - r); +#else return r ? ((i >> r) | (i << (size - r))) : i; +#endif } template diff --git a/lib/kokkos/containers/src/impl/Kokkos_StaticCrsGraph_factory.hpp b/lib/kokkos/containers/src/impl/Kokkos_StaticCrsGraph_factory.hpp index f22e5d1eca..00d3eafd23 100644 --- a/lib/kokkos/containers/src/impl/Kokkos_StaticCrsGraph_factory.hpp +++ b/lib/kokkos/containers/src/impl/Kokkos_StaticCrsGraph_factory.hpp @@ -114,15 +114,11 @@ namespace Kokkos { template inline typename StaticCrsGraphType::staticcrsgraph_type create_staticcrsgraph( const std::string& label, const std::vector& input) { - using output_type = StaticCrsGraphType; - // using input_type = std::vector; // unused - + using output_type = StaticCrsGraphType; using entries_type = typename output_type::entries_type; - - using work_type = View; + using work_type = View< + typename output_type::size_type[], typename output_type::array_layout, + typename output_type::device_type, typename output_type::memory_traits>; output_type output; @@ -161,10 +157,9 @@ inline typename StaticCrsGraphType::staticcrsgraph_type create_staticcrsgraph( static_assert(entries_type::rank == 1, "Graph entries view must be rank one"); - using work_type = View; + using work_type = View< + typename output_type::size_type[], typename output_type::array_layout, + typename output_type::device_type, typename output_type::memory_traits>; output_type output; diff --git a/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp b/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp index b06ab0846c..d7c4a5d1ff 100644 --- a/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp +++ b/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp @@ -250,8 +250,8 @@ struct UnorderedMapPrint { uint32_t list = m_map.m_hash_lists(i); for (size_type curr = list, ii = 0; curr != invalid_index; curr = m_map.m_next_index[curr], ++ii) { - printf("%d[%d]: %d->%d\n", list, ii, m_map.key_at(curr), - m_map.value_at(curr)); + KOKKOS_IMPL_DO_NOT_USE_PRINTF("%d[%d]: %d->%d\n", list, ii, + m_map.key_at(curr), m_map.value_at(curr)); } } }; diff --git a/lib/kokkos/containers/unit_tests/CMakeLists.txt b/lib/kokkos/containers/unit_tests/CMakeLists.txt index c84c5f6d5e..947d222c27 100644 --- a/lib/kokkos/containers/unit_tests/CMakeLists.txt +++ b/lib/kokkos/containers/unit_tests/CMakeLists.txt @@ -2,6 +2,7 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR}) KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/../src ) +KOKKOS_INCLUDE_DIRECTORIES(${KOKKOS_SOURCE_DIR}/core/unit_test/category_files) foreach(Tag Threads;Serial;OpenMP;HPX;Cuda;HIP;SYCL) # Because there is always an exception to the rule @@ -41,11 +42,6 @@ foreach(Tag Threads;Serial;OpenMP;HPX;Cuda;HIP;SYCL) configure_file(${dir}/dummy.cpp ${file}) list(APPEND UnitTestSources ${file}) endforeach() - list(REMOVE_ITEM UnitTestSources - ${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_Bitset.cpp - ${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_ScatterView.cpp - ${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_UnorderedMap.cpp - ) KOKKOS_ADD_EXECUTABLE_AND_TEST(UnitTest_${Tag} SOURCES ${UnitTestSources}) endif() endforeach() diff --git a/lib/kokkos/containers/unit_tests/Makefile b/lib/kokkos/containers/unit_tests/Makefile index f42b9b7519..82669fe1ab 100644 --- a/lib/kokkos/containers/unit_tests/Makefile +++ b/lib/kokkos/containers/unit_tests/Makefile @@ -26,7 +26,7 @@ override LDFLAGS += -lpthread include $(KOKKOS_PATH)/Makefile.kokkos -KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/containers/unit_tests +KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/containers/unit_tests -I${KOKKOS_PATH}/core/unit_test/category_files TEST_TARGETS = TARGETS = diff --git a/lib/kokkos/containers/unit_tests/TestCuda_Category.hpp b/lib/kokkos/containers/unit_tests/TestCuda_Category.hpp deleted file mode 100644 index 50935d7a34..0000000000 --- a/lib/kokkos/containers/unit_tests/TestCuda_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_CUDA_HPP -#define KOKKOS_TEST_CUDA_HPP - -#define TEST_CATEGORY cuda -#define TEST_EXECSPACE Kokkos::Cuda - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestDualView.hpp b/lib/kokkos/containers/unit_tests/TestDualView.hpp index 531caf0f85..3eee85ed10 100644 --- a/lib/kokkos/containers/unit_tests/TestDualView.hpp +++ b/lib/kokkos/containers/unit_tests/TestDualView.hpp @@ -114,6 +114,8 @@ struct test_dualview_combinations { a.template modify(); a.template sync(); + a.template sync( + Kokkos::DefaultExecutionSpace{}); a.h_view(5, 1) = 3; a.h_view(6, 1) = 4; @@ -122,11 +124,15 @@ struct test_dualview_combinations { ViewType b = Kokkos::subview(a, std::pair(6, 9), std::pair(0, 1)); a.template sync(); + a.template sync( + Kokkos::DefaultExecutionSpace{}); b.template modify(); Kokkos::deep_copy(b.d_view, 2); a.template sync(); + a.template sync( + Kokkos::DefaultExecutionSpace{}); Scalar count = 0; for (unsigned int i = 0; i < a.d_view.extent(0); i++) for (unsigned int j = 0; j < a.d_view.extent(1); j++) @@ -180,6 +186,7 @@ struct test_dual_view_deep_copy { } else { a.modify_device(); a.sync_host(); + a.sync_host(Kokkos::DefaultExecutionSpace{}); } // Check device view is initialized as expected @@ -208,6 +215,7 @@ struct test_dual_view_deep_copy { b.template sync(); } else { b.sync_host(); + b.sync_host(Kokkos::DefaultExecutionSpace{}); } // Perform same checks on b as done on a @@ -302,6 +310,7 @@ struct test_dualview_resize { ASSERT_EQ(a.extent(1), m / factor); a.sync_device(); + a.sync_device(Kokkos::DefaultExecutionSpace{}); // Check device view is initialized as expected a_d_sum = 0; @@ -404,19 +413,14 @@ void test_dualview_resize() { Impl::test_dualview_resize(); } -// FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, dualview_combination) { test_dualview_combinations(10, true); } -#endif TEST(TEST_CATEGORY, dualview_alloc) { test_dualview_alloc(10); } -// FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, dualview_combinations_without_init) { test_dualview_combinations(10, false); } @@ -433,8 +437,133 @@ TEST(TEST_CATEGORY, dualview_realloc) { TEST(TEST_CATEGORY, dualview_resize) { test_dualview_resize(); } + +namespace { +/** + * + * The following tests are a response to + * https://github.com/kokkos/kokkos/issues/3850 + * and + * https://github.com/kokkos/kokkos/pull/3857 + * + * DualViews were returning incorrect view types and taking + * inappropriate actions based on the templated view methods. + * + * Specifically, template view methods were always returning + * a device view if the memory space was UVM and a Kokkos::Device was passed. + * Sync/modify methods completely broke down So these tests exist to make sure + * that we keep the semantics of UVM DualViews intact. + */ +// modify if we have other UVM enabled backends +#ifdef KOKKOS_ENABLE_CUDA // OR other UVM builds +#define UVM_ENABLED_BUILD #endif +#ifdef UVM_ENABLED_BUILD +template +struct UVMSpaceFor; +#endif + +#ifdef KOKKOS_ENABLE_CUDA // specific to CUDA +template <> +struct UVMSpaceFor { + using type = Kokkos::CudaUVMSpace; +}; +#endif + +#ifdef UVM_ENABLED_BUILD +template <> +struct UVMSpaceFor { + using type = typename UVMSpaceFor::type; +}; +#else +template +struct UVMSpaceFor { + using type = typename ExecSpace::memory_space; +}; +#endif + +using ExecSpace = Kokkos::DefaultExecutionSpace; +using MemSpace = typename UVMSpaceFor::type; +using DeviceType = Kokkos::Device; + +using DualViewType = Kokkos::DualView; +using d_device = DeviceType; +using h_device = Kokkos::Device< + Kokkos::DefaultHostExecutionSpace, + typename UVMSpaceFor::type>; + +TEST(TEST_CATEGORY, dualview_device_correct_kokkos_device) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + auto v_d = dv.template view(); + using vdt = decltype(v_d); + using vdt_d = vdt::device_type; + using vdt_d_e = vdt_d::execution_space; + ASSERT_STREQ(vdt_d_e::name(), Kokkos::DefaultExecutionSpace::name()); +} +TEST(TEST_CATEGORY, dualview_host_correct_kokkos_device) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + auto v_h = dv.template view(); + using vht = decltype(v_h); + using vht_d = vht::device_type; + using vht_d_e = vht_d::execution_space; + ASSERT_STREQ(vht_d_e::name(), Kokkos::DefaultHostExecutionSpace::name()); +} + +TEST(TEST_CATEGORY, dualview_host_modify_template_device_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_host(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} + +TEST(TEST_CATEGORY, dualview_host_modify_template_device_execspace_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_host(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} + +TEST(TEST_CATEGORY, dualview_device_modify_template_host_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_device(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} +TEST(TEST_CATEGORY, dualview_device_modify_template_host_execspace_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_device(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} + +TEST(TEST_CATEGORY, + dualview_template_views_return_correct_executionspace_views) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + using hvt = decltype(dv.view()); + using dvt = decltype(dv.view()); + ASSERT_STREQ(Kokkos::DefaultExecutionSpace::name(), + dvt::device_type::execution_space::name()); + ASSERT_STREQ(Kokkos::DefaultHostExecutionSpace::name(), + hvt::device_type::execution_space::name()); +} + +} // anonymous namespace } // namespace Test #endif // KOKKOS_TEST_DUALVIEW_HPP diff --git a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp index 4b9f994417..f018793dd6 100644 --- a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp +++ b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp @@ -243,8 +243,6 @@ struct TestDynamicView { } }; -// FIXME_SYCL needs resize_serial -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, dynamic_view) { using TestDynView = TestDynamicView; @@ -252,7 +250,6 @@ TEST(TEST_CATEGORY, dynamic_view) { TestDynView::run(100000 + 100 * i); } } -#endif } // namespace Test diff --git a/lib/kokkos/containers/unit_tests/TestHIP_Category.hpp b/lib/kokkos/containers/unit_tests/TestHIP_Category.hpp deleted file mode 100644 index c2d60d1814..0000000000 --- a/lib/kokkos/containers/unit_tests/TestHIP_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_HIP_HPP -#define KOKKOS_TEST_HIP_HPP - -#define TEST_CATEGORY hip -#define TEST_EXECSPACE Kokkos::Experimental::HIP - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestOffsetView.hpp b/lib/kokkos/containers/unit_tests/TestOffsetView.hpp index 802813b13b..9ddc226e29 100644 --- a/lib/kokkos/containers/unit_tests/TestOffsetView.hpp +++ b/lib/kokkos/containers/unit_tests/TestOffsetView.hpp @@ -130,8 +130,6 @@ void test_offsetview_construction() { } } - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL const int ovmin0 = ov.begin(0); const int ovend0 = ov.end(0); const int ovmin1 = ov.begin(1); @@ -178,7 +176,6 @@ void test_offsetview_construction() { } ASSERT_EQ(OVResult, answer) << "Bad data found in OffsetView"; -#endif #endif { @@ -215,8 +212,6 @@ void test_offsetview_construction() { point3_type{{extent0, extent1, extent2}}); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifdef KOKKOS_ENABLE_SYCL int view3DSum = 0; Kokkos::parallel_reduce( rangePolicy3DZero, @@ -239,7 +234,6 @@ void test_offsetview_construction() { ASSERT_EQ(view3DSum, offsetView3DSum) << "construction of OffsetView from View and begins array broken."; -#endif #endif } view_type viewFromOV = ov.view(); @@ -266,8 +260,6 @@ void test_offsetview_construction() { Kokkos::deep_copy(aView, ov); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL int sum = 0; Kokkos::parallel_reduce( rangePolicy2D, @@ -277,7 +269,6 @@ void test_offsetview_construction() { sum); ASSERT_EQ(sum, 0) << "deep_copy(view, offsetView) broken."; -#endif #endif } @@ -288,8 +279,6 @@ void test_offsetview_construction() { Kokkos::deep_copy(ov, aView); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL int sum = 0; Kokkos::parallel_reduce( rangePolicy2D, @@ -299,7 +288,6 @@ void test_offsetview_construction() { sum); ASSERT_EQ(sum, 0) << "deep_copy(offsetView, view) broken."; -#endif #endif } } @@ -471,8 +459,6 @@ void test_offsetview_subview() { ASSERT_EQ(offsetSubview.end(1), 9); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL using range_type = Kokkos::MDRangePolicy, Kokkos::IndexType >; using point_type = typename range_type::point_type; @@ -498,7 +484,6 @@ void test_offsetview_subview() { sum); ASSERT_EQ(sum, 6 * (e0 - b0) * (e1 - b1)); -#endif #endif } @@ -701,12 +686,9 @@ void test_offsetview_offsets_rank3() { } #endif -// FIXME_SYCL needs MDRangePolicy -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, offsetview_construction) { test_offsetview_construction(); } -#endif TEST(TEST_CATEGORY, offsetview_unmanaged_construction) { test_offsetview_unmanaged_construction(); diff --git a/lib/kokkos/containers/unit_tests/TestOpenMP_Category.hpp b/lib/kokkos/containers/unit_tests/TestOpenMP_Category.hpp deleted file mode 100644 index a0169d1702..0000000000 --- a/lib/kokkos/containers/unit_tests/TestOpenMP_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_OPENMP_HPP -#define KOKKOS_TEST_OPENMP_HPP - -#define TEST_CATEGORY openmp -#define TEST_EXECSPACE Kokkos::OpenMP - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestSYCL_Category.hpp b/lib/kokkos/containers/unit_tests/TestSYCL_Category.hpp deleted file mode 100644 index 51fd3fc911..0000000000 --- a/lib/kokkos/containers/unit_tests/TestSYCL_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_SYCL_HPP -#define KOKKOS_TEST_SYCL_HPP - -#define TEST_CATEGORY sycl -#define TEST_EXECSPACE Kokkos::Experimental::SYCL - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestScatterView.hpp b/lib/kokkos/containers/unit_tests/TestScatterView.hpp index 3a3cb607a6..fdbce2d492 100644 --- a/lib/kokkos/containers/unit_tests/TestScatterView.hpp +++ b/lib/kokkos/containers/unit_tests/TestScatterView.hpp @@ -437,6 +437,10 @@ struct test_scatter_view_config { Contribution, Op, NumberType>::orig_view_type; + void compile_constructor() { + auto sv = scatter_view_def(Kokkos::view_alloc(DeviceType{}, "label"), 10); + } + void run_test(int n) { // test allocation { diff --git a/lib/kokkos/containers/unit_tests/TestSerial_Category.hpp b/lib/kokkos/containers/unit_tests/TestSerial_Category.hpp deleted file mode 100644 index 2aa09a315a..0000000000 --- a/lib/kokkos/containers/unit_tests/TestSerial_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_SERIAL_HPP -#define KOKKOS_TEST_SERIAL_HPP - -#define TEST_CATEGORY serial -#define TEST_EXECSPACE Kokkos::Serial - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp b/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp index 8bb267ce5d..a9a178f95e 100644 --- a/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp +++ b/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp @@ -285,10 +285,7 @@ void run_test_graph4() { TEST(TEST_CATEGORY, staticcrsgraph) { TestStaticCrsGraph::run_test_graph(); - // FIXME_SYCL requires MDRangePolicy -#ifndef KOKKOS_ENABLE_SYCL TestStaticCrsGraph::run_test_graph2(); -#endif TestStaticCrsGraph::run_test_graph3(1, 0); TestStaticCrsGraph::run_test_graph3(1, 1000); TestStaticCrsGraph::run_test_graph3(1, 10000); diff --git a/lib/kokkos/containers/unit_tests/TestThreads_Category.hpp b/lib/kokkos/containers/unit_tests/TestThreads_Category.hpp deleted file mode 100644 index 74a2b0da36..0000000000 --- a/lib/kokkos/containers/unit_tests/TestThreads_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_THREADS_HPP -#define KOKKOS_TEST_THREADS_HPP - -#define TEST_CATEGORY threads -#define TEST_EXECSPACE Kokkos::Threads - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp b/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp index d39e0061c7..4413cfbc80 100644 --- a/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp +++ b/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp @@ -163,7 +163,8 @@ struct TestFind { KOKKOS_INLINE_FUNCTION void operator()(typename execution_space::size_type i, value_type &errors) const { - const bool expect_to_find_i = (i < m_max_key); + const bool expect_to_find_i = + (i < typename execution_space::size_type(m_max_key)); const bool exists = m_map.exists(i); @@ -293,10 +294,11 @@ void test_deep_copy(uint32_t num_nodes) { } } -// FIXME_HIP wrong result in CI but works locally -#ifndef KOKKOS_ENABLE_HIP +// FIXME_SYCL wrong results on Nvidia GPUs but correct on Host and Intel GPUs +// FIXME_HIP // WORKAROUND MSVC -#ifndef _WIN32 +#if !(defined(KOKKOS_ENABLE_HIP) && (HIP_VERSION < 401)) && \ + !defined(_WIN32) && !defined(KOKKOS_ENABLE_SYCL) TEST(TEST_CATEGORY, UnorderedMap_insert) { for (int i = 0; i < 500; ++i) { test_insert(100000, 90000, 100, true); @@ -304,7 +306,6 @@ TEST(TEST_CATEGORY, UnorderedMap_insert) { } } #endif -#endif TEST(TEST_CATEGORY, UnorderedMap_failed_insert) { for (int i = 0; i < 1000; ++i) test_failed_insert(10000); diff --git a/lib/kokkos/core/perf_test/CMakeLists.txt b/lib/kokkos/core/perf_test/CMakeLists.txt index b7b817c910..9ff4b6006d 100644 --- a/lib/kokkos/core/perf_test/CMakeLists.txt +++ b/lib/kokkos/core/perf_test/CMakeLists.txt @@ -9,6 +9,14 @@ # that in TriBITS KokkosAlgorithms can be disabled... #INCLUDE_DIRECTORIES("${CMAKE_CURRENT_SOURCE_DIR}/../../algorithms/src") +# FIXME_OPENMPTARGET - the NVIDIA HPC compiler nvc++ in the OpenMPTarget backend does not pass the perf_tests. +IF (KOKKOS_ENABLE_OPENMPTARGET + AND (KOKKOS_CXX_COMPILER_ID STREQUAL PGI + OR KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC)) + RETURN() +ENDIF() + + SET(SOURCES PerfTestMain.cpp PerfTestGramSchmidt.cpp @@ -68,8 +76,7 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR}) # This test currently times out for MSVC -# FIXME_SYCL these tests don't compile yet (require parallel_for). -IF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL "MSVC" AND NOT Kokkos_ENABLE_SYCL) +IF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL "MSVC") KOKKOS_ADD_EXECUTABLE_AND_TEST( PerfTestExec SOURCES ${SOURCES} @@ -77,13 +84,11 @@ IF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL "MSVC" AND NOT Kokkos_ENABLE_SYCL) ) ENDIF() -# FIXME_SYCL -IF(NOT Kokkos_ENABLE_SYCL) - KOKKOS_ADD_EXECUTABLE_AND_TEST( - PerformanceTest_Atomic - SOURCES test_atomic.cpp - CATEGORIES PERFORMANCE - ) +KOKKOS_ADD_EXECUTABLE_AND_TEST( + PerformanceTest_Atomic + SOURCES test_atomic.cpp + CATEGORIES PERFORMANCE +) IF(NOT KOKKOS_ENABLE_CUDA OR KOKKOS_ENABLE_CUDA_LAMBDA) KOKKOS_ADD_EXECUTABLE_AND_TEST( @@ -98,7 +103,6 @@ KOKKOS_ADD_EXECUTABLE_AND_TEST( SOURCES test_mempool.cpp CATEGORIES PERFORMANCE ) -ENDIF() IF(NOT Kokkos_ENABLE_OPENMPTARGET) # FIXME OPENMPTARGET needs tasking diff --git a/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp b/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp index 70186283c1..dee21fd7a5 100644 --- a/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp +++ b/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp @@ -69,7 +69,7 @@ struct InvNorm2 : public Kokkos::DotSingle { KOKKOS_INLINE_FUNCTION void final(value_type& result) const { - result = std::sqrt(result); + result = Kokkos::Experimental::sqrt(result); Rjj() = result; inv() = (0 < result) ? 1.0 / result : 0; } @@ -145,7 +145,7 @@ struct ModifiedGramSchmidt { // Q(:,j) *= ( 1 / R(j,j) ); => Q(:,j) *= tmp ; Kokkos::scale(tmp, Qj); - for (size_t k = j + 1; k < count; ++k) { + for (size_type k = j + 1; k < count; ++k) { const vector_type Qk = Kokkos::subview(Q_, Kokkos::ALL(), k); const value_view Rjk = Kokkos::subview(R_, j, k); @@ -165,7 +165,7 @@ struct ModifiedGramSchmidt { //-------------------------------------------------------------------------- - static double test(const size_t length, const size_t count, + static double test(const size_type length, const size_type count, const size_t iter = 1) { multivector_type Q_("Q", length, count); multivector_type R_("R", count, count); diff --git a/lib/kokkos/core/src/CMakeLists.txt b/lib/kokkos/core/src/CMakeLists.txt index e0590a78a4..2ab0989805 100644 --- a/lib/kokkos/core/src/CMakeLists.txt +++ b/lib/kokkos/core/src/CMakeLists.txt @@ -72,8 +72,6 @@ KOKKOS_ADD_LIBRARY( ADD_BUILD_OPTIONS # core should be given all the necessary compiler/linker flags ) -SET_TARGET_PROPERTIES(kokkoscore PROPERTIES VERSION ${Kokkos_VERSION}) - KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkoscore ${KOKKOS_TOP_BUILD_DIR} ${CMAKE_CURRENT_BINARY_DIR} @@ -87,3 +85,4 @@ KOKKOS_LINK_TPL(kokkoscore PUBLIC HPX) KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBDL) KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBRT) KOKKOS_LINK_TPL(kokkoscore PUBLIC PTHREAD) +KOKKOS_LINK_TPL(kokkoscore PUBLIC ROCM) diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp index 4a30c914f0..916f109758 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp @@ -45,6 +45,10 @@ #include #ifdef KOKKOS_ENABLE_CUDA +#include +#include +#include + #include #include #include @@ -52,10 +56,6 @@ #include #include -#include -#include -#include - //#include #include #include @@ -65,6 +65,22 @@ /*--------------------------------------------------------------------------*/ /*--------------------------------------------------------------------------*/ +cudaStream_t Kokkos::Impl::cuda_get_deep_copy_stream() { + static cudaStream_t s = nullptr; + if (s == nullptr) { + cudaStreamCreate(&s); + } + return s; +} + +const std::unique_ptr &Kokkos::Impl::cuda_get_deep_copy_space( + bool initialize) { + static std::unique_ptr space = nullptr; + if (!space && initialize) + space = std::make_unique(Kokkos::Impl::cuda_get_deep_copy_stream()); + return space; +} + namespace Kokkos { namespace Impl { @@ -72,13 +88,6 @@ namespace { static std::atomic num_uvm_allocations(0); -cudaStream_t get_deep_copy_stream() { - static cudaStream_t s = nullptr; - if (s == nullptr) { - cudaStreamCreate(&s); - } - return s; -} } // namespace DeepCopy::DeepCopy(void *dst, const void *src, @@ -115,7 +124,7 @@ DeepCopy::DeepCopy(const Cuda &instance, void *dst, } void DeepCopyAsyncCuda(void *dst, const void *src, size_t n) { - cudaStream_t s = get_deep_copy_stream(); + cudaStream_t s = cuda_get_deep_copy_stream(); CUDA_SAFE_CALL(cudaMemcpyAsync(dst, src, n, cudaMemcpyDefault, s)); cudaStreamSynchronize(s); } @@ -128,14 +137,14 @@ void DeepCopyAsyncCuda(void *dst, const void *src, size_t n) { namespace Kokkos { -void CudaSpace::access_error() { +KOKKOS_DEPRECATED void CudaSpace::access_error() { const std::string msg( "Kokkos::CudaSpace::access_error attempt to execute Cuda function from " "non-Cuda space"); Kokkos::Impl::throw_runtime_exception(msg); } -void CudaSpace::access_error(const void *const) { +KOKKOS_DEPRECATED void CudaSpace::access_error(const void *const) { const std::string msg( "Kokkos::CudaSpace::access_error attempt to execute Cuda function from " "non-Cuda space"); @@ -459,79 +468,6 @@ SharedAllocationRecord::attach_texture_object( return tex_obj; } -//============================================================================== -// {{{1 - -std::string SharedAllocationRecord::get_label() const { - SharedAllocationHeader header; - - Kokkos::Impl::DeepCopy( - &header, RecordBase::head(), sizeof(SharedAllocationHeader)); - - return std::string(header.m_label); -} - -std::string SharedAllocationRecord::get_label() - const { - return std::string(RecordBase::head()->m_label); -} - -std::string -SharedAllocationRecord::get_label() const { - return std::string(RecordBase::head()->m_label); -} - -// end SharedAllocationRecord::get_label() }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -SharedAllocationRecord - *SharedAllocationRecord::allocate( - const Kokkos::CudaSpace &arg_space, const std::string &arg_label, - const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -SharedAllocationRecord - *SharedAllocationRecord::allocate( - const Kokkos::CudaUVMSpace &arg_space, const std::string &arg_label, - const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -SharedAllocationRecord - *SharedAllocationRecord::allocate( - const Kokkos::CudaHostPinnedSpace &arg_space, - const std::string &arg_label, const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -// end SharedAllocationRecord allocate() }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord *arg_rec) { - delete static_cast(arg_rec); -} - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord *arg_rec) { - delete static_cast(arg_rec); -} - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord *arg_rec) { - delete static_cast(arg_rec); -} - -// end SharedAllocationRecord deallocate }}}1 -//============================================================================== - //============================================================================== // {{{1 @@ -580,7 +516,7 @@ SharedAllocationRecord::SharedAllocationRecord( const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, #endif @@ -592,13 +528,7 @@ SharedAllocationRecord::SharedAllocationRecord( SharedAllocationHeader header; - // Fill in the Header information - header.m_record = static_cast *>(this); - - strncpy(header.m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - header.m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(header, arg_label); // Copy to device memory Kokkos::Impl::DeepCopy(RecordBase::m_alloc_ptr, &header, @@ -611,7 +541,7 @@ SharedAllocationRecord::SharedAllocationRecord( const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, #endif @@ -620,16 +550,8 @@ SharedAllocationRecord::SharedAllocationRecord( sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc), m_tex_obj(0), m_space(arg_space) { - // Fill in the Header information, directly accessible via UVM - - RecordBase::m_alloc_ptr->m_record = this; - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, + arg_label); } SharedAllocationRecord:: @@ -639,7 +561,7 @@ SharedAllocationRecord:: const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, @@ -648,319 +570,13 @@ SharedAllocationRecord:: arg_alloc_size), sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc), m_space(arg_space) { - // Fill in the Header information, directly accessible on the host - - RecordBase::m_alloc_ptr->m_record = this; - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, + arg_label); } // end SharedAllocationRecord constructors }}}1 //============================================================================== -//============================================================================== -// {{{1 - -void *SharedAllocationRecord::allocate_tracked( - const Kokkos::CudaSpace &arg_space, const std::string &arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord *const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked( - void *const arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord *const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void *SharedAllocationRecord::reallocate_tracked( - void *const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord *const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord *const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -void *SharedAllocationRecord::allocate_tracked( - const Kokkos::CudaUVMSpace &arg_space, const std::string &arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord *const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked( - void *const arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord *const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void *SharedAllocationRecord::reallocate_tracked( - void *const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord *const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord *const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -void * -SharedAllocationRecord::allocate_tracked( - const Kokkos::CudaHostPinnedSpace &arg_space, - const std::string &arg_alloc_label, const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord *const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked(void *const - arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord *const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void * -SharedAllocationRecord::reallocate_tracked( - void *const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord *const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord *const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -// end SharedAllocationRecored::(re|de|)allocate_tracked }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -SharedAllocationRecord * -SharedAllocationRecord::get_record(void *alloc_ptr) { - using RecordCuda = SharedAllocationRecord; - - using Header = SharedAllocationHeader; - - // Copy the header from the allocation - Header head; - - Header const *const head_cuda = - alloc_ptr ? Header::get_header(alloc_ptr) : nullptr; - - if (alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, head_cuda, sizeof(SharedAllocationHeader)); - } - - RecordCuda *const record = - alloc_ptr ? static_cast(head.m_record) : nullptr; - - if (!alloc_ptr || record->m_alloc_ptr != head_cuda) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::SharedAllocationRecord< Kokkos::CudaSpace , " - "void >::get_record ERROR")); - } - - return record; -} - -SharedAllocationRecord *SharedAllocationRecord< - Kokkos::CudaUVMSpace, void>::get_record(void *alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordCuda = SharedAllocationRecord; - - Header *const h = - alloc_ptr ? reinterpret_cast
(alloc_ptr) - 1 : nullptr; - - if (!alloc_ptr || h->m_record->m_alloc_ptr != h) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::SharedAllocationRecord< " - "Kokkos::CudaUVMSpace , void >::get_record ERROR")); - } - - return static_cast(h->m_record); -} - -SharedAllocationRecord - *SharedAllocationRecord::get_record( - void *alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordCuda = SharedAllocationRecord; - - Header *const h = - alloc_ptr ? reinterpret_cast
(alloc_ptr) - 1 : nullptr; - - if (!alloc_ptr || h->m_record->m_alloc_ptr != h) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::SharedAllocationRecord< " - "Kokkos::CudaHostPinnedSpace , void >::get_record ERROR")); - } - - return static_cast(h->m_record); -} - -// end SharedAllocationRecord::get_record() }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -// Iterate records to print orphaned memory ... -void SharedAllocationRecord::print_records( - std::ostream &s, const Kokkos::CudaSpace &, bool detail) { - (void)s; - (void)detail; -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord *r = &s_root_record; - - char buffer[256]; - - SharedAllocationHeader head; - - if (detail) { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - } else { - head.m_label[0] = 0; - } - - // Formatting dependent on sizeof(uintptr_t) - const char *format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = - "Cuda addr( 0x%.12lx ) list( 0x%.12lx 0x%.12lx ) extent[ 0x%.12lx " - "+ %.8ld ] count(%d) dealloc(0x%.12lx) %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = - "Cuda addr( 0x%.12llx ) list( 0x%.12llx 0x%.12llx ) extent[ " - "0x%.12llx + %.8ld ] count(%d) dealloc(0x%.12llx) %s\n"; - } - - snprintf(buffer, 256, format_string, reinterpret_cast(r), - reinterpret_cast(r->m_prev), - reinterpret_cast(r->m_next), - reinterpret_cast(r->m_alloc_ptr), r->m_alloc_size, - r->m_count, reinterpret_cast(r->m_dealloc), - head.m_label); - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } else { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - - // Formatting dependent on sizeof(uintptr_t) - const char *format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = "Cuda [ 0x%.12lx + %ld ] %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = "Cuda [ 0x%.12llx + %ld ] %s\n"; - } - - snprintf(buffer, 256, format_string, - reinterpret_cast(r->data()), r->size(), - head.m_label); - } else { - snprintf(buffer, 256, "Cuda [ 0 + 0 ]\n"); - } - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } -#else - Kokkos::Impl::throw_runtime_exception( - "SharedAllocationHeader::print_records only works with " - "KOKKOS_ENABLE_DEBUG enabled"); -#endif -} - -void SharedAllocationRecord::print_records( - std::ostream &s, const Kokkos::CudaUVMSpace &, bool detail) { - (void)s; - (void)detail; -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord::print_host_accessible_records( - s, "CudaUVM", &s_root_record, detail); -#else - Kokkos::Impl::throw_runtime_exception( - "SharedAllocationHeader::print_records only works with " - "KOKKOS_ENABLE_DEBUG enabled"); -#endif -} - -void SharedAllocationRecord::print_records( - std::ostream &s, const Kokkos::CudaHostPinnedSpace &, bool detail) { - (void)s; - (void)detail; -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord::print_host_accessible_records( - s, "CudaHostPinned", &s_root_record, detail); -#else - Kokkos::Impl::throw_runtime_exception( - "SharedAllocationHeader::print_records only works with " - "KOKKOS_ENABLE_DEBUG enabled"); -#endif -} - -// end SharedAllocationRecord::print_records() }}}1 -//============================================================================== - void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, bool to_device) { if ((ptr == nullptr) || (bytes == 0)) return; @@ -984,6 +600,29 @@ void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, } // namespace Impl } // namespace Kokkos + +//============================================================================== +// {{{1 + +#include + +namespace Kokkos { +namespace Impl { + +// To avoid additional compilation cost for something that's (mostly?) not +// performance sensitive, we explicity instantiate these CRTP base classes here, +// where we have access to the associated *_timpl.hpp header files. +template class SharedAllocationRecordCommon; +template class HostInaccessibleSharedAllocationRecordCommon; +template class SharedAllocationRecordCommon; +template class SharedAllocationRecordCommon; + +} // end namespace Impl +} // end namespace Kokkos + +// end Explicit instantiations of CRTP Base classes }}}1 +//============================================================================== + #else void KOKKOS_CORE_SRC_CUDA_CUDASPACE_PREVENT_LINK_ERROR() {} #endif // KOKKOS_ENABLE_CUDA diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp index 0d6d3bdb3a..0f4259072d 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp @@ -140,7 +140,7 @@ inline int cuda_deduce_block_size(bool early_termination, } } - if (early_termination && blocks_per_sm != 0) break; + if (early_termination && opt_block_size != 0) break; } return opt_block_size; @@ -222,7 +222,8 @@ inline size_t get_shmem_per_sm_prefer_l1(cudaDeviceProp const& properties) { case 52: case 61: return 96; case 70: - case 80: return 8; + case 80: + case 86: return 8; case 75: return 32; default: Kokkos::Impl::throw_runtime_exception( diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp index a9a62380e5..ec9c434fe6 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp @@ -175,30 +175,42 @@ class half_t { return cast_from_half(*this); } + /** + * Conversion constructors. + * + * Support implicit conversions from impl_type, float, double -> half_t + * Mixed precision expressions require upcasting which is done in the + * "// Binary Arithmetic" operator overloads below. + * + * Support implicit conversions from integral types -> half_t. + * Expressions involving half_t with integral types require downcasting + * the integral types to half_t. Existing operator overloads can handle this + * with the addition of the below implicit conversion constructors. + */ KOKKOS_FUNCTION half_t(impl_type rhs) : val(rhs) {} KOKKOS_FUNCTION - explicit half_t(float rhs) : val(cast_to_half(rhs).val) {} + half_t(float rhs) : val(cast_to_half(rhs).val) {} + KOKKOS_FUNCTION + half_t(double rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION explicit half_t(bool rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(double rhs) : val(cast_to_half(rhs).val) {} + half_t(short rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(short rhs) : val(cast_to_half(rhs).val) {} + half_t(int rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(int rhs) : val(cast_to_half(rhs).val) {} + half_t(long rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(long rhs) : val(cast_to_half(rhs).val) {} + half_t(long long rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(long long rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned short rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(unsigned short rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned int rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(unsigned int rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned long rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(unsigned long rhs) : val(cast_to_half(rhs).val) {} - KOKKOS_FUNCTION - explicit half_t(unsigned long long rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned long long rhs) : val(cast_to_half(rhs).val) {} // Unary operators KOKKOS_FUNCTION @@ -243,7 +255,7 @@ class half_t { #else float tmp = __half2float(val); --tmp; - val = __float2half(tmp); + val = __float2half(tmp); #endif return *this; } @@ -276,88 +288,317 @@ class half_t { return *this; } + template + KOKKOS_FUNCTION void operator=(T rhs) volatile { + val = cast_to_half(rhs).val; + } + // Compound operators KOKKOS_FUNCTION half_t& operator+=(half_t rhs) { #ifdef __CUDA_ARCH__ val += rhs.val; #else - val = __float2half(__half2float(val) + __half2float(rhs.val)); + val = __float2half(__half2float(val) + __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator+=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) + rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) + + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for += + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator+=(T& lhs, half_t rhs) { + lhs += static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator+=(float rhs) { + float result = static_cast(val) + rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator+=(double rhs) { + double result = static_cast(val) + rhs; + val = static_cast(result); + return *this; + } + KOKKOS_FUNCTION half_t& operator-=(half_t rhs) { #ifdef __CUDA_ARCH__ val -= rhs.val; #else - val = __float2half(__half2float(val) - __half2float(rhs.val)); + val = __float2half(__half2float(val) - __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator-=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) - rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) - + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for -= + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator-=(T& lhs, half_t rhs) { + lhs -= static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator-=(float rhs) { + float result = static_cast(val) - rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator-=(double rhs) { + double result = static_cast(val) - rhs; + val = static_cast(result); + return *this; + } + KOKKOS_FUNCTION half_t& operator*=(half_t rhs) { #ifdef __CUDA_ARCH__ val *= rhs.val; #else - val = __float2half(__half2float(val) * __half2float(rhs.val)); + val = __float2half(__half2float(val) * __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator*=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) * rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) * + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for *= + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator*=(T& lhs, half_t rhs) { + lhs *= static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator*=(float rhs) { + float result = static_cast(val) * rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator*=(double rhs) { + double result = static_cast(val) * rhs; + val = static_cast(result); + return *this; + } + KOKKOS_FUNCTION half_t& operator/=(half_t rhs) { #ifdef __CUDA_ARCH__ val /= rhs.val; #else - val = __float2half(__half2float(val) / __half2float(rhs.val)); + val = __float2half(__half2float(val) / __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator/=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) / rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) / + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for /= + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator/=(T& lhs, half_t rhs) { + lhs /= static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator/=(float rhs) { + float result = static_cast(val) / rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator/=(double rhs) { + double result = static_cast(val) / rhs; + val = static_cast(result); + return *this; + } + // Binary Arithmetic KOKKOS_FUNCTION half_t friend operator+(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val += rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) + __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) + __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator+(half_t lhs, T rhs) { + return T(lhs) + rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator+(T lhs, half_t rhs) { + return lhs + T(rhs); + } + KOKKOS_FUNCTION half_t friend operator-(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val -= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) - __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) - __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for - + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator-(half_t lhs, T rhs) { + return T(lhs) - rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator-(T lhs, half_t rhs) { + return lhs - T(rhs); + } + KOKKOS_FUNCTION half_t friend operator*(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val *= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) * __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) * __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for * + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator*(half_t lhs, T rhs) { + return T(lhs) * rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator*(T lhs, half_t rhs) { + return lhs * T(rhs); + } + KOKKOS_FUNCTION half_t friend operator/(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val /= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) / __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) / __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for / + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator/(half_t lhs, T rhs) { + return T(lhs) / rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator/(T lhs, half_t rhs) { + return lhs / T(rhs); + } + // Logical operators KOKKOS_FUNCTION bool operator!() const { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp index b8e8163458..016cb6cdcb 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp @@ -54,6 +54,7 @@ #include #include #include +#include #include #include @@ -248,11 +249,11 @@ void CudaInternal::print_configuration(std::ostream &s) const { const CudaInternalDevices &dev_info = CudaInternalDevices::singleton(); #if defined(KOKKOS_ENABLE_CUDA) - s << "macro KOKKOS_ENABLE_CUDA : defined" << std::endl; + s << "macro KOKKOS_ENABLE_CUDA : defined\n"; #endif #if defined(CUDA_VERSION) s << "macro CUDA_VERSION = " << CUDA_VERSION << " = version " - << CUDA_VERSION / 1000 << "." << (CUDA_VERSION % 1000) / 10 << std::endl; + << CUDA_VERSION / 1000 << "." << (CUDA_VERSION % 1000) / 10 << '\n'; #endif for (int i = 0; i < dev_info.m_cudaDevCount; ++i) { @@ -274,7 +275,6 @@ CudaInternal::~CudaInternal() { m_scratchConcurrentBitset) { std::cerr << "Kokkos::Cuda ERROR: Failed to call Kokkos::Cuda::finalize()" << std::endl; - std::cerr.flush(); } m_cudaDev = -1; @@ -358,8 +358,7 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { if (m_cudaArch == 0) { std::stringstream ss; - ss << "Kokkos::Cuda::initialize ERROR: likely mismatch of architecture" - << std::endl; + ss << "Kokkos::Cuda::initialize ERROR: likely mismatch of architecture\n"; std::string msg = ss.str(); Kokkos::abort(msg.c_str()); } @@ -373,7 +372,7 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { "compute capability " << compiled_major << "." << compiled_minor << " on device with compute capability " << cudaProp.major << "." - << cudaProp.minor << " is not supported by CUDA!" << std::endl; + << cudaProp.minor << " is not supported by CUDA!\n"; std::string msg = ss.str(); Kokkos::abort(msg.c_str()); } @@ -458,7 +457,7 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { Kokkos::Impl::SharedAllocationRecord; Record *const r = - Record::allocate(Kokkos::CudaSpace(), "InternalScratchBitset", + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchBitset", sizeof(uint32_t) * buffer_bound); Record::increment(r); @@ -492,17 +491,11 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { #ifdef KOKKOS_ENABLE_CUDA_UVM if (Kokkos::show_warnings() && !cuda_launch_blocking()) { - std::cerr << "Kokkos::Cuda::initialize WARNING: Cuda is allocating into " - "UVMSpace by default" - << std::endl; - std::cerr << " without setting " - "CUDA_LAUNCH_BLOCKING=1." - << std::endl; - std::cerr << " The code must call " - "Cuda().fence() after each kernel" - << std::endl; - std::cerr << " or will likely crash when " - "accessing data on the host." + std::cerr << R"warning( +Kokkos::Cuda::initialize WARNING: Cuda is allocating into UVMSpace by default + without setting CUDA_LAUNCH_BLOCKING=1. + The code must call Cuda().fence() after each kernel + or will likely crash when accessing data on the host.)warning" << std::endl; } @@ -520,19 +513,13 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { if (Kokkos::show_warnings() && (!visible_devices_one && !force_device_alloc)) { - std::cerr << "Kokkos::Cuda::initialize WARNING: Cuda is allocating into " - "UVMSpace by default" + std::cerr << R"warning( +Kokkos::Cuda::initialize WARNING: Cuda is allocating into UVMSpace by default + without setting CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 or + setting CUDA_VISIBLE_DEVICES. + This could on multi GPU systems lead to severe performance" + penalties.)warning" << std::endl; - std::cerr << " without setting " - "CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 or " - << std::endl; - std::cerr - << " setting CUDA_VISIBLE_DEVICES." - << std::endl; - std::cerr << " This could on multi GPU " - "systems lead to severe performance" - << std::endl; - std::cerr << " penalties." << std::endl; } #endif @@ -575,7 +562,7 @@ Cuda::size_type *CudaInternal::scratch_flags(const Cuda::size_type size) const { if (m_scratchFlags) Record::decrement(Record::get_record(m_scratchFlags)); Record *const r = - Record::allocate(Kokkos::CudaSpace(), "InternalScratchFlags", + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchFlags", (sizeof(ScratchGrain) * m_scratchFlagsCount)); Record::increment(r); @@ -600,7 +587,7 @@ Cuda::size_type *CudaInternal::scratch_space(const Cuda::size_type size) const { if (m_scratchSpace) Record::decrement(Record::get_record(m_scratchSpace)); Record *const r = - Record::allocate(Kokkos::CudaSpace(), "InternalScratchSpace", + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchSpace", (sizeof(ScratchGrain) * m_scratchSpaceCount)); Record::increment(r); @@ -624,7 +611,7 @@ Cuda::size_type *CudaInternal::scratch_unified( Record::decrement(Record::get_record(m_scratchUnified)); Record *const r = Record::allocate( - Kokkos::CudaHostPinnedSpace(), "InternalScratchUnified", + Kokkos::CudaHostPinnedSpace(), "Kokkos::InternalScratchUnified", (sizeof(ScratchGrain) * m_scratchUnifiedCount)); Record::increment(r); @@ -646,8 +633,9 @@ Cuda::size_type *CudaInternal::scratch_functor( if (m_scratchFunctor) Record::decrement(Record::get_record(m_scratchFunctor)); - Record *const r = Record::allocate( - Kokkos::CudaSpace(), "InternalScratchFunctor", m_scratchFunctorSize); + Record *const r = + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchFunctor", + m_scratchFunctorSize); Record::increment(r); @@ -662,7 +650,7 @@ void *CudaInternal::resize_team_scratch_space(std::int64_t bytes, if (m_team_scratch_current_size == 0) { m_team_scratch_current_size = bytes; m_team_scratch_ptr = Kokkos::kokkos_malloc( - "CudaSpace::ScratchMemory", m_team_scratch_current_size); + "Kokkos::CudaSpace::TeamScratchMemory", m_team_scratch_current_size); } if ((bytes > m_team_scratch_current_size) || ((bytes < m_team_scratch_current_size) && (force_shrink))) { @@ -676,6 +664,9 @@ void *CudaInternal::resize_team_scratch_space(std::int64_t bytes, //---------------------------------------------------------------------------- void CudaInternal::finalize() { + // skip if finalize() has already been called + if (was_finalized) return; + was_finalized = true; if (nullptr != m_scratchSpace || nullptr != m_scratchFlags) { // Only finalize this if we're the singleton @@ -719,6 +710,11 @@ void CudaInternal::finalize() { if (this == &singleton()) { cudaFreeHost(constantMemHostStaging); cudaEventDestroy(constantMemReusable); + auto &deep_copy_space = + Kokkos::Impl::cuda_get_deep_copy_space(/*initialize*/ false); + if (deep_copy_space) + deep_copy_space->impl_internal_space_instance()->finalize(); + cudaStreamDestroy(cuda_get_deep_copy_stream()); } } @@ -821,62 +817,23 @@ Cuda::size_type Cuda::device_arch() { void Cuda::impl_finalize() { Impl::CudaInternal::singleton().finalize(); } Cuda::Cuda() - : m_space_instance(&Impl::CudaInternal::singleton()), m_counter(nullptr) { + : m_space_instance(&Impl::CudaInternal::singleton(), + [](Impl::CudaInternal *) {}) { Impl::CudaInternal::singleton().verify_is_initialized( "Cuda instance constructor"); } Cuda::Cuda(cudaStream_t stream) - : m_space_instance(new Impl::CudaInternal), m_counter(new int(1)) { + : m_space_instance(new Impl::CudaInternal, [](Impl::CudaInternal *ptr) { + ptr->finalize(); + delete ptr; + }) { Impl::CudaInternal::singleton().verify_is_initialized( "Cuda instance constructor"); m_space_instance->initialize(Impl::CudaInternal::singleton().m_cudaDev, stream); } -KOKKOS_FUNCTION Cuda::Cuda(Cuda &&other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; -} - -KOKKOS_FUNCTION Cuda::Cuda(const Cuda &other) - : m_space_instance(other.m_space_instance), m_counter(other.m_counter) { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif -} - -KOKKOS_FUNCTION Cuda &Cuda::operator=(Cuda &&other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; - return *this; -} - -KOKKOS_FUNCTION Cuda &Cuda::operator=(const Cuda &other) { - m_space_instance = other.m_space_instance; - m_counter = other.m_counter; -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif - return *this; -} - -KOKKOS_FUNCTION Cuda::~Cuda() noexcept { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA - if (m_counter == nullptr) return; - int const count = Kokkos::atomic_fetch_sub(m_counter, 1); - if (count == 1) { - delete m_counter; - m_space_instance->finalize(); - delete m_space_instance; - } -#endif -} - void Cuda::print_configuration(std::ostream &s, const bool) { Impl::CudaInternal::singleton().print_configuration(s); } @@ -924,54 +881,53 @@ void CudaSpaceInitializer::fence() { Kokkos::Cuda::impl_static_fence(); } void CudaSpaceInitializer::print_configuration(std::ostream &msg, const bool detail) { - msg << "Device Execution Space:" << std::endl; - msg << " KOKKOS_ENABLE_CUDA: "; - msg << "yes" << std::endl; + msg << "Device Execution Space:\n"; + msg << " KOKKOS_ENABLE_CUDA: yes\n"; - msg << "Cuda Atomics:" << std::endl; + msg << "Cuda Atomics:\n"; msg << " KOKKOS_ENABLE_CUDA_ATOMICS: "; #ifdef KOKKOS_ENABLE_CUDA_ATOMICS - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif - msg << "Cuda Options:" << std::endl; + msg << "Cuda Options:\n"; msg << " KOKKOS_ENABLE_CUDA_LAMBDA: "; #ifdef KOKKOS_ENABLE_CUDA_LAMBDA - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUDA_LDG_INTRINSIC: "; #ifdef KOKKOS_ENABLE_CUDA_LDG_INTRINSIC - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE: "; #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUDA_UVM: "; #ifdef KOKKOS_ENABLE_CUDA_UVM - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUSPARSE: "; #ifdef KOKKOS_ENABLE_CUSPARSE - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA: "; #ifdef KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << "\nCuda Runtime Configuration:" << std::endl; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp index 13773d70c5..aaec2c2926 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp @@ -17,30 +17,24 @@ namespace Kokkos { namespace Impl { struct CudaTraits { - enum : CudaSpace::size_type { WarpSize = 32 /* 0x0020 */ }; - enum : CudaSpace::size_type { - WarpIndexMask = 0x001f /* Mask for warpindex */ - }; - enum : CudaSpace::size_type { - WarpIndexShift = 5 /* WarpSize == 1 << WarpShift */ - }; + static constexpr CudaSpace::size_type WarpSize = 32 /* 0x0020 */; + static constexpr CudaSpace::size_type WarpIndexMask = + 0x001f; /* Mask for warpindex */ + static constexpr CudaSpace::size_type WarpIndexShift = + 5; /* WarpSize == 1 << WarpShift */ - enum : CudaSpace::size_type { - ConstantMemoryUsage = 0x008000 /* 32k bytes */ - }; - enum : CudaSpace::size_type { - ConstantMemoryCache = 0x002000 /* 8k bytes */ - }; - enum : CudaSpace::size_type { - KernelArgumentLimit = 0x001000 /* 4k bytes */ - }; - enum : CudaSpace::size_type { - MaxHierarchicalParallelism = 1024 /* team_size * vector_length */ - }; + static constexpr CudaSpace::size_type ConstantMemoryUsage = + 0x008000; /* 32k bytes */ + static constexpr CudaSpace::size_type ConstantMemoryCache = + 0x002000; /* 8k bytes */ + static constexpr CudaSpace::size_type KernelArgumentLimit = + 0x001000; /* 4k bytes */ + static constexpr CudaSpace::size_type MaxHierarchicalParallelism = + 1024; /* team_size * vector_length */ using ConstantGlobalBufferType = unsigned long[ConstantMemoryUsage / sizeof(unsigned long)]; - enum { ConstantMemoryUseThreshold = 0x000200 /* 512 bytes */ }; + static constexpr int ConstantMemoryUseThreshold = 0x000200 /* 512 bytes */; KOKKOS_INLINE_FUNCTION static CudaSpace::size_type warp_count( CudaSpace::size_type i) { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp index 39404e0bf3..d892a893b3 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp @@ -158,6 +158,9 @@ inline void check_shmem_request(CudaInternal const* cuda_instance, int shmem) { } } +// This function needs to be template on DriverType and LaunchBounds +// so that the static bool is unique for each type combo +// KernelFuncPtr does not necessarily contain that type information. template inline void configure_shmem_preference(KernelFuncPtr const& func, bool prefer_shmem) { @@ -355,8 +358,7 @@ struct CudaParallelLaunchKernelInvoker< if (!Impl::is_empty_launch(grid, block)) { Impl::check_shmem_request(cuda_instance, shmem); - Impl::configure_shmem_preference( + Impl::configure_shmem_preference( base_t::get_kernel_func(), prefer_shmem); void const* args[] = {&driver}; @@ -449,8 +451,7 @@ struct CudaParallelLaunchKernelInvoker< if (!Impl::is_empty_launch(grid, block)) { Impl::check_shmem_request(cuda_instance, shmem); - Impl::configure_shmem_preference( + Impl::configure_shmem_preference( base_t::get_kernel_func(), prefer_shmem); auto* driver_ptr = Impl::allocate_driver_storage_for_kernel(driver); @@ -627,9 +628,8 @@ struct CudaParallelLaunchImpl< get_cuda_func_attributes(), block, shmem, prefer_shmem); Impl::configure_shmem_preference< - DriverType, Kokkos::LaunchBounds, - decltype(base_t::get_kernel_func())>(base_t::get_kernel_func(), - prefer_shmem); + DriverType, Kokkos::LaunchBounds>( + base_t::get_kernel_func(), prefer_shmem); KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE(); diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp new file mode 100644 index 0000000000..12b7f70a97 --- /dev/null +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp @@ -0,0 +1,37 @@ +#ifndef KOKKOS_CUDA_MDRANGEPOLICY_HPP_ +#define KOKKOS_CUDA_MDRANGEPOLICY_HPP_ + +#include + +namespace Kokkos { + +template <> +struct default_outer_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +template <> +struct default_inner_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +namespace Impl { + +// Settings for MDRangePolicy +template <> +inline TileSizeProperties get_tile_size_properties( + const Kokkos::Cuda& space) { + TileSizeProperties properties; + properties.max_threads = + space.impl_internal_space_instance()->m_maxThreadsPerSM; + properties.default_largest_tile_size = 16; + properties.default_tile_size = 2; + properties.max_total_tile_size = 512; + return properties; +} + +} // Namespace Impl +} // Namespace Kokkos +#endif diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp index 131d180980..2834e6f3de 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp @@ -60,6 +60,7 @@ #include #include #include +#include #include #include @@ -67,6 +68,7 @@ #include #include +#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -474,7 +476,7 @@ class ParallelFor, Kokkos::Cuda> { Policy const& get_policy() const { return m_policy; } - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { const Member work_stride = blockDim.y * gridDim.x; const Member work_end = m_policy.end(); @@ -537,9 +539,23 @@ class ParallelFor, Kokkos::Cuda> { const Policy m_rp; public: + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + cudaFuncAttributes attr = + CudaParallelLaunch::get_cuda_func_attributes(); + auto const& prop = pol.space().cuda_device_prop(); + // Limits due to registers/SM, MDRange doesn't have + // shared memory constraints + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast(Kokkos::Impl::CudaTraits::MaxHierarchicalParallelism)); + } Policy const& get_policy() const { return m_rp; } - - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { Kokkos::Impl::DeviceIterateTile(m_rp, m_functor) .exec_range(); @@ -689,7 +705,7 @@ class ParallelFor, public: Policy const& get_policy() const { return m_policy; } - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { // Iterate this block through the league int64_t threadid = 0; if (m_scratch_size[1] > 0) { @@ -1248,8 +1264,21 @@ class ParallelReduce, ReducerType, using DummySHMEMReductionType = int; public: + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + cudaFuncAttributes attr = + CudaParallelLaunch::get_cuda_func_attributes(); + auto const& prop = pol.space().cuda_device_prop(); + // Limits due do registers/SM + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast(Kokkos::Impl::CudaTraits::MaxHierarchicalParallelism)); + } Policy const& get_policy() const { return m_policy; } - inline __device__ void exec_range(reference_type update) const { Kokkos::Impl::Reduce::DeviceIterateTile, ReducerType, .exec_range(); } - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { /* run(Kokkos::Impl::if_c::select(1,1.0) ); } @@ -2074,7 +2103,7 @@ class ParallelScan, Kokkos::Cuda> { //---------------------------------------- - __device__ inline void initial(void) const { + __device__ inline void initial() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2110,7 +2139,7 @@ class ParallelScan, Kokkos::Cuda> { //---------------------------------------- - __device__ inline void final(void) const { + __device__ inline void final() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2195,7 +2224,7 @@ class ParallelScan, Kokkos::Cuda> { //---------------------------------------- - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { #ifdef KOKKOS_IMPL_DEBUG_CUDA_SERIAL_EXECUTION if (m_run_serial) { typename ValueTraits::value_type value; @@ -2364,7 +2393,7 @@ class ParallelScanWithTotal, //---------------------------------------- - __device__ inline void initial(void) const { + __device__ inline void initial() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2400,7 +2429,7 @@ class ParallelScanWithTotal, //---------------------------------------- - __device__ inline void final(void) const { + __device__ inline void final() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2487,7 +2516,7 @@ class ParallelScanWithTotal, //---------------------------------------- - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { #ifdef KOKKOS_IMPL_DEBUG_CUDA_SERIAL_EXECUTION if (m_run_serial) { typename ValueTraits::value_type value; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp index 4b472f5d4f..e780639015 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp @@ -661,13 +661,14 @@ KOKKOS_INLINE_FUNCTION thread, count); } -template -KOKKOS_INLINE_FUNCTION - Impl::ThreadVectorRangeBoundariesStruct - ThreadVectorRange(const Impl::CudaTeamMember& thread, iType arg_begin, - iType arg_end) { +template +KOKKOS_INLINE_FUNCTION Impl::ThreadVectorRangeBoundariesStruct< + typename std::common_type::type, Impl::CudaTeamMember> +ThreadVectorRange(const Impl::CudaTeamMember& thread, iType1 arg_begin, + iType2 arg_end) { + using iType = typename std::common_type::type; return Impl::ThreadVectorRangeBoundariesStruct( - thread, arg_begin, arg_end); + thread, iType(arg_begin), iType(arg_end)); } KOKKOS_INLINE_FUNCTION @@ -983,7 +984,7 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( //---------------------------------------------------------------------------- -/** \brief Intra-thread vector parallel exclusive prefix sum. +/** \brief Intra-thread vector parallel scan with reducer. * * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) * @@ -991,25 +992,25 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( * thread and a scan operation is performed. * The last call to closure has final == true. */ -template -KOKKOS_INLINE_FUNCTION void parallel_scan( - const Impl::ThreadVectorRangeBoundariesStruct& - loop_boundaries, - const Closure& closure) { +template +KOKKOS_INLINE_FUNCTION + typename std::enable_if::value>::type + parallel_scan(const Impl::ThreadVectorRangeBoundariesStruct< + iType, Impl::CudaTeamMember>& loop_boundaries, + const Closure& closure, const ReducerType& reducer) { (void)loop_boundaries; (void)closure; + (void)reducer; #ifdef __CUDA_ARCH__ - // Extract value_type from closure - - using value_type = typename Kokkos::Impl::FunctorAnalysis< - Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + using value_type = typename ReducerType::value_type; + value_type accum; + reducer.init(accum); + const value_type identity = accum; // Loop through boundaries by vector-length chunks // must scan at each iteration - value_type accum = 0; - // All thread "lanes" must loop the same number of times. // Determine an loop end for all thread "lanes." // Requires: @@ -1026,44 +1027,68 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( const int end = loop_boundaries.end + (rem ? blockDim.x - rem : 0); for (int i = threadIdx.x; i < end; i += blockDim.x) { - value_type val = 0; + value_type val = identity; - // First acquire per-lane contributions: - if (i < loop_boundaries.end) closure(i, val, false); + // First acquire per-lane contributions. + // This sets i's val to i-1's contribution + // to make the latter in_place_shfl_up an + // exclusive scan -- the final accumulation + // of i's val will be included in the second + // closure call later. + if (i < loop_boundaries.end && threadIdx.x > 0) closure(i - 1, val, false); - value_type sval = val; - - // Bottom up inclusive scan in triangular pattern + // Bottom up exclusive scan in triangular pattern // where each CUDA thread is the root of a reduction tree // from the zeroth "lane" to itself. // [t] += [t-1] if t >= 1 // [t] += [t-2] if t >= 2 // [t] += [t-4] if t >= 4 // ... - + // This differs from the non-reducer overload, where an inclusive scan was + // implemented, because in general the binary operator cannot be inverted + // and we would not be able to remove the inclusive contribution by + // inversion. for (int j = 1; j < (int)blockDim.x; j <<= 1) { - value_type tmp = 0; - Impl::in_place_shfl_up(tmp, sval, j, blockDim.x, active_mask); + value_type tmp = identity; + Impl::in_place_shfl_up(tmp, val, j, blockDim.x, active_mask); if (j <= (int)threadIdx.x) { - sval += tmp; + reducer.join(val, tmp); } } - // Include accumulation and remove value for exclusive scan: - val = accum + sval - val; + // Include accumulation + reducer.join(val, accum); - // Provide exclusive scan value: + // Update i's contribution into the val + // and add it to accum for next round if (i < loop_boundaries.end) closure(i, val, true); - - // Accumulate the last value in the inclusive scan: - Impl::in_place_shfl(sval, sval, mask, blockDim.x, active_mask); - - accum += sval; + Impl::in_place_shfl(accum, val, mask, blockDim.x, active_mask); } #endif } +//---------------------------------------------------------------------------- + +/** \brief Intra-thread vector parallel exclusive prefix sum. + * + * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) + * + * The range [0..N) is mapped to all vector lanes in the + * thread and a scan operation is performed. + * The last call to closure has final == true. + */ +template +KOKKOS_INLINE_FUNCTION void parallel_scan( + const Impl::ThreadVectorRangeBoundariesStruct& + loop_boundaries, + const Closure& closure) { + using value_type = typename Kokkos::Impl::FunctorAnalysis< + Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + value_type dummy; + parallel_scan(loop_boundaries, closure, Kokkos::Sum(dummy)); +} + } // namespace Kokkos namespace Kokkos { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp index f24abb377d..c55956ede9 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp @@ -139,7 +139,7 @@ struct CudaLDGFetch { template KOKKOS_INLINE_FUNCTION ValueType operator[](const iType& i) const { -#ifdef __CUDA_ARCH__ +#if defined(__CUDA_ARCH__) && (350 <= _CUDA_ARCH__) AliasType v = __ldg(reinterpret_cast(&m_ptr[i])); return *(reinterpret_cast(&v)); #else diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp index 05876a9f02..fc52e41514 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp @@ -46,6 +46,7 @@ #define KOKKOS_CUDA_WORKGRAPHPOLICY_HPP #include +#include namespace Kokkos { namespace Impl { diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp index 89135b6c45..9278d1bdc9 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp @@ -75,17 +75,6 @@ void hipOccupancy(int *numBlocks, int blockSize, int sharedmem) { hipOccupancy( numBlocks, blockSize, sharedmem); } -template -struct HIPGetMaxBlockSize; - -template -int hip_get_max_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - return HIPGetMaxBlockSize::get_block_size( - f, vector_length, shmem_extra_block, shmem_extra_thread); -} template int hip_internal_get_block_size(const F &condition_check, @@ -131,10 +120,6 @@ int hip_internal_get_block_size(const F &condition_check, int opt_block_size = (blocks_per_sm >= min_blocks_per_sm) ? block_size : min_blocks_per_sm; int opt_threads_per_sm = threads_per_sm; - // printf("BlockSizeMax: %i Shmem: %i %i %i %i Regs: %i %i Blocks: %i %i - // Achieved: %i %i Opt: %i %i\n",block_size, - // shmem_per_sm,max_shmem_per_block,functor_shmem,total_shmem, - // regs_per_sm,regs_per_wavefront,max_blocks_shmem,max_blocks_regs,blocks_per_sm,threads_per_sm,opt_block_size,opt_threads_per_sm); block_size -= HIPTraits::WarpSize; while (condition_check(blocks_per_sm) && (block_size >= HIPTraits::WarpSize)) { @@ -160,10 +145,6 @@ int hip_internal_get_block_size(const F &condition_check, opt_threads_per_sm = threads_per_sm; } } - // printf("BlockSizeMax: %i Shmem: %i %i %i %i Regs: %i %i Blocks: %i %i - // Achieved: %i %i Opt: %i %i\n",block_size, - // shmem_per_sm,max_shmem_per_block,functor_shmem,total_shmem, - // regs_per_sm,regs_per_wavefront,max_blocks_shmem,max_blocks_regs,blocks_per_sm,threads_per_sm,opt_block_size,opt_threads_per_sm); block_size -= HIPTraits::WarpSize; } return opt_block_size; @@ -178,62 +159,6 @@ int hip_get_max_block_size(const HIPInternal *hip_instance, [](int x) { return x == 0; }, hip_instance, attr, f, vector_length, shmem_block, shmem_thread); } -template -struct HIPGetMaxBlockSize { - static int get_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - int numBlocks = 0; - int blockSize = LaunchBounds::maxTperB == 0 ? 1024 : LaunchBounds::maxTperB; - int sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - - if (numBlocks > 0) return blockSize; - while (blockSize > HIPTraits::WarpSize && numBlocks == 0) { - blockSize /= 2; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - } - int blockSizeUpperBound = blockSize * 2; - while (blockSize < blockSizeUpperBound && numBlocks > 0) { - blockSize += HIPTraits::WarpSize; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - } - return blockSize - HIPTraits::WarpSize; - } -}; - -template -struct HIPGetOptBlockSize; - -template -int hip_get_opt_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - return HIPGetOptBlockSize< - DriverType, LaunchBounds, - (HIPTraits::ConstantMemoryUseThreshold < - sizeof(DriverType))>::get_block_size(f, vector_length, shmem_extra_block, - shmem_extra_thread); -} template int hip_get_opt_block_size(HIPInternal const *hip_instance, @@ -245,157 +170,6 @@ int hip_get_opt_block_size(HIPInternal const *hip_instance, shmem_block, shmem_thread); } -// FIXME_HIP the code is identical to the false struct except for -// hip_parallel_launch_constant_memory -template -struct HIPGetOptBlockSize, true> { - static int get_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - - while (blockSize < HIPTraits::MaxThreadsPerBlock) { - blockSize *= 2; - - // calculate the occupancy with that optBlockSize and check whether its - // larger than the largest one found so far - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - hipOccupancy(&numBlocks, blockSize, sharedmem); - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - return bestBlockSize; - } -}; - -template -struct HIPGetOptBlockSize, false> { - static int get_block_size(const typename DriverType::functor_type &f, - const size_t vector_length, - const size_t shmem_extra_block, - const size_t shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - - while (blockSize < HIPTraits::MaxThreadsPerBlock) { - blockSize *= 2; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - return bestBlockSize; - } -}; - -// FIXME_HIP the code is identical to the false struct except for -// hip_parallel_launch_constant_memory -template -struct HIPGetOptBlockSize< - DriverType, Kokkos::LaunchBounds, - true> { - static int get_block_size(const typename DriverType::functor_type &f, - const size_t vector_length, - const size_t shmem_extra_block, - const size_t shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - int max_threads_per_block = - std::min(MaxThreadsPerBlock, - hip_internal_maximum_warp_count() * HIPTraits::WarpSize); - - while (blockSize < max_threads_per_block) { - blockSize *= 2; - - // calculate the occupancy with that optBlockSize and check whether its - // larger than the largest one found so far - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - hipOccupancy( - &numBlocks, blockSize, sharedmem); - if (numBlocks >= static_cast(MinBlocksPerSM) && - blockSize <= static_cast(MaxThreadsPerBlock)) { - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - } - if (maxOccupancy > 0) return bestBlockSize; - return -1; - } -}; - -template -struct HIPGetOptBlockSize< - DriverType, Kokkos::LaunchBounds, - false> { - static int get_block_size(const typename DriverType::functor_type &f, - const size_t vector_length, - const size_t shmem_extra_block, - const size_t shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - int max_threads_per_block = - std::min(MaxThreadsPerBlock, - hip_internal_maximum_warp_count() * HIPTraits::WarpSize); - - while (blockSize < max_threads_per_block) { - blockSize *= 2; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy( - &numBlocks, blockSize, sharedmem); - if (numBlocks >= int(MinBlocksPerSM) && - blockSize <= int(MaxThreadsPerBlock)) { - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - } - if (maxOccupancy > 0) return bestBlockSize; - return -1; - } -}; - } // namespace Impl } // namespace Experimental } // namespace Kokkos diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp index 45512038ac..18ef10e22c 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp @@ -164,6 +164,8 @@ HIPInternal &HIPInternal::singleton() { void HIPInternal::fence() const { HIP_SAFE_CALL(hipStreamSynchronize(m_stream)); + // can reset our cycle id now as well + m_cycleId = 0; } void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { @@ -256,7 +258,7 @@ void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { void>; Record *const r = Record::allocate(Kokkos::Experimental::HIPSpace(), - "InternalScratchBitset", + "Kokkos::InternalScratchBitset", sizeof(uint32_t) * buffer_bound); Record::increment(r); @@ -303,8 +305,10 @@ Kokkos::Experimental::HIP::size_type *HIPInternal::scratch_space( Kokkos::Impl::SharedAllocationRecord; - static Record *const r = Record::allocate( - Kokkos::Experimental::HIPSpace(), "InternalScratchSpace", + if (m_scratchSpace) Record::decrement(Record::get_record(m_scratchSpace)); + + Record *const r = Record::allocate( + Kokkos::Experimental::HIPSpace(), "Kokkos::InternalScratchSpace", (sizeScratchGrain * m_scratchSpaceCount)); Record::increment(r); @@ -325,8 +329,10 @@ Kokkos::Experimental::HIP::size_type *HIPInternal::scratch_flags( Kokkos::Impl::SharedAllocationRecord; + if (m_scratchFlags) Record::decrement(Record::get_record(m_scratchFlags)); + Record *const r = Record::allocate( - Kokkos::Experimental::HIPSpace(), "InternalScratchFlags", + Kokkos::Experimental::HIPSpace(), "Kokkos::InternalScratchFlags", (sizeScratchGrain * m_scratchFlagsCount)); Record::increment(r); @@ -345,7 +351,7 @@ void *HIPInternal::resize_team_scratch_space(std::int64_t bytes, if (m_team_scratch_current_size == 0) { m_team_scratch_current_size = bytes; m_team_scratch_ptr = Kokkos::kokkos_malloc( - "HIPSpace::ScratchMemory", m_team_scratch_current_size); + "Kokkos::HIPSpace::TeamScratchMemory", m_team_scratch_current_size); } if ((bytes > m_team_scratch_current_size) || ((bytes < m_team_scratch_current_size) && (force_shrink))) { @@ -388,6 +394,40 @@ void HIPInternal::finalize() { m_team_scratch_current_size = 0; m_team_scratch_ptr = nullptr; } + if (nullptr != d_driverWorkArray) { + HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); + d_driverWorkArray = nullptr; + } +} + +char *HIPInternal::get_next_driver(size_t driverTypeSize) const { + std::lock_guard const lock(m_mutexWorkArray); + if (d_driverWorkArray == nullptr) { + HIP_SAFE_CALL( + hipHostMalloc(&d_driverWorkArray, + m_maxDriverCycles * m_maxDriverTypeSize * sizeof(char), + hipHostMallocNonCoherent)); + } + if (driverTypeSize > m_maxDriverTypeSize) { + // fence handles the cycle id reset for us + fence(); + HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); + m_maxDriverTypeSize = driverTypeSize; + if (m_maxDriverTypeSize % 128 != 0) + m_maxDriverTypeSize = + m_maxDriverTypeSize + 128 - m_maxDriverTypeSize % 128; + HIP_SAFE_CALL( + hipHostMalloc(&d_driverWorkArray, + m_maxDriverCycles * m_maxDriverTypeSize * sizeof(char), + hipHostMallocNonCoherent)); + } else { + m_cycleId = (m_cycleId + 1) % m_maxDriverCycles; + if (m_cycleId == 0) { + // ensure any outstanding kernels are completed before we wrap around + fence(); + } + } + return &d_driverWorkArray[m_maxDriverTypeSize * m_cycleId]; } //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp index 07ec8625e6..f4f88628e3 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp @@ -49,6 +49,8 @@ #include +#include + namespace Kokkos { namespace Experimental { namespace Impl { @@ -83,33 +85,46 @@ class HIPInternal { public: using size_type = ::Kokkos::Experimental::HIP::size_type; - int m_hipDev; - int m_hipArch; - unsigned m_multiProcCount; - unsigned m_maxWarpCount; - unsigned m_maxBlock; - unsigned m_maxBlocksPerSM; - unsigned m_maxSharedWords; + int m_hipDev = -1; + int m_hipArch = -1; + unsigned m_multiProcCount = 0; + unsigned m_maxWarpCount = 0; + unsigned m_maxBlock = 0; + unsigned m_maxBlocksPerSM = 0; + unsigned m_maxSharedWords = 0; int m_regsPerSM; - int m_shmemPerSM; - int m_maxShmemPerBlock; - int m_maxThreadsPerSM; + int m_shmemPerSM = 0; + int m_maxShmemPerBlock = 0; + int m_maxThreadsPerSM = 0; + + // array of DriverTypes to be allocated in host-pinned memory for async + // kernel launches + mutable char *d_driverWorkArray = nullptr; + // number of kernel launches that can be in-flight w/o synchronization + const int m_maxDriverCycles = 100; + // max size of a DriverType [bytes] + mutable size_t m_maxDriverTypeSize = 1024 * 10; + // the current index in the driverWorkArray + mutable int m_cycleId = 0; + // mutex to access d_driverWorkArray + mutable std::mutex m_mutexWorkArray; // Scratch Spaces for Reductions - size_type m_scratchSpaceCount; - size_type m_scratchFlagsCount; + size_type m_scratchSpaceCount = 0; + size_type m_scratchFlagsCount = 0; - size_type *m_scratchSpace; - size_type *m_scratchFlags; + size_type *m_scratchSpace = nullptr; + size_type *m_scratchFlags = nullptr; uint32_t *m_scratchConcurrentBitset = nullptr; hipDeviceProp_t m_deviceProp; - hipStream_t m_stream; + hipStream_t m_stream = nullptr; // Team Scratch Level 1 Space - mutable int64_t m_team_scratch_current_size; - mutable void *m_team_scratch_ptr; + mutable int64_t m_team_scratch_current_size = 0; + mutable void *m_team_scratch_ptr = nullptr; + mutable std::mutex m_team_scratch_mutex; bool was_finalized = false; @@ -117,9 +132,7 @@ class HIPInternal { int verify_is_initialized(const char *const label) const; - int is_initialized() const { - return m_hipDev >= 0; - } // 0 != m_scratchSpace && 0 != m_scratchFlags ; } + int is_initialized() const { return m_hipDev >= 0; } void initialize(int hip_device_id, hipStream_t stream = nullptr); void finalize(); @@ -128,25 +141,12 @@ class HIPInternal { void fence() const; + // returns the next driver type pointer in our work array + char *get_next_driver(size_t driverTypeSize) const; + ~HIPInternal(); - HIPInternal() - : m_hipDev(-1), - m_hipArch(-1), - m_multiProcCount(0), - m_maxWarpCount(0), - m_maxBlock(0), - m_maxSharedWords(0), - m_shmemPerSM(0), - m_maxShmemPerBlock(0), - m_maxThreadsPerSM(0), - m_scratchSpaceCount(0), - m_scratchFlagsCount(0), - m_scratchSpace(nullptr), - m_scratchFlags(nullptr), - m_stream(nullptr), - m_team_scratch_current_size(0), - m_team_scratch_ptr(nullptr) {} + HIPInternal() = default; // Resizing of reduction related scratch spaces size_type *scratch_space(const size_type size); diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp index 3e972c7346..f774423b37 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp @@ -49,9 +49,9 @@ #if defined(__HIPCC__) -#include #include #include +#include // Must use global variable on the device with HIP-Clang #ifdef __HIP__ @@ -127,19 +127,69 @@ struct HIPDispatchProperties { HIPLaunchMechanism launch_mechanism = l; }; -template , +template +struct HIPParallelLaunchKernelFunc; + +template +struct HIPParallelLaunchKernelFunc< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory> { + static auto get_kernel_func() { + return hip_parallel_launch_local_memory; + } +}; + +template +struct HIPParallelLaunchKernelFunc, + HIPLaunchMechanism::LocalMemory> { + static auto get_kernel_func() { + return hip_parallel_launch_local_memory; + } +}; + +template +struct HIPParallelLaunchKernelInvoker; + +template +struct HIPParallelLaunchKernelInvoker + : HIPParallelLaunchKernelFunc { + using base_t = HIPParallelLaunchKernelFunc; + + static void invoke_kernel(DriverType const *driver, dim3 const &grid, + dim3 const &block, int shmem, + HIPInternal const *hip_instance) { + (base_t::get_kernel_func())<<m_stream>>>( + driver); + } +}; + +template , HIPLaunchMechanism LaunchMechanism = HIPLaunchMechanism::LocalMemory> struct HIPParallelLaunch; -template struct HIPParallelLaunch< DriverType, Kokkos::LaunchBounds, - HIPLaunchMechanism::LocalMemory> { - inline HIPParallelLaunch(const DriverType &driver, const dim3 &grid, - const dim3 &block, const int shmem, - const HIPInternal *hip_instance, - const bool /*prefer_shmem*/) { + HIPLaunchMechanism::LocalMemory> + : HIPParallelLaunchKernelInvoker< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory> { + using base_t = HIPParallelLaunchKernelInvoker< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory>; + + HIPParallelLaunch(const DriverType &driver, const dim3 &grid, + const dim3 &block, const int shmem, + const HIPInternal *hip_instance, + const bool /*prefer_shmem*/) { if ((grid.x != 0) && ((block.x * block.y * block.z) != 0)) { if (hip_instance->m_maxShmemPerBlock < shmem) { Kokkos::Impl::throw_runtime_exception( @@ -148,72 +198,16 @@ struct HIPParallelLaunch< KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE(); - // FIXME_HIP -- there is currently an error copying (some) structs - // by value to the device in HIP-Clang / VDI - // As a workaround, we can malloc the DriverType and explictly copy over. - // To remove once solved in HIP - DriverType *d_driver; - HIP_SAFE_CALL(hipMalloc(&d_driver, sizeof(DriverType))); - HIP_SAFE_CALL(hipMemcpyAsync(d_driver, &driver, sizeof(DriverType), - hipMemcpyHostToDevice, - hip_instance->m_stream)); - hip_parallel_launch_local_memory - <<m_stream>>>(d_driver); - -#if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) - HIP_SAFE_CALL(hipGetLastError()); - hip_instance->fence(); -#endif - HIP_SAFE_CALL(hipFree(d_driver)); - } - } - - static hipFuncAttributes get_hip_func_attributes() { - static hipFuncAttributes attr = []() { - hipFuncAttributes attr; - HIP_SAFE_CALL(hipFuncGetAttributes( - &attr, - reinterpret_cast( - hip_parallel_launch_local_memory))); - return attr; - }(); - return attr; - } -}; - -template -struct HIPParallelLaunch, - HIPLaunchMechanism::LocalMemory> { - inline HIPParallelLaunch(const DriverType &driver, const dim3 &grid, - const dim3 &block, const int shmem, - const HIPInternal *hip_instance, - const bool /*prefer_shmem*/) { - if ((grid.x != 0) && ((block.x * block.y * block.z) != 0)) { - if (hip_instance->m_maxShmemPerBlock < shmem) { - Kokkos::Impl::throw_runtime_exception(std::string( - "HIPParallelLaunch FAILED: shared memory request is too large")); - } - - KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE(); - // Invoke the driver function on the device - - // FIXME_HIP -- see note about struct copy by value above - DriverType *d_driver; - HIP_SAFE_CALL(hipMalloc(&d_driver, sizeof(DriverType))); - HIP_SAFE_CALL(hipMemcpyAsync(d_driver, &driver, sizeof(DriverType), - hipMemcpyHostToDevice, - hip_instance->m_stream)); - hip_parallel_launch_local_memory - <<m_stream>>>(d_driver); + DriverType *d_driver = reinterpret_cast( + hip_instance->get_next_driver(sizeof(DriverType))); + std::memcpy((void *)d_driver, (void *)&driver, sizeof(DriverType)); + base_t::invoke_kernel(d_driver, grid, block, shmem, hip_instance); #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) HIP_SAFE_CALL(hipGetLastError()); hip_instance->fence(); #endif - HIP_SAFE_CALL(hipFree(d_driver)); } } @@ -221,8 +215,7 @@ struct HIPParallelLaunch, static hipFuncAttributes attr = []() { hipFuncAttributes attr; HIP_SAFE_CALL(hipFuncGetAttributes( - &attr, reinterpret_cast( - hip_parallel_launch_local_memory))); + &attr, reinterpret_cast(base_t::get_kernel_func()))); return attr; }(); return attr; diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp new file mode 100644 index 0000000000..ce1aff9586 --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp @@ -0,0 +1,37 @@ +#ifndef KOKKOS_HIP_MDRANGEPOLICY_HPP_ +#define KOKKOS_HIP_MDRANGEPOLICY_HPP_ + +#include + +namespace Kokkos { + +template <> +struct default_outer_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +template <> +struct default_inner_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +namespace Impl { + +// Settings for MDRangePolicy +template <> +inline TileSizeProperties get_tile_size_properties( + const Kokkos::Experimental::HIP& space) { + TileSizeProperties properties; + properties.max_threads = + space.impl_internal_space_instance()->m_maxThreadsPerSM; + properties.default_largest_tile_size = 16; + properties.default_tile_size = 4; + properties.max_total_tile_size = 1024; + return properties; +} + +} // Namespace Impl +} // Namespace Kokkos +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp index 6b831ff7a3..35e7d6fb85 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp @@ -49,6 +49,7 @@ #include #include #include +#include #include namespace Kokkos { @@ -72,7 +73,7 @@ class ParallelFor, ParallelFor& operator=(ParallelFor const&) = delete; public: - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { Kokkos::Impl::DeviceIterateTile(m_policy, m_functor) @@ -175,6 +176,25 @@ class ParallelFor, ParallelFor(FunctorType const& arg_functor, Policy const& arg_policy) : m_functor(arg_functor), m_policy(arg_policy) {} + + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + using closure_type = + ParallelFor, + Kokkos::Experimental::HIP>; + hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); + auto const& prop = pol.space().hip_device_prop(); + // Limits due to registers/SM, MDRange doesn't have + // shared memory constraints + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast( + Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock)); + } }; // ParallelReduce @@ -231,7 +251,7 @@ class ParallelReduce, ReducerType, DeviceIteratePattern(m_policy, m_functor, update).exec_range(); } - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { const integral_nonzero_constant word_count(ValueTraits::value_size( @@ -291,13 +311,19 @@ class ParallelReduce, ReducerType, ::Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock; int shmem_size = ::Kokkos::Impl::hip_single_inter_block_reduce_scan_shmem< false, FunctorType, WorkTag>(f, n); + using closure_type = Impl::ParallelReduce; + hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); while ( (n && (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < shmem_size)) || - (n > static_cast( - ::Kokkos::Experimental::Impl::hip_get_max_block_size< - ParallelReduce, LaunchBounds>(f, 1, shmem_size, 0)))) { + (n > + static_cast( + ::Kokkos::Experimental::Impl::hip_get_max_block_size( + m_policy.space().impl_internal_space_instance(), attr, f, 1, + shmem_size, 0)))) { n >>= 1; shmem_size = ::Kokkos::Impl::hip_single_inter_block_reduce_scan_shmem< false, FunctorType, WorkTag>(f, n); @@ -391,6 +417,23 @@ class ParallelReduce, ReducerType, memory_space>::accessible), m_scratch_space(nullptr), m_scratch_flags(nullptr) {} + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + using closure_type = + ParallelReduce, + ReducerType, Kokkos::Experimental::HIP>; + hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); + auto const& prop = pol.space().hip_device_prop(); + // Limits due do registers/SM + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast( + Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock)); + } }; } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp index 5607f1c91a..7d2825eeb4 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp @@ -92,7 +92,7 @@ class ParallelFor, public: using functor_type = FunctorType; - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { const Member work_stride = blockDim.y * gridDim.x; const Member work_end = m_policy.end(); @@ -174,11 +174,14 @@ class ParallelReduce, ReducerType, size_type* m_scratch_space = nullptr; size_type* m_scratch_flags = nullptr; - // FIXME_HIP_PERFORMANCE Need a rule to choose when to use shared memory and - // when to use shuffle +#if HIP_VERSION < 401 static bool constexpr UseShflReduction = ((sizeof(value_type) > 2 * sizeof(double)) && static_cast(ValueTraits::StaticValueSize)); +#else + static bool constexpr UseShflReduction = + static_cast(ValueTraits::StaticValueSize); +#endif private: struct ShflReductionTag {}; @@ -330,13 +333,19 @@ class ParallelReduce, ReducerType, int shmem_size = hip_single_inter_block_reduce_scan_shmem( f, n); + using closure_type = Impl::ParallelReduce; + hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); while ( (n && (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < shmem_size)) || - (n > static_cast( - Kokkos::Experimental::Impl::hip_get_max_block_size< - ParallelReduce, LaunchBounds>(f, 1, shmem_size, 0)))) { + (n > + static_cast( + ::Kokkos::Experimental::Impl::hip_get_max_block_size( + m_policy.space().impl_internal_space_instance(), attr, f, 1, + shmem_size, 0)))) { n >>= 1; shmem_size = hip_single_inter_block_reduce_scan_shmem( @@ -493,7 +502,7 @@ class ParallelScanHIPBase { //---------------------------------------- - __device__ inline void initial(void) const { + __device__ inline void initial() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -529,7 +538,7 @@ class ParallelScanHIPBase { //---------------------------------------- - __device__ inline void final(void) const { + __device__ inline void final() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -606,7 +615,7 @@ class ParallelScanHIPBase { public: //---------------------------------------- - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { if (!m_final) { initial(); } else { diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp index 5da83d289e..96c3ff2a75 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp @@ -433,6 +433,9 @@ class ParallelFor, int m_shmem_size; void* m_scratch_ptr[2]; int m_scratch_size[2]; + // Only let one ParallelFor/Reduce modify the team scratch memory. The + // constructor acquires the mutex which is released in the destructor. + std::unique_lock m_scratch_lock; template __device__ inline @@ -449,7 +452,7 @@ class ParallelFor, } public: - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { // Iterate this block through the league int64_t threadid = 0; if (m_scratch_size[1] > 0) { @@ -513,7 +516,10 @@ class ParallelFor, m_policy(arg_policy), m_league_size(arg_policy.league_size()), m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { + m_vector_size(arg_policy.impl_vector_length()), + m_scratch_lock(m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< ParallelFor, launch_bounds>::get_hip_func_attributes(); m_team_size = @@ -640,6 +646,9 @@ class ParallelReduce, const size_type m_league_size; int m_team_size; const size_type m_vector_size; + // Only let one ParallelFor/Reduce modify the team scratch memory. The + // constructor acquires the mutex which is released in the destructor. + std::unique_lock m_scratch_lock; template __device__ inline @@ -877,7 +886,10 @@ class ParallelReduce, m_scratch_ptr{nullptr, nullptr}, m_league_size(arg_policy.league_size()), m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { + m_vector_size(arg_policy.impl_vector_length()), + m_scratch_lock(m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< ParallelReduce, launch_bounds>::get_hip_func_attributes(); m_team_size = @@ -976,7 +988,10 @@ class ParallelReduce, m_scratch_ptr{nullptr, nullptr}, m_league_size(arg_policy.league_size()), m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { + m_vector_size(arg_policy.impl_vector_length()), + m_scratch_lock(m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< ParallelReduce, launch_bounds>::get_hip_func_attributes(); m_team_size = diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp index 00cef28f82..15ca089d14 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp @@ -42,12 +42,6 @@ //@HEADER */ -#include -#include -#include -#include -#include -#include #include #include @@ -57,6 +51,13 @@ #include #include +#include +#include +#include +#include +#include +#include + /*--------------------------------------------------------------------------*/ /*--------------------------------------------------------------------------*/ namespace Kokkos { @@ -172,14 +173,14 @@ void DeepCopyAsyncHIP(void* dst, void const* src, size_t n) { namespace Kokkos { -void Experimental::HIPSpace::access_error() { +KOKKOS_DEPRECATED void Experimental::HIPSpace::access_error() { const std::string msg( "Kokkos::Experimental::HIPSpace::access_error attempt to execute " "Experimental::HIP function from non-HIP space"); Kokkos::Impl::throw_runtime_exception(msg); } -void Experimental::HIPSpace::access_error(const void* const) { +KOKKOS_DEPRECATED void Experimental::HIPSpace::access_error(const void* const) { const std::string msg( "Kokkos::Experimental::HIPSpace::access_error attempt to execute " "Experimental::HIP function from non-HIP space"); @@ -326,45 +327,6 @@ SharedAllocationRecord SharedAllocationRecord< Kokkos::Experimental::HIPHostPinnedSpace, void>::s_root_record; #endif -std::string SharedAllocationRecord::get_label() const { - SharedAllocationHeader header; - - Kokkos::Impl::DeepCopy( - &header, RecordBase::head(), sizeof(SharedAllocationHeader)); - - return std::string(header.m_label); -} - -std::string SharedAllocationRecord::get_label() const { - return std::string(RecordBase::head()->m_label); -} - -SharedAllocationRecord* -SharedAllocationRecord::allocate( - const Kokkos::Experimental::HIPSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -SharedAllocationRecord* -SharedAllocationRecord:: - allocate(const Kokkos::Experimental::HIPHostPinnedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord* arg_rec) { - delete static_cast(arg_rec); -} - -void SharedAllocationRecord:: - deallocate(SharedAllocationRecord* arg_rec) { - delete static_cast(arg_rec); -} - SharedAllocationRecord::~SharedAllocationRecord() { const char* label = nullptr; @@ -393,7 +355,7 @@ SharedAllocationRecord:: const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, @@ -405,13 +367,7 @@ SharedAllocationRecord:: SharedAllocationHeader header; - // Fill in the Header information - header.m_record = static_cast*>(this); - - strncpy(header.m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - header.m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(header, arg_label); // Copy to device memory Kokkos::Impl::DeepCopy( @@ -425,7 +381,7 @@ SharedAllocationRecord:: const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, @@ -435,223 +391,8 @@ SharedAllocationRecord:: sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc), m_space(arg_space) { // Fill in the Header information, directly accessible via host pinned memory - - RecordBase::m_alloc_ptr->m_record = this; - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; -} - -//---------------------------------------------------------------------------- - -void* SharedAllocationRecord:: - allocate_tracked(const Kokkos::Experimental::HIPSpace& arg_space, - const std::string& arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord* const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked(void* const - arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord* const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void* SharedAllocationRecord:: - reallocate_tracked(void* const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord* const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord* const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -void* SharedAllocationRecord:: - allocate_tracked(const Kokkos::Experimental::HIPHostPinnedSpace& arg_space, - const std::string& arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord* const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked(void* const - arg_alloc_ptr) { - if (arg_alloc_ptr) { - SharedAllocationRecord* const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void* SharedAllocationRecord:: - reallocate_tracked(void* const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord* const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord* const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - using HIPHostPinnedSpace = Kokkos::Experimental::HIPHostPinnedSpace; - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -//---------------------------------------------------------------------------- - -SharedAllocationRecord* -SharedAllocationRecord::get_record( - void* alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordHIP = - SharedAllocationRecord; - - // Copy the header from the allocation - Header head; - - Header const* const head_hip = - alloc_ptr ? Header::get_header(alloc_ptr) : nullptr; - - if (alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, head_hip, sizeof(SharedAllocationHeader)); - } - - RecordHIP* const record = - alloc_ptr ? static_cast(head.m_record) : nullptr; - - if (!alloc_ptr || record->m_alloc_ptr != head_hip) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::SharedAllocationRecord< Kokkos::Experimental::HIPSpace " - ", void >::get_record ERROR")); - } - - return record; -} - -SharedAllocationRecord* -SharedAllocationRecord::get_record(void* alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordHIP = - SharedAllocationRecord; - - Header* const h = - alloc_ptr ? reinterpret_cast(alloc_ptr) - 1 : nullptr; - - if (!alloc_ptr || h->m_record->m_alloc_ptr != h) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::SharedAllocationRecord< " - "Kokkos::Experimental::HIPHostPinnedSpace , void >::get_record ERROR")); - } - - return static_cast(h->m_record); -} - -// Iterate records to print orphaned memory ... -void SharedAllocationRecord:: - print_records(std::ostream& s, const Kokkos::Experimental::HIPSpace&, - bool detail) { -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord* r = &s_root_record; - - char buffer[256]; - - SharedAllocationHeader head; - - if (detail) { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - } else { - head.m_label[0] = 0; - } - - // Formatting dependent on sizeof(uintptr_t) - const char* format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = - "HIP addr( 0x%.12lx ) list( 0x%.12lx 0x%.12lx ) extent[ 0x%.12lx + " - "%.8ld ] count(%d) dealloc(0x%.12lx) %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = - "HIP addr( 0x%.12llx ) list( 0x%.12llx 0x%.12llx ) extent[ " - "0x%.12llx + %.8ld ] count(%d) dealloc(0x%.12llx) %s\n"; - } - - snprintf(buffer, 256, format_string, reinterpret_cast(r), - reinterpret_cast(r->m_prev), - reinterpret_cast(r->m_next), - reinterpret_cast(r->m_alloc_ptr), r->m_alloc_size, - r->m_count, reinterpret_cast(r->m_dealloc), - head.m_label); - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } else { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - - // Formatting dependent on sizeof(uintptr_t) - const char* format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = "HIP [ 0x%.12lx + %ld ] %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = "HIP [ 0x%.12llx + %ld ] %s\n"; - } - - snprintf(buffer, 256, format_string, - reinterpret_cast(r->data()), r->size(), - head.m_label); - } else { - snprintf(buffer, 256, "HIP [ 0 + 0 ]\n"); - } - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } -#else - (void)s; - (void)detail; - throw_runtime_exception( - "Kokkos::Impl::SharedAllocationRecord::print_records" - " only works with KOKKOS_ENABLE_DEBUG enabled"); -#endif + this->base_t::_fill_host_accessible_header_info(*RecordBase::m_alloc_ptr, + arg_label); } } // namespace Impl @@ -680,63 +421,22 @@ void HIP::impl_initialize(const HIP::SelectDevice config) { void HIP::impl_finalize() { Impl::HIPInternal::singleton().finalize(); } HIP::HIP() - : m_space_instance(&Impl::HIPInternal::singleton()), m_counter(nullptr) { + : m_space_instance(&Impl::HIPInternal::singleton(), + [](Impl::HIPInternal*) {}) { Impl::HIPInternal::singleton().verify_is_initialized( "HIP instance constructor"); } HIP::HIP(hipStream_t const stream) - : m_space_instance(new Impl::HIPInternal), m_counter(new int(1)) { + : m_space_instance(new Impl::HIPInternal, [](Impl::HIPInternal* ptr) { + ptr->finalize(); + delete ptr; + }) { Impl::HIPInternal::singleton().verify_is_initialized( "HIP instance constructor"); m_space_instance->initialize(Impl::HIPInternal::singleton().m_hipDev, stream); } -KOKKOS_FUNCTION HIP::HIP(HIP&& other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; -} - -KOKKOS_FUNCTION HIP::HIP(HIP const& other) - : m_space_instance(other.m_space_instance), m_counter(other.m_counter) { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HIP_GPU - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif -} - -KOKKOS_FUNCTION HIP& HIP::operator=(HIP&& other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; - - return *this; -} - -KOKKOS_FUNCTION HIP& HIP::operator=(HIP const& other) { - m_space_instance = other.m_space_instance; - m_counter = other.m_counter; -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HIP_GPU - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif - - return *this; -} - -KOKKOS_FUNCTION HIP::~HIP() noexcept { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HIP_GPU - if (m_counter == nullptr) return; - int const count = Kokkos::atomic_fetch_sub(m_counter, 1); - if (count == 1) { - delete m_counter; - m_space_instance->finalize(); - delete m_space_instance; - } -#endif -} - void HIP::print_configuration(std::ostream& s, const bool) { Impl::HIPInternal::singleton().print_configuration(s); } @@ -810,3 +510,26 @@ void HIPSpaceInitializer::print_configuration(std::ostream& msg, } // namespace Impl } // namespace Kokkos + +//============================================================================== +// {{{1 + +#include + +namespace Kokkos { +namespace Impl { + +// To avoid additional compilation cost for something that's (mostly?) not +// performance sensitive, we explicity instantiate these CRTP base classes here, +// where we have access to the associated *_timpl.hpp header files. +template class HostInaccessibleSharedAllocationRecordCommon< + Kokkos::Experimental::HIPSpace>; +template class SharedAllocationRecordCommon; +template class SharedAllocationRecordCommon< + Kokkos::Experimental::HIPHostPinnedSpace>; + +} // end namespace Impl +} // end namespace Kokkos + +// end Explicit instantiations of CRTP Base classes }}}1 +//============================================================================== diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp index 7571510c31..fe52886ced 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp @@ -644,13 +644,14 @@ KOKKOS_INLINE_FUNCTION thread, count); } -template -KOKKOS_INLINE_FUNCTION - Impl::ThreadVectorRangeBoundariesStruct - ThreadVectorRange(const Impl::HIPTeamMember& thread, iType arg_begin, - iType arg_end) { +template +KOKKOS_INLINE_FUNCTION Impl::ThreadVectorRangeBoundariesStruct< + typename std::common_type::type, Impl::HIPTeamMember> +ThreadVectorRange(const Impl::HIPTeamMember& thread, iType1 arg_begin, + iType2 arg_end) { + using iType = typename std::common_type::type; return Impl::ThreadVectorRangeBoundariesStruct( - thread, arg_begin, arg_end); + thread, iType(arg_begin), iType(arg_end)); } KOKKOS_INLINE_FUNCTION @@ -961,7 +962,7 @@ KOKKOS_INLINE_FUNCTION //---------------------------------------------------------------------------- -/** \brief Intra-thread vector parallel exclusive prefix sum. +/** \brief Intra-thread vector parallel scan with reducer. * * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) * @@ -969,22 +970,21 @@ KOKKOS_INLINE_FUNCTION * thread and a scan operation is performed. * The last call to closure has final == true. */ -template -KOKKOS_INLINE_FUNCTION void parallel_scan( - const Impl::ThreadVectorRangeBoundariesStruct& - loop_boundaries, - const Closure& closure) { +template +KOKKOS_INLINE_FUNCTION + typename std::enable_if::value>::type + parallel_scan(const Impl::ThreadVectorRangeBoundariesStruct< + iType, Impl::HIPTeamMember>& loop_boundaries, + const Closure& closure, const ReducerType& reducer) { #ifdef __HIP_DEVICE_COMPILE__ - // Extract value_type from closure - - using value_type = typename Kokkos::Impl::FunctorAnalysis< - Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + using value_type = typename ReducerType::value_type; + value_type accum; + reducer.init(accum); + const value_type identity = accum; // Loop through boundaries by vector-length chunks // must scan at each iteration - value_type accum = 0; - // All thread "lanes" must loop the same number of times. // Determine an loop end for all thread "lanes." // Requires: @@ -997,47 +997,72 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( const int end = loop_boundaries.end + (rem ? blockDim.x - rem : 0); for (int i = threadIdx.x; i < end; i += blockDim.x) { - value_type val = 0; + value_type val = identity; - // First acquire per-lane contributions: - if (i < loop_boundaries.end) closure(i, val, false); + // First acquire per-lane contributions. + // This sets i's val to i-1's contribution + // to make the latter in_place_shfl_up an + // exclusive scan -- the final accumulation + // of i's val will be included in the second + // closure call later. + if (i < loop_boundaries.end && threadIdx.x > 0) closure(i - 1, val, false); - value_type sval = val; - - // Bottom up inclusive scan in triangular pattern + // Bottom up exclusive scan in triangular pattern // where each HIP thread is the root of a reduction tree // from the zeroth "lane" to itself. // [t] += [t-1] if t >= 1 // [t] += [t-2] if t >= 2 // [t] += [t-4] if t >= 4 // ... - + // This differs from the non-reducer overload, where an inclusive scan was + // implemented, because in general the binary operator cannot be inverted + // and we would not be able to remove the inclusive contribution by + // inversion. for (int j = 1; j < static_cast(blockDim.x); j <<= 1) { - value_type tmp = 0; - ::Kokkos::Experimental::Impl::in_place_shfl_up(tmp, sval, j, blockDim.x); + value_type tmp = identity; + ::Kokkos::Experimental::Impl::in_place_shfl_up(tmp, val, j, blockDim.x); if (j <= static_cast(threadIdx.x)) { - sval += tmp; + reducer.join(val, tmp); } } - // Include accumulation and remove value for exclusive scan: - val = accum + sval - val; + // Include accumulation + reducer.join(val, accum); - // Provide exclusive scan value: + // Update i's contribution into the val + // and add it to accum for next round if (i < loop_boundaries.end) closure(i, val, true); - - // Accumulate the last value in the inclusive scan: - ::Kokkos::Experimental::Impl::in_place_shfl(sval, sval, blockDim.x - 1, + ::Kokkos::Experimental::Impl::in_place_shfl(accum, val, blockDim.x - 1, blockDim.x); - - accum += sval; } #else (void)loop_boundaries; (void)closure; + (void)reducer; #endif } +//---------------------------------------------------------------------------- + +/** \brief Intra-thread vector parallel exclusive prefix sum. + * + * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) + * + * The range [0..N) is mapped to all vector lanes in the + * thread and a scan operation is performed. + * The last call to closure has final == true. + */ +template +KOKKOS_INLINE_FUNCTION void parallel_scan( + const Impl::ThreadVectorRangeBoundariesStruct& + loop_boundaries, + const Closure& closure) { + using value_type = typename Kokkos::Impl::FunctorAnalysis< + Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + value_type dummy; + parallel_scan(loop_boundaries, closure, Kokkos::Sum(dummy)); +} + } // namespace Kokkos namespace Kokkos { diff --git a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp index 140376425c..b7d8e62f69 100644 --- a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp +++ b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp @@ -48,17 +48,11 @@ #include #include - +#include #include #include -#include #include -#if defined(KOKKOS_ENABLE_CUDA) || \ - (defined(__HIPCC__) && defined(KOKKOS_ENABLE_HIP)) -#include -#endif - namespace Kokkos { // ------------------------------------------------------------------ // @@ -74,22 +68,14 @@ enum class Iterate template struct default_outer_direction { - using type = Iterate; -#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) - static constexpr Iterate value = Iterate::Left; -#else + using type = Iterate; static constexpr Iterate value = Iterate::Right; -#endif }; template struct default_inner_direction { - using type = Iterate; -#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) - static constexpr Iterate value = Iterate::Left; -#else + using type = Iterate; static constexpr Iterate value = Iterate::Right; -#endif }; // Iteration Pattern @@ -179,6 +165,25 @@ constexpr NVCC_WONT_LET_ME_CALL_YOU_Array to_array_potentially_narrowing( } return a; } + +struct TileSizeProperties { + int max_threads; + int default_largest_tile_size; + int default_tile_size; + int max_total_tile_size; +}; + +template +TileSizeProperties get_tile_size_properties(const ExecutionSpace&) { + // Host settings + TileSizeProperties properties; + properties.max_threads = std::numeric_limits::max(); + properties.default_largest_tile_size = 0; + properties.default_tile_size = 2; + properties.max_total_tile_size = std::numeric_limits::max(); + return properties; +} + } // namespace Impl // multi-dimensional iteration pattern @@ -208,7 +213,7 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { using launch_bounds = typename traits::launch_bounds; using member_type = typename range_policy::member_type; - enum { rank = static_cast(iteration_pattern::rank) }; + static constexpr int rank = iteration_pattern::rank; using index_type = typename traits::index_type; using array_index_type = std::int64_t; @@ -231,37 +236,20 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { point_type m_tile_end = {}; index_type m_num_tiles = 1; index_type m_prod_tile_dims = 1; + bool m_tune_tile_size = false; - /* - // NDE enum impl definition alternative - replace static constexpr int ? - enum { outer_direction = static_cast ( - (iteration_pattern::outer_direction != Iterate::Default) - ? iteration_pattern::outer_direction - : default_outer_direction< typename traits::execution_space>::value ) }; - - enum { inner_direction = static_cast ( - iteration_pattern::inner_direction != Iterate::Default - ? iteration_pattern::inner_direction - : default_inner_direction< typename traits::execution_space>::value ) }; - - enum { Right = static_cast( Iterate::Right ) }; - enum { Left = static_cast( Iterate::Left ) }; - */ - // static constexpr int rank = iteration_pattern::rank; - - static constexpr int outer_direction = static_cast( + static constexpr auto outer_direction = (iteration_pattern::outer_direction != Iterate::Default) ? iteration_pattern::outer_direction - : default_outer_direction::value); + : default_outer_direction::value; - static constexpr int inner_direction = static_cast( + static constexpr auto inner_direction = iteration_pattern::inner_direction != Iterate::Default ? iteration_pattern::inner_direction - : default_inner_direction::value); + : default_inner_direction::value; - // Ugly ugly workaround intel 14 not handling scoped enum correctly - static constexpr int Right = static_cast(Iterate::Right); - static constexpr int Left = static_cast(Iterate::Left); + static constexpr auto Right = Iterate::Right; + static constexpr auto Left = Iterate::Left; KOKKOS_INLINE_FUNCTION const typename traits::execution_space& space() const { return m_space; @@ -320,7 +308,7 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { point_type const& lower, point_type const& upper, tile_type const& tile = tile_type{}) : m_space(work_space), m_lower(lower), m_upper(upper), m_tile(tile) { - init(); + init_helper(Impl::get_tile_size_properties(work_space)); } template { m_tile(p.m_tile), m_tile_end(p.m_tile_end), m_num_tiles(p.m_num_tiles), - m_prod_tile_dims(p.m_prod_tile_dims) {} + m_prod_tile_dims(p.m_prod_tile_dims), + m_tune_tile_size(p.m_tune_tile_size) {} + + void impl_change_tile_size(const point_type& tile) { + m_tile = tile; + init_helper(Impl::get_tile_size_properties(m_space)); + } + bool impl_tune_tile_size() const { return m_tune_tile_size; } private: - void init() { - // Host - if (true -#if defined(KOKKOS_ENABLE_CUDA) - && !std::is_same::value -#endif -#if defined(KOKKOS_ENABLE_HIP) - && !std::is_same::value -#endif - ) { - index_type span; - for (int i = 0; i < rank; ++i) { - span = m_upper[i] - m_lower[i]; - if (m_tile[i] <= 0) { - if (((int)inner_direction == (int)Right && (i < rank - 1)) || - ((int)inner_direction == (int)Left && (i > 0))) { - m_tile[i] = 2; - } else { - m_tile[i] = (span == 0 ? 1 : span); - } - } - m_tile_end[i] = - static_cast((span + m_tile[i] - 1) / m_tile[i]); - m_num_tiles *= m_tile_end[i]; - m_prod_tile_dims *= m_tile[i]; - } + void init_helper(Impl::TileSizeProperties properties) { + m_prod_tile_dims = 1; + int increment = 1; + int rank_start = 0; + int rank_end = rank; + if (inner_direction == Iterate::Right) { + increment = -1; + rank_start = rank - 1; + rank_end = -1; } -#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) - else // Cuda or HIP - { - index_type span; - int increment = 1; - int rank_start = 0; - int rank_end = rank; - if ((int)inner_direction == (int)Right) { - increment = -1; - rank_start = rank - 1; - rank_end = -1; - } - bool is_cuda_exec_space = -#if defined(KOKKOS_ENABLE_CUDA) - std::is_same::value; -#else - false; -#endif - for (int i = rank_start; i != rank_end; i += increment) { - span = m_upper[i] - m_lower[i]; - if (m_tile[i] <= 0) { - // TODO: determine what is a good default tile size for Cuda and HIP - // may be rank dependent - if (((int)inner_direction == (int)Right && (i < rank - 1)) || - ((int)inner_direction == (int)Left && (i > 0))) { - if (m_prod_tile_dims < 256) { - m_tile[i] = (is_cuda_exec_space) ? 2 : 4; - } else { - m_tile[i] = 1; - } + for (int i = rank_start; i != rank_end; i += increment) { + const index_type length = m_upper[i] - m_lower[i]; + if (m_tile[i] <= 0) { + m_tune_tile_size = true; + if ((inner_direction == Iterate::Right && (i < rank - 1)) || + (inner_direction == Iterate::Left && (i > 0))) { + if (m_prod_tile_dims * properties.default_tile_size < + static_cast(properties.max_total_tile_size)) { + m_tile[i] = properties.default_tile_size; } else { - m_tile[i] = 16; + m_tile[i] = 1; } - } - m_tile_end[i] = - static_cast((span + m_tile[i] - 1) / m_tile[i]); - m_num_tiles *= m_tile_end[i]; - m_prod_tile_dims *= m_tile[i]; - } - if (m_prod_tile_dims > - 1024) { // Match Cuda restriction for ParallelReduce; 1024,1024,64 - // max per dim (Kepler), but product num_threads < 1024 - if (is_cuda_exec_space) { - printf(" Tile dimensions exceed Cuda limits\n"); - Kokkos::abort( - "Cuda ExecSpace Error: MDRange tile dims exceed maximum number " - "of threads per block - choose smaller tile dims"); } else { - printf(" Tile dimensions exceed HIP limits\n"); - Kokkos::abort( - "HIP ExecSpace Error: MDRange tile dims exceed maximum number of " - "threads per block - choose smaller tile dims"); + m_tile[i] = properties.default_largest_tile_size == 0 + ? std::max(length, 1) + : properties.default_largest_tile_size; } } + m_tile_end[i] = + static_cast((length + m_tile[i] - 1) / m_tile[i]); + m_num_tiles *= m_tile_end[i]; + m_prod_tile_dims *= m_tile[i]; + } + if (m_prod_tile_dims > static_cast(properties.max_threads)) { + printf(" Product of tile dimensions exceed maximum limit: %d\n", + static_cast(properties.max_threads)); + Kokkos::abort( + "ExecSpace Error: MDRange tile dims exceed maximum number " + "of threads per block - choose smaller tile dims"); } -#endif } }; diff --git a/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp b/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp index 8e226a078d..fb94049d7a 100644 --- a/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp +++ b/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp @@ -104,20 +104,6 @@ struct MemorySpaceAccess { enum : bool { deepcopy = true }; }; -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 1 }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void *) {} -}; - -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 1 }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void *) {} -}; - } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/core/src/Kokkos_Complex.hpp b/lib/kokkos/core/src/Kokkos_Complex.hpp index fb2925a066..6578723fc8 100644 --- a/lib/kokkos/core/src/Kokkos_Complex.hpp +++ b/lib/kokkos/core/src/Kokkos_Complex.hpp @@ -45,14 +45,13 @@ #define KOKKOS_COMPLEX_HPP #include +#include #include +#include #include +#include #include -#ifdef KOKKOS_ENABLE_SYCL -#include -#endif - namespace Kokkos { /// \class complex @@ -220,10 +219,11 @@ class // Conditional noexcept, just in case RType throws on divide-by-zero KOKKOS_CONSTEXPR_14 KOKKOS_INLINE_FUNCTION complex& operator/=( const complex& y) noexcept(noexcept(RealType{} / RealType{})) { + using Kokkos::Experimental::fabs; // Scale (by the "1-norm" of y) to avoid unwarranted overflow. // If the real part is +/-Inf and the imaginary part is -/+Inf, // this won't change the result. - const RealType s = std::fabs(y.real()) + std::fabs(y.imag()); + const RealType s = fabs(y.real()) + fabs(y.imag()); // If s is 0, then y is zero, so x/y == real(x)/0 + i*imag(x)/0. // In that case, the relation x/y == (x/s) / (y/s) doesn't hold, @@ -248,10 +248,11 @@ class KOKKOS_INLINE_FUNCTION complex& operator/=( const std::complex& y) noexcept(noexcept(RealType{} / RealType{})) { + using Kokkos::Experimental::fabs; // Scale (by the "1-norm" of y) to avoid unwarranted overflow. // If the real part is +/-Inf and the imaginary part is -/+Inf, // this won't change the result. - const RealType s = std::fabs(y.real()) + std::fabs(y.imag()); + const RealType s = fabs(y.real()) + fabs(y.imag()); // If s is 0, then y is zero, so x/y == real(x)/0 + i*imag(x)/0. // In that case, the relation x/y == (x/s) / (y/s) doesn't hold, @@ -693,35 +694,96 @@ KOKKOS_INLINE_FUNCTION RealType real(const complex& x) noexcept { return x.real(); } +//! Constructs a complex number from magnitude and phase angle +template +KOKKOS_INLINE_FUNCTION complex polar(const T& r, const T& theta = T()) { + using Kokkos::Experimental::cos; + using Kokkos::Experimental::sin; + KOKKOS_EXPECTS(r >= 0); + return complex(r * cos(theta), r * sin(theta)); +} + //! Absolute value (magnitude) of a complex number. template KOKKOS_INLINE_FUNCTION RealType abs(const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::hypot; -#else - using std::hypot; -#endif + using Kokkos::Experimental::hypot; return hypot(x.real(), x.imag()); } //! Power of a complex number -template -KOKKOS_INLINE_FUNCTION Kokkos::complex pow(const complex& x, - const RealType& e) { - RealType r = abs(x); -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan; - using cl::sycl::cos; - using cl::sycl::pow; - using cl::sycl::sin; -#else - using std::atan; - using std::cos; - using std::pow; - using std::sin; -#endif - RealType phi = atan(x.imag() / x.real()); - return pow(r, e) * Kokkos::complex(cos(phi * e), sin(phi * e)); +template +KOKKOS_INLINE_FUNCTION complex pow(const complex& x, const T& y) { + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::pow; + T r = abs(x); + T theta = atan2(x.imag(), x.real()); + return polar(pow(r, y), y * theta); +} + +template +KOKKOS_INLINE_FUNCTION complex pow(const T& x, const complex& y) { + return pow(complex(x), y); +} + +template +KOKKOS_INLINE_FUNCTION complex pow(const complex& x, + const complex& y) { + using Kokkos::Experimental::log; + + return x == T() ? T() : exp(y * log(x)); +} + +namespace Impl { +// NOTE promote would also be useful for math functions +template ::value> +struct promote { + using type = double; +}; +template +struct promote {}; +template <> +struct promote { + using type = long double; +}; +template <> +struct promote { + using type = double; +}; +template <> +struct promote { + using type = float; +}; +template +using promote_t = typename promote::type; +template +struct promote_2 { + using type = decltype(promote_t() + promote_t()); +}; +template +using promote_2_t = typename promote_2::type; +} // namespace Impl + +template ::value>> +KOKKOS_INLINE_FUNCTION complex> pow( + const T& x, const complex& y) { + using type = Impl::promote_2_t; + return pow(type(x), complex(y)); +} + +template ::value>> +KOKKOS_INLINE_FUNCTION complex> pow(const complex& x, + const U& y) { + using type = Impl::promote_2_t; + return pow(complex(x), type(y)); +} + +template +KOKKOS_INLINE_FUNCTION complex> pow( + const complex& x, const complex& y) { + using type = Impl::promote_2_t; + return pow(complex(x), complex(y)); } //! Square root of a complex number. This is intended to match the stdc++ @@ -729,26 +791,21 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex pow(const complex& x, template KOKKOS_INLINE_FUNCTION Kokkos::complex sqrt( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::abs; - using cl::sycl::sqrt; -#else - using std::abs; - using std::sqrt; -#endif + using Kokkos::Experimental::fabs; + using Kokkos::Experimental::sqrt; RealType r = x.real(); RealType i = x.imag(); if (r == RealType()) { - RealType t = sqrt(abs(i) / 2); + RealType t = sqrt(fabs(i) / 2); return Kokkos::complex(t, i < RealType() ? -t : t); } else { - RealType t = sqrt(2 * (abs(x) + abs(r))); + RealType t = sqrt(2 * (abs(x) + fabs(r))); RealType u = t / 2; - return r > RealType() - ? Kokkos::complex(u, i / t) - : Kokkos::complex(abs(i) / t, i < RealType() ? -u : u); + return r > RealType() ? Kokkos::complex(u, i / t) + : Kokkos::complex(fabs(i) / t, + i < RealType() ? -u : u); } } @@ -762,15 +819,9 @@ KOKKOS_INLINE_FUNCTION complex conj( //! Exponential of a complex number. template KOKKOS_INLINE_FUNCTION complex exp(const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::exp; - using cl::sycl::sin; -#else - using std::cos; - using std::exp; - using std::sin; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::exp; + using Kokkos::Experimental::sin; return exp(x.real()) * complex(cos(x.imag()), sin(x.imag())); } @@ -778,14 +829,9 @@ KOKKOS_INLINE_FUNCTION complex exp(const complex& x) { template KOKKOS_INLINE_FUNCTION Kokkos::complex log( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan; - using cl::sycl::log; -#else - using std::atan; - using std::log; -#endif - RealType phi = atan(x.imag() / x.real()); + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::log; + RealType phi = atan2(x.imag(), x.real()); return Kokkos::complex(log(abs(x)), phi); } @@ -793,17 +839,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex log( template KOKKOS_INLINE_FUNCTION Kokkos::complex sin( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(sin(x.real()) * cosh(x.imag()), cos(x.real()) * sinh(x.imag())); } @@ -812,17 +851,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex sin( template KOKKOS_INLINE_FUNCTION Kokkos::complex cos( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(cos(x.real()) * cosh(x.imag()), -sin(x.real()) * sinh(x.imag())); } @@ -838,17 +870,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex tan( template KOKKOS_INLINE_FUNCTION Kokkos::complex sinh( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(sinh(x.real()) * cos(x.imag()), cosh(x.real()) * sin(x.imag())); } @@ -857,17 +882,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex sinh( template KOKKOS_INLINE_FUNCTION Kokkos::complex cosh( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(cosh(x.real()) * cos(x.imag()), sinh(x.real()) * sin(x.imag())); } @@ -898,13 +916,8 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex acosh( template KOKKOS_INLINE_FUNCTION Kokkos::complex atanh( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan2; - using cl::sycl::log; -#else - using std::atan2; - using std::log; -#endif + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::log; const RealType i2 = x.imag() * x.imag(); const RealType r = RealType(1.0) - i2 - x.real() * x.real(); @@ -933,12 +946,7 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex asin( template KOKKOS_INLINE_FUNCTION Kokkos::complex acos( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::acos; - -#else - using std::acos; -#endif + using Kokkos::Experimental::acos; Kokkos::complex t = asin(x); RealType pi_2 = acos(RealType(0.0)); return Kokkos::complex(pi_2 - t.real(), -t.imag()); @@ -948,13 +956,8 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex acos( template KOKKOS_INLINE_FUNCTION Kokkos::complex atan( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan2; - using cl::sycl::log; -#else - using std::atan2; - using std::log; -#endif + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::log; const RealType r2 = x.real() * x.real(); const RealType i = RealType(1.0) - r2 - x.imag() * x.imag(); @@ -996,12 +999,13 @@ KOKKOS_INLINE_FUNCTION operator/(const complex& x, const complex& y) noexcept(noexcept(RealType1{} / RealType2{})) { + using Kokkos::Experimental::fabs; // Scale (by the "1-norm" of y) to avoid unwarranted overflow. // If the real part is +/-Inf and the imaginary part is -/+Inf, // this won't change the result. using common_real_type = typename std::common_type::type; - const common_real_type s = std::fabs(real(y)) + std::fabs(imag(y)); + const common_real_type s = fabs(real(y)) + fabs(imag(y)); // If s is 0, then y is zero, so x/y == real(x)/0 + i*imag(x)/0. // In that case, the relation x/y == (x/s) / (y/s) doesn't hold, @@ -1046,7 +1050,7 @@ std::istream& operator>>(std::istream& is, complex& x) { } template -struct reduction_identity > { +struct reduction_identity> { using t_red_ident = reduction_identity; KOKKOS_FORCEINLINE_FUNCTION constexpr static Kokkos::complex sum() noexcept { diff --git a/lib/kokkos/core/src/Kokkos_Core.hpp b/lib/kokkos/core/src/Kokkos_Core.hpp index 4dac463a66..c3771ab393 100644 --- a/lib/kokkos/core/src/Kokkos_Core.hpp +++ b/lib/kokkos/core/src/Kokkos_Core.hpp @@ -58,6 +58,7 @@ #include #include #include +#include #include #include #include @@ -86,6 +87,10 @@ struct InitArguments { int skip_device; bool disable_warnings; bool tune_internals; + bool tool_help = false; + std::string tool_lib = {}; + std::string tool_args = {}; + InitArguments(int nt = -1, int nn = -1, int dv = -1, bool dw = false, bool ti = false) : num_threads{nt}, @@ -139,6 +144,10 @@ void pre_initialize(const InitArguments& args); void post_initialize(const InitArguments& args); +void declare_configuration_metadata(const std::string& category, + const std::string& key, + const std::string& value); + } // namespace Impl bool is_initialized() noexcept; diff --git a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp index 7502719c73..fe7eba3f6e 100644 --- a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp +++ b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp @@ -50,6 +50,7 @@ // and compiler environment then sets a collection of #define macros. #include +#include #include #include @@ -180,7 +181,6 @@ using DefaultHostExecutionSpace KOKKOS_IMPL_DEFAULT_HOST_EXEC_SPACE_ANNOTATION = // a given memory space. namespace Kokkos { - namespace Impl { #if defined(KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA) && \ @@ -196,16 +196,22 @@ using ActiveExecutionMemorySpace = Kokkos::HostSpace; using ActiveExecutionMemorySpace = void; #endif -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 0 }; +template +struct MemorySpaceAccess; + +template ::accessible> +struct verify_space { + KOKKOS_FUNCTION static void check() {} }; -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 1 }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void *) {} +template +struct verify_space { + KOKKOS_FUNCTION static void check() { + Kokkos::abort( + "Kokkos::View ERROR: attempt to access inaccessible memory space"); + }; }; // Base class for exec space initializer factories @@ -220,13 +226,13 @@ class LogicalMemorySpace; } // namespace Kokkos -#define KOKKOS_RESTRICT_EXECUTION_TO_DATA(DATA_SPACE, DATA_PTR) \ - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< \ - Kokkos::Impl::ActiveExecutionMemorySpace, DATA_SPACE>::verify(DATA_PTR) +#define KOKKOS_RESTRICT_EXECUTION_TO_DATA(DATA_SPACE, DATA_PTR) \ + Kokkos::Impl::verify_space::check(); -#define KOKKOS_RESTRICT_EXECUTION_TO_(DATA_SPACE) \ - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< \ - Kokkos::Impl::ActiveExecutionMemorySpace, DATA_SPACE>::verify() +#define KOKKOS_RESTRICT_EXECUTION_TO_(DATA_SPACE) \ + Kokkos::Impl::verify_space::check(); //---------------------------------------------------------------------------- @@ -256,8 +262,7 @@ template struct ViewCopy; -template +template struct FunctorPolicyExecutionSpace; //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/Kokkos_Crs.hpp b/lib/kokkos/core/src/Kokkos_Crs.hpp index 4a573d82c0..1a10500b19 100644 --- a/lib/kokkos/core/src/Kokkos_Crs.hpp +++ b/lib/kokkos/core/src/Kokkos_Crs.hpp @@ -199,7 +199,7 @@ class CrsRowMapFromCounts { public: KOKKOS_INLINE_FUNCTION void operator()(index_type i, value_type& update, bool final_pass) const { - if (i < m_in.size()) { + if (i < static_cast(m_in.size())) { update += m_in(i); if (final_pass) m_out(i + 1) = update; } else if (final_pass) { diff --git a/lib/kokkos/core/src/Kokkos_Cuda.hpp b/lib/kokkos/core/src/Kokkos_Cuda.hpp index 81e11f3f12..7a218120bb 100644 --- a/lib/kokkos/core/src/Kokkos_Cuda.hpp +++ b/lib/kokkos/core/src/Kokkos_Cuda.hpp @@ -63,6 +63,7 @@ #include #include #include +#include /*--------------------------------------------------------------------------*/ @@ -198,16 +199,6 @@ class Cuda { Cuda(); - KOKKOS_FUNCTION Cuda(Cuda&& other) noexcept; - - KOKKOS_FUNCTION Cuda(const Cuda& other); - - KOKKOS_FUNCTION Cuda& operator=(Cuda&& other) noexcept; - - KOKKOS_FUNCTION Cuda& operator=(const Cuda& other); - - KOKKOS_FUNCTION ~Cuda() noexcept; - Cuda(cudaStream_t stream); //-------------------------------------------------------------------------- @@ -253,13 +244,12 @@ class Cuda { static const char* name(); inline Impl::CudaInternal* impl_internal_space_instance() const { - return m_space_instance; + return m_space_instance.get(); } uint32_t impl_instance_id() const noexcept { return 0; } private: - Impl::CudaInternal* m_space_instance; - int* m_counter; + Kokkos::Impl::HostSharedPtr m_space_instance; }; namespace Tools { @@ -319,38 +309,8 @@ struct MemorySpaceAccess -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = false }; - inline static void verify(void) { CudaSpace::access_error(); } - inline static void verify(const void* p) { CudaSpace::access_error(p); } -}; - } // namespace Impl } // namespace Kokkos -/*--------------------------------------------------------------------------*/ -/*--------------------------------------------------------------------------*/ - -#include -#include -#include -#include -#include -#include -#include - -#include -//---------------------------------------------------------------------------- - #endif /* #if defined( KOKKOS_ENABLE_CUDA ) */ #endif /* #ifndef KOKKOS_CUDA_HPP */ diff --git a/lib/kokkos/core/src/Kokkos_CudaSpace.hpp b/lib/kokkos/core/src/Kokkos_CudaSpace.hpp index fc1c0e2f8a..e10fae93c7 100644 --- a/lib/kokkos/core/src/Kokkos_CudaSpace.hpp +++ b/lib/kokkos/core/src/Kokkos_CudaSpace.hpp @@ -53,8 +53,10 @@ #include #include #include +#include #include +#include #include @@ -119,8 +121,8 @@ class CudaSpace { /*--------------------------------*/ /** \brief Error reporting for HostSpace attempt to access CudaSpace */ - static void access_error(); - static void access_error(const void* const); + KOKKOS_DEPRECATED static void access_error(); + KOKKOS_DEPRECATED static void access_error(const void* const); private: int m_device; ///< Which Cuda device @@ -128,42 +130,6 @@ class CudaSpace { static constexpr const char* m_name = "Cuda"; friend class Kokkos::Impl::SharedAllocationRecord; }; - -namespace Impl { -/// \brief Initialize lock array for arbitrary size atomics. -/// -/// Arbitrary atomics are implemented using a hash table of locks -/// where the hash value is derived from the address of the -/// object for which an atomic operation is performed. -/// This function initializes the locks to zero (unset). -void init_lock_arrays_cuda_space(); - -/// \brief Retrieve the pointer to the lock array for arbitrary size atomics. -/// -/// Arbitrary atomics are implemented using a hash table of locks -/// where the hash value is derived from the address of the -/// object for which an atomic operation is performed. -/// This function retrieves the lock array pointer. -/// If the array is not yet allocated it will do so. -int* atomic_lock_array_cuda_space_ptr(bool deallocate = false); - -/// \brief Retrieve the pointer to the scratch array for team and thread private -/// global memory. -/// -/// Team and Thread private scratch allocations in -/// global memory are acquired via locks. -/// This function retrieves the lock array pointer. -/// If the array is not yet allocated it will do so. -int* scratch_lock_array_cuda_space_ptr(bool deallocate = false); - -/// \brief Retrieve the pointer to the scratch array for unique identifiers. -/// -/// Unique identifiers in the range 0-Cuda::concurrency -/// are provided via locks. -/// This function retrieves the lock array pointer. -/// If the array is not yet allocated it will do so. -int* threadid_lock_array_cuda_space_ptr(bool deallocate = false); -} // namespace Impl } // namespace Kokkos /*--------------------------------------------------------------------------*/ @@ -313,6 +279,11 @@ class CudaHostPinnedSpace { namespace Kokkos { namespace Impl { +cudaStream_t cuda_get_deep_copy_stream(); + +const std::unique_ptr& cuda_get_deep_copy_space( + bool initialize = true); + static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, ""); @@ -784,104 +755,21 @@ struct DeepCopy { namespace Kokkos { namespace Impl { -/** Running in CudaSpace attempting to access HostSpace: error */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = false }; - KOKKOS_INLINE_FUNCTION static void verify(void) { - Kokkos::abort("Cuda code attempted to access HostSpace memory"); - } - - KOKKOS_INLINE_FUNCTION static void verify(const void*) { - Kokkos::abort("Cuda code attempted to access HostSpace memory"); - } -}; - -/** Running in CudaSpace accessing CudaUVMSpace: ok */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -/** Running in CudaSpace accessing CudaHostPinnedSpace: ok */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -/** Running in CudaSpace attempting to access an unknown space: error */ -template -struct VerifyExecutionCanAccessMemorySpace< - typename std::enable_if::value, - Kokkos::CudaSpace>::type, - OtherSpace> { - enum : bool { value = false }; - KOKKOS_INLINE_FUNCTION static void verify(void) { - Kokkos::abort("Cuda code attempted to access unknown Space memory"); - } - - KOKKOS_INLINE_FUNCTION static void verify(const void*) { - Kokkos::abort("Cuda code attempted to access unknown Space memory"); - } -}; - -//---------------------------------------------------------------------------- -/** Running in HostSpace attempting to access CudaSpace */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = false }; - inline static void verify(void) { CudaSpace::access_error(); } - inline static void verify(const void* p) { CudaSpace::access_error(p); } -}; - -/** Running in HostSpace accessing CudaUVMSpace is OK */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - inline static void verify(void) {} - inline static void verify(const void*) {} -}; - -/** Running in HostSpace accessing CudaHostPinnedSpace is OK */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -} // namespace Impl -} // namespace Kokkos - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - template <> class SharedAllocationRecord - : public SharedAllocationRecord { + : public HostInaccessibleSharedAllocationRecordCommon { private: friend class SharedAllocationRecord; + friend class SharedAllocationRecordCommon; + friend class HostInaccessibleSharedAllocationRecordCommon; using RecordBase = SharedAllocationRecord; + using base_t = + HostInaccessibleSharedAllocationRecordCommon; SharedAllocationRecord(const SharedAllocationRecord&) = delete; SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - static void deallocate(RecordBase*); - static ::cudaTextureObject_t attach_texture_object( const unsigned sizeof_alias, void* const alloc_ptr, const size_t alloc_size); @@ -890,39 +778,19 @@ class SharedAllocationRecord static RecordBase s_root_record; #endif - ::cudaTextureObject_t m_tex_obj; + ::cudaTextureObject_t m_tex_obj = 0; const Kokkos::CudaSpace m_space; protected: ~SharedAllocationRecord(); - SharedAllocationRecord() : RecordBase(), m_tex_obj(0), m_space() {} + SharedAllocationRecord() = default; SharedAllocationRecord( const Kokkos::CudaSpace& arg_space, const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); + const RecordBase::function_type arg_dealloc = &base_t::deallocate); public: - std::string get_label() const; - - static SharedAllocationRecord* allocate(const Kokkos::CudaSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const Kokkos::CudaSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size); - - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr); - - static SharedAllocationRecord* get_record(void* arg_alloc_ptr); - template inline ::cudaTextureObject_t attach_texture_object() { static_assert((std::is_same::value || @@ -945,57 +813,35 @@ class SharedAllocationRecord // Texture object is attached to the entire allocation range return ptr - reinterpret_cast(RecordBase::m_alloc_ptr); } - - static void print_records(std::ostream&, const Kokkos::CudaSpace&, - bool detail = false); }; template <> class SharedAllocationRecord - : public SharedAllocationRecord { + : public SharedAllocationRecordCommon { private: + friend class SharedAllocationRecordCommon; + + using base_t = SharedAllocationRecordCommon; using RecordBase = SharedAllocationRecord; SharedAllocationRecord(const SharedAllocationRecord&) = delete; SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - static void deallocate(RecordBase*); - static RecordBase s_root_record; - ::cudaTextureObject_t m_tex_obj; + ::cudaTextureObject_t m_tex_obj = 0; const Kokkos::CudaUVMSpace m_space; protected: ~SharedAllocationRecord(); - SharedAllocationRecord() : RecordBase(), m_tex_obj(0), m_space() {} + SharedAllocationRecord() = default; SharedAllocationRecord( const Kokkos::CudaUVMSpace& arg_space, const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); + const RecordBase::function_type arg_dealloc = &base_t::deallocate); public: - std::string get_label() const; - - static SharedAllocationRecord* allocate(const Kokkos::CudaUVMSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const Kokkos::CudaUVMSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size); - - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr); - - static SharedAllocationRecord* get_record(void* arg_alloc_ptr); - template inline ::cudaTextureObject_t attach_texture_object() { static_assert((std::is_same::value || @@ -1019,57 +865,32 @@ class SharedAllocationRecord // Texture object is attached to the entire allocation range return ptr - reinterpret_cast(RecordBase::m_alloc_ptr); } - - static void print_records(std::ostream&, const Kokkos::CudaUVMSpace&, - bool detail = false); }; template <> class SharedAllocationRecord - : public SharedAllocationRecord { + : public SharedAllocationRecordCommon { private: + friend class SharedAllocationRecordCommon; + using RecordBase = SharedAllocationRecord; + using base_t = SharedAllocationRecordCommon; SharedAllocationRecord(const SharedAllocationRecord&) = delete; SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - static void deallocate(RecordBase*); - static RecordBase s_root_record; const Kokkos::CudaHostPinnedSpace m_space; protected: ~SharedAllocationRecord(); - SharedAllocationRecord() : RecordBase(), m_space() {} + SharedAllocationRecord() = default; SharedAllocationRecord( const Kokkos::CudaHostPinnedSpace& arg_space, const std::string& arg_label, const size_t arg_alloc_size, const RecordBase::function_type arg_dealloc = &deallocate); - - public: - std::string get_label() const; - - static SharedAllocationRecord* allocate( - const Kokkos::CudaHostPinnedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size); - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const Kokkos::CudaHostPinnedSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size); - - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr); - - static SharedAllocationRecord* get_record(void* arg_alloc_ptr); - - static void print_records(std::ostream&, const Kokkos::CudaHostPinnedSpace&, - bool detail = false); }; } // namespace Impl diff --git a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp index 3afe081701..55aed13670 100644 --- a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp +++ b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp @@ -856,11 +856,12 @@ KOKKOS_INLINE_FUNCTION_DELETED Impl::ThreadVectorRangeBoundariesStruct ThreadVectorRange(const TeamMemberType&, const iType& count) = delete; -template -KOKKOS_INLINE_FUNCTION_DELETED - Impl::ThreadVectorRangeBoundariesStruct - ThreadVectorRange(const TeamMemberType&, const iType& arg_begin, - const iType& arg_end) = delete; +template +KOKKOS_INLINE_FUNCTION_DELETED Impl::ThreadVectorRangeBoundariesStruct< + typename std::common_type::type, TeamMemberType> +ThreadVectorRange(const TeamMemberType&, const iType1& arg_begin, + const iType2& arg_end) = delete; namespace Impl { @@ -902,85 +903,6 @@ struct ParallelConstructName { } // namespace Kokkos namespace Kokkos { -namespace Experimental { - -namespace Impl { -template -struct PolicyPropertyAdaptor; - -template class Policy, - class... Properties> -struct PolicyPropertyAdaptor, - Policy> { - using policy_in_t = Policy; - static_assert(is_execution_policy::value, ""); - using policy_out_t = Policy, - typename policy_in_t::traits::occupancy_control>; -}; - -template