diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 5016d9a644..6d1bcee2db 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -71,6 +71,7 @@ src/EXTRA-COMMAND/group_ndx.* @akohlmey src/EXTRA-COMMAND/ndx_group.* @akohlmey src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps +src/EXTRA-DUMP/dump_extxyz.* @fxcoudert src/EXTRA-FIX/fix_deform_pressure.* @jtclemm src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl src/EXTRA-PAIR/d3_parameters.h @soniasolomoni @arthurfl diff --git a/.github/release_steps.md b/.github/release_steps.md index 857acfdb85..1ffd3cb291 100644 --- a/.github/release_steps.md +++ b/.github/release_steps.md @@ -216,7 +216,7 @@ and using the CMake settings: ``` sh -D CMAKE_OSX_ARCHITECTURES=arm64;x86_64 --D CMAKE_OSX_DEPLOYMENT_TARGER=11.0 +-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0 ``` This will add the compiler flags `-arch arm64 -arch x86_64 @@ -324,6 +324,47 @@ At this point it should be possible to do a fast-forward merge of ### Push branches and tags - - ## LAMMPS Stable Update Release + +After making a stable release, bugfixes from the 'develop' branch +are selectively backported to the 'maintenance' branch. This is +done with "git cherry-pick \' wherever possible. +The LAMMPS\_UPDATE define in "src/version.h" is set to "Maintenance". + +### Prerequesites + +When a sufficient number of bugfixes has accumulated or an urgent +or important bugfix needs to be distributed a new stable update +release is made. To make this publicly visible a pull request +is submitted that will merge 'maintenance' into 'stable'. Before +merging, set LAMMPS\_UPDATE in "src/version.h" to "Update #" with +"#" indicating the update count (1, 2, and so on). +Also draft suitable release notes under https://github.com/lammps/lammps/releases + +### Fast-forward merge of 'maintenance' into 'stable', apply tag, and publish + +Do a fast-forward merge of 'maintenance' to 'stable' and then +apply the stable\_DMmmYYYY\_update# tag and push branch and tag +to GitHub. The corresponding pull request will be automatically +closed. Example: + +``` +git checkout maintenance +git pull +git checkout stable +git pull +git merge --ff-only maintenance +git tag -s -m 'Update 2 for Stable LAMMPS version 29 August 2024' stable_29Aug2024_update2 +git push git@github.com:lammps/lammps.git --tags maintenance stable +``` + +Associate draft release notes with new tag and publish as "latest release". + +On https://ci.lammps.org/ go to "dev", "stable" and manually execute +the "update\_release" task. This will update https://docs.lammps.org/stable +and prepare a stable tarball. + +### Build and upload binary packages and source tarball to GitHub + +The build procedure is the same as for the feature releases, only +that packages are built from the 'stable' branch. diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 8528ac7dff..9854689767 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -432,8 +432,8 @@ else() target_link_libraries(lammps PUBLIC mpi_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(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") +set(LAMMPS_SIZES_VALUES smallbig bigbig) set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) diff --git a/cmake/Modules/LAMMPSInterfacePlugin.cmake b/cmake/Modules/LAMMPSInterfacePlugin.cmake index fcaf604778..5b7444f62c 100644 --- a/cmake/Modules/LAMMPSInterfacePlugin.cmake +++ b/cmake/Modules/LAMMPSInterfacePlugin.cmake @@ -260,8 +260,8 @@ endif() ################ # integer size selection -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(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") +set(LAMMPS_SIZES_VALUES smallbig bigbig) set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) diff --git a/cmake/Modules/Packages/EXTRA-COMMAND.cmake b/cmake/Modules/Packages/EXTRA-COMMAND.cmake index 13c98bafd3..9e219d494a 100644 --- a/cmake/Modules/Packages/EXTRA-COMMAND.cmake +++ b/cmake/Modules/Packages/EXTRA-COMMAND.cmake @@ -1,10 +1,18 @@ # the geturl command needs libcurl -find_package(CURL QUIET COMPONENTS HTTP HTTPS) +find_package(CURL QUIET) option(WITH_CURL "Enable libcurl support" ${CURL_FOUND}) if(WITH_CURL) - find_package(CURL REQUIRED COMPONENTS HTTP HTTPS) target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL) - target_link_libraries(lammps PRIVATE CURL::libcurl) + + # need to use pkgconfig for fully static bins to find custom static libs + if (CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL") + include(FindPkgConfig) + pkg_check_modules(CURL IMPORTED_TARGET libcurl libssl libcrypto) + target_link_libraries(lammps PUBLIC PkgConfig::CURL) + else() + find_package(CURL REQUIRED) + target_link_libraries(lammps PRIVATE CURL::libcurl) + endif() endif() diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 2731b0df14..f878db654c 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -57,8 +57,8 @@ if(DOWNLOAD_KOKKOS) list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${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/4.5.01.tar.gz" CACHE STRING "URL for KOKKOS tarball") - set(KOKKOS_MD5 "4d832aa0284169d9e3fbae3165286bc6" CACHE STRING "MD5 checksum of KOKKOS tarball") + set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball") + set(KOKKOS_MD5 "61b2b69ae50d83eedcc7d47a3fa3d6cb" CACHE STRING "MD5 checksum of KOKKOS tarball") mark_as_advanced(KOKKOS_URL) mark_as_advanced(KOKKOS_MD5) GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK) @@ -83,7 +83,7 @@ if(DOWNLOAD_KOKKOS) add_dependencies(LAMMPS::KOKKOSCORE kokkos_build) add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build) elseif(EXTERNAL_KOKKOS) - find_package(Kokkos 4.5.01 REQUIRED CONFIG) + find_package(Kokkos 4.6.00 REQUIRED CONFIG) target_link_libraries(lammps PRIVATE Kokkos::kokkos) else() set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) diff --git a/cmake/presets/kokkos-cuda.cmake b/cmake/presets/kokkos-cuda.cmake index 878ce0c566..31942b8fae 100644 --- a/cmake/presets/kokkos-cuda.cmake +++ b/cmake/presets/kokkos-cuda.cmake @@ -1,6 +1,5 @@ # preset that enables KOKKOS and selects CUDA compilation with OpenMP -# enabled as well. This preselects CC 5.0 as default GPU arch, since -# that is compatible with all higher CC, but not the default CC 3.5 +# enabled as well. The GPU architecture *must* match your hardware set(PKG_KOKKOS ON CACHE BOOL "" FORCE) set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE) set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE) diff --git a/doc/Makefile b/doc/Makefile index d26e6020a6..92132e7d8c 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -17,9 +17,11 @@ MATHJAXTAG = 3.2.2 PYTHON = $(word 3,$(shell type python3)) DOXYGEN = $(word 3,$(shell type doxygen)) +PANDOC = $(word 3,$(shell type pandoc)) HAS_PYTHON3 = NO HAS_DOXYGEN = NO HAS_PDFLATEX = NO +HAS_PANDOC = NO ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0) HAS_PYTHON3 = YES @@ -31,10 +33,14 @@ endif ifeq ($(shell type pdflatex >/dev/null 2>&1; echo $$?), 0) ifeq ($(shell type latexmk >/dev/null 2>&1; echo $$?), 0) -HAS_PDFLATEX = YES +HAS_PDFLATEX = YES endif endif +ifeq ($(shell type pandoc >/dev/null 2>&1; echo $$?), 0) +HAS_PANDOC = YES +endif + # override settings for PIP commands # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org @@ -45,8 +51,9 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess # 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 html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml +.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml fasthtml-init +FASTHTMLFILES = $(patsubst $(RSTDIR)/%.rst,fasthtml/%.html,$(wildcard $(RSTDIR)/*rst)) # ------------------------------------------ help: @@ -105,6 +112,8 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\ env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\ $(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\ + env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \ + $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\ echo "############################################" ;\ deactivate ;\ ) @@ -116,25 +125,23 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ @rm -rf html/PDF/.[sg]* @echo "Build finished. The HTML pages are in doc/html." -fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) - @if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi - @$(MAKE) $(MFLAGS) -C graphviz all - @mkdir -p fasthtml - @(\ - . $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \ - sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\ - touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \ - sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\ - deactivate ;\ - ) - @rm -rf fasthtml/_sources - @rm -rf fasthtml/PDF - @rm -rf fasthtml/USER - @rm -rf fasthtml/JPG - @cp -r src/PDF fasthtml/PDF - @rm -rf fasthtml/PDF/.[sg]* +fasthtml: fasthtml-init $(FASTHTMLFILES) @echo "Fast HTML build finished. The HTML pages are in doc/fasthtml." +fasthtml-init: + @mkdir -p fasthtml/JPG + @cp src/JPG/*.* fasthtml/JPG + @cp $(RSTDIR)/accel_styles.rst $(RSTDIR)/lepton_expression.rst fasthtml/ + @cp $(BUILDDIR)/utils/pandoc.css fasthtml/ + +fasthtml/%.html: $(RSTDIR)/%.rst + @if [ "$(HAS_PANDOC)" == "NO" ] ; then echo "Make 'fasthtml' requires the 'pandoc' software" 1>&2; exit 1; fi + @mkdir -p fasthtml + @echo converting $< to $@ + @sed -e 's/\\AA/\\mathring{\\mathrm{A}}/g' $< > fasthtml/$*.temp.rst + @pandoc -s --mathml --css="pandoc.css" --template=$(BUILDDIR)/utils/pandoc.html --metadata title="$@" -o $@ fasthtml/$*.temp.rst + @rm -f fasthtml/$*.temp.rst + spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt @if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi @(\ @@ -188,6 +195,8 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\ env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\ $(PYTHON) utils/check-styles.py -s ../src -d src ;\ + env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \ + $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\ echo "############################################" ;\ deactivate ;\ ) @@ -237,6 +246,8 @@ role_check : @( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : ) @( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : ) @( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : ) + @( env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \ + $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} && exit 1 || : ) link_check : $(VENV) html @(\ diff --git a/doc/lammps.1 b/doc/lammps.1 index d6d43cc081..01dba5b277 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,7 +1,7 @@ -.TH LAMMPS "1" "4 February 2025" "2025-02-04" +.TH LAMMPS "1" "2 April 2025" "2025-04-02" .SH NAME .B LAMMPS -\- Molecular Dynamics Simulator. Version 4 February 2025 +\- Molecular Dynamics Simulator. Version 2 April 2025 .SH SYNOPSIS .B lmp diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index a38b42b4f4..2349eebf62 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -119,6 +119,13 @@ configured) and additional files like LAMMPS API headers, manpages, potential and force field files. The location of the installation tree defaults to ``${HOME}/.local``. +.. note:: + + If you have set `-D CMAKE_INSTALL_PREFIX` to install LAMMPS into a + system location on a Linux machine , you may also have to run (as + root) the `ldconfig` program to update the cache file for fast lookup + of system shared libraries. + .. _cmake_options: Configuration and build options diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index f57407f9c1..26cf776f4d 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -255,11 +255,10 @@ Traditional make Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ . You can do this manually if you prefer; follow the instructions in -``lib/gpu/README``. Note that the GPU library uses MPI calls, so you must -use the same MPI library (or the STUBS library) settings as the main -LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ , -``-DLAMMPS_SMALLBIG``\ , or ``-DLAMMPS_SMALLSMALL`` settings in whichever -Makefile you use. +``lib/gpu/README``. Note that the GPU library uses MPI calls, so you +must use the same MPI library (or the STUBS library) settings as the +main LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG`` or +``-DLAMMPS_SMALLBIG`` settings in whichever Makefile you use. You can also build the library in one step from the ``lammps/src`` dir, using a command like these, which simply invokes the ``lib/gpu/Install.py`` @@ -612,6 +611,9 @@ They must be specified in uppercase. * - ZEN3 - HOST - AMD Zen3 architecture + * - ZEN4 + - HOST + - AMD Zen4 architecture * - RISCV_SG2042 - HOST - SG2042 (RISC-V) CPUs @@ -715,7 +717,7 @@ They must be specified in uppercase. - GPU - Intel GPU Ponte Vecchio -This list was last updated for version 4.5.1 of the Kokkos library. +This list was last updated for version 4.6.0 of the Kokkos library. .. tabs:: diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index 7a969877a1..2fc29f584b 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -78,8 +78,7 @@ folder. The following ``make`` commands are available: make epub # generate LAMMPS.epub in ePUB format using Sphinx make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert - make fasthtml # generate approximate HTML in fasthtml dir using Sphinx - # some Sphinx extensions do not work correctly with this + make fasthtml # generate approximate HTML in fasthtml dir using pandoc make clean # remove intermediate RST files created by HTML build make clean-all # remove entire build folder and any cached data @@ -205,12 +204,42 @@ documentation is required and either existing files in the ``src`` folder need to be updated or new files added. These files are written in `reStructuredText `_ markup for translation with the Sphinx tool. +Testing your contribution +^^^^^^^^^^^^^^^^^^^^^^^^^ + Before contributing any documentation, please check that both the HTML -and the PDF format documentation can translate without errors. During -testing the html translation, you may use the ``make fasthtml`` command -which does an approximate translation (i.e. not all Sphinx features and -extensions will work), but runs very fast because it will only translate -files that have been changed since the last ``make fasthtml`` command. +and the PDF format documentation can translate without errors and that +there are no spelling issues. This is done with ``make html``, ``make pdf``, +and ``make spelling``, respectively. + +Fast and approximate translation to HTML +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Translating the full manual to HTML or PDF can take a long time. Thus +there is a fast and approximate way to translate the reStructuredText to +HTML as a quick-n-dirty way of checking your manual page. + +This translation uses `Pandoc `_ instead of Sphinx +and thus all special Sphinx features (cross-references, advanced tables, +embedding of Python docstrings or doxygen documentation, and so on) will +not render correctly. Most embedded math should render correctly. This +is a **very fast** way to check the syntax and layout of a documentation +file translated to HTML while writing or updating it. + +To translate **all** manual pages, you can type ``make fasthtml`` at the +command line. The translated HTML files are then in the ``fasthtml`` +folder. All subsequent ``make fasthtml`` commands will only translate +``.rst`` files that have been changed. The ``make fasthtml`` command +can be parallelized with make using the `-j` flag. You can also +directly translate only individual pages: e.g. to translate only the +``doc/src/pair_lj.rst`` page type ``make fasthtml/pair_lj.html`` + +After writing the documentation is completed, you will still need +to verify with ``make html`` and ``make pdf`` that it translates +correctly in both formats. + +Tests for consistency, completeness, and other known issues +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Please also check the output to the console for any warnings or problems. There will be multiple tests run automatically: diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index fb3ebf4b48..226e19bfc3 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -13,7 +13,8 @@ explains how to do this for building both with CMake and make. * `Size of LAMMPS integer types and size limits`_ * `Read or write compressed files`_ * `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image ` or :doc:`dump movie ` commands -* `Support for downloading files`_ +* `Support for downloading files from the input`_ +* `Prevent download of large potential files`_ * `Memory allocation alignment`_ * `Workaround for long long integers`_ * `Exception handling when using LAMMPS as a library`_ to capture errors @@ -315,7 +316,7 @@ large counters can become before "rolling over". The default setting of .. code-block:: bash - -D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall + -D LAMMPS_SIZES=value # smallbig (default) or bigbig If the variable is not set explicitly, "smallbig" is used. @@ -326,7 +327,7 @@ large counters can become before "rolling over". The default setting of .. code-block:: make - LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL + LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified @@ -335,34 +336,27 @@ LAMMPS system size restrictions .. list-table:: :header-rows: 1 - :widths: 18 27 28 27 + :widths: 27 36 37 :align: center * - - smallbig - bigbig - - smallsmall * - Total atom count - :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`) - :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`) - - :math:`2^{31}` atoms (= :math:`2.147 \cdot 10^9`) * - Total timesteps - :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`) - :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`) - - :math:`2^{31}` steps (= :math:`2.147 \cdot 10^9`) * - Atom ID values - :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)` - :math:`1 \le i \le 2^{63} (= 9.223 \cdot 10^{18})` - - :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)` * - Image flag values - :math:`-512 \le i \le 511` - :math:`- 1\,048\,576 \le i \le 1\,048\,575` - - :math:`-512 \le i \le 511` The "bigbig" setting increases the size of image flags and atom IDs over -"smallbig" and the "smallsmall" setting is only needed if your machine -does not support 64-bit integers or incurs performance penalties when -using them. +the default "smallbig" setting. These are limits for the core of the LAMMPS code, specific features or some styles may impose additional limits. The :ref:`ATC @@ -516,8 +510,8 @@ during a run. .. _libcurl: -Support for downloading files ------------------------------ +Support for downloading files from the input +-------------------------------------------- .. versionadded:: 29Aug2024 @@ -560,6 +554,25 @@ LAMMPS is compiled accordingly which needs the following settings: ---------- +.. _download_pot: + +Prevent download of large potential files +----------------------------------------- + +.. versionadded:: 8Feb2023 + +LAMMPS bundles a selection of potential files in the ``potentials`` +folder as examples of how those kinds of potential files look like and +for use with the provided input examples in the ``examples`` tree. To +keep the size of the distributed LAMMPS source package small, very large +potential files (> 5 MBytes) are not bundled, but only downloaded on +demand when the :doc:`corresponding package ` is +installed. This automatic download can be prevented when :doc:`building +LAMMPS with CMake ` by adding the setting `-D +DOWNLOAD_POTENTIALS=off` when configuring. + +---------- + .. _align: Memory allocation alignment diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 40532bdef7..3ac828670c 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -23,6 +23,7 @@ OPT. * * :doc:`bpm/rotational ` * :doc:`bpm/spring ` + * :doc:`bpm/spring/plastic ` * :doc:`class2 (ko) ` * :doc:`fene (iko) ` * :doc:`fene/expand (o) ` @@ -127,7 +128,7 @@ OPT. * :doc:`harmonic (iko) ` * :doc:`helix (o) ` * :doc:`lepton (o) ` - * :doc:`multi/harmonic (o) ` + * :doc:`multi/harmonic (ko) ` * :doc:`nharmonic (o) ` * :doc:`opls (iko) ` * :doc:`quadratic (o) ` diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst index 86dab8b731..c938937755 100644 --- a/doc/src/Commands_dump.rst +++ b/doc/src/Commands_dump.rst @@ -19,6 +19,7 @@ An alphabetic list of all LAMMPS :doc:`dump ` commands. * :doc:`custom/gz ` * :doc:`custom/zstd ` * :doc:`dcd ` + * :doc:`extxyz ` * :doc:`grid ` * :doc:`grid/vtk ` * :doc:`h5md ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 940c4e9847..1c770e446a 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -165,6 +165,8 @@ OPT. * :doc:`phonon ` * :doc:`pimd/langevin ` * :doc:`pimd/nvt ` + * :doc:`pimd/langevin/bosonic ` + * :doc:`pimd/nvt/bosonic ` * :doc:`planeforce ` * :doc:`plumed ` * :doc:`poems ` @@ -187,6 +189,7 @@ OPT. * :doc:`qeq/fire ` * :doc:`qeq/point ` * :doc:`qeq/reaxff (ko) ` + * :doc:`qeq/rel/reaxff ` * :doc:`qeq/shielded ` * :doc:`qeq/slater ` * :doc:`qmmm ` diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index de60d6636c..cea964fe79 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -1,7 +1,7 @@ Removed commands and packages ============================= -.. contents:: +.. contents:: \ ------ @@ -170,6 +170,18 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS and the :ref:`GPU package ` are maintained and allow running LAMMPS with GPU acceleration. +Compute atom/molecule +--------------------- + +.. deprecated:: 11 Dec2015 + +The atom/molecule command has been removed from LAMMPS since it was superseded +by the more general and extensible "chunk infrastructure". Here the system is +partitioned in one of many possible ways - including using molecule IDs - +through the :doc:`compute chunk/atom ` command and then +summing is done using :doc:`compute reduce/chunk ` Please +refer to the :doc:`chunk HOWTO ` section for an overview. + Fix ave/spatial and fix ave/spatial/sphere ------------------------------------------ diff --git a/doc/src/Developer.rst b/doc/src/Developer.rst index b0cfcc14fc..d4afd6f298 100644 --- a/doc/src/Developer.rst +++ b/doc/src/Developer.rst @@ -24,4 +24,5 @@ of time and requests from the LAMMPS user community. Classes Developer_platform Developer_utils + Developer_internal Developer_grid diff --git a/doc/src/Developer_internal.rst b/doc/src/Developer_internal.rst new file mode 100644 index 0000000000..89dac47be5 --- /dev/null +++ b/doc/src/Developer_internal.rst @@ -0,0 +1,120 @@ +Internal Styles +--------------- + +LAMMPS has a number of styles that are not meant to be used in an input +file and thus are not documented in the :doc:`LAMMPS command +documentation `. The differentiation between user +commands and internal commands is through the case of the command name: +user commands and styles are all lower case, internal styles are all +upper case. Internal styles are not called from the input file, but +their classes are instantiated by other styles. Often they are +created by other styles to store internal data or to perform actions +regularly at specific steps of the simulation. + +The paragraphs below document some of those styles that have general +utility and may be used to avoid redundant implementation. + +DEPRECATED Styles +^^^^^^^^^^^^^^^^^ + +The styles called DEPRECATED (e.g. pair, bond, fix, compute, region, etc.) +have the purpose to inform users that a specific style has been removed +or renamed. This is achieved by creating an alias for the deprecated +style to the corresponding class. For example, the fix style DEPRECATED +is aliased to fix style ave/spatial and fix style ave/spatial/sphere with +the following code: + +.. code-block:: c++ + + FixStyle(DEPRECATED,FixDeprecated); + FixStyle(ave/spatial,FixDeprecated); + FixStyle(ave/spatial/sphere,FixDeprecated); + +The individual class will then determine based on the style name +what action to perform: + +- inform that the style has been removed and what style replaces it, if any, and then error out +- inform that the style has been renamed and then either execute the replacement or error out +- inform that the style is no longer required, and it is thus ignored and continue + +There is also a section in the user's guide for :doc:`removed commands +and packages ` with additional explanations. + +Internal fix styles +^^^^^^^^^^^^^^^^^^^ + +These provide an implementation of features that would otherwise have +been replicated across multiple styles. The used fix ID is generally +derived from the compute or fix ID creating the fix with some string +appended. When needed, the fix can be looked up with +``Modify::get_fix_by_id()``, which returns a pointer to the fix +instance. The data managed by the fix can be accessed just as for other +fixes that can be used in input files. + +fix DUMMY +""""""""" + +Most fix classes cannot be instantiated before the simulation box has +been created since they access data that is only available then. +However, in some cases it is required that a fix must be at or close to +the top of the list of all fixes. In those cases an instance of the +DUMMY fix style may be created by calling ``Modify::add_fix()`` and then +later replaced by the intended fix through calling ``Modify::replace_fix()``. + +fix STORE/ATOM +"""""""""""""" + +Fix STORE/ATOM can be used as persistent storage of per-atom data. + +**Syntax** + +.. code-block:: LAMMPS + + fix ID group-ID STORE/ATOM N1 N2 gflag rflag + +* ID, group-ID are documented in :doc:`fix ` command +* STORE/ATOM = style name of this fix command +* N1 = 1, N2 = 0 : data is per-atom vector = single value per atom +* N1 > 1, N2 = 0 : data is per-atom array = N1 values per atom +* N1 > 0, N2 > 0 : data is per-atom tensor = N1xN2 values per atom +* gflag = 1 communicate per-atom values with ghost atoms, 0 do not update ghost atom data +* rflag = 1 store per-atom value in restart file, 0 do not store data in restart + +Similar functionality is also available through using custom per-atom +properties with :doc:`fix property/atom `. The +choice between the two fixes should be based on whether the user should +be able to access this per-atom data: if yes, then fix property/atom is +preferred, otherwise fix STORE/ATOM. + +fix STORE/GLOBAL +"""""""""""""""" + +Fix STORE/GLOBAL can be used as persistent storage of global data with support for restarts + +**Syntax** + +.. code-block:: LAMMPS + + fix ID group-ID STORE/GLOBAL N1 N2 + +* ID, group-ID are documented in :doc:`fix ` command +* STORE/GLOBAL = style name of this fix command +* N1 >=1 : number of global items to store +* N2 = 1 : data is global vector of length N1 +* N2 > 1 : data is global N1xN2 array + +fix STORE/LOCAL +""""""""""""""" + +Fix STORE/LOCAL can be used as persistent storage for local data + +**Syntax** + +.. code-block:: LAMMPS + + fix ID group-ID STORE/LOCAL Nreset Nvalues + +* ID, group-ID are documented in :doc:`fix ` command +* STORE/LOCAL = style name of this fix command +* Nreset = frequency at which local data is available +* Nvalues = number of values per local item, that is the number of columns diff --git a/doc/src/Developer_notes.rst b/doc/src/Developer_notes.rst index 3f78f33d25..4c789abb3a 100644 --- a/doc/src/Developer_notes.rst +++ b/doc/src/Developer_notes.rst @@ -7,7 +7,7 @@ typically document what a variable stores, what a small section of code does, or what a function does and its input/outputs. The topics on this page are intended to document code functionality at a higher level. -.. contents:: +.. contents:: Available notes ---- diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 96efead1a2..f2728321e6 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -1,23 +1,18 @@ -Error and warning details -========================= +Errors and warnings details +=========================== -Many errors or warnings are self-explanatory and thus straightforward to -resolve. However, there are also cases, where there is no single cause -and explanation, where LAMMPS can only detect symptoms of an error but -not the exact cause, or where the explanation needs to be more detailed -than what can be fit into a message printed by the program. The -following are discussions of such cases. +Many errors and warnings that LAMMPS outputs are self-explanatory and +thus straightforward to resolve. However, there are also cases where +there is no single cause or simple explanation that can be provided in a +short message printed by LAMMPS. Therefore, more detailed discussions +of such scenarios are provided here; first on a more general level and +then for specific errors. In the latter cases, LAMMPS will output a +short message and then provide a URL that links to a specific section on +this page. -- :ref:`Unknown identifier in data file ` -- :ref:`Incorrect format in ... section of data file ` -- :ref:`Illegal variable command: expected X arguments but found Y ` -- :ref:`Out of range atoms - cannot compute ... ` -- :ref:`Too many neighbor bins ` -- :ref:`Cannot use neighbor bins - box size \<\< cutoff ` -- :ref:`Domain too large for neighbor bins ` -- :ref:`Molecule topology/atom exceeds system topology/atom ` -- :ref:`Molecule topology type exceeds system topology type ` -- :ref:`Molecule attributes do not match system attributes ` +------- + +.. contents:: Individual paragraphs ------ @@ -27,6 +22,8 @@ General troubleshooting advice Below are suggestions that can help to understand the causes of problems with simulations leading to errors or unexpected results. +.. _hint01: + Create a small test system ^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -36,6 +33,8 @@ a small test system input that has the same issue, but will take much time until it triggers the error condition. Also, it will be easier to see what happens. +.. _hint02: + Visualize your trajectory ^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -46,6 +45,8 @@ avoid gigantic files, you can use :doc:`dump_modify delay ` to delay output until the critical section is reached, and you can use a smaller test system (see above). +.. _hint03: + Parallel versus serial ^^^^^^^^^^^^^^^^^^^^^^ @@ -55,49 +56,98 @@ only the symptoms are not triggering an error quickly. Correspondingly, errors may be triggered faster with more processors and thus smaller sub-domains. +.. _hint04: + +Segmentation Fault +^^^^^^^^^^^^^^^^^^ + +A segmentation fault is an error reported by the **operating system** +and not LAMMPS itself. It happens when a process tries to access a +memory address that is not available. This can have **many** reasons: +memory has not been allocated, a memory buffer is not large enough, a +memory address is computed from an incorrect index, a memory buffer is +used after it has been freed, some general memory corruption. When +investigating a segmentation fault (aka segfault), it is important to +determine which process is causing it; it may not always be LAMMPS. For +example, some MPI library implementations report a segmentation fault +from their "mpirun" or "mpiexec" command when the application has been +terminated unexpectedly. + +While a segmentation fault is likely an indication of a bug in LAMMPS, +it need not always be; it can also be the consequence of too aggressive +simulation settings. For time critical code paths, LAMMPS will assume +the user has chosen the settings carefully and will not make any checks +to avoid to avoid performance penalties. + +A crucial step in resolving a segmentation fault is to identify the +exact location in the code where it happens. Please see `Errors_debug` +for a couple of examples showing how to do this on a Linux machine. +With this information -- a simple way to reproduce the segmentation +fault and the exact :doc:`LAMMPS version ` and platform +you are running on -- you can contact the LAMMPS developers or post in +the LAMMPS forum to get assistance. + +.. _hint05: + Fast moving atoms ^^^^^^^^^^^^^^^^^ Fast moving atoms may be "lost" or "missing" when their velocity becomes so large that they can cross a sub-domain within one timestep. This often happens when atoms are too close, but atoms may also "move" too -fast from sub-domain to sub-domain if the box changes rapidly, e.g. when -setting a large an initial box with :doc:`shrink-wrap boundary +fast from sub-domain to sub-domain if the box changes rapidly. +E.g. when setting a large an initial box with :doc:`shrink-wrap boundary conditions ` that collapses on the first step (in this case -the solution is often using 'm' instead of 's' as boundary condition). +the solution is often using 'm' instead of 's' as a boundary condition). To reduce the impact of "close contacts", one can remove those atoms or molecules with something like :doc:`delete_atoms overlap 0.1 all all -`. With periodic boundaries, a close contact pair of atoms -may be on opposite sides of the simulation box. Another option would be -to first run a minimization (aka quench) before starting the MD. Reducing -the time step can also help. Many times, one just needs to "ease" the -system into a balanced state and can then switch to more aggressive settings. +`. With periodic boundaries, a close contact pair of +atoms may be on opposite sides of the simulation box. Another option +would be to first run a minimization (aka quench) before starting +the MD. Reducing the time step can also help. Many times, one just +needs to "ease" the system into a balanced state and can then switch to +more aggressive settings. -The speed of atoms during an MD depends on the steepness of the +The speed of atoms during an MD run depends on the steepness of the potential function and their mass. Since the positions and velocities -of atoms are computed with finite timesteps, they choice of timestep can -be too large for a stable numeric integration of the trajectory. In -those cases using (temporarily) :doc:`fix nve/limit ` or -:doc:`fix dt/reset ` can help to avoid too large updates -or adapt the timestep according to the displacements. +of atoms are computed with finite timesteps, the timestep needs to be +small enough for stable numeric integration of the trajectory. If the +timestep is too large during initialization (or other instances of +extreme dynamics), using :doc:`fix nve/limit ` or +:doc:`fix dt/reset ` temporarily can help to avoid too +large updates or adapt the timestep according to the displacements. +.. _hint06: -Pressure, forces, positions becoming NaN of Inf +Ignoring lost atoms +^^^^^^^^^^^^^^^^^^^ + +It is tempting to use the :doc:`thermo_modify lost ignore +` to avoid LAMMPS aborting with an error on lost atoms. +This setting should, however, *only* be used when atoms *should* leave +the system. In general, ignoring a problem does not solve it. + +.. _hint07: + +Pressure, forces, positions becoming NaN or Inf ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Some potentials can overflow or have a division by zero with close contacts -or bad geometries (for the given force styles in use) leading to forces -that can no longer be represented as numbers. Those will show as "NaN" or -"Inf". On most machines, the program will continue, but there is no way -to recover from it and those NaN or Inf values will propagate. So-called -:doc:`"soft-core" potentials ` or the :doc:`"soft" repulsive-only -pair style ` are less prone for this behavior (depending on the -settings in use) and can be used at the beginning of a simulation. Also, -single precision numbers can overflow much faster, so for the GPU or INTEL -package it may be beneficial to run with double precision initially before -switching to mixed or single precision for faster execution when the system -has relaxed. +Some potentials can overflow or have a division by zero with close +contacts or bad geometries (for the given force styles in use) leading +to forces that can no longer be represented as numbers. Those will show +as "NaN" or "Inf". On most machines, the program will continue, but +there is no way to recover from it and those NaN or Inf values will +propagate. So-called :doc:`"soft-core" potentials ` or +the :doc:`"soft" repulsive-only pair style ` are less prone +for this behavior (depending on the settings in use) and can be used at +the beginning of a simulation. Also, single precision numbers can +overflow much faster, so for the GPU or INTEL package it may be +beneficial to run with double precision initially before switching to +mixed or single precision for faster execution when the system has +relaxed. + +.. _hint08: Communication cutoff ^^^^^^^^^^^^^^^^^^^^ @@ -105,17 +155,19 @@ Communication cutoff The communication cutoff determines the "overlap" between sub-domains and atoms in these regions are referred to in LAMMPS as "ghost atoms". This region has to be large enough to contain all atoms of a bond, -angle, dihedral or improper with just one atom in the actual sub-domain. -Typically, this cutoff is set to the largest cutoff from the :doc:`pair -style(s) ` plus the :doc:`neighbor list skin distance -` and will be more than sufficient for all bonded -interactions. But if the pair style cutoff is small this may bot be +angle, dihedral, or improper with just one atom in the actual +sub-domain. Typically, this cutoff is set to the largest cutoff from +the :doc:`pair style(s) ` plus the :doc:`neighbor list skin +distance ` and will typically be sufficient for all bonded +interactions. But if the pair style cutoff is small, this may not be enough. LAMMPS will print a warning in this case using some heuristic -based on the equilibrium bond length, but that may not be sufficient for -cases where the force constants are small and thus bonds may be -stretched very far. The communication cutoff can be adjusted with -:doc:`comm_modify cutoff \ `, but setting this too -large will waste CPU time and memory. +based on the equilibrium bond length, but that still may not be +sufficient for cases where the force constants are small and thus bonds +may be stretched very far. The communication cutoff can be adjusted +with :doc:`comm_modify cutoff \ `, but setting this +too large will waste CPU time and memory. + +.. _hint09: Neighbor list settings ^^^^^^^^^^^^^^^^^^^^^^ @@ -125,16 +177,10 @@ for "lost" or "missing" atoms. Thus it can help to use very conservative :doc:`neighbor list settings ` and then examine the neighbor list statistics if the neighbor list rebuild can be safely delayed. Rebuilding the neighbor list less frequently -(i.e. through increasing the *delay* or *every* setting has diminishing -returns and increasing risks). +(i.e. through increasing the *delay* or *every*) setting has diminishing +returns and increasing risks. -Ignoring lost atoms -^^^^^^^^^^^^^^^^^^^ - -It is tempting to use the :doc:`thermo_modify lost ignore ` -to avoid that LAMMPS stops with an error. This setting should, however, -*only* be used when atoms *should* leave the system. In general, ignoring -a problem does not solve it. +.. _hint10: Units ^^^^^ @@ -151,23 +197,48 @@ are parameterized for other settings, most notably :doc:`ReaxFF potentials ` that use "real" units. Also, individual parameters for :doc:`pair_coeff ` commands -taken from publications or other MD software, may need to be converted +taken from publications or other MD software may need to be converted and sometimes in unexpected ways. Thus some careful checking is recommended. +.. _hint11: + No error message printed ^^^^^^^^^^^^^^^^^^^^^^^^ -In some cases - especially when running in parallel with MPI - LAMMPS -may stop without displaying an error. But that does not mean, that -there was no error message, instead it is highly likely that the message -was written to a buffer and LAMMPS was aborted before the buffer was -output. Usually, output buffers are output for every line of output, -but sometimes, this is delayed until 4096 or 8192 bytes of output have -been accumulated. This buffering for screen and logfile output can be -disabled by using the :ref:`-nb or -nonbuf ` command-line flag. -This is most often needed when debugging crashing multi-replica -calculations. +In some cases -- especially when running in parallel with MPI -- LAMMPS +may stop without displaying an error. But the fact that nothing was +displayed does not mean there was not an error message. Instead it is +highly likely that the message was written to a buffer and LAMMPS was +aborted before the buffer was output. Usually, output buffers are +output for every line of output, but sometimes this is delayed until +4096 or 8192 bytes of output have been accumulated. This buffering for +screen and logfile output can be disabled by using the :ref:`-nb +or -nonbuf ` command-line flag. This is most often needed when +debugging crashing multi-replica calculations. + +.. _hint12: + +Errors before or after the simulation box is created +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +As critical step in a LAMMPS input is when the simulation box is +defined, either with a :doc:`create_box command `, a +:doc:`read_data command `, or a :doc:`read_restart command +`. After this step, certain settings are locked in (e.g. +units, or number of atom, bond, angle, dihedral, improper types) and +cannot be changed after that. Consequently, commands that change such +settings (e.g. :doc:`units `) are only allowed before the box is +defined. Very few commands can be used before and after, like +:doc:`pair_style ` (but not :doc:`pair_coeff `). +Most LAMMPS commands must be used after the simulation box is created. + +Consequently, LAMMPS will stop with an error, if a command is used in +the wrong place. This is not always obvious. So index or string style +:doc:`variables ` can be expanded anywhere in the input, but +equal style (or similar) variables can only be expanded before the box +is defined if they do not reference anything that cannot be defined +before the box (e.g. a compute or fix reference or a thermo keyword). ------ @@ -186,19 +257,20 @@ The header section informs LAMMPS how many entries or lines are expected in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file. If there is a mismatch, LAMMPS will either keep reading beyond the end of a section or stop reading before the section has -ended. In that case the next line will not contain a recognized keyword. +ended. In that case the next line will not contain a recognized +keyword. -Such a mismatch can also happen when the first line of the data -is *not* a comment as required by the format, but a line with a valid -header keyword. That would result in LAMMPS expecting, for instance, -0 atoms because the "atoms" header line is the first line and thus -treated as a comment. +Such a mismatch can also happen when the first line of the data is *not* +a comment as required by the format, but a line with a valid header +keyword. That would result in LAMMPS expecting, for instance, 0 atoms +because the "atoms" header line is the first line and thus treated as a +comment. Another possibility to trigger this error is to have a keyword in the data file that corresponds to a fix (e.g. :doc:`fix cmap `) but the :doc:`read_data ` command is missing the (optional) -arguments that identify the fix and the header keyword and section -keyword or those arguments are inconsistent with the keywords in the +arguments that identify the fix and its header and section keywords. +Alternatively, those arguments are inconsistent with the keywords in the data file. .. _err0002: @@ -208,88 +280,264 @@ Incorrect format in ... section of data file This error happens when LAMMPS reads the contents of a section of a :doc:`data file ` and the number of parameters in the line -differs from what is expected. This most commonly happens, when the -atom style is different from what is expected for a specific data file -since changing the atom style usually changes the format of the line. +differs from what is expected. This most commonly happens when the atom +style is different from what is expected for a specific data file since +changing the atom style usually changes the format of the line. -This error can also happen when the number of entries indicated in the +This error can also occur when the number of entries indicated in the header of a data file (e.g. the number of atoms) is larger than the number of lines provided (e.g. in the corresponding Atoms section) -and then LAMMPS will continue reading into the next section and that -would have a completely different format. +causing LAMMPS to continue reading into the next section which has a +completely different format. .. _err0003: Illegal variable command: expected X arguments but found Y ---------------------------------------------------------- -This error indicates that there are the wrong number of arguments for a -specific variable command, but a common reason for that is a variable -expression that has whitespace but is not enclosed in single or double -quotes. +This error indicates that a variable command has the wrong number of +arguments. A common reason for this is that the variable expression has +whitespace, but is not enclosed in single or double quotes. To explain, the LAMMPS input parser reads and processes lines. The resulting line is broken down into "words". Those are usually -individual commands, labels, names, values separated by whitespace (a -space or tab character). For "words" that may contain whitespace, they -have to be enclosed in single (') or double (") quotes. The parser will -then remove the outermost pair of quotes and then pass that string as +individual commands, labels, names, and values separated by whitespace +(a space or tab character). For "words" that may contain whitespace, +they have to be enclosed in single (') or double (") quotes. The parser +will then remove the outermost pair of quotes and pass that string as "word" to the variable command. -Thus missing quotes or accidental extra whitespace will lead to the -error shown in the header because the unquoted whitespace will result -in the text being broken into more "words", i.e. the variable expression -being split. +Thus missing quotes or accidental extra whitespace will trigger this +error because the unquoted whitespace will result in the text being +broken into more "words", i.e. the variable expression being split. .. _err0004: Out of range atoms - cannot compute ... --------------------------------------- -The PPPM (and also PPPMDisp and MSM) methods require to assemble a grid -of electron density data derived from the (partial) charges assigned to -the atoms. This charges are smeared out across multiple grid points -(see :doc:`kspace_modify order `). When running in -parallel with MPI, LAMMPS uses a :doc:`domain decomposition scheme +The PPPM (and also PPPMDisp and MSM) methods need to assemble a grid of +electron density data derived from the (partial) charges assigned to the +atoms. These charges are smeared out across multiple grid points (see +:doc:`kspace_modify order `). When running in parallel +with MPI, LAMMPS uses a :doc:`domain decomposition scheme ` where each processor manages a subset of atoms and -thus also a grid representing the density, which covers the actual -volume of the sub-domain and some extra space corresponding to the -:doc:`neighbor list skin `. These are then :doc:`combined and -redistributed ` for parallel processing of the -long-range component of the Coulomb interaction. +thus also a grid representing the density. The processor's grid covers +the actual volume of the sub-domain and some extra space corresponding +to the :doc:`neighbor list skin `. These are then +:doc:`combined and redistributed ` for parallel +processing of the long-range component of the Coulomb interaction. -The ``Out of range atoms`` error can happen, when atoms move too fast or -the neighbor list skin is too small or the neighbor lists are not -updated frequently enough. Then the smeared charges cannot be fully +The ``Out of range atoms`` error can happen when atoms move too fast, +the neighbor list skin is too small, or the neighbor lists are not +updated frequently enough. The smeared charges cannot then be fully assigned to the density grid for all atoms. LAMMPS checks for this condition and stops with an error. Most of the time, this is an -indication of a system with very high forces, most often at the -beginning of a simulation or when boundary conditions are changed. The -error becomes more likely with more MPI processes. +indication of a system with very high forces, often at the beginning of +a simulation or when boundary conditions are changed. The error becomes +more likely with more MPI processes. There are multiple options to explore for avoiding the error. The best choice depends strongly on the individual system, and often a combination of changes is required. For example, more conservative MD parameter settings can be used (larger neighbor skin, shorter time step, more frequent neighbor list updates). Sometimes, it helps to revisit -the system generation and avoid close contacts when building it, or use -the :doc:`delete_atoms overlap` command to delete those -close contact atoms, or run a minimization before the MD. It can also -help to temporarily use a cutoff-Coulomb pair style and no kspace style -until the system has somewhat equilibrated and then switch to the -long-range solver. +the system generation and avoid close contacts when building it. +Otherwise one can use the :doc:`delete_atoms overlap` +command to delete those close contact atoms or run a minimization before +the MD. It can also help to temporarily use a cutoff-Coulomb pair style +and no kspace style until the system has somewhat equilibrated and then +switch to the long-range solver. + +.. _err0005: + +Bond (or angle, dihedral, improper, cmap, or shake) atoms missing +----------------------------------------------------------------- + +The second atom needed to compute a particular bond (or the third or +fourth atom for angle, dihedral, or improper) is missing on the +indicated timestep and processor. Typically, this is because the two +bonded atoms have become too far apart relative to the communication +cutoff distance for ghost atoms. By default, the communication cutoff +is set by the pair cutoff. However, to accommodate larger distances +between topologically connected atoms, it can be manually adjusted using +:doc:`comm_modify ` at the cost of increased communication +and more ghost atoms. However, missing bond atoms may also indicate +that there are unstable dynamics which caused the atoms to blow apart. +In this scenario, increasing the communication distance will not solve +the underlying issue. Rather, see :ref:`Fast moving atoms ` and +:ref:`Neighbor list settings ` in the general troubleshooting +section above for ideas to fix unstable dynamics. + +If atoms are intended to be lost during a simulation (e.g. due to open +boundary conditions or :doc:`fix evaporate `) such that +two bonded atoms may be lost at different times from each other, this +error can be converted to a warning or turned off using the *lost/bond* +keyword in the :doc:`thermo_modify ` command. + +.. _err0006: + +Non-numeric atom coords or pressure or box dimensions - simulation unstable +--------------------------------------------------------------------------- + +This error usually occurs due to overly aggressive simulation settings +or issues with the system geometry or the potential. See +:ref:`Pressure, forces, positions becoming NaN or Inf ` above in +the general troubleshooting section. This error is more likely to +happen during equilibration, so it can help to do a minimization before +or even add a second or third minimization after running a few +equilibration MD steps. It also is more likely when directly using a +Nose-Hoover (or other) barostat, and thus it may be advisable to run +with only a thermostat for a bit until the potential energy has +stabilized. + +.. _err007: + +Fix used in ... not computed at compatible time +----------------------------------------------- + +Many fix styles are invoked only every *nevery* timesteps, which means +their data is only valid on those steps. When data from a fix is used +as input for a compute, a dump, another fix, or thermo output, it must +read that data at timesteps when the fix in question was invoked, i.e. +on timesteps that are multiples of its *nevery* setting. If this is not +the case, LAMMPS will stop with an error. To remedy this, it may be +required to change the output frequency or the *nevery* setting of the +fix. + +.. _err0008: + +Lost atoms ... +-------------- + +A simulation stopping with an error due to lost atoms can have multiple +causes. By default, LAMMPS checks for whether the total number of atoms +is consistent with the sum of atoms "owned" by MPI processors every time +that thermodynamic output is written. In the majority of cases, lost +atoms are unexpected and a result of extremely high velocities causing +instabilities in the system. Such velocities can result from a variety +of issues. For ideas on how to track down issues with unexpected lost +atoms, see :ref:`Fast moving atoms ` and :ref:`Neighbor list +settings ` in the general troubleshooting section above. In +specific situations however, losing atoms is expected material behavior +(e.g. with sputtering and surface evaporation simulations), and an +unwanted crash can be avoided by changing the :doc:`thermo_modify lost +` keyword from the default 'error' to 'warn' or 'ignore' +(though heed the advice in :ref:`Ignoring lost atoms ` above!). .. _err0009: Too many neighbor bins ---------------------- -The simulation box has become too large relative to the size of a -neighbor bin and LAMMPS is unable to store the needed number of -bins. This typically implies the simulation box has expanded too far. -This can happen when some atoms move rapidly apart with shrink-wrap -boundaries or when a fix (like fix deform or a barostat) excessively -grows the simulation box. +The simulation box is or has become too large relative to the size of a +neighbor bin (which in turn depends on the largest pair-wise cutoff by +default) such that LAMMPS is unable to store the needed number of bins. +This typically implies the simulation box has expanded too far. That +can occur when some atoms move rapidly apart with shrink-wrap boundaries +or when a fix (like fix deform or a barostat) excessively grows the +simulation box. This can also happen if the largest pair-wise cutoff is +small. In this case, the error can be avoided by using the +:doc:`neigh_modify command ` to set the bin width to a +suitably large value. + +.. _err0010: + +Unrecognized ... style ... is part of ... package which is not enabled in this LAMMPS binary +-------------------------------------------------------------------------------------------- + +The LAMMPS executable (binary) being used was not compiled with a +package containing the specified style. This indicates that the +executable needs to be re-built after enabling the correct package in +the relevant Makefile or CMake build directory. See +:doc:`Section 3. Build LAMMPS ` for more details. One can check +if the expected package and pair style is present in the executable by +running it with the ``-help`` (or ``-h``) flag on the command line. One +common oversight, especially for beginner LAMMPS users, is enabling the +package but forgetting to run commands to rebuild (e.g., to run the +final ``make`` or ``cmake`` command). + +If this error occurs with an executable that the user does not control +(e.g., through a module on HPC clusters), the user will need to get in +contact with the relevant person or people who can update the +executable. + +.. _err011: + +Energy or stress was not tallied by pair style +---------------------------------------------- + +This warning can be printed by computes from the :ref:`TALLY package +`. Those use a callback mechanism that only work for regular +pair-wise additive pair styles like :doc:`Lennard-Jones `, +:doc:`Morse `, :doc:`Born-Meyer-Huggins `, and +similar. Such required callbacks have not been implemented for +many-body potentials so one would have to implement them to add +compatibility with these computes (which may be difficult to do in a +generic fashion). Whether this warning indicates that contributions to +the computed properties are missing depends on the groups used. At any +rate, careful testing of the results is advised when this warning +appears. + +.. _err0012: + +fmt::format_error +----------------- + +LAMMPS uses the `{fmt} library `_ for advanced string +formatting tasks. This is similar to the ``printf()`` family of +functions from the standard C library, but more flexible. If there is a +bug in the LAMMPS code and the format string does not match the list of +arguments or has some other error, this error message will be shown. +You should contact the LAMMPS developers and report the bug as a `GitHub +Bug Report Issue `_ along with +sufficient information to easily reproduce it. + + +.. _err0013: + +Substitution for illegal variable +--------------------------------- + +A variable in an input script or a variable expression was not found in +the list of valid variables. The most common reason for this is a typo +somewhere in the input file such that the expression uses an invalid +variable name. The second most common reason is omitting the curly +braces for a direct variable with a name that is not a single letter. +For example: + +.. code-block:: LAMMPS + + variable cutoff index 10.0 + pair_style lj/cut ${cutoff} # this is correct + pair_style lj/cut $cutoff # this is incorrect, LAMMPS looks for 'c' instead of 'cutoff' + variable c index 5.0 # if $c is defined, LAMMPS subsitutes only '$c' and reads: 5utoff + +Another potential source of this error may be invalid command line +variables (-var or -v argument) used when launching LAMMPS from an +interactive shell or shell scripts. An uncommon source for this error +is using the :doc:`next command ` to advance through a list of +values provided by an index style variable. If there is no remaining +element in the list, LAMMPS will delete the variable and any following +expansion or reference attempt will trigger the error. + +Users with harder-to-track variable errors might also find reading the +:doc:`Parsing rules for input scripts ` helpful. + +.. _err0014: + +Bond atom missing in image check or box size check +-------------------------------------------------- + +This can be either an error or a warning depending on your +:doc:`thermo_modify settings `. It is flagged in a part +of the LAMMPS code where it updates the domain decomposition and before +it builds the neighbor lists. It checks that both atoms of a bond are +within the communication cutoff of a subdomain. It is usually caused by +atoms moving too fast (see the :ref:`paragraph on fast moving atoms +`), or by the :doc:`communication cutoff being too small +`, or by waiting too long between :doc:`sub-domain and +neighbor list updates `. .. _err0015: @@ -297,25 +545,210 @@ Cannot use neighbor bins - box size \<\< cutoff ----------------------------------------------- LAMMPS is unable to build neighbor bins since the size of the box is -much smaller than an interaction cutoff in at least one of its dimensions. -Typically, this error is triggered when the simulation box has one very -thin dimension. If a cubic neighbor bin had to fit exactly within -the thin dimension, then an inordinate amount of bins would be created to -fill space. This error can be avoided using the generally slower -:doc:`nsq neighbor style ` or by increasing the size of the -smallest box lengths. +much smaller than an interaction cutoff in at least one of its +dimensions. Typically, this error is triggered when the simulation box +has one very thin dimension. If a cubic neighbor bin had to fit exactly +within the thin dimension, then an inordinate amount of bins would be +created to fill space. This error can be avoided using the generally +slower :doc:`nsq neighbor style ` or by increasing the size of +the smallest box lengths. + +.. _err0016: + +Did not assign all atoms correctly +---------------------------------- + +This error happens most commonly when :doc:`reading a data file +` under :doc:`non-periodic boundary conditions`. +Only atoms with positions **inside** the simulation box will be read and +thus any atoms outside the box will be skipped and the total atom count +will not match, which triggers the error. This does not happen with +periodic boundary conditions where atoms outside the principal box will +be "wrapped" into the principal box and their image flags set +accordingly. + +Similar errors can happen with the :doc:`replicate command` +or the :doc:`read_restart command`. In these cases the +cause may be a problematic geometry, an insufficient communication +cutoff, or a bug in the LAMMPS source code. In these cases it is +advisable to set up :ref:`small test case ` for testing and +debugging. This will be required in case you need to get help from a +LAMMPS developer. .. _err0017: Domain too large for neighbor bins ---------------------------------- -The domain has become extremely large so that neighbor bins cannot -be used. Too many neighbor bins would need to be created to fill space -Most likely, one or more atoms have been blown out of the simulation -box to a great distance or a fix (like fix deform or a barostat) has +The domain has become extremely large so that neighbor bins cannot be +used. Too many neighbor bins would need to be created to fill space. +Most likely, one or more atoms have been blown a great distance out of +the simulation box or a fix (like fix deform or a barostat) has excessively grown the simulation box. +.. _err0018: + +Step X: (h)bondchk failed +------------------------- + +This error is a consequence of the heuristic memory allocations for +buffers of the regular ReaxFF version. In ReaxFF simulations, the lists +of bonds and hydrogen bonds can change due to chemical reactions. The +default approach, however, assumes that these changes are not very +large, so it allocates buffers for the current system setup plus a +safety margin. This can be adjusted with the :doc:`safezone, mincap, +and minhbonds settings of the pair style `, but only to +some extent. When equilibrating a new system, or simulating a sparse +system in parallel, this can be difficult to control and become +wasteful. A simple workaround is often to break a simulation down in +multiple chunks. A better approach, however, is to compile and use the +KOKKOS package version of ReaxFF (you do not need a GPU for that, but +can also compile it in serial or OpenMP mode), which uses a more robust +memory allocation approach. + +.. _err0019: + +Numeric index X is out of bounds +-------------------------------- + +This error most commonly happens when setting force field coefficients +with either the :doc:`pair_coeff `, the :doc:`bond_coeff +`, the :doc:`angle_coeff `, the +:doc:`dihedral_coeff `, or the :doc:`improper_coeff +` command. These commands accept type labels, explicit +numbers, and wildcards for ranges of numbers. If the numeric value of +any of these is outside the valid range (defined by the number of +corresponding types), LAMMPS will stop with this error. A few other +commands and styles also allow ranges of numbers and check using the +same method and thus print the same kind of error. + +The cause is almost always a typo in the input or a logic error when +defining the values or ranges. So one needs to carefully review the +input. Along with the error, LAMMPS will print the valid range as a +hint. + +.. _err0020: + +Compute, fix, or variable vector or array is accessed out-of-range +------------------------------------------------------------------ + +When accessing an individual element of a global vector or array or a +per-atom vector or array provided by a compute or fix or atom-style or +vector-style variable or data from a specific atom, an index in square +brackets ("[ ]") (or two indices) must be provided to determine which +element to access and it must be in a valid range or else LAMMPS would +access invalid data or crash with a segmentation fault. In the two most +common cases, where this data is accessed, :doc:`variable expressions +` and :doc:`thermodynamic output `, LAMMPS will +check for valid indices and stop with an error otherwise. + +While LAMMPS is written in C++ (which uses 0 based indexing) these +indices start at 1 (i.e. similar to Fortran). Any index smaller than 1 +or larger than the maximum allowed value should trigger this error. +Since this kind of error frequently happens with rather complex +expressions, it is recommended to test these with small test systems, +where the values can be tracked with output files for all relevant +properties at every step. + +.. _err0021: + +Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients) +------------------------------------------------------------------------------------- + +The parameters in the :doc:`pair_coeff ` command for a +specified :doc:`pair_style ` have a missing or erroneous +argument. The same applies when seeing this error for :doc:`bond_coeff +`, :doc:`angle_coeff `, :doc:`dihedral_coeff +`, or :doc:`improper_coeff ` and their +respective style commands when using the MOLECULE or EXTRA-MOLECULE +packages. The cases below describe some ways to approach pair +coefficient errors, but the same strategies apply to bonded systems as +well. + +Outside of normal typos, this error can have several sources. In all +cases, the first step is to compare the command arguments to the +expected format found in the corresponding :doc:`pair_style +` page. This can reveal cases where, for example, a pair +style was changed, but the pair coefficients were not updated. This can +happen especially with pair style variants such as :doc:`pair_style eam +` vs. :doc:`pair_style eam/alloy ` that look very +similar but accept different parameters (the latter 'eam/alloy' variant +takes element type names while 'eam' does not). + +Another common source of coefficient errors is when using multiple pair +styles with commands such as :doc:`pair_style hybrid `. +Using hybrid pair styles requires adding an extra "label" argument in +the coefficient commands that designates which pair style the command +line refers to. Moreover, if the same pair style is used multiple +times, this label must be followed by an additional numeric argument. +Also, different pair styles may require different arguments. + +This error message might also require a close look at other LAMMPS input +files that are read in by the input script, such as data files or +restart files. + +.. _err0022: + +Energy was not tallied on needed timestep (also virial, per-atom energy, per-atom virial) +----------------------------------------------------------------------------------------- + +This error is generated when LAMMPS attempts to access an out-of-date or +non-existent energy, pressure, or virial. For efficiency reasons, +LAMMPS does *not* calculate these quantities when the forces are +calculated on every timestep or iteration. Global quantities are only +calculated when they are needed for :doc:`thermo ` output +(at the beginning, end, and at regular intervals specified by the +:doc:`thermo ` command). Similarly, per-atom quantities are +only calculated if they are needed to write per-atom energy or virial to +a dump file. This system works fine for simple input scripts. However, +the many user-specified `variable`, `fix`, and `compute` commands that +LAMMPS provides make it difficult to anticipate when a quantity will be +requested. In some use cases, LAMMPS will figure out that a quantity is +needed and arrange for it to be calculated on that timestep e.g. if it +is requested by :doc:`fix ave/time ` or similar commands. +If that fails, it can be detected by a mismatch between the current +timestep and when a quantity was last calculated, in which case an error +message of this type is generated. + +The most common cause of this type of error is requesting a quantity +before the start of the simulation. + +.. code-block:: LAMMPS + + # run 0 post no # this will fix the error + variable e equal pe # requesting energy compute + print "Potential energy = $e" # this will generate the error + run 1000 # start of simulation + +This situation can be avoided by adding in a "run 0" command, as +explained in more detail in the "Variable Accuracy" section of the +:doc:`variable ` doc page. + +Another cause is requesting a quantity on a timestep that is not a +thermo or dump output timestep. This can often be remedied by +increasing the frequency of thermo or dump output. + +.. _err0023: + +Molecule auto special bond generation overflow +---------------------------------------------- + +In order to correctly apply the :doc:`special_bonds ` +settings (also known as "exclusions"), LAMMPS needs to maintain for each +atom a list of atoms that are connected to this atom, either directly +with a bond or indirectly through bonding with an intermediate atom(s). +The purpose is to either remove or tag those pairs of atoms in the +neighbor list. This information is stored with individual atoms and +thus the maximum number of such "special" neighbors is set when the +simulation box is created. When reading (relative) geometry and +topology of a 'molecule' from a :doc:`molecule file `, LAMMPS +will build the list of such "special" neighbors for the molecule atom +(if not given in the molecule file explicitly). The error is triggered +when the resulting list is too long for the space reserved when creating +the simulation box. The solution is to increase the corresponding +setting. Overestimating this value will only consume more memory, and +is thus a safe choice. + .. _err0024: Molecule topology/atom exceeds system topology/atom @@ -323,13 +756,13 @@ Molecule topology/atom exceeds system topology/atom LAMMPS uses :doc:`domain decomposition ` to distribute data (i.e. atoms) across the MPI processes in parallel runs. -This includes topology data, that is data about bonds, angles, -dihedrals, impropers and :doc:`"special" neighbors `. -This information is stored with either one or all atoms involved in such -a topology entry (which of the two option applies depends on the -:doc:`newton ` setting for bonds. When reading a data file, -LAMMPS analyzes the requirements for this file and then the values -are "locked in" and cannot be extended. +This includes topology data about bonds, angles, dihedrals, impropers +and :doc:`"special" neighbors `. This information is +stored with either one or all atoms involved in such a topology entry +(which of the two option applies depends on the :doc:`newton ` +setting for bonds). When reading a data file, LAMMPS analyzes the +requirements for this file and then the values are "locked in" and +cannot be extended. So loading a molecule file that requires more of the topology per atom storage or adding a data file with such needs will lead to an error. To @@ -345,10 +778,10 @@ Molecule topology type exceeds system topology type --------------------------------------------------- The total number of atom, bond, angle, dihedral, and improper types is -"locked in" when LAMMPS creates the simulation box. This can happen +"locked in" when LAMMPS creates the simulation box. This can happen through either the :doc:`create_box `, the :doc:`read_data `, or the :doc:`read_restart ` command. After -this it is not possible to refer to an additional type. So loading a +this it is not possible to refer to an additional type. So loading a molecule file that uses additional types or adding a data file that would require additional types will lead to an error. To avoid the error, one or more of the `extra/XXX/types` keywords are required to @@ -367,3 +800,185 @@ example, are usually not a per-atom property, but defined through the atom type. Thus it would not be required to have a Masses section and the included data would be ignored. LAMMPS prints this warning to inform about this case. + +.. _err0027: + +Inconsistent image flags +------------------------ + +This warning happens when the distance between the *unwrapped* x-, y-, +or z-components of the coordinates of a bond is larger than half the box +with periodic boundaries or larger than the box with non-periodic +boundaries. It means that the positions and image flags have become +inconsistent. LAMMPS will still compute bonded interactions based on +the closest periodic images of the atoms and thus in most cases the +results will be correct. However they can cause problems when such +atoms are used with the fix rigid or replicate commands. Thus, it is +good practice to update the system so that the message does not appear. +It will help with future manipulations of the system. + +There is one case where this warning *must* appear: when you have a +chain of connected bonds that pass through the entire box and connect +back to the first atom in the chain through periodic boundaries, +i.e. some kind of "infinite polymer". In that case, the bond image +flags *must* be inconsistent for the one bond that reaches back to the +beginning of the chain. + + +.. _err0028: + +No fixes with time integration, atoms won't move +------------------------------------------------ + +This warning will be issued if LAMMPS encounters a :doc:`run ` +command that does not have a preceding :doc:`fix ` command that +updates atom/object positions and velocities per step. In other words, +there are no fixes detected that perform velocity-Verlet time +integration, such as :doc:`fix nve `. Note that this alert +does not mean that there are no active fixes. LAMMPS has a very wide +variety of fixes, many of which do not move objects but also operate +through steps, such as printing outputs (e.g. :doc:`fix print +`), performing calculations (e.g. :doc:`fix ave/time +`), or changing other system parameters (e.g. :doc:`fix +dt/reset `). It is up to the user to determine whether +the lack of a time-integrating fix is intentional or not. + + +.. _err0029: + +System is not charge neutral, net charge = ... +---------------------------------------------- + +the sum of charges in the system is not zero. When a system is not +charge-neutral, methods that evolve/manipulate per-atom charges, +evaluate Coulomb interactions, evaluate Coulomb forces, or +evaluate/manipulate other properties relying on per-atom charges may +raise this warning. A non-zero net charge most commonly arises after +setting per-atom charges :doc:`set ` such that the sum is non-zero +or by reading in a system through :doc:`read_data ` where the +per-atom charges do not sum to zero. However, a loss of charge +neutrality may occur in other less common ways, like when charge +equilibration methods (e.g., :doc:`fix qeq `) fail. + +A similar warning/error may be raised when using certain charge +equilibration methods: :doc:`fix qeq `, :doc:`fix qeq/comb +`, :doc:`fix qeq/reaxff `, and :doc:`fix +qtpie/reaxff `. In such cases, this warning/error +will be raised for the fix :doc:`group ` when the group has a +non-zero net charge. + +When the system is expected to be charge-neutral, this warning often +arises due to an error in the lammps input (e.g., an incorrect :doc:`set +` command, error in the data file read by :doc:`read_data +`, incorrectly grouping atoms with charge, etc.). If the +system is NOT expected to be charge-neutral, the user should make sure +that the method(s) used are appropriate for systems with a non-zero net +charge. Some commonly used fixes for charge equilibration :doc:`fix qeq +`, pair styles that include charge interactions +:doc:`pair_style coul/XXX `, and kspace methods +:doc:`kspace_style ` can, in theory, support systems with +non-zero net charge. However, non-zero net charge can lead to spurious +artifacts. The severity of these artifacts depends on the magnitude of +total charge, system size, and methods used. Before running simulations +or calculations for systems with non-zero net charge, users should test +for artifacts and convergence of properties. + +.. _err0030: + +Variable evaluation before simulation box is defined +---------------------------------------------------- + +This error happens, when trying to expand or use an equal- or atom-style +variable (or an equivalent style), where the expression contains a +reference to something (e.g. a compute reference, a property of an atom, +or a thermo keyword) that is not allowed to be used before the +simulation box is defined. See the paragraph on :ref:`errors before or +after the simulation box is created ` for additional +information. + +.. _err0031: + +Invalid thermo keyword 'X' in variable formula +---------------------------------------------- + +This error message is often misleading. It is caused when evaluating a +:doc:`variable command ` expression and LAMMPS comes across a +string that it does not recognize. LAMMPS first checks if a string is a +reference to a compute, fix, custom property, or another variable by +looking at the first 2-3 characters (and if it is, it checks whether the +referenced item exists). Next LAMMPS checks if the string matches one +of the available functions or constants. If that fails, LAMMPS will +assume that this string is a :doc:`thermo keyword ` and +let the code for printing thermodynamic output return the corresponding +value. However, if this fails too, since the string is not a thermo +keyword, LAMMPS stops with the 'Invalid thermo keyword' error. But it +is also possible, that there is just a typo in the name of a valid +variable function. Thus it is recommended to check the failing variable +expression very carefully. + +.. _err0032: + +One or more atoms are time integrated more than once +---------------------------------------------------- + +This is probably an error since you typically do not want to advance the +positions or velocities of an atom more than once per timestep. This +typically happens when there are multiple fix commands that advance atom +positions with overlapping groups. Also, for some fix styles it is not +immediately obvious that they include time integration. Please check +the documentation carefully. + +.. _err0033: + +XXX command before simulation box is defined +-------------------------------------------- + +This error occurs when trying to execute a LAMMPS command that requires +information about the system dimensions, or the number atom, bond, +angle, dihedral, or improper types, or the number of atoms or similar +data that is only available *after* the simulation box has been created. +See the paragraph on :ref:`errors before or after the simulation box is +created ` for additional information. + +.. _err0034: + +XXX command after simulation box is defined +-------------------------------------------- + +This error occurs when trying to execute a LAMMPS command that changes a +global setting *after* it is locked in when the simulation box is +created (for instance defining the :doc:`atom style `, +:doc:`dimension `, :doc:`newton `, or :doc:`units +` setting). These settings may only be changed *before* the +simulation box has been created. See the paragraph on :ref:`errors +before or after the simulation box is created ` for additional +information. + +.. _err0035: + +Error messages ending in 'Please contact the LAMMPS developers' +--------------------------------------------------------------- + +Such error messages indicate that something unexpected has happened and +that it will require a good understanding of the details of the design +of LAMMPS to resolve this. This can be due to some bug in contributed +code, and oversight when updating functionality, a feature that is +scheduled to be removed or reaching a combination of flags and settings +that should not be possible or similar. + +Even if you find a way to work around this error or warning, you should +contact the LAMMPS developers and prepare a minimal set of inputs that +can be used to reproduce this error or warning. By providing the input, +the LAMMPS developers can then assess whether additional action is +needed and who else to contact about this, if needed. + +There are multiple ways to get into contact and report your issue. In +order of preference there are: + +- Submit a bug report `issue in the LAMMPS GitHub + ` repository +- Post a message in the "LAMMPS Development" forum in the + `MatSci Community Discourse `_ +- Send an email to ``developers@lammps.org`` +- Send an email to an :doc:`individual LAMMPS developer ` + that you know and trust diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index bfc395067a..d1318ceffe 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -1,11 +1,15 @@ Error messages ============== -This is an alphabetic list of the ERROR messages LAMMPS prints out and -the reason why. If the explanation here is not sufficient, the -documentation for the offending command may help. Error messages also -list the source file and line number where the error was generated. -For example, a message like this: +This is an alphabetic list of some of the ERROR messages LAMMPS prints +out and the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. This is a historic +list and no longer updated. Instead the LAMMPS developers are trying +to provide more details right with the error message or link to a +paragraph with :doc:`detailed explanations `. + +Error messages also list the source file and line number where the error +was generated. For example, a message like this: .. parsed-literal:: @@ -14,20 +18,10 @@ For example, a message like this: means that line #78 in the file src/velocity.cpp generated the error. Looking in the source code may help you figure out what went wrong. -Doc page with :doc:`WARNING messages ` +Please also see the page with :doc:`Warning messages `. ---------- -*1-3 bond count is inconsistent* - An inconsistency was detected when computing the number of 1-3 - neighbors for each atom. This likely means something is wrong with - the bond topologies you have defined. - -*1-4 bond count is inconsistent* - An inconsistency was detected when computing the number of 1-4 - neighbors for each atom. This likely means something is wrong with - the bond topologies you have defined. - *Accelerator sharing is not currently supported on system* Multiple MPI processes cannot share the accelerator on your system. For NVIDIA GPUs, see the nvidia-smi command to change this @@ -37,15 +31,6 @@ Doc page with :doc:`WARNING messages ` All angle coefficients must be set in the data file or by the angle_coeff command before running a simulation. -*All atom IDs = 0 but atom_modify id = yes* - Self-explanatory. - -*All atoms of a swapped type must have same charge.* - Self-explanatory. - -*All atoms of a swapped type must have the same charge.* - Self-explanatory. - *All bond coeffs are not set* All bond coefficients must be set in the data file or by the bond_coeff command before running a simulation. @@ -79,12 +64,6 @@ Doc page with :doc:`WARNING messages ` the x,y,z fields, else LAMMPS cannot reconstruct the unscaled coordinates. -*All universe/uloop variables must have same # of values* - Self-explanatory. - -*All variables in next command must be same style* - Self-explanatory. - *Angle atom missing in delete_bonds* The delete_bonds command cannot find one or more atoms in a particular angle on a particular processor. The pairwise cutoff is too short or @@ -95,18 +74,6 @@ Doc page with :doc:`WARNING messages ` a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid angle. -*Angle atoms %d %d %d missing on proc %d at step %ld* - One or more of three atoms needed to compute a particular angle are - missing on this processor. Typically this is because the pairwise - cutoff is set too short or the angle has blown apart and an atom is - too far away. - -*Angle atoms missing on proc %d at step %ld* - One or more of three atoms needed to compute a particular angle are - missing on this processor. Typically this is because the pairwise - cutoff is set too short or the angle has blown apart and an atom is - too far away. - *Angle coeff for hybrid has invalid style* Angle style hybrid uses another angle style as one of its coefficients. The angle style used in the angle_coeff command or read @@ -124,18 +91,6 @@ Doc page with :doc:`WARNING messages ` *Angle potential must be defined for SHAKE* When shaking angles, an angle_style potential must be used. -*Angle style hybrid cannot have hybrid as an argument* - Self-explanatory. - -*Angle style hybrid cannot have none as an argument* - Self-explanatory. - -*Angle style hybrid cannot use same angle style twice* - Self-explanatory. - -*Angle table must range from 0 to 180 degrees* - Self-explanatory. - *Angle table parameters did not set N* List of angle table parameters must include N setting. @@ -171,27 +126,6 @@ Doc page with :doc:`WARNING messages ` *Arcsin of invalid value in variable formula* Argument of arcsin() must be between -1 and 1. -*Assigning body parameters to non-body atom* - Self-explanatory. - -*Assigning ellipsoid parameters to non-ellipsoid atom* - Self-explanatory. - -*Assigning line parameters to non-line atom* - Self-explanatory. - -*Assigning quat to non-body atom* - Self-explanatory. - -*Assigning tri parameters to non-tri atom* - Self-explanatory. - -*At least one atom of each swapped type must be present to define charges.* - Self-explanatory. - -*Atom IDs must be consecutive for velocity create loop all* - Self-explanatory. - *Atom IDs must be used for molecular systems* Atom IDs are used to identify and find partner atoms in bonds. @@ -215,21 +149,12 @@ Doc page with :doc:`WARNING messages ` This is an internal LAMMPS error. Please report it to the developers. -*Atom style hybrid cannot have hybrid as an argument* - Self-explanatory. - -*Atom style hybrid cannot use same atom style twice* - Self-explanatory. - *Atom style template molecule must have atom types* The defined molecule(s) does not specify atom types. *Atom style was redefined after using fix property/atom* This is not allowed. -*Atom type must be zero in fix gcmc mol command* - Self-explanatory. - *Atom vector in equal-style variable formula* Atom vectors generate one value per atom which is not allowed in an equal-style variable. @@ -246,28 +171,13 @@ Doc page with :doc:`WARNING messages ` The atom_modify map command cannot be used after a read_data, read_restart, or create_box command. -*Atom_modify sort and first options cannot be used together* - Self-explanatory. - *Atom_style command after simulation box is defined* The atom_style command cannot be used after a read_data, read_restart, or create_box command. -*Atom_style line can only be used in 2d simulations* - Self-explanatory. - -*Atom_style tri can only be used in 3d simulations* - Self-explanatory. - *Atomfile variable could not read values* Check the file assigned to the variable. -*Atomfile variable in equal-style variable formula* - Self-explanatory. - -*Atomfile-style variable in equal-style variable formula* - Self-explanatory. - *Attempt to pop empty stack in fix box/relax* Internal LAMMPS error. Please report it to the developers. @@ -277,9 +187,6 @@ Doc page with :doc:`WARNING messages ` *Attempting to rescale a 0.0 temperature* Cannot rescale a temperature that is already 0.0. -*Attempting to insert more particles than available lattice points* - Self-explanatory. - *Bad FENE bond* Two atoms in a FENE bond have become so far apart that the bond cannot be computed. @@ -386,26 +293,11 @@ Doc page with :doc:`WARNING messages ` bond on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid bond. -*Bond atom missing in image check* - The second atom in a particular bond is missing on this processor. - Typically this is because the pairwise cutoff is set too short or the - bond has blown apart and an atom is too far away. - *Bond atom missing in set command* The set command cannot find one or more atoms in a particular bond on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid bond. -*Bond atoms %d %d missing on proc %d at step %ld* - The second atom needed to compute a particular bond is missing on this - processor. Typically this is because the pairwise cutoff is set too - short or the bond has blown apart and an atom is too far away. - -*Bond atoms missing on proc %d at step %ld* - The second atom needed to compute a particular bond is missing on this - processor. Typically this is because the pairwise cutoff is set too - short or the bond has blown apart and an atom is too far away. - *Bond coeff for hybrid has invalid style* Bond style hybrid uses another bond style as one of its coefficients. The bond style used in the bond_coeff command or read from a restart @@ -423,15 +315,6 @@ Doc page with :doc:`WARNING messages ` *Bond potential must be defined for SHAKE* Cannot use fix shake unless bond potential is defined. -*Bond style hybrid cannot have hybrid as an argument* - Self-explanatory. - -*Bond style hybrid cannot have none as an argument* - Self-explanatory. - -*Bond style hybrid cannot use same bond style twice* - Self-explanatory. - *Bond style quartic cannot be used with 3,4-body interactions* No angle, dihedral, or improper styles can be defined when using bond style quartic. @@ -476,12 +359,6 @@ Doc page with :doc:`WARNING messages ` *Bonds defined but no bond types* The data file header lists bonds but no bond types. -*Both restart files must use % or neither* - Self-explanatory. - -*Both restart files must use MPI-IO or neither* - Self-explanatory. - *Both sides of boundary must be periodic* Cannot specify a boundary as periodic only on the lo or hi side. Must be periodic on both sides. @@ -510,21 +387,6 @@ Doc page with :doc:`WARNING messages ` Only triclinic boxes can be used with off-diagonal pressure components. See the region prism command for details. -*Can only use -plog with multiple partitions* - Self-explanatory. See page discussion of command-line switches. - -*Can only use -pscreen with multiple partitions* - Self-explanatory. See page discussion of command-line switches. - -*Can only use Kokkos supported regions with Kokkos package* - Self-explanatory. - -*Can only use NEB with 1-processor replicas* - This is current restriction for NEB as implemented in LAMMPS. - -*Can only use TAD with 1-processor replicas for NEB* - This is current restriction for NEB as implemented in LAMMPS. - *Cannot (yet) do analytic differentiation with pppm/gpu* This is a current restriction of this command. @@ -561,18 +423,6 @@ Doc page with :doc:`WARNING messages ` *Cannot (yet) use kspace_style pppm/stagger with triclinic systems* This feature is not yet supported. -*Cannot (yet) use molecular templates with Kokkos* - Self-explanatory. - -*Cannot (yet) use respa with Kokkos* - Self-explanatory. - -*Cannot (yet) use rigid bodies with fix deform and Kokkos* - Self-explanatory. - -*Cannot (yet) use rigid bodies with fix nh and Kokkos* - Self-explanatory. - *Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)* Single precision cannot be used with MSM. @@ -583,9 +433,6 @@ Doc page with :doc:`WARNING messages ` The simulation box must be defined with edges aligned with the Cartesian axes. -*Cannot balance in z dimension for 2d simulation* - Self-explanatory. - *Cannot change box ortho/triclinic with certain fixes defined* This is because those fixes store the shape of the box. You need to use unfix to discard the fix, change the box, then redefine a new @@ -599,12 +446,6 @@ Doc page with :doc:`WARNING messages ` *Cannot change box tilt factors for orthogonal box* Cannot use tilt factors unless the simulation box is non-orthogonal. -*Cannot change box to orthogonal when tilt is non-zero* - Self-explanatory. - -*Cannot change box z boundary to non-periodic for a 2d simulation* - Self-explanatory. - *Cannot change dump_modify every for dump dcd* The frequency of writing dump dcd snapshots cannot be changed. @@ -619,20 +460,11 @@ Doc page with :doc:`WARNING messages ` This is because fix pour pre-computes the time delay for particles to fall out of the insertion volume due to gravity. -*Cannot change to comm_style brick from tiled layout* - Self-explanatory. - *Cannot change_box after reading restart file with per-atom info* This is because the restart file info cannot be migrated with the atoms. You can get around this by performing a 0-timestep run which will assign the restart file info to actual atoms. -*Cannot change_box in xz or yz for 2d simulation* - Self-explanatory. - -*Cannot change_box in z dimension for 2d simulation* - Self-explanatory. - *Cannot clear group all* This operation is not allowed. @@ -668,27 +500,6 @@ Doc page with :doc:`WARNING messages ` *Cannot currently use pair reax with pair hybrid* This is not yet supported. -*Cannot currently use pppm/gpu with fix balance.* - Self-explanatory. - -*Cannot delete group all* - Self-explanatory. - -*Cannot delete group currently used by a compute* - Self-explanatory. - -*Cannot delete group currently used by a dump* - Self-explanatory. - -*Cannot delete group currently used by a fix* - Self-explanatory. - -*Cannot delete group currently used by atom_modify first* - Self-explanatory. - -*Cannot delete_atoms bond yes for non-molecular systems* - Self-explanatory. - *Cannot displace_atoms after reading restart file with per-atom info* This is because the restart file info cannot be migrated with the atoms. You can get around this by performing a 0-timestep run which @@ -702,9 +513,6 @@ Doc page with :doc:`WARNING messages ` This is a restriction due to the way atoms are organized in a list to enable the atom_modify first command. -*Cannot dump sort on atom IDs with no atom IDs defined* - Self-explanatory. - *Cannot dump sort when multiple dump files are written* In this mode, each processor dumps its atoms to a file, so no sorting is allowed. @@ -717,30 +525,15 @@ Doc page with :doc:`WARNING messages ` This is a restriction due to the way atoms are organized in a list to enable the atom_modify first command. -*Cannot find create_bonds group ID* - Self-explanatory. - *Cannot find delete_bonds group ID* Group ID used in the delete_bonds command does not exist. -*Cannot find specified group ID for core particles* - Self-explanatory. - -*Cannot find specified group ID for shell particles* - Self-explanatory. - *Cannot have both pair_modify shift and tail set to yes* These 2 options are contradictory. *Cannot intersect groups using a dynamic group* This operation is not allowed. -*Cannot mix molecular and molecule template atom styles* - Self-explanatory. - -*Cannot open -reorder file* - Self-explanatory. - *Cannot open ADP potential file %s* The specified ADP potential file cannot be opened. Check that the path and name are correct. @@ -801,16 +594,10 @@ Doc page with :doc:`WARNING messages ` The specified Vashishta potential file cannot be opened. Check that the path and name are correct. -*Cannot open balance output file* - Self-explanatory. - *Cannot open coul/streitz potential file %s* The specified coul/streitz potential file cannot be opened. Check that the path and name are correct. -*Cannot open custom file* - Self-explanatory. - *Cannot open data file %s* The specified file cannot be opened. Check that the path and name are correct. @@ -819,9 +606,6 @@ Doc page with :doc:`WARNING messages ` Using a "\*" in the name of the restart file will open the current directory to search for matching file names. -*Cannot open dump file* - Self-explanatory. - *Cannot open dump file %s* The output file for the dump command cannot be opened. Check that the path and name are correct. @@ -851,9 +635,6 @@ Doc page with :doc:`WARNING messages ` The specified file cannot be opened. Check that the path and name are correct. -*Cannot open fix balance output file* - Self-explanatory. - *Cannot open fix poems file %s* The specified file cannot be opened. Check that the path and name are correct. @@ -897,9 +678,6 @@ Doc page with :doc:`WARNING messages ` LAMMPS was compiled without support for reading and writing gzipped files through a pipeline to the gzip program with -DLAMMPS_GZIP. -*Cannot open input script %s* - Self-explanatory. - *Cannot open log.cite file* This file is created when you use some LAMMPS features, to indicate what paper you should cite on behalf of those who implemented @@ -934,15 +712,6 @@ Doc page with :doc:`WARNING messages ` The specified polymorphic potential file cannot be opened. Check that the path and name are correct. -*Cannot open print file %s* - Self-explanatory. - -*Cannot open processors output file* - Self-explanatory. - -*Cannot open restart file %s* - Self-explanatory. - *Cannot open restart file for reading - MPI error: %s* This error was generated by MPI when reading/writing an MPI-IO restart file. @@ -956,9 +725,6 @@ Doc page with :doc:`WARNING messages ` opened. Check that the directory you are running in allows for files to be created. -*Cannot open temporary file for world counter.* - Self-explanatory. - *Cannot open universe log file* For a multi-partition run, the master log file cannot be opened. Check that the directory you are running in allows for files to be @@ -973,9 +739,6 @@ Doc page with :doc:`WARNING messages ` This error was generated by MPI when reading/writing an MPI-IO restart file. -*Cannot read_data without add keyword after simulation box is defined* - Self-explanatory. - *Cannot read_restart after simulation box is defined* The read_restart command cannot be used after a read_data, read_restart, or create_box command. @@ -1017,40 +780,10 @@ Doc page with :doc:`WARNING messages ` all together (pair), or in pieces (inner/middle/outer). You can't do both. -*Cannot set cutoff/multi before simulation box is defined* - Self-explanatory. - -*Cannot set dpd/theta for this atom style* - Self-explanatory. - -*Cannot set dump_modify flush for dump xtc* - Self-explanatory. - *Cannot set mass for this atom style* This atom style does not support mass settings for each atom type. Instead they are defined on a per-atom basis in the data file. -*Cannot set meso/cv for this atom style* - Self-explanatory. - -*Cannot set meso/e for this atom style* - Self-explanatory. - -*Cannot set meso/rho for this atom style* - Self-explanatory. - -*Cannot set non-zero image flag for non-periodic dimension* - Self-explanatory. - -*Cannot set non-zero z velocity for 2d simulation* - Self-explanatory. - -*Cannot set quaternion for atom that has none* - Self-explanatory. - -*Cannot set quaternion with xy components for 2d system* - Self-explanatory. - *Cannot set respa hybrid and any of pair/inner/middle/outer* In the rRESPA integrator, you must compute pairwise potentials either all together (pair), with different cutoff regions (inner/middle/outer), @@ -1064,39 +797,18 @@ Doc page with :doc:`WARNING messages ` This error was generated by MPI when reading/writing an MPI-IO restart file. -*Cannot set smd/contact/radius for this atom style* - Self-explanatory. - -*Cannot set smd/mass/density for this atom style* - Self-explanatory. - *Cannot set temperature for fix rigid/nph* The temp keyword cannot be specified. -*Cannot set theta for atom that is not a line* - Self-explanatory. - *Cannot set this attribute for this atom style* The attribute being set does not exist for the defined atom style. -*Cannot set variable z velocity for 2d simulation* - Self-explanatory. - -*Cannot skew triclinic box in z for 2d simulation* - Self-explanatory. - *Cannot subtract groups using a dynamic group* This operation is not allowed. *Cannot union groups using a dynamic group* This operation is not allowed. -*Cannot use -kokkos on without KOKKOS installed* - Self-explanatory. - -*Cannot use -reorder after -partition* - Self-explanatory. See page discussion of command-line switches. - *Cannot use Ewald with 2d simulation* The kspace style ewald cannot be used in 2d simulations. You can use 2d Ewald in a 3d simulation; see the kspace_modify command. @@ -1109,15 +821,9 @@ Doc page with :doc:`WARNING messages ` *Cannot use EwaldDisp with 2d simulation* This is a current restriction of this command. -*Cannot use Kokkos pair style with rRESPA inner/middle* - Self-explanatory. - *Cannot use NEB unless atom map exists* Use the atom_modify command to create an atom map. -*Cannot use NEB with a single replica* - Self-explanatory. - *Cannot use NEB with atom_modify sort enabled* This is current restriction for NEB implemented in LAMMPS. @@ -1166,109 +872,40 @@ Doc page with :doc:`WARNING messages ` The boundary style of the face where atoms are added can not be of type p (periodic). -*Cannot use atomfile-style variable unless atom map exists* - Self-explanatory. See the atom_modify command to create a map. - -*Cannot use both com and bias with compute temp/chunk* - Self-explanatory. - -*Cannot use chosen neighbor list style with buck/coul/cut/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with buck/coul/long/kk* - Self-explanatory. - *Cannot use chosen neighbor list style with buck/kk* That style is not supported by Kokkos. *Cannot use chosen neighbor list style with coul/cut/kk* That style is not supported by Kokkos. -*Cannot use chosen neighbor list style with coul/debye/kk* - Self-explanatory. - *Cannot use chosen neighbor list style with coul/dsf/kk* That style is not supported by Kokkos. *Cannot use chosen neighbor list style with coul/wolf/kk* That style is not supported by Kokkos. -*Cannot use chosen neighbor list style with lj/charmm/coul/charmm/implicit/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with lj/charmm/coul/charmm/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with lj/charmm/coul/long/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with lj/class2/coul/cut/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with lj/class2/coul/long/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with lj/class2/kk* - Self-explanatory. - *Cannot use chosen neighbor list style with lj/cut/coul/cut/kk* That style is not supported by Kokkos. -*Cannot use chosen neighbor list style with lj/cut/coul/debye/kk* - Self-explanatory. - *Cannot use chosen neighbor list style with lj/cut/coul/long/kk* That style is not supported by Kokkos. *Cannot use chosen neighbor list style with lj/cut/kk* That style is not supported by Kokkos. -*Cannot use chosen neighbor list style with lj/expand/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with lj/gromacs/coul/gromacs/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with lj/gromacs/kk* - Self-explanatory. - *Cannot use chosen neighbor list style with lj/spica/kk* That style is not supported by Kokkos. *Cannot use chosen neighbor list style with pair eam/kk* That style is not supported by Kokkos. -*Cannot use chosen neighbor list style with pair eam/kk/alloy* - Self-explanatory. - -*Cannot use chosen neighbor list style with pair eam/kk/fs* - Self-explanatory. - -*Cannot use chosen neighbor list style with pair sw/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with tersoff/kk* - Self-explanatory. - -*Cannot use chosen neighbor list style with tersoff/zbl/kk* - Self-explanatory. - -*Cannot use compute chunk/atom bin z for 2d model* - Self-explanatory. - *Cannot use compute cluster/atom unless atoms have IDs* Atom IDs are used to identify clusters. -*Cannot use create_atoms rotate unless single style* - Self-explanatory. - *Cannot use create_bonds unless atoms have IDs* This command requires a mapping from global atom IDs to local atoms, but the atoms that have been defined have no IDs. -*Cannot use create_bonds with non-molecular system* - Self-explanatory. - *Cannot use cwiggle in variable formula between runs* This is a function of elapsed time. @@ -1283,12 +920,6 @@ Doc page with :doc:`WARNING messages ` *Cannot use delete_bonds with non-molecular system* Your choice of atom style does not have bonds. -*Cannot use dump_modify fileper without % in dump file name* - Self-explanatory. - -*Cannot use dump_modify nfile without % in dump file name* - Self-explanatory. - *Cannot use dynamic group with fix adapt atom* This is not yet supported. @@ -1340,28 +971,13 @@ Doc page with :doc:`WARNING messages ` *Cannot use fix deform trate on a box with zero tilt* The trate style alters the current strain. -*Cannot use fix deposit rigid and not molecule* - Self-explanatory. - *Cannot use fix deposit rigid and shake* These two attributes are conflicting. -*Cannot use fix deposit shake and not molecule* - Self-explanatory. - -*Cannot use fix enforce2d with 3d simulation* - Self-explanatory. - *Cannot use fix gcmc in a 2d simulation* Fix gcmc is set up to run in 3d only. No 2d simulations with fix gcmc are allowed. -*Cannot use fix gcmc shake and not molecule* - Self-explanatory. - -*Cannot use fix msst without per-type mass defined* - Self-explanatory. - *Cannot use fix npt and fix deform on same component of stress tensor* This would be changing the same box dimension twice. @@ -1374,15 +990,6 @@ Doc page with :doc:`WARNING messages ` When specifying a diagonal pressure component, the dimension must be periodic. -*Cannot use fix nvt/npt/nph with both xy dynamics and xy scaling* - Self-explanatory. - -*Cannot use fix nvt/npt/nph with both xz dynamics and xz scaling* - Self-explanatory. - -*Cannot use fix nvt/npt/nph with both yz dynamics and yz scaling* - Self-explanatory. - *Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension* The second dimension in the barostatted tilt factor must be periodic. @@ -1392,15 +999,9 @@ Doc page with :doc:`WARNING messages ` *Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension* The second dimension in the barostatted tilt factor must be periodic. -*Cannot use fix pour rigid and not molecule* - Self-explanatory. - *Cannot use fix pour rigid and shake* These two attributes are conflicting. -*Cannot use fix pour shake and not molecule* - Self-explanatory. - *Cannot use fix pour with triclinic box* This option is not yet supported. @@ -1408,15 +1009,6 @@ Doc page with :doc:`WARNING messages ` These commands both change the box size/shape, so you cannot use both together. -*Cannot use fix press/berendsen on a non-periodic dimension* - Self-explanatory. - -*Cannot use fix press/berendsen with triclinic box* - Self-explanatory. - -*Cannot use fix reax/bonds without pair_style reax* - Self-explanatory. - *Cannot use fix rigid npt/nph and fix deform on same component of stress tensor* This would be changing the same box dimension twice. @@ -1437,202 +1029,20 @@ Doc page with :doc:`WARNING messages ` *Cannot use fix ttm with triclinic box* This is a current restriction of this fix due to the grid it creates. -*Cannot use fix tune/kspace without a kspace style* - Self-explanatory. - *Cannot use fix tune/kspace without a pair style* This fix (tune/kspace) can only be used when a pair style has been specified. -*Cannot use fix wall in periodic dimension* - Self-explanatory. - -*Cannot use fix wall zlo/zhi for a 2d simulation* - Self-explanatory. - -*Cannot use fix wall/reflect in periodic dimension* - Self-explanatory. - -*Cannot use fix wall/reflect zlo/zhi for a 2d simulation* - Self-explanatory. - -*Cannot use fix wall/srd in periodic dimension* - Self-explanatory. - *Cannot use fix wall/srd more than once* Nor is their a need to since multiple walls can be specified in one command. -*Cannot use fix wall/srd without fix srd* - Self-explanatory. - -*Cannot use fix wall/srd zlo/zhi for a 2d simulation* - Self-explanatory. - -*Cannot use fix_deposit unless atoms have IDs* - Self-explanatory. - -*Cannot use fix_pour unless atoms have IDs* - Self-explanatory. - -*Cannot use include command within an if command* - Self-explanatory. - *Cannot use lines with fix srd unless overlap is set* This is because line segments are connected to each other. -*Cannot use multiple fix wall commands with pair brownian* - Self-explanatory. - -*Cannot use multiple fix wall commands with pair lubricate* - Self-explanatory. - -*Cannot use multiple fix wall commands with pair lubricate/poly* - Self-explanatory. - -*Cannot use multiple fix wall commands with pair lubricateU* - Self-explanatory. - *Cannot use neigh_modify exclude with GPU neighbor builds* This is a current limitation of the GPU implementation in LAMMPS. -*Cannot use neighbor bins - box size << cutoff* - Too many neighbor bins will be created. This typically happens when - the simulation box is very small in some dimension, compared to the - neighbor cutoff. Use the "nsq" style instead of "bin" style. - -*Cannot use newton pair with beck/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with born/coul/long/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with born/coul/wolf/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with born/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with buck/coul/cut/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with buck/coul/long/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with buck/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with colloid/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with coul/cut/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with coul/debye/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with coul/dsf/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with coul/long/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with dipole/cut/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with dipole/sf/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with dpd/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with dpd/tstat/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with eam/alloy/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with eam/fs/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with eam/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with gauss/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with gayberne/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/charmm/coul/long/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/class2/coul/long/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/class2/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/cubic/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/cut/coul/cut/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/cut/coul/debye/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/cut/coul/dsf/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/cut/coul/long/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/cut/coul/msm/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/cut/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/expand/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/gromacs/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/spica/coul/long/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj/spica/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with lj96/cut/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with mie/cut/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with morse/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with resquared/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with soft/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with table/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with yukawa/colloid/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with yukawa/gpu pair style* - Self-explanatory. - -*Cannot use newton pair with zbl/gpu pair style* - Self-explanatory. - *Cannot use non-zero forces in an energy minimization* Fix setforce cannot be used in this manner. Use fix addforce instead. @@ -1660,9 +1070,6 @@ Doc page with :doc:`WARNING messages ` boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. -*Cannot use order greater than 8 with pppm/gpu.* - Self-explanatory. - *Cannot use package gpu neigh yes with triclinic box* This is a current restriction in LAMMPS. @@ -1675,18 +1082,6 @@ Doc page with :doc:`WARNING messages ` *Cannot use ramp in variable formula between runs* This is because the ramp() function is time dependent. -*Cannot use read_data add before simulation box is defined* - Self-explanatory. - -*Cannot use read_data extra with add flag* - Self-explanatory. - -*Cannot use read_data offset without add flag* - Self-explanatory. - -*Cannot use read_data shift without add flag* - Self-explanatory. - *Cannot use region INF or EDGE when box does not exist* Regions that extend to the box boundaries can only be used after the create_box command has been used. @@ -1694,18 +1089,12 @@ Doc page with :doc:`WARNING messages ` *Cannot use set atom with no atom IDs defined* Atom IDs are not defined, so they cannot be used to identify an atom. -*Cannot use set mol with no molecule IDs defined* - Self-explanatory. - *Cannot use swiggle in variable formula between runs* This is a function of elapsed time. *Cannot use tris with fix srd unless overlap is set* This is because triangles are connected to each other. -*Cannot use variable energy with constant efield in fix efield* - LAMMPS computes the energy itself when the E-field is constant. - *Cannot use variable energy with constant force in fix addforce* This is because for constant force, LAMMPS can compute the change in energy directly. @@ -1720,22 +1109,10 @@ Doc page with :doc:`WARNING messages ` *Cannot use vdisplace in variable formula between runs* This is a function of elapsed time. -*Cannot use velocity bias command without temp keyword* - Self-explanatory. - *Cannot use velocity create loop all unless atoms have IDs* Atoms in the simulation to do not have IDs, so this style of velocity creation cannot be performed. -*Cannot use wall in periodic dimension* - Self-explanatory. - -*Cannot use write_restart fileper without % in restart file name* - Self-explanatory. - -*Cannot use write_restart nfile without % in restart file name* - Self-explanatory. - *Cannot wiggle and shear fix wall/gran* Cannot specify both options at the same time. @@ -1746,12 +1123,6 @@ Doc page with :doc:`WARNING messages ` *Cannot yet use KSpace solver with grid with comm style tiled* This is current restriction in LAMMPS. -*Cannot yet use comm_style tiled with multi-mode comm* - Self-explanatory. - -*Cannot yet use comm_style tiled with triclinic box* - Self-explanatory. - *Cannot yet use compute tally with Kokkos* This feature is not yet supported. @@ -1774,50 +1145,11 @@ Doc page with :doc:`WARNING messages ` *Cannot zero gld force for zero atoms* There are no atoms currently in the group. -*Cannot zero momentum of no atoms* - Self-explanatory. - -*Change_box command before simulation box is defined* - Self-explanatory. - *Change_box volume used incorrectly* The "dim volume" option must be used immediately following one or two settings for "dim1 ..." (and optionally "dim2 ...") and must be for a different dimension, i.e. dim != dim1 and dim != dim2. -*Chunk/atom compute does not exist for compute angmom/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute com/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute gyration/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute inertia/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute msd/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute omega/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute property/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute temp/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute torque/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for compute vcm/chunk* - Self-explanatory. - -*Chunk/atom compute does not exist for fix ave/chunk* - Self-explanatory. - *Comm tiled invalid index in box drop brick* Internal error check in comm_style tiled which should not occur. Contact the developers. @@ -1826,12 +1158,6 @@ Doc page with :doc:`WARNING messages ` Internal error check in comm_style tiled which should not occur. Contact the developers. -*Comm_modify group != atom_modify first group* - Self-explanatory. - -*Communication cutoff for comm_style tiled cannot exceed periodic box length* - Self-explanatory. - *Communication cutoff too small for SNAP micro load balancing* This can happen if you change the neighbor skin after your pair_style command or if your box dimensions grow during a run. You can set the @@ -1840,69 +1166,12 @@ Doc page with :doc:`WARNING messages ` *Compute %s does not allow use of dynamic group* Dynamic groups have not yet been enabled for this compute. -*Compute for fix pafi does not calculate a local array* - Self-explanatory. - -*Compute for fix pafi must have 9 fields per atom* - Self-explanatory. - -*Compute ID for compute chunk /atom does not exist* - Self-explanatory. - -*Compute ID for compute chunk/atom does not exist* - Self-explanatory. - -*Compute gyration ID does not exist for compute gyration/shape* - Self-explanatory. Provide a valid compute ID. - -*Compute gyration/shape compute ID does not point to a gyration compute* - Self-explanatory. Provide and ID of a compute gyration command. - -*Compute ID for compute reduce does not exist* - Self-explanatory. - -*Compute ID for compute slice does not exist* - Self-explanatory. - -*Compute ID for fix ave/atom does not exist* - Self-explanatory. - -*Compute ID for fix ave/chunk does not exist* - Self-explanatory. - -*Compute ID for fix ave/correlate does not exist* - Self-explanatory. - -*Compute ID for fix ave/histo does not exist* - Self-explanatory. - -*Compute ID for fix ave/time does not exist* - Self-explanatory. - -*Compute ID for fix numdiff does not exist* - Self-explanatory. - -*Compute ID for fix numdiff/virial does not exist* - Self-explanatory. - -*Compute ID for fix store/state does not exist* - Self-explanatory. - -*Compute ID for fix vector does not exist* - Self-explanatory. - -*Compute ID must be alphanumeric or underscore characters* - Self-explanatory. - *Compute angle/local used when angles are not allowed* The atom style does not support angles. *Compute angmom/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. -*Compute body/local requires atom style body* - Self-explanatory. - *Compute bond/local used when bonds are not allowed* The atom style does not support bonds. @@ -1916,46 +1185,10 @@ Doc page with :doc:`WARNING messages ` *Compute chunk/atom bin/sphere radius is too large for periodic box* Radius cannot be bigger than 1/2 of any periodic dimension. -*Compute chunk/atom compute array is accessed out-of-range* - The index for the array is out of bounds. - -*Compute chunk/atom compute does not calculate a per-atom array* - Self-explanatory. - -*Compute chunk/atom compute does not calculate a per-atom vector* - Self-explanatory. - -*Compute chunk/atom compute does not calculate per-atom values* - Self-explanatory. - -*Compute chunk/atom cylinder axis must be z for 2d* - Self-explanatory. - -*Compute chunk/atom fix array is accessed out-of-range* - The index for the array is out of bounds. - -*Compute chunk/atom fix does not calculate a per-atom array* - Self-explanatory. - -*Compute chunk/atom fix does not calculate a per-atom vector* - Self-explanatory. - -*Compute chunk/atom fix does not calculate per-atom values* - Self-explanatory. - -*Compute chunk/atom for triclinic boxes requires units reduced* - Self-explanatory. - *Compute chunk/atom ids once but nchunk is not once* You cannot assign chunks IDs to atom permanently if the number of chunks may change. -*Compute chunk/atom molecule for non-molecular system* - Self-explanatory. - -*Compute chunk/atom sphere z origin must be 0.0 for 2d* - Self-explanatory. - *Compute chunk/atom stores no IDs for compute property/chunk* It will only store IDs if its compress option is enabled. @@ -1968,9 +1201,6 @@ Doc page with :doc:`WARNING messages ` *Compute chunk/atom stores no coord3 for compute property/chunk* Only certain binning options for compute chunk/atom store coordinates. -*Compute chunk/atom variable is not atom-style variable* - Self-explanatory. - *Compute chunk/atom without bins cannot use discard mixed* That discard option only applies to the binning styles. @@ -1981,28 +1211,13 @@ Doc page with :doc:`WARNING messages ` This is so that the pair style defines a cutoff distance which is used to find clusters. -*Compute cna/atom cutoff is longer than pairwise cutoff* - Self-explanatory. - -*Compute cna/atom requires a pair style be defined* - Self-explanatory. - *Compute com/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. -*Compute contact/atom requires a pair style be defined* - Self-explanatory. - -*Compute contact/atom requires atom style sphere* - Self-explanatory. - *Compute coord/atom cutoff is longer than pairwise cutoff* Cannot compute coordination at distances longer than the pair cutoff, since those atoms are not in the neighbor list. -*Compute coord/atom requires a pair style be defined* - Self-explanatory. - *Compute damage/atom requires peridynamic potential* Damage is a Peridynamic-specific metric. It requires you to be running a Peridynamics simulation. @@ -2010,65 +1225,29 @@ Doc page with :doc:`WARNING messages ` *Compute dihedral/local used when dihedrals are not allowed* The atom style does not support dihedrals. -*Compute dilatation/atom cannot be used with this pair style* - Self-explanatory. - -*Compute dilatation/atom requires Peridynamic pair style* - Self-explanatory. - *Compute does not allow an extra compute or fix to be reset* This is an internal LAMMPS error. Please report it to the developers. -*Compute erotate/asphere requires atom style ellipsoid or line or tri* - Self-explanatory. - *Compute erotate/asphere requires extended particles* This compute cannot be used with point particles. -*Compute erotate/rigid with non-rigid fix-ID* - Self-explanatory. - -*Compute erotate/sphere requires atom style sphere* - Self-explanatory. - -*Compute erotate/sphere/atom requires atom style sphere* - Self-explanatory. - *Compute event/displace has invalid fix event assigned* This is an internal LAMMPS error. Please report it to the developers. -*Compute group/group group ID does not exist* - Self-explanatory. - *Compute gyration/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. -*Compute heat/flux compute ID does not compute ke/atom* - Self-explanatory. - -*Compute heat/flux compute ID does not compute pe/atom* - Self-explanatory. - -*Compute heat/flux compute ID does not compute stress/atom* - Self-explanatory. - *Compute hexorder/atom cutoff is longer than pairwise cutoff* Cannot compute order parameter beyond cutoff. -*Compute hexorder/atom requires a pair style be defined* - Self-explanatory. - *Compute improper/local used when impropers are not allowed* The atom style does not support impropers. *Compute inertia/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. -*Compute ke/rigid with non-rigid fix-ID* - Self-explanatory. - *Compute msd/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. @@ -2077,24 +1256,12 @@ Doc page with :doc:`WARNING messages ` the number of chunks is changing. Compute chunk/atom allows setting nchunk to be static. -*Compute nve/asphere requires atom style ellipsoid* - Self-explanatory. - -*Compute nvt/nph/npt asphere requires atom style ellipsoid* - Self-explanatory. - -*Compute nvt/nph/npt body requires atom style body* - Self-explanatory. - *Compute omega/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. *Compute orientorder/atom cutoff is longer than pairwise cutoff* Cannot compute order parameter beyond cutoff. -*Compute orientorder/atom requires a pair style be defined* - Self-explanatory. - *Compute pair must use group all* Pair styles accumulate energy on all atoms. @@ -2102,12 +1269,6 @@ Doc page with :doc:`WARNING messages ` Energies computed by potentials (pair, bond, etc) are computed on all atoms. -*Compute plasticity/atom cannot be used with this pair style* - Self-explanatory. - -*Compute plasticity/atom requires Peridynamic pair style* - Self-explanatory. - *Compute pressure must use group all* Virial contributions computed by potentials (pair, bond, etc) are computed on all atoms. @@ -2123,9 +1284,6 @@ Doc page with :doc:`WARNING messages ` The command is accessing a vector added by the fix property/atom command, that does not exist. -*Compute property/atom for atom property that is not allocated* - Self-explanatory. - *Compute property/atom integer vector does not exist* The command is accessing a vector added by the fix property/atom command, that does not exist. @@ -2137,117 +1295,18 @@ Doc page with :doc:`WARNING messages ` Only inputs that generate the same number of datums can be used together. E.g. bond and angle quantities cannot be mixed. -*Compute property/local does not (yet) work with atom_style template* - Self-explanatory. - -*Compute property/local for property that is not allocated* - Self-explanatory. - -*Compute rdf requires a pair style be defined* - Self-explanatory. - -*Compute reduce compute array is accessed out-of-range* - An index for the array is out of bounds. - *Compute reduce compute calculates global values* A compute that calculates peratom or local values is required. -*Compute reduce compute does not calculate a local array* - Self-explanatory. - -*Compute reduce compute does not calculate a local vector* - Self-explanatory. - -*Compute reduce compute does not calculate a per-atom array* - Self-explanatory. - -*Compute reduce compute does not calculate a per-atom vector* - Self-explanatory. - -*Compute reduce fix array is accessed out-of-range* - An index for the array is out of bounds. - *Compute reduce fix calculates global values* A fix that calculates peratom or local values is required. -*Compute reduce fix does not calculate a local array* - Self-explanatory. - -*Compute reduce fix does not calculate a local vector* - Self-explanatory. - -*Compute reduce fix does not calculate a per-atom array* - Self-explanatory. - -*Compute reduce fix does not calculate a per-atom vector* - Self-explanatory. - -*Compute reduce replace requires min or max mode* - Self-explanatory. - -*Compute reduce variable is not atom-style variable* - Self-explanatory. - -*Compute slice compute array is accessed out-of-range* - An index for the array is out of bounds. - -*Compute slice compute does not calculate a global array* - Self-explanatory. - -*Compute slice compute does not calculate a global vector* - Self-explanatory. - -*Compute slice compute does not calculate global vector or array* - Self-explanatory. - -*Compute slice compute vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Compute slice fix array is accessed out-of-range* - An index for the array is out of bounds. - -*Compute slice fix does not calculate a global array* - Self-explanatory. - -*Compute slice fix does not calculate a global vector* - Self-explanatory. - -*Compute slice fix does not calculate global vector or array* - Self-explanatory. - -*Compute slice fix vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Compute sna/atom cutoff is longer than pairwise cutoff* - Self-explanatory. - -*Compute sna/atom requires a pair style be defined* - Self-explanatory. - -*Compute snad/atom cutoff is longer than pairwise cutoff* - Self-explanatory. - -*Compute snad/atom requires a pair style be defined* - Self-explanatory. - -*Compute snav/atom cutoff is longer than pairwise cutoff* - Self-explanatory. - -*Compute snav/atom requires a pair style be defined* - Self-explanatory. - *Compute stress/atom temperature ID does not compute temperature* The specified compute must compute temperature. -*Compute temp/asphere requires atom style ellipsoid* - Self-explanatory. - *Compute temp/asphere requires extended particles* This compute cannot be used with point particles. -*Compute temp/body requires atom style body* - Self-explanatory. - *Compute temp/body requires bodies* This compute can only be applied to body particles. @@ -2260,27 +1319,6 @@ Doc page with :doc:`WARNING messages ` *Compute temp/cs used when bonds are not allowed* This compute only works on pairs of bonded particles. -*Compute temp/partial cannot use vz for 2d systemx* - Self-explanatory. - -*Compute temp/profile cannot bin z for 2d systems* - Self-explanatory. - -*Compute temp/profile cannot use vz for 2d systemx* - Self-explanatory. - -*Compute temp/sphere requires atom style sphere* - Self-explanatory. - -*Compute ti kspace style does not exist* - Self-explanatory. - -*Compute ti pair style does not exist* - Self-explanatory. - -*Compute ti tail when pair style does not compute tail corrections* - Self-explanatory. - *Compute torque/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. @@ -2304,9 +1342,6 @@ Doc page with :doc:`WARNING messages ` *Compute vcm/chunk does not use chunk/atom compute* The style of the specified compute is not chunk/atom. -*Computed temperature for fix temp/berendsen cannot be 0.0* - Self-explanatory. - *Computed temperature for fix temp/rescale cannot be 0.0* Cannot rescale the temperature to a new value if the current temperature is 0.0. @@ -2368,67 +1403,19 @@ Doc page with :doc:`WARNING messages ` The specified constraints did not allow this style of grid to be created. -*Could not evaluate Python function input variable* - Self-explanatory. - *Could not find Python function* The provided Python code was run successfully, but it not define a callable function with the required name. -*Could not find atom_modify first group ID* - Self-explanatory. - *Could not find change_box group ID* Group ID used in the change_box command does not exist. -*Could not find compute ID for PRD* - Self-explanatory. - -*Could not find compute ID for TAD* - Self-explanatory. - -*Could not find compute ID for temperature bias* - Self-explanatory. - -*Could not find compute ID to delete* - Self-explanatory. - -*Could not find compute displace/atom fix ID* - Self-explanatory. - -*Could not find compute event/displace fix ID* - Self-explanatory. - -*Could not find compute group ID* - Self-explanatory. - -*Could not find compute heat/flux compute ID* - Self-explanatory. - -*Could not find compute msd fix ID* - Self-explanatory. - *Could not find compute msd/chunk fix ID* The compute creates an internal fix, which has been deleted. *Could not find compute pressure temperature ID* The compute ID for calculating temperature does not exist. -*Could not find compute stress/atom temperature ID* - Self-explanatory. - -*Could not find compute vacf fix ID* - Self-explanatory. - -*Could not find compute/voronoi surface group ID* - Self-explanatory. - -*Could not find compute_modify ID* - Self-explanatory. - -*Could not find custom per-atom property ID* - Self-explanatory. - *Could not find delete_atoms group ID* Group ID used in the delete_atoms command does not exist. @@ -2438,61 +1425,16 @@ Doc page with :doc:`WARNING messages ` *Could not find displace_atoms group ID* Group ID used in the displace_atoms command does not exist. -*Could not find dump custom compute ID* - Self-explanatory. - -*Could not find dump custom fix ID* - Self-explanatory. - -*Could not find dump custom variable name* - Self-explanatory. - *Could not find dump group ID* A group ID used in the dump command does not exist. -*Could not find dump local compute ID* - Self-explanatory. - -*Could not find dump local fix ID* - Self-explanatory. - -*Could not find dump modify compute ID* - Self-explanatory. - -*Could not find dump modify custom atom floating point property ID* - Self-explanatory. - -*Could not find dump modify custom atom integer property ID* - Self-explanatory. - -*Could not find dump modify fix ID* - Self-explanatory. - -*Could not find dump modify variable name* - Self-explanatory. - -*Could not find fix ID to delete* - Self-explanatory. - *Could not find fix adapt storage fix ID* This should not happen unless you explicitly deleted a secondary fix that fix adapt created internally. -*Could not find fix halt variable name* - Self-explanatory. - -*Could not find fix gcmc exclusion group ID* - Self-explanatory. - -*Could not find fix gcmc rotation group ID* - Self-explanatory. - *Could not find fix group ID* A group ID used in the fix command does not exist. -*Could not find fix msst compute ID* - Self-explanatory. - *Could not find fix poems group ID* A group ID used in the fix poems command does not exist. @@ -2502,9 +1444,6 @@ Doc page with :doc:`WARNING messages ` *Could not find fix rigid group ID* A group ID used in the fix rigid command does not exist. -*Could not find fix srd group ID* - Self-explanatory. - *Could not find fix_modify ID* A fix ID used in the fix_modify command does not exist. @@ -2514,12 +1453,6 @@ Doc page with :doc:`WARNING messages ` *Could not find fix_modify temperature ID* The compute ID for computing temperature does not exist. -*Could not find group clear group ID* - Self-explanatory. - -*Could not find group delete group ID* - Self-explanatory. - *Could not find pair fix ID* A fix is created internally by the pair style to store shear history information. You cannot delete it. @@ -2527,9 +1460,6 @@ Doc page with :doc:`WARNING messages ` *Could not find set group ID* Group ID specified in set command does not exist. -*Could not find specified fix gcmc group ID* - Self-explanatory. - *Could not find thermo compute ID* Compute ID specified in thermo_style command does not exist. @@ -2541,15 +1471,9 @@ Doc page with :doc:`WARNING messages ` The fix ID needed by thermo style custom to compute a requested quantity does not exist. -*Could not find thermo custom variable name* - Self-explanatory. - *Could not find thermo fix ID* Fix ID specified in thermo_style command does not exist. -*Could not find thermo variable name* - Self-explanatory. - *Could not find thermo_modify pressure ID* The compute ID needed by thermo style custom to compute pressure does not exist. @@ -2572,15 +1496,6 @@ Doc page with :doc:`WARNING messages ` Could not initialize at least one of the devices specified for the gpu package -*Could not grab element entry from EIM potential file* - Self-explanatory - -*Could not grab global entry from EIM potential file* - Self-explanatory. - -*Could not grab pair entry from EIM potential file* - Self-explanatory. - *Could not initialize embedded Python* The main module in Python was not accessible. @@ -2616,9 +1531,6 @@ Doc page with :doc:`WARNING messages ` *Coulombic cut not supported in pair_style lj/long/dipole/long* Must use long-range Coulombic interactions. -*Cound not find dump_modify ID* - Self-explanatory. - *Create_atoms command before simulation box is defined* The create_atoms command cannot be used before a read_data, read_restart, or create_box command. @@ -2635,9 +1547,6 @@ Doc page with :doc:`WARNING messages ` *Create_atoms region ID does not exist* A region ID used in the create_atoms command does not exist. -*Create_bonds command before simulation box is defined* - Self-explanatory. - *Create_bonds command requires no kspace_style be defined* This is so that atom pairs that are already bonded to not appear in the neighbor list. @@ -2649,12 +1558,6 @@ Doc page with :doc:`WARNING messages ` *Create_bonds max distance > neighbor cutoff* Can only create bonds for atom pairs that will be in neighbor list. -*Create_bonds requires a pair style be defined* - Self-explanatory. - -*Create_box region ID does not exist* - Self-explanatory. - *Create_box region does not support a bounding box* Not all regions represent bounded volumes. You cannot use such a region with the create_box command. @@ -2667,21 +1570,6 @@ Doc page with :doc:`WARNING messages ` The command is accessing a vector added by the fix property/atom command, that does not exist. -*Custom per-atom property ID is not floating point* - Self-explanatory. - -*Custom per-atom property ID is not integer* - Self-explanatory. - -*Cut-offs missing in pair_style lj/long/dipole/long* - Self-explanatory. - -*Cutoffs missing in pair_style buck/long/coul/long* - Self-explanatory. - -*Cutoffs missing in pair_style lj/long/coul/long* - Self-explanatory. - *Cyclic loop in joint connections* Fix poems cannot (yet) work with coupled bodies whose joints connect the bodies in a ring (or cycle). @@ -2689,9 +1577,6 @@ Doc page with :doc:`WARNING messages ` *Degenerate lattice primitive vectors* Invalid set of 3 lattice vectors for lattice command. -*Delete region ID does not exist* - Self-explanatory. - *Delete_atoms command before simulation box is defined* The delete_atoms command cannot be used before a read_data, read_restart, or create_box command. @@ -2713,14 +1598,6 @@ Doc page with :doc:`WARNING messages ` *Delete_bonds command with no atoms existing* No atoms are yet defined so the delete_bonds command cannot be used. -*Deposition region extends outside simulation box* - Self-explanatory. - -*Did not assign all atoms correctly* - Atoms read in from a data file were not assigned correctly to - processors. This is likely due to some atom coordinates being - outside a non-periodic simulation box. - *Did not assign all restart atoms correctly* Atoms read in from the restart file were not assigned correctly to processors. This is likely due to some atom coordinates being outside @@ -2743,12 +1620,6 @@ Doc page with :doc:`WARNING messages ` *Did not set pressure for fix rigid/nph* The press keyword must be specified. -*Did not set temp for fix rigid/nvt/small* - Self-explanatory. - -*Did not set temp or press for fix rigid/npt/small* - Self-explanatory. - *Did not set temperature for fix rigid/nvt* The temp keyword must be specified. @@ -2765,18 +1636,6 @@ Doc page with :doc:`WARNING messages ` on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid dihedral. -*Dihedral atoms %d %d %d %d missing on proc %d at step %ld* - One or more of 4 atoms needed to compute a particular dihedral are - missing on this processor. Typically this is because the pairwise - cutoff is set too short or the dihedral has blown apart and an atom is - too far away. - -*Dihedral atoms missing on proc %d at step %ld* - One or more of 4 atoms needed to compute a particular dihedral are - missing on this processor. Typically this is because the pairwise - cutoff is set too short or the dihedral has blown apart and an atom is - too far away. - *Dihedral charmm is incompatible with Pair style* Dihedral style charmm must be used with a pair style charmm in order for the 1-4 epsilon/sigma parameters to be defined. @@ -2790,15 +1649,6 @@ Doc page with :doc:`WARNING messages ` No dihedral coefficients have been assigned in the data file or via the dihedral_coeff command. -*Dihedral style hybrid cannot have hybrid as an argument* - Self-explanatory. - -*Dihedral style hybrid cannot have none as an argument* - Self-explanatory. - -*Dihedral style hybrid cannot use same dihedral style twice* - Self-explanatory. - *Dihedral/improper extent > half of periodic box length* This error was detected by the neigh_modify check yes setting. It is an error because the dihedral atoms are so far apart it is ambiguous @@ -2830,9 +1680,6 @@ Doc page with :doc:`WARNING messages ` The dimension command cannot be used after a read_data, read_restart, or create_box command. -*Disk limit not supported by OS or illegal path* - Self-explanatory. - *Dispersion PPPMDisp order has been reduced below minorder* The default minimum order is 2. This can be reset by the kspace_modify minorder command. @@ -2841,9 +1688,6 @@ Doc page with :doc:`WARNING messages ` The displace_atoms command cannot be used before a read_data, read_restart, or create_box command. -*Distance must be > 0 for compute event/displace* - Self-explanatory. - *Divide by 0 in influence function* This should not normally occur. It is likely a problem with your model. @@ -2852,23 +1696,9 @@ Doc page with :doc:`WARNING messages ` This should not normally occur. It is likely a problem with your model. -*Divide by 0 in variable formula* - Self-explanatory. - -*Domain too large for neighbor bins* - The domain has become extremely large so that neighbor bins cannot be - used. Most likely, one or more atoms have been blown out of the - simulation box to a great distance. - -*Double precision is not supported on this accelerator* - Self-explanatory - *Dump atom/gz only writes compressed files* The dump atom/gz output file name must have a .gz suffix. -*Dump cfg arguments can not mix xs\|ys\|zs with xsu\|ysu\|zsu* - Self-explanatory. - *Dump cfg arguments must start with 'mass type xs ys zs' or 'mass type xsu ysu zsu'* This is a requirement of the CFG output format. See the dump cfg doc page for more details. @@ -2883,30 +1713,6 @@ Doc page with :doc:`WARNING messages ` The fix must produce per-atom quantities on timesteps that dump custom needs them. -*Dump custom compute does not calculate per-atom array* - Self-explanatory. - -*Dump custom compute does not calculate per-atom vector* - Self-explanatory. - -*Dump custom compute does not compute per-atom info* - Self-explanatory. - -*Dump custom compute vector is accessed out-of-range* - Self-explanatory. - -*Dump custom fix does not compute per-atom array* - Self-explanatory. - -*Dump custom fix does not compute per-atom info* - Self-explanatory. - -*Dump custom fix does not compute per-atom vector* - Self-explanatory. - -*Dump custom fix vector is accessed out-of-range* - Self-explanatory. - *Dump custom variable is not atom-style variable* Only atom-style variables generate per-atom quantities, needed for dump output. @@ -2927,132 +1733,36 @@ Doc page with :doc:`WARNING messages ` This is because a % signifies one file per processor and MPI-IO creates one large file for all processors. -*Dump file does not contain requested snapshot* - Self-explanatory. - -*Dump file is incorrectly formatted* - Self-explanatory. - -*Dump image body yes requires atom style body* - Self-explanatory. - -*Dump image bond not allowed with no bond types* - Self-explanatory. - -*Dump image cannot perform sorting* - Self-explanatory. - -*Dump image line requires atom style line* - Self-explanatory. - *Dump image requires one snapshot per file* Use a "\*" in the filename. -*Dump image tri requires atom style tri* - Self-explanatory. - *Dump local and fix not computed at compatible times* The fix must produce per-atom quantities on timesteps that dump local needs them. -*Dump local attributes contain no compute or fix* - Self-explanatory. - *Dump local cannot sort by atom ID* This is because dump local does not really dump per-atom info. -*Dump local compute does not calculate local array* - Self-explanatory. - -*Dump local compute does not calculate local vector* - Self-explanatory. - -*Dump local compute does not compute local info* - Self-explanatory. - -*Dump local compute vector is accessed out-of-range* - Self-explanatory. - *Dump local count is not consistent across input fields* Every column of output must be the same length. -*Dump local fix does not compute local array* - Self-explanatory. - -*Dump local fix does not compute local info* - Self-explanatory. - -*Dump local fix does not compute local vector* - Self-explanatory. - -*Dump local fix vector is accessed out-of-range* - Self-explanatory. - -*Dump modify bcolor not allowed with no bond types* - Self-explanatory. - -*Dump modify bdiam not allowed with no bond types* - Self-explanatory. - -*Dump modify compute ID does not compute per-atom array* - Self-explanatory. - -*Dump modify compute ID does not compute per-atom info* - Self-explanatory. - -*Dump modify compute ID does not compute per-atom vector* - Self-explanatory. - -*Dump modify compute ID vector is not large enough* - Self-explanatory. - *Dump modify element names do not match atom types* Number of element names must equal number of atom types. -*Dump modify fix ID does not compute per-atom array* - Self-explanatory. - -*Dump modify fix ID does not compute per-atom info* - Self-explanatory. - -*Dump modify fix ID does not compute per-atom vector* - Self-explanatory. - -*Dump modify fix ID vector is not large enough* - Self-explanatory. - -*Dump modify variable is not atom-style variable* - Self-explanatory. - -*Dump sort column is invalid* - Self-explanatory. - *Dump xtc requires sorting by atom ID* Use the dump_modify sort command to enable this. *Dump xyz/gz only writes compressed files* The dump xyz/gz output file name must have a .gz suffix. -*Dump_modify buffer yes not allowed for this style* - Self-explanatory. - *Dump_modify format string is too short* There are more fields to be dumped in a line of output than your format string specifies. -*Dump_modify region ID does not exist* - Self-explanatory. - *Dumping an atom property that is not allocated* The chosen atom style does not define the per-atom quantity being dumped. -*Duplicate atom IDs exist* - Self-explanatory. - -*Duplicate fields in read_dump command* - Self-explanatory. - *Duplicate particle in PeriDynamic bond - simulation box is too small* This is likely because your box length is shorter than 2 times the bond length. @@ -3067,20 +1777,9 @@ Doc page with :doc:`WARNING messages ` There is no variable syntax that uses empty brackets. Check the variable doc page. -*Energy was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to - have tallied energy, but they did not on this timestep. See the - variable page for ideas on how to make this work. - -*Epsilon or sigma reference not set by pair style in PPPMDisp* - Self-explanatory. - *Epsilon or sigma reference not set by pair style in ewald/n* The pair style is not providing the needed epsilon or sigma values. -*Error in MEAM parameter file: keyword %s (further information)* - Self-explanatory. Check the parameter file. - *Error in vdw spline: inner radius > outer radius* A pre-tabulated spline is invalid. Likely a problem with the potential parameters. @@ -3118,57 +1817,9 @@ Doc page with :doc:`WARNING messages ` *File variable could not read value* Check the file assigned to the variable. -*Final box dimension due to fix deform is < 0.0* - Self-explanatory. - *Fix %s does not allow use of dynamic group* Dynamic groups have not yet been enabled for this fix. -*Fix ID for compute chunk/atom does not exist* - Self-explanatory. - -*Fix ID for compute erotate/rigid does not exist* - Self-explanatory. - -*Fix ID for compute ke/rigid does not exist* - Self-explanatory. - -*Fix ID for compute reduce does not exist* - Self-explanatory. - -*Fix ID for compute slice does not exist* - Self-explanatory. - -*Fix ID for fix ave/atom does not exist* - Self-explanatory. - -*Fix ID for fix ave/chunk does not exist* - Self-explanatory. - -*Fix ID for fix ave/correlate does not exist* - Self-explanatory. - -*Fix ID for fix ave/histo does not exist* - Self-explanatory. - -*Fix ID for fix ave/time does not exist* - Self-explanatory. - -*Fix ID for fix store/state does not exist* - Self-explanatory - -*Fix ID for fix vector does not exist* - Self-explanatory. - -*Fix ID for read_data does not exist* - Self-explanatory. - -*Fix ID for velocity does not exist* - Self-explanatory. - -*Fix ID must be alphanumeric or underscore characters* - Self-explanatory. - *Fix SRD: bad bin assignment for SRD advection* Something has gone wrong in your SRD model; try using more conservative settings. @@ -3191,12 +1842,6 @@ Doc page with :doc:`WARNING messages ` *Fix adapt interface to this pair style not supported* New coding for the pair style would need to be done. -*Fix adapt kspace style does not exist* - Self-explanatory. - -*Fix adapt pair style does not exist* - Self-explanatory - *Fix adapt pair style param not supported* The pair style does not know about the parameter you specified. @@ -3206,30 +1851,15 @@ Doc page with :doc:`WARNING messages ` *Fix adapt requires atom attribute diameter* The atom style being used does not specify an atom diameter. -*Fix adapt type pair range is not valid for pair hybrid sub-style* - Self-explanatory. - *Fix append/atoms requires a lattice be defined* Use the lattice command for this purpose. -*Fix ave/atom compute array is accessed out-of-range* - Self-explanatory. - -*Fix ave/atom compute does not calculate a per-atom array* - Self-explanatory. - *Fix ave/atom compute does not calculate a per-atom vector* A compute used by fix ave/atom must generate per-atom values. *Fix ave/atom compute does not calculate per-atom values* A compute used by fix ave/atom must generate per-atom values. -*Fix ave/atom fix array is accessed out-of-range* - Self-explanatory. - -*Fix ave/atom fix does not calculate a per-atom array* - Self-explanatory. - *Fix ave/atom fix does not calculate a per-atom vector* A fix used by fix ave/atom must generate per-atom values. @@ -3239,145 +1869,13 @@ Doc page with :doc:`WARNING messages ` *Fix ave/atom variable is not atom-style variable* A variable used by fix ave/atom must generate per-atom values. -*Fix ave/chunk compute does not calculate a per-atom array* - Self-explanatory. - -*Fix ave/chunk compute does not calculate a per-atom vector* - Self-explanatory. - -*Fix ave/chunk compute does not calculate per-atom values* - Self-explanatory. - -*Fix ave/chunk compute vector is accessed out-of-range* - Self-explanatory. - *Fix ave/chunk does not use chunk/atom compute* The specified compute is not for a compute chunk/atom command. -*Fix ave/chunk fix does not calculate a per-atom array* - Self-explanatory. - -*Fix ave/chunk fix does not calculate a per-atom vector* - Self-explanatory. - -*Fix ave/chunk fix does not calculate per-atom values* - Self-explanatory. - -*Fix ave/chunk fix vector is accessed out-of-range* - Self-explanatory. - -*Fix ave/chunk variable is not atom-style variable* - Self-explanatory. - -*Fix ave/correlate compute does not calculate a scalar* - Self-explanatory. - -*Fix ave/correlate compute does not calculate a vector* - Self-explanatory. - -*Fix ave/correlate compute vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Fix ave/correlate fix does not calculate a scalar* - Self-explanatory. - -*Fix ave/correlate fix does not calculate a vector* - Self-explanatory. - -*Fix ave/correlate fix vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Fix ave/correlate variable is not equal-style variable* - Self-explanatory. - -*Fix ave/histo cannot input local values in scalar mode* - Self-explanatory. - -*Fix ave/histo cannot input per-atom values in scalar mode* - Self-explanatory. - -*Fix ave/histo compute array is accessed out-of-range* - Self-explanatory. - -*Fix ave/histo compute does not calculate a global array* - Self-explanatory. - -*Fix ave/histo compute does not calculate a global scalar* - Self-explanatory. - -*Fix ave/histo compute does not calculate a global vector* - Self-explanatory. - -*Fix ave/histo compute does not calculate a local array* - Self-explanatory. - -*Fix ave/histo compute does not calculate a local vector* - Self-explanatory. - -*Fix ave/histo compute does not calculate a per-atom array* - Self-explanatory. - -*Fix ave/histo compute does not calculate a per-atom vector* - Self-explanatory. - -*Fix ave/histo compute does not calculate local values* - Self-explanatory. - -*Fix ave/histo compute does not calculate per-atom values* - Self-explanatory. - -*Fix ave/histo compute vector is accessed out-of-range* - Self-explanatory. - -*Fix ave/histo fix array is accessed out-of-range* - Self-explanatory. - -*Fix ave/histo fix does not calculate a global array* - Self-explanatory. - -*Fix ave/histo fix does not calculate a global scalar* - Self-explanatory. - -*Fix ave/histo fix does not calculate a global vector* - Self-explanatory. - -*Fix ave/histo fix does not calculate a local array* - Self-explanatory. - -*Fix ave/histo fix does not calculate a local vector* - Self-explanatory. - -*Fix ave/histo fix does not calculate a per-atom array* - Self-explanatory. - -*Fix ave/histo fix does not calculate a per-atom vector* - Self-explanatory. - -*Fix ave/histo fix does not calculate local values* - Self-explanatory. - -*Fix ave/histo fix does not calculate per-atom values* - Self-explanatory. - -*Fix ave/histo fix vector is accessed out-of-range* - Self-explanatory. - -*Fix ave/histo input is invalid compute* - Self-explanatory. - -*Fix ave/histo input is invalid fix* - Self-explanatory. - -*Fix ave/histo input is invalid variable* - Self-explanatory. - *Fix ave/histo inputs are not all global, peratom, or local* All inputs in a single fix ave/histo command must be of the same style. -*Fix ave/histo/weight value and weight vector lengths do not match* - Self-explanatory. - *Fix ave/time cannot set output array intensive/extensive from these inputs* One of more of the vector inputs has individual elements which are flagged as intensive or extensive. Such an input cannot be flagged as @@ -3386,48 +1884,6 @@ Doc page with :doc:`WARNING messages ` *Fix ave/time cannot use variable with vector mode* Variables produce scalar values. -*Fix ave/time columns are inconsistent lengths* - Self-explanatory. - -*Fix ave/time compute array is accessed out-of-range* - An index for the array is out of bounds. - -*Fix ave/time compute does not calculate a scalar* - Self-explanatory. - -*Fix ave/time compute does not calculate a vector* - Self-explanatory. - -*Fix ave/time compute does not calculate an array* - Self-explanatory. - -*Fix ave/time compute vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Fix ave/time fix array cannot be variable length* - Self-explanatory. - -*Fix ave/time fix array is accessed out-of-range* - An index for the array is out of bounds. - -*Fix ave/time fix does not calculate a scalar* - Self-explanatory. - -*Fix ave/time fix does not calculate a vector* - Self-explanatory. - -*Fix ave/time fix does not calculate an array* - Self-explanatory. - -*Fix ave/time fix vector cannot be variable length* - Self-explanatory. - -*Fix ave/time fix vector is accessed out-of-range* - The index for the vector is out of bounds. - -*Fix ave/time variable is not equal-style variable* - Self-explanatory. - *Fix balance rcb cannot be used with comm_style brick* Comm_style tiled must be used instead. @@ -3439,19 +1895,10 @@ Doc page with :doc:`WARNING messages ` acquire needed info, The comm_modify cutoff command can be used to extend the communication range. -*Fix bond/create angle type is invalid* - Self-explanatory. - *Fix bond/create cutoff is longer than pairwise cutoff* This is not allowed because bond creation is done using the pairwise neighbor list. -*Fix bond/create dihedral type is invalid* - Self-explanatory. - -*Fix bond/create improper type is invalid* - Self-explanatory. - *Fix bond/create induced too many angles/dihedrals/impropers per atom* See the read_data command for info on using the "extra/angle/per/atom", (or dihedral, improper) keywords to allow for additional @@ -3498,15 +1945,6 @@ Doc page with :doc:`WARNING messages ` comm_modify cutoff command can be used to extend the communication range. -*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted* - Self-explanatory. - -*Fix bond/react: First neighbors of chiral atoms must be of mutually different types* - Self-explanatory. - -*Fix bond/react: Chiral atoms must have exactly four first neighbors* - Self-explanatory. - *Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword* The coordinates of atoms in the pre-reacted template are used to determine chirality. @@ -3524,12 +1962,6 @@ Doc page with :doc:`WARNING messages ` *Fix bond/swap cannot use dihedral or improper styles* These styles cannot be defined when using this fix. -*Fix bond/swap requires pair and bond styles* - Self-explanatory. - -*Fix bond/swap requires special_bonds = 0,1,1* - Self-explanatory. - *Fix box/relax generated negative box length* The pressure being applied is likely too large. Try applying it incrementally, to build to the high pressure. @@ -3555,12 +1987,6 @@ Doc page with :doc:`WARNING messages ` *Fix deform volume setting is invalid* Cannot use volume style unless other dimensions are being controlled. -*Fix deposit and fix rigid/small not using same molecule template ID* - Self-explanatory. - -*Fix deposit and fix shake not using same molecule template ID* - Self-explanatory. - *Fix deposit molecule must have atom types* The defined molecule does not specify atom types. @@ -3578,9 +2004,6 @@ Doc page with :doc:`WARNING messages ` Not all regions represent bounded volumes. You cannot use such a region with the fix deposit command. -*Fix deposit shake fix does not exist* - Self-explanatory. - *Fix efield requires atom attribute q or mu* The atom style defined does not have this attribute. @@ -3628,28 +2051,16 @@ Doc page with :doc:`WARNING messages ` *Fix freeze requires atom attribute torque* The atom style defined does not have this attribute. -*Fix gcmc and fix shake not using same molecule template ID* - Self-explanatory. - -*Fix gcmc atom has charge, but atom style does not* - Self-explanatory. - *Fix gcmc cannot exchange individual atoms belonging to a molecule* This is an error since you should not delete only one atom of a molecule. The user has specified atomic (non-molecular) gas exchanges, but an atom belonging to a molecule could be deleted. -*Fix gcmc does not (yet) work with atom_style template* - Self-explanatory. - *Fix gcmc molecule command requires that atoms have molecule attributes* Should not choose the gcmc molecule feature if no molecules are being simulated. The general molecule flag is off, but gcmc's molecule flag is on. -*Fix gcmc molecule has charges, but atom style does not* - Self-explanatory. - *Fix gcmc molecule must have atom types* The defined molecule does not specify atom types. @@ -3676,39 +2087,6 @@ Doc page with :doc:`WARNING messages ` Not all regions represent bounded volumes. You cannot use such a region with the fix gcmc command. -*Fix gcmc region extends outside simulation box* - Self-explanatory. - -*Fix gcmc shake fix does not exist* - Self-explanatory. - -*Fix gld c coefficients must be >= 0* - Self-explanatory. - -*Fix gld needs more prony series coefficients* - Self-explanatory. - -*Fix gld prony terms must be > 0* - Self-explanatory. - -*Fix gld series type must be pprony for now* - Self-explanatory. - -*Fix gld start temperature must be >= 0* - Self-explanatory. - -*Fix gld stop temperature must be >= 0* - Self-explanatory. - -*Fix gld tau coefficients must be > 0* - Self-explanatory. - -*Fix halt variable is not equal-style variable* - Self-explanatory. - -*Fix heat group has no atoms* - Self-explanatory. - *Fix heat kinetic energy of an atom went negative* This will cause the velocity rescaling about to be performed by fix heat to be invalid. @@ -3724,69 +2102,24 @@ Doc page with :doc:`WARNING messages ` *Fix langevin angmom is not yet implemented with kokkos* This option is not yet available. -*Fix langevin angmom requires atom style ellipsoid* - Self-explanatory. - *Fix langevin angmom requires extended particles* This fix option cannot be used with point particles. -*Fix langevin gjf and respa are not compatible* - Self-explanatory. - *Fix langevin gjf cannot have period equal to dt/2* If the period is equal to dt/2 then division by zero will happen. -*Fix langevin gjf should come before fix nve* - Self-explanatory. - *Fix langevin gjf with tbias is not yet implemented with kokkos* This option is not yet available. *Fix langevin omega is not yet implemented with kokkos* This option is not yet available. -*Fix langevin omega requires atom style sphere* - Self-explanatory. - *Fix langevin omega requires extended particles* One of the particles has radius 0.0. *Fix langevin period must be > 0.0* The time window for temperature relaxation must be > 0 -*Fix langevin variable returned negative temperature* - Self-explanatory. - -*Fix momentum group has no atoms* - Self-explanatory. - -*Fix move cannot define z or vz variable for 2d problem* - Self-explanatory. - -*Fix move cannot rotate aroung non z-axis for 2d problem* - Self-explanatory. - -*Fix move cannot set linear z motion for 2d problem* - Self-explanatory. - -*Fix move cannot set wiggle z motion for 2d problem* - Self-explanatory. - -*Fix msst compute ID does not compute potential energy* - Self-explanatory. - -*Fix msst compute ID does not compute pressure* - Self-explanatory. - -*Fix msst compute ID does not compute temperature* - Self-explanatory. - -*Fix msst requires a periodic box* - Self-explanatory. - -*Fix msst tscale must satisfy 0 <= tscale < 1* - Self-explanatory. - *Fix npt/nph has tilted box too far in one step - periodic cell is too far from equilibrium state* Self-explanatory. The change in the box tilt is too extreme on a short timescale. @@ -3806,61 +2139,22 @@ Doc page with :doc:`WARNING messages ` *Fix nve/asphere requires extended particles* This fix can only be used for particles with a shape setting. -*Fix nve/asphere/noforce requires atom style ellipsoid* - Self-explanatory. - *Fix nve/asphere/noforce requires extended particles* One of the particles is not an ellipsoid. -*Fix nve/body requires atom style body* - Self-explanatory. - *Fix nve/body requires bodies* This fix can only be used for particles that are bodies. -*Fix nve/line can only be used for 2d simulations* - Self-explanatory. - -*Fix nve/line requires atom style line* - Self-explanatory. - -*Fix nve/line requires line particles* - Self-explanatory. - *Fix nve/sphere dipole requires atom attribute mu* An atom style with this attribute is needed. -*Fix nve/sphere requires atom style sphere* - Self-explanatory. - *Fix nve/sphere requires extended particles* This fix can only be used for particles of a finite size. -*Fix nve/tri can only be used for 3d simulations* - Self-explanatory. - -*Fix nve/tri requires atom style tri* - Self-explanatory. - -*Fix nve/tri requires tri particles* - Self-explanatory. - *Fix nvt/nph/npt asphere requires extended particles* The shape setting for a particle in the fix group has shape = 0.0, which means it is a point particle. -*Fix nvt/nph/npt body requires bodies* - Self-explanatory. - -*Fix nvt/nph/npt sphere requires atom style sphere* - Self-explanatory. - -*Fix nvt/npt/nph damping parameters must be > 0.0* - Self-explanatory. - -*Fix nvt/npt/nph dilate group ID does not exist* - Self-explanatory. - *Fix nvt/sphere requires extended particles* This fix can only be used for particles of a finite size. @@ -3879,15 +2173,6 @@ Doc page with :doc:`WARNING messages ` *Fix peri neigh does not exist* Somehow a fix that the pair style defines has been deleted. -*Fix pour and fix rigid/small not using same molecule template ID* - Self-explanatory. - -*Fix pour and fix shake not using same molecule template ID* - Self-explanatory. - -*Fix pour insertion count per timestep is 0* - Self-explanatory. - *Fix pour molecule must have atom types* The defined molecule does not specify atom types. @@ -3898,12 +2183,6 @@ Doc page with :doc:`WARNING messages ` When using atom_style template, you cannot pour molecules that are not in that template. -*Fix pour polydisperse fractions do not sum to 1.0* - Self-explanatory. - -*Fix pour region ID does not exist* - Self-explanatory. - *Fix pour region cannot be dynamic* Only static regions can be used with fix pour. @@ -3914,187 +2193,49 @@ Doc page with :doc:`WARNING messages ` *Fix pour requires atom attributes radius, rmass* The atom style defined does not have these attributes. -*Fix pour rigid fix does not exist* - Self-explanatory. - -*Fix pour shake fix does not exist* - Self-explanatory. - -*Fix press/berendsen damping parameters must be > 0.0* - Self-explanatory. - -*Fix property/atom cannot specify mol twice* - Self-explanatory. - -*Fix property/atom cannot specify q twice* - Self-explanatory. - -*Fix property/atom mol when atom_style already has molecule attribute* - Self-explanatory. - -*Fix property/atom q when atom_style already has charge attribute* - Self-explanatory. - *Fix property/atom vector name already exists* The name for an integer or floating-point vector must be unique. -*Fix qeq has negative upper Taper radius cutoff* - Self-explanatory. - -*Fix qeq/comb group has no atoms* - Self-explanatory. - *Fix qeq/comb requires atom attribute q* An atom style with charge must be used to perform charge equilibration. -*Fix qeq/dynamic group has no atoms* - Self-explanatory. - -*Fix qeq/dynamic requires atom attribute q* - Self-explanatory. - -*Fix qeq/fire group has no atoms* - Self-explanatory. - -*Fix qeq/fire requires atom attribute q* - Self-explanatory. - -*Fix qeq/point group has no atoms* - Self-explanatory. - *Fix qeq/point has insufficient QEq matrix size* Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and re-compile. -*Fix qeq/point requires atom attribute q* - Self-explanatory. - -*Fix qeq/shielded group has no atoms* - Self-explanatory. - *Fix qeq/shielded has insufficient QEq matrix size* Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and re-compile. -*Fix qeq/shielded requires atom attribute q* - Self-explanatory. - *Fix qeq/slater could not extract params from pair coul/streitz* This should not happen unless pair coul/streitz has been altered. -*Fix qeq/slater group has no atoms* - Self-explanatory. - *Fix qeq/slater has insufficient QEq matrix size* Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and re-compile. -*Fix qeq/slater requires atom attribute q* - Self-explanatory. - *Fix reax/bonds numbonds > nsbmax_most* The limit of the number of bonds expected by the ReaxFF force field was exceeded. -*Fix recenter group has no atoms* - Self-explanatory. - -*Fix restrain requires an atom map, see atom_modify* - Self-explanatory. - *Fix rigid atom has non-zero image flag in a non-periodic dimension* Image flags for non-periodic dimensions should not be set. -*Fix rigid file has no lines* - Self-explanatory. - -*Fix rigid langevin period must be > 0.0* - Self-explanatory. - -*Fix rigid molecule requires atom attribute molecule* - Self-explanatory. - -*Fix rigid npt/nph dilate group ID does not exist* - Self-explanatory. - *Fix rigid npt/nph does not yet allow triclinic box* This is a current restriction in LAMMPS. -*Fix rigid npt/nph period must be > 0.0* - Self-explanatory. - -*Fix rigid npt/small t_chain should not be less than 1* - Self-explanatory. - -*Fix rigid npt/small t_order must be 3 or 5* - Self-explanatory. - -*Fix rigid nvt/npt/nph damping parameters must be > 0.0* - Self-explanatory. - -*Fix rigid nvt/small t_chain should not be less than 1* - Self-explanatory. - -*Fix rigid nvt/small t_iter should not be less than 1* - Self-explanatory. - -*Fix rigid nvt/small t_order must be 3 or 5* - Self-explanatory. - -*Fix rigid xy torque cannot be on for 2d simulation* - Self-explanatory. - -*Fix rigid z force cannot be on for 2d simulation* - Self-explanatory. - -*Fix rigid/npt period must be > 0.0* - Self-explanatory. - -*Fix rigid/npt temperature order must be 3 or 5* - Self-explanatory. - -*Fix rigid/npt/small period must be > 0.0* - Self-explanatory. - -*Fix rigid/nvt period must be > 0.0* - Self-explanatory. - -*Fix rigid/nvt temperature order must be 3 or 5* - Self-explanatory. - -*Fix rigid/nvt/small period must be > 0.0* - Self-explanatory. - *Fix rigid/small atom has non-zero image flag in a non-periodic dimension* Image flags for non-periodic dimensions should not be set. -*Fix rigid/small langevin period must be > 0.0* - Self-explanatory. - *Fix rigid/small molecule must have atom types* The defined molecule does not specify atom types. *Fix rigid/small molecule must have coordinates* The defined molecule does not specify coordinates. -*Fix rigid/small npt/nph period must be > 0.0* - Self-explanatory. - -*Fix rigid/small nvt/npt/nph damping parameters must be > 0.0* - Self-explanatory. - -*Fix rigid/small nvt/npt/nph dilate group ID does not exist* - Self-explanatory. - -*Fix rigid/small requires an atom map, see atom_modify* - Self-explanatory. - -*Fix rigid/small requires atom attribute molecule* - Self-explanatory. - *Fix rigid: Bad principal moments* The principal moments of inertia computed for a rigid body are not within the required tolerances. @@ -4106,9 +2247,6 @@ Doc page with :doc:`WARNING messages ` *Fix shake molecule template must have shake info* The defined molecule does not specify SHAKE information. -*Fix spring couple group ID does not exist* - Self-explanatory. - *Fix srd can only currently be used with comm_style brick* This is a current restriction in LAMMPS. @@ -4119,18 +2257,9 @@ Doc page with :doc:`WARNING messages ` This is because the SRD collisions will impart torque to the solute particles. -*Fix srd requires SRD particles all have same mass* - Self-explanatory. - *Fix srd requires ghost atoms store velocity* Use the comm_modify vel yes command to enable this. -*Fix srd requires newton pair on* - Self-explanatory. - -*Fix store/state compute array is accessed out-of-range* - Self-explanatory. - *Fix store/state compute does not calculate a per-atom array* The compute calculates a per-atom vector. @@ -4141,9 +2270,6 @@ Doc page with :doc:`WARNING messages ` Computes that calculate global or local quantities cannot be used with fix store/state. -*Fix store/state fix array is accessed out-of-range* - Self-explanatory. - *Fix store/state fix does not calculate a per-atom array* The fix calculates a per-atom vector. @@ -4154,71 +2280,20 @@ Doc page with :doc:`WARNING messages ` Fixes that calculate global or local quantities cannot be used with fix store/state. -*Fix store/state for atom property that is not allocated* - Self-explanatory. - *Fix store/state variable is not atom-style variable* Only atom-style variables calculate per-atom quantities. -*Fix temp/berendsen period must be > 0.0* - Self-explanatory. - -*Fix temp/berendsen variable returned negative temperature* - Self-explanatory. - *Fix temp/csld is not compatible with fix rattle or fix shake* These two commands cannot currently be used together with fix temp/csld. -*Fix temp/csld variable returned negative temperature* - Self-explanatory. - -*Fix temp/csvr variable returned negative temperature* - Self-explanatory. - -*Fix temp/rescale variable returned negative temperature* - Self-explanatory. - -*Fix tfmc displacement length must be > 0* - Self-explanatory. - *Fix tfmc is not compatible with fix shake* These two commands cannot currently be used together. -*Fix tfmc temperature must be > 0* - Self-explanatory. - -*Fix thermal/conductivity swap value must be positive* - Self-explanatory. - *Fix tmd must come after integration fixes* Any fix tmd command must appear in the input script after all time integration fixes (nve, nvt, npt). See the fix tmd documentation for details. -*Fix ttm electron temperatures must be > 0.0* - Self-explanatory. - -*Fix ttm electronic_density must be > 0.0* - Self-explanatory. - -*Fix ttm electronic_specific_heat must be > 0.0* - Self-explanatory. - -*Fix ttm electronic_thermal_conductivity must be >= 0.0* - Self-explanatory. - -*Fix ttm gamma_p must be > 0.0* - Self-explanatory. - -*Fix ttm gamma_s must be >= 0.0* - Self-explanatory. - -*Fix ttm number of nodes must be > 0* - Self-explanatory. - -*Fix ttm v_0 must be >= 0.0* - Self-explanatory. - *Fix used in compute chunk/atom not computed at compatible time* The chunk/atom compute cannot query the output of the fix on a timestep it is needed. @@ -4235,39 +2310,6 @@ Doc page with :doc:`WARNING messages ` The inputs to the command have conflicting intensive/extensive attributes. You need to use more than one fix vector command. -*Fix vector compute does not calculate a scalar* - Self-explanatory. - -*Fix vector compute does not calculate a vector* - Self-explanatory. - -*Fix vector compute vector is accessed out-of-range* - Self-explanatory. - -*Fix vector fix does not calculate a scalar* - Self-explanatory. - -*Fix vector fix does not calculate a vector* - Self-explanatory. - -*Fix vector fix vector is accessed out-of-range* - Self-explanatory. - -*Fix vector variable is not equal-style variable* - Self-explanatory. - -*Fix viscosity swap value must be positive* - Self-explanatory. - -*Fix viscosity vtarget value must be positive* - Self-explanatory. - -*Fix wall cutoff <= 0.0* - Self-explanatory. - -*Fix wall/colloid requires atom style sphere* - Self-explanatory. - *Fix wall/colloid requires extended particles* One of the particles has radius 0.0. @@ -4275,21 +2317,12 @@ Doc page with :doc:`WARNING messages ` Must use a granular pair style to define the parameters needed for this fix. -*Fix wall/gran requires atom style sphere* - Self-explanatory. - *Fix wall/piston command only available at zlo* The face keyword must be zlo. -*Fix wall/region colloid requires atom style sphere* - Self-explanatory. - *Fix wall/region colloid requires extended particles* One of the particles has radius 0.0. -*Fix wall/region cutoff <= 0.0* - Self-explanatory. - *Fix_modify pressure ID does not compute pressure* The compute ID assigned to the fix must compute pressure. @@ -4303,12 +2336,6 @@ Doc page with :doc:`WARNING messages ` *Found no restart file matching pattern* When using a "\*" in the restart file name, no matching file was found. -*GPU library not compiled for this accelerator* - Self-explanatory. - -*GPU package does not (yet) work with atom_style template* - Self-explanatory. - *GPU particle split must be set to 1 for this pair style.* For this pair style, you cannot run part of the force calculation on the host. See the package command. @@ -4325,21 +2352,12 @@ Doc page with :doc:`WARNING messages ` *Gravity changed since fix pour was created* The gravity vector defined by fix gravity must be static. -*Gravity must point in -y to use with fix pour in 2d* - Self-explanatory. - -*Gravity must point in -z to use with fix pour in 3d* - Self-explanatory. - *Grmask function in equal-style variable formula* Grmask is per-atom operation. *Group ID does not exist* A group ID used in the group command does not exist. -*Group ID in variable formula does not exist* - Self-explanatory. - *Group all cannot be made dynamic* This operation is not allowed. @@ -4347,15 +2365,6 @@ Doc page with :doc:`WARNING messages ` The group command cannot be used before a read_data, read_restart, or create_box command. -*Group dynamic cannot reference itself* - Self-explanatory. - -*Group dynamic parent group cannot be dynamic* - Self-explanatory. - -*Group dynamic parent group does not exist* - Self-explanatory. - *Group region ID does not exist* A region ID used in the group command does not exist. @@ -4388,19 +2397,10 @@ Doc page with :doc:`WARNING messages ` One or more of the coefficients defined in the potential file is invalid. -*Illegal compute voronoi/atom command (occupation and (surface or edges))* - Self-explanatory. - *Illegal coul/streitz parameter* One or more of the coefficients defined in the potential file is invalid. -*Illegal dump_modify sfactor value (must be > 0.0)* - Self-explanatory. - -*Illegal dump_modify tfactor value (must be > 0.0)* - Self-explanatory. - *Illegal fix gcmc gas mass <= 0* The computed mass of the designated gas molecule or atom type was less than or equal to zero. @@ -4411,9 +2411,6 @@ Doc page with :doc:`WARNING messages ` *Illegal fix wall/piston velocity* The piston velocity must be positive. -*Illegal integrate style* - Self-explanatory. - *Illegal nb3b/harmonic parameter* One or more of the coefficients defined in the potential file is invalid. @@ -4462,18 +2459,6 @@ Doc page with :doc:`WARNING messages ` on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid improper. -*Improper atoms %d %d %d %d missing on proc %d at step %ld* - One or more of 4 atoms needed to compute a particular improper are - missing on this processor. Typically this is because the pairwise - cutoff is set too short or the improper has blown apart and an atom is - too far away. - -*Improper atoms missing on proc %d at step %ld* - One or more of 4 atoms needed to compute a particular improper are - missing on this processor. Typically this is because the pairwise - cutoff is set too short or the improper has blown apart and an atom is - too far away. - *Improper coeff for hybrid has invalid style* Improper style hybrid uses another improper style as one of its coefficients. The improper style used in the improper_coeff command @@ -4483,15 +2468,6 @@ Doc page with :doc:`WARNING messages ` No improper coefficients have been assigned in the data file or via the improper_coeff command. -*Improper style hybrid cannot have hybrid as an argument* - Self-explanatory. - -*Improper style hybrid cannot have none as an argument* - Self-explanatory. - -*Improper style hybrid cannot use same improper style twice* - Self-explanatory. - *Improper_coeff command before improper_style is defined* Coefficients cannot be set in the data file or via the improper_coeff command until an improper_style has been assigned. @@ -4554,24 +2530,6 @@ Doc page with :doc:`WARNING messages ` *Incorrect SNAP parameter file* The file cannot be parsed correctly, check its internal syntax. -*Incorrect args for angle coefficients* - Self-explanatory. Check the input script or data file. - -*Incorrect args for bond coefficients* - Self-explanatory. Check the input script or data file. - -*Incorrect args for dihedral coefficients* - Self-explanatory. Check the input script or data file. - -*Incorrect args for improper coefficients* - Self-explanatory. Check the input script or data file. - -*Incorrect args for pair coefficients* - Self-explanatory. Check the input script or data file. - -*Incorrect args in pair_style command* - Self-explanatory. - *Incorrect atom format in data file* Number of values per atom line in the data file is not consistent with the atom style. @@ -4610,10 +2568,6 @@ Doc page with :doc:`WARNING messages ` *Incorrect element names in EAM potential file* The element names in the EAM file do not match those requested. -*Incorrect format of ... section in data file* - Number or type of values per line in the given section of the data file - is not consistent with the requirements for this section. - *Incorrect format in COMB potential file* Incorrect number of words per line in the potential file. @@ -4650,49 +2604,25 @@ Doc page with :doc:`WARNING messages ` *Incorrect integer value in Bodies section of data file* See page for body style. -*Incorrect multiplicity arg for dihedral coefficients* - Self-explanatory. Check the input script or data file. - -*Incorrect number of elements in potential file* - Self-explanatory. - *Incorrect rigid body format in fix rigid file* The number of fields per line is not what expected. *Incorrect rigid body format in fix rigid/small file* The number of fields per line is not what expected. -*Incorrect sign arg for dihedral coefficients* - Self-explanatory. Check the input script or data file. - -*Incorrect table format check for element types* - Self-explanatory. - *Incorrect velocity format in data file* Each atom style defines a format for the Velocity section of the data file. The read-in lines do not match. -*Incorrect weight arg for dihedral coefficients* - Self-explanatory. Check the input script or data file. - -*Index between variable brackets must be positive* - Self-explanatory. - *Indexed per-atom vector in variable formula without atom map* Accessing a value from an atom vector requires the ability to lookup an atom index, which is provided by an atom map. An atom map does not exist (by default) for non-molecular problems. Using the atom_modify map command will force an atom map to be created. -*Initial temperatures not all set in fix ttm* - Self-explanatory. - *Input line quote not followed by white-space* An end quote must be followed by white-space. -*Insertion region extends outside simulation box* - Self-explanatory. - *Insufficient Jacobi rotations for POEMS body* Eigensolve for rigid body was not sufficiently accurate. @@ -4716,62 +2646,17 @@ Doc page with :doc:`WARNING messages ` *Internal error in atom_style body* This error should not occur. Contact the developers. -*Invalid -reorder N value* - Self-explanatory. - -*Invalid Angles section in molecule file* - Self-explanatory. - -*Invalid Bonds section in molecule file* - Self-explanatory. - -*Invalid Boolean syntax in if command* - Self-explanatory. - -*Invalid Charges section in molecule file* - Self-explanatory. - -*Invalid Coords section in molecule file* - Self-explanatory. - -*Invalid Diameters section in molecule file* - Self-explanatory. - -*Invalid Dihedrals section in molecule file* - Self-explanatory. - -*Invalid Impropers section in molecule file* - Self-explanatory. - -*Invalid Kokkos command-line args* - Self-explanatory. See Section 2.7 of the manual for details. - *Invalid LAMMPS restart file* The file does not appear to be a LAMMPS restart file since it does not contain the correct magic string at the beginning. -*Invalid Masses section in molecule file* - Self-explanatory. - *Invalid molecule ID in molecule file* Molecule ID must be a non-zero positive integer. -*Invalid Molecules section in molecule file* - Self-explanatory. - *Invalid REAX atom type* There is a mis-match between LAMMPS atom types and the elements listed in the ReaxFF force field file. -*Invalid Special Bond Counts section in molecule file* - Self-explanatory. - -*Invalid Types section in molecule file* - Self-explanatory. - -*Invalid angle count in molecule file* - Self-explanatory. - *Invalid angle table length* Length must be 2 or greater. @@ -4779,12 +2664,6 @@ Doc page with :doc:`WARNING messages ` Angle type must be positive integer and within range of specified angle types. -*Invalid angle type in Angles section of molecule file* - Self-explanatory. - -*Invalid angle type index for fix shake* - Self-explanatory. - *Invalid args for non-hybrid pair coefficients* "NULL" is only supported in pair_coeff calls when using pair hybrid @@ -4800,9 +2679,6 @@ Doc page with :doc:`WARNING messages ` Atom IDs must be positive integers and within range of defined atoms. -*Invalid atom ID in Angles section of molecule file* - Self-explanatory. - *Invalid atom ID in Atoms section of data file* Atom IDs must be positive integers. @@ -4814,9 +2690,6 @@ Doc page with :doc:`WARNING messages ` Atom IDs must be positive integers and within range of defined atoms. -*Invalid atom ID in Bonds section of molecule file* - Self-explanatory. - *Invalid atom ID in Bonus section of data file* Atom IDs must be positive integers and within range of defined atoms. @@ -4825,9 +2698,6 @@ Doc page with :doc:`WARNING messages ` Atom IDs must be positive integers and within range of defined atoms. -*Invalid atom ID in Fragments section of molecule file* - Self-explanatory. - *Invalid atom ID in Impropers section of data file* Atom IDs must be positive integers and within range of defined atoms. @@ -4836,15 +2706,6 @@ Doc page with :doc:`WARNING messages ` Atom IDs must be positive integers and within range of defined atoms. -*Invalid atom ID in dihedrals section of molecule file* - Self-explanatory. - -*Invalid atom ID in impropers section of molecule file* - Self-explanatory. - -*Invalid atom ID in variable file* - Self-explanatory. - *Invalid atom IDs in neb file* An ID in the file was not found in the system. @@ -4873,12 +2734,6 @@ Doc page with :doc:`WARNING messages ` *Invalid atom type in fix atom/swap command* The atom type specified in the atom/swap command does not exist. -*Invalid atom type in fix bond/create command* - Self-explanatory. - -*Invalid atom type in fix deposit command* - Self-explanatory. - *Invalid atom type in fix deposit mol command* The atom types in the defined molecule are added to the value specified in the create_atoms command, as an offset. The final value @@ -4888,9 +2743,6 @@ Doc page with :doc:`WARNING messages ` *Invalid atom type in fix gcmc command* The atom type specified in the gcmc command does not exist. -*Invalid atom type in fix pour command* - Self-explanatory. - *Invalid atom type in fix pour mol command* The atom types in the defined molecule are added to the value specified in the create_atoms command, as an offset. The final value @@ -4915,18 +2767,6 @@ Doc page with :doc:`WARNING messages ` *Invalid atom_style body command* No body style argument was provided. -*Invalid atom_style command* - Self-explanatory. - -*Invalid attribute in dump custom command* - Self-explanatory. - -*Invalid attribute in dump local command* - Self-explanatory. - -*Invalid attribute in dump modify command* - Self-explanatory. - *Invalid basis setting in create_atoms command* The basis index must be between 1 to N where N is the number of basis atoms in the lattice. The type index must be between 1 to N where N @@ -4946,9 +2786,6 @@ Doc page with :doc:`WARNING messages ` *Invalid body nparticle command* Arguments in atom-style command are not correct. -*Invalid bond count in molecule file* - Self-explanatory. - *Invalid bond table length* Length must be 2 or greater. @@ -4956,21 +2793,6 @@ Doc page with :doc:`WARNING messages ` Bond type must be positive integer and within range of specified bond types. -*Invalid bond type in Bonds section of molecule file* - Self-explanatory. - -*Invalid bond type in create_bonds command* - Self-explanatory. - -*Invalid bond type in fix bond/break command* - Self-explanatory. - -*Invalid bond type in fix bond/create command* - Self-explanatory. - -*Invalid bond type index for fix shake* - Self-explanatory. Check the fix shake command in the input script. - *Invalid coeffs for this dihedral style* Cannot set class 2 coeffs in data file for this dihedral style. @@ -5074,22 +2896,10 @@ Doc page with :doc:`WARNING messages ` *Invalid density in set command* Density must be > 0.0. -*Invalid diameter in set command* - Self-explanatory. - -*Invalid dihedral count in molecule file* - Self-explanatory. - *Invalid dihedral type in Dihedrals section of data file* Dihedral type must be positive integer and within range of specified dihedral types. -*Invalid dihedral type in dihedrals section of molecule file* - Self-explanatory. - -*Invalid dipole length in set command* - Self-explanatory. - *Invalid displace_atoms rotate axis for 2d* Axis must be in z direction. @@ -5129,15 +2939,9 @@ Doc page with :doc:`WARNING messages ` *Invalid dump_modify threshold operator* Operator keyword used for threshold specification in not recognized. -*Invalid entry in -reorder file* - Self-explanatory. - *Invalid fix ID in variable formula* The fix is not recognized. -*Invalid fix ave/time off column* - Self-explanatory. - *Invalid fix box/relax command for a 2d simulation* Fix box/relax styles involving the z dimension cannot be used in a 2d simulation. @@ -5148,12 +2952,6 @@ Doc page with :doc:`WARNING messages ` *Invalid fix box/relax pressure settings* Settings for coupled dimensions must be the same. -*Invalid fix halt attribute* - Self-explanatory. - -*Invalid fix halt operator* - Self-explanatory. - *Invalid fix nvt/npt/nph command for a 2d simulation* Cannot control z dimension in a 2d model. @@ -5208,94 +3006,22 @@ Doc page with :doc:`WARNING messages ` *Invalid group function in variable formula* Group function is not recognized. -*Invalid group in comm_modify command* - Self-explanatory. - *Invalid image up vector* Up vector cannot be (0,0,0). *Invalid immediate variable* Syntax of immediate value is incorrect. -*Invalid improper count in molecule file* - Self-explanatory. - *Invalid improper type in Impropers section of data file* Improper type must be positive integer and within range of specified improper types. -*Invalid improper type in impropers section of molecule file* - Self-explanatory. - *Invalid index for non-body particles in compute body/local command* Only indices 1,2,3 can be used for non-body particles. -*Invalid index in compute body/local command* - Self-explanatory. - -*Invalid is_active() function in variable formula* - Self-explanatory. - -*Invalid is_available() function in variable formula* - Self-explanatory. - -*Invalid is_defined() function in variable formula* - Self-explanatory. - -*Invalid keyword in angle table parameters* - Self-explanatory. - -*Invalid keyword in bond table parameters* - Self-explanatory. - -*Invalid keyword in compute angle/local command* - Self-explanatory. - -*Invalid keyword in compute bond/local command* - Self-explanatory. - -*Invalid keyword in compute dihedral/local command* - Self-explanatory. - -*Invalid keyword in compute improper/local command* - Self-explanatory. - -*Invalid keyword in compute pair/local command* - Self-explanatory. - -*Invalid keyword in compute property/atom command* - Self-explanatory. - -*Invalid keyword in compute property/chunk command* - Self-explanatory. - -*Invalid keyword in compute property/local command* - Self-explanatory. - -*Invalid keyword in dump cfg command* - Self-explanatory. - *Invalid keyword in pair table parameters* Keyword used in list of table parameters is not recognized. -*Invalid length in set command* - Self-explanatory. - -*Invalid mass in set command* - Self-explanatory. - -*Invalid mass line in data file* - Self-explanatory. - -*Invalid mass value* - Self-explanatory. - -*Invalid math function in variable formula* - Self-explanatory. - -*Invalid math/group/special function in variable formula* - Self-explanatory. - *Invalid option in lattice command for non-custom style* Certain lattice keywords are not supported unless the lattice style is "custom". @@ -5336,9 +3062,6 @@ Doc page with :doc:`WARNING messages ` *Invalid random number seed in set command* Random number seed must be > 0. -*Invalid replace values in compute reduce* - Self-explanatory. - *Invalid rigid body ID in fix rigid file* The ID does not match the number of an existing ID of rigid bodies that are defined by the fix rigid command. @@ -5351,12 +3074,6 @@ Doc page with :doc:`WARNING messages ` The number of timesteps must fit in a 32-bit integer. If you want to run for more steps than this, perform multiple shorter runs. -*Invalid run command start/stop value* - Self-explanatory. - -*Invalid run command upto value* - Self-explanatory. - *Invalid seed for Marsaglia random # generator* The initial seed for this random number generator must be a positive integer less than or equal to 900 million. @@ -5365,45 +3082,9 @@ Doc page with :doc:`WARNING messages ` The initial seed for this random number generator must be a positive integer. -*Invalid shake angle type in molecule file* - Self-explanatory. - -*Invalid shake atom in molecule file* - Self-explanatory. - -*Invalid shake bond type in molecule file* - Self-explanatory. - -*Invalid shake flag in molecule file* - Self-explanatory. - -*Invalid shape in Ellipsoids section of data file* - Self-explanatory. - *Invalid shape in Triangles section of data file* Two or more of the triangle corners are duplicate points. -*Invalid shape in set command* - Self-explanatory. - -*Invalid shear direction for fix wall/gran* - Self-explanatory. - -*Invalid special atom index in molecule file* - Self-explanatory. - -*Invalid special function in variable formula* - Self-explanatory. - -*Invalid style in pair_write command* - Self-explanatory. Check the input script. - -*Invalid syntax in variable formula* - Self-explanatory. - -*Invalid t_event in prd command* - Self-explanatory. - *Invalid t_event in tad command* The value must be greater than 0. @@ -5415,9 +3096,6 @@ Doc page with :doc:`WARNING messages ` The template indices must be between 1 to N, where N is the number of molecules in the template. -*Invalid thermo keyword in variable formula* - The keyword is not recognized. - *Invalid threads_per_atom specified.* For 3-body potentials on the GPU, the threads_per_atom setting cannot be greater than 4 for NVIDIA GPUs. @@ -5469,9 +3147,6 @@ Doc page with :doc:`WARNING messages ` *Invalid variable evaluation in variable formula* A variable used in a formula could not be evaluated. -*Invalid variable in next command* - Self-explanatory. - *Invalid variable name* Variable name used in an input script line is invalid. @@ -5488,21 +3163,6 @@ Doc page with :doc:`WARNING messages ` *Invalid volume in set command* Volume must be > 0.0. -*Invalid wiggle direction for fix wall/gran* - Self-explanatory. - -*Invoked angle equil angle on angle style none* - Self-explanatory. - -*Invoked angle single on angle style none* - Self-explanatory. - -*Invoked bond equil distance on bond style none* - Self-explanatory. - -*Invoked bond single on bond style none* - Self-explanatory. - *Invoked pair single on pair style none* A command (e.g. a dump) attempted to invoke the single() function on a pair style none, which is illegal. You are probably attempting to @@ -5519,12 +3179,6 @@ Doc page with :doc:`WARNING messages ` Model. Please contact the OpenKIM database maintainers to verify and potentially correct this. -*KOKKOS package does not yet support comm_style tiled* - Self-explanatory. - -*KOKKOS package requires a kokkos enabled atom_style* - Self-explanatory. - *KSpace accuracy must be > 0* The kspace accuracy designated in the input must be greater than zero. @@ -5549,9 +3203,6 @@ Doc page with :doc:`WARNING messages ` Setting a kspace style requires that a pair style with matching long-range Coulombic or dispersion components be used. -*Keyword %s in MEAM parameter file not recognized* - Self-explanatory. - *Kokkos has been compiled for CUDA but no GPUs are requested* One or more GPUs must be used when Kokkos is compiled for CUDA. @@ -5565,39 +3216,18 @@ Doc page with :doc:`WARNING messages ` the required accuracy via *force/disp/real* as well as *force/disp/kspace* is set. -*Kspace style does not support compute group/group* - Self-explanatory. - -*Kspace style pppm/disp/tip4p requires newton on* - Self-explanatory. - -*Kspace style pppm/tip4p requires newton on* - Self-explanatory. - *Kspace style requires atom attribute q* The atom style defined does not have these attributes. -*Kspace_modify eigtol must be smaller than one* - Self-explanatory. - *LAMMPS is not built with Python embedded* This is done by including the PYTHON package before LAMMPS is built. This is required to use python-style variables. -*LAMMPS unit_style lj not supported by KIM models* - Self-explanatory. Check the input script or data file. - -*LJ6 off not supported in pair_style buck/long/coul/long* - Self-explanatory. - *Label map is incomplete: all types must be assigned a unique type label* For a given type-kind (atom types, bond types, etc.) to be written to the data file, all associated types must be assigned a type label, and each type label can be assigned to only one numeric type. -*Label wasn't found in input script* - Self-explanatory. - *Labelmap command before simulation box is defined* The labelmap command cannot be used before a read_data, read_restart, or create_box command. @@ -5625,19 +3255,9 @@ Doc page with :doc:`WARNING messages ` 2d simulation can use sq, sq2, or hex lattice. 3d simulation can use sc, bcc, or fcc lattice. -*Log of zero/negative value in variable formula* - Self-explanatory. - *Lost atoms via balance: original %ld current %ld* This should not occur. Report the problem to the developers. -*Lost atoms: original %ld current %ld* - Lost atoms are checked for each time thermo output is done. See the - thermo_modify lost command for options. Lost atoms usually indicate - bad dynamics, e.g. atoms have been blown far out of the simulation - box, or moved further than one processor's subdomain away before - reneighboring. - *MEAM library error %d* A call to the MEAM Fortran library returned an error. @@ -5678,9 +3298,6 @@ Doc page with :doc:`WARNING messages ` The minimize command cannot be used before a read_data, read_restart, or create_box command. -*Mismatched brackets in variable* - Self-explanatory. - *Mismatched compute in variable formula* A compute is referenced incorrectly or a compute that produces per-atom values is used in an equal-style variable formula. @@ -5697,52 +3314,10 @@ Doc page with :doc:`WARNING messages ` produces per-atom values is used in an equal-style variable formula. -*Modulo 0 in variable formula* - Self-explanatory. - *Molecule IDs too large for compute chunk/atom* The IDs must not be larger than can be stored in a 32-bit integer since chunk IDs are 32-bit integers. -*Molecule auto special bond generation overflow* - Counts exceed maxspecial setting for other atoms in system. - -*Molecule file has angles but no nangles setting* - Self-explanatory. - -*Molecule file has body params but no setting for them* - Self-explanatory. - -*Molecule file has bonds but no nbonds setting* - Self-explanatory. - -*Molecule file has dihedrals but no ndihedrals setting* - Self-explanatory. - -*Molecule file has fragments but no nfragments setting* - Self-explanatory. - -*Molecule file has impropers but no nimpropers setting* - Self-explanatory. - -*Molecule file has no Body Doubles section* - Self-explanatory. - -*Molecule file has no Body Integers section* - Self-explanatory. - -*Molecule file has no Fragments section* - Self-explanatory. - -*Molecule file has special flags but no bonds* - Self-explanatory. - -*Molecule file needs both Special Bond sections* - Self-explanatory. - -*Molecule file requires atom style body* - Self-explanatory. - *Molecule file shake flags not before shake atoms* The order of the two sections is important. @@ -5755,52 +3330,6 @@ Doc page with :doc:`WARNING messages ` *Molecule file special list does not match special count* The number of values in an atom's special list does not match count. -*Molecule file z center-of-mass must be 0.0 for 2d* - Self-explanatory. - -*Molecule file z coord must be 0.0 for 2d* - Self-explanatory. - -*Molecule natoms must be 1 for body particle* - Self-explanatory. - -*Molecule sizescale must be 1.0 for body particle* - Self-explanatory. - -*Molecule template ID for atom_style template does not exist* - Self-explanatory. - -*Molecule template ID for create_atoms does not exist* - Self-explanatory. - -*Molecule template ID for fix deposit does not exist* - Self-explanatory. - -*Molecule template ID for fix gcmc does not exist* - Self-explanatory. - -*Molecule template ID for fix pour does not exist* - Self-explanatory. - -*Molecule template ID for fix rigid/small does not exist* - Self-explanatory. - -*Molecule template ID for fix shake does not exist* - Self-explanatory. - -*Molecule template ID must be alphanumeric or underscore characters* - Self-explanatory. - -*Molecule topology/atom exceeds system topology/atom* - The number of bonds, angles, etc per-atom in the molecule exceeds the - system setting. See the create_box command for how to specify these - values. - -*Molecule topology type exceeds system topology type* - The number of bond, angle, etc types in the molecule exceeds the - system setting. See the create_box command for how to specify these - values. - *More than one fix deform* Only one fix deform can be defined at a time. @@ -5811,9 +3340,6 @@ Doc page with :doc:`WARNING messages ` *More than one fix shake* Only one fix shake can be defined. -*Mu not allowed when not using semi-grand in fix atom/swap command* - Self-explanatory. - *Must define angle_style before Angle Coeffs* Must use an angle_style command before reading a data file that defines Angle Coeffs. @@ -5874,9 +3400,6 @@ Doc page with :doc:`WARNING messages ` Cannot use the temper command with only one processor partition. Use the -partition command-line option. -*Must not have multiple fixes change box parameter ...* - Self-explanatory. - *Must read Angle Type Labels before Angles* An Angle Type Labels section of a data file must come before the Angles section. @@ -5941,21 +3464,6 @@ Doc page with :doc:`WARNING messages ` *Must specify a region in fix deposit* The region keyword must be specified with this fix. -*Must specify a region in fix pour* - Self-explanatory. - -*Must specify at least 2 types in fix atom/swap command* - Self-explanatory. - -*Must use 'kim_style init' command before simulation box is defined* - Self-explanatory. - -*Must use 'kim_style define' command after simulation box is defined* - Self-explanatory. - -*Must use 'kim_style init' command before 'kim_style define'* - Self-explanatory. - *Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM* The kspace scalar pressure option cannot (yet) be used with rRESPA. @@ -5979,22 +3487,10 @@ Doc page with :doc:`WARNING messages ` *Must use Kokkos half/thread or full neighbor list with threads or GPUs* Using Kokkos half-neighbor lists with threading is not allowed. -*Must use a block or cylinder region with fix pour* - Self-explanatory. - -*Must use a block region with fix pour for 2d simulations* - Self-explanatory. - *Must use a bond style with TIP4P potential* TIP4P potentials assume bond lengths in water are constrained by a fix shake command. -*Must use a molecular atom style with fix poems molecule* - Self-explanatory. - -*Must use a z-axis cylinder region with fix pour* - Self-explanatory. - *Must use an angle style with TIP4P potential* TIP4P potentials assume angles in water are constrained by a fix shake command. @@ -6002,12 +3498,6 @@ Doc page with :doc:`WARNING messages ` *Must use atom map style array with Kokkos* See the atom_modify map command. -*Must use atom style with molecule IDs with fix bond/swap* - Self-explanatory. - -*Must use pair_style comb or comb3 with fix qeq/comb* - Self-explanatory. - *Must use variable energy with fix addforce* Must define an energy variable when applying a dynamic force during minimization. @@ -6016,21 +3506,12 @@ Doc page with :doc:`WARNING messages ` You must define an energy when performing a minimization with a variable E-field. -*NEB command before simulation box is defined* - Self-explanatory. - *NEB requires damped dynamics minimizer* Use a different minimization style. -*NEB requires use of fix neb* - Self-explanatory. - *NL ramp in wall/piston only implemented in zlo for now* The ramp keyword can only be used for piston applied to face zlo. -*Need nswaptypes mu values in fix atom/swap command* - Self-explanatory. - *Needed bonus data not in data file* Some atom styles require bonus data. See the read_data page for details. @@ -6039,12 +3520,6 @@ Doc page with :doc:`WARNING messages ` The header of the data file indicated bonds, angles, etc would be included, but they are not present. -*Neigh_modify exclude molecule requires atom attribute molecule* - Self-explanatory. - -*Neigh_modify include group != atom_modify first group* - Self-explanatory. - *Neighbor delay must be 0 or multiple of every setting* The delay and every parameters set via the neigh_modify command are inconsistent. If the delay setting is non-zero, then it must be a @@ -6061,12 +3536,6 @@ Doc page with :doc:`WARNING messages ` *Neighbor multi not yet enabled for ghost neighbors* This is a current restriction within LAMMPS. -*Neighbor multi not yet enabled for granular* - Self-explanatory. - -*Neighbor multi not yet enabled for rRESPA* - Self-explanatory. - *Neighbor page size must be >= 10x the one atom setting* This is required to prevent wasting too much memory. @@ -6094,19 +3563,10 @@ Doc page with :doc:`WARNING messages ` *Next command must list all universe and uloop variables* This is to ensure they stay in sync. -*No Kspace style defined for compute group/group* - Self-explanatory. - *No OpenMP support compiled in* An OpenMP flag is set, but LAMMPS was not built with OpenMP support. -*No angle style is defined for compute angle/local* - Self-explanatory. - -*No angles allowed with this atom style* - Self-explanatory. - *No atoms in data file* The header of the data file indicated that atoms would be included, but they are not present. @@ -6114,52 +3574,16 @@ Doc page with :doc:`WARNING messages ` *No basis atoms in lattice* Basis atoms must be defined for lattice style user. -*No bodies allowed with this atom style* - Self-explanatory. Check data file. - -*No bond style is defined for compute bond/local* - Self-explanatory. - -*No bonds allowed with this atom style* - Self-explanatory. - -*No box information in dump. You have to use 'box no'* - Self-explanatory. - *No count or invalid atom count in molecule file* The number of atoms must be specified. -*No dihedral style is defined for compute dihedral/local* - Self-explanatory. - -*No dihedrals allowed with this atom style* - Self-explanatory. - *No dump custom arguments specified* The dump custom command requires that atom quantities be specified to output to dump file. -*No dump local arguments specified* - Self-explanatory. - -*No ellipsoids allowed with this atom style* - Self-explanatory. Check data file. - *No fix gravity defined for fix pour* Gravity is required to use fix pour. -*No improper style is defined for compute improper/local* - Self-explanatory. - -*No impropers allowed with this atom style* - Self-explanatory. - -*No input values for fix ave/spatial* - Self-explanatory. - -*No lines allowed with this atom style* - Self-explanatory. Check data file. - *No matching element in ADP potential file* The ADP potential file does not contain elements that match the requested elements. @@ -6172,69 +3596,29 @@ Doc page with :doc:`WARNING messages ` The data file cannot specify the number of bonds, angles, etc, because this info if inferred from the molecule templates. -*No overlap of box and region for create_atoms* - Self-explanatory. - *No pair coul/streitz for fix qeq/slater* These commands must be used together. -*No pair hbond/dreiding coefficients set* - Self-explanatory. - *No pair style defined for compute group/group* Cannot calculate group interactions without a pair style defined. -*No pair style is defined for compute pair/local* - Self-explanatory. - -*No pair style is defined for compute property/local* - Self-explanatory. - *No rigid bodies defined* The fix specification did not end up defining any rigid bodies. -*No triangles allowed with this atom style* - Self-explanatory. Check data file. - -*No values in fix ave/chunk command* - Self-explanatory. - -*No values in fix ave/time command* - Self-explanatory. - -*Non digit character between brackets in variable* - Self-explanatory. - *Non integer # of swaps in temper command* Swap frequency in temper command must evenly divide the total # of timesteps. -*Non-numeric box dimensions - simulation unstable* - The box size has apparently blown up. - -*Non-zero atom IDs with atom_modify id = no* - Self-explanatory. - -*Non-zero read_data shift z value for 2d simulation* - Self-explanatory. - -*Nprocs not a multiple of N for -reorder* - Self-explanatory. - *Number of core atoms != number of shell atoms* There must be a one-to-one pairing of core and shell atoms. -*Numeric index is out of bounds* - A command with an argument that specifies an integer or range of - integers is using a value that is less than 1 or greater than the - maximum allowed limit. - *One or more Atom IDs is negative* Atom IDs must be positive integers. *One or more atom IDs is too big* - The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL - setting in your LAMMPS build. See the :doc:`Build settings ` page for more info. + The limit on atom IDs is set by the SMALLBIG, BIGBIG + setting in your LAMMPS build. See the + :doc:`Build settings ` page for more info. *One or more atom IDs is zero* Either all atoms IDs must be zero or none of them. @@ -6243,70 +3627,10 @@ Doc page with :doc:`WARNING messages ` Two or more rigid bodies defined by the fix rigid command cannot contain the same atom. -*One or more rigid bodies are a single particle* - Self-explanatory. - *One or zero atoms in rigid body* Any rigid body defined by the fix rigid command must contain 2 or more atoms. -*Only 2 types allowed when not using semi-grand in fix atom/swap command* - Self-explanatory. - -*Only one cut-off allowed when requesting all long* - Self-explanatory. - -*Only one cutoff allowed when requesting all long* - Self-explanatory. - -*Only zhi currently implemented for fix append/atoms* - Self-explanatory. - -*Out of range atoms - cannot compute MSM* - One or more atoms are attempting to map their charge to a MSM grid point - that is not owned by a processor. This is likely for one of two - reasons, both of them bad. First, it may mean that an atom near the - boundary of a processor's subdomain has moved more than 1/2 the - :doc:`neighbor skin distance ` without neighbor lists being - rebuilt and atoms being migrated to new processors. This also means - you may be missing pairwise interactions that need to be computed. - The solution is to change the re-neighboring criteria via the - :doc:`neigh_modify ` command. The safest settings are - "delay 0 every 1 check yes". Second, it may mean that an atom has - moved far outside a processor's subdomain or even the entire - simulation box. This indicates bad physics, e.g. due to highly - overlapping atoms, too large a timestep, etc. - -*Out of range atoms - cannot compute PPPM* - One or more atoms are attempting to map their charge to a PPPM grid - point that is not owned by a processor. This is likely for one of two - reasons, both of them bad. First, it may mean that an atom near the - boundary of a processor's subdomain has moved more than 1/2 the - :doc:`neighbor skin distance ` without neighbor lists being - rebuilt and atoms being migrated to new processors. This also means - you may be missing pairwise interactions that need to be computed. - The solution is to change the re-neighboring criteria via the - :doc:`neigh_modify ` command. The safest settings are - "delay 0 every 1 check yes". Second, it may mean that an atom has - moved far outside a processor's subdomain or even the entire - simulation box. This indicates bad physics, e.g. due to highly - overlapping atoms, too large a timestep, etc. - -*Out of range atoms - cannot compute PPPMDisp* - One or more atoms are attempting to map their charge to a PPPM grid - point that is not owned by a processor. This is likely for one of two - reasons, both of them bad. First, it may mean that an atom near the - boundary of a processor's subdomain has moved more than 1/2 the - :doc:`neighbor skin distance ` without neighbor lists being - rebuilt and atoms being migrated to new processors. This also means - you may be missing pairwise interactions that need to be computed. - The solution is to change the re-neighboring criteria via the - :doc:`neigh_modify ` command. The safest settings are - "delay 0 every 1 check yes". Second, it may mean that an atom has - moved far outside a processor's subdomain or even the entire - simulation box. This indicates bad physics, e.g. due to highly - overlapping atoms, too large a timestep, etc. - *Overflow of allocated fix vector storage* This should not normally happen if the fix correctly calculated how long the vector will grow to. Contact the developers. @@ -6362,12 +3686,6 @@ Doc page with :doc:`WARNING messages ` The prd command cannot be used before a read_data, read_restart, or create_box command. -*PRD nsteps must be multiple of t_event* - Self-explanatory. - -*PRD t_corr must be multiple of t_event* - Self-explanatory. - *Package command after simulation box is defined* The package command cannot be used after a read_data, read_restart, or create_box command. @@ -6388,30 +3706,18 @@ Doc page with :doc:`WARNING messages ` The OPENMP package must be installed via "make yes-openmp" before LAMMPS is built. -*Pair body requires atom style body* - Self-explanatory. - *Pair body requires body style nparticle* This pair style is specific to the nparticle body style. -*Pair brownian requires atom style sphere* - Self-explanatory. - *Pair brownian requires extended particles* One of the particles has radius 0.0. *Pair brownian requires monodisperse particles* All particles must be the same finite size. -*Pair brownian/poly requires atom style sphere* - Self-explanatory. - *Pair brownian/poly requires extended particles* One of the particles has radius 0.0. -*Pair brownian/poly requires newton pair off* - Self-explanatory. - *Pair coeff for hybrid has invalid style* Style in pair coeff must have been listed in pair_style command. @@ -6447,18 +3753,6 @@ Doc page with :doc:`WARNING messages ` Each atom type involved in pair_style gayberne must have these 3 coefficients set at least once. -*Pair gayberne requires atom style ellipsoid* - Self-explanatory. - -*Pair gayberne requires atoms with same type have same shape* - Self-explanatory. - -*Pair gayberne/gpu requires atom style ellipsoid* - Self-explanatory. - -*Pair gayberne/gpu requires atoms with same type have same shape* - Self-explanatory. - *Pair granular requires atom attributes radius, rmass* The atom style defined does not have these attributes. @@ -6469,9 +3763,6 @@ Doc page with :doc:`WARNING messages ` This is a current restriction of the implementation of pair granular styles with history. -*Pair hybrid single calls do not support per sub-style special bond values* - Self-explanatory. - *Pair hybrid sub-style does not support single call* You are attempting to invoke a single() call on a pair style that does not support it. @@ -6487,36 +3778,21 @@ Doc page with :doc:`WARNING messages ` *Pair inner cutoff >= Pair outer cutoff* The specified cutoffs for the pair style are inconsistent. -*Pair line/lj requires atom style line* - Self-explanatory. - *Pair lj/long/dipole/long requires atom attributes mu, torque* The atom style defined does not have these attributes. -*Pair lubricate requires atom style sphere* - Self-explanatory. - *Pair lubricate requires ghost atoms store velocity* Use the comm_modify vel yes command to enable this. *Pair lubricate requires monodisperse particles* All particles must be the same finite size. -*Pair lubricate/poly requires atom style sphere* - Self-explanatory. - *Pair lubricate/poly requires extended particles* One of the particles has radius 0.0. *Pair lubricate/poly requires ghost atoms store velocity* Use the comm_modify vel yes command to enable this. -*Pair lubricate/poly requires newton pair off* - Self-explanatory. - -*Pair lubricateU requires atom style sphere* - Self-explanatory. - *Pair lubricateU requires ghost atoms store velocity* Use the comm_modify vel yes command to enable this. @@ -6526,9 +3802,6 @@ Doc page with :doc:`WARNING messages ` *Pair lubricateU/poly requires ghost atoms store velocity* Use the comm_modify vel yes command to enable this. -*Pair lubricateU/poly requires newton pair off* - Self-explanatory. - *Pair peri lattice is not identical in x, y, and z* The lattice defined by the lattice command must be cubic. @@ -6539,24 +3812,6 @@ Doc page with :doc:`WARNING messages ` Even for atomic systems, an atom map is required to find Peridynamic bonds. Use the atom_modify command to define one. -*Pair resquared epsilon a,b,c coeffs are not all set* - Self-explanatory. - -*Pair resquared epsilon and sigma coeffs are not all set* - Self-explanatory. - -*Pair resquared requires atom style ellipsoid* - Self-explanatory. - -*Pair resquared requires atoms with same type have same shape* - Self-explanatory. - -*Pair resquared/gpu requires atom style ellipsoid* - Self-explanatory. - -*Pair resquared/gpu requires atoms with same type have same shape* - Self-explanatory. - *Pair style AIREBO requires atom IDs* This is a requirement to use the AIREBO potential. @@ -6574,9 +3829,6 @@ Doc page with :doc:`WARNING messages ` *Pair style COMB requires atom IDs* This is a requirement to use the AIREBO potential. -*Pair style COMB requires atom attribute q* - Self-explanatory. - *Pair style COMB requires newton pair on* See the newton command. This is a restriction to use the COMB potential. @@ -6584,9 +3836,6 @@ Doc page with :doc:`WARNING messages ` *Pair style COMB3 requires atom IDs* This is a requirement to use the COMB3 potential. -*Pair style COMB3 requires atom attribute q* - Self-explanatory. - *Pair style COMB3 requires newton pair on* See the newton command. This is a restriction to use the COMB3 potential. @@ -6670,9 +3919,6 @@ Doc page with :doc:`WARNING messages ` *Pair style coul/long/gpu requires atom attribute q* The atom style defined does not have these attributes. -*Pair style coul/streitz requires atom attribute q* - Self-explanatory. - *Pair style does not have extra field requested by compute pair/local* The pair style does not support the pN value requested by the compute pair/local command. @@ -6709,24 +3955,9 @@ Doc page with :doc:`WARNING messages ` Atoms in the simulation do not have IDs, so history effects cannot be tracked by the granular pair potential. -*Pair style hbond/dreiding requires an atom map, see atom_modify* - Self-explanatory. - -*Pair style hbond/dreiding requires atom IDs* - Self-explanatory. - -*Pair style hbond/dreiding requires molecular system* - Self-explanatory. - *Pair style hbond/dreiding requires newton pair on* See the newton command for details. -*Pair style hybrid cannot have hybrid as an argument* - Self-explanatory. - -*Pair style hybrid cannot have none as an argument* - Self-explanatory. - *Pair style is incompatible with KSpace style* If a pair style with a long-range Coulombic component is selected, then a kspace style must also be used. @@ -6826,9 +4057,6 @@ Doc page with :doc:`WARNING messages ` *Pair style nm/cut/coul/long requires atom attribute q* The atom style defined does not have this attribute. -*Pair style peri requires atom style peri* - Self-explanatory. - *Pair style polymorphic requires atom IDs* This is a requirement to use the polymorphic potential. @@ -6848,9 +4076,6 @@ Doc page with :doc:`WARNING messages ` *Pair style requires a KSpace style* No kspace style is defined. -*Pair style requires use of kspace_style ewald/disp* - Self-explanatory. - *Pair style sw/gpu requires atom IDs* This is a requirement to use this potential. @@ -6903,38 +4128,17 @@ Doc page with :doc:`WARNING messages ` *Pair tersoff/zbl/kk requires metal or real units* This is a current restriction of this pair potential. -*Pair tri/lj requires atom style tri* - Self-explanatory. - -*Pair yukawa/colloid requires atom style sphere* - Self-explanatory. - -*Pair yukawa/colloid requires atoms with same type have same radius* - Self-explanatory. - -*Pair yukawa/colloid/gpu requires atom style sphere* - Self-explanatory. - *PairKIM only works with 3D problems* This is a current limitation. -*Pair_coeff command before pair_style is defined* - Self-explanatory. - *Pair_coeff command before simulation box is defined* The pair_coeff command cannot be used before a read_data, read_restart, or create_box command. -*Pair_modify command before pair_style is defined* - Self-explanatory. - *Pair_modify special setting for pair hybrid incompatible with global special_bonds setting* Cannot override a setting of 0.0 or 1.0 or change a setting between 0.0 and 1.0. -*Pair_write command before pair_style is defined* - Self-explanatory. - *Particle on or inside fix wall surface* Particles must be "exterior" to the wall in order for energy/force to be calculated. @@ -6946,26 +4150,13 @@ Doc page with :doc:`WARNING messages ` *Per-atom compute in equal-style variable formula* Equal-style variables cannot use per-atom quantities. -*Per-atom energy was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to - have tallied energy, but they did not on this timestep. See the - variable page for ideas on how to make this work. - *Per-atom fix in equal-style variable formula* Equal-style variables cannot use per-atom quantities. -*Per-atom virial was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to have - tallied the virial, but they did not on this timestep. See the - variable page for ideas on how to make this work. - *Per-processor system is too big* The number of owned atoms plus ghost atoms on a single processor must fit in 32-bit integer. -*Potential energy ID for fix neb does not exist* - Self-explanatory. - *Potential energy ID for fix nvt/nph/npt does not exist* A compute for potential energy must be defined. @@ -6975,79 +4166,22 @@ Doc page with :doc:`WARNING messages ` *Potential file is missing an entry* The potential file does not have a needed entry. -*Power by 0 in variable formula* - Self-explanatory. - *Pressure ID for fix box/relax does not exist* The compute ID needed to compute pressure for the fix does not exist. -*Pressure ID for fix modify does not exist* - Self-explanatory. - -*Pressure ID for fix npt/nph does not exist* - Self-explanatory. - *Pressure ID for fix press/berendsen does not exist* The compute ID needed to compute pressure for the fix does not exist. -*Pressure ID for fix rigid npt/nph does not exist* - Self-explanatory. - *Pressure ID for thermo does not exist* The compute ID needed to compute pressure for thermodynamics does not exist. -*Pressure control can not be used with fix nvt* - Self-explanatory. - -*Pressure control can not be used with fix nvt/asphere* - Self-explanatory. - -*Pressure control can not be used with fix nvt/body* - Self-explanatory. - -*Pressure control can not be used with fix nvt/sllod* - Self-explanatory. - -*Pressure control can not be used with fix nvt/sphere* - Self-explanatory. - -*Pressure control must be used with fix nph* - Self-explanatory. - -*Pressure control must be used with fix nph/asphere* - Self-explanatory. - -*Pressure control must be used with fix nph/body* - Self-explanatory. - -*Pressure control must be used with fix nph/small* - Self-explanatory. - -*Pressure control must be used with fix nph/sphere* - Self-explanatory. - *Pressure control must be used with fix nphug* A pressure control keyword (iso, aniso, tri, x, y, or z) must be provided. -*Pressure control must be used with fix npt* - Self-explanatory. - -*Pressure control must be used with fix npt/asphere* - Self-explanatory. - -*Pressure control must be used with fix npt/body* - Self-explanatory. - -*Pressure control must be used with fix npt/sphere* - Self-explanatory. - -*Processor count in z must be 1 for 2d simulation* - Self-explanatory. - *Processor partitions do not match number of allocated processors* The total number of processors in all partitions must match the number of processors LAMMPS is running on. @@ -7068,12 +4202,6 @@ Doc page with :doc:`WARNING messages ` *Processors part option and grid style are incompatible* Cannot use gstyle numa or custom with the part option. -*Processors twogrid requires proc count be a multiple of core count* - Self-explanatory. - -*Pstart and Pstop must have the same value* - Self-explanatory. - *Python function evaluation failed* The Python function did not run successfully and/or did not return a value (if it is supposed to return a value). This is probably due to @@ -7100,9 +4228,6 @@ Doc page with :doc:`WARNING messages ` *R0 < 0 for fix spring command* Equilibrium spring length is invalid. -*RATTLE coordinate constraints are not satisfied up to desired tolerance* - Self-explanatory. - *RATTLE determinant = 0.0* The determinant of the matrix being solved for a single cluster specified by the fix rattle command is numerically invalid. @@ -7110,19 +4235,10 @@ Doc page with :doc:`WARNING messages ` *RATTLE failed* Certain constraints were not satisfied. -*RATTLE velocity constraints are not satisfied up to desired tolerance* - Self-explanatory. - *Read data add offset is too big* It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit integer. -*Read dump of atom property that is not allocated* - Self-explanatory. - -*Read rerun dump file timestep > specified stop* - Self-explanatory. - *Read restart MPI-IO input not allowed with % in filename* This is because a % signifies one file per processor and MPI-IO creates one large file for all processors. @@ -7138,16 +4254,10 @@ Doc page with :doc:`WARNING messages ` The read_dump command cannot be used before a read_data, read_restart, or create_box command. -*Read_dump field not found in dump file* - Self-explanatory. - *Read_dump triclinic status does not match simulation* Both the dump snapshot and the current LAMMPS simulation must be using either an orthogonal or triclinic box. -*Read_dump xyz fields do not have consistent scaling/wrapping* - Self-explanatory. - *Reax_defs.h setting for NATDEF is too small* Edit the setting in the ReaxFF library and re-compile the library and re-build LAMMPS. @@ -7159,66 +4269,6 @@ Doc page with :doc:`WARNING messages ` *Receiving partition in processors part command is already a receiver* Cannot specify a partition to be a receiver twice. -*Region ID for compute chunk/atom does not exist* - Self-explanatory. - -*Region ID for compute reduce/region does not exist* - Self-explanatory. - -*Region ID for compute temp/region does not exist* - Self-explanatory. - -*Region ID for dump custom does not exist* - Self-explanatory. - -*Region ID for fix addforce does not exist* - Self-explanatory. - -*Region ID for fix atom/swap does not exist* - Self-explanatory. - -*Region ID for fix ave/spatial does not exist* - Self-explanatory. - -*Region ID for fix aveforce does not exist* - Self-explanatory. - -*Region ID for fix deposit does not exist* - Self-explanatory. - -*Region ID for fix efield does not exist* - Self-explanatory. - -*Region ID for fix evaporate does not exist* - Self-explanatory. - -*Region ID for fix gcmc does not exist* - Self-explanatory. - -*Region ID for fix heat does not exist* - Self-explanatory. - -*Region ID for fix setforce does not exist* - Self-explanatory. - -*Region ID for fix wall/region does not exist* - Self-explanatory. - -*Region ID for group dynamic does not exist* - Self-explanatory. - -*Region ID in variable formula does not exist* - Self-explanatory. - -*Region cannot have 0 length rotation vector* - Self-explanatory. - -*Region for fix oneway does not exist* - Self-explanatory. - -*Region intersect region ID does not exist* - Self-explanatory. - *Region union or intersect cannot be dynamic* The sub-regions can be dynamic, but not the combined region. @@ -7255,18 +4305,12 @@ Doc page with :doc:`WARNING messages ` The rerun command cannot be used before a read_data, read_restart, or create_box command. -*Rerun dump file does not contain requested snapshot* - Self-explanatory. - *Resetting timestep size is not allowed with fix move* This is because fix move is moving atoms based on elapsed time. *Respa inner cutoffs are invalid* The first cutoff must be <= the second cutoff. -*Respa levels must be >= 1* - Self-explanatory. - *Respa middle cutoffs are invalid* The first cutoff must be <= the second cutoff. @@ -7355,12 +4399,6 @@ Doc page with :doc:`WARNING messages ` The run command cannot be used before a read_data, read_restart, or create_box command. -*Run command start value is after start of run* - Self-explanatory. - -*Run command stop value is before end of run* - Self-explanatory. - *Run_style command before simulation box is defined* The run_style command cannot be used before a read_data, read_restart, or create_box command. @@ -7381,9 +4419,6 @@ Doc page with :doc:`WARNING messages ` See the inside keyword if you want this message to be an error vs warning. -*Same dimension twice in fix ave/spatial* - Self-explanatory. - *Sending partition in processors part command is already a sender* Cannot specify a partition to be a sender twice. @@ -7391,12 +4426,6 @@ Doc page with :doc:`WARNING messages ` The set command cannot be used before a read_data, read_restart, or create_box command. -*Set command floating point vector does not exist* - Self-explanatory. - -*Set command integer vector does not exist* - Self-explanatory. - *Set command with no atoms existing* No atoms are yet defined so the set command cannot be used. @@ -7470,12 +4499,6 @@ Doc page with :doc:`WARNING messages ` The 3d grid of processors defined by the processors command does not match the number of processors LAMMPS is being run on. -*Specified target stress must be uniaxial or hydrostatic* - Self-explanatory. - -*Sqrt of negative value in variable formula* - Self-explanatory. - *Subsequent read data induced too many angles per atom* See the extra/angle/per/atom keyword for the create_box or the read_data command to set this limit larger @@ -7492,10 +4515,6 @@ Doc page with :doc:`WARNING messages ` See the extra/improper/per/atom keyword for the create_box or the read_data command to set this limit larger -*Substitution for illegal variable* - Input script line contained a variable that could not be substituted - for. - *Support for writing images in JPEG format not included* LAMMPS was not built with the -DLAMMPS_JPEG switch in the Makefile. @@ -7512,9 +4531,6 @@ Doc page with :doc:`WARNING messages ` The total charge on all atoms on the system is not 0.0. For some KSpace solvers this is an error. -*TAD nsteps must be multiple of t_event* - Self-explanatory. - *TIP4P hydrogen has incorrect atom type* The TIP4P pairwise computation found an H atom whose type does not agree with the specified H type. @@ -7527,9 +4543,6 @@ Doc page with :doc:`WARNING messages ` The target file for the fix tmd command did not list all atoms in the fix group. -*Tad command before simulation box is defined* - Self-explanatory. - *Tagint setting in lmptype.h is invalid* Tagint must be as large or larger than smallint. @@ -7537,107 +4550,17 @@ Doc page with :doc:`WARNING messages ` Format of tagint stored in restart file is not consistent with LAMMPS version you are running. See the settings in src/lmptype.h -*Target pressure for fix rigid/nph cannot be < 0.0* - Self-explanatory. - -*Target pressure for fix rigid/npt/small cannot be < 0.0* - Self-explanatory. - -*Target temperature for fix nvt/npt/nph cannot be 0.0* - Self-explanatory. - -*Target temperature for fix rigid/npt cannot be 0.0* - Self-explanatory. - -*Target temperature for fix rigid/npt/small cannot be 0.0* - Self-explanatory. - -*Target temperature for fix rigid/nvt cannot be 0.0* - Self-explanatory. - -*Target temperature for fix rigid/nvt/small cannot be 0.0* - Self-explanatory. - *Temper command before simulation box is defined* The temper command cannot be used before a read_data, read_restart, or create_box command. -*Temperature ID for fix bond/swap does not exist* - Self-explanatory. - -*Temperature ID for fix box/relax does not exist* - Self-explanatory. - -*Temperature ID for fix nvt/npt does not exist* - Self-explanatory. - -*Temperature ID for fix press/berendsen does not exist* - Self-explanatory. - -*Temperature ID for fix rigid nvt/npt/nph does not exist* - Self-explanatory. - -*Temperature ID for fix temp/berendsen does not exist* - Self-explanatory. - -*Temperature ID for fix temp/csld does not exist* - Self-explanatory. - -*Temperature ID for fix temp/csvr does not exist* - Self-explanatory. - -*Temperature ID for fix temp/rescale does not exist* - Self-explanatory. - *Temperature compute degrees of freedom < 0* This should not happen if you are calculating the temperature on a valid set of atoms. -*Temperature control can not be used with fix nph* - Self-explanatory. - -*Temperature control can not be used with fix nph/asphere* - Self-explanatory. - -*Temperature control can not be used with fix nph/body* - Self-explanatory. - -*Temperature control can not be used with fix nph/sphere* - Self-explanatory. - *Temperature control must be used with fix nphug* The temp keyword must be provided. -*Temperature control must be used with fix npt* - Self-explanatory. - -*Temperature control must be used with fix npt/asphere* - Self-explanatory. - -*Temperature control must be used with fix npt/body* - Self-explanatory. - -*Temperature control must be used with fix npt/sphere* - Self-explanatory. - -*Temperature control must be used with fix nvt* - Self-explanatory. - -*Temperature control must be used with fix nvt/asphere* - Self-explanatory. - -*Temperature control must be used with fix nvt/body* - Self-explanatory. - -*Temperature control must be used with fix nvt/sllod* - Self-explanatory. - -*Temperature control must be used with fix nvt/sphere* - Self-explanatory. - -*Temperature control must not be used with fix nph/small* - Self-explanatory. - *Temperature for fix nvt/sllod does not have a bias* The specified compute must compute temperature with a bias. @@ -7655,31 +4578,10 @@ Doc page with :doc:`WARNING messages ` *Test_descriptor_string already allocated* This is an internal error. Contact the developers. -*The package gpu command is required for gpu styles* - Self-explanatory. - *Thermo and fix not computed at compatible times* Fixes generate values on specific timesteps. The thermo output does not match these timesteps. -*Thermo compute array is accessed out-of-range* - Self-explanatory. - -*Thermo compute does not compute array* - Self-explanatory. - -*Thermo compute does not compute scalar* - Self-explanatory. - -*Thermo compute does not compute vector* - Self-explanatory. - -*Thermo compute vector is accessed out-of-range* - Self-explanatory. - -*Thermo custom variable cannot be indexed* - Self-explanatory. - *Thermo custom variable is not equal-style variable* Only equal-style variables can be output with thermodynamics, not atom-style variables. @@ -7687,21 +4589,6 @@ Doc page with :doc:`WARNING messages ` *Thermo every variable returned a bad timestep* The variable must return a timestep greater than the current timestep. -*Thermo fix array is accessed out-of-range* - Self-explanatory. - -*Thermo fix does not compute array* - Self-explanatory. - -*Thermo fix does not compute scalar* - Self-explanatory. - -*Thermo fix does not compute vector* - Self-explanatory. - -*Thermo fix vector is accessed out-of-range* - Self-explanatory. - *Thermo keyword in variable requires thermo to use/init pe* You are using a thermo keyword in a variable that requires potential energy to be calculated, but your thermo output @@ -7728,9 +4615,6 @@ Doc page with :doc:`WARNING messages ` *Thermo_modify every variable returned a bad timestep* The returned timestep is less than or equal to the current timestep. -*Thermo_modify int format does not contain d character* - Self-explanatory. - *Thermo_modify pressure ID does not compute pressure* The specified compute ID does not compute pressure. @@ -7765,15 +4649,6 @@ Doc page with :doc:`WARNING messages ` Table size specified via pair_modify command does not work with your machine's floating point representation. -*Too few lines in %s section of data file* - Self-explanatory. - -*Too few values in body lines in data file* - Self-explanatory. - -*Too few values in body section of molecule file* - Self-explanatory. - *Too many -pk arguments in command-line* The string formed by concatenating the arguments is too long. Use a package command in the input script instead. @@ -7843,10 +4718,6 @@ Doc page with :doc:`WARNING messages ` *Too many molecules for fix rigid* The limit is 2\^31 = ~2 billion molecules. -*Too many neighbor bins* - This is likely due to an immense simulation box that has blown up - to a large size. - *Too many timesteps* The cumulative timesteps must fit in a 64-bit integer. @@ -7861,12 +4732,6 @@ Doc page with :doc:`WARNING messages ` Table size specified via pair_modify command is too large. Note that a value of N generates a 2\^N size table. -*Too many values in body lines in data file* - Self-explanatory. - -*Too many values in body section of molecule file* - Self-explanatory. - *Too much buffered per-proc info for dump* The size of the buffered string must fit in a 32-bit integer for a dump. @@ -7883,9 +4748,6 @@ Doc page with :doc:`WARNING messages ` Fix poems cannot (yet) work with coupled bodies whose joints connect the bodies in a tree structure. -*Tried to convert a double to int, but input_double > INT_MAX* - Self-explanatory. - *Trying to build an occasional neighbor list before initialization completed* This is not allowed. Source code caller needs to be modified. @@ -7894,9 +4756,6 @@ Doc page with :doc:`WARNING messages ` chunk assignments persist for some number of timesteps, but are doing it in different ways. -*Two groups cannot be the same in fix spring couple* - Self-explanatory. - *The %s type label %s is already in use for type %s* For a given type-kind (atom types, bond types, etc.), a given type label can be assigned to only one numeric type. @@ -7911,9 +4770,6 @@ Doc page with :doc:`WARNING messages ` No matching end double quote was found following a leading double quote. -*Unexpected end of -reorder file* - Self-explanatory. - *Unexpected empty line in Angle Coeffs section* Read a blank line where there should be coefficient data. @@ -7929,9 +4785,6 @@ Doc page with :doc:`WARNING messages ` *Unexpected empty line in Pair Coeffs section* Read a blank line where there should be coefficient data. -*Unexpected end of custom file* - Self-explanatory. - *Unexpected end of data file* LAMMPS hit the end of the data file while attempting to read a section. Something is wrong with the format of the data file. @@ -7945,9 +4798,6 @@ Doc page with :doc:`WARNING messages ` *Unexpected end of fix rigid/small file* A read operation from the file failed. -*Unexpected end of molecule file* - Self-explanatory. - *Unexpected end of neb file* A read operation from the file failed. @@ -7959,93 +4809,15 @@ Doc page with :doc:`WARNING messages ` A universe or uloop style variable must specify a number of values >= to the number of processor partitions. -*Unrecognized angle style* - The choice of angle style is unknown. - -*Unrecognized atom style* - The choice of atom style is unknown. - -*Unrecognized body style* - The choice of body style is unknown. - -*Unrecognized bond style* - The choice of bond style is unknown. - -*Unknown category for info is_active()* - Self-explanatory. - -*Unknown category for info is_available()* - Self-explanatory. - -*Unknown category for info is_defined()* - Self-explanatory. - -*Unrecognized command: %s* - The command is not known to LAMMPS. Check the input script. - -*Unrecognized compute style* - The choice of compute style is unknown. - -*Unrecognized dihedral style* - The choice of dihedral style is unknown. - -*Unrecognized dump reader style* - The choice of dump reader style via the format keyword is unknown. - -*Unrecognized dump style* - The choice of dump style is unknown. - -*Unknown error in GPU library* - Self-explanatory. - -*Unrecognized fix style* - The choice of fix style is unknown. - -*Unknown identifier in data file: %s* - A section of the data file cannot be read by LAMMPS. - -*Unrecognized improper style* - The choice of improper style is unknown. - *Unknown keyword in thermo_style custom command* One or more specified keywords are not recognized. -*Unrecognized kspace style* - The choice of kspace style is unknown. - -*Unknown name for info newton category* - Self-explanatory. - -*Unknown name for info package category* - Self-explanatory. - -*Unknown name for info pair category* - Self-explanatory. - -*Unrecognized pair style* - The choice of pair style is unknown. - *Unknown pair_modify hybrid sub-style* The choice of sub-style is unknown. -*Unrecognized region style* - The choice of region style is unknown. - -*Unknown section in molecule file* - Self-explanatory. - -*Unknown table style in angle style table* - Self-explanatory. - -*Unknown table style in bond style table* - Self-explanatory. - *Unknown table style in pair_style command* Style of table is invalid for use with pair_style table command. -*Unknown unit_style* - Self-explanatory. Check the input script or data file. - *Unrecognized lattice type in MEAM library file* The lattice type in an entry of the MEAM library file is not valid. @@ -8054,9 +4826,6 @@ Doc page with :doc:`WARNING messages ` The lattice type in an entry of the MEAM parameter file is not valid. -*Unrecognized pair style in compute pair command* - Self-explanatory. - *Unsupported mixing rule in kspace_style ewald/disp* Only geometric mixing is supported. @@ -8066,9 +4835,6 @@ Doc page with :doc:`WARNING messages ` *Unsupported order in kspace_style pppm/disp, pair_style %s* Only pair styles with 1/r and 1/r\^6 dependence are currently supported. -*Unsupported parameter in MEAM library file* - Self-explanatory. - *Use cutoff keyword to set cutoff in single mode* Mode is single so cutoff/multi keyword cannot be used. @@ -8079,9 +4845,6 @@ Doc page with :doc:`WARNING messages ` Fix nvt/sllod requires that deforming atoms have a velocity profile provided by "remap v" as a fix deform option. -*Using fix nvt/sllod with no fix deform defined* - Self-explanatory. - *Using fix srd with inconsistent fix deform remap option* When shearing the box in an SRD simulation, the remap v option for fix deform needs to be used. @@ -8092,27 +4855,6 @@ Doc page with :doc:`WARNING messages ` *Using pair lubricate/poly with inconsistent fix deform remap option* If fix deform is used, the remap v option is required. -*Using suffix gpu without GPU package installed* - Self-explanatory. - -*Using suffix intel without INTEL package installed* - Self-explanatory. - -*Using suffix kk without KOKKOS package enabled* - Self-explanatory. - -*Using suffix omp without OPENMP package installed* - Self-explanatory. - -*Using update dipole flag requires atom attribute mu* - Self-explanatory. - -*Using update dipole flag requires atom style sphere* - Self-explanatory. - -*Variable ID in variable formula does not exist* - Self-explanatory. - *Variable atom ID is too large* Specified ID is larger than the maximum allowed atom ID. @@ -8126,9 +4868,6 @@ Doc page with :doc:`WARNING messages ` *Variable evaluation in region gave bad value* Variable returned a radius < 0.0. -*Variable for compute ti is invalid style* - Self-explanatory. - *Variable for create_atoms is invalid style* The variables must be equal-style variables. @@ -8153,9 +4892,6 @@ Doc page with :doc:`WARNING messages ` *Variable for fix adapt is invalid style* Only equal-style variables can be used. -*Variable for fix addforce is invalid style* - Self-explanatory. - *Variable for fix aveforce is invalid style* Only equal-style variables can be used. @@ -8219,9 +4955,6 @@ Doc page with :doc:`WARNING messages ` *Variable for region is invalid style* Only equal-style variables can be used. -*Variable for region is not equal style* - Self-explanatory. - *Variable for region sphere is invalid style* Only equal-style variables are allowed. @@ -8237,173 +4970,11 @@ Doc page with :doc:`WARNING messages ` *Variable for velocity set is invalid style* Only atom-style variables can be used. -*Variable for voronoi radius is not atom style* - Self-explanatory. - -*Variable formula compute array is accessed out-of-range* - Self-explanatory. - -*Variable formula compute vector is accessed out-of-range* - Self-explanatory. - -*Variable formula fix array is accessed out-of-range* - Self-explanatory. - -*Variable formula fix vector is accessed out-of-range* - Self-explanatory. - *Variable has circular dependency* A circular dependency is when variable "a" in used by variable "b" and variable "b" is also used by variable "a". Circular dependencies with longer chains of dependence are also not allowed. -*Variable name between brackets must be alphanumeric or underscore characters* - Self-explanatory. - -*Variable name for compute chunk/atom does not exist* - Self-explanatory. - -*Variable name for compute reduce does not exist* - Self-explanatory. - -*Variable name for compute ti does not exist* - Self-explanatory. - -*Variable name for create_atoms does not exist* - Self-explanatory. - -*Variable name for displace_atoms does not exist* - Self-explanatory. - -*Variable name for dump every does not exist* - Self-explanatory. - -*Variable name for dump image center does not exist* - Self-explanatory. - -*Variable name for dump image phi does not exist* - Self-explanatory. - -*Variable name for dump image theta does not exist* - Self-explanatory. - -*Variable name for dump image zoom does not exist* - Self-explanatory. - -*Variable name for fix adapt does not exist* - Self-explanatory. - -*Variable name for fix addforce does not exist* - Self-explanatory. - -*Variable name for fix ave/atom does not exist* - Self-explanatory. - -*Variable name for fix ave/chunk does not exist* - Self-explanatory. - -*Variable name for fix ave/correlate does not exist* - Self-explanatory. - -*Variable name for fix ave/histo does not exist* - Self-explanatory. - -*Variable name for fix ave/spatial does not exist* - Self-explanatory. - -*Variable name for fix ave/time does not exist* - Self-explanatory. - -*Variable name for fix aveforce does not exist* - Self-explanatory. - -*Variable name for fix deform does not exist* - Self-explanatory. - -*Variable name for fix efield does not exist* - Self-explanatory. - -*Variable name for fix gravity does not exist* - Self-explanatory. - -*Variable name for fix heat does not exist* - Self-explanatory. - -*Variable name for fix indent does not exist* - Self-explanatory. - -*Variable name for fix langevin does not exist* - Self-explanatory. - -*Variable name for fix move does not exist* - Self-explanatory. - -*Variable name for fix setforce does not exist* - Self-explanatory. - -*Variable name for fix store/state does not exist* - Self-explanatory. - -*Variable name for fix temp/berendsen does not exist* - Self-explanatory. - -*Variable name for fix temp/csld does not exist* - Self-explanatory. - -*Variable name for fix temp/csvr does not exist* - Self-explanatory. - -*Variable name for fix temp/rescale does not exist* - Self-explanatory. - -*Variable name for fix vector does not exist* - Self-explanatory. - -*Variable name for fix wall does not exist* - Self-explanatory. - -*Variable name for fix wall/reflect does not exist* - Self-explanatory. - -*Variable name for fix wall/srd does not exist* - Self-explanatory. - -*Variable name for group does not exist* - Self-explanatory. - -*Variable name for group dynamic does not exist* - Self-explanatory. - -*Variable name for region cylinder does not exist* - Self-explanatory. - -*Variable name for region does not exist* - Self-explanatory. - -*Variable name for region sphere does not exist* - Self-explanatory. - -*Variable name for restart does not exist* - Self-explanatory. - -*Variable name for set command does not exist* - Self-explanatory. - -*Variable name for thermo every does not exist* - Self-explanatory. - -*Variable name for velocity set does not exist* - Self-explanatory. - -*Variable name for voronoi radius does not exist* - Self-explanatory. - -*Variable name must be alphanumeric or underscore characters* - Self-explanatory. - -*Variable uses atom property that is not allocated* - Self-explanatory. - *Velocity command before simulation box is defined* The velocity command cannot be used before a read_data, read_restart, or create_box command. @@ -8411,12 +4982,6 @@ Doc page with :doc:`WARNING messages ` *Velocity command with no atoms existing* A velocity command has been used, but no atoms yet exist. -*Velocity ramp in z for a 2d problem* - Self-explanatory. - -*Velocity rigid used with non-rigid fix-ID* - Self-explanatory. - *Velocity temperature ID does calculate a velocity bias* The specified compute must compute a bias for temperature. @@ -8440,23 +5005,9 @@ Doc page with :doc:`WARNING messages ` This is so there is an equal number of Rspace processors for every Kspace processor. -*Virial was not tallied on needed timestep* - You are using a thermo keyword that requires potentials to - have tallied the virial, but they did not on this timestep. See the - variable page for ideas on how to make this work. - *Voro++ error: narea and neigh have a different size* This error is returned by the Voro++ library. -*Wall defined twice in fix wall command* - Self-explanatory. - -*Wall defined twice in fix wall/reflect command* - Self-explanatory. - -*Wall defined twice in fix wall/srd command* - Self-explanatory. - *Water H epsilon must be 0.0 for pair style lj/cut/tip4p/cut* This is because LAMMPS does not compute the Lennard-Jones interactions with these particles for efficiency reasons. @@ -8473,18 +5024,6 @@ Doc page with :doc:`WARNING messages ` A world-style variable must specify a number of values equal to the number of processor partitions. -*Write_data command before simulation box is defined* - Self-explanatory. - *Write_restart command before simulation box is defined* The write_restart command cannot be used before a read_data, read_restart, or create_box command. - -*Zero length rotation vector with displace_atoms* - Self-explanatory. - -*Zero length rotation vector with fix move* - Self-explanatory. - -*Zero-length lattice orient vector* - Self-explanatory. diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 25aa87f162..3f18ddd2ca 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -1,11 +1,15 @@ Warning messages ================ -This is an alphabetic list of the WARNING messages LAMMPS prints out -and the reason why. If the explanation here is not sufficient, the -documentation for the offending command may help. Warning messages -also list the source file and line number where the warning was -generated. For example, a message like this: +This is an alphabetic list of some of the WARNING messages LAMMPS prints +out and the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. This is a historic +list and no longer updated. Instead the LAMMPS developers are trying +to provide more details right with the error message or link to a +paragraph with :doc:`detailed explanations `. + +Warning messages also list the source file and line number where the +warning was generated. For example, a message like this: .. parsed-literal:: @@ -14,7 +18,7 @@ generated. For example, a message like this: means that line #187 in the file src/domain.cpp generated the error. Looking in the source code may help you figure out what went wrong. -Doc page with :doc:`ERROR messages ` +Please also see the page with :doc:`Error messages ` ---------- @@ -28,16 +32,10 @@ Doc page with :doc:`ERROR messages ` cutoff is set too short or the angle has blown apart and an atom is too far away. -*Angle style in data file differs from currently defined angle style* - Self-explanatory. - *Angles are defined but no angle style is set* The topology contains angles, but there are no angle forces computed since there was no angle_style command. -*Atom style in data file differs from currently defined atom style* - Self-explanatory. - *Bond atom missing in box size check* The second atom needed to compute a particular bond is missing on this processor. Typically this is because the pairwise cutoff is set too @@ -53,9 +51,6 @@ Doc page with :doc:`ERROR messages ` processor. Typically this is because the pairwise cutoff is set too short or the bond has blown apart and an atom is too far away. -*Bond style in data file differs from currently defined bond style* - Self-explanatory. - *Bonds are defined but no bond style is set* The topology contains bonds, but there are no bond forces computed since there was no bond_style command. @@ -68,9 +63,6 @@ Doc page with :doc:`ERROR messages ` length, multiplying by the number of bonds in the interaction (e.g. 3 for a dihedral) and adding a small amount of stretch. -*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero* - Self-explanatory. - *Calling write_dump before a full system init.* The write_dump command is used before the system has been fully initialized as part of a 'run' or 'minimize' command. Not all dump @@ -86,18 +78,6 @@ Doc page with :doc:`ERROR messages ` This means the temperature associated with the rigid bodies may be incorrect on this timestep. -*Cannot include log terms without 1/r terms; setting flagHI to 1* - Self-explanatory. - -*Cannot include log terms without 1/r terms; setting flagHI to 1.* - Self-explanatory. - -*Charges are set, but coulombic solver is not used* - Self-explanatory. - -*Charges did not converge at step %ld: %lg* - Self-explanatory. - *Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost* The communication cutoff defaults to the maximum of what is inferred from pair and bond styles (will be zero, if none are defined) and what is specified @@ -123,9 +103,6 @@ Doc page with :doc:`ERROR messages ` is not changed automatically and the warning may be ignored depending on the specific system being simulated. -*Communication cutoff is too small for SNAP micro load balancing, increased to %lf* - Self-explanatory. - *Compute cna/atom cutoff may be too large to find ghost atom neighbors* The neighbor cutoff used may not encompass enough ghost atoms to perform this operation correctly. @@ -158,9 +135,6 @@ Doc page with :doc:`ERROR messages ` Conformation of the 4 listed dihedral atoms is extreme; you may want to check your simulation geometry. -*Dihedral style in data file differs from currently defined dihedral style* - Self-explanatory. - *Dihedrals are defined but no dihedral style is set* The topology contains dihedrals, but there are no dihedral forces computed since there was no dihedral_style command. @@ -177,9 +151,6 @@ Doc page with :doc:`ERROR messages ` *Estimated error in splitting of dispersion coeffs is %g* Error is greater than 0.0001 percent. -*Ewald/disp Newton solver failed, using old method to estimate g_ewald* - Self-explanatory. Choosing a different cutoff value may help. - *FENE bond too long* A FENE bond has stretched dangerously far. It's interaction strength will be truncated to attempt to prevent the bond from blowing up. @@ -192,9 +163,6 @@ Doc page with :doc:`ERROR messages ` A FENE bond has stretched dangerously far. It's interaction strength will be truncated to attempt to prevent the bond from blowing up. -*Fix halt condition for fix-id %s met on step %ld with value %g* - Self explanatory. - *Fix SRD walls overlap but fix srd overlap not set* You likely want to set this in your input script. @@ -238,21 +206,12 @@ Doc page with :doc:`ERROR messages ` *Fix property/atom mol or charge w/out ghost communication* A model typically needs these properties defined for ghost atoms. -*Fix qeq CG convergence failed (%g) after %d iterations at %ld step* - Self-explanatory. - *Fix qeq has non-zero lower Taper radius cutoff* Absolute value must be <= 0.01. *Fix qeq has very low Taper radius cutoff* Value should typically be >= 5.0. -*Fix qeq/dynamic tolerance may be too small for damped dynamics* - Self-explanatory. - -*Fix qeq/fire tolerance may be too small for damped fires* - Self-explanatory. - *Fix rattle should come after all other integration fixes* This fix is designed to work after all other integration fixes change atom positions. Thus it should be the last integration fix specified. @@ -285,9 +244,6 @@ Doc page with :doc:`ERROR messages ` The user-specified force accuracy cannot be achieved unless the table feature is disabled by using 'pair_modify table 0'. -*Geometric mixing assumed for 1/r\^6 coefficients* - Self-explanatory. - *Group for fix_modify temp != fix group* The fix_modify command is specifying a temperature computation that computes a temperature on a different group of atoms than the fix @@ -310,46 +266,14 @@ Doc page with :doc:`ERROR messages ` Conformation of the 4 listed improper atoms is extreme; you may want to check your simulation geometry. -*Improper style in data file differs from currently defined improper style* - Self-explanatory. - *Impropers are defined but no improper style is set* The topology contains impropers, but there are no improper forces computed since there was no improper_style command. -*Inconsistent image flags* - The image flags for a pair on bonded atoms appear to be inconsistent. - Inconsistent means that when the coordinates of the two atoms are - unwrapped using the image flags, the two atoms are far apart. - Specifically they are further apart than half a periodic box length. - Or they are more than a box length apart in a non-periodic dimension. - This is usually due to the initial data file not having correct image - flags for the two atoms in a bond that straddles a periodic boundary. - They should be different by 1 in that case. This is a warning because - inconsistent image flags will not cause problems for dynamics or most - LAMMPS simulations. However they can cause problems when such atoms - are used with the fix rigid or replicate commands. Note that if you - have an infinite periodic crystal with bonds then it is impossible to - have fully consistent image flags, since some bonds will cross - periodic boundaries and connect two atoms with the same image - flag. - *Increasing communication cutoff for GPU style* The pair style has increased the communication cutoff to be consistent with the communication cutoff requirements for this pair style when run on the GPU. -*KIM Model does not provide 'energy'; Potential energy will be zero* - Self-explanatory. - -*KIM Model does not provide 'forces'; Forces will be zero* - Self-explanatory. - -*KIM Model does not provide 'particleEnergy'; energy per atom will be zero* - Self-explanatory. - -*KIM Model does not provide 'particleVirial'; virial per atom will be zero* - Self-explanatory. - *Kspace_modify slab param < 2.0 may cause unphysical behavior* The kspace_modify slab parameter should be larger to ensure periodic grids padded with empty space do not overlap. @@ -401,20 +325,10 @@ Doc page with :doc:`ERROR messages ` box, or moved further than one processor's subdomain away before reneighboring. -*MSM mesh too small, increasing to 2 points in each direction* - Self-explanatory. - *Mismatch between velocity and compute groups* The temperature computation used by the velocity command will not be on the same group of atoms that velocities are being set for. -*Mixing forced for lj coefficients* - Self-explanatory. - -*Molecule attributes do not match system attributes* - An attribute is specified (e.g. diameter, charge) that is - not defined for the specified atom style. - *Molecule has bond topology but no special bond settings* This means the bonded atoms will not be excluded in pairwise interactions. @@ -449,9 +363,6 @@ Doc page with :doc:`ERROR messages ` *More than one compute damage/atom* It is not efficient to use compute ke/atom more than once. -*More than one compute dilatation/atom* - Self-explanatory. - *More than one compute erotate/sphere/atom* It is not efficient to use compute erorate/sphere/atom more than once. @@ -464,24 +375,6 @@ Doc page with :doc:`ERROR messages ` *More than one compute orientorder/atom* It is not efficient to use compute orientorder/atom more than once. -*More than one compute plasticity/atom* - Self-explanatory. - -*More than one compute sna/atom* - Self-explanatory. - -*More than one compute sna/grid* - Self-explanatory. - -*More than one compute sna/grid/local* - Self-explanatory. - -*More than one compute snad/atom* - Self-explanatory. - -*More than one compute snav/atom* - Self-explanatory. - *More than one fix poems* It is not efficient to use fix poems more than once. @@ -557,21 +450,12 @@ Doc page with :doc:`ERROR messages ` *Pair COMB charge %.10f with force %.10f hit min barrier* Something is possibly wrong with your model. -*Pair brownian needs newton pair on for momentum conservation* - Self-explanatory. - -*Pair dpd needs newton pair on for momentum conservation* - Self-explanatory. - *Pair dsmc: num_of_collisions > number_of_A* Collision model in DSMC is breaking down. *Pair dsmc: num_of_collisions > number_of_B* Collision model in DSMC is breaking down. -*Pair style in data file differs from currently defined pair style* - Self-explanatory. - *Pair style restartinfo set but has no restart support* This pair style has a bug, where it does not support reading and writing information to a restart file, but does not set the member @@ -681,9 +565,6 @@ Doc page with :doc:`ERROR messages ` cluster specified by the fix shake command is numerically suspect. LAMMPS will set it to 0.0 and continue. -*Shell command '%s' failed with error '%s'* - Self-explanatory. - *Shell command returned with non-zero status* This may indicate the shell command did not operate as expected. @@ -694,15 +575,9 @@ Doc page with :doc:`ERROR messages ` This will lead to invalid constraint forces in the SHAKE/RATTLE computation. -*Simulations might be very slow because of large number of structure factors* - Self-explanatory. - *Slab correction not needed for MSM* Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. -*Specifying an 'subset' value of '0' is equivalent to no 'subset' keyword* - Self-explanatory. - *System is not charge neutral, net charge = %g* The total charge on all atoms on the system is not 0.0. For some KSpace solvers this is only a warning. @@ -734,9 +609,6 @@ Doc page with :doc:`ERROR messages ` assumed to also be for all atoms. Thus the pressure printed by thermo could be inaccurate. -*The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015* - Self-explanatory. - *The minimizer does not re-orient dipoles when using fix efield* This means that only the atom coordinates will be minimized, not the orientation of the dipoles. @@ -745,9 +617,6 @@ Doc page with :doc:`ERROR messages ` More than the maximum # of neighbors was found multiple times. This was unexpected. -*Too many inner timesteps in fix ttm* - Self-explanatory. - *Too many neighbors in CNA for %d atoms* More than the maximum # of neighbors was found multiple times. This was unexpected. @@ -775,24 +644,6 @@ Doc page with :doc:`ERROR messages ` The deformation will heat the SRD particles so this can be dangerous. -*Using kspace solver on system with no charge* - Self-explanatory. - -*Using largest cut-off for lj/long/dipole/long long long* - Self-explanatory. - -*Using largest cutoff for buck/long/coul/long* - Self-explanatory. - -*Using largest cutoff for lj/long/coul/long* - Self-explanatory. - -*Using largest cutoff for pair_style lj/long/tip4p/long* - Self-explanatory. - -*Using package gpu without any pair style defined* - Self-explanatory. - *Using pair potential shift with pair_modify compute no* The shift effects will thus not be computed. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 683cbd0500..d80fc8aa4c 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -54,7 +54,7 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | body | body particles, 2d system | +-------------+------------------------------------------------------------------+ -| bpm | BPM simulations of pouring elastic grains and plate impact | +| bpm | simulations of solid elastic/plastic deformation and fracture | +-------------+------------------------------------------------------------------+ | cmap | CMAP 5-body contributions to CHARMM force field | +-------------+------------------------------------------------------------------+ diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst index ea0ade5cf4..0a8434f63d 100644 --- a/doc/src/Fortran.rst +++ b/doc/src/Fortran.rst @@ -2773,8 +2773,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type END SUBROUTINE external_callback END INTERFACE - where ``c_bigint`` is ``c_int`` if ``-DLAMMPS_SMALLSMALL`` was used and - ``c_int64_t`` otherwise; and ``c_tagint`` is ``c_int64_t`` if + where ``c_bigint`` is ``c_int64_t`` and ``c_tagint`` is ``c_int64_t`` if ``-DLAMMPS_BIGBIG`` was used and ``c_int`` otherwise. The argument *caller* to :f:subr:`set_fix_external_callback` is unlimited diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 2031e40fdd..9134a32022 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -40,6 +40,7 @@ Settings howto Howto_walls Howto_nemd Howto_dispersion + Howto_bulk2slab Analysis howto ============== diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst index f2aa1fc0a3..f632ee6172 100644 --- a/doc/src/Howto_bpm.rst +++ b/doc/src/Howto_bpm.rst @@ -42,12 +42,14 @@ such as those created by pouring grains using :doc:`fix pour ---------- -Currently, there are two types of bonds included in the BPM package. The +Currently, there are three types of bonds included in the BPM package. The first bond style, :doc:`bond bpm/spring `, only applies pairwise, central body forces. Point particles must have :doc:`bond atom style ` and may be thought of as nodes in a spring network. An optional multibody term can be used to adjust the network's -Poisson's ratio. Alternatively, the second bond style, :doc:`bond bpm/rotational +Poisson's ratio. The :doc:`bpm/spring/plastic ` +bond style is similar except it adds a plastic yield strain. +Alternatively, the third bond style, :doc:`bond bpm/rotational `, resolves tangential forces and torques arising with the shearing, bending, and twisting of the bond due to rotation or displacement of particles. Particles are similar to those used in the diff --git a/doc/src/Howto_bulk2slab.rst b/doc/src/Howto_bulk2slab.rst new file mode 100644 index 0000000000..2c26961522 --- /dev/null +++ b/doc/src/Howto_bulk2slab.rst @@ -0,0 +1,160 @@ +=========================== +Convert bulk system to slab +=========================== + +A regularly encountered simulation problem is how to convert a bulk +system that has been run for a while to equilibrate into a slab system +with some vacuum space and free surfaces. The challenge here is that +one cannot just change the box dimensions with the :doc:`change_box +command ` or edit the box boundaries in a data file because +some atoms will have non-zero image flags from diffusing around. + +Changing the box dimensions results in an undesired displacement of +those atoms, since the image flags indicate how many times the box +length in x-, y-, or z-direction needs to be added or subtracted to get +the "unwrapped" coordinates. By changing the box dimension this +distance is changed and thus those atoms move unphysically relative to +their neighbors with zero image flags. Setting image flags forcibly to +zero creates problems because that could break apart molecules by having +one atom of a bond on the top of the system and the other at the bottom. + +.. _bulk2slab: +.. figure:: JPG/rhodo-both.jpg + :figwidth: 80% + :figclass: align-center + + Snapshots of the bulk Rhodopsin in lipid layer and water system (right) + and the generated slab geometry (left) + +.. admonition:: Disclaimer + :class: note + + The following workflow will work for many bulk systems, but not all. + Some systems cannot be converted (e.g. polymers with bonds to the + same molecule across periodic boundaries, sometimes called "infinite + polymers"). The amount of vacuum that needs to be added depends on + the length of the molecules where the system is split (the example + here splits where there is water with short molecules). In some + cases, the system may need to be re-centered in the box first using + the :doc:`displace_atoms command `. Also, the time + spent on strong thermalization and equilibration will depend on the + specific system and its thermodynamic conditions. + +Below is a suggested workflow using the :doc:`Rhodopsin benchmark input +` for demonstration. The figure shows the state *before* +the procedure on the left (with unwrapped atoms that have diffused out +of the box) and *after* on the right (with the vacuum added above and +below). The procedure is implemented by modifying a copy of the +``in.rhodo`` input file. The first lines up to and including the +:doc:`read_data command ` remain unchanged. Then we insert +the following lines to add vacuum to the z direction above and below the +system: + +.. code-block:: LAMMPS + + variable delta index 10.0 + reset_atoms image all + write_dump all custom rhodo-unwrap.lammpstrj id xu yu zu + change_box all z final $(zlo-2.0*v_delta) $(zhi+2.0*v_delta) & + boundary p p f + read_dump rhodo-unwrap.lammpstrj 0 x y z box no replace yes + kspace_modify slab 3.0 + +Specifically, the :doc:`variable delta ` (set to 10.0) +represents a distance that determines the amount of vacuum added: we add +twice its value in each direction to the z-dimension; thus in total +:math:`40 \AA` get added. The :doc:`reset_atoms image all +` command shall reset any image flags to become either 0 or +:math:`\pm 1` and thus have the minimum distance from the center of the +simulation box, but the correct relative distance for bonded atoms. + +The :doc:`write_dump command ` then writes out the resulting +*unwrapped* coordinates of the system. After expanding the box, +coordinates that were outside the box should now be inside and the +unwrapped coordinates will become "wrapped", while atoms outside the +periodic boundaries will be wrapped back into the box and their image +flags in those directions restored. + +The :doc:`change_box command ` adds the desired +distance to the low and high box boundary in z-direction and then changes +the :doc:`boundary to "p p f" ` which will force the image +flags in z-direction to zero and create an undesired displacement for +the atoms with non-zero image flags. + +With the :doc:`read_dump command ` we read back and replace +partially incorrect coordinates with the previously saved, unwrapped +coordinates. It is important to ignore the box dimensions stored in the +dump file. We want to preserve the expanded box. Finally, we turn on +the slab correction for the PPPM long-range solver with the +:doc:`kspace_modify command ` as required when using a +long range Coulomb solver for non-periodic z-dimension. + +Next we replace the :doc:`fix npt command ` with: + +.. code-block:: LAMMPS + + fix 2 nvt temp 300.0 300.0 10.0 + +We now have an open system and thus the adjustment of the cell in +z-direction is no longer required. Since splitting the bulk water +region where the vacuum is inserted, creates surface atoms with high +potential energy, we reduce the thermostat time constant from 100.0 to +10.0 to remove excess kinetic energy resulting from that change faster. + +Also the high potential energy of the surface atoms can cause that some +of them are ejected from the slab. In order to suppress that, we add +soft harmonic walls to push back any atoms that want to leave the slab. +To determine the position of the wall, we first need to to determine the +extent of the atoms in z-direction and then place the harmonic walls +based on that information: + +.. code-block:: LAMMPS + + compute zmin all reduce min z + compute zmax all reduce max z + thermo_style custom zlo c_zmin zhi c_zmax + run 0 post no + fix 3 all wall/harmonic zhi $(c_zmax+v_delta) 10.0 0.0 ${delta} & + zlo $(c_zmin-v_delta) 10.0 0.0 ${delta} + +The two :doc:`compute reduce ` command determine the +minimum and maximum z-coordinate across all atoms. In order to trigger +the execution of the compute commands we need to "consume" them. This +is done with the :doc:`thermo_style custom ` command +followed by the :doc:`run 0 ` command. This avoids and error +accessing the min/max values determined by the compute commands to +compute the location of the wall in lower and upper direction. This +uses the previously defined *delta* variable to determine the distance +of the wall from the extent of the system and the cutoff for the wall +interaction. This way only atoms that move beyond the min/max values in +z-direction will experience a restoring force, nudging them back to the +slab. The force constant of :math:`10.0 \frac{\mathrm{kcal/mol}}{\AA}` +was determined empirically. + +Adding these "restoring" soft walls assist in making the free surfaces +above and below the slab flat, instead of having rugged or ondulated +surfaces. The impact of the walls can be changed by adjusting the force +constant, cutoff, and position of the wall. + +Finally, we replace the :doc:`run 100 ` of the original input with: + +.. code-block:: LAMMPS + + run 1000 post no + + unfix 3 + fix 2 all nvt temp 300.0 300.0 100.0 + run 1000 post no + + write_data data.rhodo-slab + +This runs the system converted to a slab first for 1000 MD steps using +the walls and stronger Nose-Hoover thermostat. Then the walls are +removed with :doc:`unfix 3 ` and the thermostat time constant +reset to 100.0 and the system run for another 1000 steps. Finally the +resulting slab geometry is written to a new data file +``data.rhodo-slab`` with a :doc:`write_data command `. The +number of MD steps required to reach a proper equilibrium state is very +likely larger. The number of 1000 steps (corresponding to 2 +picoseconds) was chosen for demonstration purposes, so that the +procedure can be easily and quickly tested. diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 78a05f113c..b53a2edbc7 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -487,10 +487,10 @@ updates are back-ported from the *develop* branch to the *maintenance* branch and occasionally merged to *stable* as an update release. Furthermore, the naming of the release tags now follow the pattern -"patch_" to simplify comparisons between releases. -For stable releases additional "stable_" tags are +"patch\_" to simplify comparisons between releases. +For stable releases additional "stable\_" tags are applied and update releases are tagged with -"stable__update", Finally, all releases and +"stable\_\_update", Finally, all releases and submissions are subject to automatic testing and code checks to make sure they compile with a variety of compilers and popular operating systems. Some unit and regression testing is applied as well. diff --git a/doc/src/Howto_lammps_gui.rst b/doc/src/Howto_lammps_gui.rst index 63cf859c57..adf0c836fb 100644 --- a/doc/src/Howto_lammps_gui.rst +++ b/doc/src/Howto_lammps_gui.rst @@ -21,10 +21,11 @@ to the online LAMMPS documentation for known LAMMPS commands and styles. Sur or later), and Windows (version 10 or later) :ref:`are available ` for download. Non-MPI LAMMPS executables (as ``lmp``) for running LAMMPS from the command-line and :doc:`some - LAMMPS tools ` compiled executables are also included. - Also, the pre-compiled LAMMPS-GUI packages include the WHAM executables + LAMMPS tools ` compiled executables are also included. Also, + the pre-compiled LAMMPS-GUI packages include the WHAM executables from http://membrane.urmc.rochester.edu/content/wham/ for use with - LAMMPS tutorials. + LAMMPS tutorials documented in this paper (:ref:`Gravelle1 + `). The source code for LAMMPS-GUI is included in the LAMMPS source code distribution and can be found in the ``tools/lammps-gui`` folder. It @@ -720,6 +721,19 @@ output, charts, slide show, variables, or snapshot images. The default settings for their visibility can be changed in the *Preferences* dialog. +Tutorials +^^^^^^^^^ + +The *Tutorials* menu is to support the set of LAMMPS tutorials for +beginners and intermediate LAMMPS users documented in (:ref:`Gravelle1 +`). From the drop down menu you can select which of the eight +currently available tutorial sessions you want to start and then will be +taken to a 'wizard' dialog where you can choose in which folder you want +to work, whether you want that folder to be cleared, and also whether +you want to download the solutions files (can be large). The dialog +will then start downloading the files requested and load the first input +file for the selected session into LAMMPS-GUI. + About ^^^^^ @@ -848,6 +862,11 @@ General Settings: the plots in the *Charts* window in milliseconds. The default is to redraw the plots every 500 milliseconds. This is just for the drawing, data collection is managed with the previous setting. +- *HTTPS proxy setting:* Allows to enter a URL for an HTTPS proxy. This + may be needed when the LAMMPS input contains :doc:`geturl commands ` + or for downloading tutorial files from the *Tutorials* menu. If the + ``https_proxy`` environment variable was set externally, its value is + displayed but cannot be changed. Accelerators: ^^^^^^^^^^^^^ @@ -976,10 +995,21 @@ available (On macOS use the Command key instead of Ctrl/Control). - Ctrl+Shift+T - LAMMPS Tutorial -Further editing keybindings `are documented with the Qt documentation +Further keybindings of the editor window `are documented with the Qt +documentation `_. In case of conflicts the list above takes precedence. All other windows only support a subset of keyboard shortcuts listed above. Typically, the shortcuts `Ctrl-/` (Stop Run), `Ctrl-W` (Close Window), and `Ctrl-Q` (Quit Application) are supported. + +------------- + +.. _Gravelle1: + +**(Gravelle1)** Gravelle, Gissinger, Kohlmeyer, `arXiv:2503.14020 \[physics.comp-ph\] `_ (2025) + +.. _Gravelle2: + +**(Gravelle2)** Gravelle https://lammpstutorials.github.io/ diff --git a/doc/src/Howto_moltemplate.rst b/doc/src/Howto_moltemplate.rst index 1b34169a4f..cd5a1fb100 100644 --- a/doc/src/Howto_moltemplate.rst +++ b/doc/src/Howto_moltemplate.rst @@ -2,14 +2,18 @@ Moltemplate Tutorial ==================== In this tutorial, we are going to use the tool :ref:`Moltemplate -` to set up a classical molecular dynamic simulation using -the :ref:`OPLS-AA force field `. The first -task is to describe an organic compound and create a complete input deck -for LAMMPS. The second task is to map the OPLS-AA force field to a -molecular sample created with an external tool, e.g. PACKMOL, and -exported as a PDB file. The files used in this tutorial can be found -in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS -source code distribution. +` from https://moltemplate.org/ to set up a classical +molecular dynamic simulation using the :ref:`OPLS-AA force field +`. The first task is to describe an organic compound and +create a complete input deck for LAMMPS. The second task is to use +moltemplate to build a polymer. The third task is to map the OPLS-AA +force field to a molecular sample created with an external tool, +e.g. PACKMOL, and exported as a PDB file. The files used in this +tutorial can be found in the ``tools/moltemplate/tutorial-files`` folder +of the LAMMPS source code distribution. + +Many more examples can be found here: https://moltemplate.org/examples.html + Simulating an organic solvent """"""""""""""""""""""""""""" @@ -17,14 +21,13 @@ Simulating an organic solvent This example aims to create a cubic box of the organic solvent formamide. -The first step is to create a molecular topology in the -LAMMPS-template (LT) file format representing a single molecule, which -will be stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``. +The first step is to create a molecular topology in the LAMMPS-template +(LT) file format representing a single molecule, which will be +stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``. This command states that the object ``_FAM`` is based on an existing object called ``OPLSAA``, which contains OPLS-AA parameters, atom type definitions, partial charges, masses and bond-angle rules for many organic and biological compounds. - The atomic structure is the starting point to populate the command ``write('Data Atoms') {}``, which will write the ``Atoms`` section in the LAMMPS data file. The OPLS-AA force field uses the ``atom_style full``, @@ -36,21 +39,23 @@ to the ``molID``, except that the same variable is used for the whole molecule. The atom types are assigned using ``@``-type variables. The assignment of atom types (e.g. ``@atom:177``, ``@atom:178``) is done using the OPLS-AA atom types defined in the "In Charges" section of the file -``oplsaa.lt``, looking for a reasonable match with the description of the atom. +``oplsaa2024.lt``, looking for a reasonable match with the description of the atom. The resulting file (``formamide.lt``) follows: .. code-block:: bash + import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt # defines OPLSAA + _FAM inherits OPLSAA { # atomID molID atomType charge coordX coordY coordZ write('Data Atoms') { - $atom:C00 $mol @atom:177 0.00 0.100 0.490 0.0 - $atom:O01 $mol @atom:178 0.00 1.091 -0.250 0.0 - $atom:N02 $mol @atom:179 0.00 -1.121 -0.181 0.0 - $atom:H03 $mol @atom:182 0.00 -2.013 0.272 0.0 - $atom:H04 $mol @atom:182 0.00 -1.056 -1.190 0.0 - $atom:H05 $mol @atom:221 0.00 0.144 1.570 0.0 + $atom:C00 $mol @atom:235 0.00 0.100 0.490 0.0 + $atom:O01 $mol @atom:236 0.00 1.091 -0.250 0.0 + $atom:N02 $mol @atom:237 0.00 -1.121 -0.181 0.0 + $atom:H03 $mol @atom:240 0.00 -2.013 0.272 0.0 + $atom:H04 $mol @atom:240 0.00 -1.056 -1.190 0.0 + $atom:H05 $mol @atom:279 0.00 0.144 1.570 0.0 } # A list of the bonds in the molecule: @@ -64,16 +69,17 @@ The resulting file (``formamide.lt``) follows: } } -You don't have to specify the charge in this example because they will -be assigned according to the atom type. Analogously, only a -"Data Bond List" section is needed as the atom type will determine the -bond type. The other bonded interactions (e.g. angles, -dihedrals, and impropers) will be automatically generated by +You don't have to specify the charge in this example because the OPLSAA +force-field assigns charge according to the atom type. (This is not true +when using other force fields.) A "Data Bond List" section is needed as +the atom type will determine the bond type. The other bonded interactions +(e.g. angles, dihedrals, and impropers) will be automatically generated by Moltemplate. -If the simulation is non-neutral, or Moltemplate complains that you have -missing bond, angle, or dihedral types, this means at least one of your -atom types is incorrect. +If the simulation is not charge-neutral, or Moltemplate complains that +you have missing bond, angle, or dihedral types, this probably means that +at least one of your atom types is incorrect (or that perhaps there is no +suitable atom type currently defined in the ``oplsaa2024.lt`` file). The second step is to create a master file with instructions to build a starting structure and the LAMMPS commands to run an NPT simulation. The @@ -81,11 +87,9 @@ master file (``solv_01.lt``) follows: .. code-block:: bash - # Import the force field. - import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt - import formamide.lt # after oplsaa.lt, as it depends on it. + import formamide.lt # Defines "_FAM" and OPLSAA - # Create the input sample. + # Distribute the molecules on a 5x5x5 cubic grid with spacing 4.6 solv = new _FAM [5].move( 4.6, 0, 0) [5].move( 0, 4.6, 0) [5].move( 0, 0, 4.6) @@ -98,8 +102,11 @@ master file (``solv_01.lt``) follows: -11.5 11.5 zlo zhi } - # Create an input deck for LAMMPS. - write_once("In Init"){ + # Note: The lines below in the "In Run" section are often omitted. + + write_once("In Run"){ + # Create an input deck for LAMMPS. + # Run an NPT simulation. # Input variables. variable run string solv_01 # output name variable ts equal 1 # timestep @@ -109,12 +116,6 @@ master file (``solv_01.lt``) follows: variable equi equal 5000 # Equilibration steps variable prod equal 30000 # Production steps - # PBC (set them before the creation of the box). - boundary p p p - } - - # Run an NPT simulation. - write_once("In Run"){ # Derived variables. variable tcouple equal \$\{ts\}*100 variable pcouple equal \$\{ts\}*1000 @@ -143,7 +144,7 @@ master file (``solv_01.lt``) follows: unfix NPT } -The first two commands insert the content of files ``oplsaa.lt`` and +The first two commands insert the content of files ``oplsaa2024.lt`` and ``formamide.lt`` into the master file. At this point, we can use the command ``solv = new _FAM [N]`` to create N copies of a molecule of type ``_FAM``. In this case, we create an array of 5*5*5 molecules on a cubic @@ -153,21 +154,37 @@ the sample was created from scratch, we also specify the simulation box size in the "Data Boundary" section. The LAMMPS setting for the force field are specified in the file -``oplsaa.lt`` and are written automatically in the input deck. We also +``oplsaa2024.lt`` and are written automatically in the input deck. We also specify the boundary conditions and a set of variables in -the "In Init" section. The remaining commands to run an NPT simulation +the "In Init" section. + +The remaining commands to run an NPT simulation are written in the "In Run" section. Note that in this script, LAMMPS variables are protected with the escape character ``\`` to distinguish them from Moltemplate variables, e.g. ``\$\{run\}`` is a LAMMPS variable that is written in the input deck as ``${run}``. +(Note: Moltemplate can be slow to run, so you need to change you run +settings frequently, I recommended moving those commands (from "In Run") +out of your .lt files and into a separate file. Moltemplate creates a +file named ``run.in.EXAMPLE`` for this purpose. You can put your run +settings and fixes that file and then invoke LAMMPS using +``mpirun -np 4 lmp -in run.in.EXAMPLE`` instead.) + + Compile the master file with: .. code-block:: bash - moltemplate.sh -overlay-all solv_01.lt + moltemplate.sh solv_01.lt + cleanup_moltemplate.sh # <-- optional: see below -And execute the simulation with the following: +(Note: The optional "cleanup_moltemplate.sh" command deletes +unused atom types, which sometimes makes LAMMPS run faster. +But it does not work with many-body pair styles or dreiding-style h-bonds. +Fortunately most force fields, including OPLSAA, don't use those features.) + +Then execute the simulation with the following: .. code-block:: bash @@ -180,15 +197,116 @@ And execute the simulation with the following: Snapshot of the sample at the beginning and end of the simulation. Rendered with Ovito. + +Building a simple polymer +""""""""""""""""""""""""" +Moltemplate is particularly useful for building polymers (and other molecules +with sub-units). As an simple example, consider butane: + +.. figure:: JPG/butane.jpg + +The ``butane.lt`` file below defines Butane as a polymer containing +4 monomers (of type ``CH3``, ``CH2``, ``CH2``, ``CH3``). + +.. code-block:: bash + + import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt # defines OPLSAA + + CH3 inherits OPLSAA { + + # atomID molID atomType charge coordX coordY coordZ + write("Data Atoms") { + $atom:c $mol:... @atom:54 0.0 0.000000 0.4431163 0.000000 + $atom:h1 $mol:... @atom:60 0.0 0.000000 1.0741603 0.892431 + $atom:h2 $mol:... @atom:60 0.0 0.000000 1.0741603 -0.892431 + $atom:h3 $mol:... @atom:60 0.0 -0.892431 -0.1879277 0.000000 + } + # (Using "$mol:..." indicates this object ("CH3") is part of a larger + # molecule. Moltemplate will share the molecule-ID with that molecule.) + + # A list of the bonds within the "CH3" molecular sub-unit: + # BondID AtomID1 AtomID2 + write('Data Bond List') { + $bond:ch1 $atom:c $atom:h1 + $bond:ch2 $atom:c $atom:h2 + $bond:ch3 $atom:c $atom:h3 + } + } + + CH2 inherits OPLSAA { + + # atomID molID atomType charge coordX coordY coordZ + write("Data Atoms") { + $atom:c $mol:... @atom:57 0.0 0.000000 0.4431163 0.000000 + $atom:h1 $mol:... @atom:60 0.0 0.000000 1.0741603 0.892431 + $atom:h2 $mol:... @atom:60 0.0 0.000000 1.0741603 -0.892431 + } + + # A list of the bonds within the "CH2" molecular sub-unit: + # BondID AtomID1 AtomID2 + write('Data Bond List') { + $bond:ch1 $atom:c $atom:h1 + $bond:ch2 $atom:c $atom:h2 + } + } + + Butane inherits OPLSAA { + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + # - Create 4 monomers + # - Move them along the X axis using ".move()", + # - Rotate them 180 degrees with respect to the previous monomer + monomer1 = new CH3 + monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0) + monomer3 = new CH2.move(2.5066446,0,0) + monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0) + + # A list of the bonds connecting different monomers together: + write('Data Bond List') { + $bond:b1 $atom:monomer1/c $atom:monomer2/c + $bond:b2 $atom:monomer2/c $atom:monomer3/c + $bond:b3 $atom:monomer3/c $atom:monomer4/c + } + } + +Again, you don't have to specify the charge in this example because OPLSAA +assigns charges according to the atom type. + +This ``Butane`` object is a molecule which can be used anywhere other molecules +can be used. (You can arrange ``Butane`` molecules on a lattice, as we did previously. +You can also modify individual butane molecules by adding or deleting atoms or bonds. +You can add bonds between specific butane molecules or use ``Butane`` as a +sub-unit to define even larger molecules. See the moltemplate manual for details.) + + + + + + +How to build a complex polymer +"""""""""""""""""""""""""""""""""""""""""" +A similar procedure can be used to create more complicated polymers, +such as the NIPAM polymer example shown below. For details, see: + +https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/NIPAM_polymer+water+ions + + + + Mapping an existing structure """"""""""""""""""""""""""""" Another helpful way to use Moltemplate is mapping an existing molecular -sample to a force field. This is useful when a complex sample is -assembled from different simulations or created with specialized -software (e.g. PACKMOL). As in the previous example, all molecular -species in the sample must be defined using single-molecule Moltemplate -objects. For this example, we use a short polymer in a box containing +sample to a force field. This is useful when a complex sample is assembled +from different simulations or created with specialized software (e.g. PACKMOL). +(Note: The previous link shows how to build this entire system from scratch +using only moltemplate. However here we will assume instead that we obtained +a PDB file for this system using PACKMOL.) + +As in the previous examples, all molecular species in the sample +are defined using single-molecule Moltemplate objects. +For this example, we use a short polymer in a box containing water molecules and ions in the PDB file ``model.pdb``. It is essential to understand that the order of atoms in the PDB file @@ -246,25 +364,25 @@ The resulting master LT file defining short annealing at a fixed volume .. code-block:: bash # Use the OPLS-AA force field for all species. - import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt + import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt import PolyNIPAM.lt # Define the SPC water and ions as in the OPLS-AA Ca inherits OPLSAA { write("Data Atoms"){ - $atom:a1 $mol:. @atom:354 0.0 0.00000 0.00000 0.000000 + $atom:a1 $mol:. @atom:412 0.0 0.00000 0.00000 0.000000 } } Cl inherits OPLSAA { write("Data Atoms"){ - $atom:a1 $mol:. @atom:344 0.0 0.00000 0.00000 0.000000 + $atom:a1 $mol:. @atom:401 0.0 0.00000 0.00000 0.000000 } } SPC inherits OPLSAA { write("Data Atoms"){ - $atom:O $mol:. @atom:76 0. 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:77 0. 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590 + $atom:O $mol:. @atom:9991 0. 0.0000000 0.00000 0.0000000 + $atom:H1 $mol:. @atom:9990 0. 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:9990 0. -0.8164904 0.00000 0.5773590 } write("Data Bond List") { $bond:OH1 $atom:O $atom:H1 @@ -285,8 +403,15 @@ The resulting master LT file defining short annealing at a fixed volume 0 26 zlo zhi } - # Define the input variables. write_once("In Init"){ + boundary p p p # "p p p" is the default. This line is optional. + neighbor 3 bin # (This line is also optional in this example.) + } + + # Note: The lines below in the "In Run" section are often omitted. + + # Run an NVT simulation. + write_once("In Run"){ # Input variables. variable run string sample01 # output name variable ts equal 2 # timestep @@ -294,13 +419,6 @@ The resulting master LT file defining short annealing at a fixed volume variable p equal 1. # equilibrium pressure variable equi equal 30000 # equilibration steps - # PBC (set them before the creation of the box). - boundary p p p - neighbor 3 bin - } - - # Run an NVT simulation. - write_once("In Run"){ # Set the output. thermo 1000 thermo_style custom step etotal evdwl ecoul elong ebond eangle & @@ -314,8 +432,8 @@ The resulting master LT file defining short annealing at a fixed volume write_data \$\{run\}.min # Set the constrains. - group watergroup type @atom:76 @atom:77 - fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043 + group watergroup type @atom:9991 @atom:9990 + fix 0 watergroup shake 0.0001 10 0 b @bond:spcO_spcH a @angle:spcH_spcO_spcH # Short annealing. timestep \$\{ts\} @@ -327,7 +445,7 @@ The resulting master LT file defining short annealing at a fixed volume In this example, the water model is SPC and it is defined in the -``oplsaa.lt`` file with atom types ``@atom:76`` and ``@atom:77``. For +``oplsaa2024.lt`` file with atom types ``@atom:9991`` and ``@atom:9990``. For water we also use the ``group`` and ``fix shake`` commands with Moltemplate ``@``-type variables, to ensure consistency with the numerical values assigned during compilation. To identify the bond and @@ -336,19 +454,20 @@ are: .. code-block:: bash - replace{ @atom:76 @atom:76_b042_a042_d042_i042 } - replace{ @atom:77 @atom:77_b043_a043_d043_i043 } + replace{ @atom:9991 @atom:9991_bspcO_aspcO_dspcO_ispcO } + replace{ @atom:9990 @atom:9990_bspcH_aspcH_dspcH_ispcH } From which we can identify the following "Data Bonds By Type": -``@bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i*`` and -"Data Angles By Type": ``@angle:043_042_043 @atom:*_b*_a043*_d*_i* -@atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i*`` +``@bond:spcO_spcH @atom:*_bspcO*_a*_d*_i* @atom:*_bspcH*_a*_d*_i*`` +and "Data Angles By Type": +``@angle:spcH_spcO_spcH @atom:*_b*_aspcH*_d*_i* @atom:*_b*_aspcO*_d*_i* @atom:*_b*_aspcH*_d*_i*`` Compile the master file with: .. code-block:: bash - moltemplate.sh -overlay-all -pdb model.pdb sample01.lt + moltemplate.sh -pdb model.pdb sample01.lt + cleanup_moltemplate.sh And execute the simulation with the following: @@ -363,8 +482,13 @@ And execute the simulation with the following: Sample visualized with Ovito loading the trajectory into the DATA file written after minimization. + ------------ -.. _OPLSAA96: +.. _oplsaa2024: -**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996). +**(OPLS-AA)** Jorgensen, W.L., Ghahremanpour, M.M., Saar, A., Tirado-Rives, J., J. Phys. Chem. B, 128(1), 250-262 (2024). + +.. _Moltemplate1: + +**(Moltemplate)** Jewett et al., J. Mol. Biol., 433(11), 166841 (2021) diff --git a/doc/src/Howto_peri.rst b/doc/src/Howto_peri.rst index 29eb685c81..fa299e7f84 100644 --- a/doc/src/Howto_peri.rst +++ b/doc/src/Howto_peri.rst @@ -197,7 +197,7 @@ The LPS model has a force scalar state .. math:: \underline{t} = \frac{3K\theta}{m}\underline{\omega}\,\underline{x} + - \alpha \underline{\omega}\,\underline{e}^{\rm d}, \qquad\qquad\textrm{(3)} + \alpha \underline{\omega}\,\underline{e}^\mathrm{d}, \qquad\qquad\textrm{(3)} with :math:`K` the bulk modulus and :math:`\alpha` related to the shear modulus :math:`G` as @@ -242,14 +242,14 @@ scalar state are defined, respectively, as .. math:: - \underline{e}^{\rm i}=\frac{\theta \underline{x}}{3}, \qquad - \underline{e}^{\rm d} = \underline{e}- \underline{e}^{\rm i}, + \underline{e}^\mathrm{i}=\frac{\theta \underline{x}}{3}, \qquad + \underline{e}^\mathrm{d} = \underline{e}- \underline{e}^\mathrm{i}, where the arguments of the state functions and the vectors on which they operate are omitted for simplicity. We note that the LPS model is linear in the dilatation :math:`\theta`, and in the deviatoric part of the -extension :math:`\underline{e}^{\rm d}`. +extension :math:`\underline{e}^\mathrm{d}`. .. note:: diff --git a/doc/src/Howto_python.rst b/doc/src/Howto_python.rst index bfb182d989..ee919e96e7 100644 --- a/doc/src/Howto_python.rst +++ b/doc/src/Howto_python.rst @@ -62,17 +62,17 @@ with :ref:`PNG, JPEG and FFMPEG output support ` enabled. cd $LAMMPS_DIR/src - # add packages if necessary + # add LAMMPS packages if necessary make yes-MOLECULE make yes-PYTHON # compile shared library using Makefile make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg" -Step 2: Installing the LAMMPS Python package -"""""""""""""""""""""""""""""""""""""""""""" +Step 2: Installing the LAMMPS Python module +""""""""""""""""""""""""""""""""""""""""""" -Next install the LAMMPS Python package into your current Python installation with: +Next install the LAMMPS Python module into your current Python installation with: .. code-block:: bash @@ -89,6 +89,29 @@ privileges) or into your personal Python module folder. Recompiling the shared library requires re-installing the Python package. +.. _externally_managed: + +.. admonition:: Handling an "externally-managed-environment" Error + :class: Hint + + Some Python installations made through Linux distributions + (e.g. Ubuntu 24.04LTS or later) will prevent installing the LAMMPS + Python module into a system folder or a corresponding folder of the + individual user as attempted by ``make install-python`` with an error + stating that an *externally managed* python installation must be only + managed by the same package package management tool. This is an + optional setting, so not all Linux distributions follow it currently + (Spring 2025). The reasoning and explanations for this error can be + found in the `Python Packaging User Guide + `_ + + These guidelines suggest to create a virtual environment and install + the LAMMPS Python module there (see below). This is generally a good + idea and the LAMMPS developers recommend this, too. If, however, you + want to proceed and install the LAMMPS Python module regardless, you + can install the "wheel" file (see above) manually with the ``pip`` + command by adding the ``--break-system-packages`` flag. + Installation inside of a virtual environment ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 3529579d65..24ac66e103 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -249,23 +249,23 @@ as follows: .. math:: - a = & {\rm lx} \\ - b^2 = & {\rm ly}^2 + {\rm xy}^2 \\ - c^2 = & {\rm lz}^2 + {\rm xz}^2 + {\rm yz}^2 \\ - \cos{\alpha} = & \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\ - \cos{\beta} = & \frac{\rm xz}{c} \\ - \cos{\gamma} = & \frac{\rm xy}{b} \\ + a = & \mathrm{lx} \\ + b^2 = & \mathrm{ly}^2 + \mathrm{xy}^2 \\ + c^2 = & \mathrm{lz}^2 + \mathrm{xz}^2 + \mathrm{yz}^2 \\ + \cos{\alpha} = & \frac{\mathrm{xy}*\mathrm{xz} + \mathrm{ly}*\mathrm{yz}}{b*c} \\ + \cos{\beta} = & \frac{\mathrm{xz}}{c} \\ + \cos{\gamma} = & \frac{\mathrm{xy}}{b} \\ The inverse relationship can be written as follows: .. math:: - {\rm lx} = & a \\ - {\rm xy} = & b \cos{\gamma} \\ - {\rm xz} = & c \cos{\beta}\\ - {\rm ly}^2 = & b^2 - {\rm xy}^2 \\ - {\rm yz} = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\ - {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\ + \mathrm{lx} = & a \\ + \mathrm{xy} = & b \cos{\gamma} \\ + \mathrm{xz} = & c \cos{\beta}\\ + \mathrm{ly}^2 = & b^2 - \mathrm{xy}^2 \\ + \mathrm{yz} = & \frac{b*c \cos{\alpha} - \mathrm{xy}*\mathrm{xz}}{\mathrm{ly}} \\ + \mathrm{lz}^2 = & c^2 - \mathrm{xz}^2 - \mathrm{yz}^2 \\ The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and :math:`\gamma` can be printed out or accessed by computes using the diff --git a/doc/src/Install_mac.rst b/doc/src/Install_mac.rst index 452a8fd460..c8e21e8cfe 100644 --- a/doc/src/Install_mac.rst +++ b/doc/src/Install_mac.rst @@ -5,8 +5,7 @@ LAMMPS can be downloaded, built, and configured for macOS with `Homebrew `_. (Alternatively, see the installation instructions for :doc:`downloading an executable via Conda `.) The following LAMMPS packages are unavailable at this time because of -additional requirements not yet met: GPU, KOKKOS, MSCG, POEMS, -VORONOI. +additional requirements not yet met: GPU, KOKKOS. After installing Homebrew, you can install LAMMPS on your system with the following commands: diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index 57fa7fbfb6..0f777a9adc 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -20,13 +20,21 @@ acceleration. .. _lws: https://www.lammps.org .. _omp: https://www.openmp.org -LAMMPS is written in C++ and requires a compiler that is at least -compatible with the C++-11 standard. Earlier versions were written in -F77, F90, and C++-98. See the `History page +LAMMPS is written in C++ and currently requires a compiler that is at +least compatible with the C++-11 standard. Earlier versions were +written in F77, F90, and C++-98. See the `History page `_ of the website for details. All versions can be downloaded as source code from the `LAMMPS website `_. +Through a :ref:`C language API ` LAMMPS functionality can +be accessed and managed from other programming languages rather than +running the LAMMPS executable. Ready to use modules for :ref:`Python +` and :ref:`Fortran ` exist, and +an example :ref:`SWIG interface file ` as well as example C files +for dynamically loading LAMMPS as a shared library into other +executables are provided. + LAMMPS is designed to be easy to modify or extend with new capabilities, such as new force fields, atom types, boundary conditions, or diagnostics. See the :doc:`Modify` section of for more details. diff --git a/doc/src/Intro_portability.rst b/doc/src/Intro_portability.rst index 8bb716833f..63ae147b8c 100644 --- a/doc/src/Intro_portability.rst +++ b/doc/src/Intro_portability.rst @@ -15,7 +15,7 @@ Most of the C++ code currently requires a compiler compatible with the C++11 standard, the KOKKOS package currently requires C++17. Most of the Python code is written to be compatible with Python 3.6 or later. -.. deprecated:: TBD +.. deprecated:: 2Apr2025 Python 2.x is no longer supported and trying to use it, e.g. for the LAMMPS Python module should result in an error. If you come across diff --git a/doc/src/JPG/PolyNIPAM.jpg b/doc/src/JPG/PolyNIPAM.jpg index 4ad3ce8274..372a712de1 100644 Binary files a/doc/src/JPG/PolyNIPAM.jpg and b/doc/src/JPG/PolyNIPAM.jpg differ diff --git a/doc/src/JPG/butane.jpg b/doc/src/JPG/butane.jpg new file mode 100644 index 0000000000..41a9a9edd1 Binary files /dev/null and b/doc/src/JPG/butane.jpg differ diff --git a/doc/src/JPG/rhodo-both.jpg b/doc/src/JPG/rhodo-both.jpg new file mode 100644 index 0000000000..47cc863d8f Binary files /dev/null and b/doc/src/JPG/rhodo-both.jpg differ diff --git a/doc/src/Library_add.rst b/doc/src/Library_add.rst index 8777ebbcad..e955422984 100644 --- a/doc/src/Library_add.rst +++ b/doc/src/Library_add.rst @@ -19,9 +19,9 @@ there are now a few requirements for including new changes or extensions. be added. - New features should also be implemented and documented not just for the C interface, but also the Python and Fortran interfaces. - - All additions should work and be compatible with ``-DLAMMPS_BIGBIG``, - ``-DLAMMPS_SMALLBIG``, ``-DLAMMPS_SMALLSMALL`` as well as when - compiling with and without MPI support. + - All additions should work and be compatible with + ``-DLAMMPS_BIGBIG``, ``-DLAMMPS_SMALLBIG`` as well as when compiling + with and without MPI support. - The ``library.h`` file should be kept compatible to C code at a level similar to C89. Its interfaces may not reference any custom data types (e.g. ``bigint``, ``tagint``, and so on) that diff --git a/doc/src/Library_utility.rst b/doc/src/Library_utility.rst index e555b79c0b..b9cd568da9 100644 --- a/doc/src/Library_utility.rst +++ b/doc/src/Library_utility.rst @@ -20,6 +20,7 @@ functions. They do not directly call the LAMMPS library. - :cpp:func:`lammps_force_timeout` - :cpp:func:`lammps_has_error` - :cpp:func:`lammps_get_last_error_message` +- :cpp:func:`lammps_set_show_error` - :cpp:func:`lammps_python_api_version` The :cpp:func:`lammps_free` function is a clean-up function to free @@ -110,6 +111,11 @@ where such memory buffers were allocated that require the use of ----------------------- +.. doxygenfunction:: lammps_set_show_error + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_python_api_version :project: progguide diff --git a/doc/src/Manual_version.rst b/doc/src/Manual_version.rst index 1bfaffaf6d..0c757fc0ea 100644 --- a/doc/src/Manual_version.rst +++ b/doc/src/Manual_version.rst @@ -2,9 +2,15 @@ What does a LAMMPS version mean ------------------------------- The LAMMPS "version" is the date when it was released, such as 1 May -2014. LAMMPS is updated continuously, and we aim to keep it working -correctly and reliably at all times. Also, several variants of static -code analysis are run regularly to maintain or improve the overall code +2014. LAMMPS is updated continuously, and with the help of extensive +automated testing (mostly applied *before* changes are included) we aim +to keep it working correctly and reliably at all times, but there also +are regular *feature releases* with new and expanded functionality, and +there are designated *stable releases* that receive updates with bug +fixes back-ported from the development branch. + +In addition to automated testing, several variants of static code +analysis are run regularly to maintain or improve the overall code quality, consistency, and compliance with programming standards, best practices and style conventions. You can follow its development in a public `git repository on GitHub `_. @@ -19,17 +25,18 @@ Identifying the Version The version date is printed to the screen and log file every time you run LAMMPS. There also is an indication, if a LAMMPS binary was -compiled from version with modifications **after** a release. -It is also visible in the file src/version.h and in the LAMMPS directory -name created when you unpack a downloaded tarball. And it is on the -first page of the :doc:`manual `. +compiled from version with modifications **after** a release, either +from the development version or the maintenance version of the last +stable release. It is also visible in the file src/version.h and in the +LAMMPS directory name created when you unpack a downloaded tarball. And +it is on the first page of the :doc:`manual `. * If you browse the HTML pages of the online version of the LAMMPS manual, they will by default describe the most current feature release version of LAMMPS. In the navigation bar on the bottom left, there is the option to view instead the documentation for the most recent *stable* version or the documentation corresponding to the state of - the development branch. + the development branch *develop*. * If you browse the HTML pages included in your downloaded tarball, they describe the version you have, which may be older than the online version. @@ -48,8 +55,9 @@ Development Modifications of the LAMMPS source code (like bug fixes, code refactoring, updates to existing features, or addition of new features) are organized into pull requests. Pull requests will be merged into the -*develop* branch of the git repository after they pass automated testing -and code review by the LAMMPS developers. +*develop* branch of the LAMMPS git repository on GitHub after they pass +automated testing and code review by :doc:`core LAMMPS developers +`. Feature Releases """""""""""""""" @@ -62,8 +70,7 @@ repository is updated with every such *feature release* and a tag in the format ``patch_1May2014`` is added. A summary of the most important changes of these releases for the current year are posted on `this website page `_. More detailed release -notes are `available on GitHub -`_. +notes are `available on GitHub `_. Stable Releases """"""""""""""" @@ -71,18 +78,18 @@ Stable Releases About once a year, we release a *stable release* version of LAMMPS. This is done after a "stabilization period" where we apply only bug fixes and small, non-intrusive changes to the *develop* branch but no -new features. At the same time, the code is subjected to more detailed -and thorough manual testing than the default automated testing. -After such a *stable release*, both the *release* and the *stable* -branches are updated and two tags are applied, a ``patch_1May2014`` format -and a ``stable_1May2014`` format tag. +new features to the core code. At the same time, the code is subjected +to more detailed and thorough manual testing than the default automated +testing. After such a *stable release*, both the *release* and the +*stable* branches are updated and two tags are applied, a +``patch_1May2014`` format and a ``stable_1May2014`` format tag. Stable Release Updates """""""""""""""""""""" -Between *stable releases*, we collect bug fixes and updates back-ported -from the *develop* branch in a branch called *maintenance*. From the -*maintenance* branch we make occasional *stable update releases* and -update the *stable* branch accordingly. The first update to the -``stable_1May2014`` release would be tagged as +Between *stable releases*, we collect bug fixes and updates that are +back-ported from the *develop* branch in a branch called *maintenance*. +From the *maintenance* branch we make occasional *stable update +releases* and update the *stable* branch accordingly. The first update +to the ``stable_1May2014`` release would be tagged as ``stable_1May2014_update1``. These updates contain no new features. diff --git a/doc/src/Modify_compute.rst b/doc/src/Modify_compute.rst index ea603985dd..1d7b528d90 100644 --- a/doc/src/Modify_compute.rst +++ b/doc/src/Modify_compute.rst @@ -1,19 +1,21 @@ Compute styles ============== -Classes that compute scalar and vector quantities like temperature -and the pressure tensor, as well as classes that compute per-atom -quantities like kinetic energy and the centro-symmetry parameter -are derived from the Compute class. New styles can be created -to add new calculations to LAMMPS. +Classes that compute scalar and vector quantities like temperature and +the pressure tensor, as well as classes that compute per-atom quantities +like kinetic energy and the centro-symmetry parameter are derived from +the Compute class. New styles can be created to add new calculations to +LAMMPS. -Compute_temp.cpp is a simple example of computing a scalar -temperature. Compute_ke_atom.cpp is a simple example of computing -per-atom kinetic energy. +The ``src/compute_temp.cpp`` file is a simple example of computing a +scalar temperature. The ``src/compute_ke_atom.cpp`` file is a simple +example of computing per-atom kinetic energy. Here is a brief description of methods you define in your new derived -class. See compute.h for details. +class. See ``src/compute.h`` for additional details. ++-----------------------+------------------------------------------------------------------+ +| post_constructor | perform tasks that cannot be run in the constructor (optional) | +-----------------------+------------------------------------------------------------------+ | init | perform one time setup (required) | +-----------------------+------------------------------------------------------------------+ @@ -50,10 +52,11 @@ class. See compute.h for details. | memory_usage | tally memory usage (optional) | +-----------------------+------------------------------------------------------------------+ -Tally-style computes are a special case, as their computation is done -in two stages: the callback function is registered with the pair style -and then called from the Pair::ev_tally() function, which is called for -each pair after force and energy has been computed for this pair. Then -the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The :doc:`compute styles in the TALLY package ` -provide *examples* for utilizing this mechanism. +Tally-style computes are a special case, as their computation is done in +two stages: the callback function is registered with the pair style and +then called from the Pair::ev_tally() function, which is called for each +pair after force and energy has been computed for this pair. Then the +tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The :doc:`compute styles in +the TALLY package ` provide *examples* for utilizing this +mechanism. diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst index 0e697c28dd..18b51d6e13 100644 --- a/doc/src/Modify_fix.rst +++ b/doc/src/Modify_fix.rst @@ -1,23 +1,25 @@ Fix styles ========== -In LAMMPS, a "fix" is any operation that is computed during -timestepping that alters some property of the system. Essentially -everything that happens during a simulation besides force computation, -neighbor list construction, and output, is a "fix". This includes -time integration (update of coordinates and velocities), force -constraints or boundary conditions (SHAKE or walls), and diagnostics -(compute a diffusion coefficient). New styles can be created to add -new options to LAMMPS. +In LAMMPS, a "fix" is any operation that is computed during timestepping +that alters some property of the system. Essentially everything that +happens during a simulation besides force computation, neighbor list +construction, and output, is a "fix". This includes time integration +(update of coordinates and velocities), force constraints or boundary +conditions (SHAKE or walls), and diagnostics (compute a diffusion +coefficient). New styles can be created to add new options to LAMMPS. -Fix_setforce.cpp is a simple example of setting forces on atoms to -prescribed values. There are dozens of fix options already in LAMMPS; -choose one as a template that is similar to what you want to -implement. +The file ``src/fix_setforce.cpp`` is a simple example of setting forces +on atoms to prescribed values. There are dozens of fix options already +in LAMMPS; choose one as a template that is similar to what you want to +implement. There also is a detailed discussion of :doc:`how to write +new fix styles ` in LAMMPS. Here is a brief description of methods you can define in your new -derived class. See fix.h for details. +derived class. See ``src/fix.h`` for additional details. ++---------------------------+--------------------------------------------------------------------------------------------+ +| post_constructor | perform tasks that cannot be run in the constructor (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ | setmask | determines when the fix is called during the timestep (required) | +---------------------------+--------------------------------------------------------------------------------------------+ @@ -130,10 +132,11 @@ derived class. See fix.h for details. Typically, only a small fraction of these methods are defined for a particular fix. Setmask is mandatory, as it determines when the fix -will be invoked during the timestep. Fixes that perform time -integration (\ *nve*, *nvt*, *npt*\ ) implement initial_integrate() and -final_integrate() to perform velocity Verlet updates. Fixes that -constrain forces implement post_force(). +will be invoked during :doc:`the evolution of a timestep +`. Fixes that perform time integration (\ *nve*, *nvt*, +*npt*\ ) implement initial_integrate() and final_integrate() to perform +velocity Verlet updates. Fixes that constrain forces implement +post_force(). Fixes that perform diagnostics typically implement end_of_step(). For an end_of_step fix, one of your fix arguments must be the variable @@ -143,13 +146,13 @@ is the first argument the fix defines (after the ID, group-ID, style). If the fix needs to store information for each atom that persists from timestep to timestep, it can manage that memory and migrate the info -with the atoms as they move from processors to processor by -implementing the grow_arrays, copy_arrays, pack_exchange, and -unpack_exchange methods. Similarly, the pack_restart and -unpack_restart methods can be implemented to store information about -the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the :doc:`run_style ` -command), the initial_integrate, post_force_integrate, and -final_integrate_respa methods can be implemented. The thermo method -enables a fix to contribute values to thermodynamic output, as printed -quantities and/or to be summed to the potential energy of the system. +with the atoms as they move from processors to processor by implementing +the grow_arrays, copy_arrays, pack_exchange, and unpack_exchange +methods. Similarly, the pack_restart and unpack_restart methods can be +implemented to store information about the fix in restart files. If you +wish an integrator or force constraint fix to work with rRESPA (see the +:doc:`run_style ` command), the initial_integrate, +post_force_integrate, and final_integrate_respa methods can be +implemented. The thermo method enables a fix to contribute values to +thermodynamic output, as printed quantities and/or to be summed to the +potential energy of the system. diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 1e53a99914..e225327c06 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -7,7 +7,7 @@ LAMMPS shared library through the Python `ctypes `_ module. Because of the dynamic loading, it is required that LAMMPS is compiled in :ref:`"shared" mode `. -.. versionchanged:: TBD +.. versionchanged:: 2Apr2025 LAMMPS currently only supports Python version 3.6 or later. @@ -110,13 +110,16 @@ folder that the dynamic loader searches or inside of the installed .. code-block:: bash - python install.py -p -l -v [-n] + python install.py -p -l -v [-n] [-f] * The ``-p`` flag points to the ``lammps`` Python package folder to be installed, * the ``-l`` flag points to the LAMMPS shared library file to be installed, * the ``-v`` flag points to the LAMMPS version header file to extract the version date, - * and the optional ``-n`` instructs the script to only build a wheel file - but not attempt to install it. + * the optional ``-n`` instructs the script to only build a wheel file but not attempt + to install it, + * and the optional ``-f`` argument instructs the script to force installation even if + pip would otherwise refuse installation with an + :ref:`error about externally managed environments `. .. tab:: Virtual environment @@ -198,6 +201,10 @@ folder that the dynamic loader searches or inside of the installed The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package! +In case you run into an "externally-managed-environment" error when +trying to install the LAMMPS Python module, please refer to +:ref:`corresponding paragraph ` in the Python HOWTO +page to learn about options for handling this error. To verify if LAMMPS can be successfully started from Python, start the Python interpreter, load the ``lammps`` Python module and create a diff --git a/doc/src/Python_scatter.rst b/doc/src/Python_scatter.rst index da045d7b6b..16bb5b128c 100644 --- a/doc/src/Python_scatter.rst +++ b/doc/src/Python_scatter.rst @@ -3,17 +3,16 @@ Scatter/gather operations .. code-block:: python - data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID - # name = "x", "charge", "type", etc - data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered) - data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs + data = lmp.gather_atoms(name,dtype,count) # return per-atom property of all atoms gathered into data, ordered by atom ID + # name = "x", "q", "type", etc + data = lmp.gather_atoms_concat(name,dtype,count) # ditto, but concatenated atom values from each proc (unordered) + data = lmp.gather_atoms_subset(name,dtype,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs - lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID - # name = "x", "charge", "type", etc - # count = # of per-atom values, 1 or 3, etc - - lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs + lmp.scatter_atoms(name,dtype,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID + # name = "x", "q", "type", etc + # count = # of per-atom values, 1 or 3, etc + lmp.scatter_atoms_subset(name,dtype,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs The gather methods collect peratom info of the requested type (atom coords, atom types, forces, etc) from all processors, and returns the @@ -22,6 +21,12 @@ functions do the inverse. They distribute a vector of peratom values, passed by all calling processors, to individual atoms, which may be owned by different processors. +The *dtype* parameter is 0 for ``int`` values and 1 for ``double`` +values. The *count* parameter is 1 for per-atom vectors like "type" +or "q" and 3 for per-atom arrays like "x", "v", "f". Use *count* = 3 +with name = "image" if you want the single integer storing the image +flags unpacked into 3 components ("x", "y", and "z"). + Note that the data returned by the gather methods, e.g. :py:meth:`gather_atoms("x") `, is different from the data structure returned by diff --git a/doc/src/Run_formats.rst b/doc/src/Run_formats.rst new file mode 100644 index 0000000000..d03227f091 --- /dev/null +++ b/doc/src/Run_formats.rst @@ -0,0 +1,416 @@ + +File formats used by LAMMPS +=========================== + +This page provides a general overview of the kinds of files and file +formats that LAMMPS is reading and writing. + +.. contents:: On this page + :depth: 2 + :backlinks: top + +------------------- + +Character Encoding +^^^^^^^^^^^^^^^^^^ + +For processing text files, the LAMMPS source code assumes `ASCII +character encoding `_ which +represents the digits 0 to 9, the lower and upper case letters a to z, +some common punctuation and other symbols and a few whitespace +characters including a regular "space character", "line feed", "carriage +return", "tabulator". These characters are all represented by single +bytes with a value smaller than 128 and only 95 of those 128 values +represent printable characters. This list is sufficient to represent +most English text, but misses accented characters or umlauts or Greek +symbols and more. + +Modern text often uses `UTF-8 character encoding +`_ instead. This encoding is a way +to represent many more different characters as defined by the Unicode +standard. UFT-8 is compatible with ASCII, since the first 128 values +are identical with the ASCII encoding. It is important to note, +however, that there are Unicode characters that *look* similar to ASCII +characters, but have a different binary representation. As a general +rule, these characters may not be correctly recognized by LAMMPS. For +some parts of LAMMPS' text processing, translation tables with known +"lookalike" characters are used. The tables are used to substitute +non-ASCII characters with their ASCII equivalents. Non-ASCII lookalike +characters are often used by web browsers or PDF viewers to improve the +readability of text. Thus, when using copy and paste to transfer text +from such an application to your input file, you may unintentionally +create text that is not exclusively using ASCII encoding and may cause +errors when LAMMPS is trying to read it. + +Lines with non-printable and non-ASCII characters in text files can be +detected for example with a (Linux) command like the following: + +.. code-block:: bash + + env LC_ALL=C grep -n '[^ -~]' some_file.txt + +Number Formatting +^^^^^^^^^^^^^^^^^ + +Different countries and languages have different conventions to format +numbers. While in some regions commas are used for fractions and points +to indicate thousand, million and so on, this is reversed in other +regions. Modern operating systems have facilities to adjust input and +output accordingly that are collectively referred to as "native language +support" (NLS). The exact rules are often applied according to the +value of the ``$LANG`` environment variable (e.g. "en_US.utf8" for +English text in UTF-8 encoding). + +For the sake of simplicity of the implementation and transferability of +results, LAMMPS does not support this and instead expects numbers being +formatted in the generic or "C" locale. The "C" locale has no +punctuation for thousand, million and so on and uses a decimal point for +fractions. One thousand would be represented as "1000.0" and not as +"1,000.0" nor as "1.000,0". Having native language support enabled for +a locale other than "C" will result in different behavior when +converting or formatting numbers that can trigger unexpected errors. + +LAMMPS also only accepts integer numbers when an integer is required, so +using floating point equivalents like "1.0" are not accepted; you *must* +use "1" instead. + +For floating point numbers in scientific notation, the Fortran double +precision notation "1.1d3" is not accepted; you have to use "1100", +"1100.0" or "1.1e3". + +Input file +^^^^^^^^^^ + +A LAMMPS input file is a text file with commands. It is read +line-by-line and each line is processed *immediately*. Before looking +for commands and executing them, there is a pre-processing step where +comments (non-quoted text starting with a pound sign '#') are removed, +``${variable}`` and ``$(expression)`` constructs are expanded or +evaluated, and lines that end in the ampersand character '&' are +combined with the next line (similar to Fortran 90 free-format source +code). After the pre-processing, lines are split into "words" and +evaluated. The first word must be a :doc:`command ` and +all following words are arguments. Below are some example lines: + +.. code-block:: LAMMPS + + # full line comment + + # some global settings + units lj + atom_style atomic + # ^^ command ^^ argument(s) + + variable x index 1 # may be overridden from command line with -var x + variable xx equal 20*$x # variable "xx" is always 20 times "x" + + lattice fcc 0.8442 + + # example of a command written across multiple lines + # the "region" command uses spacing from "lattice" command, unless "units box" is specified + region box block 0.0 ${xx} & + 0.0 40.0 & + 0.0 30.0 + # create simulation box and fill with atoms according to lattice setting + create_box 1 box + create_atoms 1 box + + # set force field and parameters + mass 1 1.0 + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 2.5 + + # run simulation + fix 1 all nve + run 1000 + +The pivotal command in this example input is the :doc:`create_box +command `. It defines the simulation system and many +parameters that go with it: units, atom style, number of atom types (and +other types) and more. Those settings are *locked in* after the box is +created. Commands that change these kind of settings are only allowed +**before** a simulation box is created and many other commands are only +allowed **after** the simulation box is defined (e.g. :doc:`pair_coeff +`). Very few commands (e.g. :doc:`pair_style `) +may be used in either part of the input. The :doc:`read_data +` and :doc:`read_restart ` commands also create +the system box and thus have a similar pivotal function. + +The LAMMPS input syntax has minimal support for conditionals and loops, +but if more complex operations are required, it is recommended to use +the library interface, e.g. :doc:`from Python using the LAMMPS Python +module `. + +There is a frequent misconception about the :doc:`if command `: +this is a command for conditional execution **outside** a run or +minimization. To trigger actions on specific conditions **during** +a run is a non-trivial operation that usually requires adopting one +of the available "fix" commands or creating a new "fix" command. + +LAMMPS commands change the internal state and thus the order of commands +matters and reordering them can produce different results. For example, +the region defined by the :doc:`region command ` in the example +above depends on the :doc:`lattice setting ` and thus its +dimensions will be different depending on the order of the two commands. + +Each line must have an "end-of-line" character (line feed or carriage +return plus line feed). Some text editors do not automatically insert +one which may cause LAMMPS to ignore the last command. It is thus +recommended to always have an empty line at the end of an input file. + +The specific details describing how LAMMPS input is processed and parsed +are explained in :doc:`Commands_parse`. + +Data file +^^^^^^^^^ + +A LAMMPS data file contains a description of a system suitable for +reading with the :doc:`read_data command `. Data files are +commonly used for setting up complex molecular systems that can be +difficult to achieve with the commands :doc:`create_box ` +and :doc:`create_atoms ` alone. Also, data files can be +used as a portable alternatives to a :doc:`binary restart file +`. A restart file can be converted into a data file from the +:doc:`command line `. + +Data files have a header section at the very beginning of the file and +multiple titled sections such as "Atoms", Masses", "Pair Coeffs", and so +on. Header keywords can only be used *before* the first title section. + +The data file **always** starts with a "title" line, which will be +**ignored** by LAMMPS. Omitting the title line can lead to unexpected +behavior because a line of the header with an actual setting may be +ignored. In this case, the mistakenly ignored line often contains the +"atoms" keyword, which results in LAMMPS assuming that there are no +atoms in the data file and thus throwing an error on the contents of the +"Atoms" section. The title line may contain some keywords that can be +used by external programs to convey information about the system +(included as comments), that is not required and not read by LAMMPS. + +The line following a section title is also **ignored**. An error will +occur if an empty line is not placed after a section title. The number +of lines in titled sections depends on header keywords, like the number +of atom types, the number of atoms, the number of bond types, the number +of bonds, and so on. The data in those sections has to be complete. A +special case are the "Pair Coeffs" and "PairIJ Coeffs" sections; the +former is for force fields and pair styles that use mixing of non-bonded +potential parameters, the latter for pair styles and force fields +requiring explicit coefficients. Thus with *N* being the number of atom +types, the "Pair Coeffs" section has *N* entries while "PairIJ Coeffs" +has :math:`N \cdot (N-1)` entries. Internally, these sections will be +converted to :doc:`pair_coeff ` commands. Thus the +corresponding :doc:`pair style ` must have been set *before* +the :doc:`read_data command ` reads the data file. + +Data files may contain comments, which start with the pound sign '#'. +There must be at least one blank between a valid keyword and the pound +sign. Below is a simple example case of a data file for :doc:`atom style +full `. + +.. code-block:: bash + + LAMMPS Title line (ignored) + # full line comment + + 10 atoms # comment + 4 atom types + + -36.840194 64.211560 xlo xhi + -41.013691 68.385058 ylo yhi + -29.768095 57.139462 zlo zhi + + Masses + + 1 12.0110 + 2 12.0110 + 3 15.9990 + 4 1.0080 + + Pair Coeffs # this section is optional + + 1 0.110000 3.563595 0.110000 3.563595 + 2 0.080000 3.670503 0.010000 3.385415 + 3 0.120000 3.029056 0.120000 2.494516 + 4 0.022000 2.351973 0.022000 2.351973 + + Atoms # full + + 1 1 1 0.560 43.99993 58.52678 36.78550 0 0 0 + 2 1 2 -0.270 45.10395 58.23499 35.86693 0 0 0 + 3 1 3 -0.510 43.81519 59.54928 37.43995 0 0 0 + 4 1 4 0.090 45.71714 57.34797 36.13434 0 0 0 + 5 1 4 0.090 45.72261 59.13657 35.67007 0 0 0 + 6 1 4 0.090 44.66624 58.09539 34.85538 0 0 0 + 7 1 3 -0.470 43.28193 57.47427 36.91953 0 0 0 + 8 1 4 0.070 42.07157 57.45486 37.62418 0 0 0 + 9 1 1 0.510 42.19985 57.57789 39.12163 0 0 0 + 10 1 1 0.510 41.88641 58.62251 39.70398 0 0 0 + # ^^atomID ^^molID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord ^^image^^flags (optional) + + Velocities # this section is optional + + 1 0.0050731 -0.00398928 0.00391473 + 2 -0.0175184 0.0173484 -0.00489207 + 3 0.00597225 -0.00202006 0.00166454 + 4 -0.010395 -0.0082582 0.00316419 + 5 -0.00390877 0.00470331 -0.00226911 + 6 -0.00111157 -0.00374545 -0.0169374 + 7 0.00209054 -0.00594936 -0.000124563 + 8 0.00635002 -0.0120093 -0.0110999 + 9 -0.004955 -0.0123375 0.000403422 + 10 0.00265028 -0.00189329 -0.00293198 + +The common problem is processing the "Atoms" section, since its format +depends on the :doc:`atom style ` used, and that setting +must be done in the input file *before* reading the data file. To +assist with detecting incompatible data files, a comment is appended to +the "Atoms" title indicating the atom style used (or intended) when +*writing* the data file. For example, below is an "Atoms" section for +:doc:`atom style charge `, which omits the molecule ID +column. + +.. code-block:: bash + + Atoms # charge + + 1 1 0.560 43.99993 58.52678 36.78550 + 2 2 -0.270 45.10395 58.23499 35.86693 + 3 3 -0.510 43.81519 59.54928 37.43995 + 4 4 0.090 45.71714 57.34797 36.13434 + 5 4 0.090 45.72261 59.13657 35.67007 + 6 4 0.090 44.66624 58.09539 34.85538 + 7 3 -0.470 43.28193 57.47427 36.91953 + 8 4 0.070 42.07157 57.45486 37.62418 + 9 1 0.510 42.19985 57.57789 39.12163 + 10 1 0.510 41.88641 58.62251 39.70398 + # ^^atomID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord + +Another source of confusion about the "Atoms" section format is the +ordering of columns. The three atom style variants `atom_style full`, +`atom_style hybrid charge molecular`, and `atom_style hybrid molecular +charge` all carry the same per-atom information. However, in data files, +the Atoms section has the columns 'Atom-ID Molecule-ID Atom-type Charge +X Y Z' for atom style full, but for hybrid atom styles the first columns +are always 'Atom-ID Atom-type X Y Z' followed by any *additional* data +added by the hybrid styles, for example, 'Charge Molecule-ID' for the +first hybrid style and 'Molecule-ID Charge' in the second hybrid style +variant. Finally, an alternative to a hybrid atom style is to use fix +property/atom, e.g. to add molecule IDs to atom style charge. In this +case the "Atoms" section is formatted according to atom style charge and +a new section, "Molecules" is added that contains lines with 'Atom-ID +Molecule-ID', one for each atom in the system. For adding charges to +atom style molecular with fix property/atom, the "Atoms" section is now +formatted according to the atom style and a "Charges" section is added. + +Molecule file +^^^^^^^^^^^^^ + +Molecule files for use with the :doc:`molecule command ` look +quite similar to data files but they do not have a compatible format, +i.e., one cannot use a data file as molecule file and vice versa. Below +is a simple example for a water molecule (SPC/E model). Same as a data +file, there is an ignored title line and you can use comments. However, +there is no information about the number of types or the box dimensions. +These parameters are set when the simulation box is created. Thus the +header only has the count of atoms, bonds, and so on. + +Molecule files have a header followed by sections (just as in data +files), but the section names are different than those of a data file. +There is no "Atoms" section and the section formats in molecule files is +independent of the atom style. Its information is split across multiple +sections, like "Coords", "Types", and "Charges". Note that no "Masses" +section is needed here. The atom masses are by default tied to the atom +type and set with a data file or the :doc:`mass command `. A +"Masses" section would only be required for atom styles with per-atom +masses, e.g. atom style sphere, where in data files you would provide +the density and the diameter instead of the mass. + +Since the entire file is a 'molecule', LAMMPS will assign a new +molecule-ID (if supported by the atom style) when atoms are instantiated +from a molecule file, e.g. with the :doc:`create_atoms command +`. It is possible to include a "Molecules" section to +indicate that the atoms belong to multiple 'molecules'. Atom-IDs and +molecule-IDs in the molecule file are relative for the file +(i.e. starting from 1) and will be translated into actual atom-IDs also +when the atoms from the molecule are created. + +.. code-block:: bash + + # Water molecule. SPC/E model. + + 3 atoms + 2 bonds + 1 angles + + Coords + + 1 1.12456 0.09298 1.27452 + 2 1.53683 0.75606 1.89928 + 3 0.49482 0.56390 0.65678 + + Types + + 1 1 + 2 2 + 3 2 + + Charges + + 1 -0.8472 + 2 0.4236 + 3 0.4236 + + Bonds + + 1 1 1 2 + 2 1 1 3 + + Angles + + 1 1 2 1 3 + + +There are also optional sections, e.g. about :doc:`SHAKE ` +and :doc:`special bonds `. Those sections are only needed +if the molecule command is issued *before* the simulation box is +defined. Otherwise, the molecule command can derive the required +settings internally. + +Restart file +^^^^^^^^^^^^ + +LAMMPS restart files are binary files and not available in text format. +They can be identified by the first few bytes that contain the (C-style) +string ``LammpS RestartT`` as `magic string +`_. This string is followed +by a 16-bit integer of the number 1 used for detecting whether the +computer writing the restart has the same `endianness +`_ as the computer reading it. +If not, the file cannot be read correctly. This integer is followed by +a 32-bit integer indicating the file format revision (currently 3), +which can be used to implement backward compatibility for reading older +revisions. + +This information has been added to the `Unix "file" command's +` "magic" file so that restart files +can be identified without opening them. If you have a fairly recent +version, it should already be included. If you have an older version, +the LAMMPS source package :ref:`contains a file with the necessary +additions `. + +The rest of the file is organized in sections of a 32-bit signed integer +constant indicating the kind of content and the corresponding value (or +values). If those values are arrays (including C-style strings), then +the integer constant is followed by a 32-bit integer indicating the +length of the array. This mechanism will read the data regardless of +the ordering of the sections. Symbolic names of the section constants +are in the ``lmprestart.h`` header file. + +LAMMPS restart files are not expected to be portable between platforms +or LAMMPS versions, but changes to the file format are rare. + +.. Native Dump file +.. ^^^^^^^^^^^^^^^^ +.. +.. Potential files +.. ^^^^^^^^^^^^^^^ diff --git a/doc/src/Run_head.rst b/doc/src/Run_head.rst index 5da5942d9b..6739df5cbb 100644 --- a/doc/src/Run_head.rst +++ b/doc/src/Run_head.rst @@ -1,10 +1,11 @@ Run LAMMPS ********** -These pages explain how to run LAMMPS once you have :doc:`installed an executable ` or :doc:`downloaded the source code ` -and :doc:`built an executable `. The :doc:`Commands ` -doc page describes how input scripts are structured and the commands -they can contain. +These pages explain how to run LAMMPS once you have :doc:`installed an +executable ` or :doc:`downloaded the source code ` and +:doc:`built an executable `. The :doc:`Commands ` doc +page describes how input scripts are structured and the commands they +can contain. .. toctree:: :maxdepth: 1 @@ -12,4 +13,5 @@ they can contain. Run_basics Run_options Run_output + Run_formats Run_windows diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index 7821214c83..3f72e5d715 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -44,11 +44,6 @@ section below for examples where this has been done. system the crossover (in single precision) is often about 50K-100K atoms per GPU. When performing double precision calculations the crossover point can be significantly smaller. -* Both KOKKOS and GPU package compute bonded interactions (bonds, angles, - etc) on the CPU. If the GPU package is running with several MPI processes - assigned to one GPU, the cost of computing the bonded interactions is - spread across more CPUs and hence the GPU package can run faster in these - cases. * When using LAMMPS with multiple MPI ranks assigned to the same GPU, its performance depends to some extent on the available bandwidth between the CPUs and the GPU. This can differ significantly based on the @@ -85,10 +80,10 @@ section below for examples where this has been done. code (with a performance penalty due to having data transfers between host and GPU). * The GPU package requires neighbor lists to be built on the CPU when using - exclusion lists, or a triclinic simulation box. -* The GPU package can be compiled for CUDA or OpenCL and thus supports - both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically - resulting in equal or better performance over OpenCL. + hybrid pair styles, exclusion lists, or a triclinic simulation box. +* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus supports + NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is + typically resulting in equal or better performance over OpenCL. * OpenCL in the GPU package does theoretically also support Intel CPUs or Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL) is superior. diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index d13a6d384f..e502480ce5 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -930,7 +930,7 @@ dependencies and redirects the download to the local cache. mkdir build cd build - cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake + cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake -D DOWNLOAD_POTENTIALS=off ../cmake make -j 8 deactivate_caches @@ -1276,11 +1276,13 @@ Those scripts were written by Steve Plimpton sjplimp at gmail.com valgrind tool ------------- -The ``valgrind`` folder contains additional suppressions fur LAMMPS when using -valgrind's memcheck tool to search for memory access violation and memory -leaks. These suppressions are automatically invoked when running tests through -CMake "ctest -T memcheck". See the provided README file to add these -suppressions when running LAMMPS. +The ``valgrind`` folder contains additional suppressions fur LAMMPS when +using `valgrind's `_ ` `memcheck tool +`_ to search for memory +access violation and memory leaks. These suppressions are automatically +invoked when running tests through CMake "ctest -T memcheck". See the +instruction in the ``README`` file to add these suppressions when using +valgrind with LAMMPS or other programs. ---------- diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 88d63c901d..27962c81a1 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -10,7 +10,7 @@ Syntax bond_style bpm/spring keyword value attribute1 attribute2 ... -* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* or *volume/factor* +* optional keyword = *overlay/pair* or *store/local* or *smooth* or *normalize* or *break* or *volume/factor* .. parsed-literal:: @@ -141,7 +141,8 @@ calculated using bond lengths squared and the cube root in the above equation is accordingly replaced with a square root. This approximation assumes bonds are evenly distributed on a spherical surface and neglects constant prefactors which are irrelevant since only the ratio of volumes matters. This term may be -used to adjust the Poisson's ratio. +used to adjust the Poisson's ratio. See the simulation in the +``examples/bpm/poissons_ratio`` directory for a demonstration of this effect. If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting (or adding) that bond's contribution. @@ -152,7 +153,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) Additionally, if *volume/factor* is set to *yes*, a fourth coefficient @@ -214,11 +215,11 @@ for an overview of LAMMPS output options. The vector or array will be floating point values that correspond to the specified attribute. -The single() function of this bond style returns 0.0 for the energy -of a bonded interaction, since energy is not conserved in these -dissipative potentials. The single() function also calculates an -extra bond quantity, the initial distance :math:`r_0`. This -extra quantity can be accessed by the +The potential energy and the single() function of this bond style return +:math:`k (r - r_0)^2 / 2` as a proxy of the energy of a bonded interaction, +ignoring any volumetric/smoothing factors or dissipative forces. The single() +function also calculates an extra bond quantity, the initial distance +:math:`r_0`. This extra quantity can be accessed by the :doc:`compute bond/local ` command as *b1*\ . Restrictions diff --git a/doc/src/bond_bpm_spring_plastic.rst b/doc/src/bond_bpm_spring_plastic.rst new file mode 100644 index 0000000000..e19e520d0e --- /dev/null +++ b/doc/src/bond_bpm_spring_plastic.rst @@ -0,0 +1,184 @@ +.. index:: bond_style bpm/spring/plastic + +bond_style bpm/spring/plastic command +===================================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + bond_style bpm/spring/plastic keyword value attribute1 attribute2 ... + +* optional keyword = *overlay/pair* or *store/local* or *smooth* or *normalize* or *break* + + .. parsed-literal:: + + *store/local* values = fix_ID N attributes ... + * fix_ID = ID of associated internal fix to store data + * N = prepare data for output every this many timesteps + * attributes = zero or more of the below attributes may be appended + + *id1, id2* = IDs of two atoms in the bond + *time* = the timestep the bond broke + *x, y, z* = the center of mass position of the two atoms when the bond broke (distance units) + *x/ref, y/ref, z/ref* = the initial center of mass position of the two atoms (distance units) + + *overlay/pair* value = *yes* or *no* + bonded particles will still interact with pair forces + + *smooth* value = *yes* or *no* + smooths bond forces near the breaking point + + *normalize* value = *yes* or *no* + normalizes bond forces by the reference length + + *break* value = *yes* or *no* + indicates whether bonds break during a run + +Examples +"""""""" + +.. code-block:: LAMMPS + + bond_style bpm/spring/plastic + bond_coeff 1 1.0 0.05 0.1 0.02 + + bond_style bpm/spring/plastic myfix 1000 time id1 id2 + dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3] + dump_modify 1 write_header no + +Description +""""""""""" + +.. versionadded:: 2Apr2025 + +The *bpm/spring/plastic* bond style computes forces based on +deviations from the initial reference state of the two atoms and the +strain history. The reference length of the bond :math:`r_0` is stored +by each bond when it is first computed in the setup of a run. Initially, +the equilibrium length of each bond :math:`r_\mathrm{eq}` is set equal +to :math:`r_0` but can evolve. data is then preserved across run commands +and is written to :doc:`binary restart files ` such that restarting +the system will not modify either of these quantities. + +This bond style only applies central-body forces which conserve the +translational and rotational degrees of freedom of a bonded set of +particles. The force has a magnitude of + +.. math:: + + F = -k (r_\mathrm{eq} - r) w + +where :math:`k` is a stiffness, :math:`r` is the current distance between +the two particles, and :math:`w` is an optional smoothing factor discussed +below. If the bond stretches beyond a strain of :math:`\epsilon_p` in compression +or extension, it will plastically activate and :math:`r_\mathrm{eq}` will evolve +to ensure :math:`|(r-r_\mathrm{eq})/r_\mathrm{eq}|` never exceeds :math:`\epsilon_p`. +Therefore, if a bond is continually loaded in either tension or compression, the +force will initially grow elastically before plateauing. See +:ref:`(Clemmer) ` for more details on these mechanics. + +Bonds will break at a strain of :math:`\epsilon_c`. This is done by setting +the bond type to 0 such that forces are no longer computed. + +An additional damping force is applied to the bonded +particles. This forces is proportional to the difference in the +normal velocity of particles: + +.. math:: + + F_D = - \gamma w (\hat{r} \bullet \vec{v}) + +where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the +radial normal vector, and :math:`\vec{v}` is the velocity difference +between the two particles. + +The smoothing factor :math:`w` is constructed such that forces smoothly +go to zero, avoiding discontinuities, as bonds approach the critical +breaking strain + +.. math:: + + w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 . + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data +` or :doc:`read_restart ` commands: + +* :math:`k` (force/distance units) +* :math:`\epsilon_c` (unitless) +* :math:`\gamma` (force/velocity units) +* :math:`\epsilon_p` (unitless) + +See the :doc:`bpm/spring doc page ` for information on +the *smooth*, *normalize*, *break*, *overlay/pair*, and *store/local* +keywords. + +Note that when unbroken bonds are dumped to a file via the +:doc:`dump local ` command, bonds with type 0 (broken bonds) +are not included. +The :doc:`delete_bonds ` command can also be used to +query the status of broken bonds or permanently delete them, e.g.: + +.. code-block:: LAMMPS + + delete_bonds all stats + delete_bonds all bond 0 remove + +---------- + +Restart and other info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This bond style writes the reference state and plastic history of each +bond to :doc:`binary restart files `. Loading a restart file +will properly restore bonds. However, the reference state is NOT written +to data files. Therefore reading a data file will not restore bonds and +will cause their reference states to be redefined. + +The potential energy and the single() function of this bond style +returns zero. The single() function also calculates two extra bond +quantities, the initial distance :math:`r_0` and the current equilibrium +length :math:`r_eq`. These extra quantities can be accessed by the +:doc:`compute bond/local ` command as *b1* and *b2*, +respectively. + +Restrictions +"""""""""""" + +This bond style is part of the BPM package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +By default if pair interactions between bonded atoms are to be disabled, +this bond style requires setting + +.. code-block:: LAMMPS + + special_bonds lj 0 1 1 coul 1 1 1 + +and :doc:`newton ` must be set to bond off. If the *overlay/pair* +keyword is set to *yes*, this bond style alternatively requires setting + +.. code-block:: LAMMPS + + special_bonds lj/coul 1 1 1 + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`bond bpm/spring ` + +Default +""""""" + +The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes* + +---------- + +.. _plastic-Clemmer: + +**(Clemmer)** Clemmer and Lechman, Powder Technology (2025). + diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index a76cc54746..70e652bb4a 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -60,6 +60,8 @@ Related commands """""""""""""""" :doc:`bond_coeff `, :doc:`delete_bonds ` +:doc:`bond style harmonic/shift `, +:doc:`bond style harmonic/shift/cut ` Default """"""" diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index 43e10bde00..e57d464af8 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -31,9 +31,15 @@ the potential E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] -where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance. -The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is -:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. +where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the +critical distance. The potential energy has the value +:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`. This +bond style differs from :doc:`bond_style harmonic ` +by the value of the potential energy. + +The equivalent spring constant value *K* for use with :doc:`bond_style +harmonic ` can be computed using :math:`K = +U_{\text{min}} / [(r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the :doc:`bond_coeff ` command as in the example above, or in @@ -41,9 +47,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) - * :math:`r_0` (distance) - * :math:`r_c` (distance) ---------- @@ -63,7 +67,8 @@ Related commands """""""""""""""" :doc:`bond_coeff `, :doc:`delete_bonds `, -:doc:`bond_harmonic ` +:doc:`bond style harmonic `, +:doc:`bond style harmonic/shift/cut ` Default """"""" diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index d8d4a792b7..964ae4b9ba 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -31,9 +31,14 @@ uses the potential E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] -where :math:`r_0` is the equilibrium bond distance, and rc the critical distance. -The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}` -at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. +where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the +critical distance. The bond potential is zero and thus its force also +zero for distances :math:`r > r_c`. The potential energy has the value +:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`. + +The equivalent spring constant value *K* for use with :doc:`bond_style +harmonic ` for :math:`r <= r_c`, can be computed using +:math:`K = U_{\text{min}} / [(r_0-r_c)^2]` The following coefficients must be defined for each bond type via the :doc:`bond_coeff ` command as in the example above, or in diff --git a/doc/src/bond_rheo_shell.rst b/doc/src/bond_rheo_shell.rst index 090f5ab7aa..ef8d7d4249 100644 --- a/doc/src/bond_rheo_shell.rst +++ b/doc/src/bond_rheo_shell.rst @@ -94,7 +94,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) Unlike other BPM-style bonds, this bond style does not update special diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index 590f7c8cba..a30fb9e812 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -10,7 +10,7 @@ Syntax bond_style style args -* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table* +* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *bpm/spring/plastic* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table* * args = none for any style except *hybrid* @@ -86,6 +86,7 @@ accelerated styles exist. * :doc:`bpm/rotational ` - breakable bond with forces and torques based on deviation from reference state * :doc:`bpm/spring ` - breakable bond with forces based on deviation from reference length +* :doc:`bpm/spring/plastic ` - a similar breakable bond with plastic yield * :doc:`class2 ` - COMPASS (class 2) bond * :doc:`fene ` - FENE (finite-extensible non-linear elastic) bond * :doc:`fene/expand ` - FENE bonds with variable size particles diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index 9bca1e26d1..24c2e2e47c 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -217,13 +217,16 @@ scaled differently in the two different dimensions to transform them into ellipses). The created bins (and hence the chunk IDs) are numbered consecutively -from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*, the -numbering varies most rapidly in the first dimension (which could be -*x*, *y*, or *z*), next rapidly in the second dimension, and most slowly in the -third dimension. For *bin/sphere*, the bin with smallest radii is chunk -1 and the bin with largest radii is chunk Nchunk = *ncbin*\ . For -*bin/cylinder*, the numbering varies most rapidly in the dimension -along the cylinder axis and most slowly in the radial direction. +from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*, the +numbering varies fastest in the last dimension (which could be +*x*, *y*, or *z*), slower in the second dimension, and slowest in the +first dimension. For *bin/sphere*, the bin with smallest radius is chunk +1 and the bin with largest radius is chunk Nchunk = *ncbin*\ . For +*bin/cylinder*, the numbering varies faster in the dimension +along the cylinder axis and slower in the radial direction. +In all cases, for a given dimension, the numbering increases +with increasing value of the coordinate (Cartesian coordinate, +sphere or cylinder radius, axial position). Each time this compute is invoked, each atom is mapped to a bin based on its current position. Note that between reneighboring timesteps, diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index 925159951c..33329d88d6 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -67,7 +67,7 @@ following relation should also be satisfied: .. math:: - r_c + r_s > 2*{\rm cutoff} + r_c + r_s > 2*\mathrm{cutoff} where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is the skin diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst index 41fdb8324e..94dec390f4 100644 --- a/doc/src/compute_cnp_atom.rst +++ b/doc/src/compute_cnp_atom.rst @@ -74,7 +74,7 @@ following relation should also be satisfied: .. math:: - r_c + r_s > 2*{\rm cutoff} + r_c + r_s > 2*\mathrm{cutoff} where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is the skin diff --git a/doc/src/compute_efield_wolf_atom.rst b/doc/src/compute_efield_wolf_atom.rst index 93bfa55151..572ca59ab4 100644 --- a/doc/src/compute_efield_wolf_atom.rst +++ b/doc/src/compute_efield_wolf_atom.rst @@ -50,9 +50,9 @@ the potential energy using the Wolf summation method, described in .. math:: E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} + \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()* are error-function and complementary error-function terms. This diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 1fb8113a89..ea937f2e00 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -40,7 +40,7 @@ is a complex number (stored as two real numbers) defined as follows: .. math:: - q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\bf r}_{ij})} + q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\textbf{r}}_{ij})} where the sum is over the *nnn* nearest neighbors of the central atom. The angle :math:`\theta` diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index 01535aa880..08153fe496 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -49,7 +49,7 @@ For each atom, :math:`Q_\ell` is a real number defined as follows: .. math:: - \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) \bigr) \\ + \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( \mathbf{r}_{ij} ), \phi( \mathbf{r}_{ij} ) \bigr) \\ Q_\ell = & \sqrt{\frac{4 \pi}{2 \ell + 1} \sum_{m = -\ell }^{m = \ell } \bar{Y}_{\ell m} \bar{Y}^*_{\ell m}} The first equation defines the local order parameters as averages diff --git a/doc/src/compute_slcsa_atom.rst b/doc/src/compute_slcsa_atom.rst index 7338b92d59..f7852cd4c7 100644 --- a/doc/src/compute_slcsa_atom.rst +++ b/doc/src/compute_slcsa_atom.rst @@ -19,7 +19,7 @@ Syntax * lr_decision_file = file name of file containing the scaling matrix for logistic regression classification * lr_bias_file = file name of file containing the bias vector for logistic regression classification * maha_file = file name of file containing for each crystal structure: the Mahalanobis distance threshold for sanity check purposes, the average reduced descriptor and the inverse of the corresponding covariance matrix -* c_ID[*] = compute ID of previously required *compute sna/atom* command +* c_ID[1] = compute ID and output data column of previously defined *compute sna/atom* command Examples """""""" @@ -27,7 +27,7 @@ Examples .. code-block:: LAMMPS compute b1 all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.3 - compute b2 all slcsa/atom 8 4 mean_descriptors.dat lda_scalings.dat lr_decision.dat lr_bias.dat maha_thresholds.dat c_b1[*] + compute b2 all slcsa/atom 8 4 mean_descriptors.dat lda_scalings.dat lr_decision.dat lr_bias.dat maha_thresholds.dat c_b1[1] Description """"""""""" diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 2572093499..2f8c4c4f5d 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -139,11 +139,11 @@ mapped on to a third polar angle :math:`\theta_0` defined by, .. math:: - \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi + \theta_0 = \mathsf{rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi In this way, all possible neighbor positions are mapped on to a subset -of the 3-sphere. Points south of the latitude :math:`\theta_0` = -*rfac0* :math:`\pi` are excluded. +of the 3-sphere. Points south of the latitude +:math:`\theta_0 = \mathsf{rfac0} \pi` are excluded. The natural basis for functions on the 3-sphere is formed by the representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, @@ -204,7 +204,7 @@ components summed separately for each LAMMPS atom type: .. math:: - -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i} + -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial \mathbf{r}_i} The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*, this compute evaluates the above expression for each direction, each @@ -216,7 +216,7 @@ derivatives: .. math:: - -{\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i} + -\mathbf{r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial \mathbf{r}_i} Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom *i*, this compute evaluates the above expression for each of the six diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index e047423640..6c4e0b690c 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -65,7 +65,7 @@ In case of compute *stress/atom*, the virial contribution is: W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) \\ & + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\ - & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} + & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} The first term is a pairwise energy contribution where :math:`n` loops over the :math:`N_p` neighbors of atom :math:`I`, :math:`\mathbf{r}_1` @@ -97,7 +97,7 @@ In case of compute *centroid/stress/atom*, the virial contribution is: .. math:: W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\ - & + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} + & + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} As with compute *stress/atom*, the first, second, third, fourth and fifth terms are pairwise, bond, angle, dihedral and improper diff --git a/doc/src/compute_vacf_chunk.rst b/doc/src/compute_vacf_chunk.rst index f9d22e22a1..6ae676edaf 100644 --- a/doc/src/compute_vacf_chunk.rst +++ b/doc/src/compute_vacf_chunk.rst @@ -24,7 +24,7 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 2Apr2025 Define a computation that calculates the velocity auto-correlation function (VACF) for multiple chunks of atoms. diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index 176d3815dc..3656ad814a 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -1,10 +1,11 @@ .. index:: dihedral_style multi/harmonic +.. index:: dihedral_style multi/harmonic/kk .. index:: dihedral_style multi/harmonic/omp dihedral_style multi/harmonic command ===================================== -Accelerator Variants: *multi/harmonic/omp* +Accelerator Variants: *multi/harmonic/kk*, *multi/harmonic/omp* Syntax """""" diff --git a/doc/src/dump.rst b/doc/src/dump.rst index a8175fa612..62f9909073 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -3,6 +3,7 @@ .. index:: dump cfg .. index:: dump custom .. index:: dump dcd +.. index:: dump extxyz .. index:: dump grid .. index:: dump grid/vtk .. index:: dump local @@ -59,7 +60,7 @@ Syntax * ID = user-assigned name for the dump * group-ID = ID of the group of atoms to be dumped -* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml* +* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *extxyz* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml* * N = dump on timesteps which are multiples of N * file = name of file to write dump info to * attribute1,attribute2,... = list of attributes for a particular style @@ -77,6 +78,7 @@ Syntax *custom*, *custom/gz*, *custom/zstd* attributes = see below *custom/adios* attributes = same as *custom* attributes, discussed on :doc:`dump custom/adios ` page *dcd* attributes = none + *extxyz* attributes = none *h5md* attributes = discussed on :doc:`dump h5md ` page *grid* attributes = see below *grid/vtk* attributes = see below @@ -242,28 +244,29 @@ all the processors or multiple smaller files. frames consistently to the same atom. This can lead to incorrect visualizations or results. LAMMPS will print a warning in such cases. -For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting -is off by default. For the *dcd*, *grid/vtk*, *xtc*, *xyz*, and +For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting is +off by default. For the *dcd*, *extxyz*, *grid/vtk*, *xtc*, *xyz*, and *molfile* styles, sorting by atom ID or grid ID is on by default. See the :doc:`dump_modify ` page for details. The *style* keyword determines what kind of data is written to the dump file(s) and in what format. -Note that *atom*, *custom*, *dcd*, *xtc*, *xyz*, and *yaml* style dump -files can be read directly by `VMD `_, -a popular tool for visualizing and analyzing trajectories from atomic -and molecular systems. For reading *netcdf* style dump files, the -netcdf plugin needs to be recompiled from source using a NetCDF version -compatible with the one used by LAMMPS. The bundled plugin binary -uses a very old version of NetCDF that is not compatible with LAMMPS. +Note that *atom*, *custom*, *dcd*, *extxyz*, *xtc*, *xyz*, and *yaml* +style dump files can be read directly by `VMD +`_, a popular tool for visualizing +and analyzing trajectories from atomic and molecular systems. For +reading *netcdf* style dump files, the netcdf plugin needs to be +recompiled from source using a NetCDF version compatible with the one +used by LAMMPS. The bundled plugin binary uses a very old version of +NetCDF that is not compatible with LAMMPS. Likewise the `OVITO visualization package `_, -popular for materials modeling, can read the *atom*, *custom*, +popular for materials modeling, can read the *atom*, *custom*, *extxyz*, *local*, *xtc*, *cfg*, *netcdf*, and *xyz* style atom dump files -directly. With version 3.8 and above, OVITO can also read and -visualize *grid* style dump files with grid cell data, including -iso-surface images of the grid cell values. +directly. With version 3.8 and above, OVITO can also read and visualize +*grid* style dump files with grid cell data, including iso-surface +images of the grid cell values. Note that settings made via the :doc:`dump_modify ` command can also alter the format of individual values and content of @@ -475,6 +478,24 @@ label). This option will help many visualization programs to guess bonds and colors. You can use the :doc:`dump_modify types labels ` option to replace numeric atom types with :doc:`type labels `. +.. versionadded:: 2Apr2025 + +The *extxyz* style writes XYZ files compatible with the Extended XYZ (or +ExtXYZ) format as defined as defined in `the libAtoms specification +`_. Specifically, the following +information will be dumped: + +* timestep +* time, which can be disabled with :doc:`dump_modify time no ` +* simulation box lattice and pbc conditions +* atomic forces, which can be disabled with :doc:`dump_modify forces no ` +* atomic velocities, which can be disabled with :doc:`dump_modify vel no ` +* atomic masses, if enabled with :doc:`dump_modify mass yes ` + +Dump style *extxyz* requires either that a :doc:`type label map for atoms types +` is defined or :doc:`dump_modify element ` is used to +set up an atom type number to atom name mapping. + .. versionadded:: 22Dec2022 The *grid/vtk* style writes VTK files for grid data on a regular @@ -607,8 +628,8 @@ with the processor ID from :math:`0` to :math:`P-1`. For example, tmp.dump.% becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.:math:`P-1`, etc. This creates smaller files and can be a fast mode of output on parallel machines that support parallel I/O for output. This option is -**not** available for the *dcd*, *xtc*, *xyz*, *grid/vtk*, and *yaml* -styles. +**not** available for the *dcd*, *extxyz*, *xtc*, *xyz*, *grid/vtk*, and +*yaml* styles. By default, :math:`P` is the the number of processors, meaning one file per processor, but :math:`P` can be set to a smaller value via the *nfile* or @@ -1017,9 +1038,9 @@ the COMPRESS package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -The *xtc*, *dcd*, and *yaml* styles are part of the EXTRA-DUMP package. -They are only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` page for more info. +The *dcd*, *extxyz*, *xtc*, and *yaml* styles are part of the EXTRA-DUMP +package. They are only enabled if LAMMPS was built with that package. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 1f2b1c8e0e..4786ea3c8f 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -92,6 +92,15 @@ Syntax see the :doc:`dump image ` doc page for details +* these keywords apply only to the extxyz dump style +* keyword = *forces* or *mass* or *vel* + + .. parsed-literal:: + + *forces* arg = *yes* or *no* + *mass* arg = *yes* or *no* + *vel* arg = *yes* or *no* + * these keywords apply only to the */gz* and */zstd* dump styles * keyword = *compression_level* @@ -972,9 +981,11 @@ The option defaults are * fileper = # of processors * first = no * flush = yes +* forces = yes * format = %d and %g for each integer or floating point value * image = no * label = ENTRIES +* mass = no * maxfiles = -1 * nfile = 1 * pad = 0 @@ -990,6 +1001,7 @@ The option defaults are * types = numeric * units = no * unwrap = no +* vel = yes * compression_level = 9 (gz variants) * compression_level = 0 (zstd variants) diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst index de52e0545b..e1f2c47c60 100644 --- a/doc/src/fitpod_command.rst +++ b/doc/src/fitpod_command.rst @@ -263,10 +263,10 @@ then the globally defined weights from the ``fitting_weight_energy`` and POD Potential """"""""""""" -We consider a multi-element system of *N* atoms with :math:`N_{\rm e}` +We consider a multi-element system of *N* atoms with :math:`N_\mathrm{e}` unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n` position vector and type of an atom *n* in the system, -respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e} +respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_\mathrm{e} \}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots, \boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1, Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 643ba61f06..6934d6c9fe 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -344,6 +344,8 @@ accelerated styles exist. * :doc:`phonon ` - calculate dynamical matrix from MD simulations * :doc:`pimd/langevin ` - Feynman path-integral molecular dynamics with stochastic thermostat * :doc:`pimd/nvt ` - Feynman path-integral molecular dynamics with Nose-Hoover thermostat +* :doc:`pimd/langevin/bosonic ` - Bosonic Feynman path-integral molecular dynamics for with stochastic thermostat +* :doc:`pimd/nvt/bosonic ` - Bosonic Feynman path-integral molecular dynamics with Nose-Hoover thermostat * :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 @@ -366,6 +368,7 @@ accelerated styles exist. * :doc:`qeq/fire ` - charge equilibration via FIRE minimizer * :doc:`qeq/point ` - charge equilibration via point method * :doc:`qeq/reaxff ` - charge equilibration for ReaxFF potential +* :doc:`qeq/rel/reaxff ` - charge equilibration for ReaxFF potential with alternate efield implementation * :doc:`qeq/shielded ` - charge equilibration via shielded method * :doc:`qeq/slater ` - charge equilibration via Slater method * :doc:`qmmm ` - functionality to enable a quantum mechanics/molecular mechanics coupling diff --git a/doc/src/fix_acks2_reaxff.rst b/doc/src/fix_acks2_reaxff.rst index 79a9cf8ea6..c198ae8a08 100644 --- a/doc/src/fix_acks2_reaxff.rst +++ b/doc/src/fix_acks2_reaxff.rst @@ -123,8 +123,10 @@ components in non-periodic directions. Related commands """""""""""""""" -:doc:`pair_style reaxff `, :doc:`fix qeq/reaxff `, -:doc:`fix qtpi/reaxff ` +:doc:`pair_style reaxff `, +:doc:`fix qeq/reaxff `, +:doc:`fix qtpie/reaxff `, +:doc:`fix qeq/rel/reaxff ` Default """"""" diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 93bd8da041..2eec2eb457 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -14,7 +14,7 @@ Syntax * adapt = style name of this fix command * N = adapt simulation settings every this many timesteps * one or more attribute/arg pairs may be appended -* attribute = *pair* or *bond* or *angle* or *kspace* or *atom* +* attribute = *pair* or *bond* or *angle* or *improper* or *kspace* or *atom* .. parsed-literal:: @@ -33,6 +33,11 @@ Syntax aparam = parameter to adapt over time I = type angle to set parameter for (integer or type label) v_name = variable with name that calculates value of aparam + *improper* args = istyle iparam I v_name + istyle = improper style name (e.g., cvff) + iparam = parameter to adapt over time + I = type improper to set parameter for (integer or type label) + v_name = variable with name that calculates value of iparam *kspace* arg = v_name v_name = variable with name that calculates scale factor on :math:`k`-space terms *atom* args = atomparam v_name @@ -178,10 +183,14 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lennard/mdf ` | A,B | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj96/cut ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/class2 ` | epsilon,sigma | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma,coulombic_cutoff | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/cubic ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/cut ` | epsilon,sigma | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma,coulombic_cutoff | type pairs | @@ -196,6 +205,8 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/lj/gromacs ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/mdf ` | epsilon,sigma | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/sf/dipole/sf ` | epsilon,sigma,scale | type pairs | @@ -216,6 +227,8 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`pace, pace/extrapolation ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`pedone ` | c0,d0,r0,alpha | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`quip ` | scale | type global | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`snap ` | scale | type pairs | @@ -236,6 +249,8 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`wf/cut ` | epsilon,sigma,nu,mu | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`yukawa ` | alpha | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ .. note:: @@ -418,6 +433,56 @@ this fix uses to reset theta0 needs to generate values in radians. ---------- +.. versionadded:: 2Apr2025 + +The *improper* keyword uses the specified variable to change the value of +an improper coefficient over time, very similar to how the *angle* keyword +operates. The only difference is that now an improper coefficient for a +given improper type is adapted. + +A wild-card asterisk can be used in place of or in conjunction with the +improper type argument to set the coefficients for multiple improper types. +This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is +the number of improper types, then an asterisk with no numeric values means +all types from 1 to :math:`N`. A leading asterisk means all types from +1 to n (inclusive). A trailing asterisk means all types from m to +:math:`N` (inclusive). A middle asterisk means all types from m to n +(inclusive). + +If :doc:`improper_style hybrid ` is used, *istyle* should be a +sub-style name. The improper styles that currently work with fix adapt are: + ++---------------------------------------------------------+----------------+----------------+ +| :doc:`amoeba ` | k | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`class2 ` | k,chi0 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`cossq ` | k,chi0 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`cvff ` | k,d,n | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`distance ` | k2,k4 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`distharm ` | k,d0 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`fourier ` | k,C0,C1,C2 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`harmonic ` | k,chi0 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`inversion/harmonic ` | k,w0 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`ring ` | k,theta0 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`umbrella ` | k,w0 | type impropers | ++---------------------------------------------------------+----------------+----------------+ +| :doc:`sqdistharm ` | k | type impropers | ++---------------------------------------------------------+----------------+----------------+ + +Note that internally, chi0 and theta0 are stored in radians, so the variable +this fix use to reset chi0 or theta0 needs to generate values in radians. + +---------- + The *kspace* keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever :math:`k`-space solver is defined by the :doc:`kspace_style ` command. If the diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index 76c7ec4cfc..704019d46a 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -459,8 +459,8 @@ output. This option can only be used with the *ave running* setting. The *format* keyword sets the numeric format of each value when it is printed to a file via the *file* keyword. Note that all values are -floating point quantities. The default format is %g. You can specify -a higher precision if desired (e.g., %20.16g). +floating point quantities. The default format is " %g". You can specify +a higher precision if desired (e.g., " %20.16g"). The *title1* and *title2* and *title3* keywords allow specification of the strings that will be printed as the first three lines of the output diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 659e15105c..91f5c701aa 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -32,13 +32,14 @@ Syntax .. parsed-literal:: - *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* + *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* or *first* auto = correlate each value with itself upper = correlate each value with each succeeding value lower = correlate each value with each preceding value auto/upper = auto + upper auto/lower = auto + lower full = correlate each value with every other value, including itself = auto + upper + lower + first = correlate each value with the first value *ave* args = *one* or *running* one = zero the correlation accumulation every Nfreq steps running = accumulate correlations continuously @@ -257,6 +258,9 @@ time. * If *type* is set to *full* then each input value is correlated with itself and every other value (i.e., :math:`C_{ij} = V_i V_j` for :math:`\{i,j\} = \{1,N\}`, so :math:`N_\text{pair} = N^2`). +* If *type* is set to *first* then each input value is correlated with + the first input value (i.e., :math:`C_{ij} = V_1 V_j` for + :math:`\{j\} = \{1,N\}`, so :math:`N_\text{pair} = N`). The *ave* keyword determines what happens to the accumulation of correlation samples every :math:`N_\text{freq}` timesteps. If the *ave* setting is *one*, @@ -369,6 +373,8 @@ above. * For *type* = *full*, the :math:`N_\text{pair} = N^2` columns are ordered: :math:`C_{11}, C_{12}, \dotsc, C_{1N}, C_{21}, C_{22}, \dotsc, C_{2N}, C_{31}, \dotsc, C_{3N}, \dotsc, C_{N1}, \dotsc, C_{N,N-1}, C_{NN}` +* For *type* = *first*, the :math:`N_\text{pair} = N` columns are ordered: + :math:`C_{11}, C_{12}, \dotsc, C_{1N}` The array values calculated by this fix are treated as extensive. If you need to divide them by the number of atoms, you must do this in a diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index 003bdf897d..22fac89706 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -31,13 +31,14 @@ Syntax .. parsed-literal:: - *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* + *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* or *first* auto = correlate each value with itself upper = correlate each value with each succeeding value lower = correlate each value with each preceding value auto/upper = auto + upper auto/lower = auto + lower full = correlate each value with every other value, including itself = auto + upper + lower + first = correlate each value with the first value *start* args = Nstart Nstart = start accumulating correlations on this time step *file* arg = filename diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 00771a1422..661ea2d466 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -304,8 +304,8 @@ output. This option can only be used with the *ave running* setting. The *format* keyword sets the numeric format of each value when it is printed to a file via the *file* keyword. Note that all values are -floating point quantities. The default format is %g. You can specify -a higher precision if desired (e.g., %20.16g). +floating point quantities. The default format is " %g". You can specify +a higher precision if desired (e.g., " %20.16g"). The *title1* and *title2* and *title3* keywords allow specification of the strings that will be printed as the first 2 or 3 lines of the diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 08c2f5fb9d..542407d7ff 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -28,9 +28,10 @@ Syntax *no* = no reaction site stabilization (default) group_prefix = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction xmax = value that is used by an internally-created :doc:`nve/limit ` integrator - *reset_mol_ids* values = *yes* or *no* + *reset_mol_ids* values = *yes* or *no* or *molmap* *yes* = update molecule IDs based on new global topology (default) *no* = do not update molecule IDs + *molmap* = customize how molecule IDs are updated * react = mandatory argument indicating new reaction specification * react-ID = user-assigned name for the reaction @@ -188,12 +189,30 @@ due to the internal dynamic grouping performed by fix bond/react. If the group-ID is an existing static group, react-group-IDs should also be specified as this static group or a subset. -The *reset_mol_ids* keyword invokes the :doc:`reset_atoms mol -` command after a reaction occurs, to ensure that -molecule IDs are consistent with the new bond topology. The group-ID -used for :doc:`reset_atoms mol ` is the group-ID for this -fix. Resetting molecule IDs is necessarily a global operation, so it -can be slow for very large systems. +.. versionadded:: 2Apr2025 + + New *molmap* option + +If the *reset_mol_ids* keyword is set to *yes* (default), the +:doc:`reset_atoms mol ` command is invoked after a reaction +occurs, to ensure that molecule IDs are consistent with the new bond +topology. The group-ID used for :doc:`reset_atoms mol ` is +the group-ID for this fix. Resetting molecule IDs is necessarily a +global operation, so it can be slow for very large systems. If the +*reset_mol_ids* keyword is set to *no*, molecule IDs are not updated. +If the *reset_mol_ids* keyword is set to *molmap*, molecule IDs are +updated consistently with the molecule IDs listed in the *Molecules* +section of the pre- and post-reaction templates. If a post-reaction +atom has the same molecule ID as one or more pre-reaction atoms in the +templates, then the post-reaction simulation atom will be assigned the +same simulation molecule ID that those corresponding pre-reaction +simulation atoms had before the reaction. The *molmap* option is only +guaranteed to work correctly if all the pre-reaction atoms that have +equivalent template molecule IDs also have equivalent molecule IDs in +the simulation. No check is performed to test for this consistency. +For post-reaction atoms that have a template molecule ID that does not +exist in pre-reaction template, they are assigned a new molecule ID that +does not currently exist in the simulation. The following comments pertain to each *react* argument (in other words, they can be customized for each reaction, or reaction step): @@ -420,9 +439,10 @@ within a distance :math:`R` of any created atom, including the effect of periodic boundary conditions if applicable. :math:`R` is defined by the *overlap* sub-keyword. Note that the default value for :math:`R` is 0.0, which will allow atoms to strongly overlap if you are inserting where other -atoms are present. The velocity of each created atom is initialized in -a random direction with a magnitude calculated from the instantaneous -temperature of the reaction site. +atoms are present. The molecule ID of a created atom is zero, unless the +*reset_mol_ids molmap* option is used. The velocity of each created atom is +initialized in a random direction with a magnitude calculated from the +instantaneous temperature of the reaction site. .. note:: diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 104fa79c20..df95b736df 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -49,7 +49,7 @@ computed according to the following relation: where *m* is the number of species, :math:`c_{i,j}` is the concentration of species *j* in particle *i*, :math:`u_j` is the -internal energy of species j, :math:`\Delta H_{f,j} is the heat of +internal energy of species j, :math:`\Delta H_{f,j}` is the heat of formation of species *j*, N is the number of molecules represented by the coarse-grained particle, :math:`k_B` is the Boltzmann constant, and :math:`T` is the temperature of the system. Additionally, it is diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index ba26f7a51b..8c24275cb4 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -60,9 +60,9 @@ With this fix active, the force on the *j*\ th atom is given as .. math:: - {\bf F}_{j}(t) = & {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\ + \mathbf{F}_{j}(t) = & \mathbf{F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) \mathbf{v}_j(s)~\text{d}s + \mathbf{F}^R_j(t) \\ \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ - \langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s) + \langle\mathbf{F}^R_j(t),\mathbf{F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s) Here, the first term is representative of all conservative (pairwise, bonded, etc) forces external to this fix, the second is the temporally diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 0bcf2fb5ea..aa6490a879 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -25,13 +25,14 @@ Syntax * operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^" * avalue = numeric value to compare attribute to * zero or more keyword/value pairs may be appended -* keyword = *error* or *message* or *path* +* keyword = *error* or *message* or *path* or *universe* .. parsed-literal:: *error* value = *hard* or *soft* or *continue* *message* value = *yes* or *no* *path* value = path to check for free space (may be in quotes) + *universe* value = *yes* or *no* Examples @@ -40,8 +41,10 @@ Examples .. code-block:: LAMMPS fix 10 all halt 1 bondmax > 1.5 - fix 10 all halt 10 v_myCheck != 0 error soft + fix 10 all halt 10 v_myCheck != 0 error soft message no fix 10 all halt 100 diskfree < 100000.0 path "dump storage/." + fix 2 all halt 100 v_curtime > ${maxtime} universe yes + Description """"""""""" @@ -141,33 +144,52 @@ The optional *error* keyword determines how the current run is halted. If its value is *hard*, then LAMMPS will stop with an error message. If its value is *soft*, LAMMPS will exit the current run, but continue -to execute subsequent commands in the input script. However, -additional :doc:`run ` or :doc:`minimize ` commands will be -skipped. For example, this allows a script to output the current -state of the system, e.g. via a :doc:`write_dump ` or -:doc:`write_restart ` command. +to execute subsequent commands in the input script. However, additional +:doc:`run ` or :doc:`minimize ` commands will be skipped. +For example, this allows a script to output the current state of the +system, e.g. via a :doc:`write_dump ` or :doc:`write_restart +` command. To re-enable regular runs after *fix halt* +stopped a run, you need to issue a :doc:`timer timeout unlimited +` command. If its value is *continue*, the behavior is the same as for *soft*, except subsequent :doc:`run ` or :doc:`minimize ` commands are executed. This allows your script to remedy the condition that -triggered the halt, if necessary. Note that you may wish use the -:doc:`unfix ` command on the fix halt ID, so that the same -condition is not immediately triggered in a subsequent run. +triggered the halt, if necessary. This is the equivalent of stopping +with *error soft* and followed by :doc:`timer timeout unlimited +` command. This can have undesired consequences, when a +:doc:`run command ` uses the *every* keyword, so using *error soft* +and resetting the timer manually may be the preferred option. + +You may wish use the :doc:`unfix ` command on the *fix halt* ID +before starting a subsequent run, so that the same condition is not +immediately triggered again. The optional *message* keyword determines whether a message is printed to the screen and logfile when the halt condition is triggered. If *message* is set to yes, a one line message with the values that -triggered the halt is printed. If *message* is set to no, no message -is printed; the run simply exits. The latter may be desirable for +triggered the halt is printed. If *message* is set to no, no message is +printed; the run simply exits. The latter may be desirable for post-processing tools that extract thermodynamic information from log files. +.. versionadded:: 2Apr2025 + +The optional *universe* keyword determines whether the halt request +should be synchronized across the partitions of a :doc:`multi-partition +run `. If *universe* is set to yes, fix halt will check if +there is a specific message received from any of the other partitions +requesting to stop the run on this partition as well. Consequently, if +fix halt determines to halt the simulation, the fix will send messages +to all other partitions so they stop their runs, too. + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various :doc:`output commands `. +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to this fix. 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. @@ -183,4 +205,4 @@ Related commands Default """"""" -The option defaults are error = soft, message = yes, and path = ".". +The option defaults are error = soft, message = yes, path = ".", and universe = no. diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index f58c4780b0..9eae426098 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -131,14 +131,15 @@ timesteps is simply t_{hyper} = \sum_{i=1,N} B-i \cdot dt where *dt* is the timestep size defined by the :doc:`timestep ` -command. The effective time acceleration due to GHD is thus t_hyper / -N\*dt, where N\*dt is elapsed time for a normal MD run of N timesteps. +command. The effective time acceleration due to GHD is thus +:math:`t_{hyper} / N * dt`, where N\*dt is elapsed time for a normal MD run +of N timesteps. -Note that in GHD, the boost factor varies from timestep to timestep. -Likewise, which bond has :math:`E^{max}` strain and thus which pair of -atoms the bias potential is added to, will also vary from timestep to timestep. -This is in contrast to local hyperdynamics (LHD) where the boost -factor is an input parameter; see the :doc:`fix hyper/local ` page for details. +Note that in GHD, the boost factor varies from timestep to timestep. Likewise, +which bond has :math:`E^{max}` strain and thus which pair of atoms the bias +potential is added to, will also vary from timestep to timestep. This is in +contrast to local hyperdynamics (LHD) where the boost factor is an input +parameter; see the :doc:`fix hyper/local ` page for details. ---------- @@ -178,7 +179,7 @@ time-accurate trajectory of the system. Note that if *Vmax* is set too small, the GHD simulation will run correctly. There will just be fewer events because the hyper time -(t_hyper equation above) will be shorter. +(:math:`t_{hyper}` equation above) will be shorter. .. note:: diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 499a12b9bc..46d73daa66 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -111,7 +111,7 @@ requirement, and thus a bias potential :math:`V^{max}_{ij}` will be applied to many bonds on the same timestep. In LHD, all bonds store a :math:`C_{ij}` prefactor which appears in -the :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}equations above. Note +the :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}` equations above. Note that the :math:`C_{ij}` factor scales the strength of the bias energy and forces whenever bond *ij* is the maximum strain bond in its neighborhood. @@ -269,7 +269,7 @@ inverse of the alpha parameter discussed in The *Btarget* argument is the desired time boost factor (a value > 1) that all the atoms in the system will experience. The elapsed time -t_hyper for an LHD simulation running for *N* timesteps is simply +:math:`t_{hyper}` for an LHD simulation running for *N* timesteps is simply .. math:: @@ -294,7 +294,7 @@ is the specified temperature of the system Note that if *Btarget* is set smaller than this, the LHD simulation will run correctly. There will just be fewer events because the hyper -time (t_hyper equation above) will be shorter. +time (:math:`t_{hyper}` equation above) will be shorter. .. note:: diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index a461175f71..e49831986b 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -130,7 +130,7 @@ calculated as: .. math:: - {\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha} + \mathbf{F}_{j \alpha} = \gamma \left(\mathbf{v}_n - \mathbf{u}_f \right) \zeta_{j\alpha} where :math:`\mathbf{v}_n` is the velocity of the MD particle, :math:`\mathbf{u}_f` is the fluid velocity interpolated to the particle diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index 265803c213..42e64226d1 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -12,7 +12,7 @@ Syntax * fix-ID = ID of the fix to modify * one or more keyword/value pairs may be appended -* keyword = *bodyforces* or *colname* or *dynamic/dof* or *energy* or *press* or *respa* or *temp* or *virial* +* keyword = *bodyforces* or *colname* or *dynamic/dof* or *energy* or *pad* or *press* or *respa* or *temp* or *virial* .. parsed-literal:: @@ -25,6 +25,7 @@ Syntax *dynamic/dof* value = *yes* or *no* yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature *energy* value = *yes* or *no* + *pad* arg = Nchar = # of characters to convert timestep to *press* value = compute ID that calculates a pressure *respa* value = *1* to *max respa level* or *0* (for outermost level) *temp* value = compute ID that calculates a temperature @@ -184,6 +185,18 @@ replaces the string for that specific keyword. The *colname* keyword can be used multiple times. If multiple *colname* settings refer to the same keyword, the last setting has precedence. +.. versionadded:: 2Apr2025 + +The *pad* keyword only applies when a fix produces a file and the output +filename is specified with a wildcard "\*" character which becomes the +timestep. If *pad* is 0, which is the default, the timestep is +converted into a string of unpadded length (e.g., 100 or 12000 or +2000000). When *pad* is specified with *Nchar* :math:`>` 0, the string +is padded with leading zeroes so they are all the same length = *Nchar*\ +. For example, pad 7 would yield 0000100, 0012000, 2000000. This can +be useful so that post-processing programs can easily read the files in +ascending timestep order. Please see the documentation of the individual +fix styles if this keyword is supported. Restrictions """""""""""" diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 3fde5f0861..a493678143 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -35,11 +35,12 @@ Syntax v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL * zero or more keyword/value pairs may be appended -* keyword = *units* +* keyword = *units* or *update* .. parsed-literal:: *units* value = *box* or *lattice* + *update* value = *dipole* Examples """""""" @@ -49,7 +50,7 @@ Examples fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0 fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL - fix 3 boundary move transrot 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 1.0 5.0 units box + fix 3 boundary move transrot 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 1.0 5.0 units box update dipole Description """"""""""" @@ -217,6 +218,15 @@ been previously used to define the lattice spacing. Each of these 3 quantities may be dependent on the x,y,z dimension, since the lattice spacings can be different in x,y,z. +.. versionadded:: 2Apr2025 + +If the *update dipole* keyword/value pair is used together with the +*rotate* or *transrot* style, then the orientation of the dipole moment +of each particle is also updated appropriately to correspond with the rotation. +This option should be used for models where a dipole moment is assigned to +finite-size particles, e.g. spheroids via use of the :doc:`atom_style hybrid +sphere dipole ` command. + ---------- Restart, fix_modify, output, run start/stop, minimize info diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 51066675b8..0dbf4f5a18 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -180,7 +180,7 @@ force is added. By default, no additional forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their -respective local minima. By using the key word *end*, additional forces +respective local minima. By using the keyword *end*, additional forces can be applied to the first and/or last replicas, to enable them to relax toward a MEP while constraining their energy E to the target energy ETarget. diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 0cfbc8f921..0a4076364c 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -208,19 +208,19 @@ The relaxation rate of the barostat is set by its inertia :math:`W`: .. math:: - W = (N + 1) k_B T_{\rm target} P_{\rm damp}^2 + W = (N + 1) k_B T_\mathrm{target} P_\mathrm{damp}^2 where :math:`N` is the number of atoms, :math:`k_B` is the Boltzmann constant, -and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) `. -If a thermostat is defined, :math:`T_{\rm target}` is the target temperature -of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}` +and :math:`T_\mathrm{target}` is the target temperature of the barostat :ref:`(Martyna) `. +If a thermostat is defined, :math:`T_\mathrm{target}` is the target temperature +of the thermostat. If a thermostat is not defined, :math:`T_\mathrm{target}` is set to the current temperature of the system when the barostat is initialized. If this temperature is too low the simulation will quit with an error. -Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to +Note: in previous versions of LAMMPS, :math:`T_\mathrm{target}` would default to a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature of exactly zero. -If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be +If a thermostat is not specified by this fix, :math:`T_\mathrm{target}` can be manually specified using the *Ptemp* parameter. This may be useful if the barostat is initialized when the current temperature does not reflect the steady state temperature of the system. This keyword may also be useful in @@ -512,8 +512,8 @@ according to the following factorization of the Liouville propagator .. math:: \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E} - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\ &\times \left[ @@ -526,8 +526,8 @@ according to the following factorization of the Liouville propagator &\times \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ &+ \mathcal{O} \left(\Delta t^3 \right) This factorization differs somewhat from that of Tuckerman et al, in diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 6764f88eee..862a0b546e 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -426,8 +426,8 @@ according to the following factorization of the Liouville propagator .. math:: \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E} - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\ &\times \left[ @@ -440,8 +440,8 @@ according to the following factorization of the Liouville propagator &\times \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ &+ \mathcal{O} \left(\Delta t^3 \right) This factorization differs somewhat from that of Tuckerman et al, in diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 7e30b7bb01..881ae6c45c 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -62,19 +62,19 @@ The potential energy added to atom I is given by these formulas .. math:: - \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(1\right) \\ + \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(1\right) \\ \\ - \xi_{\rm IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^{\rm J} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(2\right)\\ + \xi_\mathrm{IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^\mathrm{J} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(2\right)\\ \\ - \xi_{\rm low} = & {\rm cutlo} \, \xi_{\rm IJ} \qquad\qquad\qquad\left(3\right)\\ - \xi_{\rm high} = & {\rm cuthi} \, \xi_{\rm IJ} \qquad\qquad\qquad\left(4\right) \\ + \xi_\mathrm{low} = & \mathrm{cutlo} \, \xi_\mathrm{IJ} \qquad\qquad\qquad\left(3\right)\\ + \xi_\mathrm{high} = & \mathrm{cuthi} \, \xi_\mathrm{IJ} \qquad\qquad\qquad\left(4\right) \\ \\ - \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \qquad\qquad\left(5\right)\\ + \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_\mathrm{low}}{\xi_\mathrm{high} - \xi_\mathrm{low}} \qquad\qquad\left(5\right)\\ \\ - u_{i} = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_{\rm low}\\ - = & {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2} - \qquad \mathrm{ for }\qquad \xi_{\rm low} < \xi_{i} < \xi_{\rm high} \quad \left(6\right) \\ - = & {\rm dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_{\rm high} < \xi_{i} + u_{i} = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_\mathrm{low}\\ + = & \mathrm{dE}\,\frac{1 - \cos(2 \omega_{i})}{2} + \qquad \mathrm{for }\qquad \xi_\mathrm{low} < \xi_{i} < \xi_\mathrm{high} \quad \left(6\right) \\ + = & \mathrm{dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_\mathrm{high} < \xi_{i} which are fully explained in :ref:`(Janssens) `. For fcc crystals this order parameter Xi for atom I in equation (1) is a sum over the diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 0c7f763ced..0f37260194 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -1,5 +1,7 @@ .. index:: fix pimd/langevin .. index:: fix pimd/nvt +.. index:: fix pimd/langevin/bosonic +.. index:: fix pimd/nvt/bosonic fix pimd/langevin command ========================= @@ -7,6 +9,12 @@ fix pimd/langevin command fix pimd/nvt command ==================== +fix pimd/langevin/bosonic command +================================= + +fix pimd/nvt/bosonic command +============================ + Syntax """""" @@ -15,39 +23,42 @@ Syntax fix ID group-ID style keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* style = *pimd/langevin* or *pimd/nvt* = style name of this fix command +* style = *pimd/langevin* or *pimd/nvt* or *pimd/langevin/bosonic* or *pimd/nvt/bosonic* = style name of this fix command * zero or more keyword/value pairs may be appended * keywords for style *pimd/nvt* .. parsed-literal:: - *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc* - *method* value = *pimd* or *nmpimd* or *cmd* - *fmass* value = scaling factor on mass - *sp* value = scaling factor on Planck constant - *temp* value = temperature (temperature units) - *nhc* value = Nc = number of chains in Nose-Hoover thermostat + + *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc* + *method* value = *pimd* or *nmpimd* or *cmd* + *fmass* value = scaling factor on mass + *sp* value = scaling factor on Planck constant + *temp* value = temperature (temperature units) + *nhc* value = Nc = number of chains in Nose-Hoover thermostat * keywords for style *pimd/langevin* .. parsed-literal:: - *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj* - *method* value = *nmpimd* (default) or *pimd* - *integrator* value = *obabo* or *baoab* - *fmmode* value = *physical* or *normal* - *fmass* value = scaling factor on mass - *temp* value = temperature (temperature unit) + + *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj* + *method* value = *nmpimd* (default) or *pimd* + *integrator* value = *obabo* or *baoab* + *ensemble* value = *nvt* or *nve* or *nph* or *npt* + *fmmode* value = *physical* or *normal* + *fmass* value = scaling factor on mass + *temp* value = temperature (temperature unit) temperature = target temperature of the thermostat - *thermostat* values = style seed + *thermostat* values = style seed style value = *PILE_L* seed = random number generator seed - *tau* value = thermostat damping parameter (time unit) - *scale* value = scaling factor of the damping times of non-centroid modes of PILE_L thermostat - *iso* or *aniso* values = pressure (pressure unit) + *tau* value = thermostat damping parameter (time unit) + *scale* value = scaling factor of the damping times of non-centroid modes of PILE_L thermostat + *iso* or *aniso* values = pressure (pressure unit) pressure = scalar external pressure of the barostat - *barostat* value = *BZP* or *MTTK* - *taup* value = barostat damping parameter (time unit) - *fixcom* value = *yes* or *no* - *lj* values = epsilon sigma mass planck mvv2e + *barostat* value = *BZP* or *MTTK* + *taup* value = barostat damping parameter (time unit) + *fixcom* value = *yes* or *no* + *lj* values = epsilon sigma mass planck mvv2e epsilon = energy scale for reduced units (energy units) sigma = length scale for reduced units (length units) mass = mass scale for reduced units (mass units) @@ -62,6 +73,8 @@ Examples fix 1 all pimd/nvt method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4 fix 1 all pimd/langevin ensemble npt integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0 iso 1.0 barostat BZP taup 1.0 +Example input files are provided in the examples/PACKAGES/pimd directory. + Description """"""""""" @@ -76,12 +89,20 @@ partition function for the original system to a classical partition function for a ring-polymer system is exploited, to efficiently sample configurations from the canonical ensemble :ref:`(Feynman) `. -The classical partition function and its components are given +.. versionadded:: 2Apr2025 + + Fix *pimd/langevin/bosonic* and *pimd/nvt/bosonic* were added. + +Fix *pimd/nvt* and fix *pimd/langevin* simulate *distinguishable* quantum particles. +Simulations of bosons, including exchange effects, are supported with the +fix *pimd/langevin/bosonic* and the *pimd/nvt/bosonic* commands. + +For distinguishable particles, the isomorphic classical partition function and its components are given by the following equations: .. math:: - Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\ + Z = & \int d\mathbf{q} d\mathbf{p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\ H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\ V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg] @@ -153,15 +174,17 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics Mode *pimd* added to fix pimd/langevin. -Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default value is *nmpimd*. -If *method* is *nmpimd*, the normal mode representation is used to integrate the equations of motion. -The exact solution of harmonic oscillator is used to propagate the free ring polymer part of the Hamiltonian. -If *method* is *pimd*, the Cartesian representation is used to integrate the equations of motion. -The harmonic force is added to the total force of the system, and the numerical integrator is used to propagate the Hamiltonian. +Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default +value is *nmpimd*. If *method* is *nmpimd*, the normal mode representation is +used to integrate the equations of motion. The exact solution of harmonic +oscillator is used to propagate the free ring polymer part of the Hamiltonian. +If *method* is *pimd*, the Cartesian representation is used to integrate the +equations of motion. The harmonic force is added to the total force of the +system, and the numerical integrator is used to propagate the Hamiltonian. -The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*. -See :ref:`(Liu) ` for a discussion on the OBABO and BAOAB splitting schemes. Typically -either of the two should work fine. +The keyword *integrator* specifies the Trotter splitting method used by *fix +pimd/langevin*. See :ref:`(Liu) ` for a discussion on the OBABO and BAOAB +splitting schemes. Typically either of the two should work fine. The keyword *fmass* sets a further scaling factor for the fictitious masses of beads, which can be used for the Partial Adiabatic CMD @@ -211,8 +234,8 @@ a positive floating-point number. For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature. -The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only -be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti `), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator. +The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. +*style* can only be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti `), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator. .. note:: @@ -222,7 +245,7 @@ be *PILE_L* (path integral Langevin equation local thermostat, as described in : The keyword *tau* specifies the thermostat damping time parameter for fix style *pimd/langevin*. It is in time unit. It only works on the centroid mode. The keyword *scale* specifies a scaling parameter for the damping times of the non-centroid modes for fix style *pimd/langevin*. The default -damping time of the non-centroid mode :math:`i` is :math:`\frac{P}{\beta\hbar}\sqrt{\lambda_i\times\mathrm{fmass}}` (*fmmode* is *physical*) or :math:`\frac{P}{\beta\hbar}\sqrt{\mathrm{fmass}}` (*fmmode* is *normal*). The damping times of all non-centroid modes are the default values divided by *scale*. +damping time of the non-centroid mode :math:`i` is :math:`\frac{P}{\beta\hbar}\sqrt{\lambda_i\times\mathrm{fmass}}` (*fmmode* is *physical*) or :math:`\frac{P}{\beta\hbar}\sqrt{\mathrm{fmass}}` (*fmmode* is *normal*). The damping times of all non-centroid modes are the default values divided by *scale*. This keyword should be used only with *method*=*nmpimd*. The barostat parameters for fix style *pimd/langevin* with *npt* or *nph* ensemble is specified using one of *iso* and *aniso* keywords. A *pressure* value should be given with pressure unit. The keyword *iso* means couple all 3 diagonal components together when pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. The keyword *aniso* means x, y, and z dimensions are controlled independently using the Pxx, Pyy, and Pzz components of the stress tensor as the driving forces, and the specified scalar external pressure. @@ -334,8 +357,8 @@ it outputs multiple log files, and different log files contain information about different beads or modes (see detailed explanations below). If *ensemble* is *nve* or *nvt*, the vector has 10 values: - #. kinetic energy of the normal mode - #. spring elastic energy of the normal mode + #. kinetic energy of the bead (if *method*=*pimd*) or normal mode (if *method*=*nmpimd*) + #. spring elastic energy of the bead (if *method*=*pimd*) or normal mode (if *method*=*nmpimd*) #. potential energy of the bead #. total energy of all beads (conserved if *ensemble* is *nve*) #. primitive kinetic energy estimator @@ -398,7 +421,12 @@ LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Fix *pimd/nvt* cannot be used with :doc:`lj units `. -Fix *pimd/langevin* can be used with :doc:`lj units `. See the above part for how to use it. +Fix *pimd/langevin* can be used with :doc:`lj units `. +See the documentation above for how to use it. + +Only some combinations of fix styles and their options support +partitions with multiple processors. LAMMPS will stop with an +error if multi-processor partitions are not supported. A PIMD simulation can be initialized with a single data file read via the :doc:`read_data ` command. However, this means all @@ -412,12 +440,20 @@ variable, e.g. velocity all create 300.0 1234${ibead} rot yes dist gaussian +Related commands +"""""""""""""""" + +:doc:`fix ipi ` + Default """"""" The keyword defaults for fix *pimd/nvt* are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0, and nhc = 2. +The keyword defaults for fix *pimd/langevin* are integrator = obabo, method = nmpimd, ensemble = nvt, fmmode = physical, fmass = 1.0, +scale = 1, temp = 298.15, thermostat = PILE_L, tau = 1.0, iso = 1.0, taup = 1.0, barostat = BZP, fixcom = yes, and lj = 1 for all its arguments. + ---------- .. _Feynman: diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 06a1f98375..ac0bca84f1 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -304,7 +304,7 @@ Chemistry, 95, 3358-3363 (1991). .. _CTIP1: **(CTIP)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson, -in preparation +J Chemical Physics, 162, 054709 (2025) .. _vanDuin: diff --git a/doc/src/fix_qeq_reaxff.rst b/doc/src/fix_qeq_reaxff.rst index e1a09c4fc3..7441138396 100644 --- a/doc/src/fix_qeq_reaxff.rst +++ b/doc/src/fix_qeq_reaxff.rst @@ -59,7 +59,7 @@ extracted from the :doc:`pair_style reaxff ` command and the ReaxFF force field file it reads in. If a file name is specified for *params*, then the parameters are taken from the specified file and the file must contain one line for each atom type. The latter -form must be used when performing QeQ with a non-ReaxFF potential. +form must be used when performing QEq with a non-ReaxFF potential. Each line should be formatted as follows: .. parsed-literal:: @@ -140,7 +140,8 @@ Related commands """""""""""""""" :doc:`pair_style reaxff `, :doc:`fix qeq/shielded `, -:doc:`fix acks2/reaxff `, :doc:`fix qtpie/reaxff ` +:doc:`fix acks2/reaxff `, :doc:`fix qtpie/reaxff `, +:doc:`fix qeq/rel/reaxff ` Default """"""" diff --git a/doc/src/fix_qeq_rel_reaxff.rst b/doc/src/fix_qeq_rel_reaxff.rst new file mode 100644 index 0000000000..012980e230 --- /dev/null +++ b/doc/src/fix_qeq_rel_reaxff.rst @@ -0,0 +1,195 @@ +.. index:: fix qeq/rel/reaxff + +fix qeq/rel/reaxff command +========================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + fix ID group-ID qeq/rel/reaxff Nevery cutlo cuthi tolerance params gfile args + +* ID, group-ID are documented in :doc:`fix ` command +* qeq/rel/reaxff = style name of this fix command +* Nevery = perform QEqR every this many steps +* cutlo,cuthi = lo and hi cutoff for Taper radius +* tolerance = precision to which charges will be equilibrated +* params = reaxff or a filename +* gfile = the name of a file containing Gaussian orbital exponents +* one or more keywords or keyword/value pairs may be appended + + .. parsed-literal:: + + keyword = *scale* or *maxiter* or *nowarn* + *scale* beta = set value of scaling factor *beta* (determines strength of electric polarization) + *maxiter* N = limit the number of iterations to *N* + *nowarn* = do not print a warning message if the maximum number of iterations is reached + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all qeq/rel/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qeqr + fix 1 all qeq/rel/reaxff 1 0.0 10.0 1.0e-6 params.qeqr exp.qeqr scale 1.5 maxiter 500 nowarn + +Description +""""""""""" + +.. versionadded:: 19Nov2024 + +This fix implements the QEqR method for charge equilibration, which +differs from the QEq charge equilibration method :ref:`(Rappe and +Goddard) ` only in how external electric fields are accounted +for. This fix therefore raises a warning when used without :doc:`fix +efield ` since :doc:`fix qeq/reaxff ` should +be used without an external electric field. Charges are computed with +the QEqR method by minimizing the electrostatic energy of the system in +the same way as the QEq method but where the absolute electronegativity, +:math:`\chi_i`, of each atom in the QEq method is replaced with an +effective electronegativity given by + +.. math:: + \chi_{\mathrm{r}i} = \chi_i + \frac{\sum_{j=1}^{N} \beta(\phi_i - \phi_j) S_{ij}} + {\sum_{m=1}^{N}S_{im}}, + +where :math:`N` is the number of atoms in the system, :math:`\beta` is a +scaling factor, :math:`\phi_i` and :math:`\phi_j` are the electric +potentials at the positions of atoms :math:`i` and :math:`j` due to the +external electric field and :math:`S_{ij}` is the overlap integral +between atoms :math:`i` and :math:`j`. This formulation is advantageous +over the method used by :doc:`fix qeq/reaxff ` to +account for an external electric field in that it permits periodic +boundaries in the direction of an external electric field and in that it +does not worsen long-range charge transfer seen with QEq. + +This fix is typically used in conjunction with the ReaxFF force field +model as implemented in the :doc:`pair_style reaxff ` +command, but it can be used with any potential in LAMMPS, so long as it +defines and uses charges on each atom. For more technical details about +the charge equilibration performed by *fix qeq/rel/reaxff*, which is the +same as in :doc:`fix qeq/reaxff ` except for the use of +:math:`\chi_{\mathrm{r}i}`, please refer to :ref:`(Aktulga) +`. To be explicit, *fix qeq/rel/reaxff* replaces +:math:`\chi_k` of eq. 3 in :ref:`(Aktulga) ` with +:math:`\chi_{\mathrm{r}k}` when an external electric field is applied. + +This fix requires the absolute electronegativity, :math:`\chi`, in eV, +the self-Coulomb potential, :math:`\eta`, in eV, and the shielded +Coulomb constant, :math:`\gamma`, in :math:`\AA^{-1}`. If the *params* +setting above is the word "reaxff", then these are extracted from the +:doc:`pair_style reaxff ` command and the ReaxFF force +field file it reads in. If a file name is specified for *params*, then +the parameters are taken from the specified file and the file must +contain one line for each atom type. The latter form must be used when +using this fix with a non-ReaxFF potential. Each line should be +formatted as follows, ensuring that the parameters are given in units of +eV, eV, and :math:`\AA^{-1}`, respectively: + +.. parsed-literal:: + + itype chi eta gamma + +where *itype* is the atom type from 1 to Ntypes. Note that eta is +defined here as twice the eta value in the ReaxFF file. + +The overlap integrals :math:`S_{ij}` are computed by using normalized 1s +Gaussian type orbitals. The Gaussian orbital exponents, :math:`\alpha`, +that are needed to compute the overlap integrals are taken from the file +given by *gfile*. This file must contain one line for each atom type +and provide the Gaussian orbital exponent for each atom type in units of +inverse square Bohr radius. Each line should be formatted as follows: + +.. parsed-literal:: + + itype alpha + +Empty lines or any text following the pound sign (#) are ignored. An +example *gfile* for a system with two atom types is + +.. parsed-literal:: + + # An example gfile. Exponents are taken from Table 2.2 of Chen, J. (2009). + # Theory and applications of fluctuating-charge models. + # The units of the exponents are 1 / (Bohr radius)^2 . + 1 0.2240 # O + 2 0.5434 # H + +The optional *scale* keyword sets the value of :math:`\beta` in the +equation for :math:`\chi_{\mathrm{r}i}`. The default value is 1.0. + +The optional *maxiter* keyword allows changing the max number of +iterations in the linear solver. The default value is 200. + +The optional *nowarn* keyword silences the warning message printed when +the maximum number of iterations is reached. This can be useful for +comparing serial and parallel results where having the same fixed number +of iterations is desired, which can be achieved by using a very small +tolerance and setting *maxiter* to the desired number of iterations. + +.. note:: + + In order to solve the self-consistent equations for electronegativity + equalization, LAMMPS imposes the additional constraint that all the + charges in the fix group must add up to zero. The initial charge + assignments should also satisfy this constraint. LAMMPS will print a + warning if that is not the case. + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files +`. This fix computes a global scalar (the number of +iterations) and a per-atom vector (the effective electronegativity), +which can be accessed 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 invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + +This fix is part of the REAXFF package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. + +This fix does not correctly handle interactions involving multiple +periodic images of the same atom. Hence, it should not be used for +periodic cell dimensions smaller than the non-bonded cutoff radius, +which is typically :math:`10~\AA` for ReaxFF simulations. + +This fix may be used in combination with :doc:`fix efield ` +and will apply the external electric field during charge equilibration, +but there may be only one fix efield instance used and the electric +field must be applied to all atoms in the system. Consequently, `fix +efield` must be used with *group-ID* all and must not be used with the +keyword *region*. Equal-style variables can be used for electric field +vector components without any further settings. Atom-style variables can +be used for spatially-varying electric field vector components, but the +resulting electric potential must be specified as an atom-style variable +using the *potential* keyword for `fix efield`. + +Related commands +"""""""""""""""" + +:doc:`pair_style reaxff `, :doc:`fix qeq/reaxff `, +:doc:`fix acks2/reaxff `, :doc:`fix qtpie/reaxff ` + +Default +""""""" + +scale = 1.0 and maxiter = 200 + +---------- + +.. _Rappe4: + +**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95, +3358-3363 (1991). + +.. _qeq-Aktulga3: + +**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, +245-259 (2012). diff --git a/doc/src/fix_qtpie_reaxff.rst b/doc/src/fix_qtpie_reaxff.rst index e96cbec459..08ae24e164 100644 --- a/doc/src/fix_qtpie_reaxff.rst +++ b/doc/src/fix_qtpie_reaxff.rst @@ -21,8 +21,10 @@ Syntax .. parsed-literal:: - keyword = *maxiter* + keyword = *scale* or *maxiter* or *nowarn* + *scale* beta = set value of scaling factor *beta* (determines strength of electric polarization) *maxiter* N = limit the number of iterations to *N* + *nowarn* = do not print a warning message if the maximum number of iterations is reached Examples """""""" @@ -30,7 +32,7 @@ Examples .. code-block:: LAMMPS fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qtpie - fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 params.qtpie exp.qtpie maxiter 500 + fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 params.qtpie exp.qtpie scale 1.5 maxiter 500 nowarn Description """"""""""" @@ -46,7 +48,7 @@ same way as the QEq method but where the absolute electronegativity, electronegativity given by :ref:`(Chen) ` .. math:: - \chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j) S_{ij}} + \tilde{\chi}_{i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j) S_{ij}} {\sum_{m=1}^{N}S_{im}}, which acts to penalize long-range charge transfer seen with the QEq charge @@ -61,11 +63,11 @@ electric field by using the effective electronegativity given in :ref:`(Gergs) `: .. math:: - \chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \phi_i - \phi_j) S_{ij}} + \tilde{\chi}_{\mathrm{r}i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \beta(\phi_i - \phi_j)) S_{ij}} {\sum_{m=1}^{N}S_{im}}, -where :math:`\phi_i` and :math:`\phi_j` are the electric -potentials at the positions of atom :math:`i` and :math:`j` +where :math:`\beta` is a scaling factor and :math:`\phi_i` and :math:`\phi_j` +are the electric potentials at the positions of atoms :math:`i` and :math:`j` due to the external electric field. This fix is typically used in conjunction with the ReaxFF force @@ -74,9 +76,12 @@ command, but it can be used with any potential in LAMMPS, so long as it defines and uses charges on each atom. For more technical details about the charge equilibration performed by `fix qtpie/reaxff`, which is the same as in :doc:`fix qeq/reaxff ` except for the use of -:math:`\chi_{\mathrm{eff},i}`, please refer to :ref:`(Aktulga) `. +:math:`\tilde{\chi}_{i}` or :math:`\tilde{\chi}_{\mathrm{r}i}`, +please refer to :ref:`(Aktulga) `. To be explicit, this fix replaces :math:`\chi_k` of eq. 3 in -:ref:`(Aktulga) ` with :math:`\chi_{\mathrm{eff},k}`. +:ref:`(Aktulga) ` with :math:`\tilde{\chi}_{k}` when no external +electric field is applied and with :math:`\tilde{\chi}_{\mathrm{r}k}` when an +external electric field is applied. This fix requires the absolute electronegativity, :math:`\chi`, in eV, the self-Coulomb potential, :math:`\eta`, in eV, and the shielded Coulomb @@ -97,7 +102,7 @@ respectively: where *itype* is the atom type from 1 to Ntypes. Note that eta is defined here as twice the eta value in the ReaxFF file. -The overlap integrals in the equation for :math:`\chi_{\mathrm{eff},i}` +The overlap integrals :math:`S_{ij}` are computed by using normalized 1s Gaussian type orbitals. The Gaussian orbital exponents, :math:`\alpha`, that are needed to compute the overlap integrals are taken from the file given by *gfile*. @@ -120,15 +125,26 @@ Empty lines or any text following the pound sign (#) are ignored. An example 1 0.2240 # O 2 0.5434 # H +The optional *scale* keyword sets the value of :math:`\beta` in the equation for +:math:`\tilde{\chi}_{\mathrm{r}i}`. This keyword only affects the computed charges +when :doc:`fix efield ` is used. The default value is 1.0. + The optional *maxiter* keyword allows changing the max number of iterations in the linear solver. The default value is 200. +The optional *nowarn* keyword silences the warning message printed +when the maximum number of iterations is reached. This can be +useful for comparing serial and parallel results where having the +same fixed number of iterations is desired, which can be achieved +by using a very small tolerance and setting *maxiter* to the desired +number of iterations. + .. note:: In order to solve the self-consistent equations for electronegativity equalization, LAMMPS imposes the additional constraint that all the - charges in the fix group must add up to zero. The initial charge - assignments should also satisfy this constraint. LAMMPS will print a + charges in the fix group must add up to zero. The initial charge + assignments should also satisfy this constraint. LAMMPS will print a warning if that is not the case. Restart, fix_modify, output, run start/stop, minimize info @@ -170,12 +186,13 @@ Related commands """""""""""""""" :doc:`pair_style reaxff `, :doc:`fix qeq/reaxff `, -:doc:`fix acks2/reaxff ` +:doc:`fix acks2/reaxff `, +:doc:`fix qeq/rel/reaxff ` Default """"""" -maxiter 200 +scale = 1.0 and maxiter = 200 ---------- diff --git a/doc/src/fix_reaxff_bonds.rst b/doc/src/fix_reaxff_bonds.rst index 15fd9abafa..1194af617c 100644 --- a/doc/src/fix_reaxff_bonds.rst +++ b/doc/src/fix_reaxff_bonds.rst @@ -56,16 +56,28 @@ If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write. +.. versionadded:: 2Apr2025 + +If the filename contains the wildcard character "\*", a new file is +created on every timestep there bond information is written. The "\*" +character is replaced with the timestep value. Note that the +:doc:`fix_modify pad ` command can be used so that all +timestep numbers have the same length by adding leading zeroes +(e.g. 00010 for a pad value of 5). The default pad value is 0, i.e. no +leading zeroes. + ---------- Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. 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 `. +No information about this fix is written to :doc:`binary restart files +`. This fix supports the :doc:`fix_modify pad ` +option. 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 `. ---------- @@ -76,10 +88,10 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -The fix reaxff/bonds command requires that the :doc:`pair_style reaxff ` is invoked. This fix is part of the -REAXFF package. It is only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` page for more -info. +The fix reaxff/bonds command requires that the :doc:`pair_style reaxff +` is invoked. This fix is part of the REAXFF package. It +is only enabled if LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. To write gzipped bond files, you must compile LAMMPS with the -DLAMMPS_GZIP option. @@ -92,4 +104,4 @@ Related commands Default """"""" -none +pad = 0 diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst index 068d1de995..badcf72a56 100644 --- a/doc/src/fix_reaxff_species.rst +++ b/doc/src/fix_reaxff_species.rst @@ -207,6 +207,9 @@ 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 `. +This fix supports dynamic groups only if the *Nrepeat* setting is 1, +i.e. there is no averaging. + ---------- .. include:: accel_styles.rst diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index d60d8cb731..9102cc579e 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -33,7 +33,7 @@ Syntax *box* = the wall position is defined in simulation box units .. - FIXME: There are several "undocumented" key words for this fix: *rough*, + FIXME: There are several "undocumented" keywords for this fix: *rough*, *rampNL1*, *rampNL2*, *rampNL3*, *rampNL4*, and *rampNL5*. Examples diff --git a/doc/src/geturl.rst b/doc/src/geturl.rst index acf1e21a3e..11145f898a 100644 --- a/doc/src/geturl.rst +++ b/doc/src/geturl.rst @@ -58,6 +58,32 @@ behave as expected. If the argument is *no*, geturl will operate silently and only report the error status number provided by libcurl, in case of a failure. +.. _geturl_proxy: + +.. admonition:: Using *geturl* with proxies for http or https + :class: note + + The `libcurl library `_ supports `routing + traffic through proxies + `_ by setting + suitable environment variables (e.g. ``http_proxy`` or + ``https_proxy``) as required by some institutional or corporate + security protocols. In that case you probably also want to use the + *verify* *no* setting. + + Using a proxy may also be needed if you are running on an HPC cluster + where only the login or head nodes have access to the internet, but + not the compute nodes. In this case the following input can be adapted + and used for your local HPC environment: + + .. code-block:: LAMMPS + + variable headnode getenv PBS_O_HOST # use SLURM_SUBMIT_HOST when using SLURM instead of Torque/PBS + shell ssh -N -f -D 8001 ${headnode} # start SOCKS5 proxy with backgrounded ssh connection to cluster head node + shell putenv http_proxy=socks5://localhost:8001 https_proxy=socks5://localhost:8001 + geturl https://download.lammps.org/tars/SHA256SUMS # download a file using proxy + shell head SHA256SUMS # check if the download was successful + ---------- Restrictions diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index d36f19b0d5..9e4cb4fbc6 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -98,14 +98,14 @@ all atoms .. math:: - || \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right) + || \vec{F} ||_{max} = \mathrm{max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right) The *inf* norm takes the maximum component across the forces of all atoms in the system: .. math:: - || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) + || \vec{F} ||_{inf} = \mathrm{max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) For the min styles *spin*, *spin/cg* and *spin/lbfgs*, the force norm is replaced by the spin-torque norm. diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 9b6841ae8c..c6ae2f26b1 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -50,9 +50,9 @@ system: .. math:: - {\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|} + {\Delta t}_\mathrm{max} = \frac{2\pi}{\kappa \left|\vec{\omega}_\mathrm{max} \right|} -with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precession +with :math:`\left|\vec{\omega}_\mathrm{max}\right|` the norm of the largest precession frequency in the system (across all processes, and across all replicas if a spin/neb calculation is performed). diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index c201e53340..84ee4b99fc 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -108,12 +108,12 @@ potential energy of the system as a function of the N atom coordinates: .. math:: - E(r_1,r_2, \ldots ,r_N) = & \sum_{i,j} E_{\it pair}(r_i,r_j) + - \sum_{ij} E_{\it bond}(r_i,r_j) + - \sum_{ijk} E_{\it angle}(r_i,r_j,r_k) + \\ - & \sum_{ijkl} E_{\it dihedral}(r_i,r_j,r_k,r_l) + - \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) + - \sum_i E_{\it fix}(r_i) + E(r_1,r_2, \ldots ,r_N) = & \sum_{i,j} E_{pair}(r_i,r_j) + + \sum_{ij} E_{bond}(r_i,r_j) + + \sum_{ijk} E_{angle}(r_i,r_j,r_k) + \\ + & \sum_{ijkl} E_{dihedral}(r_i,r_j,r_k,r_l) + + \sum_{ijkl} E_{improper}(r_i,r_j,r_k,r_l) + + \sum_i E_{fix}(r_i) where the first term is the sum of all non-bonded :doc:`pairwise interactions ` including :doc:`long-range Coulombic diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 62ca9f32cb..ba8ea3a7cd 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -148,7 +148,7 @@ spin i, :math:`\omega_i^{\nu}` is a rotation angle defined as: .. math:: - \omega_i^{\nu} = (\nu - 1) \Delta \omega_i {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1} + \omega_i^{\nu} = (\nu - 1) \Delta \omega_i \mathrm{~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1} with :math:`\nu` the image number, Q the total number of images, and :math:`\omega_i` the total rotation between the initial and final spins. diff --git a/doc/src/package.rst b/doc/src/package.rst index ddb3656027..cde9855c5f 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -15,115 +15,115 @@ Syntax .. parsed-literal:: - *gpu* args = Ngpu keyword value ... - Ngpu = # of GPUs per node - zero or more keyword/value pairs may be appended - keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *blocksize* or *omp* or *platform* or *device_type* or *ocl_args* - *neigh* value = *yes* or *no* - *yes* = neighbor list build on GPU (default) - *no* = neighbor list build on CPU - *newton* = *off* or *on* - *off* = set Newton pairwise flag off (default and required) - *on* = set Newton pairwise flag on (currently not allowed) - *pair/only* = *off* or *on* - *off* = apply "gpu" suffix to all available styles in the GPU package (default) - *on* = apply "gpu" suffix only pair styles - *binsize* value = size - size = bin size for neighbor list construction (distance units) - *split* = fraction - fraction = fraction of atoms assigned to GPU (default = 1.0) - *tpa* value = Nlanes - Nlanes = # of GPU vector lanes (CUDA threads) used per atom - *blocksize* value = size - size = thread block size for pair force computation - *omp* value = Nthreads - Nthreads = number of OpenMP threads to use on CPU (default = 0) - *platform* value = id - id = For OpenCL, platform ID for the GPU or accelerator - *gpuID* values = id - id = ID of first GPU to be used on each node - *device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom*,val1,val2,... - val1,val2,... = custom OpenCL accelerator configuration parameters (see below for details) - *ocl_args* value = args - args = List of additional OpenCL compiler arguments delimited by colons - *intel* args = NPhi keyword value ... - Nphi = # of co-processors per node - zero or more keyword/value pairs may be appended - keywords = *mode* or *omp* or *lrt* or *balance* or *ghost* or *tpc* or *tptask* or *pppm_table* or *no_affinity* - *mode* value = *single* or *mixed* or *double* - single = perform force calculations in single precision - mixed = perform force calculations in mixed precision - double = perform force calculations in double precision - *omp* value = Nthreads - Nthreads = number of OpenMP threads to use on CPU (default = 0) - *lrt* value = *yes* or *no* - *yes* = use additional thread dedicated for some PPPM calculations - *no* = do not dedicate an extra thread for some PPPM calculations - *balance* value = split - split = fraction of work to offload to co-processor, -1 for dynamic - *ghost* value = *yes* or *no* - *yes* = include ghost atoms for offload - *no* = do not include ghost atoms for offload - *tpc* value = Ntpc - Ntpc = max number of co-processor threads per co-processor core (default = 4) - *tptask* value = Ntptask - Ntptask = max number of co-processor threads per MPI task (default = 240) - *pppm_table* value = *yes* or *no* - *yes* = Precompute pppm values in table (doesn't change accuracy) - *no* = Compute pppm values on the fly - *no_affinity* values = none - *kokkos* args = keyword value ... - zero or more keyword/value pairs may be appended - keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *atom/map* or *gpu/aware* or *pair/only* - *neigh* value = *full* or *half* - full = full neighbor list - half = half neighbor list built in thread-safe manner - *neigh/qeq* value = *full* or *half* - full = full neighbor list - half = half neighbor list built in thread-safe manner - *neigh/thread* value = *off* or *on* - *off* = thread only over atoms - *on* = thread over both atoms and neighbors - *neigh/transpose* value = *off* or *on* - *off* = use same memory layout for GPU neigh list build as pair style - *on* = use transposed memory layout for GPU neigh list build - *newton* = *off* or *on* - *off* = set Newton pairwise and bonded flags off - *on* = set Newton pairwise and bonded flags on - *binsize* value = size - size = bin size for neighbor list construction (distance units) - *comm* value = *no* or *host* or *device* - use value for comm/exchange and comm/forward and comm/pair/forward and comm/fix/forward and comm/reverse - *comm/exchange* value = *no* or *host* or *device* - *comm/forward* value = *no* or *host* or *device* - *comm/pair/forward* value = *no* or *device* - *comm/fix/forward* value = *no* or *device* - *comm/reverse* value = *no* or *host* or *device* - *no* = perform communication pack/unpack in non-KOKKOS mode - *host* = perform pack/unpack on host (e.g. with OpenMP threading) - *device* = perform pack/unpack on device (e.g. on GPU) - *comm/pair/reverse* value = *no* or *device* - *no* = perform communication pack/unpack in non-KOKKOS mode - *device* = perform pack/unpack on device (e.g. on GPU) - *sort* value = *no* or *device* - *no* = perform atom sorting in non-KOKKOS mode - *device* = perform atom sorting on device (e.g. on GPU) - *atom/map* value = *no* or *device* - *no* = build atom map in non-KOKKOS mode - *device* = build atom map on device (e.g. on GPU) - *gpu/aware* = *off* or *on* - *off* = do not use GPU-aware MPI - *on* = use GPU-aware MPI (default) - *pair/only* = *off* or *on* - *off* = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default) - *on* = use device acceleration only for pair styles (and host acceleration for others) - *omp* args = Nthreads keyword value ... - Nthreads = # of OpenMP threads to associate with each MPI process - zero or more keyword/value pairs may be appended - keywords = *neigh* - *neigh* value = *yes* or *no* - *yes* = threaded neighbor list build (default) - *no* = non-threaded neighbor list build + *gpu* args = Ngpu keyword value ... + Ngpu = # of GPUs per node + zero or more keyword/value pairs may be appended + keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *blocksize* or *omp* or *platform* or *device_type* or *ocl_args* + *neigh* value = *yes* or *no* + *yes* = neighbor list build on GPU (default) + *no* = neighbor list build on CPU + *newton* = *off* or *on* + *off* = set Newton pairwise flag off (default and required) + *on* = set Newton pairwise flag on (currently not allowed) + *pair/only* = *off* or *on* + *off* = apply "gpu" suffix to all available styles in the GPU package (default) + *on* = apply "gpu" suffix only pair styles + *binsize* value = size + size = bin size for neighbor list construction (distance units) + *split* = fraction + fraction = fraction of atoms assigned to GPU (default = 1.0) + *tpa* value = Nlanes + Nlanes = # of GPU vector lanes (CUDA threads) used per atom + *blocksize* value = size + size = thread block size for pair force computation + *omp* value = Nthreads + Nthreads = number of OpenMP threads to use on CPU (default = 0) + *platform* value = id + id = For OpenCL, platform ID for the GPU or accelerator + *gpuID* values = id + id = ID of first GPU to be used on each node + *device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom*,val1,val2,... + val1,val2,... = custom OpenCL accelerator configuration parameters (see below for details) + *ocl_args* value = args + args = List of additional OpenCL compiler arguments delimited by colons + *intel* args = NPhi keyword value ... + Nphi = # of co-processors per node + zero or more keyword/value pairs may be appended + keywords = *mode* or *omp* or *lrt* or *balance* or *ghost* or *tpc* or *tptask* or *pppm_table* or *no_affinity* + *mode* value = *single* or *mixed* or *double* + single = perform force calculations in single precision + mixed = perform force calculations in mixed precision + double = perform force calculations in double precision + *omp* value = Nthreads + Nthreads = number of OpenMP threads to use on CPU (default = 0) + *lrt* value = *yes* or *no* + *yes* = use additional thread dedicated for some PPPM calculations + *no* = do not dedicate an extra thread for some PPPM calculations + *balance* value = split + split = fraction of work to offload to co-processor, -1 for dynamic + *ghost* value = *yes* or *no* + *yes* = include ghost atoms for offload + *no* = do not include ghost atoms for offload + *tpc* value = Ntpc + Ntpc = max number of co-processor threads per co-processor core (default = 4) + *tptask* value = Ntptask + Ntptask = max number of co-processor threads per MPI task (default = 240) + *pppm_table* value = *yes* or *no* + *yes* = Precompute pppm values in table (doesn't change accuracy) + *no* = Compute pppm values on the fly + *no_affinity* values = none + *kokkos* args = keyword value ... + zero or more keyword/value pairs may be appended + keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *atom/map* or *gpu/aware* or *pair/only* + *neigh* value = *full* or *half* + full = full neighbor list + half = half neighbor list built in thread-safe manner + *neigh/qeq* value = *full* or *half* + full = full neighbor list + half = half neighbor list built in thread-safe manner + *neigh/thread* value = *off* or *on* + *off* = thread only over atoms + *on* = thread over both atoms and neighbors + *neigh/transpose* value = *off* or *on* + *off* = use same memory layout for GPU neigh list build as pair style + *on* = use transposed memory layout for GPU neigh list build + *newton* = *off* or *on* + *off* = set Newton pairwise and bonded flags off + *on* = set Newton pairwise and bonded flags on + *binsize* value = size + size = bin size for neighbor list construction (distance units) + *comm* value = *no* or *host* or *device* + use value for comm/exchange and comm/forward and comm/pair/forward and comm/fix/forward and comm/reverse + *comm/exchange* value = *no* or *host* or *device* + *comm/forward* value = *no* or *host* or *device* + *comm/pair/forward* value = *no* or *device* + *comm/fix/forward* value = *no* or *device* + *comm/reverse* value = *no* or *host* or *device* + *no* = perform communication pack/unpack in non-KOKKOS mode + *host* = perform pack/unpack on host (e.g. with OpenMP threading) + *device* = perform pack/unpack on device (e.g. on GPU) + *comm/pair/reverse* value = *no* or *device* + *no* = perform communication pack/unpack in non-KOKKOS mode + *device* = perform pack/unpack on device (e.g. on GPU) + *sort* value = *no* or *device* + *no* = perform atom sorting in non-KOKKOS mode + *device* = perform atom sorting on device (e.g. on GPU) + *atom/map* value = *no* or *device* + *no* = build atom map in non-KOKKOS mode + *device* = build atom map on device (e.g. on GPU) + *gpu/aware* = *off* or *on* + *off* = do not use GPU-aware MPI + *on* = use GPU-aware MPI (default) + *pair/only* = *off* or *on* + *off* = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default) + *on* = use device acceleration only for pair styles (and host acceleration for others) + *omp* args = Nthreads keyword value ... + Nthreads = # of OpenMP threads to associate with each MPI process + zero or more keyword/value pairs may be appended + keywords = *neigh* + *neigh* value = *yes* or *no* + *yes* = threaded neighbor list build (default) + *no* = non-threaded neighbor list build Examples """""""" @@ -200,7 +200,7 @@ number of compute cores. If there are more devices than MPI tasks, the additional devices will be unused. The auto-selection of GPUs/ accelerator devices and platforms can be restricted by specifying a non-zero value for *Ngpu* and / or using the *gpuID*, *platform*, -and *device_type* keywords as described below. If there are more MPI +and *device\_type* keywords as described below. If there are more MPI tasks (per node) than GPUs, multiple MPI tasks will share each GPU. Optional keyword/value pairs can also be specified. Each has a @@ -274,8 +274,8 @@ the other particles. The *gpuID* keyword is used to specify the first ID for the GPU or other accelerator that LAMMPS will use. For example, if the ID is 1 and *Ngpu* is 3, GPUs 1-3 will be used. Device IDs should be -determined from the output of nvc_get_devices, ocl_get_devices, -or hip_get_devices +determined from the output of nvc\_get\_devices, ocl\_get\_devices, +or hip\_get\_devices as provided in the lib/gpu directory. When using OpenCL with accelerators that have main memory NUMA, the accelerators can be split into smaller virtual accelerators for more efficient use @@ -308,15 +308,15 @@ The meaning of *Nthreads* is exactly the same for the GPU, INTEL, and GPU packages. The *platform* keyword is only used with OpenCL to specify the ID for -an OpenCL platform. See the output from ocl_get_devices in the lib/gpu +an OpenCL platform. See the output from ocl\_get\_devices in the lib/gpu directory. In LAMMPS only one platform can be active at a time and by default (id=-1) the platform is auto-selected to find the GPU with the most compute cores. When *Ngpu* or other keywords are specified, the auto-selection is appropriately restricted. For example, if *Ngpu* is 3, only platforms with at least 3 accelerators are considered. Similar -restrictions can be enforced by the *gpuID* and *device_type* keywords. +restrictions can be enforced by the *gpuID* and *device\_type* keywords. -The *device_type* keyword can be used for OpenCL to specify the type of +The *device\_type* keyword can be used for OpenCL to specify the type of GPU to use or specify a custom configuration for an accelerator. In most cases this selection will be automatic and there is no need to use the keyword. The *applegpu* type is not specific to a particular GPU vendor, @@ -324,25 +324,25 @@ but is separate due to the more restrictive Apple OpenCL implementation. For expert users, to specify a custom configuration, the *custom* keyword followed by the next parameters can be specified: -CONFIG_ID, SIMD_SIZE, MEM_THREADS, SHUFFLE_AVAIL, FAST_MATH, -THREADS_PER_ATOM, THREADS_PER_CHARGE, THREADS_PER_THREE, BLOCK_PAIR, -BLOCK_BIO_PAIR, BLOCK_ELLIPSE, PPPM_BLOCK_1D, BLOCK_NBOR_BUILD, -BLOCK_CELL_2D, BLOCK_CELL_ID, MAX_SHARED_TYPES, MAX_BIO_SHARED_TYPES, -PPPM_MAX_SPLINE, NBOR_PREFETCH. +CONFIG\_ID, SIMD\_SIZE, MEM\_THREADS, SHUFFLE\_AVAIL, FAST\_MATH, +THREADS\_PER\_ATOM, THREADS\_PER\_CHARGE, THREADS\_PER\_THREE, BLOCK\_PAIR, +BLOCK\_BIO\_PAIR, BLOCK\_ELLIPSE, PPPM\_BLOCK\_1D, BLOCK\_NBOR\_BUILD, +BLOCK\_CELL\_2D, BLOCK\_CELL\_ID, MAX\_SHARED\_TYPES, MAX\_BIO\_SHARED\_TYPES, +PPPM\_MAX\_SPLINE, NBOR\_PREFETCH. -CONFIG_ID can be 0. SHUFFLE_AVAIL in {0,1} indicates that inline-PTX +CONFIG\_ID can be 0. SHUFFLE\_AVAIL in {0,1} indicates that inline-PTX (NVIDIA) or OpenCL extensions (Intel) should be used for horizontal -vector operations. FAST_MATH in {0,1} indicates that OpenCL fast math +vector operations. FAST\_MATH in {0,1} indicates that OpenCL fast math optimizations are used during the build and hardware-accelerated -transcendental functions are used when available. THREADS_PER_* give the +transcendental functions are used when available. THREADS\_PER\_\* give the default *tpa* values for ellipsoidal models, styles using charge, and -any other styles. The BLOCK_* parameters specify the block sizes for -various kernel calls and the MAX_*SHARED*_ parameters are used to +any other styles. The BLOCK\_\* parameters specify the block sizes for +various kernel calls and the MAX\_\*SHARED\_\* parameters are used to determine the amount of local shared memory to use for storing model parameters. For OpenCL, the routines are compiled at runtime for the specified GPU -or accelerator architecture. The *ocl_args* keyword can be used to +or accelerator architecture. The *ocl\_args* keyword can be used to specify additional flags for the runtime build. ---------- @@ -381,7 +381,7 @@ force calculation. The *lrt* keyword can be used to enable "Long Range Thread (LRT)" mode. It can take a value of *yes* to enable and *no* to disable. LRT mode generates an extra thread (in addition to any OpenMP threads -specified with the OMP_NUM_THREADS environment variable or the *omp* +specified with the OMP\_NUM\_THREADS environment variable or the *omp* keyword). The extra thread is dedicated for performing part of the :doc:`PPPM solver ` computations and communications. This can improve parallel performance on processors supporting diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst index b84202e69e..b7c33e9c86 100644 --- a/doc/src/pair_aip_water_2dm.rst +++ b/doc/src/pair_aip_water_2dm.rst @@ -53,14 +53,14 @@ materials as described in :ref:`(Feng1) ` and :ref:`(Feng2) `. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \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 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 42b9c54406..013dcbc46b 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -32,20 +32,20 @@ Description """"""""""" The *bop* pair style computes Bond-Order Potentials (BOP) based on -quantum mechanical theory incorporating both :math:`\sigma` and :math:`\pi` bonding. -By analytically deriving the BOP from quantum mechanical theory its -transferability to different phases can approach that of quantum -mechanical methods. This potential is similar to the original BOP -developed by Pettifor (:ref:`Pettifor_1 `, -:ref:`Pettifor_2 `, :ref:`Pettifor_3 `) and later updated -by Murdick, Zhou, and Ward (:ref:`Murdick `, :ref:`Ward `). -Currently, BOP potential files for these systems are provided with -LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A system with -only a subset of these elements, including a single element (e.g. C or -Cu or Al or Ga or Zn or CdZn), can also be modeled by using the -appropriate alloy file and assigning all atom types to the -single element or subset of elements via the pair_coeff command, as -discussed below. +quantum mechanical theory incorporating both :math:`\sigma` and +:math:`\pi` bonding. By analytically deriving the BOP from quantum +mechanical theory its transferability to different phases can approach +that of quantum mechanical methods. This potential is similar to the +original BOP developed by Pettifor (:ref:`Pettifor_1 `, +:ref:`Pettifor_2 `, :ref:`Pettifor_3 `) and +later updated by Murdick, Zhou, and Ward (:ref:`Murdick `, +:ref:`Ward `). Currently, BOP potential files for these systems +are provided with LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A +system with only a subset of these elements, including a single element +(e.g. C or Cu or Al or Ga or Zn or CdZn), can also be modeled by using +the appropriate alloy file and assigning all atom types to the single +element or subset of elements via the :doc:`pair_coeff command +`, as discussed below. The BOP potential consists of three terms: @@ -58,7 +58,7 @@ representing the repulsion between a pair of ion cores, :math:`\beta_{\sigma,ij}(r_{ij})` and :math:`\beta_{\sigma,ij}(r_{ij})` are respectively sigma and :math:`\pi` bond integrals, :math:`\Theta_{\sigma,ij}` and :math:`\Theta_{\pi,ij}` are :math:`\sigma` and :math:`\pi` -bond-orders, and U_prom is the promotion energy for sp-valent systems. +bond-orders, and U\_prom is the promotion energy for sp-valent systems. The detailed formulas for this potential are given in Ward (:ref:`Ward `); here we provide only a brief description. @@ -96,7 +96,7 @@ length 4. This enables the incorporation of dihedral angles effects. .. note:: Note that unlike for other potentials, cutoffs for BOP - potentials are not set in the pair_style or pair_coeff command; they + potentials are not set in the pair\_style or pair\_coeff command; they are specified in the BOP potential files themselves. Likewise, the BOP potential files list atomic masses; thus you do not need to use the :doc:`mass ` command to specify them. Note that for BOP @@ -106,7 +106,7 @@ length 4. This enables the incorporation of dihedral angles effects. :doc:`pair_coeff ` command to read the BOP potential file. -One option can be specified as a keyword with the pair_style command. +One option can be specified as a keyword with the pair\_style command. The *save* keyword gives you the option to calculate in advance and store a set of distances, angles, and derivatives of angles. The @@ -118,10 +118,10 @@ system configuration. ---------- -Only a single pair_coeff command is used with the *bop* style which +Only a single pair\_coeff command is used with the *bop* style which specifies a BOP potential file, with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, +N additional arguments after the filename in the pair\_coeff command, where N is the number of LAMMPS atom types: * filename @@ -130,7 +130,7 @@ where N is the number of LAMMPS atom types: As an example, imagine the CdTe.bop file has BOP values for Cd and Te. If your LAMMPS simulation has 4 atoms types and you want the first 3 to be Cd, and the fourth to be Te, you would use the following -pair_coeff command: +pair\_coeff command: .. code-block:: LAMMPS @@ -143,8 +143,8 @@ element in the BOP file. The final Te argument maps LAMMPS atom type BOP files in the *potentials* directory of the LAMMPS distribution have a ".bop" suffix. The potentials are in tabulated form containing -pre-tabulated pair functions for phi_ij(r_ij), beta_(sigma,ij)(r_ij), -and beta_pi,ij)(r_ij). +pre-tabulated pair functions for phi\_ij(r\_ij), beta\_(sigma,ij)(r\_ij), +and beta\_pi,ij)(r\_ij). The parameters/coefficients format for the different kinds of BOP files are given below with variables matching the formulation of Ward @@ -170,89 +170,89 @@ the tabulated functions are given. * Line 1: nr, nBOt (nr is the number of divisions the radius is broken into for function tables and MUST be a factor of 5; nBOt is the number - of divisions for the tabulated values of THETA_(S,ij) -* Line 2: delta_1-delta_7 (if all are not used in the particular + of divisions for the tabulated values of THETA\_(S,ij) +* Line 2: delta\_1-delta\_7 (if all are not used in the particular * formulation, set unused values to 0.0) -Following this N lines for e_1-e_N containing p_pi. +Following this N lines for e\_1-e\_N containing p\_pi. -* Line 3: p_pi (for e_1) -* Line 4: p_pi (for e_2 and continues to e_N) +* Line 3: p\_pi (for e\_1) +* Line 4: p\_pi (for e\_2 and continues to e\_N) The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N +interaction types e\_i-e\_j, with i=1->N, j=i->N -* Line 1: r_cut (for e_1-e_1 interactions) -* Line 2: c_sigma, a_sigma, c_pi, a_pi -* Line 3: delta_sigma, delta_pi -* Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of +* Line 1: r\_cut (for e\_1-e\_1 interactions) +* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi +* Line 3: delta\_sigma, delta\_pi +* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of the previous section but is interaction type dependent) The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N +e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N -* Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for - g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. :ref:`Ward ` +* Line 1: g\_(sigma0), g\_(sigma1), g\_(sigma2) (These are coefficients for + g\_(sigma,jik)(THETA\_ijk) for e\_1-e\_1-e\_1 interaction. :ref:`Ward ` contains the full expressions for the constants as functions of - b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) -* Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) + b\_(sigma,ijk), p\_(sigma,ijk), u\_(sigma,ijk)) +* Line 2: g\_(sigma0), g\_(sigma1), g\_(sigma2) (for e\_1-e\_1-e\_2) The next section contains a block for each interaction type for the -phi_ij(r_ij). Each block has nr entries with 5 entries per line. +phi\_ij(r\_ij). Each block has nr entries with 5 entries per line. -* Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e_1-e_1 +* Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e\_1-e\_1 interaction type) * Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues until nr) * ... -* Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the - e_1-e_1 interaction type) +* Line nr/5\_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the + e\_1-e\_1 interaction type) The next section contains a block for each interaction type for the -beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per +beta\_(sigma,ij)(r\_ij). Each block has nr entries with 5 entries per line. -* Line 1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), beta_sigma(r4), - beta_sigma(r5) (for the e_1-e_1 interaction type) -* Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9), - beta_sigma(r10) (this continues until nr) +* Line 1: beta\_sigma(r1), beta\_sigma(r2), beta\_sigma(r3), beta\_sigma(r4), + beta\_sigma(r5) (for the e\_1-e\_1 interaction type) +* Line 2: beta\_sigma(r6), beta\_sigma(r7), beta\_sigma(r8), beta\_sigma(r9), + beta\_sigma(r10) (this continues until nr) * ... -* Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), - beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) +* Line nr/5+1: beta\_sigma(r1), beta\_sigma(r2), beta\_sigma(r3), + beta\_sigma(r4), beta\_sigma(r5) (for the e\_1-e\_2 interaction type) The next section contains a block for each interaction type for -beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line. +beta\_(pi,ij)(r\_ij). Each block has nr entries with 5 entries per line. -* Line 1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), beta_pi(r5) - (for the e_1-e_1 interaction type) -* Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9), - beta_pi(r10) (this continues until nr) +* Line 1: beta\_pi(r1), beta\_pi(r2), beta\_pi(r3), beta\_pi(r4), beta\_pi(r5) + (for the e\_1-e\_1 interaction type) +* Line 2: beta\_pi(r6), beta\_pi(r7), beta\_pi(r8), beta\_pi(r9), + beta\_pi(r10) (this continues until nr) * ... -* Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), - beta_pi(r5) (for the e_1-e_2 interaction type) +* Line nr/5+1: beta\_pi(r1), beta\_pi(r2), beta\_pi(r3), beta\_pi(r4), + beta\_pi(r5) (for the e\_1-e\_2 interaction type) The next section contains a block for each interaction type for the -THETA_(S,ij)((THETA_(sigma,ij))\^(1/2), f_(sigma,ij)). Each block has +THETA\_(S,ij)((THETA\_(sigma,ij))\^(1/2), f\_(sigma,ij)). Each block has nBOt entries with 5 entries per line. -* Line 1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), - THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) -* Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8), - THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) +* Line 1: THETA\_(S,ij)(r1), THETA\_(S,ij)(r2), THETA\_(S,ij)(r3), + THETA\_(S,ij)(r4), THETA\_(S,ij)(r5) (for the e\_1-e\_2 interaction type) +* Line 2: THETA\_(S,ij)(r6), THETA\_(S,ij)(r7), THETA\_(S,ij)(r8), + THETA\_(S,ij)(r9), THETA\_(S,ij)(r10) (this continues until nBOt) * ... -* Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), - THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) +* Line nBOt/5+1: THETA\_(S,ij)(r1), THETA\_(S,ij)(r2), THETA\_(S,ij)(r3), + THETA\_(S,ij)(r4), THETA\_(S,ij)(r5) (for the e\_1-e\_2 interaction type) -The next section contains a block of N lines for e_1-e_N +The next section contains a block of N lines for e\_1-e\_N -* Line 1: delta\^mu (for e_1) -* Line 2: delta\^mu (for e_2 and repeats to e_N) +* Line 1: delta\^mu (for e\_1) +* Line 2: delta\^mu (for e\_2 and repeats to e\_N) -The last section contains more constants for e_i-e_j interactions with +The last section contains more constants for e\_i-e\_j interactions with i=0->N, j=i->N -* Line 1: (A_ij)\^(mu\*nu) (for e1-e1) -* Line 2: (A_ij)\^(mu\*nu) (for e1-e2 and repeats as above) +* Line 1: (A\_ij)\^(mu\*nu) (for e1-e1) +* Line 2: (A\_ij)\^(mu\*nu) (for e1-e2 and repeats as above) ---------- @@ -274,34 +274,34 @@ the tabulated functions are given. * Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken into for function tables and MUST be a factor of 5; ntheta is the power of the power of the spline used to fit the angular function; nBOt is the number - of divisions for the tabulated values of THETA_(S,ij) -* Line 2: delta_1-delta_7 (if all are not used in the particular + of divisions for the tabulated values of THETA\_(S,ij) +* Line 2: delta\_1-delta\_7 (if all are not used in the particular * formulation, set unused values to 0.0) -Following this N lines for e_1-e_N containing p_pi. +Following this N lines for e\_1-e\_N containing p\_pi. -* Line 3: p_pi (for e_1) -* Line 4: p_pi (for e_2 and continues to e_N) +* Line 3: p\_pi (for e\_1) +* Line 4: p\_pi (for e\_2 and continues to e\_N) The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N +interaction types e\_i-e\_j, with i=1->N, j=i->N -* Line 1: r_cut (for e_1-e_1 interactions) -* Line 2: c_sigma, a_sigma, c_pi, a_pi -* Line 3: delta_sigma, delta_pi -* Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of +* Line 1: r\_cut (for e\_1-e\_1 interactions) +* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi +* Line 3: delta\_sigma, delta\_pi +* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of the previous section but is interaction type dependent) The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N +e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N * Line 1: g0, g1, g2... (These are coefficients for the angular spline - of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The + of the g\_(sigma,jik)(THETA\_ijk) for e\_1-e\_1-e\_1 interaction. The function can contain up to 10 term thus 10 constants. The first line can contain up to five constants. If the spline has more than five terms the second line will contain the remaining constants The following lines will then contain the constants for the remaining g0, - g1, g2... (for e_1-e_1-e_2) and the other three body + g1, g2... (for e\_1-e\_1-e\_2) and the other three body interactions The rest of the table has the same structure as the previous section @@ -327,34 +327,34 @@ the tabulated functions are given. * Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken into for function tables and MUST be a factor of 5; ntheta is the number of divisions for the tabulated values of the g angular function; nBOt is the number - of divisions for the tabulated values of THETA_(S,ij) -* Line 2: delta_1-delta_7 (if all are not used in the particular + of divisions for the tabulated values of THETA\_(S,ij) +* Line 2: delta\_1-delta\_7 (if all are not used in the particular * formulation, set unused values to 0.0) -Following this N lines for e_1-e_N containing p_pi. +Following this N lines for e\_1-e\_N containing p\_pi. -* Line 3: p_pi (for e_1) -* Line 4: p_pi (for e_2 and continues to e_N) +* Line 3: p\_pi (for e\_1) +* Line 4: p\_pi (for e\_2 and continues to e\_N) The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N +interaction types e\_i-e\_j, with i=1->N, j=i->N -* Line 1: r_cut (for e_1-e_1 interactions) -* Line 2: c_sigma, a_sigma, c_pi, a_pi -* Line 3: delta_sigma, delta_pi -* Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of +* Line 1: r\_cut (for e\_1-e\_1 interactions) +* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi +* Line 3: delta\_sigma, delta\_pi +* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of the previous section but is interaction type dependent) The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N +e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N -* Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e_1-e_1-e_1 +* Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e\_1-e\_1-e\_1 interaction type) * Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues until ntheta) * ... * Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the - e_1-e_1-e_2 interaction type) + e\_1-e\_1-e\_2 interaction type) The rest of the table has the same structure as the previous section (see above). diff --git a/doc/src/pair_bpm_spring.rst b/doc/src/pair_bpm_spring.rst index 53375d86b8..19ba4cdbec 100644 --- a/doc/src/pair_bpm_spring.rst +++ b/doc/src/pair_bpm_spring.rst @@ -117,6 +117,10 @@ 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. +The potential energy and the single() function of this pair style returns +:math:`k (r - r_c)^2 / 2 + k_a (r - r_c)^4 / 4` for a proxy +of the energy of a pair interaction, ignoring any smoothing or dissipative forces. + ---------- Restrictions diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 77c0e0b18b..c673561237 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -241,9 +241,9 @@ summation method, described in :ref:`Wolf `, given by: .. math:: E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} + \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()* are error-function and complementary error-function terms. This @@ -471,7 +471,7 @@ Phys, 110, 8254 (1999). .. _Plummer1: **(Plummer)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson, -in preparation +J Chemical Physics, 162, 054709 (2025). .. _Jorgensen3: diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index a7f99500f5..5f580f9037 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -40,8 +40,8 @@ the pair style :doc:`ilp/graphene/hbn ` .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + V_{ij} = & \mathrm{Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\ + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_dispersion_d3.rst b/doc/src/pair_dispersion_d3.rst index a9249299d0..a78bf17a40 100644 --- a/doc/src/pair_dispersion_d3.rst +++ b/doc/src/pair_dispersion_d3.rst @@ -55,7 +55,7 @@ factor, and :math:`f_n^{damp}` are damping functions. contributions, according to, for example, the Axilrod-Teller-Muto model. -.. versionchanged:: TBD +.. versionchanged:: 2Apr2025 renamed *zero* keyword to *original* to avoid conflicts with :doc:`pair style zero ` when used as :doc:`hybrid diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index 1caed4689b..e84001235a 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -62,8 +62,8 @@ a sum of 3 terms \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}}\\ + 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}^\mathrm{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}^\mathrm{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` diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index c84bce9d53..2de2a124e2 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -37,10 +37,11 @@ energy of the system E is given by E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left(r_{ij}\right) + \sum_{i=1}^{N}E_i\left(q_i,\sigma_i\right) The first term is a double pairwise sum over the J neighbors of all I -atoms, where :math:`\phi_{ij}` is a pair potential. The second term sums over -the embedding energy E_i of atom I, which is a function of its charge -q_i and the electrical potential :math:`\sigma_i` at its location. E_i, q_i, -and :math:`sigma_i` are calculated as +atoms, where :math:`\phi_{ij}` is a pair potential. The second term +sums over the embedding energy :math:`E_i` of atom I, which is a +function of its charge :math:`q_i` and the electrical potential +:math:`\sigma_i` at its location. :math:`E_i`, :math:`q_i`, and +:math:`\sigma_i` are calculated as .. math:: @@ -77,7 +78,7 @@ atoms in the atomic pair. charge on each atom and thus requires you to assign a charge to each atom, e.g. the *charge* or *full* atom styles. This is because the EIM potential infers the charge on an atom from the equation above for - q_i; you do not assign charges explicitly. + :math:`q_i`; you do not assign charges explicitly. ---------- @@ -90,15 +91,15 @@ A system with any combination of these elements can be modeled. This file is parameterized in terms of LAMMPS :doc:`metal units `. Note that unlike other potentials, cutoffs for EIM potentials are not -set in the pair_style or pair_coeff command; they are specified in the +set in the pair\_style or pair\_coeff command; they are specified in the EIM potential file itself. Likewise, the EIM potential file lists atomic masses; thus you do not need to use the :doc:`mass ` command to specify them. -Only a single pair_coeff command is used with the *eim* style which +Only a single pair\_coeff command is used with the *eim* style which specifies an EIM potential file and the element(s) to extract information for. The EIM elements are mapped to LAMMPS atom types by -specifying N additional arguments after the filename in the pair_coeff +specifying N additional arguments after the filename in the pair\_coeff command, where N is the number of LAMMPS atom types: * Elem1, Elem2, ... @@ -111,7 +112,7 @@ to specify the path for the potential file. As an example like one of those above, suppose you want to model a system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms types and you want the first 3 to be Na, and the fourth to be Cl, you would -use the following pair_coeff command: +use the following pair\_coeff command: .. code-block:: LAMMPS @@ -147,9 +148,9 @@ radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive energy (LAMMPS ignores it), and q0 (must be 0). Lines starting with "pair:" are entered as: element 1, element 2, -r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e, -alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta, -r_(s,psi), and p. +r\_(c,phi), r\_(c,phi) (redundant for historical reasons), E\_b, r\_e, +alpha, beta, r\_(c,eta), A\_(eta), r\_(s,eta), r\_(c,psi), A\_(psi), zeta, +r\_(s,psi), and p. The lines in the file can be in any order; LAMMPS extracts the info it needs. diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index f54079daf1..4ae59a587f 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -29,6 +29,9 @@ Examples pair_style granular pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji + pair_style granular + pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping coeff_restitution synchronized_verlet + pair_style granular pair_coeff 1 * jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall pair_coeff 2 2 hertz 200.0 100.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall @@ -103,11 +106,12 @@ on particle *i* due to contact with particle *j* is given by: \mathbf{F}_{ne, Hooke} = k_n \delta_{ij} \mathbf{n} Where :math:`\delta_{ij} = R_i + R_j - \|\mathbf{r}_{ij}\|` is the particle -overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = \mathbf{r}_i - \mathbf{r}_j` is the vector separating the two -particle centers (note the i-j ordering so that :math:`\mathbf{F}_{ne}` is -positive for repulsion), and :math:`\mathbf{n} = \frac{\mathbf{r}_{ij}}{\|\mathbf{r}_{ij}\|}`. Therefore, -for *hooke*, the units of the spring constant :math:`k_n` are -*force*\ /\ *distance*, or equivalently *mass*\ /*time\^2*. +overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = +\mathbf{r}_i - \mathbf{r}_j` is the vector separating the two particle centers +(note the i-j ordering so that :math:`\mathbf{F}_{ne}` is positive for repulsion), +and :math:`\mathbf{n} = \frac{\mathbf{r}_{ij}}{\|\mathbf{r}_{ij}\|}`. Therefore, +for *hooke*, the units of the spring constant :math:`k_n` are *force*\ /\ +*distance*, or equivalently *mass*\ /*time\^2*. For the *hertz* model, the normal component of force is given by: @@ -313,7 +317,8 @@ following general form: \mathbf{F}_{n,damp} = -\eta_n \mathbf{v}_{n,rel} -Here, :math:`\mathbf{v}_{n,rel} = (\mathbf{v}_j - \mathbf{v}_i) \cdot \mathbf{n}\ \mathbf{n}` is the component of relative velocity along +Here, :math:`\mathbf{v}_{n,rel} = (\mathbf{v}_j - \mathbf{v}_i) \cdot +\mathbf{n}\ \mathbf{n}` is the component of relative velocity along :math:`\mathbf{n}`. The optional *damping* keyword to the *pair_coeff* command followed by @@ -488,7 +493,8 @@ the normal force: F_{n0} = \|\mathbf{F}_n\| For cohesive models such as *jkr* and *dmt*, the critical force is -adjusted so that the critical tangential force approaches :math:`\mu_t F_{pulloff}`, see :ref:`Marshall `, equation 43, and +adjusted so that the critical tangential force approaches +:math:`\mu_t F_{pulloff}`, see :ref:`Marshall `, equation 43, and :ref:`Thornton `. For both models, :math:`F_{n0}` takes the form: @@ -578,7 +584,6 @@ of :math:`a`, the radius of the contact region. The tangential force is given by \mathbf{F}_t = -\min(\mu_t F_{n0}, \|-k_t a \mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t} - Here, :math:`a` is the radius of the contact region, given by :math:`a =\sqrt{R\delta}` for all normal contact models, except for *jkr*, where it is given implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see @@ -694,9 +699,11 @@ the tangential force: \mathbf{F}_{roll,0} = k_{roll} \mathbf{\xi}_{roll} - \gamma_{roll} \mathbf{v}_{roll} -Here, :math:`\mathbf{v}_{roll} = -R(\boldsymbol{\Omega}_i - \boldsymbol{\Omega}_j) \times \mathbf{n}` is the relative rolling -velocity, as given in :ref:`Wang et al ` and -:ref:`Luding `. This differs from the expressions given by :ref:`Kuhn and Bagi ` and used in :ref:`Marshall `; see :ref:`Wang et al ` for details. The rolling displacement is given by: +Here, :math:`\mathbf{v}_{roll} = -R(\boldsymbol{\Omega}_i - \boldsymbol{\Omega}_j) +\times \mathbf{n}` is the relative rolling velocity, as given in +:ref:`Wang et al ` and :ref:`Luding `. This differs from the +expressions given by :ref:`Kuhn and Bagi ` and used in :ref:`Marshall `; +see :ref:`Wang et al ` for details. The rolling displacement is given by: .. math:: @@ -753,9 +760,10 @@ the most straightforward treatment: \tau_{twist,0} = -k_{twist}\xi_{twist} - \gamma_{twist}\Omega_{twist} -Here :math:`\xi_{twist} = \int_{t_0}^t \Omega_{twist} (\tau) \mathrm{d}\tau` is the twisting angular displacement, and -:math:`\Omega_{twist} = (\mathbf{\Omega}_i - \mathbf{\Omega}_j) \cdot \mathbf{n}` is the relative twisting angular velocity. The torque -is then truncated according to: +Here :math:`\xi_{twist} = \int_{t_0}^t \Omega_{twist} (\tau) \mathrm{d}\tau` is +the twisting angular displacement, and +:math:`\Omega_{twist} = (\mathbf{\Omega}_i - \mathbf{\Omega}_j) \cdot \mathbf{n}` +is the relative twisting angular velocity. The torque is then truncated according to: .. math:: @@ -809,6 +817,19 @@ attractive force. This keyword cannot be used with the JKR or DMT models. ---------- +The standard velocity-Verlet integration scheme's half-step staggering of +position and velocity can introduce inaccuracies in frictional tangential +force calculations, resulting in unphysical kinematics in certain systems. +These effects are particularly pronounced in polydisperse frictional flows +characterized by large-to-small size ratios exceeding three. The +*synchronized_verlet* flag implements an alternate Velocity-Verlet integration +scheme, as detailed in :ref:`Vyas et al `, that synchronizes position +and velocity updates for force evaluation. By refining tangential force +calculations, the *synchronized_verlet* method ensures physically consistent +results without significantly impacting computational cost. + +---------- + The optional *heat* keyword enables heat conduction. The options currently supported are: @@ -923,8 +944,9 @@ or E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij}^2)} -These pair styles write their information to :doc:`binary restart files `, so a pair_style command does not need to be -specified in an input script that reads a restart file. +These pair styles write their information to :doc:`binary restart files `, +so a pair_style command does 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 @@ -954,8 +976,8 @@ maximum number of extra quantities in a model but the order of quantities is determined by each model's specific set of sub-models. Any unused quantities are zeroed. -These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*, *p2*, ..., -*p12*\ . +These extra quantities can be accessed by the :doc:`compute pair/local +` command, as *p1*, *p2*, ..., *p12*\ . ---------- @@ -1118,3 +1140,8 @@ I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302. Heat conduction in granular materials. AIChE Journal, 47(5), 1052-1059. +.. _Vyas2025: + +**(Vyas et al, 2025)** Vyas D. R., Ottino J. M., Lueptow R. M., & Umbanhowar P. B. (2025). +Improved Velocity-Verlet Algorithm for the Discrete Element Method. +Computer Physics Communications, 109524. diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index a122fc5ea2..2c5059ffa9 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -68,21 +68,21 @@ force field, given by: .. math:: - E = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\ - = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\ + E = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_\mathrm{in} \\ + = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_\mathrm{in} < r < r_\mathrm{out} \\ + = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_\mathrm{out} \\ LJ(r) = & AR^{-12}-BR^{-10}cos^n\theta= \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}- 6\left[ \frac{\sigma}{r}\right]^{10} \right\rbrace cos^n\theta\\ Morse(r) = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta= D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right\rbrace cos^n\theta \\ - S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} - { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } + S(r) = & \frac{ \left[r_\mathrm{out}^2 - r^2\right]^2 + \left[r_\mathrm{out}^2 + 2r^2 - 3{r_\mathrm{in}^2}\right]} + { \left[r_\mathrm{out}^2 - {r_\mathrm{in}}^2\right]^3 } -where :math:`r_{\rm in}` is the inner spline distance cutoff, -:math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is +where :math:`r_\mathrm{in}` is the inner spline distance cutoff, +:math:`r_\mathrm{out}` is the outer distance cutoff, :math:`\theta_c` is the angle cutoff, and :math:`n` is the power of the cosine of the angle :math:`\theta`. @@ -189,8 +189,8 @@ follows: * :math:`\epsilon` (energy units) * :math:`\sigma` (distance units) * *n* = exponent in formula above -* distance cutoff :math:`r_{\rm in}` (distance units) -* distance cutoff :math:`r_{\rm out}` (distance units) +* distance cutoff :math:`r_\mathrm{in}` (distance units) +* distance cutoff :math:`r_\mathrm{out}` (distance units) * angle cutoff (degrees) For the *hbond/dreiding/morse* style the list of coefficients is as @@ -202,7 +202,7 @@ follows: * :math:`\alpha` (1/distance units) * :math:`r_0` (distance units) * *n* = exponent in formula above -* distance cutoff :math:`r_{\rm in}` (distance units) +* distance cutoff :math:`r_\mathrm{in}` (distance units) * distance cutoff :math:`r_{out}` (distance units) * angle cutoff (degrees) diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index 36e971ef62..e50509497f 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -44,14 +44,14 @@ in :ref:`(Kolmogorov) `. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \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 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_ilp_tmd.rst b/doc/src/pair_ilp_tmd.rst index 575bafdc91..f486f73c69 100644 --- a/doc/src/pair_ilp_tmd.rst +++ b/doc/src/pair_ilp_tmd.rst @@ -41,14 +41,14 @@ as described in :ref:`(Ouyang7) ` and :ref:`(Jiang) `. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \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 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 @@ -67,7 +67,7 @@ calculating the normals. normal vectors used for graphene and h-BN is no longer valid for TMDs. In :ref:`(Ouyang7) `, a new definition is proposed, where for each atom `i`, its six nearest neighboring atoms belonging to the same - sub-layer are chosen to define the normal vector `{\bf n}_i`. + sub-layer are chosen to define the normal vector `\mathbf{n}_i`. The parameter file (e.g. TMD.ILP), is intended for use with *metal* :doc:`units `, with energies in meV. Two additional parameters, diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 1a4706dd6f..2af56cbf9b 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -37,8 +37,8 @@ No simplification is made, 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} \\ - \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 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot \mathbf{n}_{i})^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot \mathbf{n}_{j})^2 \\ f(\rho) & = e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n} It is important to have a sufficiently large cutoff to ensure smooth diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 1a099e009b..b1e25cfc9f 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -68,7 +68,7 @@ LJ cutoff specified in the pair_style command is used. Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing distance for the potential, *not* as the energy minimum at -:math:`r_0 = 2^{\frac{1}{6}} \sigma`. The _same_ potential function becomes: +:math:`r_0 = 2^{\frac{1}{6}} \sigma`. The *same* potential function becomes: .. math:: diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index aa5f7a2620..da39ac1645 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -194,9 +194,9 @@ summation method, described in :ref:`Wolf `, given by: .. math:: E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} + \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and erfc() is the complementary error-function terms. This potential is essentially a diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 6674b013ba..269701ee27 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -200,7 +200,7 @@ force :math:`F_{ij}^C` are expressed as \mathbf{F}_{ij}^{D} & = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij} \\ \mathbf{F}_{ij}^{R} & = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij} \\ \omega_{C}(r) & = 1 - r/r_c \\ - \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^{\rm power_f} \\ + \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^\mathrm{power_f} \\ \sigma^2 = 2\gamma k_B T The concentration flux between two tDPD particles includes the Fickian @@ -211,7 +211,7 @@ by Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\ Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\ - w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power_{cc}} \\ + w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^\mathrm{power_{cc}} \\ \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho where the parameters kappa and epsilon determine the strength of the diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 92bf9cd738..e492e555ac 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -33,7 +33,7 @@ elemental bulk material in the form .. math:: - E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega ) + E_\mathrm{tot}(\mathbf{R}_1 \ldots \mathbf{R}_N) = NE_\mathrm{vol}(\Omega ) + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega ) + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega ) + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega ) diff --git a/doc/src/pair_saip_metal.rst b/doc/src/pair_saip_metal.rst index ed011894c9..211e5e9359 100644 --- a/doc/src/pair_saip_metal.rst +++ b/doc/src/pair_saip_metal.rst @@ -41,14 +41,14 @@ potential (ILP) potential for hetero-junctions formed with hexagonal .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \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 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 @@ -63,8 +63,8 @@ calculating the normals. .. note:: To account for the isotropic nature of the isolated gold atom - electron cloud, their corresponding normal vectors (`{\bf n}_i`) are - assumed to lie along the interatomic vector `{\bf r}_ij`. Notably, this + electron cloud, their corresponding normal vectors (`\mathbf{n}_i`) are + assumed to lie along the interatomic vector `\mathbf{r}_ij`. Notably, this assumption is suitable for many bulk material surfaces, for example, for systems possessing s-type valence orbitals or metallic surfaces, whose valence electrons are mostly diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index c38bba03ae..faa2bc7461 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -43,7 +43,7 @@ vector omega and mechanical force between particles I and J. .. math:: - \mathcal{H}_{\rm long} & = + \mathcal{H}_\mathrm{long} & = -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi} \sum_{i,j,i\neq j}^{N} \frac{g_i g_j}{r_{ij}^3} diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 282da39ff7..bb98c72d84 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -52,7 +52,7 @@ particle i: .. math:: \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) - ~~{\rm and}~~ + ~~\mathrm{and}~~ \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) More details about the derivation of these torques/forces are reported in diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index 553af72983..a922c45a8d 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -94,7 +94,7 @@ submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} \left(r_{ij} \right)\,\vec{s}_{j} - ~~{\rm and}~~ + ~~\mathrm{and}~~ \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij} diff --git a/doc/src/region2vmd.rst b/doc/src/region2vmd.rst index 54216bb925..792155d9eb 100644 --- a/doc/src/region2vmd.rst +++ b/doc/src/region2vmd.rst @@ -33,9 +33,9 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 2Apr2025 -Write a `VMD `_ Tcl script file with +Write a `VMD `_ Tcl script file with commands that aim to create a visualization of :doc:`regions `. There may be multiple region visualizations stored in a single file. diff --git a/doc/src/timer.rst b/doc/src/timer.rst index 13d5a92473..46a67c89b2 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -87,7 +87,7 @@ negative, if the timeout time is expired and positive if there is time remaining and in this case the value of the variable are the number of seconds remaining. -When the *timeout* key word is used a second time, the timer is +When the *timeout* keyword is used a second time, the timer is restarted with a new time limit. The timeout *elapse* value can be specified as *off* or *unlimited* to impose a no timeout condition (which is the default). The *elapse* setting can be specified as diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 2b59aeb65d..75a13e47e1 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -51,12 +51,12 @@ Syntax thermo keywords = vol, ke, press, etc from :doc:`thermo_style ` math operators = (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x - math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), + math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), - vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x) + vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) group functions = count(group), mass(group), charge(group), xcm(group,dim), vcm(group,dim), fcm(group,dim), bound(group,dir), gyration(group), ke(group), @@ -541,7 +541,7 @@ variables. +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x | +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x) | +| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) | +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) | +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ @@ -692,6 +692,11 @@ sqrt() of the product of one atom's y and z coordinates. Most of the math functions perform obvious operations. The ln() is the natural log; log() is the base 10 log. +.. versionadded:: 4Feb2025 + +The sign(x) function returns 1.0 if the value is greater than or equal +to 0.0, and -1.0 otherwise. + The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z = seed. It generates a uniform random number between lo and hi. The normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and @@ -860,9 +865,6 @@ run, according to one of these formulas, where omega = 2 PI / period: where dt = the timestep size. -The sign(x) function returns 1.0 if the value is greater than or equal -to 0.0, and -1.0 otherwise. - The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. 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+$abstract$ +
+$endif$ +
+$endif$ +$if(toc)$ + +$endif$ +$body$ +$for(include-after)$ +$include-after$ +$endfor$ + + diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index d842f47c11..fbb161baa5 100644 --- a/doc/utils/requirements.txt +++ b/doc/utils/requirements.txt @@ -1,4 +1,4 @@ -Sphinx >= 5.3.0, <8.2.0 +Sphinx >= 5.3.0, <8.3.0 sphinxcontrib-spelling sphinxcontrib-jquery sphinx-design diff --git a/doc/utils/sphinx-config/_static/up.png b/doc/utils/sphinx-config/_static/up.png new file mode 100644 index 0000000000..2a940a7da7 Binary files /dev/null and b/doc/utils/sphinx-config/_static/up.png differ diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html index 83fdb7054b..e78b54f8f0 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html @@ -129,7 +129,7 @@
{#- SIDE NAV, TOGGLES ON MOBILE #}
diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index e4b461397d..073143a7e9 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -208,13 +208,11 @@ html_favicon = '_static/lammps.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ['_static',] # These paths are either relative to html_static_path # or fully qualified paths (eg. https://...) -html_css_files = [ - 'css/lammps.css', -] +html_css_files = ['css/lammps.css',] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 621507d389..f4ef07c39e 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -8,6 +8,7 @@ abi abo Abramyan absTol +Acad Acc Accelerys Accelrys @@ -340,6 +341,7 @@ bodyflag bodyforce bodystyle Bogaerts +Bogoliubov Bogusz Bohrs boltz @@ -359,6 +361,8 @@ boostostat boostostatting Boresch borophene +bosonic +bosons Botero Botu Bouguet @@ -724,6 +728,7 @@ dashpot dat datafile datatype +dataset datums Davidchack Daw @@ -735,6 +740,7 @@ dE De deallocate deallocated +deallocation debye Debye Decius @@ -855,6 +861,7 @@ DNi Dobnikar Dobson docenv +docstrings Dodds dodgerblue dof @@ -1082,6 +1089,7 @@ estretch esu esub esw +esynch et etag etap @@ -1145,6 +1153,7 @@ fdotr fdt fe Fehlberg +Feldman Fellinger femtosecond femtoseconds @@ -1154,6 +1163,8 @@ Fennell fep FEP fermi +fermion +fermions Fermionic Ferrand fexternal @@ -1194,6 +1205,7 @@ Finnis Fiorin fitpod fivebody +fixcom fixID fj Fji @@ -1214,6 +1226,7 @@ fmag fmass fmatch fmm +fmmode fmt fmtlib fmx @@ -1324,10 +1337,12 @@ geturl gewald Gezelter gfile +gflag Gflop gfortran ghostneigh ghostwhite +Ghahremanpour Giacomo GiB gif @@ -1488,6 +1503,7 @@ hgrid hhmrr Hibbs Higdon +Higer hiID Hijazi Hilger @@ -2079,6 +2095,7 @@ lubricateU lucas lucy Luding +Lueptow Luijten lunit Lunkad @@ -2613,6 +2630,7 @@ nn nnodes npits npj +nmpimd nO Nocedal nocite @@ -2741,6 +2759,7 @@ nylo nz Nz nzlo +obabo ochre ocl octahedral @@ -2770,6 +2789,7 @@ omegaz Omelyan omp OMP +ondulated oneAPI onebody onelevel @@ -2805,6 +2825,7 @@ orthorhombic Ortner os oso +Ottino Otype Ouadfel Ouldridge @@ -2940,6 +2961,7 @@ Pieniazek Pieter pIm pimd +pimdb Piola pIp pipelining @@ -2953,6 +2975,7 @@ pKa pKb pKs planeforce +plastically Plathe Plimpton plog @@ -3103,9 +3126,11 @@ qE qeff qelectron qeq +qeqr Qamar QeQ QEq +QEqR qfactor qfile qi @@ -3248,6 +3273,7 @@ resquared REsquared restartfile restartinfo +reStructuredText Restrepo rethrowing Revenga @@ -3255,6 +3281,7 @@ rewrap rezwanur rfac rfile +rflag rg Rg Rhaphson @@ -3289,6 +3316,7 @@ RiRj Risi Rix Riy +Rizzi rj Rj Rjinner @@ -3722,6 +3750,7 @@ Tanmoy Tartakovsky taskset taubi +taup Tavenner taylor tb @@ -3940,6 +3969,7 @@ uloop ulsph Ultrafast uMech +Umbanhowar umin Umin un @@ -3995,6 +4025,7 @@ username usleep usolve usr +utf util utils utsa diff --git a/examples/COUPLE/multiple/in.chain b/examples/COUPLE/multiple/in.chain index ed72441aa1..6aa3b455ad 100644 --- a/examples/COUPLE/multiple/in.chain +++ b/examples/COUPLE/multiple/in.chain @@ -1,5 +1,5 @@ # FENE beadspring benchmark - +variable t index 1.0 units lj atom_style bond special_bonds fene diff --git a/examples/COUPLE/plugin/liblammpsplugin.c b/examples/COUPLE/plugin/liblammpsplugin.c index 619b8828fc..87cf58729c 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.c +++ b/examples/COUPLE/plugin/liblammpsplugin.c @@ -204,6 +204,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(has_error); ADDSYM(get_last_error_message); } + ADDSYM(set_show_error); ADDSYM(python_api_version); return lmp; diff --git a/examples/COUPLE/plugin/liblammpsplugin.h b/examples/COUPLE/plugin/liblammpsplugin.h index c765b0adc3..3732b3a5c0 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.h +++ b/examples/COUPLE/plugin/liblammpsplugin.h @@ -24,7 +24,7 @@ * Follow the behavior of regular LAMMPS compilation and assume * -DLAMMPS_SMALLBIG when no define is set. */ -#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL) +#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) #define LAMMPS_SMALLBIG #endif @@ -100,8 +100,6 @@ extern "C" { #if defined(LAMMPS_BIGBIG) typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **); -#elif defined(LAMMPS_SMALLSMALL) -typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **); #else typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **); #endif @@ -111,6 +109,7 @@ struct _liblammpsplugin { int abiversion; int has_exceptions; void *handle; + #if defined(LAMMPS_LIB_MPI) void *(*open)(int, char **, MPI_Comm, void **); #else @@ -189,7 +188,7 @@ struct _liblammpsplugin { * the ifdef ensures they are compatible with rest of LAMMPS * caller must match to how LAMMPS library is built */ -#ifndef LAMMPS_BIGBIG +#if !defined(LAMMPS_BIGBIG) int (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int); #else int (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int); @@ -257,6 +256,7 @@ struct _liblammpsplugin { int (*has_error)(void *); int (*get_last_error_message)(void *, char *, int); + int (*set_show_error)(void *, const int); int (*python_api_version)(); }; diff --git a/examples/PACKAGES/atc/elastic/Au_u3.eam b/examples/PACKAGES/atc/elastic/Au_u3.eam new file mode 120000 index 0000000000..2ace8a4162 --- /dev/null +++ b/examples/PACKAGES/atc/elastic/Au_u3.eam @@ -0,0 +1 @@ +../../../../potentials/Au_u3.eam \ No newline at end of file diff --git a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long index 91ddddf4ec..29315a5901 100644 --- a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long +++ b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long @@ -15,12 +15,12 @@ Masses PairIJ Coeffs # dpd/coul/slater/long -1 1 78 4.5 yes 1 -1 2 78 4.5 yes 1 -1 3 78 4.5 yes 1 -2 2 78 4.5 no 1 -2 3 78 4.5 no 1 -3 3 78 4.5 no 1 +1 1 78 4.5 no 1 +1 2 78 4.5 no 1 +1 3 78 4.5 no 1 +2 2 78 4.5 yes 1 +2 3 78 4.5 yes 1 +3 3 78 4.5 yes 1 Atoms # full diff --git a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long index bd405aad37..dc73aa887b 100644 --- a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long +++ b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long @@ -10,49 +10,47 @@ variable cut_coul equal 2.0 # Initialize LAMMPS run for 3-d periodic #------------------------------------------------------------------------------- -units lj -boundary p p p # periodic at all axes -atom_style full -dimension 3 +units lj +boundary p p p # periodic at all axes +atom_style full +dimension 3 -bond_style none -angle_style none -dihedral_style none -improper_style none +bond_style none +angle_style none +dihedral_style none +improper_style none -newton on -comm_modify vel yes # store info of ghost atoms btw processors +newton on +comm_modify vel yes # store info of ghost atoms btw processors #------------------------------------------------------------------------------- # Box creation and configuration #------------------------------------------------------------------------------- # Define pair style and coefficients -pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul} - -read_data data.dpd_coul_slater_long +pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul} # Enable long range electrostatics solver -kspace_style pppm 1e-04 +kspace_style pppm 1e-04 + +read_data data.dpd_coul_slater_long # Construct neighbors every steps -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes #------------------------------------------------------------------------------- # Run the simulation #------------------------------------------------------------------------------- -thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax -thermo_modify norm no -thermo 100 +thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax +thermo_modify norm no +thermo 100 -timestep 0.01 -run_style verlet +timestep 0.01 +run_style verlet -fix 1 all nve +fix 1 all nve -run 1000 - -unfix 1 +run 1000 diff --git a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.1 b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.1 deleted file mode 100644 index 39c0ded481..0000000000 --- a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.1 +++ /dev/null @@ -1,147 +0,0 @@ -LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# DPD Ionic Fluid - -variable T equal 1.0 -variable cut_DPD equal 1.0 -variable seed equal 165412 -variable lambda equal 0.25 -variable cut_coul equal 2.0 - -#------------------------------------------------------------------------------- -# Initialize LAMMPS run for 3-d periodic -#------------------------------------------------------------------------------- - -units lj -boundary p p p # periodic at all axes -atom_style full -dimension 3 - -bond_style none -angle_style none -dihedral_style none -improper_style none - -newton on -comm_modify vel yes # store info of ghost atoms btw processors - -#------------------------------------------------------------------------------- -# Box creation and configuration -#------------------------------------------------------------------------------- - -# Define pair style and coefficients -pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul} -pair_style dpd/coul/slater/long 1 1 165412 0.25 2 - -read_data data.dpd_coul_slater_long -Reading data file ... - orthogonal box = (0 0 0) to (5 5 5) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 375 atoms - reading velocities ... - 375 velocities -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.003 seconds - -# Enable long range electrostatics solver -kspace_style pppm 1e-04 - -# Construct neighbors every steps -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -#------------------------------------------------------------------------------- -# Run the simulation -#------------------------------------------------------------------------------- - -thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax -thermo_modify norm no -thermo 100 - -timestep 0.01 -run_style verlet - -fix 1 all nve - -run 1000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 1.4828454 - grid = 20 20 20 - stencil order = 5 - estimated absolute RMS force accuracy = 7.7240141e-05 - estimated relative force accuracy = 7.7240141e-05 - using double precision FFTW3 - 3d grid and FFT values/proc = 24389 8000 -Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3 - ghost atom cutoff = 3 - binsize = 1.5, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair dpd/coul/slater/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes - Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax - 0 0.9849949 69.271905 125 4673.0443 0 -30.365103 4642.6792 552.58214 646.76798 65.851035 - 100 1.0614027 69.794624 125 4659.0139 0 -31.906319 4627.1075 595.44692 612.94396 60.338653 - 200 0.9422517 68.721098 125 4687.8862 0 -33.81531 4654.0709 528.6032 620.25627 62.726994 - 300 0.8956649 69.323482 125 4721.0824 0 -33.854275 4687.2281 502.46801 670.22699 73.087908 - 400 0.99584547 69.670416 125 4713.9086 0 -30.783633 4683.125 558.66931 607.65881 59.224652 - 500 1.0565931 69.497816 125 4701.2584 0 -26.80545 4674.4529 592.74873 646.18907 71.398122 - 600 1.0071523 70.26222 125 4659.2061 0 -29.98909 4629.217 565.01243 630.00244 58.264115 - 700 1.0507355 67.920078 125 4695.255 0 -32.649209 4662.6058 589.46259 651.80459 70.573524 - 800 0.98561942 68.279591 125 4745.7603 0 -28.98491 4716.7754 552.9325 627.14371 67.196483 - 900 0.96470105 70.742864 125 4706.3605 0 -30.271633 4676.0889 541.19729 644.43036 79.474998 - 1000 1.0204819 70.164419 125 4654.6077 0 -27.797433 4626.8103 572.49035 624.19728 71.825307 -Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms - -Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/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 | 1.1779 | 1.1779 | 1.1779 | 0.0 | 56.05 -Bond | 6.507e-05 | 6.507e-05 | 6.507e-05 | 0.0 | 0.00 -Kspace | 0.74636 | 0.74636 | 0.74636 | 0.0 | 35.51 -Neigh | 0.12903 | 0.12903 | 0.12903 | 0.0 | 6.14 -Comm | 0.039726 | 0.039726 | 0.039726 | 0.0 | 1.89 -Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 0.01 -Modify | 0.0037596 | 0.0037596 | 0.0037596 | 0.0 | 0.18 -Other | | 0.004451 | | | 0.21 - -Nlocal: 375 ave 375 max 375 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3613 ave 3613 max 3613 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62354 ave 62354 max 62354 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 62354 -Ave neighs/atom = 166.27733 -Ave special neighs/atom = 0 -Neighbor list builds = 65 -Dangerous builds = 0 - -unfix 1 - -Total wall time: 0:00:02 diff --git a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.4 b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.4 deleted file mode 100644 index 445baac0f7..0000000000 --- a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.4 +++ /dev/null @@ -1,147 +0,0 @@ -LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# DPD Ionic Fluid - -variable T equal 1.0 -variable cut_DPD equal 1.0 -variable seed equal 165412 -variable lambda equal 0.25 -variable cut_coul equal 2.0 - -#------------------------------------------------------------------------------- -# Initialize LAMMPS run for 3-d periodic -#------------------------------------------------------------------------------- - -units lj -boundary p p p # periodic at all axes -atom_style full -dimension 3 - -bond_style none -angle_style none -dihedral_style none -improper_style none - -newton on -comm_modify vel yes # store info of ghost atoms btw processors - -#------------------------------------------------------------------------------- -# Box creation and configuration -#------------------------------------------------------------------------------- - -# Define pair style and coefficients -pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul} -pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul} -pair_style dpd/coul/slater/long 1 1 165412 0.25 2 - -read_data data.dpd_coul_slater_long -Reading data file ... - orthogonal box = (0 0 0) to (5 5 5) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 375 atoms - reading velocities ... - 375 velocities -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.003 seconds - -# Enable long range electrostatics solver -kspace_style pppm 1e-04 - -# Construct neighbors every steps -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -#------------------------------------------------------------------------------- -# Run the simulation -#------------------------------------------------------------------------------- - -thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax -thermo_modify norm no -thermo 100 - -timestep 0.01 -run_style verlet - -fix 1 all nve - -run 1000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 1.4828454 - grid = 20 20 20 - stencil order = 5 - estimated absolute RMS force accuracy = 7.7240141e-05 - estimated relative force accuracy = 7.7240141e-05 - using double precision FFTW3 - 3d grid and FFT values/proc = 10469 2000 -Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3 - ghost atom cutoff = 3 - binsize = 1.5, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair dpd/coul/slater/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes - Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax - 0 0.9849949 69.076433 125 4673.0443 0 -30.365103 4642.6792 552.58214 613.18374 70.700582 - 100 0.95374867 69.110009 125 4681.1097 0 -31.260804 4649.8489 535.053 629.95109 62.05418 - 200 1.0076152 69.824904 125 4670.7458 0 -28.382203 4642.3636 565.27213 656.8501 72.049813 - 300 1.0014752 69.666331 125 4696.454 0 -26.943577 4669.5105 561.8276 631.49861 74.737274 - 400 0.98863876 69.731774 125 4700.7552 0 -23.816077 4676.9391 554.62634 637.74742 68.928573 - 500 0.95782852 68.588075 125 4698.588 0 -29.249543 4669.3385 537.3418 646.31897 68.800569 - 600 0.97443232 70.864079 125 4674.8821 0 -26.415644 4648.4664 546.65653 606.50755 78.664429 - 700 0.98783988 68.908299 125 4692.5536 0 -28.092022 4664.4616 554.17817 638.98401 69.691814 - 800 0.98000145 69.83977 125 4706.6365 0 -29.648365 4676.9881 549.78082 626.84362 73.133934 - 900 1.0526251 69.466078 125 4671.9648 0 -30.941117 4641.0237 590.52269 618.1049 62.333546 - 1000 0.98340746 69.527121 125 4728.2894 0 -31.869907 4696.4195 551.69159 630.14208 61.392611 -Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms - -Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/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 | 0.30761 | 0.34974 | 0.38864 | 4.9 | 37.67 -Bond | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 | 0.0 | 0.01 -Kspace | 0.39038 | 0.42976 | 0.47215 | 4.4 | 46.28 -Neigh | 0.033986 | 0.035576 | 0.036791 | 0.5 | 3.83 -Comm | 0.10247 | 0.10324 | 0.10481 | 0.3 | 11.12 -Output | 0.00024145 | 0.00027404 | 0.00036867 | 0.0 | 0.03 -Modify | 0.0022402 | 0.0025068 | 0.0026343 | 0.3 | 0.27 -Other | | 0.007356 | | | 0.79 - -Nlocal: 93.75 ave 96 max 93 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 2289.75 ave 2317 max 2271 min -Histogram: 1 1 0 0 1 0 0 0 0 1 -Neighs: 15590.2 ave 16765 max 14540 min -Histogram: 1 0 1 0 0 1 0 0 0 1 - -Total # of neighbors = 62361 -Ave neighs/atom = 166.296 -Ave special neighs/atom = 0 -Neighbor list builds = 64 -Dangerous builds = 0 - -unfix 1 - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.1 b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.1 new file mode 100644 index 0000000000..4b2509550f --- /dev/null +++ b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.1 @@ -0,0 +1,145 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# DPD Ionic Fluid + +variable T equal 1.0 +variable cut_DPD equal 1.0 +variable seed equal 165412 +variable lambda equal 0.25 +variable cut_coul equal 2.0 + +#------------------------------------------------------------------------------- +# Initialize LAMMPS run for 3-d periodic +#------------------------------------------------------------------------------- + +units lj +boundary p p p # periodic at all axes +atom_style full +dimension 3 + +bond_style none +angle_style none +dihedral_style none +improper_style none + +newton on +comm_modify vel yes # store info of ghost atoms btw processors + +#------------------------------------------------------------------------------- +# Box creation and configuration +#------------------------------------------------------------------------------- + +# Define pair style and coefficients +pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul} +pair_style dpd/coul/slater/long 1 1 165412 0.25 2 + +# Enable long range electrostatics solver +kspace_style pppm 1e-04 + +read_data data.dpd_coul_slater_long +Reading data file ... + orthogonal box = (0 0 0) to (5 5 5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 375 atoms + reading velocities ... + 375 velocities +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.004 seconds + +# Construct neighbors every steps +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +#------------------------------------------------------------------------------- +# Run the simulation +#------------------------------------------------------------------------------- + +thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax +thermo_modify norm no +thermo 100 + +timestep 0.01 +run_style verlet + +fix 1 all nve + +run 1000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 1.4828454 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 7.7240141e-05 + estimated relative force accuracy = 7.7240141e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 24389 8000 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3 + ghost atom cutoff = 3 + binsize = 1.5, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair dpd/coul/slater/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes + Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax + 0 0.9849949 69.242343 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 646.89929 65.851035 + 100 1.023885 69.716134 125 4676.9465 -4.9878506 -34.092864 4637.8658 574.39949 663.35845 94.350026 + 200 1.0286646 69.674249 125 4636.201 -4.6314926 -33.406897 4598.1626 577.08087 614.52805 62.295431 + 300 0.9745797 69.689534 125 4679.9157 -4.3964184 -30.560567 4644.9588 546.73921 603.46282 60.56253 + 400 0.99487931 69.17085 125 4678.0362 -4.9518269 -34.446596 4638.6378 558.12729 656.99738 88.090014 + 500 0.97732377 69.551562 125 4684.3709 -5.0851581 -33.863212 4645.4226 548.27864 647.12533 75.851935 + 600 0.95396337 68.358297 125 4706.824 -4.269168 -33.634096 4668.9207 535.17345 604.31276 63.41042 + 700 0.99397324 68.365109 125 4669.1062 -4.700146 -35.014001 4629.3921 557.61899 633.29262 74.300913 + 800 1.0157864 69.263686 125 4664.1398 -4.0142381 -34.372669 4625.7529 569.85616 595.81462 67.046561 + 900 0.9925779 70.008922 125 4652.3023 -2.7845751 -33.095293 4616.4224 556.8362 620.13154 82.785317 + 1000 0.97336501 68.973657 125 4688.8002 -5.5239266 -36.42345 4646.8529 546.05777 625.66451 64.948859 +Loop time of 0.755094 on 1 procs for 1000 steps with 375 atoms + +Performance: 1144228.093 tau/day, 1324.338 timesteps/s, 496.627 katom-step/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 | 0.14421 | 0.14421 | 0.14421 | 0.0 | 19.10 +Bond | 3.8885e-05 | 3.8885e-05 | 3.8885e-05 | 0.0 | 0.01 +Kspace | 0.53292 | 0.53292 | 0.53292 | 0.0 | 70.58 +Neigh | 0.056741 | 0.056741 | 0.056741 | 0.0 | 7.51 +Comm | 0.017676 | 0.017676 | 0.017676 | 0.0 | 2.34 +Output | 0.00024925 | 0.00024925 | 0.00024925 | 0.0 | 0.03 +Modify | 0.0016688 | 0.0016688 | 0.0016688 | 0.0 | 0.22 +Other | | 0.001588 | | | 0.21 + +Nlocal: 375 ave 375 max 375 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3570 ave 3570 max 3570 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19729 ave 19729 max 19729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19729 +Ave neighs/atom = 52.610667 +Ave special neighs/atom = 0 +Neighbor list builds = 66 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.4 b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.4 new file mode 100644 index 0000000000..52d50716c9 --- /dev/null +++ b/examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.4 @@ -0,0 +1,145 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# DPD Ionic Fluid + +variable T equal 1.0 +variable cut_DPD equal 1.0 +variable seed equal 165412 +variable lambda equal 0.25 +variable cut_coul equal 2.0 + +#------------------------------------------------------------------------------- +# Initialize LAMMPS run for 3-d periodic +#------------------------------------------------------------------------------- + +units lj +boundary p p p # periodic at all axes +atom_style full +dimension 3 + +bond_style none +angle_style none +dihedral_style none +improper_style none + +newton on +comm_modify vel yes # store info of ghost atoms btw processors + +#------------------------------------------------------------------------------- +# Box creation and configuration +#------------------------------------------------------------------------------- + +# Define pair style and coefficients +pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul} +pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul} +pair_style dpd/coul/slater/long 1 1 165412 0.25 2 + +# Enable long range electrostatics solver +kspace_style pppm 1e-04 + +read_data data.dpd_coul_slater_long +Reading data file ... + orthogonal box = (0 0 0) to (5 5 5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 375 atoms + reading velocities ... + 375 velocities +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +# Construct neighbors every steps +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +#------------------------------------------------------------------------------- +# Run the simulation +#------------------------------------------------------------------------------- + +thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax +thermo_modify norm no +thermo 100 + +timestep 0.01 +run_style verlet + +fix 1 all nve + +run 1000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 1.4828454 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 7.7240141e-05 + estimated relative force accuracy = 7.7240141e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 10469 2000 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3 + ghost atom cutoff = 3 + binsize = 1.5, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair dpd/coul/slater/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes + Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax + 0 0.9849949 69.04687 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 613.14254 70.700582 + 100 1.0206537 69.308834 125 4676.3153 -4.5693306 -33.647673 4638.0983 572.58672 630.70953 76.020236 + 200 0.99990746 68.572978 125 4707.1556 -3.4977853 -33.275671 4670.3821 560.94809 633.00167 77.040049 + 300 0.91055241 69.390592 125 4685.5268 -2.9764038 -29.986737 4652.5637 510.8199 614.61006 62.799933 + 400 1.0080135 69.442971 125 4677.3078 -4.8740989 -32.908722 4639.525 565.49557 649.20121 61.033612 + 500 0.99500653 68.275189 125 4718.6774 -4.2475783 -35.206868 4679.223 558.19867 657.3073 74.738502 + 600 1.052925 70.601712 125 4703.6749 -2.8511316 -34.085418 4666.7383 590.69094 641.70441 59.043346 + 700 0.96467445 69.502018 125 4720.4257 -4.3345734 -34.310005 4681.7811 541.18237 656.24965 72.433637 + 800 1.0657358 70.960958 125 4685.5637 -5.8903418 -35.207202 4644.4661 597.87781 595.54446 61.462159 + 900 1.0273388 68.735518 125 4693.5106 -2.4175829 -28.602387 4662.4906 576.33707 598.80294 71.747886 + 1000 0.9702835 69.885576 125 4701.4385 -3.6513555 -29.487331 4668.2999 544.32904 666.55262 73.231425 +Loop time of 0.270344 on 4 procs for 1000 steps with 375 atoms + +Performance: 3195929.791 tau/day, 3698.993 timesteps/s, 1.387 Matom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031268 | 0.035485 | 0.039491 | 1.6 | 13.13 +Bond | 3.3378e-05 | 3.4848e-05 | 3.5667e-05 | 0.0 | 0.01 +Kspace | 0.18632 | 0.19083 | 0.19556 | 0.8 | 70.59 +Neigh | 0.012413 | 0.012991 | 0.013598 | 0.4 | 4.81 +Comm | 0.028195 | 0.028407 | 0.028626 | 0.1 | 10.51 +Output | 0.00013369 | 0.00015738 | 0.00022498 | 0.0 | 0.06 +Modify | 0.00055373 | 0.00059062 | 0.00068807 | 0.0 | 0.22 +Other | | 0.001846 | | | 0.68 + +Nlocal: 93.75 ave 95 max 92 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 2286 ave 2307 max 2269 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 4945 ave 5443 max 4513 min +Histogram: 1 0 1 0 0 1 0 0 0 1 + +Total # of neighbors = 19780 +Ave neighs/atom = 52.746667 +Ave special neighs/atom = 0 +Neighbor list builds = 66 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pafi/in.pafi b/examples/PACKAGES/pafi/in.pafi index 9e9efb156b..ebfe419a6d 100644 --- a/examples/PACKAGES/pafi/in.pafi +++ b/examples/PACKAGES/pafi/in.pafi @@ -9,7 +9,7 @@ read_data pafipath.4.data fix pa NULL PafiPath ## EAM potential pair_style eam/fs -pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe +pair_coeff * * Fe_mm.eam.fs Fe mass * 55.85 thermo 100 diff --git a/examples/PACKAGES/pimd_bosonic/README b/examples/PACKAGES/pimd_bosonic/README new file mode 100644 index 0000000000..9e8e3cf527 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/README @@ -0,0 +1,11 @@ +This directory contains example input files for the pimd/nvt/bosonic and pimd/langevin/bosonic fix commands. +The demonstrated system is that of 3 non-interacting bosons in a harmonic trap. +The input files initiate a simulation of 100 steps using 4 beads. The expected output log files are included. + +The input files can be edited to provide a physically meaningful output, by extending the simulations to a few nanoseconds +and increasing the number of beads (32 beads should be enough). +The total energy can be computed by summing the potential energy and either the virial or primitive kinetic energy estimator, and averaging over time. +Notice that for pimd/langevin/bosonic the summed value of either kinetic estimator is printed across all log files. +It should be taken from a single log file, with all files providing the same output. +For pimd/nvt/bosonic, one has to sum over the output of all log files. For the potential energy, summing over log files is required for both fix commands. +The obtained energy should be compared to the analytical value of 0.00058031 Hartree. diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp new file mode 100644 index 0000000000..f5d984eed4 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp @@ -0,0 +1,57 @@ +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no + +# Outputs +variable prim_kinetic equal f_pimdb[5] +variable virial equal f_pimdb[6] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ new file mode 100644 index 0000000000..3d91f7ea87 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ @@ -0,0 +1,2 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Running on 4 partitions of processors diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0 new file mode 100644 index 0000000000..cb5c5c236a --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0 @@ -0,0 +1,238 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 0 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188891 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no +fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no + +# Outputs +variable prim_kinetic equal f_pimdb[5] +variable virial equal f_pimdb[6] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +Initializing PI Langevin equation thermostat... + Bead ID | omega | tau | c1 | c2 + 0 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02 + 1 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02 + 2 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02 + 3 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02 + PILE_L thermostat successfully initialized! + +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 1.3661449e-08 0.0009918329 + 1 1.3158398e-09 1.8742641e-09 0.00099182267 + 2 5.0818396e-09 7.1801177e-09 0.00099180053 + 3 1.2446727e-08 1.4372388e-08 0.00099176038 + 4 2.1754941e-08 3.1274072e-08 0.00099170266 + 5 3.2927703e-08 5.2470231e-08 0.00099162511 + 6 4.7293056e-08 7.2301291e-08 0.00099153 + 7 6.526455e-08 9.5440683e-08 0.00099141194 + 8 8.6974168e-08 1.1669162e-07 0.00099127168 + 9 1.1249595e-07 1.3551097e-07 0.00099109846 + 10 1.4190482e-07 1.6050328e-07 0.00099089759 + 11 1.7313555e-07 1.8645705e-07 0.0009906735 + 12 2.0672874e-07 2.1181418e-07 0.00099042271 + 13 2.4042615e-07 2.4218941e-07 0.00099012073 + 14 2.7524432e-07 2.7507982e-07 0.00098977876 + 15 3.1513375e-07 3.1771012e-07 0.00098940169 + 16 3.6161087e-07 3.6075963e-07 0.00098900826 + 17 4.0813191e-07 4.0059005e-07 0.00098859985 + 18 4.5194598e-07 4.3883585e-07 0.00098817535 + 19 4.9898075e-07 4.8036287e-07 0.00098770764 + 20 5.5458728e-07 5.2362451e-07 0.00098721266 + 21 6.1220768e-07 5.7705077e-07 0.00098670407 + 22 6.6573849e-07 6.3271105e-07 0.00098617081 + 23 7.2475089e-07 6.9382916e-07 0.00098557406 + 24 7.804837e-07 7.5979853e-07 0.0009849612 + 25 8.3194987e-07 8.232213e-07 0.00098434971 + 26 8.8723792e-07 8.9901705e-07 0.0009836645 + 27 9.3837241e-07 9.7033126e-07 0.0009830068 + 28 9.897077e-07 1.0444697e-06 0.00098229311 + 29 1.043431e-06 1.1208219e-06 0.00098150213 + 30 1.0900368e-06 1.1899315e-06 0.00098077686 + 31 1.1303314e-06 1.2560026e-06 0.00098003518 + 32 1.1725968e-06 1.3287355e-06 0.00097921099 + 33 1.2081344e-06 1.399856e-06 0.0009784037 + 34 1.2449387e-06 1.4769272e-06 0.00097754491 + 35 1.2852285e-06 1.5642459e-06 0.00097667479 + 36 1.3234189e-06 1.6571388e-06 0.00097572641 + 37 1.3666391e-06 1.7603492e-06 0.00097475881 + 38 1.4102743e-06 1.8666516e-06 0.00097373763 + 39 1.454172e-06 1.9696572e-06 0.0009727081 + 40 1.5031422e-06 2.0910539e-06 0.00097155807 + 41 1.5538491e-06 2.2198868e-06 0.00097030871 + 42 1.6079193e-06 2.3576614e-06 0.00096896762 + 43 1.6637051e-06 2.496284e-06 0.00096760456 + 44 1.7189714e-06 2.637657e-06 0.00096619083 + 45 1.7656688e-06 2.795845e-06 0.00096470693 + 46 1.8092153e-06 2.9727162e-06 0.00096303835 + 47 1.8415769e-06 3.1451673e-06 0.00096140406 + 48 1.8664597e-06 3.3241907e-06 0.00095971129 + 49 1.8940033e-06 3.5094834e-06 0.00095790964 + 50 1.9211844e-06 3.7049195e-06 0.00095603039 + 51 1.9533838e-06 3.9139587e-06 0.0009540918 + 52 1.9833776e-06 4.1289537e-06 0.0009520767 + 53 2.0106231e-06 4.3481079e-06 0.00095003676 + 54 2.0429292e-06 4.5702968e-06 0.00094802906 + 55 2.0747842e-06 4.7928135e-06 0.00094600351 + 56 2.1043981e-06 5.0253448e-06 0.0009438419 + 57 2.1474343e-06 5.2569331e-06 0.00094169256 + 58 2.2115003e-06 5.4997767e-06 0.00093948055 + 59 2.2773037e-06 5.7547729e-06 0.00093714003 + 60 2.3402972e-06 6.0074589e-06 0.00093480857 + 61 2.4107157e-06 6.2647899e-06 0.00093244785 + 62 2.4953095e-06 6.5384938e-06 0.00092998209 + 63 2.58923e-06 6.8124372e-06 0.00092751453 + 64 2.682021e-06 7.0913777e-06 0.00092505171 + 65 2.7538688e-06 7.3773956e-06 0.00092256944 + 66 2.8444661e-06 7.6811232e-06 0.00091984092 + 67 2.9532286e-06 7.9951107e-06 0.0009170037 + 68 3.0551339e-06 8.3096758e-06 0.00091414977 + 69 3.1625164e-06 8.6232285e-06 0.00091137219 + 70 3.2717759e-06 8.9388929e-06 0.00090857909 + 71 3.3924986e-06 9.2524846e-06 0.00090583473 + 72 3.5236727e-06 9.5688611e-06 0.00090308342 + 73 3.6440162e-06 9.8873586e-06 0.00090026584 + 74 3.7692169e-06 1.0203245e-05 0.00089755256 + 75 3.8946044e-06 1.0523755e-05 0.00089485804 + 76 4.0498738e-06 1.0848398e-05 0.00089217189 + 77 4.2099346e-06 1.1164286e-05 0.00088956967 + 78 4.3589564e-06 1.1466652e-05 0.00088700311 + 79 4.5069481e-06 1.177381e-05 0.00088439373 + 80 4.6635354e-06 1.2059606e-05 0.00088199635 + 81 4.8398269e-06 1.233837e-05 0.0008797438 + 82 5.0191539e-06 1.261531e-05 0.00087745162 + 83 5.205285e-06 1.2899972e-05 0.00087506863 + 84 5.3708116e-06 1.3160246e-05 0.00087288444 + 85 5.5534416e-06 1.3438712e-05 0.00087052617 + 86 5.7613e-06 1.372546e-05 0.00086818634 + 87 5.9645662e-06 1.4017631e-05 0.00086572407 + 88 6.1830289e-06 1.4328439e-05 0.000862992 + 89 6.423646e-06 1.4640964e-05 0.00086017364 + 90 6.688219e-06 1.4978644e-05 0.0008570595 + 91 6.9305603e-06 1.5307214e-05 0.00085411601 + 92 7.1857573e-06 1.5649328e-05 0.00085112325 + 93 7.4653538e-06 1.6015833e-05 0.0008479391 + 94 7.8132911e-06 1.6393131e-05 0.00084474237 + 95 8.1540941e-06 1.674573e-05 0.00084165639 + 96 8.4943231e-06 1.7094435e-05 0.00083858996 + 97 8.8504733e-06 1.7451741e-05 0.00083536142 + 98 9.2042324e-06 1.780703e-05 0.00083221292 + 99 9.5058078e-06 1.8141862e-05 0.00082913227 + 100 9.8087647e-06 1.8457846e-05 0.00082619877 +Loop time of 0.00116399 on 1 procs for 100 steps with 3 atoms + +Performance: 3711359336.904 fs/day, 0.000 hours/fs, 85911.096 timesteps/s, 257.733 katom-step/s +89.8% 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 | 1.292e-06 | 1.292e-06 | 1.292e-06 | 0.0 | 0.11 +Comm | 1.2305e-05 | 1.2305e-05 | 1.2305e-05 | 0.0 | 1.06 +Output | 0.00018105 | 0.00018105 | 0.00018105 | 0.0 | 15.55 +Modify | 0.00090255 | 0.00090255 | 0.00090255 | 0.0 | 77.54 +Other | | 6.68e-05 | | | 5.74 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 33 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1 new file mode 100644 index 0000000000..a170220ef0 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1 @@ -0,0 +1,230 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 1 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188892 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no +fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no + +# Outputs +variable prim_kinetic equal f_pimdb[5] +variable virial equal f_pimdb[6] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 1.3661449e-08 0.0009918329 + 1 7.3810761e-10 1.8742641e-09 0.00099182267 + 2 3.0654593e-09 7.1801177e-09 0.00099180053 + 3 6.4534507e-09 1.4372388e-08 0.00099176038 + 4 1.1681892e-08 3.1274072e-08 0.00099170266 + 5 1.8404818e-08 5.2470231e-08 0.00099162511 + 6 2.6171374e-08 7.2301291e-08 0.00099153 + 7 3.5990441e-08 9.5440683e-08 0.00099141194 + 8 4.9770229e-08 1.1669162e-07 0.00099127168 + 9 6.6159035e-08 1.3551097e-07 0.00099109846 + 10 8.7281867e-08 1.6050328e-07 0.00099089759 + 11 1.1505206e-07 1.8645705e-07 0.0009906735 + 12 1.4564491e-07 2.1181418e-07 0.00099042271 + 13 1.8674942e-07 2.4218941e-07 0.00099012073 + 14 2.3275077e-07 2.7507982e-07 0.00098977876 + 15 2.833552e-07 3.1771012e-07 0.00098940169 + 16 3.3078875e-07 3.6075963e-07 0.00098900826 + 17 3.7783787e-07 4.0059005e-07 0.00098859985 + 18 4.3007763e-07 4.3883585e-07 0.00098817535 + 19 4.8592613e-07 4.8036287e-07 0.00098770764 + 20 5.4429898e-07 5.2362451e-07 0.00098721266 + 21 6.0140068e-07 5.7705077e-07 0.00098670407 + 22 6.6036274e-07 6.3271105e-07 0.00098617081 + 23 7.3748601e-07 6.9382916e-07 0.00098557406 + 24 8.1086859e-07 7.5979853e-07 0.0009849612 + 25 8.8638234e-07 8.232213e-07 0.00098434971 + 26 9.8252709e-07 8.9901705e-07 0.0009836645 + 27 1.0768657e-06 9.7033126e-07 0.0009830068 + 28 1.1810654e-06 1.0444697e-06 0.00098229311 + 29 1.2964318e-06 1.1208219e-06 0.00098150213 + 30 1.4097624e-06 1.1899315e-06 0.00098077686 + 31 1.5368367e-06 1.2560026e-06 0.00098003518 + 32 1.6777082e-06 1.3287355e-06 0.00097921099 + 33 1.8186759e-06 1.399856e-06 0.0009784037 + 34 1.9730383e-06 1.4769272e-06 0.00097754491 + 35 2.1285065e-06 1.5642459e-06 0.00097667479 + 36 2.2809575e-06 1.6571388e-06 0.00097572641 + 37 2.4393024e-06 1.7603492e-06 0.00097475881 + 38 2.6212592e-06 1.8666516e-06 0.00097373763 + 39 2.8115312e-06 1.9696572e-06 0.0009727081 + 40 3.0115212e-06 2.0910539e-06 0.00097155807 + 41 3.2325069e-06 2.2198868e-06 0.00097030871 + 42 3.4582526e-06 2.3576614e-06 0.00096896762 + 43 3.6838101e-06 2.496284e-06 0.00096760456 + 44 3.9267475e-06 2.637657e-06 0.00096619083 + 45 4.1942569e-06 2.795845e-06 0.00096470693 + 46 4.4694976e-06 2.9727162e-06 0.00096303835 + 47 4.7570486e-06 3.1451673e-06 0.00096140406 + 48 5.0917213e-06 3.3241907e-06 0.00095971129 + 49 5.4581889e-06 3.5094834e-06 0.00095790964 + 50 5.8607381e-06 3.7049195e-06 0.00095603039 + 51 6.2673583e-06 3.9139587e-06 0.0009540918 + 52 6.6764632e-06 4.1289537e-06 0.0009520767 + 53 7.0828028e-06 4.3481079e-06 0.00095003676 + 54 7.4858144e-06 4.5702968e-06 0.00094802906 + 55 7.8711706e-06 4.7928135e-06 0.00094600351 + 56 8.2756726e-06 5.0253448e-06 0.0009438419 + 57 8.6667628e-06 5.2569331e-06 0.00094169256 + 58 9.0585083e-06 5.4997767e-06 0.00093948055 + 59 9.4634766e-06 5.7547729e-06 0.00093714003 + 60 9.8696653e-06 6.0074589e-06 0.00093480857 + 61 1.0308345e-05 6.2647899e-06 0.00093244785 + 62 1.0757919e-05 6.5384938e-06 0.00092998209 + 63 1.1183568e-05 6.8124372e-06 0.00092751453 + 64 1.1585073e-05 7.0913777e-06 0.00092505171 + 65 1.1993605e-05 7.3773956e-06 0.00092256944 + 66 1.2382612e-05 7.6811232e-06 0.00091984092 + 67 1.2768116e-05 7.9951107e-06 0.0009170037 + 68 1.3181941e-05 8.3096758e-06 0.00091414977 + 69 1.3605472e-05 8.6232285e-06 0.00091137219 + 70 1.4027012e-05 8.9388929e-06 0.00090857909 + 71 1.4471706e-05 9.2524846e-06 0.00090583473 + 72 1.4896833e-05 9.5688611e-06 0.00090308342 + 73 1.5345003e-05 9.8873586e-06 0.00090026584 + 74 1.5779905e-05 1.0203245e-05 0.00089755256 + 75 1.6189898e-05 1.0523755e-05 0.00089485804 + 76 1.6654778e-05 1.0848398e-05 0.00089217189 + 77 1.7131363e-05 1.1164286e-05 0.00088956967 + 78 1.7572176e-05 1.1466652e-05 0.00088700311 + 79 1.8000817e-05 1.177381e-05 0.00088439373 + 80 1.838117e-05 1.2059606e-05 0.00088199635 + 81 1.8762432e-05 1.233837e-05 0.0008797438 + 82 1.9099052e-05 1.261531e-05 0.00087745162 + 83 1.9507863e-05 1.2899972e-05 0.00087506863 + 84 1.9885648e-05 1.3160246e-05 0.00087288444 + 85 2.0266439e-05 1.3438712e-05 0.00087052617 + 86 2.0612316e-05 1.372546e-05 0.00086818634 + 87 2.0959061e-05 1.4017631e-05 0.00086572407 + 88 2.13065e-05 1.4328439e-05 0.000862992 + 89 2.1634898e-05 1.4640964e-05 0.00086017364 + 90 2.2023174e-05 1.4978644e-05 0.0008570595 + 91 2.2431573e-05 1.5307214e-05 0.00085411601 + 92 2.2872283e-05 1.5649328e-05 0.00085112325 + 93 2.338476e-05 1.6015833e-05 0.0008479391 + 94 2.3912199e-05 1.6393131e-05 0.00084474237 + 95 2.437725e-05 1.674573e-05 0.00084165639 + 96 2.4828999e-05 1.7094435e-05 0.00083858996 + 97 2.5286762e-05 1.7451741e-05 0.00083536142 + 98 2.5769956e-05 1.780703e-05 0.00083221292 + 99 2.624134e-05 1.8141862e-05 0.00082913227 + 100 2.6731735e-05 1.8457846e-05 0.00082619877 +Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms + +Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s +88.4% 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 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.773e-06 | 1.773e-06 | 1.773e-06 | 0.0 | 0.15 +Comm | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 | 0.0 | 1.27 +Output | 0.00021888 | 0.00021888 | 0.00021888 | 0.0 | 18.58 +Modify | 0.00086503 | 0.00086503 | 0.00086503 | 0.0 | 73.42 +Other | | 7.754e-05 | | | 6.58 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 44 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2 new file mode 100644 index 0000000000..cb5b5a1a95 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2 @@ -0,0 +1,230 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 2 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188893 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no +fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no + +# Outputs +variable prim_kinetic equal f_pimdb[5] +variable virial equal f_pimdb[6] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 1.3661449e-08 0.0009918329 + 1 8.3480048e-10 1.8742641e-09 0.00099182267 + 2 2.8201389e-09 7.1801177e-09 0.00099180053 + 3 7.3605781e-09 1.4372388e-08 0.00099176038 + 4 1.4967393e-08 3.1274072e-08 0.00099170266 + 5 2.4978087e-08 5.2470231e-08 0.00099162511 + 6 3.5908849e-08 7.2301291e-08 0.00099153 + 7 4.8226614e-08 9.5440683e-08 0.00099141194 + 8 6.3621045e-08 1.1669162e-07 0.00099127168 + 9 8.0119736e-08 1.3551097e-07 0.00099109846 + 10 9.7965614e-08 1.6050328e-07 0.00099089759 + 11 1.1538858e-07 1.8645705e-07 0.0009906735 + 12 1.365443e-07 2.1181418e-07 0.00099042271 + 13 1.5920175e-07 2.4218941e-07 0.00099012073 + 14 1.8252589e-07 2.7507982e-07 0.00098977876 + 15 2.0858909e-07 3.1771012e-07 0.00098940169 + 16 2.3676046e-07 3.6075963e-07 0.00098900826 + 17 2.689757e-07 4.0059005e-07 0.00098859985 + 18 3.0022172e-07 4.3883585e-07 0.00098817535 + 19 3.3127637e-07 4.8036287e-07 0.00098770764 + 20 3.6044366e-07 5.2362451e-07 0.00098721266 + 21 3.8484646e-07 5.7705077e-07 0.00098670407 + 22 4.1435067e-07 6.3271105e-07 0.00098617081 + 23 4.4508994e-07 6.9382916e-07 0.00098557406 + 24 4.7879333e-07 7.5979853e-07 0.0009849612 + 25 5.0918223e-07 8.232213e-07 0.00098434971 + 26 5.4733661e-07 8.9901705e-07 0.0009836645 + 27 5.7932115e-07 9.7033126e-07 0.0009830068 + 28 6.1775401e-07 1.0444697e-06 0.00098229311 + 29 6.6883535e-07 1.1208219e-06 0.00098150213 + 30 7.0943445e-07 1.1899315e-06 0.00098077686 + 31 7.4477897e-07 1.2560026e-06 0.00098003518 + 32 7.8183156e-07 1.3287355e-06 0.00097921099 + 33 8.1987667e-07 1.399856e-06 0.0009784037 + 34 8.5514962e-07 1.4769272e-06 0.00097754491 + 35 8.9607784e-07 1.5642459e-06 0.00097667479 + 36 9.4986753e-07 1.6571388e-06 0.00097572641 + 37 1.0024729e-06 1.7603492e-06 0.00097475881 + 38 1.0526731e-06 1.8666516e-06 0.00097373763 + 39 1.103419e-06 1.9696572e-06 0.0009727081 + 40 1.1640352e-06 2.0910539e-06 0.00097155807 + 41 1.2292837e-06 2.2198868e-06 0.00097030871 + 42 1.3024454e-06 2.3576614e-06 0.00096896762 + 43 1.3788736e-06 2.496284e-06 0.00096760456 + 44 1.4503248e-06 2.637657e-06 0.00096619083 + 45 1.5334106e-06 2.795845e-06 0.00096470693 + 46 1.6246777e-06 2.9727162e-06 0.00096303835 + 47 1.715884e-06 3.1451673e-06 0.00096140406 + 48 1.8096683e-06 3.3241907e-06 0.00095971129 + 49 1.916714e-06 3.5094834e-06 0.00095790964 + 50 2.0374848e-06 3.7049195e-06 0.00095603039 + 51 2.1747488e-06 3.9139587e-06 0.0009540918 + 52 2.3236882e-06 4.1289537e-06 0.0009520767 + 53 2.4790586e-06 4.3481079e-06 0.00095003676 + 54 2.6478101e-06 4.5702968e-06 0.00094802906 + 55 2.8275135e-06 4.7928135e-06 0.00094600351 + 56 3.0338638e-06 5.0253448e-06 0.0009438419 + 57 3.2428318e-06 5.2569331e-06 0.00094169256 + 58 3.4414566e-06 5.4997767e-06 0.00093948055 + 59 3.6324968e-06 5.7547729e-06 0.00093714003 + 60 3.8269172e-06 6.0074589e-06 0.00093480857 + 61 4.0183315e-06 6.2647899e-06 0.00093244785 + 62 4.2263009e-06 6.5384938e-06 0.00092998209 + 63 4.4382735e-06 6.8124372e-06 0.00092751453 + 64 4.6488232e-06 7.0913777e-06 0.00092505171 + 65 4.8707403e-06 7.3773956e-06 0.00092256944 + 66 5.1178339e-06 7.6811232e-06 0.00091984092 + 67 5.377713e-06 7.9951107e-06 0.0009170037 + 68 5.63843e-06 8.3096758e-06 0.00091414977 + 69 5.8975743e-06 8.6232285e-06 0.00091137219 + 70 6.168921e-06 8.9388929e-06 0.00090857909 + 71 6.4488238e-06 9.2524846e-06 0.00090583473 + 72 6.7115203e-06 9.5688611e-06 0.00090308342 + 73 6.995134e-06 9.8873586e-06 0.00090026584 + 74 7.284199e-06 1.0203245e-05 0.00089755256 + 75 7.6029528e-06 1.0523755e-05 0.00089485804 + 76 7.9431391e-06 1.0848398e-05 0.00089217189 + 77 8.2768015e-06 1.1164286e-05 0.00088956967 + 78 8.6058917e-06 1.1466652e-05 0.00088700311 + 79 8.9683477e-06 1.177381e-05 0.00088439373 + 80 9.3324487e-06 1.2059606e-05 0.00088199635 + 81 9.6876036e-06 1.233837e-05 0.0008797438 + 82 1.0061754e-05 1.261531e-05 0.00087745162 + 83 1.0457019e-05 1.2899972e-05 0.00087506863 + 84 1.0866064e-05 1.3160246e-05 0.00087288444 + 85 1.1298832e-05 1.3438712e-05 0.00087052617 + 86 1.1762526e-05 1.372546e-05 0.00086818634 + 87 1.2264941e-05 1.4017631e-05 0.00086572407 + 88 1.2784125e-05 1.4328439e-05 0.000862992 + 89 1.332533e-05 1.4640964e-05 0.00086017364 + 90 1.3897966e-05 1.4978644e-05 0.0008570595 + 91 1.4473024e-05 1.5307214e-05 0.00085411601 + 92 1.5067033e-05 1.5649328e-05 0.00085112325 + 93 1.5677943e-05 1.6015833e-05 0.0008479391 + 94 1.6254294e-05 1.6393131e-05 0.00084474237 + 95 1.6791089e-05 1.674573e-05 0.00084165639 + 96 1.7362795e-05 1.7094435e-05 0.00083858996 + 97 1.7961498e-05 1.7451741e-05 0.00083536142 + 98 1.8568337e-05 1.780703e-05 0.00083221292 + 99 1.9188379e-05 1.8141862e-05 0.00082913227 + 100 1.9789011e-05 1.8457846e-05 0.00082619877 +Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms + +Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s +89.6% 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 | 1.582e-06 | 1.582e-06 | 1.582e-06 | 0.0 | 0.14 +Comm | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 | 0.0 | 1.15 +Output | 0.00017996 | 0.00017996 | 0.00017996 | 0.0 | 15.49 +Modify | 0.00090771 | 0.00090771 | 0.00090771 | 0.0 | 78.14 +Other | | 5.907e-05 | | | 5.09 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 41 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3 new file mode 100644 index 0000000000..a587bfd3af --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3 @@ -0,0 +1,230 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 3 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188894 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no +fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no + +# Outputs +variable prim_kinetic equal f_pimdb[5] +variable virial equal f_pimdb[6] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 1.3661449e-08 0.0009918329 + 1 8.448696e-10 1.8742641e-09 0.00099182267 + 2 3.5286528e-09 7.1801177e-09 0.00099180053 + 3 8.2936659e-09 1.4372388e-08 0.00099176038 + 4 1.4586045e-08 3.1274072e-08 0.00099170266 + 5 2.4161875e-08 5.2470231e-08 0.00099162511 + 6 3.8801085e-08 7.2301291e-08 0.00099153 + 7 5.9758384e-08 9.5440683e-08 0.00099141194 + 8 8.5838823e-08 1.1669162e-07 0.00099127168 + 9 1.1684437e-07 1.3551097e-07 0.00099109846 + 10 1.4954974e-07 1.6050328e-07 0.00099089759 + 11 1.8686687e-07 1.8645705e-07 0.0009906735 + 12 2.2747543e-07 2.1181418e-07 0.00099042271 + 13 2.807392e-07 2.4218941e-07 0.00099012073 + 14 3.3827867e-07 2.7507982e-07 0.00098977876 + 15 3.9918359e-07 3.1771012e-07 0.00098940169 + 16 4.6034561e-07 3.6075963e-07 0.00098900826 + 17 5.2315136e-07 4.0059005e-07 0.00098859985 + 18 5.8457073e-07 4.3883585e-07 0.00098817535 + 19 6.5273892e-07 4.8036287e-07 0.00098770764 + 20 7.2150647e-07 5.2362451e-07 0.00098721266 + 21 8.0596691e-07 5.7705077e-07 0.00098670407 + 22 8.946994e-07 6.3271105e-07 0.00098617081 + 23 9.9120142e-07 6.9382916e-07 0.00098557406 + 24 1.09722e-06 7.5979853e-07 0.0009849612 + 25 1.2053692e-06 8.232213e-07 0.00098434971 + 26 1.3196547e-06 8.9901705e-07 0.0009836645 + 27 1.4380033e-06 9.7033126e-07 0.0009830068 + 28 1.5700587e-06 1.0444697e-06 0.00098229311 + 29 1.7089133e-06 1.1208219e-06 0.00098150213 + 30 1.839944e-06 1.1899315e-06 0.00098077686 + 31 1.9718088e-06 1.2560026e-06 0.00098003518 + 32 2.1244847e-06 1.3287355e-06 0.00097921099 + 33 2.2823018e-06 1.399856e-06 0.0009784037 + 34 2.4607034e-06 1.4769272e-06 0.00097754491 + 35 2.6410061e-06 1.5642459e-06 0.00097667479 + 36 2.8395019e-06 1.6571388e-06 0.00097572641 + 37 3.0476467e-06 1.7603492e-06 0.00097475881 + 38 3.2661567e-06 1.8666516e-06 0.00097373763 + 39 3.4857766e-06 1.9696572e-06 0.0009727081 + 40 3.7310241e-06 2.0910539e-06 0.00097155807 + 41 3.9947356e-06 2.2198868e-06 0.00097030871 + 42 4.2722057e-06 2.3576614e-06 0.00096896762 + 43 4.5444932e-06 2.496284e-06 0.00096760456 + 44 4.8307956e-06 2.637657e-06 0.00096619083 + 45 5.1356773e-06 2.795845e-06 0.00096470693 + 46 5.4835294e-06 2.9727162e-06 0.00096303835 + 47 5.8235502e-06 3.1451673e-06 0.00096140406 + 48 6.1541132e-06 3.3241907e-06 0.00095971129 + 49 6.4796693e-06 3.5094834e-06 0.00095790964 + 50 6.8009213e-06 3.7049195e-06 0.00095603039 + 51 7.1253629e-06 3.9139587e-06 0.0009540918 + 52 7.4712081e-06 4.1289537e-06 0.0009520767 + 53 7.8322309e-06 4.3481079e-06 0.00095003676 + 54 8.1941694e-06 4.5702968e-06 0.00094802906 + 55 8.579188e-06 4.7928135e-06 0.00094600351 + 56 8.9656493e-06 5.0253448e-06 0.0009438419 + 57 9.351102e-06 5.2569331e-06 0.00094169256 + 58 9.7645407e-06 5.4997767e-06 0.00093948055 + 59 1.0230434e-05 5.7547729e-06 0.00093714003 + 60 1.0724041e-05 6.0074589e-06 0.00093480857 + 61 1.1207453e-05 6.2647899e-06 0.00093244785 + 62 1.171285e-05 6.5384938e-06 0.00092998209 + 63 1.221299e-05 6.8124372e-06 0.00092751453 + 64 1.2743686e-05 7.0913777e-06 0.00092505171 + 65 1.3295725e-05 7.3773956e-06 0.00092256944 + 66 1.3906023e-05 7.6811232e-06 0.00091984092 + 67 1.4511348e-05 7.9951107e-06 0.0009170037 + 68 1.5116776e-05 8.3096758e-06 0.00091414977 + 69 1.571005e-05 8.6232285e-06 0.00091137219 + 70 1.6297136e-05 8.9388929e-06 0.00090857909 + 71 1.6849099e-05 9.2524846e-06 0.00090583473 + 72 1.7417168e-05 9.5688611e-06 0.00090308342 + 73 1.7971613e-05 9.8873586e-06 0.00090026584 + 74 1.8509472e-05 1.0203245e-05 0.00089755256 + 75 1.9047825e-05 1.0523755e-05 0.00089485804 + 76 1.9510646e-05 1.0848398e-05 0.00089217189 + 77 1.9903304e-05 1.1164286e-05 0.00088956967 + 78 2.0300948e-05 1.1466652e-05 0.00088700311 + 79 2.0696905e-05 1.177381e-05 0.00088439373 + 80 2.1058218e-05 1.2059606e-05 0.00088199635 + 81 2.139726e-05 1.233837e-05 0.0008797438 + 82 2.1755155e-05 1.261531e-05 0.00087745162 + 83 2.2051018e-05 1.2899972e-05 0.00087506863 + 84 2.2294567e-05 1.3160246e-05 0.00087288444 + 85 2.2559076e-05 1.3438712e-05 0.00087052617 + 86 2.2815918e-05 1.372546e-05 0.00086818634 + 87 2.3062616e-05 1.4017631e-05 0.00086572407 + 88 2.3324206e-05 1.4328439e-05 0.000862992 + 89 2.3559323e-05 1.4640964e-05 0.00086017364 + 90 2.3792776e-05 1.4978644e-05 0.0008570595 + 91 2.3990667e-05 1.5307214e-05 0.00085411601 + 92 2.4198637e-05 1.5649328e-05 0.00085112325 + 93 2.4419398e-05 1.6015833e-05 0.0008479391 + 94 2.4625252e-05 1.6393131e-05 0.00084474237 + 95 2.4816363e-05 1.674573e-05 0.00084165639 + 96 2.4982897e-05 1.7094435e-05 0.00083858996 + 97 2.5153682e-05 1.7451741e-05 0.00083536142 + 98 2.5288512e-05 1.780703e-05 0.00083221292 + 99 2.5384836e-05 1.8141862e-05 0.00082913227 + 100 2.5401412e-05 1.8457846e-05 0.00082619877 +Loop time of 0.00116067 on 1 procs for 100 steps with 3 atoms + +Performance: 3721997782.310 fs/day, 0.000 hours/fs, 86157.356 timesteps/s, 258.472 katom-step/s +88.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.441e-06 | 1.441e-06 | 1.441e-06 | 0.0 | 0.12 +Comm | 1.2111e-05 | 1.2111e-05 | 1.2111e-05 | 0.0 | 1.04 +Output | 0.00018148 | 0.00018148 | 0.00018148 | 0.0 | 15.64 +Modify | 0.0009054 | 0.0009054 | 0.0009054 | 0.0 | 78.01 +Other | | 6.023e-05 | | | 5.19 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 42 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/run.sh b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/run.sh new file mode 100644 index 0000000000..c1329f646a --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/run.sh @@ -0,0 +1 @@ +mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp new file mode 100644 index 0000000000..56d6d3932a --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp @@ -0,0 +1,60 @@ +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Number of Nose-Hoover chains +variable nhc equal 4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc} + +# Outputs +variable virial equal f_pimdb[3] +variable prim_kinetic equal f_pimdb[4] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ new file mode 100644 index 0000000000..3d91f7ea87 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ @@ -0,0 +1,2 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Running on 4 partitions of processors diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0 new file mode 100644 index 0000000000..460e1cf198 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0 @@ -0,0 +1,237 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 0 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Number of Nose-Hoover chains +variable nhc equal 4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188891 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 + +# Outputs +variable virial equal f_pimdb[3] +variable prim_kinetic equal f_pimdb[4] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.2139311e-05 (kcal/mol/A^2) + +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 0 0.00024794798 + 1 8.5849317e-10 4.5664581e-10 0.00024794215 + 2 3.4338094e-09 1.3424585e-09 0.00024793325 + 3 7.7255501e-09 2.6573351e-09 0.00024792129 + 4 1.3733112e-08 4.4011211e-09 0.00024790626 + 5 2.1455686e-08 6.5736113e-09 0.00024788818 + 6 3.0892259e-08 9.1745487e-09 0.00024786704 + 7 4.2041614e-08 1.2203626e-08 0.00024784285 + 8 5.4902328e-08 1.5660483e-08 0.0002478156 + 9 6.9472776e-08 1.9544712e-08 0.00024778532 + 10 8.5751128e-08 2.385585e-08 0.00024775199 + 11 1.0373535e-07 2.8593386e-08 0.00024771564 + 12 1.234232e-07 3.3756758e-08 0.00024767626 + 13 1.4481225e-07 3.9345352e-08 0.00024763386 + 14 1.6789985e-07 4.5358504e-08 0.00024758844 + 15 1.9268316e-07 5.1795501e-08 0.00024754003 + 16 2.1915914e-07 5.8655576e-08 0.00024748862 + 17 2.4732452e-07 6.5937915e-08 0.00024743423 + 18 2.7717588e-07 7.3641654e-08 0.00024737686 + 19 3.0870956e-07 8.1765876e-08 0.00024731653 + 20 3.4192172e-07 9.0309618e-08 0.00024725324 + 21 3.7680831e-07 9.9271863e-08 0.00024718701 + 22 4.1336509e-07 1.0865155e-07 0.00024711785 + 23 4.5158762e-07 1.1844756e-07 0.00024704578 + 24 4.9147126e-07 1.2865874e-07 0.0002469708 + 25 5.3301119e-07 1.3928387e-07 0.00024689293 + 26 5.7620236e-07 1.5032169e-07 0.00024681218 + 27 6.2103957e-07 1.6177089e-07 0.00024672857 + 28 6.675174e-07 1.7363012e-07 0.00024664212 + 29 7.1563024e-07 1.8589798e-07 0.00024655283 + 30 7.6537229e-07 1.9857299e-07 0.00024646073 + 31 8.1673756e-07 2.1165368e-07 0.00024636584 + 32 8.6971988e-07 2.2513849e-07 0.00024626816 + 33 9.2431288e-07 2.3902582e-07 0.00024616772 + 34 9.8051001e-07 2.5331402e-07 0.00024606453 + 35 1.0383045e-06 2.6800143e-07 0.00024595862 + 36 1.0976895e-06 2.8308629e-07 0.00024585001 + 37 1.1586578e-06 2.9856682e-07 0.0002457387 + 38 1.2212021e-06 3.1444121e-07 0.00024562473 + 39 1.2853151e-06 3.3070757e-07 0.00024550812 + 40 1.350989e-06 3.4736399e-07 0.00024538888 + 41 1.4182159e-06 3.644085e-07 0.00024526703 + 42 1.4869879e-06 3.8183911e-07 0.00024514261 + 43 1.5572969e-06 3.9965375e-07 0.00024501562 + 44 1.6291343e-06 4.1785034e-07 0.0002448861 + 45 1.7024917e-06 4.3642673e-07 0.00024475406 + 46 1.7773604e-06 4.5538075e-07 0.00024461954 + 47 1.8537315e-06 4.7471016e-07 0.00024448255 + 48 1.9315959e-06 4.9441271e-07 0.00024434312 + 49 2.0109445e-06 5.1448608e-07 0.00024420127 + 50 2.0917677e-06 5.3492792e-07 0.00024405703 + 51 2.1740562e-06 5.5573584e-07 0.00024391043 + 52 2.2578001e-06 5.769074e-07 0.00024376149 + 53 2.3429895e-06 5.9844014e-07 0.00024361023 + 54 2.4296146e-06 6.2033154e-07 0.00024345669 + 55 2.5176649e-06 6.4257904e-07 0.00024330088 + 56 2.6071302e-06 6.6518005e-07 0.00024314285 + 57 2.6980001e-06 6.8813194e-07 0.00024298261 + 58 2.7902637e-06 7.1143203e-07 0.0002428202 + 59 2.8839103e-06 7.3507763e-07 0.00024265563 + 60 2.9789289e-06 7.5906598e-07 0.00024248895 + 61 3.0753084e-06 7.833943e-07 0.00024232018 + 62 3.1730376e-06 8.0805977e-07 0.00024214934 + 63 3.2721049e-06 8.3305953e-07 0.00024197647 + 64 3.372499e-06 8.5839069e-07 0.00024180161 + 65 3.474208e-06 8.8405032e-07 0.00024162477 + 66 3.5772201e-06 9.1003545e-07 0.00024144598 + 67 3.6815235e-06 9.3634309e-07 0.00024126529 + 68 3.7871058e-06 9.6297021e-07 0.00024108272 + 69 3.893955e-06 9.8991374e-07 0.0002408983 + 70 4.0020586e-06 1.0171706e-06 0.00024071206 + 71 4.1114041e-06 1.0447376e-06 0.00024052403 + 72 4.2219789e-06 1.0726116e-06 0.00024033425 + 73 4.3337702e-06 1.1007895e-06 0.00024014274 + 74 4.4467651e-06 1.1292679e-06 0.00023994955 + 75 4.5609507e-06 1.1580437e-06 0.0002397547 + 76 4.6763137e-06 1.1871136e-06 0.00023955822 + 77 4.792841e-06 1.2164741e-06 0.00023936014 + 78 4.9105191e-06 1.2461221e-06 0.00023916051 + 79 5.0293346e-06 1.276054e-06 0.00023895935 + 80 5.149274e-06 1.3062666e-06 0.00023875669 + 81 5.2703234e-06 1.3367563e-06 0.00023855257 + 82 5.392469e-06 1.3675198e-06 0.00023834703 + 83 5.515697e-06 1.3985535e-06 0.00023814009 + 84 5.6399934e-06 1.4298539e-06 0.00023793178 + 85 5.7653439e-06 1.4614174e-06 0.00023772215 + 86 5.8917344e-06 1.4932406e-06 0.00023751123 + 87 6.0191505e-06 1.5253199e-06 0.00023729904 + 88 6.1475779e-06 1.5576515e-06 0.00023708563 + 89 6.277002e-06 1.590232e-06 0.00023687102 + 90 6.4074081e-06 1.6230576e-06 0.00023665526 + 91 6.5387817e-06 1.6561246e-06 0.00023643837 + 92 6.6711079e-06 1.6894294e-06 0.00023622039 + 93 6.8043718e-06 1.7229682e-06 0.00023600135 + 94 6.9385585e-06 1.7567372e-06 0.00023578129 + 95 7.0736529e-06 1.7907328e-06 0.00023556024 + 96 7.2096401e-06 1.8249512e-06 0.00023533824 + 97 7.3465046e-06 1.8593885e-06 0.00023511531 + 98 7.4842314e-06 1.8940408e-06 0.0002348915 + 99 7.622805e-06 1.9289045e-06 0.00023466684 + 100 7.76221e-06 1.9639756e-06 0.00023444136 +Loop time of 0.00193128 on 1 procs for 100 steps with 3 atoms + +Performance: 2236858456.568 fs/day, 0.000 hours/fs, 51779.131 timesteps/s, 155.337 katom-step/s +36.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.454e-06 | 1.454e-06 | 1.454e-06 | 0.0 | 0.08 +Comm | 2.3033e-05 | 2.3033e-05 | 2.3033e-05 | 0.0 | 1.19 +Output | 0.00030824 | 0.00030824 | 0.00030824 | 0.0 | 15.96 +Modify | 0.001541 | 0.001541 | 0.001541 | 0.0 | 79.79 +Other | | 5.754e-05 | | | 2.98 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 24 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1 new file mode 100644 index 0000000000..7e01637f3d --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1 @@ -0,0 +1,235 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 1 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Number of Nose-Hoover chains +variable nhc equal 4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188892 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 + +# Outputs +variable virial equal f_pimdb[3] +variable prim_kinetic equal f_pimdb[4] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 0 0.00024796164 + 1 8.5850843e-10 5.313724e-10 0.00024796083 + 2 3.4339027e-09 1.4919466e-09 0.00024795841 + 3 7.7257901e-09 2.8816048e-09 0.00024795438 + 4 1.3733516e-08 4.7001635e-09 0.00024794873 + 5 2.1456164e-08 6.9473741e-09 0.00024794148 + 6 3.0892555e-08 9.6229225e-09 0.00024793261 + 7 4.2041252e-08 1.2726429e-08 0.00024792214 + 8 5.4900553e-08 1.6257449e-08 0.00024791006 + 9 6.9468499e-08 2.0215473e-08 0.00024789638 + 10 8.5742867e-08 2.4599926e-08 0.0002478811 + 11 1.0372118e-07 2.9410168e-08 0.00024786422 + 12 1.2340069e-07 3.4645495e-08 0.00024784576 + 13 1.447784e-07 4.0305136e-08 0.0002478257 + 14 1.6785106e-07 4.6388259e-08 0.00024780406 + 15 1.9261515e-07 5.2893965e-08 0.00024778084 + 16 2.190669e-07 5.9821291e-08 0.00024775605 + 17 2.4720228e-07 6.7169211e-08 0.00024772969 + 18 2.7701701e-07 7.4936635e-08 0.00024770176 + 19 3.0850655e-07 8.312241e-08 0.00024767228 + 20 3.416661e-07 9.1725317e-08 0.00024764125 + 21 3.7649064e-07 1.0074408e-07 0.00024760868 + 22 4.1297485e-07 1.1017735e-07 0.00024757457 + 23 4.511132e-07 1.2002372e-07 0.00024753893 + 24 4.9089989e-07 1.3028173e-07 0.00024750177 + 25 5.3232887e-07 1.4094984e-07 0.0002474631 + 26 5.7539386e-07 1.5202647e-07 0.00024742293 + 27 6.2008832e-07 1.6350996e-07 0.00024738126 + 28 6.6640547e-07 1.7539859e-07 0.00024733811 + 29 7.1433828e-07 1.876906e-07 0.00024729348 + 30 7.6387949e-07 2.0038414e-07 0.00024724738 + 31 8.150216e-07 2.1347732e-07 0.00024719983 + 32 8.6775685e-07 2.2696818e-07 0.00024715084 + 33 9.2207727e-07 2.4085472e-07 0.0002471004 + 34 9.7797464e-07 2.5513485e-07 0.00024704855 + 35 1.0354405e-06 2.6980645e-07 0.00024699528 + 36 1.0944662e-06 2.8486732e-07 0.00024694061 + 37 1.1550427e-06 3.0031522e-07 0.00024688456 + 38 1.2171611e-06 3.1614785e-07 0.00024682713 + 39 1.2808118e-06 3.3236283e-07 0.00024676833 + 40 1.3459853e-06 3.4895776e-07 0.00024670818 + 41 1.4126717e-06 3.6593016e-07 0.0002466467 + 42 1.4808611e-06 3.832775e-07 0.0002465839 + 43 1.5505431e-06 4.009972e-07 0.00024651978 + 44 1.6217074e-06 4.1908663e-07 0.00024645437 + 45 1.6943431e-06 4.3754308e-07 0.00024638767 + 46 1.7684394e-06 4.5636381e-07 0.00024631971 + 47 1.8439852e-06 4.7554603e-07 0.0002462505 + 48 1.9209691e-06 4.9508689e-07 0.00024618005 + 49 1.9993796e-06 5.1498348e-07 0.00024610839 + 50 2.079205e-06 5.3523286e-07 0.00024603551 + 51 2.1604333e-06 5.5583202e-07 0.00024596145 + 52 2.2430524e-06 5.7677791e-07 0.00024588621 + 53 2.32705e-06 5.9806742e-07 0.00024580981 + 54 2.4124135e-06 6.1969741e-07 0.00024573228 + 55 2.4991302e-06 6.4166468e-07 0.00024565362 + 56 2.5871872e-06 6.6396597e-07 0.00024557386 + 57 2.6765714e-06 6.8659801e-07 0.00024549301 + 58 2.7672695e-06 7.0955745e-07 0.00024541108 + 59 2.859268e-06 7.328409e-07 0.00024532811 + 60 2.9525533e-06 7.5644494e-07 0.00024524409 + 61 3.0471115e-06 7.8036609e-07 0.00024515907 + 62 3.1429287e-06 8.0460083e-07 0.00024507304 + 63 3.2399907e-06 8.2914562e-07 0.00024498603 + 64 3.3382831e-06 8.5399683e-07 0.00024489807 + 65 3.4377915e-06 8.7915084e-07 0.00024480916 + 66 3.5385011e-06 9.0460395e-07 0.00024471933 + 67 3.6403972e-06 9.3035245e-07 0.0002446286 + 68 3.7434648e-06 9.5639257e-07 0.00024453698 + 69 3.8476886e-06 9.8272051e-07 0.0002444445 + 70 3.9530535e-06 1.0093324e-06 0.00024435118 + 71 4.0595439e-06 1.0362244e-06 0.00024425703 + 72 4.1671443e-06 1.0633926e-06 0.00024416208 + 73 4.275839e-06 1.0908331e-06 0.00024406635 + 74 4.3856121e-06 1.1185418e-06 0.00024396985 + 75 4.4964475e-06 1.1465147e-06 0.00024387262 + 76 4.6083292e-06 1.1747478e-06 0.00024377466 + 77 4.7212408e-06 1.2032371e-06 0.00024367601 + 78 4.835166e-06 1.2319783e-06 0.00024357668 + 79 4.9500883e-06 1.2609674e-06 0.00024347669 + 80 5.0659909e-06 1.2902001e-06 0.00024337607 + 81 5.1828572e-06 1.3196723e-06 0.00024327483 + 82 5.3006702e-06 1.3493797e-06 0.000243173 + 83 5.419413e-06 1.379318e-06 0.0002430706 + 84 5.5390685e-06 1.4094831e-06 0.00024296765 + 85 5.6596194e-06 1.4398705e-06 0.00024286417 + 86 5.7810485e-06 1.4704759e-06 0.00024276019 + 87 5.9033384e-06 1.501295e-06 0.00024265573 + 88 6.0264715e-06 1.5323234e-06 0.00024255081 + 89 6.1504303e-06 1.5635565e-06 0.00024244545 + 90 6.275197e-06 1.5949902e-06 0.00024233967 + 91 6.400754e-06 1.6266197e-06 0.0002422335 + 92 6.5270834e-06 1.6584408e-06 0.00024212696 + 93 6.6541672e-06 1.6904488e-06 0.00024202007 + 94 6.7819875e-06 1.7226394e-06 0.00024191285 + 95 6.9105262e-06 1.7550078e-06 0.00024180534 + 96 7.0397651e-06 1.7875497e-06 0.00024169754 + 97 7.169686e-06 1.8202604e-06 0.00024158948 + 98 7.3002707e-06 1.8531354e-06 0.00024148118 + 99 7.4315008e-06 1.88617e-06 0.00024137268 + 100 7.563358e-06 1.9193596e-06 0.00024126398 +Loop time of 0.00190888 on 1 procs for 100 steps with 3 atoms + +Performance: 2263110719.025 fs/day, 0.000 hours/fs, 52386.822 timesteps/s, 157.160 katom-step/s +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 2.774e-06 | 2.774e-06 | 2.774e-06 | 0.0 | 0.15 +Comm | 2.3215e-05 | 2.3215e-05 | 2.3215e-05 | 0.0 | 1.22 +Output | 0.00042246 | 0.00042246 | 0.00042246 | 0.0 | 22.13 +Modify | 0.0013744 | 0.0013744 | 0.0013744 | 0.0 | 72.00 +Other | | 8.601e-05 | | | 4.51 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 23 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2 new file mode 100644 index 0000000000..9540baaf27 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2 @@ -0,0 +1,235 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 2 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Number of Nose-Hoover chains +variable nhc equal 4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188893 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 + +# Outputs +variable virial equal f_pimdb[3] +variable prim_kinetic equal f_pimdb[4] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 0 0.00024796164 + 1 8.5850845e-10 -3.6831179e-10 0.0002479594 + 2 3.4338783e-09 -3.0736303e-10 0.00024795267 + 3 7.7256433e-09 1.8277487e-10 0.00024794145 + 4 1.3733026e-08 1.1019528e-09 0.00024792576 + 5 2.145494e-08 2.449944e-09 0.00024790558 + 6 3.0889985e-08 4.226444e-09 0.00024788093 + 7 4.2036455e-08 6.4310711e-09 0.00024785181 + 8 5.4892332e-08 9.0633658e-09 0.00024781823 + 9 6.9455288e-08 1.2122792e-08 0.00024778019 + 10 8.572269e-08 1.5608734e-08 0.0002477377 + 11 1.0369159e-07 1.9520504e-08 0.00024769077 + 12 1.2335875e-07 2.3857331e-08 0.00024763941 + 13 1.4472059e-07 2.8618373e-08 0.00024758363 + 14 1.6777327e-07 3.3802708e-08 0.00024752344 + 15 1.9251262e-07 3.940934e-08 0.00024745886 + 16 2.1893415e-07 4.5437194e-08 0.00024738989 + 17 2.4703311e-07 5.1885122e-08 0.00024731656 + 18 2.768044e-07 5.8751899e-08 0.00024723887 + 19 3.0824267e-07 6.6036227e-08 0.00024715685 + 20 3.4134222e-07 7.3736729e-08 0.00024707051 + 21 3.7609709e-07 8.1851958e-08 0.00024697986 + 22 4.1250102e-07 9.0380389e-08 0.00024688494 + 23 4.5054742e-07 9.9320426e-08 0.00024678575 + 24 4.9022945e-07 1.086704e-07 0.00024668231 + 25 5.3153996e-07 1.1842856e-07 0.00024657466 + 26 5.744715e-07 1.285931e-07 0.00024646281 + 27 6.1901635e-07 1.3916212e-07 0.00024634678 + 28 6.6516648e-07 1.5013367e-07 0.0002462266 + 29 7.1291361e-07 1.6150571e-07 0.00024610229 + 30 7.6224914e-07 1.7327614e-07 0.00024597388 + 31 8.1316422e-07 1.8544279e-07 0.0002458414 + 32 8.6564969e-07 1.9800342e-07 0.00024570487 + 33 9.1969614e-07 2.109557e-07 0.00024556432 + 34 9.7529388e-07 2.2429727e-07 0.00024541978 + 35 1.0324329e-06 2.3802567e-07 0.00024527128 + 36 1.0911031e-06 2.5213838e-07 0.00024511886 + 37 1.1512938e-06 2.6663282e-07 0.00024496253 + 38 1.2129943e-06 2.8150634e-07 0.00024480234 + 39 1.2761936e-06 2.9675622e-07 0.00024463831 + 40 1.3408803e-06 3.1237968e-07 0.00024447049 + 41 1.407043e-06 3.2837388e-07 0.0002442989 + 42 1.4746698e-06 3.447359e-07 0.00024412359 + 43 1.5437487e-06 3.6146277e-07 0.00024394458 + 44 1.6142674e-06 3.7855146e-07 0.00024376192 + 45 1.6862132e-06 3.9599886e-07 0.00024357564 + 46 1.7595735e-06 4.1380182e-07 0.00024338577 + 47 1.8343351e-06 4.3195711e-07 0.00024319237 + 48 1.9104848e-06 4.5046147e-07 0.00024299547 + 49 1.9880091e-06 4.6931154e-07 0.00024279511 + 50 2.0668943e-06 4.8850394e-07 0.00024259132 + 51 2.1471263e-06 5.0803521e-07 0.00024238416 + 52 2.228691e-06 5.2790184e-07 0.00024217367 + 53 2.311574e-06 5.4810027e-07 0.00024195988 + 54 2.3957606e-06 5.6862687e-07 0.00024174285 + 55 2.481236e-06 5.8947797e-07 0.00024152261 + 56 2.5679851e-06 6.1064984e-07 0.00024129922 + 57 2.6559926e-06 6.3213871e-07 0.00024107271 + 58 2.7452431e-06 6.5394073e-07 0.00024084313 + 59 2.8357209e-06 6.7605203e-07 0.00024061054 + 60 2.9274101e-06 6.9846868e-07 0.00024037498 + 61 3.0202947e-06 7.2118669e-07 0.00024013649 + 62 3.1143583e-06 7.4420204e-07 0.00023989513 + 63 3.2095846e-06 7.6751065e-07 0.00023965094 + 64 3.3059569e-06 7.911084e-07 0.00023940398 + 65 3.4034585e-06 8.1499113e-07 0.00023915429 + 66 3.5020722e-06 8.3915461e-07 0.00023890193 + 67 3.601781e-06 8.6359461e-07 0.00023864694 + 68 3.7025676e-06 8.8830681e-07 0.00023838939 + 69 3.8044144e-06 9.132869e-07 0.00023812931 + 70 3.9073038e-06 9.3853048e-07 0.00023786677 + 71 4.0112181e-06 9.6403314e-07 0.00023760182 + 72 4.1161392e-06 9.8979043e-07 0.00023733451 + 73 4.2220491e-06 1.0157978e-06 0.0002370649 + 74 4.3289295e-06 1.0420509e-06 0.00023679303 + 75 4.4367621e-06 1.068545e-06 0.00023651897 + 76 4.5455283e-06 1.0952755e-06 0.00023624277 + 77 4.6552095e-06 1.1222378e-06 0.00023596449 + 78 4.7657869e-06 1.1494273e-06 0.00023568418 + 79 4.8772416e-06 1.1768393e-06 0.0002354019 + 80 4.9895545e-06 1.2044689e-06 0.00023511771 + 81 5.1027067e-06 1.2323116e-06 0.00023483166 + 82 5.2166788e-06 1.2603625e-06 0.00023454381 + 83 5.3314515e-06 1.2886168e-06 0.00023425422 + 84 5.4470054e-06 1.3170697e-06 0.00023396295 + 85 5.5633208e-06 1.3457162e-06 0.00023367006 + 86 5.6803783e-06 1.3745516e-06 0.0002333756 + 87 5.798158e-06 1.403571e-06 0.00023307963 + 88 5.9166402e-06 1.4327693e-06 0.00023278222 + 89 6.0358049e-06 1.4621418e-06 0.00023248341 + 90 6.1556323e-06 1.4916833e-06 0.00023218329 + 91 6.2761023e-06 1.5213889e-06 0.00023188189 + 92 6.3971948e-06 1.5512537e-06 0.00023157929 + 93 6.5188897e-06 1.5812727e-06 0.00023127554 + 94 6.6411667e-06 1.6114407e-06 0.0002309707 + 95 6.7640056e-06 1.6417527e-06 0.00023066484 + 96 6.8873862e-06 1.6722038e-06 0.00023035801 + 97 7.011288e-06 1.7027888e-06 0.00023005028 + 98 7.1356907e-06 1.7335027e-06 0.0002297417 + 99 7.2605738e-06 1.7643404e-06 0.00022943234 + 100 7.3859169e-06 1.7952968e-06 0.00022912226 +Loop time of 0.00195857 on 1 procs for 100 steps with 3 atoms + +Performance: 2205688634.372 fs/day, 0.000 hours/fs, 51057.607 timesteps/s, 153.173 katom-step/s +39.2% 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 | 1.602e-06 | 1.602e-06 | 1.602e-06 | 0.0 | 0.08 +Comm | 1.6951e-05 | 1.6951e-05 | 1.6951e-05 | 0.0 | 0.87 +Output | 0.00032627 | 0.00032627 | 0.00032627 | 0.0 | 16.66 +Modify | 0.0015486 | 0.0015486 | 0.0015486 | 0.0 | 79.07 +Other | | 6.514e-05 | | | 3.33 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 24 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3 new file mode 100644 index 0000000000..de7655776f --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3 @@ -0,0 +1,235 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Processor partition = 3 + using 1 OpenMP thread(s) per MPI task +# Units and dimensions +units electron +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +pair_style none + +# Time step (in femtoseconds) +timestep 0.5 + +# Temperature (in Kelvin) +variable Temp equal 17.4 + +# Number of Nose-Hoover chains +variable nhc equal 4 + +# Force constant (in Hartree energies per Bohr radius squared) +variable k equal 1.2154614120000001e-08 + +# Number of beads +variable Nbeads equal 4 +variable ibead uloop ${Nbeads} pad +variable ibead uloop 4 pad +variable seed equal 18889 + +# Create box and atoms. All distances are in Bohr +region box block -1500 1500 -1500 1500 -1500 1500 +create_box 1 box +Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + 1 by 1 by 1 MPI processor grid +variable a loop 3 +label loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14.5 ${y1} ${z1} +create_atoms 1 single -14.5 9.5 ${z1} +create_atoms 1 single -14.5 9.5 1.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -14 ${y1} ${z1} +create_atoms 1 single -14 9 ${z1} +create_atoms 1 single -14 9 2 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop +variable x1 equal -15.0+0.5*v_a +variable y1 equal 10.0-0.5*v_a +variable z1 equal 1+0.5*v_a +create_atoms 1 single ${x1} ${y1} ${z1} +create_atoms 1 single -13.5 ${y1} ${z1} +create_atoms 1 single -13.5 8.5 ${z1} +create_atoms 1 single -13.5 8.5 2.5 +Created 1 atoms + using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) + create_atoms CPU = 0.000 seconds +next a +jump SELF loop + +# Electron mass (in amu) +mass 1 0.00054858 + +# Initialize velocities +velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian +velocity all create 17.4 188894 mom yes rot yes dist gaussian + +# Add harmonic external force +fix harm all spring/self ${k} +fix harm all spring/self 1.215461412e-08 + +# Add harmonic potential energy to total energy and potential energy +fix_modify harm energy yes + +# PIMD command +fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 + +# Outputs +variable virial equal f_pimdb[3] +variable prim_kinetic equal f_pimdb[4] + +thermo_style custom step pe v_virial v_prim_kinetic +thermo 1 + +run 100 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) +Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes + Step PotEng v_virial v_prim_kinetic + 0 0 0 0.00024796164 + 1 8.5847879e-10 4.4463719e-10 0.00024796024 + 2 3.4336684e-09 1.3183829e-09 0.00024795602 + 3 7.7250055e-09 2.6210625e-09 0.000247949 + 4 1.3731669e-08 4.3524371e-09 0.00024793917 + 5 2.1452581e-08 6.5122035e-09 0.00024792653 + 6 3.0886407e-08 9.0999942e-09 0.0002479111 + 7 4.2031554e-08 1.2115377e-08 0.00024789287 + 8 5.4886174e-08 1.5557858e-08 0.00024787185 + 9 6.9448162e-08 1.9426875e-08 0.00024784804 + 10 8.5715159e-08 2.3721806e-08 0.00024782146 + 11 1.0368455e-07 2.8441963e-08 0.0002477921 + 12 1.2335346e-07 3.3586595e-08 0.00024775998 + 13 1.4471878e-07 3.9154888e-08 0.0002477251 + 14 1.6777712e-07 4.5145965e-08 0.00024768748 + 15 1.9252485e-07 5.1558884e-08 0.00024764712 + 16 2.1895809e-07 5.8392642e-08 0.00024760403 + 17 2.4707272e-07 6.5646173e-08 0.00024755823 + 18 2.7686434e-07 7.3318348e-08 0.00024750973 + 19 3.0832834e-07 8.1407976e-08 0.00024745854 + 20 3.4145982e-07 8.9913804e-08 0.00024740467 + 21 3.7625367e-07 9.8834518e-08 0.00024734813 + 22 4.127045e-07 1.0816874e-07 0.00024728895 + 23 4.5080671e-07 1.1791504e-07 0.00024722714 + 24 4.9055443e-07 1.2807191e-07 0.00024716271 + 25 5.3194155e-07 1.3863779e-07 0.00024709568 + 26 5.7496174e-07 1.4961107e-07 0.00024702607 + 27 6.1960841e-07 1.6099007e-07 0.00024695389 + 28 6.6587473e-07 1.7277305e-07 0.00024687917 + 29 7.1375365e-07 1.8495821e-07 0.00024680191 + 30 7.6323786e-07 1.975437e-07 0.00024672216 + 31 8.1431984e-07 2.1052759e-07 0.00024663991 + 32 8.6699183e-07 2.2390793e-07 0.0002465552 + 33 9.2124582e-07 2.3768267e-07 0.00024646805 + 34 9.7707361e-07 2.5184974e-07 0.00024637847 + 35 1.0344667e-06 2.6640698e-07 0.0002462865 + 36 1.0934165e-06 2.813522e-07 0.00024619215 + 37 1.1539141e-06 2.9668313e-07 0.00024609545 + 38 1.2159503e-06 3.1239747e-07 0.00024599643 + 39 1.2795157e-06 3.2849286e-07 0.00024589511 + 40 1.344601e-06 3.4496686e-07 0.00024579151 + 41 1.4111961e-06 3.61817e-07 0.00024568566 + 42 1.4792913e-06 3.7904076e-07 0.0002455776 + 43 1.5488762e-06 3.9663555e-07 0.00024546734 + 44 1.6199404e-06 4.1459874e-07 0.00024535492 + 45 1.6924734e-06 4.3292764e-07 0.00024524035 + 46 1.7664643e-06 4.5161952e-07 0.00024512369 + 47 1.841902e-06 4.7067159e-07 0.00024500494 + 48 1.9187753e-06 4.90081e-07 0.00024488415 + 49 1.9970729e-06 5.0984488e-07 0.00024476135 + 50 2.076783e-06 5.2996028e-07 0.00024463656 + 51 2.1578939e-06 5.5042422e-07 0.00024450981 + 52 2.2403935e-06 5.7123366e-07 0.00024438115 + 53 2.3242696e-06 5.9238553e-07 0.0002442506 + 54 2.4095099e-06 6.138767e-07 0.00024411819 + 55 2.4961017e-06 6.3570399e-07 0.00024398396 + 56 2.5840323e-06 6.5786419e-07 0.00024384795 + 57 2.6732887e-06 6.8035404e-07 0.00024371018 + 58 2.7638579e-06 7.0317021e-07 0.0002435707 + 59 2.8557265e-06 7.2630938e-07 0.00024342953 + 60 2.9488811e-06 7.4976814e-07 0.00024328672 + 61 3.0433081e-06 7.7354305e-07 0.0002431423 + 62 3.1389936e-06 7.9763065e-07 0.00024299631 + 63 3.2359238e-06 8.2202741e-07 0.00024284878 + 64 3.3340844e-06 8.4672977e-07 0.00024269976 + 65 3.4334612e-06 8.7173415e-07 0.00024254927 + 66 3.5340397e-06 8.970369e-07 0.00024239736 + 67 3.6358055e-06 9.2263435e-07 0.00024224406 + 68 3.7387437e-06 9.4852279e-07 0.00024208942 + 69 3.8428394e-06 9.7469849e-07 0.00024193348 + 70 3.9480777e-06 1.0011576e-06 0.00024177626 + 71 4.0544433e-06 1.0278964e-06 0.00024161782 + 72 4.1619211e-06 1.054911e-06 0.0002414582 + 73 4.2704954e-06 1.0821976e-06 0.00024129742 + 74 4.3801508e-06 1.1097521e-06 0.00024113554 + 75 4.4908716e-06 1.1375706e-06 0.0002409726 + 76 4.6026419e-06 1.1656492e-06 0.00024080863 + 77 4.7154459e-06 1.1939839e-06 0.00024064367 + 78 4.8292673e-06 1.2225706e-06 0.00024047778 + 79 4.9440901e-06 1.2514052e-06 0.00024031099 + 80 5.059898e-06 1.2804837e-06 0.00024014333 + 81 5.1766745e-06 1.309802e-06 0.00023997487 + 82 5.2944032e-06 1.3393558e-06 0.00023980562 + 83 5.4130674e-06 1.369141e-06 0.00023963565 + 84 5.5326505e-06 1.3991534e-06 0.00023946499 + 85 5.6531355e-06 1.4293887e-06 0.00023929369 + 86 5.7745057e-06 1.4598429e-06 0.00023912178 + 87 5.8967439e-06 1.4905114e-06 0.00023894931 + 88 6.0198332e-06 1.5213902e-06 0.00023877633 + 89 6.1437564e-06 1.5524748e-06 0.00023860287 + 90 6.2684962e-06 1.5837609e-06 0.00023842898 + 91 6.3940353e-06 1.6152441e-06 0.00023825471 + 92 6.5203562e-06 1.6469202e-06 0.0002380801 + 93 6.6474416e-06 1.6787847e-06 0.00023790518 + 94 6.7752739e-06 1.7108332e-06 0.00023773001 + 95 6.9038354e-06 1.7430613e-06 0.00023755463 + 96 7.0331085e-06 1.7754645e-06 0.00023737908 + 97 7.1630755e-06 1.8080385e-06 0.00023720341 + 98 7.2937187e-06 1.8407787e-06 0.00023702765 + 99 7.4250201e-06 1.8736806e-06 0.00023685186 + 100 7.5569619e-06 1.9067398e-06 0.00023667607 +Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms + +Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s +37.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.652e-06 | 1.652e-06 | 1.652e-06 | 0.0 | 0.08 +Comm | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 | 0.0 | 0.91 +Output | 0.00036011 | 0.00036011 | 0.00036011 | 0.0 | 18.27 +Modify | 0.0015231 | 0.0015231 | 0.0015231 | 0.0 | 77.28 +Other | | 6.806e-05 | | | 3.45 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 24 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh new file mode 100644 index 0000000000..c1329f646a --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh @@ -0,0 +1 @@ +mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt index fb0324cabe..f19eee339d 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt @@ -58,4 +58,4 @@ thermo_style custom step temp press density f_myrxns[*] # cumulative reaction co run 200 # write_restart restart_longrun -# write_data restart_longrun.data +# write_data restart_longrun.data nofix diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized index 4998ea7d9d..06ac9d5cb7 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized @@ -43,7 +43,6 @@ thermo 50 fix myrxns all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & - react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes fix 1 statted_grp_REACT nvt temp 300 300 100 @@ -59,4 +58,4 @@ thermo_style custom step temp press density f_myrxns[*] run 10000 # write_restart restart_longrun -# write_data restart_longrun.data +# write_data restart_longrun.data nofix diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability index 4b268cf0d9..80f86db1ec 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability @@ -62,4 +62,4 @@ thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[*] run ${runsteps} # write_restart restart_longrun -# write_data restart_longrun.data +# write_data restart_longrun.data nofix diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized index 3ecf552174..74f521d74e 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized @@ -55,4 +55,4 @@ thermo_style custom step temp press density f_myrxns[*] run 1000 # write_restart restart_longrun -# write_data restart_longrun.data +# write_data restart_longrun.data nofix diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized index 34346d9ef7..f181b24ee5 100644 --- a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized +++ b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized @@ -56,5 +56,5 @@ thermo_style custom step temp press density f_rxn1[*] run 10000 -# write_restart restart_longrun nofix -# write_data restart_longrun.data +# write_restart restart_longrun +# write_data restart_longrun.data nofix diff --git a/examples/PACKAGES/ti/in.ti_spring b/examples/PACKAGES/ti/in.ti_spring index 383d4b688c..05f4902aad 100644 --- a/examples/PACKAGES/ti/in.ti_spring +++ b/examples/PACKAGES/ti/in.ti_spring @@ -13,7 +13,7 @@ create_atoms 1 box pair_style eam/alloy - pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu + pair_coeff * * Cu_mishin1.eam.alloy Cu #------------------------------------------------------------------------------# diff --git a/examples/SPIN/read_restart/Norm_randXY_8x8x32.data b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data index d239bb6ca0..cc3dc7998c 100644 --- a/examples/SPIN/read_restart/Norm_randXY_8x8x32.data +++ b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data @@ -1,8207 +1,2066 @@ -LAMMPS data file via write_data, version 4 May 2017, timestep = 0 +LAMMPS data file via write_data, version 4 Feb 2025, timestep = 0, units = metal -8192 atoms +1024 atoms 1 atom types -0.0000000000000000e+00 2.8320000000000000e+01 xlo xhi -0.0000000000000000e+00 2.8320000000000000e+01 ylo yhi -0.0000000000000000e+00 1.1328000000000000e+02 zlo zhi +0 15 xlo xhi +0 28.32 ylo yhi +0 13.68 zlo zhi Masses -1 58.93 +1 58.9332 Atoms # spin -1 1 1.72 0.0 0.0 0.0 0.52887 -0.848703 1.0 -2 1 1.72 1.77 1.77 0.0 -0.745115 -0.666936 1.0 -3 1 1.72 1.77 0.0 1.77 -0.989437 -0.144964 1.0 -4 1 1.72 0.0 1.77 1.77 0.999926 -0.0121449 1.0 -5 1 1.72 3.54 0.0 0.0 0.377063 -0.926188 1.0 -6 1 1.72 5.31 1.77 0.0 0.412944 0.910756 1.0 -7 1 1.72 5.31 0.0 1.77 -0.999979 0.00650985 1.0 -8 1 1.72 3.54 1.77 1.77 0.535453 -0.844565 1.0 -9 1 1.72 7.0799999 0.0 0.0 -0.986135 0.165942 1.0 -10 1 1.72 8.8500004 1.77 0.0 -0.37352 -0.927622 1.0 -11 1 1.72 8.8500004 0.0 1.77 -0.926878 0.375363 1.0 -12 1 1.72 7.0799999 1.77 1.77 -0.690063 -0.72375 1.0 -13 1 1.72 10.6199999 0.0 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0 +1013 0 0 0 +1014 0 0 0 +1015 0 0 0 +1016 0 0 0 +1017 0 0 0 +1018 0 0 0 +1019 0 0 0 +1020 0 0 0 +1021 0 0 0 +1022 0 0 0 +1023 0 0 0 +1024 0 0 0 diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data index b2b55a9fcb..0875ad0f9d 100644 --- a/examples/SPIN/read_restart/in.spin.read_data +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -1,45 +1,46 @@ -units metal -dimension 3 -boundary p p p +units metal +dimension 3 +boundary p p p -atom_style spin +atom_style spin # necessary for the serial algorithm (sametag) -atom_modify map array -read_data Norm_randXY_8x8x32.data +atom_modify map array +read_data Norm_randXY_8x8x32.data +replicate 1 1 2 -mass 1 58.93 +mass 1 58.93 -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice moving -timestep 0.0001 +fix 3 all nve/spin lattice moving +timestep 0.0001 # define outputs and computes -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] thermo 20 thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal thermo_modify format float %20.15g -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 1 sort id +run 100 diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart index 985da65eb4..72ed6b1b09 100644 --- a/examples/SPIN/read_restart/in.spin.restart +++ b/examples/SPIN/read_restart/in.spin.restart @@ -1,49 +1,49 @@ # start a spin-lattice simulation from a data file -units metal -atom_style spin +units metal +atom_style spin -dimension 3 -boundary p p p +dimension 3 +boundary p p p # necessary for the serial algorithm (sametag) -atom_modify map array +atom_modify map array -read_restart restart_hcp_cobalt.equil +read_restart restart_hcp_cobalt.equil # setting mass, mag. moments, and interactions -mass 1 58.93 +mass 1 58.93 -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice moving -timestep 0.0001 +fix 3 all nve/spin lattice moving +timestep 0.0001 # define outputs -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] thermo 20 thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal thermo_modify format float %20.15g -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] -run 100 +run 100 diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart index 19ab8e6b30..d0e8f79e1b 100644 --- a/examples/SPIN/read_restart/in.spin.write_restart +++ b/examples/SPIN/read_restart/in.spin.write_restart @@ -1,54 +1,54 @@ # fcc cobalt in a 3d periodic box -units metal -atom_style spin +units metal +atom_style spin -dimension 3 -boundary p p p +dimension 3 +boundary p p p # necessary for the serial algorithm (sametag) -atom_modify map array +atom_modify map array -lattice hcp 2.5071 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -create_atoms 1 box +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box # setting mass, mag. moments, and interactions for cobalt -mass 1 58.93 +mass 1 58.93 -set group all spin/random 31 1.72 +set group all spin/atom/random 31 1.72 -pair_style spin/exchange 4.0 -pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 -neighbor 0.1 bin -neigh_modify every 10 check yes delay 20 +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 100.0 0.01 21 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 -fix 3 all nve/spin lattice frozen -timestep 0.0001 +fix 3 all nve/spin lattice frozen +timestep 0.0001 # compute and output options -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] thermo_style custom step time v_magnorm pe v_emag temp etotal thermo 100 -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 1000 -write_restart restart_hcp_cobalt.equil +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 100 sort id +run 1000 +write_restart restart_hcp_cobalt.equil diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 new file mode 100644 index 0000000000..8edfd17527 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 @@ -0,0 +1,136 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data +Reading data file ... + orthogonal box = (0 0 0) to (15 28.32 13.68) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1024 atoms + reading velocities ... + 1024 velocities + read_data CPU = 0.004 seconds +replicate 1 1 2 +Replication is creating a 1x1x2 = 2 times larger system... + orthogonal box = (0 0 0) to (15 28.32 27.36) + 1 by 1 by 1 MPI processor grid + 2048 atoms + replicate CPU = 0.001 seconds + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs and computes + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 1 sort id +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 5 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.082 | 9.082 | 9.082 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 0 0 0.99566943155533 116726.359107918 -852.392312873949 34.9207785637842 0 116726.359107918 + 20 0.002 0.995669416541629 70905.5692189811 -849.222504107045 34.647400481739 172820.122486868 116632.998844426 + 40 0.004 0.995669401356638 71221.2391274615 -848.368415908416 34.9759984641547 171555.103338675 116613.950357609 + 60 0.006 0.995669394598344 69647.7523345612 -845.585158124559 36.100016238044 177502.681559427 116614.166097826 + 80 0.008 0.995669395756676 107415.560454437 -846.200871523815 37.9775024824566 35031.4099604677 116684.714477685 + 100 0.01 0.995669403283478 63849.6798250643 -836.341677782106 39.680777051272 199492.565587335 116634.518317396 +Loop time of 2.97847 on 1 procs for 100 steps with 2048 atoms + +Performance: 0.290 ns/day, 82.735 hours/ns, 33.574 timesteps/s, 68.760 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0361 | 1.0361 | 1.0361 | 0.0 | 34.79 +Neigh | 0.78559 | 0.78559 | 0.78559 | 0.0 | 26.38 +Comm | 0.013262 | 0.013262 | 0.013262 | 0.0 | 0.45 +Output | 0.00026908 | 0.00026908 | 0.00026908 | 0.0 | 0.01 +Modify | 1.1415 | 1.1415 | 1.1415 | 0.0 | 38.33 +Other | | 0.001761 | | | 0.06 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7952 ave 7952 max 7952 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 314944 ave 314944 max 314944 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 629888 ave 629888 max 629888 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 629888 +Ave neighs/atom = 307.5625 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:03 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 new file mode 100644 index 0000000000..9945bc79fd --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 @@ -0,0 +1,136 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data +Reading data file ... + orthogonal box = (0 0 0) to (15 28.32 13.68) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1024 atoms + reading velocities ... + 1024 velocities + read_data CPU = 0.004 seconds +replicate 1 1 2 +Replication is creating a 1x1x2 = 2 times larger system... + orthogonal box = (0 0 0) to (15 28.32 27.36) + 1 by 2 by 2 MPI processor grid + 2048 atoms + replicate CPU = 0.002 seconds + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs and computes + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 1 sort id +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 5 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.812 | 5.812 | 5.812 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 0 0 0.995669431555328 116726.359107923 -852.39231287395 34.9207785637843 0 116726.359107923 + 20 0.002 0.995669419512638 70905.5692199804 -849.222502855646 34.6474282239503 172820.122483292 116632.998844479 + 40 0.004 0.995669419108591 71221.2391285209 -848.368412494784 34.97611050919 171555.103335676 116613.950357875 + 60 0.006 0.99566940895435 69647.7523345112 -845.585157291247 36.1001312564486 177502.681560664 116614.166098104 + 80 0.008 0.995669417344697 107415.560454912 -846.200874451992 37.9776090859263 35031.4099596403 116684.714477941 + 100 0.01 0.995669427709463 63849.6798245944 -836.341678212079 39.6809090980074 199492.565591024 116634.518317902 +Loop time of 0.991506 on 4 procs for 100 steps with 2048 atoms + +Performance: 0.871 ns/day, 27.542 hours/ns, 100.857 timesteps/s, 206.554 katom-step/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.31016 | 0.31287 | 0.31496 | 0.3 | 31.56 +Neigh | 0.21999 | 0.22957 | 0.23793 | 1.7 | 23.15 +Comm | 0.015231 | 0.025975 | 0.036137 | 6.0 | 2.62 +Output | 0.00012037 | 0.00014855 | 0.0001849 | 0.0 | 0.01 +Modify | 0.4213 | 0.42166 | 0.42201 | 0.0 | 42.53 +Other | | 0.001272 | | | 0.13 + +Nlocal: 512 ave 521 max 503 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 4112 ave 4121 max 4103 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 78736 ave 80265 max 77207 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 157472 ave 160276 max 154668 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 629888 +Ave neighs/atom = 307.5625 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:01 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 new file mode 100644 index 0000000000..9ca8ef3521 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 @@ -0,0 +1,135 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil +Reading restart file ... + restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025 + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 1 by 1 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + read_restart CPU = 0.000 seconds + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.255 | 5.255 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 1000 0.1 0.0932563992120983 -2200.23506043127 -5.23510819573568 2608.1272233749 0 -2200.23506043127 + 1020 0.102 0.0932564226983496 -2200.24431693921 -5.24438874766875 2636.89284253705 0.143502110493468 -2200.23506093651 + 1040 0.104 0.0932564330551733 -2200.27026761331 -5.27068764778909 2646.09012775508 0.545814389665464 -2200.23506214178 + 1060 0.106 0.0932564065525508 -2200.30841491752 -5.31025431862422 2627.26990645217 1.13721564075693 -2200.23506358487 + 1080 0.108 0.0932563850278094 -2200.35339675793 -5.35874497582981 2585.24230543411 1.83458183455181 -2200.23506473927 + 1100 0.11 0.0932563977118321 -2200.40087596139 -5.41289411193204 2540.00857034711 2.5706738278606 -2200.23506541119 +Loop time of 0.473574 on 1 procs for 100 steps with 500 atoms + +Performance: 1.824 ns/day, 13.155 hours/ns, 211.160 timesteps/s, 105.580 katom-step/s +98.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12025 | 0.12025 | 0.12025 | 0.0 | 25.39 +Neigh | 0.14912 | 0.14912 | 0.14912 | 0.0 | 31.49 +Comm | 0.0047587 | 0.0047587 | 0.0047587 | 0.0 | 1.00 +Output | 0.07234 | 0.07234 | 0.07234 | 0.0 | 15.28 +Modify | 0.12645 | 0.12645 | 0.12645 | 0.0 | 26.70 +Other | | 0.0006494 | | | 0.14 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2534 ave 2534 max 2534 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36500 ave 36500 max 36500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 73000 ave 73000 max 73000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 new file mode 100644 index 0000000000..2fe8f44691 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 @@ -0,0 +1,136 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil +Reading restart file ... + restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025 +WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:628) + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 2 by 2 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + read_restart CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) +Per MPI rank memory allocation (min/avg/max) = 5.188 | 5.188 | 5.188 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 1000 0.1 0.0932563992120983 -2200.23506043087 -5.23510819573568 2608.1272233749 0 -2200.23506043087 + 1020 0.102 0.0932564663999882 -2200.24431693996 -5.24438874845296 2636.89226887198 0.14350212264756 -2200.23506093648 + 1040 0.104 0.0932565837400281 -2200.27026761822 -5.27068765273516 2646.08966888271 0.545814465748645 -2200.23506214179 + 1060 0.106 0.0932567073488227 -2200.30841492456 -5.31025432590717 2627.27001685206 1.13721574991944 -2200.23506358486 + 1080 0.108 0.0932567401022577 -2200.35339675946 -5.35874497805351 2585.24242001276 1.83458185842719 -2200.23506473925 + 1100 0.11 0.0932566884738387 -2200.4008759633 -5.41289411525345 2540.00813568378 2.57067385759474 -2200.23506541119 +Loop time of 0.180477 on 4 procs for 100 steps with 500 atoms + +Performance: 4.787 ns/day, 5.013 hours/ns, 554.088 timesteps/s, 277.044 katom-step/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 | 0.033968 | 0.034363 | 0.035109 | 0.2 | 19.04 +Neigh | 0.035043 | 0.03728 | 0.040013 | 0.9 | 20.66 +Comm | 0.0049574 | 0.0073867 | 0.0089549 | 1.7 | 4.09 +Output | 0.021087 | 0.023594 | 0.026417 | 1.3 | 13.07 +Modify | 0.074785 | 0.07749 | 0.079892 | 0.7 | 42.94 +Other | | 0.0003627 | | | 0.20 + +Nlocal: 125 ave 136 max 117 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 1387 ave 1395 max 1376 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 9125 ave 9972 max 8559 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +FullNghs: 18250 ave 19856 max 17082 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 new file mode 100644 index 0000000000..b1dc9fbba6 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + create_atoms CPU = 0.000 seconds + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/atom/random 31 1.72 +Setting atom values ... + 500 settings made for spin/atom/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +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 100.0 0.01 21 + +fix 3 all nve/spin lattice frozen +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm pe v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 100 sort id +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.78 | 4.78 | 4.78 Mbytes + Step Time v_magnorm PotEng v_emag Temp TotEng + 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 + 100 0.01 0.077627966 0.36694275 0.36694275 0 0.36694275 + 200 0.02 0.076678387 -0.20241504 -0.20241504 0 -0.20241504 + 300 0.03 0.079174207 -0.67593525 -0.67593525 0 -0.67593525 + 400 0.04 0.085031074 -1.5172826 -1.5172826 0 -1.5172826 + 500 0.05 0.087026279 -2.042653 -2.042653 0 -2.042653 + 600 0.06 0.087064628 -2.6297295 -2.6297295 0 -2.6297295 + 700 0.07 0.089787949 -3.3144767 -3.3144767 0 -3.3144767 + 800 0.08 0.091698615 -4.028707 -4.028707 0 -4.028707 + 900 0.09 0.090031988 -4.6007241 -4.6007241 0 -4.6007241 + 1000 0.1 0.093256399 -5.2351082 -5.2351082 0 -5.2351082 +Loop time of 0.710555 on 1 procs for 1000 steps with 500 atoms + +Performance: 12.160 ns/day, 1.974 hours/ns, 1407.350 timesteps/s, 703.675 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12852 | 0.12852 | 0.12852 | 0.0 | 18.09 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012387 | 0.012387 | 0.012387 | 0.0 | 1.74 +Output | 0.00014522 | 0.00014522 | 0.00014522 | 0.0 | 0.02 +Modify | 0.56835 | 0.56835 | 0.56835 | 0.0 | 79.99 +Other | | 0.001145 | | | 0.16 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1221 ave 1221 max 1221 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 10000 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 new file mode 100644 index 0000000000..1d5c10bc67 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 @@ -0,0 +1,142 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/atom/random 31 1.72 +Setting atom values ... + 500 settings made for spin/atom/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +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 100.0 0.01 21 + +fix 3 all nve/spin lattice frozen +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm pe v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 100 sort id +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.732 | 4.732 | 4.733 Mbytes + Step Time v_magnorm PotEng v_emag Temp TotEng + 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 + 100 0.01 0.078299852 0.44131103 0.44131103 0 0.44131103 + 200 0.02 0.081260369 -0.2174146 -0.2174146 0 -0.2174146 + 300 0.03 0.081195064 -0.87039697 -0.87039697 0 -0.87039697 + 400 0.04 0.087298284 -1.7069593 -1.7069593 0 -1.7069593 + 500 0.05 0.087663192 -2.1882865 -2.1882865 0 -2.1882865 + 600 0.06 0.091713114 -2.926766 -2.926766 0 -2.926766 + 700 0.07 0.093779218 -3.3532704 -3.3532704 0 -3.3532704 + 800 0.08 0.097960251 -3.9343481 -3.9343481 0 -3.9343481 + 900 0.09 0.10193598 -4.7944099 -4.7944099 0 -4.7944099 + 1000 0.1 0.10832963 -5.3823924 -5.3823924 0 -5.3823924 +Loop time of 0.40066 on 4 procs for 1000 steps with 500 atoms + +Performance: 21.564 ns/day, 1.113 hours/ns, 2495.885 timesteps/s, 1.248 Matom-step/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 | 0.032435 | 0.033013 | 0.033957 | 0.3 | 8.24 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.016106 | 0.016898 | 0.017915 | 0.5 | 4.22 +Output | 0.00012331 | 0.00013523 | 0.00016852 | 0.0 | 0.03 +Modify | 0.34913 | 0.34974 | 0.35017 | 0.1 | 87.29 +Other | | 0.0008755 | | | 0.22 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 597.5 ave 600 max 595 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2500 ave 2500 max 2500 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1 deleted file mode 100644 index 4a744700f9..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1 +++ /dev/null @@ -1,110 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -units metal -dimension 3 -boundary p p p - -atom_style spin - -# necessary for the serial algorithm (sametag) -atom_modify map array -read_data Norm_randXY_8x8x32.data - orthogonal box = (0 0 0) to (28.32 28.32 113.28) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 8192 atoms - read_data CPU = 0.022048 secs - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs and computes - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 8 8 31 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 19.99 | 19.99 | 19.99 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 0 0 0.0177864461018737 -36558.7284872918 -661.829206399896 1274.398774669 0 -36558.7284872918 - 20 0.002 0.0177864377256184 -36558.7389378387 -661.839683504936 1259.94171978912 0.00986992693139795 -36558.7284878577 - 40 0.004 0.017786472977471 -36558.7684525639 -661.869582914286 1224.05894016152 0.0377451568363827 -36558.7284891299 - 60 0.006 0.0177865119543331 -36558.8126238543 -661.915330492427 1184.24369688088 0.0794631076347515 -36558.728490712 - 80 0.008 0.0177865172048059 -36558.8659242367 -661.972562482488 1152.05459929593 0.129803482511904 -36558.7284922233 - 100 0.01 0.0177865063752424 -36558.9229549739 -662.037138807935 1129.51470280479 0.183667498513087 -36558.7284933644 -Loop time of 14.3276 on 1 procs for 100 steps with 8192 atoms - -Performance: 0.060 ns/day, 397.988 hours/ns, 6.980 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 | 4.0409 | 4.0409 | 4.0409 | 0.0 | 28.20 -Neigh | 3.6219 | 3.6219 | 3.6219 | 0.0 | 25.28 -Comm | 0.055327 | 0.055327 | 0.055327 | 0.0 | 0.39 -Output | 2.4259 | 2.4259 | 2.4259 | 0.0 | 16.93 -Modify | 4.1688 | 4.1688 | 4.1688 | 0.0 | 29.10 -Other | | 0.01477 | | | 0.10 - -Nlocal: 8192 ave 8192 max 8192 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 14621 ave 14621 max 14621 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 573440 ave 573440 max 573440 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1146880 -Ave neighs/atom = 140 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:14 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4 deleted file mode 100644 index 6ce648abf3..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4 +++ /dev/null @@ -1,110 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -units metal -dimension 3 -boundary p p p - -atom_style spin - -# necessary for the serial algorithm (sametag) -atom_modify map array -read_data Norm_randXY_8x8x32.data - orthogonal box = (0 0 0) to (28.32 28.32 113.28) - 1 by 1 by 4 MPI processor grid - reading atoms ... - 8192 atoms - read_data CPU = 0.013634 secs - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs and computes - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 8 8 31 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.961 | 9.047 | 9.29 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 0 0 0.0177864461018739 -36558.7284872997 -661.829206399894 1274.398774669 0 -36558.7284872997 - 20 0.002 0.0177863981273124 -36558.7389378386 -661.839683504262 1259.94177798388 0.00986992629371963 -36558.7284878582 - 40 0.004 0.0177864622701489 -36558.7684525586 -661.869582908114 1224.05908191331 0.0377451510479599 -36558.7284891308 - 60 0.006 0.0177865625037858 -36558.8126238326 -661.915330472361 1184.24389640891 0.0794630890177406 -36558.72849071 - 80 0.008 0.0177865898045059 -36558.8659241943 -661.972562439245 1152.05483020781 0.129803443061299 -36558.7284922226 - 100 0.01 0.017786565190115 -36558.9229549058 -662.037138735432 1129.51495182843 0.183667434061771 -36558.7284933646 -Loop time of 4.35911 on 4 procs for 100 steps with 8192 atoms - -Performance: 0.198 ns/day, 121.086 hours/ns, 22.940 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.0924 | 1.1043 | 1.1117 | 0.7 | 25.33 -Neigh | 0.93575 | 0.94926 | 0.98325 | 2.0 | 21.78 -Comm | 0.044663 | 0.088288 | 0.11128 | 8.7 | 2.03 -Output | 0.64199 | 0.6587 | 0.67226 | 1.4 | 15.11 -Modify | 1.5412 | 1.5535 | 1.5706 | 0.9 | 35.64 -Other | | 0.005046 | | | 0.12 - -Nlocal: 2048 ave 2061 max 2035 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 5765 ave 5778 max 5752 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 143360 ave 144262 max 142469 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -FullNghs: 286720 ave 288540 max 284900 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 1146880 -Ave neighs/atom = 140 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:04 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1 b/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1 deleted file mode 100644 index 652f7da474..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1 +++ /dev/null @@ -1,116 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# start a spin-lattice simulation from a data file -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -read_restart restart_hcp_cobalt.equil -WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.cpp:736) - restoring atom style spin from restart - orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 1 by 1 MPI processor grid - restoring pair style spin/exchange from restart - 500 atoms - read_restart CPU = 0.00179696 secs - -# setting mass, mag. moments, and interactions - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 4 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.422 | 7.422 | 7.422 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 1000 0 0.108317262557656 -2200.38241212222 -5.38245988668244 2538.4247868621 0 -2200.38241212222 - 1020 0.002 0.108317318495042 -2200.39172132133 -5.39179331134703 2513.42968070374 0.144319963844279 -2200.38241256643 - 1040 0.004 0.108317415558744 -2200.41811580407 -5.418541526637 2478.87571728648 0.553516420254567 -2200.38241354532 - 1060 0.006 0.108317473592946 -2200.45801216332 -5.45990062771403 2449.77257658726 1.17203792179707 -2200.38241476526 - 1080 0.008 0.108317450745396 -2200.5068824087 -5.51245983698347 2427.25022669715 1.92968606059505 -2200.3824160902 - 1100 0.01 0.108317381572202 -2200.55976028827 -5.57250071024394 2400.86131889957 2.74946927499959 -2200.38241728649 -Loop time of 0.954493 on 1 procs for 100 steps with 500 atoms - -Performance: 0.905 ns/day, 26.514 hours/ns, 104.768 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 | 0.27043 | 0.27043 | 0.27043 | 0.0 | 28.33 -Neigh | 0.26148 | 0.26148 | 0.26148 | 0.0 | 27.40 -Comm | 0.0071123 | 0.0071123 | 0.0071123 | 0.0 | 0.75 -Output | 0.14169 | 0.14169 | 0.14169 | 0.0 | 14.84 -Modify | 0.2726 | 0.2726 | 0.2726 | 0.0 | 28.56 -Other | | 0.001178 | | | 0.12 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2534 ave 2534 max 2534 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 36500 ave 36500 max 36500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 73000 ave 73000 max 73000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 73000 -Ave neighs/atom = 146 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4 b/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4 deleted file mode 100644 index c22c672f6b..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4 +++ /dev/null @@ -1,115 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# start a spin-lattice simulation from a data file -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -read_restart restart_hcp_cobalt.equil - restoring atom style spin from restart - orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 2 by 2 MPI processor grid - restoring pair style spin/exchange from restart - 500 atoms - read_restart CPU = 0.00173593 secs - -# setting mass, mag. moments, and interactions - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 4 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.324 | 7.324 | 7.324 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 1000 0 0.108317262557656 -2200.38241212182 -5.38245988668244 2538.4247868621 0 -2200.38241212182 - 1020 0.002 0.108317316216432 -2200.39172132147 -5.39179331147409 2513.42945241007 0.14431996581917 -2200.38241256644 - 1040 0.004 0.108317347939802 -2200.41811580574 -5.41854152831072 2478.87544274124 0.553516446104432 -2200.38241354532 - 1060 0.006 0.108317342440309 -2200.45801216927 -5.45990063373049 2449.77218633122 1.17203801398165 -2200.38241476526 - 1080 0.008 0.108317320345284 -2200.50688241767 -5.51245984623572 2427.2497145488 1.92968619968329 -2200.3824160902 - 1100 0.01 0.10831728372281 -2200.55976028296 -5.57250070536486 2400.86059511731 2.74946919265255 -2200.38241728649 -Loop time of 0.405615 on 4 procs for 100 steps with 500 atoms - -Performance: 2.130 ns/day, 11.267 hours/ns, 246.539 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.075661 | 0.076798 | 0.077343 | 0.2 | 18.93 -Neigh | 0.063154 | 0.064974 | 0.066991 | 0.5 | 16.02 -Comm | 0.012538 | 0.013787 | 0.015151 | 0.8 | 3.40 -Output | 0.039155 | 0.040842 | 0.042502 | 0.6 | 10.07 -Modify | 0.20709 | 0.20883 | 0.21036 | 0.3 | 51.49 -Other | | 0.0003826 | | | 0.09 - -Nlocal: 125 ave 127 max 122 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Nghost: 1387 ave 1390 max 1385 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 9125 ave 9272 max 8945 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -FullNghs: 18250 ave 18542 max 17812 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 73000 -Ave neighs/atom = 146 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1 deleted file mode 100644 index 8ad14c55c0..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1 +++ /dev/null @@ -1,120 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# fcc cobalt in a 3d periodic box - -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -lattice hcp 2.5071 -Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - create_atoms CPU = 0.000952005 secs - -# setting mass, mag. moments, and interactions for cobalt - -mass 1 58.93 - -set group all spin/random 31 1.72 - 500 settings made for spin/random - -pair_style spin/exchange 4.0 -pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -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 100.0 0.01 21 - -fix 3 all nve/spin lattice frozen -timestep 0.0001 - -# compute and output options - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo_style custom step time v_magnorm pe v_emag temp etotal -thermo 100 - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 1000 -Neighbor list info ... - update every 10 steps, delay 20 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.1 - ghost atom cutoff = 4.1 - binsize = 2.05, bins = 7 11 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes -Step Time v_magnorm PotEng v_emag Temp TotEng - 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 - 100 0.01 0.077628154 0.36693917 0.36693917 0 0.36693917 - 200 0.02 0.076678996 -0.20242315 -0.20242315 0 -0.20242315 - 300 0.03 0.079174837 -0.67595514 -0.67595514 0 -0.67595514 - 400 0.04 0.085031632 -1.5172851 -1.5172851 0 -1.5172851 - 500 0.05 0.08702747 -2.0426628 -2.0426628 0 -2.0426628 - 600 0.06 0.087066482 -2.6297745 -2.6297745 0 -2.6297745 - 700 0.07 0.089788894 -3.314538 -3.314538 0 -3.314538 - 800 0.08 0.091699611 -4.0287043 -4.0287043 0 -4.0287043 - 900 0.09 0.090038899 -4.600601 -4.600601 0 -4.600601 - 1000 0.1 0.093257309 -5.2352261 -5.2352261 0 -5.2352261 -Loop time of 3.30071 on 1 procs for 1000 steps with 500 atoms - -Performance: 2.618 ns/day, 9.169 hours/ns, 302.965 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 | 0.3844 | 0.3844 | 0.3844 | 0.0 | 11.65 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.019863 | 0.019863 | 0.019863 | 0.0 | 0.60 -Output | 1.3844 | 1.3844 | 1.3844 | 0.0 | 41.94 -Modify | 1.5084 | 1.5084 | 1.5084 | 0.0 | 45.70 -Other | | 0.00367 | | | 0.11 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1221 ave 1221 max 1221 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 10000 ave 10000 max 10000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 10000 -Ave neighs/atom = 20 -Neighbor list builds = 0 -Dangerous builds = 0 -write_restart restart_hcp_cobalt.equil - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4 deleted file mode 100644 index c0c1ec130c..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4 +++ /dev/null @@ -1,120 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# fcc cobalt in a 3d periodic box - -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -lattice hcp 2.5071 -Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - create_atoms CPU = 0.000663042 secs - -# setting mass, mag. moments, and interactions for cobalt - -mass 1 58.93 - -set group all spin/random 31 1.72 - 500 settings made for spin/random - -pair_style spin/exchange 4.0 -pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -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 100.0 0.01 21 - -fix 3 all nve/spin lattice frozen -timestep 0.0001 - -# compute and output options - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo_style custom step time v_magnorm pe v_emag temp etotal -thermo 100 - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 1000 -Neighbor list info ... - update every 10 steps, delay 20 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.1 - ghost atom cutoff = 4.1 - binsize = 2.05, bins = 7 11 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.868 | 6.868 | 6.868 Mbytes -Step Time v_magnorm PotEng v_emag Temp TotEng - 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 - 100 0.01 0.078299981 0.44129792 0.44129792 0 0.44129792 - 200 0.02 0.081260508 -0.21742361 -0.21742361 0 -0.21742361 - 300 0.03 0.081195603 -0.87041046 -0.87041046 0 -0.87041046 - 400 0.04 0.087298495 -1.7069519 -1.7069519 0 -1.7069519 - 500 0.05 0.087663924 -2.1883045 -2.1883045 0 -2.1883045 - 600 0.06 0.091713683 -2.9267461 -2.9267461 0 -2.9267461 - 700 0.07 0.093779119 -3.353314 -3.353314 0 -3.353314 - 800 0.08 0.097960611 -3.9344284 -3.9344284 0 -3.9344284 - 900 0.09 0.10193463 -4.7944004 -4.7944004 0 -4.7944004 - 1000 0.1 0.10831726 -5.3824599 -5.3824599 0 -5.3824599 -Loop time of 1.7839 on 4 procs for 1000 steps with 500 atoms - -Performance: 4.843 ns/day, 4.955 hours/ns, 560.569 timesteps/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.10068 | 0.10749 | 0.11461 | 1.5 | 6.03 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.052378 | 0.062171 | 0.07177 | 2.8 | 3.49 -Output | 0.4054 | 0.42334 | 0.44025 | 2.0 | 23.73 -Modify | 1.174 | 1.1893 | 1.2043 | 1.1 | 66.67 -Other | | 0.001558 | | | 0.09 - -Nlocal: 125 ave 125 max 125 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 597.5 ave 600 max 595 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 2500 ave 2500 max 2500 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 10000 -Ave neighs/atom = 20 -Neighbor list builds = 0 -Dangerous builds = 0 -write_restart restart_hcp_cobalt.equil - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/SPIN/read_restart/restart_hcp_cobalt.equil b/examples/SPIN/read_restart/restart_hcp_cobalt.equil index d7f92285db..8caa9da7dd 100644 Binary files a/examples/SPIN/read_restart/restart_hcp_cobalt.equil and b/examples/SPIN/read_restart/restart_hcp_cobalt.equil differ 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 38c669e166..1d98901702 100644 --- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve +++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve @@ -50,5 +50,5 @@ 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 10000 # run 1 diff --git a/examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 b/examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 new file mode 100644 index 0000000000..249c7b1bfe --- /dev/null +++ b/examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 @@ -0,0 +1,188 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin +# atom_style spin/kk + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 3.0 0.0 3.0 0.0 3.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 54 atoms + using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin/random 31 2.2 +Setting atom values ... +WARNING: Set attribute spin/random is deprecated. Please use spin/atom/random instead. (src/set.cpp:293) + 54 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +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 0.0 0.00 21 +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable emag equal c_out_mag[5] +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 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.773367 + ghost atom cutoff = 5.773367 + binsize = 2.8866835, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 5.7733670002446 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Dump 1 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) +Per MPI rank memory allocation (min/avg/max) = 5.626 | 5.626 | 5.626 Mbytes + Step Time v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 1836.2373 100.00358 -0.26674297 0.6851033 -231.38675 -230.70164 + 200 0.02 1751.0384 48.019015 -0.27512361 0.32896808 -231.03061 -230.70164 + 400 0.04 1776.2639 19.035769 -0.28188188 0.13041001 -230.83205 -230.70164 + 600 0.06 1787.5802 60.069761 -0.2772323 0.41152518 -231.11317 -230.70164 + 800 0.08 1706.5552 50.79606 -0.27292548 0.34799302 -231.04963 -230.70164 + 1000 0.1 2120.1611 44.605193 -0.26987056 0.3055807 -231.00722 -230.70164 + 1200 0.12 1754.9393 64.57232 -0.26943293 0.44237126 -231.14401 -230.70164 + 1400 0.14 1912.6009 44.177766 -0.26857448 0.3026525 -231.00429 -230.70164 + 1600 0.16 1875.5315 40.249733 -0.27481087 0.27574238 -230.97738 -230.70164 + 1800 0.18 1837.1786 62.817536 -0.28092582 0.4303496 -231.13199 -230.70164 + 2000 0.2 1860.1719 54.167659 -0.28282659 0.37109113 -231.07273 -230.70164 + 2200 0.22 1691.658 46.643932 -0.29528237 0.31954767 -231.02119 -230.70164 + 2400 0.24 1525.2579 57.361866 -0.30189945 0.39297397 -231.09462 -230.70164 + 2600 0.26 1505.1726 56.239347 -0.30898994 0.38528383 -231.08693 -230.70164 + 2800 0.28 1415.9555 47.818074 -0.31351411 0.32759147 -231.02923 -230.70164 + 3000 0.3 1248.4308 49.608492 -0.31727375 0.33985725 -231.0415 -230.70164 + 3200 0.32 1200.7605 51.495405 -0.31565357 0.35278409 -231.05443 -230.70164 + 3400 0.34 1746.137 56.967184 -0.30906485 0.39027008 -231.09191 -230.70164 + 3600 0.36 1805.3667 55.030692 -0.30799197 0.37700359 -231.07865 -230.70164 + 3800 0.38 1609.9498 59.452017 -0.30520539 0.40729315 -231.10894 -230.70164 + 4000 0.4 1686.1863 57.338707 -0.30240026 0.39281531 -231.09446 -230.70164 + 4200 0.42 1961.3516 41.421108 -0.30479326 0.28376722 -230.98541 -230.70164 + 4400 0.44 1971.1808 54.038289 -0.30876936 0.37020484 -231.07185 -230.70164 + 4600 0.46 1819.428 56.766201 -0.3129157 0.38889319 -231.09054 -230.70164 + 4800 0.48 1494.1263 47.402453 -0.32868332 0.32474414 -231.02639 -230.70164 + 5000 0.5 1601.6127 63.404101 -0.33283819 0.43436803 -231.13601 -230.70164 + 5200 0.52 1567.7429 62.783792 -0.34753005 0.43011843 -231.13176 -230.70164 + 5400 0.54 1686.234 40.450417 -0.3603489 0.27711722 -230.97876 -230.70164 + 5600 0.56 1651.1927 64.255456 -0.36569031 0.44020049 -231.14184 -230.70164 + 5800 0.58 1380.639 75.386226 -0.36870019 0.51645503 -231.2181 -230.70164 + 6000 0.6 1539.07 40.611642 -0.36303517 0.27822173 -230.97986 -230.70164 + 6200 0.62 1442.2286 50.254503 -0.36560331 0.34428293 -231.04592 -230.70164 + 6400 0.64 1263.6928 69.095161 -0.36822748 0.47335628 -231.175 -230.70164 + 6600 0.66 1468.1529 54.534243 -0.37319988 0.37360252 -231.07524 -230.70164 + 6800 0.68 1289.4927 60.381892 -0.38478834 0.41366352 -231.11531 -230.70164 + 7000 0.7 1121.6702 58.691171 -0.39652609 0.40208075 -231.10372 -230.70164 + 7200 0.72 1018.1068 53.528417 -0.40711639 0.36671182 -231.06835 -230.70164 + 7400 0.74 1115.0342 78.62129 -0.41729373 0.53861776 -231.24026 -230.70164 + 7600 0.76 1329.4621 65.650574 -0.41928751 0.44975815 -231.1514 -230.70164 + 7800 0.78 1154.164 45.603278 -0.41263444 0.31241837 -231.01406 -230.70164 + 8000 0.8 1090.2959 62.148282 -0.40987933 0.42576469 -231.12741 -230.70164 + 8200 0.82 1303.4698 63.864431 -0.41301445 0.43752166 -231.13916 -230.70164 + 8400 0.84 1144.2181 52.222297 -0.41645089 0.35776387 -231.05941 -230.70164 + 8600 0.86 1005.3359 61.59129 -0.41282114 0.42194885 -231.12359 -230.70164 + 8800 0.88 1453.8465 70.876149 -0.41920851 0.48555745 -231.1872 -230.70164 + 9000 0.9 1325.9116 63.675151 -0.42450864 0.43622494 -231.13787 -230.70164 + 9200 0.92 1213.5738 58.297881 -0.42722791 0.3993864 -231.10103 -230.70164 + 9400 0.94 1227.437 57.375795 -0.44309693 0.39306939 -231.09471 -230.70164 + 9600 0.96 1192.79 65.822598 -0.44760999 0.45093664 -231.15258 -230.70164 + 9800 0.98 1231.5166 69.119896 -0.45335245 0.47352573 -231.17517 -230.70164 + 10000 1 1284.2809 66.166068 -0.45872955 0.45328969 -231.15493 -230.70164 +Loop time of 5.97474 on 1 procs for 10000 steps with 54 atoms + +Performance: 14.461 ns/day, 1.660 hours/ns, 1673.714 timesteps/s, 90.381 katom-step/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 | 2.501 | 2.501 | 2.501 | 0.0 | 41.86 +Neigh | 0.016481 | 0.016481 | 0.016481 | 0.0 | 0.28 +Comm | 0.37576 | 0.37576 | 0.37576 | 0.0 | 6.29 +Output | 0.12311 | 0.12311 | 0.12311 | 0.0 | 2.06 +Modify | 2.9317 | 2.9317 | 2.9317 | 0.0 | 49.07 +Other | | 0.02661 | | | 0.45 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 777 ave 777 max 777 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1700 ave 1700 max 1700 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3400 ave 3400 max 3400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3400 +Ave neighs/atom = 62.962963 +Neighbor list builds = 58 +Dangerous builds = 0 +# run 1 +Total wall time: 0:00:06 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 a1f739fe54..e65aff510f 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice @@ -49,4 +49,4 @@ variable tmag equal c_out_mag[6] thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo 200 -run 200000 +run 20000 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 102f76a2a6..f88c2c51a2 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin @@ -32,7 +32,7 @@ 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 0.0 0.0 0.0 48279 +fix 2 all langevin 0.0 0.0 0.001 48279 fix 3 all langevin/spin 200.0 0.01 321 fix 4 all nve/spin lattice moving timestep 0.001 @@ -50,4 +50,4 @@ variable tmag equal c_out_mag[6] thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo 200 -run 200000 +run 20000 diff --git a/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 new file mode 100644 index 0000000000..11ba5e8c1e --- /dev/null +++ b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 @@ -0,0 +1,240 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin +# atom_style spin/kk + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 3.0 0.0 3.0 0.0 3.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 54 atoms + using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin 2.2 0.0 0.0 1.0 +Setting atom values ... +WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268) + 54 settings made for spin +velocity all create 400 4928459 rot yes dist gaussian + +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 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 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_tmag temp v_emag ke pe etotal +thermo 200 + +run 20000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.773367 + ghost atom cutoff = 5.773367 + binsize = 2.8866835, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 5.7733670002446 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) pair spin/neel, perpetual, copy from (2) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes + Step Time v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 1.4336203e-31 400.01433 -22.021022 2.7404132 -253.14103 -250.40061 + 200 0.2 0.26275543 188.91786 -21.983513 1.2942362 -251.94911 -250.65488 + 400 0.4 0.56095049 204.95947 -21.977046 1.4041338 -251.914 -250.50987 + 600 0.6 0.81480981 203.28763 -21.98548 1.3926804 -251.88478 -250.4921 + 800 0.8 0.97590428 184.8694 -21.974142 1.266501 -251.73716 -250.47066 + 1000 1 1.1324742 184.65547 -21.986309 1.2650354 -252.03248 -250.76744 + 1200 1.2 1.5284342 207.55788 -21.974821 1.421935 -251.7769 -250.35497 + 1400 1.4 1.8310776 220.75396 -21.979994 1.5123385 -251.93989 -250.42755 + 1600 1.6 2.2057174 236.04272 -21.973951 1.6170785 -251.98625 -250.36917 + 1800 1.8 2.7760928 195.92697 -21.96808 1.3422541 -251.7495 -250.40725 + 2000 2 3.2171354 161.33811 -21.975129 1.1052932 -251.86337 -250.75808 + 2200 2.2 3.8284998 193.21861 -21.968067 1.3236997 -251.86609 -250.54239 + 2400 2.4 4.4109629 203.79368 -21.971813 1.3961472 -251.92264 -250.52649 + 2600 2.6 4.5056291 200.81431 -21.960649 1.3757362 -251.80976 -250.43403 + 2800 2.8 4.6221125 185.57027 -21.972664 1.2713025 -252.0384 -250.76709 + 3000 3 4.9059897 216.00877 -21.966875 1.4798302 -252.13406 -250.65423 + 3200 3.2 5.3958965 152.77626 -21.956779 1.0466377 -251.66 -250.61337 + 3400 3.4 5.9881406 170.70538 -21.964189 1.1694663 -251.9061 -250.73663 + 3600 3.6 6.134982 210.99981 -21.945137 1.4455149 -251.75025 -250.30474 + 3800 3.8 6.5940545 239.12527 -21.953159 1.6381964 -251.90813 -250.26993 + 4000 4 6.9355034 181.99614 -21.938591 1.2468169 -251.59724 -250.35043 + 4200 4.2 7.3712919 242.52183 -21.932318 1.6614656 -251.71104 -250.04957 + 4400 4.4 7.5924709 164.34328 -21.942361 1.1258809 -251.64032 -250.51444 + 4600 4.6 8.1833481 205.94973 -21.941491 1.4109179 -251.57627 -250.16536 + 4800 4.8 8.40416 169.96914 -21.945774 1.1644225 -251.87887 -250.71444 + 5000 5 8.4422416 189.79518 -21.94955 1.3002465 -251.80055 -250.50031 + 5200 5.2 8.3667008 195.86473 -21.934302 1.3418277 -251.64678 -250.30495 + 5400 5.4 8.7075519 204.82319 -21.947339 1.4032002 -251.85712 -250.45392 + 5600 5.6 8.6582399 191.25854 -21.933614 1.3102717 -251.51648 -250.2062 + 5800 5.8 8.896287 180.44446 -21.923523 1.2361867 -251.68003 -250.44384 + 6000 6 9.1379808 248.49596 -21.938845 1.7023931 -251.84502 -250.14263 + 6200 6.2 8.9724294 181.67979 -21.939567 1.2446497 -251.81639 -250.57174 + 6400 6.4 8.7735241 198.31668 -21.952115 1.3586255 -251.97841 -250.61979 + 6600 6.6 9.0394523 218.6735 -21.934717 1.4980857 -251.85133 -250.35325 + 6800 6.8 9.5779186 203.83536 -21.937873 1.3964328 -251.98448 -250.58804 + 7000 7 9.7893273 185.56096 -21.949319 1.2712387 -252.09057 -250.81934 + 7200 7.2 9.5292481 205.53224 -21.936466 1.4080577 -251.98037 -250.57231 + 7400 7.4 9.7369072 200.76528 -21.944609 1.3754003 -251.88128 -250.50588 + 7600 7.6 9.9385522 217.68239 -21.920768 1.4912959 -251.6169 -250.1256 + 7800 7.8 9.8656638 219.17274 -21.92302 1.5015059 -251.50189 -250.00039 + 8000 8 9.2380618 264.13229 -21.936112 1.8095143 -251.71532 -249.9058 + 8200 8.2 9.3384949 239.58029 -21.941834 1.6413137 -251.73551 -250.0942 + 8400 8.4 9.1684312 207.27974 -21.938426 1.4200295 -251.59062 -250.17059 + 8600 8.6 8.8407032 200.79452 -21.933328 1.3756006 -251.48006 -250.10446 + 8800 8.8 8.84683 218.44316 -21.949738 1.4965077 -251.92925 -250.43275 + 9000 9 9.0686442 216.06373 -21.942255 1.4802067 -251.79797 -250.31776 + 9200 9.2 9.2783597 187.56662 -21.93374 1.2849791 -251.87884 -250.59386 + 9400 9.4 9.2794158 203.78139 -21.955284 1.396063 -252.09328 -250.69722 + 9600 9.6 9.3563189 196.15871 -21.948544 1.3438417 -251.85685 -250.51301 + 9800 9.8 9.6458819 215.38334 -21.94895 1.4755455 -251.92219 -250.44665 + 10000 10 9.5073837 178.61601 -21.955281 1.2236604 -251.97306 -250.7494 + 10200 10.2 9.3510908 185.21136 -21.94749 1.2688437 -251.83233 -250.56349 + 10400 10.4 9.8171891 194.92192 -21.945394 1.3353687 -251.86067 -250.5253 + 10600 10.6 9.5996138 213.90302 -21.945461 1.4654042 -251.72508 -250.25968 + 10800 10.8 9.8602813 208.57912 -21.936736 1.4289312 -251.55778 -250.12885 + 11000 11 10.652287 202.88507 -21.933085 1.3899225 -251.69631 -250.30639 + 11200 11.2 10.413298 171.86972 -21.919711 1.1774429 -251.16232 -249.98488 + 11400 11.4 10.589727 179.33897 -21.927537 1.2286132 -251.65266 -250.42405 + 11600 11.6 11.099271 176.43012 -21.925025 1.2086853 -251.65796 -250.44927 + 11800 11.8 11.49558 216.78529 -21.935923 1.48515 -251.51958 -250.03443 + 12000 12 11.190687 206.45545 -21.941866 1.4143824 -251.55494 -250.14055 + 12200 12.2 11.372777 216.26373 -21.934028 1.4815769 -251.75482 -250.27324 + 12400 12.4 11.303952 218.67625 -21.928577 1.4981046 -251.73908 -250.24098 + 12600 12.6 11.065605 188.25083 -21.925979 1.2896665 -251.49808 -250.20841 + 12800 12.8 11.289265 209.423 -21.933529 1.4347125 -251.85142 -250.41671 + 13000 13 11.412931 148.86392 -21.93732 1.0198351 -251.88347 -250.86364 + 13200 13.2 11.677538 187.03356 -21.923919 1.2813272 -251.52124 -250.23991 + 13400 13.4 12.451801 237.44268 -21.93385 1.6266694 -251.70112 -250.07445 + 13600 13.6 12.981208 196.47947 -21.926751 1.3460391 -251.80509 -250.45905 + 13800 13.8 13.301789 191.61721 -21.921891 1.3127288 -251.85541 -250.54268 + 14000 14 13.726635 212.61693 -21.922086 1.4565934 -252.06804 -250.61145 + 14200 14.2 13.715662 197.51397 -21.915949 1.3531263 -251.71314 -250.36002 + 14400 14.4 13.340257 210.15601 -21.927197 1.4397342 -251.73271 -250.29297 + 14600 14.6 14.118672 175.1782 -21.923635 1.2001087 -251.54286 -250.34275 + 14800 14.8 14.52801 211.5541 -21.919371 1.4493122 -251.74119 -250.29188 + 15000 15 14.522566 207.59406 -21.919623 1.4221828 -251.74192 -250.31974 + 15200 15.2 15.1446 191.32404 -21.902291 1.3107204 -251.52754 -250.21682 + 15400 15.4 15.815481 160.35385 -21.918453 1.0985502 -251.75506 -250.65651 + 15600 15.6 16.942896 211.32891 -21.89554 1.4477695 -251.42064 -249.97287 + 15800 15.8 17.339057 213.03178 -21.903747 1.4594355 -251.5815 -250.12207 + 16000 16 17.610695 211.72009 -21.899083 1.4504494 -251.51043 -250.05998 + 16200 16.2 18.352293 236.99887 -21.9043 1.623629 -251.79466 -250.17103 + 16400 16.4 17.898896 208.62272 -21.904247 1.42923 -251.66653 -250.2373 + 16600 16.6 18.005606 169.07581 -21.910252 1.1583025 -251.84184 -250.68353 + 16800 16.8 18.884686 198.75251 -21.900417 1.3616113 -251.8573 -250.49569 + 17000 17 19.454235 182.70172 -21.904544 1.2516507 -251.66187 -250.41021 + 17200 17.2 19.497759 157.47203 -21.904461 1.0788075 -251.88582 -250.80701 + 17400 17.4 19.470705 215.43531 -21.887158 1.4759016 -251.82426 -250.34836 + 17600 17.6 19.553888 212.82066 -21.89372 1.4579892 -251.79955 -250.34157 + 17800 17.8 19.646117 236.85339 -21.8983 1.6226323 -251.75304 -250.13041 + 18000 18 20.205554 253.85283 -21.909061 1.7390919 -251.84228 -250.10319 + 18200 18.2 20.065135 233.11058 -21.882631 1.5969911 -251.54972 -249.95273 + 18400 18.4 20.76763 209.7018 -21.895306 1.4366225 -251.79971 -250.36309 + 18600 18.6 21.369833 214.39422 -21.882332 1.4687693 -251.53344 -250.06467 + 18800 18.8 21.939164 216.25928 -21.89097 1.4815464 -251.82112 -250.33958 + 19000 19 22.817363 215.27695 -21.882698 1.4748166 -251.82572 -250.3509 + 19200 19.2 23.705114 182.22745 -21.879076 1.2484016 -251.43044 -250.18204 + 19400 19.4 23.441248 222.83743 -21.879144 1.5266119 -251.76376 -250.23715 + 19600 19.6 23.435558 218.16026 -21.86114 1.4945696 -251.59729 -250.10272 + 19800 19.8 24.074607 222.78958 -21.87264 1.5262841 -251.7863 -250.26001 + 20000 20 23.618814 222.44332 -21.870985 1.5239119 -251.37299 -249.84908 +Loop time of 22.6158 on 1 procs for 20000 steps with 54 atoms + +Performance: 76.407 ns/day, 0.314 hours/ns, 884.338 timesteps/s, 47.754 katom-step/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 | 8.9116 | 8.9116 | 8.9116 | 0.0 | 39.40 +Neigh | 0.26535 | 0.26535 | 0.26535 | 0.0 | 1.17 +Comm | 0.65637 | 0.65637 | 0.65637 | 0.0 | 2.90 +Output | 0.0036141 | 0.0036141 | 0.0036141 | 0.0 | 0.02 +Modify | 12.725 | 12.725 | 12.725 | 0.0 | 56.26 +Other | | 0.05425 | | | 0.24 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 632 ave 632 max 632 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1677 ave 1677 max 1677 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3354 ave 3354 max 3354 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3354 +Ave neighs/atom = 62.111111 +Neighbor list builds = 1000 +Dangerous builds = 1000 +Total wall time: 0:00:22 diff --git a/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 new file mode 100644 index 0000000000..e8a14b259c --- /dev/null +++ b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 @@ -0,0 +1,241 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin +# atom_style spin/kk + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 3.0 0.0 3.0 0.0 3.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 54 atoms + using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin 2.2 0.0 0.0 1.0 +Setting atom values ... +WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268) + 54 settings made for spin +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 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 0.0 0.0 0.001 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 + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_tmag temp v_emag ke pe etotal +thermo 200 + +run 20000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.773367 + ghost atom cutoff = 5.773367 + binsize = 2.8866835, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 5.7733670002446 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) pair spin/neel, perpetual, copy from (2) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes + Step Time v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 1.4336203e-31 0 -22.021022 0 -253.14103 -253.14103 + 200 0.2 185.03537 7.1508965e-05 -21.172867 4.8989274e-07 -252.29287 -252.29287 + 400 0.4 209.70221 8.8414079e-05 -21.060203 6.0570608e-07 -252.1802 -252.1802 + 600 0.6 185.48899 0.00010245242 -21.112413 7.0187977e-07 -252.23241 -252.23241 + 800 0.8 223.05275 8.1457051e-05 -21.018423 5.5804496e-07 -252.13842 -252.13842 + 1000 1 213.0164 8.9515898e-05 -21.048926 6.1325441e-07 -252.16892 -252.16892 + 1200 1.2 246.36673 0.0001154676 -20.930718 7.9104402e-07 -252.05072 -252.05072 + 1400 1.4 196.53774 6.2911172e-05 -21.154732 4.3099109e-07 -252.27473 -252.27473 + 1600 1.6 182.01716 0.00010355261 -21.16282 7.0941692e-07 -252.28282 -252.28282 + 1800 1.8 210.96677 8.7541641e-05 -21.088701 5.997292e-07 -252.2087 -252.2087 + 2000 2 253.99717 0.00010826381 -20.86351 7.416924e-07 -251.98351 -251.98351 + 2200 2.2 216.1501 9.6113637e-05 -21.030784 6.5845412e-07 -252.15078 -252.15078 + 2400 2.4 223.43699 8.5950374e-05 -21.009537 5.8882776e-07 -252.12954 -252.12954 + 2600 2.6 218.14727 0.00010110952 -20.970036 6.9267987e-07 -252.09004 -252.09004 + 2800 2.8 232.40923 0.00011013217 -20.973661 7.5449212e-07 -252.09366 -252.09366 + 3000 3 237.03942 0.0001227047 -20.923005 8.4062388e-07 -252.043 -252.043 + 3200 3.2 193.18057 6.4453691e-05 -21.192632 4.4155855e-07 -252.31263 -252.31263 + 3400 3.4 215.89559 0.00010926778 -20.99777 7.4857038e-07 -252.11777 -252.11777 + 3600 3.6 166.54235 7.286928e-05 -21.241556 4.9921196e-07 -252.36156 -252.36156 + 3800 3.8 159.38579 5.7560855e-05 -21.290065 3.9433719e-07 -252.41007 -252.41007 + 4000 4 170.59358 7.7217892e-05 -21.234059 5.2900339e-07 -252.35406 -252.35406 + 4200 4.2 215.77287 8.7497504e-05 -21.031438 5.9942683e-07 -252.15144 -252.15144 + 4400 4.4 197.99439 8.3188835e-05 -21.136708 5.6990905e-07 -252.25671 -252.25671 + 4600 4.6 225.89271 0.00015400081 -20.963516 1.0550269e-06 -252.08352 -252.08352 + 4800 4.8 202.99311 0.00014034452 -21.013112 9.614705e-07 -252.13311 -252.13311 + 5000 5 213.82643 0.00011505981 -21.058401 7.8825036e-07 -252.1784 -252.1784 + 5200 5.2 185.50349 8.6160092e-05 -21.172207 5.902645e-07 -252.29221 -252.29221 + 5400 5.4 201.98179 0.00010791717 -21.096481 7.3931764e-07 -252.21648 -252.21648 + 5600 5.6 171.20549 6.8869235e-05 -21.197869 4.718085e-07 -252.31787 -252.31787 + 5800 5.8 227.95465 0.00012603913 -21.009323 8.6346729e-07 -252.12932 -252.12932 + 6000 6 200.21111 0.00010449734 -21.110701 7.1588912e-07 -252.2307 -252.2307 + 6200 6.2 160.58077 7.2836942e-05 -21.267151 4.9899042e-07 -252.38715 -252.38715 + 6400 6.4 200.05407 9.0509705e-05 -21.073988 6.2006277e-07 -252.19399 -252.19399 + 6600 6.6 190.65275 0.0001033421 -21.158207 7.0797478e-07 -252.27821 -252.27821 + 6800 6.8 228.26898 0.00014786596 -20.911618 1.0129983e-06 -252.03162 -252.03162 + 7000 7 181.38559 7.164051e-05 -21.178965 4.9079392e-07 -252.29897 -252.29897 + 7200 7.2 206.68689 0.00014900154 -20.996098 1.0207779e-06 -252.1161 -252.1161 + 7400 7.4 192.31745 7.9639216e-05 -21.152927 5.4559136e-07 -252.27293 -252.27293 + 7600 7.6 190.74433 8.1341909e-05 -21.140079 5.5725615e-07 -252.26008 -252.26008 + 7800 7.8 174.0955 6.4367878e-05 -21.239195 4.4097067e-07 -252.3592 -252.35919 + 8000 8 160.00011 0.00012761576 -21.159302 8.7426845e-07 -252.2793 -252.2793 + 8200 8.2 210.43151 0.00014479042 -21.034928 9.9192846e-07 -252.15493 -252.15493 + 8400 8.4 234.76455 0.00017824488 -20.929712 1.2211178e-06 -252.04971 -252.04971 + 8600 8.6 186.41675 8.9522862e-05 -21.152624 6.1330212e-07 -252.27262 -252.27262 + 8800 8.8 182.51437 8.1196096e-05 -21.169538 5.5625721e-07 -252.28954 -252.28954 + 9000 9 205.7602 8.1712224e-05 -21.069704 5.597931e-07 -252.1897 -252.1897 + 9200 9.2 169.12461 4.5311332e-05 -21.260803 3.1041832e-07 -252.3808 -252.3808 + 9400 9.4 226.30809 0.00011391282 -20.976322 7.8039252e-07 -252.09632 -252.09632 + 9600 9.6 167.17205 9.1023114e-05 -21.226931 6.2358003e-07 -252.34693 -252.34693 + 9800 9.8 204.63476 0.00010727562 -21.045363 7.3492253e-07 -252.16536 -252.16536 + 10000 10 236.18563 8.998006e-05 -20.973452 6.1643429e-07 -252.09345 -252.09345 + 10200 10.2 194.32863 7.2352023e-05 -21.144235 4.9566835e-07 -252.26424 -252.26424 + 10400 10.4 212.89479 0.00011913313 -21.041706 8.1615576e-07 -252.16171 -252.1617 + 10600 10.6 215.20168 9.7714692e-05 -21.032571 6.6942261e-07 -252.15257 -252.15257 + 10800 10.8 297.63322 0.00013498385 -20.721355 9.2474566e-07 -251.84135 -251.84135 + 11000 11 221.40055 0.00010205784 -21.051231 6.9917662e-07 -252.17123 -252.17123 + 11200 11.2 242.39307 0.00013617253 -20.890742 9.3288909e-07 -252.01074 -252.01074 + 11400 11.4 165.26613 7.2237463e-05 -21.24741 4.9488352e-07 -252.36741 -252.36741 + 11600 11.6 216.24435 8.1150764e-05 -21.036156 5.5594665e-07 -252.15616 -252.15616 + 11800 11.8 183.53912 0.00010117662 -21.186918 6.9313953e-07 -252.30692 -252.30692 + 12000 12 220.44994 9.647801e-05 -21.023611 6.6095036e-07 -252.14361 -252.14361 + 12200 12.2 225.17986 9.472867e-05 -21.009823 6.48966e-07 -252.12982 -252.12982 + 12400 12.4 216.68616 8.9352492e-05 -21.025818 6.1213495e-07 -252.14582 -252.14582 + 12600 12.6 179.65027 6.5355297e-05 -21.199208 4.4773526e-07 -252.31921 -252.31921 + 12800 12.8 210.22912 7.5167585e-05 -21.071447 5.1495716e-07 -252.19145 -252.19145 + 13000 13 157.423 9.2895323e-05 -21.250615 6.3640614e-07 -252.37062 -252.37061 + 13200 13.2 204.52025 0.00012645764 -21.049044 8.6633447e-07 -252.16904 -252.16904 + 13400 13.4 198.28053 0.00012118522 -21.066084 8.3021421e-07 -252.18609 -252.18608 + 13600 13.6 237.99318 8.644348e-05 -20.978488 5.9220593e-07 -252.09849 -252.09849 + 13800 13.8 222.81023 0.00015789536 -20.951387 1.0817076e-06 -252.07139 -252.07139 + 14000 14 218.31245 0.00011842157 -21.008674 8.1128101e-07 -252.12867 -252.12867 + 14200 14.2 197.5018 0.00011399102 -21.081911 7.8092826e-07 -252.20191 -252.20191 + 14400 14.4 228.11014 0.00015934606 -20.963235 1.091646e-06 -252.08323 -252.08323 + 14600 14.6 216.45102 9.6033576e-05 -21.034352 6.5790564e-07 -252.15435 -252.15435 + 14800 14.8 205.97376 0.00014278574 -21.018847 9.7819479e-07 -252.13885 -252.13885 + 15000 15 230.09259 0.00012803086 -20.986446 8.7711221e-07 -252.10645 -252.10644 + 15200 15.2 248.21379 0.0001784321 -20.84502 1.2224004e-06 -251.96502 -251.96502 + 15400 15.4 223.07119 0.00013057001 -20.984451 8.9450744e-07 -252.10445 -252.10445 + 15600 15.6 194.42126 8.4530618e-05 -21.127055 5.7910131e-07 -252.24705 -252.24705 + 15800 15.8 207.23453 0.00013807606 -21.035173 9.4592974e-07 -252.15517 -252.15517 + 16000 16 175.93234 8.2440767e-05 -21.208299 5.6478419e-07 -252.3283 -252.3283 + 16200 16.2 225.63746 7.4767651e-05 -21.012845 5.1221731e-07 -252.13285 -252.13284 + 16400 16.4 149.12667 6.624179e-05 -21.331981 4.5380844e-07 -252.45198 -252.45198 + 16600 16.6 211.41275 0.00012606898 -21.042094 8.6367183e-07 -252.16209 -252.16209 + 16800 16.8 199.88466 8.2345231e-05 -21.116203 5.641297e-07 -252.2362 -252.2362 + 17000 17 212.37144 0.00010445794 -21.041826 7.1561919e-07 -252.16183 -252.16183 + 17200 17.2 160.83603 5.4109632e-05 -21.294207 3.706936e-07 -252.41421 -252.41421 + 17400 17.4 254.84209 0.00013687967 -20.886397 9.3773358e-07 -252.0064 -252.0064 + 17600 17.6 237.6091 0.00012462019 -20.958967 8.5374644e-07 -252.07897 -252.07897 + 17800 17.8 194.26242 7.0286952e-05 -21.145006 4.8152099e-07 -252.26501 -252.26501 + 18000 18 175.14964 6.1470052e-05 -21.239458 4.2111827e-07 -252.35946 -252.35946 + 18200 18.2 181.99258 7.2295849e-05 -21.195184 4.9528351e-07 -252.31519 -252.31519 + 18400 18.4 197.11115 9.9207898e-05 -21.116471 6.7965225e-07 -252.23647 -252.23647 + 18600 18.6 211.2814 8.4543325e-05 -21.074729 5.7918837e-07 -252.19473 -252.19473 + 18800 18.8 198.62813 9.4052117e-05 -21.097909 6.4433109e-07 -252.21791 -252.21791 + 19000 19 226.11003 0.00013827389 -20.951669 9.4728506e-07 -252.07167 -252.07167 + 19200 19.2 233.61049 0.00013363448 -20.917911 9.1550145e-07 -252.03791 -252.03791 + 19400 19.4 182.94749 9.0400181e-05 -21.139686 6.1931245e-07 -252.25969 -252.25968 + 19600 19.6 155.99677 5.9871119e-05 -21.282519 4.1016433e-07 -252.40252 -252.40252 + 19800 19.8 179.57217 8.5624245e-05 -21.193447 5.8659353e-07 -252.31345 -252.31345 + 20000 20 243.60222 0.00015451915 -20.911769 1.0585779e-06 -252.03177 -252.03177 +Loop time of 21.9748 on 1 procs for 20000 steps with 54 atoms + +Performance: 78.636 ns/day, 0.305 hours/ns, 910.134 timesteps/s, 49.147 katom-step/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 | 8.1863 | 8.1863 | 8.1863 | 0.0 | 37.25 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.77445 | 0.77445 | 0.77445 | 0.0 | 3.52 +Output | 0.0037256 | 0.0037256 | 0.0037256 | 0.0 | 0.02 +Modify | 12.954 | 12.954 | 12.954 | 0.0 | 58.95 +Other | | 0.05601 | | | 0.25 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 801 ave 801 max 801 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1728 ave 1728 max 1728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3456 ave 3456 max 3456 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3456 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:22 diff --git a/examples/bpm/plasticity/in.bpm.plasticity b/examples/bpm/plasticity/in.bpm.plasticity new file mode 100644 index 0000000000..4cf8f277a8 --- /dev/null +++ b/examples/bpm/plasticity/in.bpm.plasticity @@ -0,0 +1,103 @@ +# Load then unload four cantilevers with different plastic yield strains +# model from DOI: 10.1016/j.powtec.2024.120563 + +units lj +dimension 3 +boundary p s s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +region box block 0 20 -1 41 -5 5 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +mass * 1.0 + +# Create initial disordered geometry somewhat near jamming + +region cantilever block 3.0 12.0 0 40 -2.5 2.5 units box +region cantileverw block 2.0 13.0 -1 41 -3.5 3.5 units box +create_atoms 1 region cantilever + +velocity all create 0.1 345910 + +pair_style bpm/spring +pair_coeff * * 1.0 1.0 1.0 + +fix 1 all nve +fix wtemp all wall/region cantileverw harmonic 1.0 1.0 1.0 + +thermo_style custom step ke pe pxx pyy pzz +thermo 100 + +timestep 0.1 +run 20000 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group c1 region r1 +group c2 region r2 +group c3 region r3 +group c4 region r4 + +set group c2 type 2 +set group c3 type 3 +set group c4 type 4 + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many c1 c1 1 0.0 1.5 +create_bonds many c2 c2 2 0.0 1.5 +create_bonds many c3 c3 3 0.0 1.5 +create_bonds many c4 c4 4 0.0 1.5 + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring/plastic break no smooth no +bond_coeff 1 1.0 0 1.0 1.0 +bond_coeff 2 1.0 0 1.0 0.022 +bond_coeff 3 1.0 0 1.0 0.0185 +bond_coeff 4 1.0 0 1.0 0.017 + +# apply load + +region anchor block EDGE EDGE EDGE 2.0 EDGE EDGE units box +region load block EDGE EDGE 38.0 EDGE EDGE EDGE units box +group anchor region anchor +group load region load + +variable fload equal ramp(0.0,-0.0005) +fix 2 anchor setforce 0.0 0.0 0.0 +fix 3 load addforce 0.0 0.0 v_fload +fix 4 all viscous 0.0016 + +compute zmin1 c1 reduce min z +compute zmin2 c2 reduce min z +compute zmin3 c3 reduce min z +compute zmin4 c4 reduce min z + +thermo_style custom step ke c_zmin1 c_zmin2 c_zmin3 c_zmin4 +#dump 1 all custom 1000 atomDump id type x y z + +run 30000 + +# hold load + +unfix 3 +fix 3 load addforce 0.0 0.0 -0.0005 +run 50000 + +# remove load + +unfix 3 +run 60000 diff --git a/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 b/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 new file mode 100644 index 0000000000..e51437b585 --- /dev/null +++ b/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 @@ -0,0 +1,2024 @@ +LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1034-ged627579f6-modified) +# Load then unload four cantilevers with different plastic yield strains +# model from DOI: 10.1016/j.powtec.2024.120563 + +units lj +dimension 3 +boundary p s s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +Lattice spacing in x,y,z = 1.4156209 1.4156209 1.4156209 +region box block 0 20 -1 41 -5 5 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +Created orthogonal box = (0 -1 -5) to (20 41 5) + 1 by 1 by 1 MPI processor grid +mass * 1.0 + +# Create initial disordered geometry somewhat near jamming + +region cantilever block 3.0 12.0 0 40 -2.5 2.5 units box +region cantileverw block 2.0 13.0 -1 41 -3.5 3.5 units box +create_atoms 1 region cantilever +Created 2394 atoms + using lattice units in orthogonal box = (0 -1.0042 -5.001) to (20 41.0042 5.001) + create_atoms CPU = 0.001 seconds + +velocity all create 0.1 345910 + +pair_style bpm/spring +pair_coeff * * 1.0 1.0 1.0 + +fix 1 all nve +fix wtemp all wall/region cantileverw harmonic 1.0 1.0 1.0 + +thermo_style custom step ke pe pxx pyy pzz +thermo 100 + +timestep 0.1 +run 20000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 31 65 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.752 | 9.752 | 9.752 Mbytes + Step KinEng PotEng Pxx Pyy Pzz + 0 0.14993734 0 0.071514461 0.070121562 0.071454556 + 100 0.0066788839 0.0029982274 0.016637041 0.016868542 0.015823802 + 200 0.0019715508 0.00071490141 0.007843495 0.0076223765 0.0067662021 + 300 0.00087217257 0.00026043228 0.003985349 0.004259066 0.0040664397 + 400 0.00050307484 0.00011882009 0.0024899485 0.0025393633 0.0024477801 + 500 0.00033241763 6.5955939e-05 0.0016895447 0.0018048761 0.0017308071 + 600 0.00023663671 4.4828066e-05 0.0013515511 0.001353668 0.0013208904 + 700 0.0001837694 2.7185024e-05 0.00094852029 0.0010286312 0.00099370739 + 800 0.00014655165 1.8873405e-05 0.00075979673 0.0008230931 0.00075345331 + 900 0.00012145909 1.4344012e-05 0.00060702604 0.00068683252 0.00061213385 + 1000 0.00010239299 1.2153676e-05 0.00055078741 0.00060838425 0.00054159268 + 1100 8.8075366e-05 9.9954299e-06 0.00045915185 0.00057179945 0.00047014896 + 1200 7.8336822e-05 7.4598572e-06 0.00038286385 0.000423282 0.00040077777 + 1300 6.8617848e-05 7.4071518e-06 0.00038962894 0.00045042653 0.00042176853 + 1400 6.1816066e-05 5.7757188e-06 0.00035626235 0.00037452754 0.00033148835 + 1500 5.5158763e-05 5.3010672e-06 0.00032659745 0.00035059437 0.0003143055 + 1600 5.0680523e-05 4.4203877e-06 0.00027420802 0.00032194903 0.00030193132 + 1700 4.6020086e-05 4.0228214e-06 0.00026909527 0.00029969818 0.00027492066 + 1800 4.1968387e-05 3.9751303e-06 0.00027184181 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1.0582884e-05 1.2673246e-05 1.3298389e-05 + 18700 1.8742478e-06 4.4718119e-08 1.5344401e-05 1.2546575e-05 1.1764246e-05 + 18800 1.8650878e-06 3.7704721e-08 1.07802e-05 1.2917662e-05 9.5373738e-06 + 18900 1.8685713e-06 3.6504734e-08 1.0815769e-05 1.3268273e-05 9.2228416e-06 + 19000 1.8510631e-06 3.5157873e-08 1.2534306e-05 1.2128038e-05 1.0355377e-05 + 19100 1.844547e-06 3.5807341e-08 1.1011196e-05 1.2288462e-05 1.042938e-05 + 19200 1.8237482e-06 4.4374495e-08 1.0976301e-05 1.0525434e-05 1.3496339e-05 + 19300 1.809658e-06 4.663351e-08 1.0427019e-05 1.2761301e-05 1.2443509e-05 + 19400 1.8047595e-06 3.7730816e-08 1.2549441e-05 9.4564734e-06 1.159109e-05 + 19500 1.7912254e-06 3.9882052e-08 1.3940679e-05 1.220604e-05 1.1210472e-05 + 19600 1.789224e-06 3.7125586e-08 1.0231473e-05 1.2070753e-05 1.1047121e-05 + 19700 1.7845362e-06 3.456485e-08 1.12335e-05 1.042505e-05 9.0484867e-06 + 19800 1.7683141e-06 3.8353201e-08 1.29417e-05 1.0764969e-05 1.116828e-05 + 19900 1.7664071e-06 3.2153664e-08 9.4515931e-06 1.1051242e-05 1.0924767e-05 + 20000 1.7618892e-06 2.2689236e-08 8.4011955e-06 7.5721128e-06 8.9521609e-06 +Loop time of 1.48476 on 1 procs for 20000 steps with 2394 atoms + +Performance: 116382628.128 tau/day, 13470.212 timesteps/s, 32.248 Matom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.63885 | 0.63885 | 0.63885 | 0.0 | 43.03 +Bond | 0.00053413 | 0.00053413 | 0.00053413 | 0.0 | 0.04 +Neigh | 0.15112 | 0.15112 | 0.15112 | 0.0 | 10.18 +Comm | 0.0056225 | 0.0056225 | 0.0056225 | 0.0 | 0.38 +Output | 0.0032158 | 0.0032158 | 0.0032158 | 0.0 | 0.22 +Modify | 0.61597 | 0.61597 | 0.61597 | 0.0 | 41.49 +Other | | 0.06945 | | | 4.68 + +Nlocal: 2394 ave 2394 max 2394 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 11170 ave 11170 max 11170 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 11170 +Ave neighs/atom = 4.6658312 +Ave special neighs/atom = 0 +Neighbor list builds = 199 +Dangerous builds = 0 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 +Replication is creating a 4x1x1 = 4 times larger system... + orthogonal box = (0 -0.0019118212 -2.5018545) to (80 40.003414 2.5021045) + 1 by 1 by 1 MPI processor grid + 9576 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 0 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group c1 region r1 +2394 atoms in group c1 +group c2 region r2 +2394 atoms in group c2 +group c3 region r3 +2394 atoms in group c3 +group c4 region r4 +2394 atoms in group c4 + +set group c2 type 2 +Setting atom values ... + 2394 settings made for type +set group c3 type 3 +Setting atom values ... + 2394 settings made for type +set group c4 type 4 +Setting atom values ... + 2394 settings made for type + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many c1 c1 1 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 13760 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.001 seconds +create_bonds many c2 c2 2 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 27520 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds many c3 c3 3 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 41280 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds many c4 c4 4 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 55040 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring/plastic break no smooth no +bond_coeff 1 1.0 0 1.0 1.0 +bond_coeff 2 1.0 0 1.0 0.022 +bond_coeff 3 1.0 0 1.0 0.0185 +bond_coeff 4 1.0 0 1.0 0.017 + +# apply load + +region anchor block EDGE EDGE EDGE 2.0 EDGE EDGE units box +region load block EDGE EDGE 38.0 EDGE EDGE EDGE units box +group anchor region anchor +512 atoms in group anchor +group load region load +592 atoms in group load + +variable fload equal ramp(0.0,-0.0005) +fix 2 anchor setforce 0.0 0.0 0.0 +fix 3 load addforce 0.0 0.0 v_fload +fix 4 all viscous 0.0016 + +compute zmin1 c1 reduce min z +compute zmin2 c2 reduce min z +compute zmin3 c3 reduce min z +compute zmin4 c4 reduce min z + +thermo_style custom step ke c_zmin1 c_zmin2 c_zmin3 c_zmin4 +dump 1 all custom 1000 atomDump id type x y z + +run 30000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- BPM bond style: doi:10.1039/D3SM01373A + +@Article{Clemmer2024, + author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.}, + title = {A soft departure from jamming: the compaction of deformable + granular matter under high pressures}, + journal = {Soft Matter}, + year = 2024, + volume = 20, + number = 8, + pages = {1702--1718} +} + +- BPM/spring/plastic bond style: doi:10.1016/j.powtec.2024.120563 + +@Article{Clemmer2025, + author = {Clemmer, Joel T. and Lechman, Jeremy B.}, + title = {Onset and impact of plastic deformation in granular compaction}, + journal = {Powder Technology}, + year = 2025, + volume = 452, + number = 28, + pages = {120563} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 124 62 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 20.02 | 20.02 | 20.02 Mbytes + Step KinEng c_zmin1 c_zmin2 c_zmin3 c_zmin4 + 20000 0 -2.5009426 -2.5009426 -2.5009426 -2.5009426 + 20100 1.2351668e-12 -2.5009426 -2.5009426 -2.5009426 -2.5009426 + 20200 1.6504342e-11 -2.50094 -2.50094 -2.50094 -2.50094 + 20300 7.2443173e-11 -2.5009238 -2.5009238 -2.5009238 -2.5009238 + 20400 2.0430679e-10 -2.5009047 -2.5009047 -2.5009047 -2.5009047 + 20500 4.5403534e-10 -2.5014106 -2.5014106 -2.5014106 -2.5014106 + 20600 8.6883638e-10 -2.5021368 -2.5021368 -2.5021368 -2.5021368 + 20700 1.5005944e-09 -2.5032627 -2.5032627 -2.5032627 -2.5032627 + 20800 2.4020834e-09 -2.5048635 -2.5048635 -2.5048635 -2.5048635 + 20900 3.620123e-09 -2.5068127 -2.5068127 -2.5068127 -2.5068127 + 21000 5.1981536e-09 -2.5091315 -2.5091315 -2.5091315 -2.5091315 + 21100 7.1838766e-09 -2.5118405 -2.5118405 -2.5118405 -2.5118405 + 21200 9.6334884e-09 -2.5149609 -2.5149609 -2.5149609 -2.5149609 + 21300 1.2612436e-08 -2.5185116 -2.5185116 -2.5185116 -2.5185116 + 21400 1.6194239e-08 -2.5224995 -2.5224995 -2.5224995 -2.5224995 + 21500 2.0460353e-08 -2.5269165 -2.5269165 -2.5269165 -2.5269165 + 21600 2.5502476e-08 -2.5317485 -2.5317485 -2.5317485 -2.5317485 + 21700 3.1420875e-08 -2.5369872 -2.5369872 -2.5369872 -2.5369872 + 21800 3.831695e-08 -2.5426357 -2.5426357 -2.5426357 -2.5426357 + 21900 4.6285399e-08 -2.5487084 -2.5487084 -2.5487084 -2.5487084 + 22000 5.540962e-08 -2.5552276 -2.5552276 -2.5552276 -2.5552276 + 22100 6.5761039e-08 -2.5622201 -2.5622201 -2.5622201 -2.5622201 + 22200 7.7400349e-08 -2.5697151 -2.5697151 -2.5697151 -2.5697151 + 22300 9.0377386e-08 -2.5777426 -2.5777426 -2.5777426 -2.5777426 + 22400 1.047309e-07 -2.5863331 -2.5863331 -2.5863331 -2.5863331 + 22500 1.2049105e-07 -2.5955148 -2.5955148 -2.5955148 -2.5955148 + 22600 1.3768365e-07 -2.6053118 -2.6053118 -2.6053118 -2.6053118 + 22700 1.5633289e-07 -2.6157454 -2.6157454 -2.6157454 -2.6157454 + 22800 1.7646087e-07 -2.6268375 -2.6268375 -2.6268375 -2.6268375 + 22900 1.9808425e-07 -2.6386137 -2.6386137 -2.6386137 -2.6386137 + 23000 2.2121115e-07 -2.6511024 -2.6511024 -2.6511024 -2.6511024 + 23100 2.4583965e-07 -2.6643302 -2.6643302 -2.6643302 -2.6643302 + 23200 2.7195651e-07 -2.678336 -2.678336 -2.678336 -2.678336 + 23300 2.9953549e-07 -2.6934773 -2.6934773 -2.6934773 -2.6934773 + 23400 3.2853628e-07 -2.7094153 -2.7094153 -2.7094153 -2.7094153 + 23500 3.5890539e-07 -2.7261413 -2.7261413 -2.7261413 -2.7261413 + 23600 3.9057925e-07 -2.7436388 -2.7436388 -2.7436388 -2.7436388 + 23700 4.2348784e-07 -2.7618864 -2.7618864 -2.7618864 -2.7618864 + 23800 4.5755714e-07 -2.7808597 -2.7808597 -2.7808597 -2.7808597 + 23900 4.9271044e-07 -2.8005353 -2.8005353 -2.8005353 -2.8005353 + 24000 5.2886942e-07 -2.8208926 -2.8208926 -2.8208926 -2.8208926 + 24100 5.6595503e-07 -2.8419149 -2.8419149 -2.8419149 -2.8419149 + 24200 6.0388753e-07 -2.8635875 -2.8635875 -2.8635875 -2.8635875 + 24300 6.4258508e-07 -2.885895 -2.885895 -2.885895 -2.885895 + 24400 6.8196158e-07 -2.9088193 -2.9088193 -2.9088193 -2.9088193 + 24500 7.2192513e-07 -2.9323405 -2.9323405 -2.9323405 -2.9323405 + 24600 7.6237754e-07 -2.9564391 -2.9564391 -2.9564391 -2.9564391 + 24700 8.0321442e-07 -2.9810988 -2.9810988 -2.9810988 -2.9810988 + 24800 8.4432539e-07 -3.0063086 -3.0063086 -3.0063086 -3.0063086 + 24900 8.8559455e-07 -3.0320638 -3.0320638 -3.0320638 -3.0320638 + 25000 9.2690186e-07 -3.0583647 -3.0583647 -3.0583647 -3.0583647 + 25100 9.6812534e-07 -3.0852155 -3.0852155 -3.0852155 -3.0852155 + 25200 1.0091433e-06 -3.1126219 -3.1126219 -3.1126219 -3.1126219 + 25300 1.0498359e-06 -3.1405884 -3.1405884 -3.1405884 -3.1405884 + 25400 1.0900852e-06 -3.1691161 -3.1691161 -3.1691161 -3.1691161 + 25500 1.1297762e-06 -3.1982005 -3.1982005 -3.1982005 -3.1982005 + 25600 1.1687961e-06 -3.227832 -3.227832 -3.227832 -3.227832 + 25700 1.2070344e-06 -3.257997 -3.257997 -3.257997 -3.257997 + 25800 1.2443825e-06 -3.2886792 -3.2886792 -3.2886792 -3.2886792 + 25900 1.2807322e-06 -3.3198613 -3.3198613 -3.3198613 -3.3198613 + 26000 1.3159765e-06 -3.3515247 -3.3515247 -3.3515247 -3.3515247 + 26100 1.3500098e-06 -3.3836487 -3.3836487 -3.3836487 -3.3836487 + 26200 1.3827298e-06 -3.4162094 -3.4162094 -3.4162094 -3.4162094 + 26300 1.4140396e-06 -3.449179 -3.449179 -3.449179 -3.449179 + 26400 1.4438488e-06 -3.4825256 -3.4825256 -3.4825256 -3.4825256 + 26500 1.4720759e-06 -3.5162134 -3.5162134 -3.5162134 -3.5162134 + 26600 1.4986491e-06 -3.5502047 -3.5502047 -3.5502047 -3.5502047 + 26700 1.5235069e-06 -3.5844612 -3.5844612 -3.5844612 -3.5844612 + 26800 1.5465982e-06 -3.6189462 -3.6189462 -3.6189462 -3.6189462 + 26900 1.567881e-06 -3.6536265 -3.6536265 -3.6536265 -3.6536265 + 27000 1.5873207e-06 -3.6884733 -3.6884733 -3.6884733 -3.6884733 + 27100 1.6048891e-06 -3.7234623 -3.7234623 -3.7234623 -3.7234623 + 27200 1.6205631e-06 -3.758573 -3.758573 -3.758573 -3.758573 + 27300 1.6343242e-06 -3.7937872 -3.7937872 -3.7937872 -3.7937872 + 27400 1.6461586e-06 -3.8290884 -3.8290884 -3.8290884 -3.8290884 + 27500 1.6560567e-06 -3.8644611 -3.8644611 -3.8644611 -3.8644611 + 27600 1.6640149e-06 -3.899891 -3.899891 -3.899891 -3.899891 + 27700 1.6700356e-06 -3.9353655 -3.9353655 -3.9353655 -3.9353655 + 27800 1.6741283e-06 -3.9708734 -3.9708734 -3.9708734 -3.9708734 + 27900 1.6763095e-06 -4.0064055 -4.0064055 -4.0064055 -4.0064055 + 28000 1.6766027e-06 -4.0419539 -4.0419539 -4.0419539 -4.0419539 + 28100 1.6750373e-06 -4.077511 -4.077511 -4.077511 -4.077511 + 28200 1.6716485e-06 -4.1130688 -4.1130688 -4.1130688 -4.1130688 + 28300 1.666476e-06 -4.148617 -4.148617 -4.148617 -4.148617 + 28400 1.6595633e-06 -4.1841425 -4.1841425 -4.1841425 -4.1841425 + 28500 1.6509568e-06 -4.2196283 -4.2196283 -4.2196283 -4.2196283 + 28600 1.6407058e-06 -4.2550543 -4.2550543 -4.2550543 -4.2550543 + 28700 1.6288629e-06 -4.2903975 -4.2903975 -4.2903975 -4.2903975 + 28800 1.6154837e-06 -4.3256335 -4.3256335 -4.3256335 -4.3256335 + 28900 1.6006277e-06 -4.3607374 -4.3607374 -4.3607374 -4.3607374 + 29000 1.5843585e-06 -4.3956842 -4.3956842 -4.3956842 -4.3956842 + 29100 1.5667441e-06 -4.4304495 -4.4304495 -4.4304495 -4.4304495 + 29200 1.5478572e-06 -4.4650097 -4.4650097 -4.4650097 -4.4650097 + 29300 1.5277745e-06 -4.4993416 -4.4993416 -4.4993416 -4.4993416 + 29400 1.5065765e-06 -4.5334229 -4.5334229 -4.5334229 -4.5334229 + 29500 1.4843462e-06 -4.5672325 -4.5672325 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0.037787 | 0.0 | 0.16 +Output | 0.17723 | 0.17723 | 0.17723 | 0.0 | 0.77 +Modify | 2.4504 | 2.4504 | 2.4504 | 0.0 | 10.69 +Other | | 0.4793 | | | 2.09 + +Nlocal: 9576 ave 9576 max 9576 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 44684 ave 44684 max 44684 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 44684 +Ave neighs/atom = 4.666249 +Ave special neighs/atom = 11.495405 +Neighbor list builds = 62 +Dangerous builds = 0 + +# hold load + +unfix 3 +fix 3 load addforce 0.0 0.0 -0.0005 +run 50000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 22.14 | 22.14 | 22.14 Mbytes + Step KinEng c_zmin1 c_zmin2 c_zmin3 c_zmin4 + 50000 4.0265078e-06 -9.2049257 -10.073506 -11.003853 -11.624781 + 50100 4.078797e-06 -9.2250318 -10.115223 -11.061622 -11.691546 + 50200 4.1270084e-06 -9.2449811 -10.157097 -11.119697 -11.758608 + 50300 4.1711893e-06 -9.2647179 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+Pair | 5.1258 | 5.1258 | 5.1258 | 0.0 | 12.24 +Bond | 31.193 | 31.193 | 31.193 | 0.0 | 74.48 +Neigh | 0.37652 | 0.37652 | 0.37652 | 0.0 | 0.90 +Comm | 0.044633 | 0.044633 | 0.044633 | 0.0 | 0.11 +Output | 0.29854 | 0.29854 | 0.29854 | 0.0 | 0.71 +Modify | 4.0413 | 4.0413 | 4.0413 | 0.0 | 9.65 +Other | | 0.8001 | | | 1.91 + +Nlocal: 9576 ave 9576 max 9576 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 44699 ave 44699 max 44699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 44699 +Ave neighs/atom = 4.6678154 +Ave special neighs/atom = 11.495405 +Neighbor list builds = 87 +Dangerous builds = 0 + +# remove load + +unfix 3 +run 60000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 22.79 | 22.79 | 22.79 Mbytes + Step KinEng c_zmin1 c_zmin2 c_zmin3 c_zmin4 + 100000 3.9853122e-10 -9.3641487 -12.537084 -17.318766 -22.862977 + 100100 3.5487181e-07 -9.347706 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time of 49.2753 on 1 procs for 60000 steps with 9576 atoms + +Performance: 10520476.677 tau/day, 1217.648 timesteps/s, 11.660 Matom-step/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.0276 | 6.0276 | 6.0276 | 0.0 | 12.23 +Bond | 36.671 | 36.671 | 36.671 | 0.0 | 74.42 +Neigh | 0.63507 | 0.63507 | 0.63507 | 0.0 | 1.29 +Comm | 0.063752 | 0.063752 | 0.063752 | 0.0 | 0.13 +Output | 0.3562 | 0.3562 | 0.3562 | 0.0 | 0.72 +Modify | 4.5593 | 4.5593 | 4.5593 | 0.0 | 9.25 +Other | | 0.9622 | | | 1.95 + +Nlocal: 9576 ave 9576 max 9576 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 44691 ave 44691 max 44691 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 44691 +Ave neighs/atom = 4.6669799 +Ave special neighs/atom = 11.495405 +Neighbor list builds = 147 +Dangerous builds = 0 +Total wall time: 0:01:55 diff --git a/examples/bpm/poissons_ratio/in.bpm.poissons_ratio b/examples/bpm/poissons_ratio/in.bpm.poissons_ratio new file mode 100644 index 0000000000..71052ad417 --- /dev/null +++ b/examples/bpm/poissons_ratio/in.bpm.poissons_ratio @@ -0,0 +1,90 @@ +# Squish four pillars with different Poisson's ratios +# going from nearly incompressible to auxetic +# from left to right, nu ~ 0.5, 0.25, 0, <0 +# calibration from DOI: 10.1039/d3sm01373a + +units lj +dimension 3 +boundary p p s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +region box block 0 20 -10 10 -1 21 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +mass * 1.0 + +# Create initial disordered geometry somewhat near jamming + +region pillar cylinder z 10.0 0.0 7.0 0.0 20.0 units box +region pillarw cylinder z 10.0 0.0 8.0 -1.0 21.0 units box +create_atoms 1 region pillar + +velocity all create 0.1 345910 + +pair_style bpm/spring +pair_coeff * * 1.0 1.0 1.0 + +fix 1 all nve +fix wtemp all wall/region pillarw harmonic 1.0 1.0 1.0 + +thermo_style custom step ke pe pxx pyy pzz +thermo 100 + +timestep 0.1 +run 20000 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group p1 region r1 +group p2 region r2 +group p3 region r3 +group p4 region r4 + +set group p2 type 2 +set group p3 type 3 +set group p4 type 4 + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many p1 p1 1 0.0 1.5 +create_bonds many p2 p2 2 0.0 1.5 +create_bonds many p3 p3 3 0.0 1.5 +create_bonds many p4 p4 4 0.0 1.5 + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring break no smooth no volume/factor yes +bond_coeff 1 1.0 0 1.0 -0.8 +bond_coeff 2 1.0 0 1.0 0.0 +bond_coeff 3 1.0 0 1.0 2.0 +bond_coeff 4 1.0 0 1.0 10.0 + +# squish + +region b block EDGE EDGE EDGE EDGE -1.0 2.0 units box +region t block EDGE EDGE EDGE EDGE 18.0 21.0 units box +group bot region b +group top region t + +velocity top set 0.0 0.0 -0.0025 +fix 2 bot setforce 0.0 0.0 0.0 +fix 3 top setforce 0.0 0.0 0.0 + +compute zmax all reduce max z + +thermo_style custom step ke pe pxx pyy pzz c_zmax +#dump 1 all custom 100 atomDump id type x y z + +run 10000 diff --git a/examples/bpm/poissons_ratio/log.19Nov2024.bpm.poissons_ratio.g++.1 b/examples/bpm/poissons_ratio/log.19Nov2024.bpm.poissons_ratio.g++.1 new file mode 100644 index 0000000000..e4a95e2b70 --- /dev/null +++ b/examples/bpm/poissons_ratio/log.19Nov2024.bpm.poissons_ratio.g++.1 @@ -0,0 +1,635 @@ +LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1028-g800a5f6310-modified) +# Squish three pillars with different Poisson's ratios +# from left to right, nu ~ 0.5, nu = 0.25 nu ~ 0, nu << 0 + +units lj +dimension 3 +boundary p p s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +Lattice spacing in x,y,z = 1.4156209 1.4156209 1.4156209 +region box block 0 20 -10 10 -1 21 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +Created orthogonal box = (0 -10 -1) to (20 10 21) + 1 by 1 by 1 MPI processor grid +mass * 1.0 + +# Create roughly jammed initial disordered geometry + +region pillar cylinder z 10.0 0.0 7.0 0.0 20.0 units box +region pillarw cylinder z 10.0 0.0 8.0 -1.0 21.0 units box +create_atoms 1 region pillar +Created 4348 atoms + using lattice units in orthogonal box = (0 -10 -1.0022) to (20 10 21.0022) + create_atoms CPU = 0.001 seconds + +velocity all create 0.1 345910 + +pair_style bpm/spring +pair_coeff * * 1.0 1.0 1.0 + +fix 1 all nve +fix wtemp all wall/region pillarw harmonic 1.0 1.0 1.0 + +thermo_style custom step ke pe pxx pyy pzz +thermo 100 + +timestep 0.1 +run 20000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 31 31 34 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.863 | 9.863 | 9.863 Mbytes + Step KinEng PotEng Pxx Pyy Pzz + 0 0.1499655 0 0.055275974 0.054026613 0.05516469 + 100 0.0045460156 0.0041409796 0.020750379 0.02025897 0.02055488 + 200 0.0013178069 0.0013493823 0.011925094 0.011431479 0.012133526 + 300 0.00061239509 0.00063111128 0.0078970462 0.0079941921 0.0081233289 + 400 0.00035752073 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3.3411556e-05 + 19900 2.2007538e-05 2.6295204e-08 4.5722301e-05 4.441743e-05 3.4023953e-05 + 20000 2.2006515e-05 2.6089093e-08 4.4621124e-05 4.5449725e-05 3.2126359e-05 +Loop time of 7.03939 on 1 procs for 20000 steps with 4348 atoms + +Performance: 24547586.015 tau/day, 2841.156 timesteps/s, 12.353 Matom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.55 | 4.55 | 4.55 | 0.0 | 64.64 +Bond | 0.00067765 | 0.00067765 | 0.00067765 | 0.0 | 0.01 +Neigh | 0.3745 | 0.3745 | 0.3745 | 0.0 | 5.32 +Comm | 0.013687 | 0.013687 | 0.013687 | 0.0 | 0.19 +Output | 0.006889 | 0.006889 | 0.006889 | 0.0 | 0.10 +Modify | 1.9222 | 1.9222 | 1.9222 | 0.0 | 27.31 +Other | | 0.1715 | | | 2.44 + +Nlocal: 4348 ave 4348 max 4348 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23350 ave 23350 max 23350 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 23350 +Ave neighs/atom = 5.3702852 +Ave special neighs/atom = 0 +Neighbor list builds = 222 +Dangerous builds = 0 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 +Replication is creating a 4x1x1 = 4 times larger system... + orthogonal box = (0 -10 -0.0025658844) to (80 10 20.002511) + 1 by 1 by 1 MPI processor grid + 17392 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 0 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.001 seconds + replicate CPU = 0.003 seconds + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group p1 region r1 +4348 atoms in group p1 +group p2 region r2 +4348 atoms in group p2 +group p3 region r3 +4348 atoms in group p3 +group p4 region r4 +4348 atoms in group p4 + +set group p2 type 2 +Setting atom values ... + 4348 settings made for type +set group p3 type 3 +Setting atom values ... + 4348 settings made for type +set group p4 type 4 +Setting atom values ... + 4348 settings made for type + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many p1 p1 1 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 29229 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds many p2 p2 2 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 58458 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.003 seconds +create_bonds many p3 p3 3 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 87687 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.004 seconds +create_bonds many p4 p4 4 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 116916 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.005 seconds + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring break no smooth no volume/factor yes +bond_coeff 1 1.0 0 1.0 -0.8 +bond_coeff 2 1.0 0 1.0 0.0 +bond_coeff 3 1.0 0 1.0 2.0 +bond_coeff 4 1.0 0 1.0 10.0 + +# squish + +region b block EDGE EDGE EDGE EDGE -1.0 2.0 units box +region t block EDGE EDGE EDGE EDGE 18.0 21.0 units box +group bot region b +2040 atoms in group bot +group top region t +2036 atoms in group top + +velocity top set 0.0 0.0 -0.0025 +fix 2 bot setforce 0.0 0.0 0.0 +fix 3 top setforce 0.0 0.0 0.0 + +compute zmax all reduce max z + +thermo_style custom step ke pe pxx pyy pzz c_zmax +dump 1 all custom 100 atomDump id type x y z + +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- BPM bond style: doi:10.1039/D3SM01373A + +@Article{Clemmer2024, + author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.}, + title = {A soft departure from jamming: the compaction of deformable + granular matter under high pressures}, + journal = {Soft Matter}, + year = 2024, + volume = 20, + number = 8, + pages = {1702--1718} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 124 31 31 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 33.55 | 33.55 | 33.55 Mbytes + Step KinEng PotEng Pxx Pyy Pzz c_zmax + 20000 7.3311514e-07 0 5.5082149e-05 5.6035691e-05 0.00016879881 20.000342 + 20100 3.1226194e-06 4.1766539e-06 -0.00013996263 -0.00014393529 0.0029331928 19.964952 + 20200 2.5567295e-06 1.4988852e-05 -0.00027674096 -0.00027610139 0.0056641847 19.929561 + 20300 2.5665365e-06 3.3513395e-05 -0.00042198157 -0.0004191815 0.0083802213 19.894171 + 20400 2.4143831e-06 5.9638373e-05 -0.00055373017 -0.00055236369 0.011083701 19.85878 + 20500 2.2440232e-06 9.3155125e-05 -0.00070411826 -0.00070166982 0.013871936 19.82339 + 20600 2.3036882e-06 0.00013415012 -0.00084108079 -0.00084004876 0.016564858 19.787999 + 20700 2.4894579e-06 0.00018252868 -0.00098164122 -0.00097848101 0.019243173 19.752609 + 20800 2.3533488e-06 0.0002383092 -0.0011196916 -0.0011163409 0.021906836 19.717218 + 20900 2.3312562e-06 0.000301439 -0.0012662271 -0.0012625903 0.024743687 19.681828 + 21000 2.3806649e-06 0.00037188609 -0.0014035798 -0.0013992731 0.02739958 19.646437 + 21100 2.3212779e-06 0.00044964779 -0.0015396059 -0.0015348733 0.030041098 19.611047 + 21200 2.3908442e-06 0.00053469194 -0.001674797 -0.0016694993 0.03266844 19.575656 + 21300 2.3622478e-06 0.00062699617 -0.001822934 -0.0018167895 0.035552232 19.540266 + 21400 2.349964e-06 0.00072653051 -0.0019569691 -0.0019503123 0.038170924 19.504875 + 21500 2.3567592e-06 0.00083327134 -0.0020899915 -0.0020827032 0.040775314 19.469484 + 21600 2.3616263e-06 0.00094719631 -0.0022220661 -0.0022140075 0.043365368 19.434094 + 21700 2.353721e-06 0.0010682808 -0.0023711759 -0.0023623886 0.046296241 19.398703 + 21800 2.3646799e-06 0.0011965 -0.0025021157 -0.0024925265 0.048877326 19.363313 + 21900 2.3550746e-06 0.0013318277 -0.0026319662 -0.0026215842 0.051443901 19.327922 + 22000 2.3552825e-06 0.0014742397 -0.0027607166 -0.0027495396 0.053995979 19.292532 + 22100 2.3588762e-06 0.0016237112 -0.0028884164 -0.0028763855 0.05653356 19.257141 + 22200 2.3566445e-06 0.0017802179 -0.0030385388 -0.0030255211 0.05951687 19.221751 + 22300 2.3569128e-06 0.0019437341 -0.0031650443 -0.0031511287 0.062044959 19.18636 + 22400 2.3573615e-06 0.0021142342 -0.0032904648 -0.0032756057 0.064558413 19.15097 + 22500 2.3556792e-06 0.0022916926 -0.003414791 -0.0033989599 0.067057238 19.115579 + 22600 2.3559622e-06 0.0024760839 -0.0035658051 -0.0035488398 0.070087637 19.080189 + 22700 2.3565188e-06 0.0026673826 -0.0036888874 -0.0036708796 0.072576558 19.044798 + 22800 2.3554654e-06 0.0028655631 -0.0038108556 -0.0037917743 0.075050709 19.009408 + 22900 2.3556755e-06 0.0030705996 -0.0039317038 -0.0039115206 0.07751008 18.974017 + 23000 2.3553906e-06 0.0032824663 -0.0040835075 -0.0040620186 0.080587643 18.938627 + 23100 2.3549893e-06 0.0035011372 -0.0042030492 -0.0041803845 0.08303667 18.903236 + 23200 2.3549869e-06 0.0037265864 -0.0043214571 -0.004297582 0.085470779 18.867846 + 23300 2.3548674e-06 0.0039587875 -0.0044387217 -0.004413608 0.087889956 18.832455 + 23400 2.3544804e-06 0.0041977141 -0.0045911895 -0.0045645946 0.091014737 18.797065 + 23500 2.3543814e-06 0.0044433399 -0.0047070844 -0.0046791718 0.093423108 18.761674 + 23600 2.3541461e-06 0.0046956382 -0.0048218198 -0.0047925569 0.09581641 18.726284 + 23700 2.3539051e-06 0.0049545823 -0.0049353928 -0.0049047458 0.098194634 18.690893 + 23800 2.3537612e-06 0.0052201456 -0.0050478006 -0.0050157354 0.10055777 18.655502 + 23900 2.3535618e-06 0.0054923012 -0.0052005398 -0.0051667526 0.10373359 18.620112 + 24000 2.353333e-06 0.005771022 -0.0053114912 -0.0052762067 0.10608529 18.584721 + 24100 2.3531619e-06 0.006056281 -0.0054212598 -0.0053844406 0.10842176 18.549331 + 24200 2.3529697e-06 0.0063480511 -0.0055298409 -0.0054914515 0.11074298 18.51394 + 24300 2.352776e-06 0.0066463046 -0.0056829436 -0.0056426256 0.11396569 18.47855 + 24400 2.3526011e-06 0.0069510143 -0.0057899993 -0.0057480274 0.11627496 18.443159 + 24500 2.3524078e-06 0.0072621525 -0.0058958481 -0.0058521853 0.11856882 18.407769 + 24600 2.3522128e-06 0.0075796913 -0.0060004865 -0.0059550957 0.12084728 18.372378 + 24700 2.3520292e-06 0.0079036029 -0.0061538145 -0.0061062726 0.12411681 18.336988 + 24800 2.3518453e-06 0.0082338593 -0.0062568585 -0.0062074978 0.12638278 18.301597 + 24900 2.3516643e-06 0.0085704324 -0.0063586718 -0.0063074546 0.12863317 18.266207 + 25000 2.3514892e-06 0.0089132938 -0.0064592514 -0.0064061393 0.13086797 18.230816 + 25100 2.3513106e-06 0.0092624151 -0.0066126575 -0.0065571568 0.13418421 18.195426 + 25200 2.3511362e-06 0.0096177679 -0.0067115701 -0.0066540785 0.13640596 18.160035 + 25300 2.3509678e-06 0.0099793234 -0.0068092292 -0.0067497066 0.13861195 18.124645 + 25400 2.3508006e-06 0.010347053 -0.0069056318 -0.0068440373 0.14080217 18.089254 + 25500 2.3506356e-06 0.010720927 -0.0070007749 -0.0069370671 0.14297661 18.053864 + 25600 2.3504737e-06 0.011100917 -0.0071536223 -0.0070872122 0.14634153 18.018473 + 25700 2.3503117e-06 0.011486993 -0.007247006 -0.0071783805 0.14850216 17.983083 + 25800 2.3501529e-06 0.011879126 -0.0073391102 -0.0072682259 0.15064682 17.947692 + 25900 2.3499998e-06 0.012277287 -0.0074299315 -0.0073567446 0.1527755 17.912302 + 26000 2.3498505e-06 0.012681445 -0.0075824884 -0.0075063219 0.15618632 17.876911 + 26100 2.3497046e-06 0.013091571 -0.0076714736 -0.0075928957 0.15830056 17.84152 + 26200 2.3495632e-06 0.013507634 -0.0077591555 -0.0076781204 0.16039862 17.80613 + 26300 2.349426e-06 0.013929604 -0.0078455309 -0.0077619923 0.1624805 17.770739 + 26400 2.3492932e-06 0.014357451 -0.0079976262 -0.0079108096 0.16593692 17.735349 + 26500 2.349166e-06 0.014791144 -0.008082087 -0.0079926504 0.16800369 17.699958 + 26600 2.3490444e-06 0.015230653 -0.0081652207 -0.0080731154 0.17005406 17.664568 + 26700 2.3489277e-06 0.015675946 -0.008247024 -0.0081522008 0.17208804 17.629177 + 26800 2.3488161e-06 0.016126992 -0.0083984781 -0.008300055 0.17558967 17.593787 + 26900 2.3487105e-06 0.016583761 -0.0084782861 -0.0083770201 0.17760782 17.558396 + 27000 2.3486117e-06 0.017046219 -0.0085567431 -0.008452582 0.17960935 17.523006 + 27100 2.3485201e-06 0.017514336 -0.0086338458 -0.0085267367 0.18159424 17.487615 + 27200 2.3484365e-06 0.017988079 -0.0087095911 -0.0085994803 0.18356247 17.452225 + 27300 2.3483611e-06 0.018467417 -0.008859495 -0.0087453549 0.18710893 17.416834 + 27400 2.3482941e-06 0.018952317 -0.0089331441 -0.0088158653 0.18906038 17.381444 + 27500 2.3482362e-06 0.019442747 -0.0090054148 -0.0088849402 0.19099494 17.346053 + 27600 2.3481885e-06 0.019938673 -0.009076304 -0.0089525756 0.19291257 17.310663 + 27700 2.3481517e-06 0.020440063 -0.0092251203 -0.0090969772 0.19650266 17.275272 + 27800 2.3481263e-06 0.020946883 -0.0092938279 -0.0091622823 0.1984027 17.239882 + 27900 2.3481132e-06 0.0214591 -0.0093611327 -0.0092261226 0.20028558 17.204491 + 28000 2.3481132e-06 0.02197668 -0.0094270316 -0.0092884939 0.20215126 17.169101 + 28100 2.3481274e-06 0.02249959 -0.0095745512 -0.0094311779 0.20578425 17.13371 + 28200 2.348157e-06 0.023027794 -0.0096381809 -0.0094911175 0.20763145 17.09832 + 28300 2.3482036e-06 0.023561259 -0.0097003831 -0.0095495617 0.20946119 17.062929 + 28400 2.3482687e-06 0.024099949 -0.0097611548 -0.0096065059 0.21127344 17.027538 + 28500 2.3480319e-06 0.024643805 -0.0099071195 -0.0097471709 0.21494867 16.992148 + 28600 2.3475123e-06 0.025192783 -0.0099654368 -0.0098014823 0.21674185 16.956757 + 28700 2.3465283e-06 0.02574682 -0.010022297 -0.0098542782 0.21851751 16.921367 + 28800 2.3462245e-06 0.026305935 -0.010077643 -0.0099055665 0.2202753 16.885976 + 28900 2.3465001e-06 0.026870106 -0.010131548 -0.0099553377 0.22201519 16.850586 + 29000 2.3468383e-06 0.027439281 -0.010274668 -0.010092595 0.22572932 16.815195 + 29100 2.3470511e-06 0.028013406 -0.010326047 -0.010139547 0.22744875 16.779805 + 29200 2.3477211e-06 0.02859243 -0.010375939 -0.01018496 0.22915025 16.744414 + 29300 2.348195e-06 0.029176333 -0.010424252 -0.010228763 0.23083364 16.709024 + 29400 2.3486217e-06 0.02976508 -0.010565133 -0.010363233 0.2345875 16.673633 + 29500 2.3494547e-06 0.030358578 -0.010610824 -0.010404093 0.2362499 16.638243 + 29600 2.350246e-06 0.030956806 -0.010654741 -0.010443743 0.23789521 16.602852 + 29700 2.350645e-06 0.031559783 -0.010697062 -0.01048188 0.23952237 16.567462 + 29800 2.3513205e-06 0.032167468 -0.010835186 -0.010613742 0.24331694 16.532071 + 29900 2.3500682e-06 0.03277985 -0.010874694 -0.010649336 0.2449217 16.496681 + 30000 2.348814e-06 0.033396866 -0.010912585 -0.010683036 0.24650812 16.46129 +Loop time of 96.3898 on 1 procs for 10000 steps with 17392 atoms + +Performance: 896360.661 tau/day, 103.745 timesteps/s, 1.804 Matom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.4048 | 2.4048 | 2.4048 | 0.0 | 2.49 +Bond | 89.472 | 89.472 | 89.472 | 0.0 | 92.82 +Neigh | 0.25526 | 0.25526 | 0.25526 | 0.0 | 0.26 +Comm | 0.0489 | 0.0489 | 0.0489 | 0.0 | 0.05 +Output | 1.6355 | 1.6355 | 1.6355 | 0.0 | 1.70 +Modify | 1.8578 | 1.8578 | 1.8578 | 0.0 | 1.93 +Other | | 0.7153 | | | 0.74 + +Nlocal: 17392 ave 17392 max 17392 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 77 ave 77 max 77 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 102662 ave 102662 max 102662 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 102662 +Ave neighs/atom = 5.9028289 +Ave special neighs/atom = 13.444802 +Neighbor list builds = 23 +Dangerous builds = 0 + 10000 +ERROR: Unknown command: 10000 (../input.cpp:314) +Last input line: 10000 diff --git a/examples/granular/3ps.dat b/examples/granular/3ps.dat new file mode 100644 index 0000000000..88360e2d06 --- /dev/null +++ b/examples/granular/3ps.dat @@ -0,0 +1,20 @@ +LAMMPS data file + +3 atoms +2 atom types + +-0.03 0.03 xlo xhi +-0.02 0.02 ylo yhi +-0.02 0.02 zlo zhi + +Atoms # sphere + +1 2 0.0005 2500 0.005 2.7937481665024794E-05 0.0016005372526493155 0 0 0 +2 1 0.01 2500 0.01 0.0 0.0 0 0 0 +3 1 0.01 2500 0.0 0.0 0.0 0 0 0 + +Velocities + +1 0 0 0 0 0 0 +2 0 0 0 0 0 0 +3 0 0 0 0 0 0 diff --git a/examples/granular/in.sync_verlet b/examples/granular/in.sync_verlet new file mode 100644 index 0000000000..6626c8694d --- /dev/null +++ b/examples/granular/in.sync_verlet @@ -0,0 +1,31 @@ +# Example problem demonstrating the use of synchronized_verlet +# Refer https://doi.org/10.1016/j.cpc.2025.109524 for further details + +units si +atom_style sphere +newton off + +boundary p p f +read_data 3ps.dat + +group ps type 1 +group fine type 2 + +pair_style granular +pair_coeff * * hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution synchronized_verlet +# pair_coeff * * hertz/material 5e8 0.5 0.3 tangential mindlin NULL 0.0 0.5 damping coeff_restitution #synchronized_verlet + +timestep 1e-6 +fix frz ps freeze +fix g fine gravity 9.81 vector 0 0 -1 +fix 1 fine nve/sphere +fix 2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane $(zlo) $(zhi) + +# dump 1 all custom 3000 op.dump id x y z vx vy vz type diameter + +comm_modify vel yes + +thermo 3000 +thermo_style custom step ke +run_style verlet +run 300000 diff --git a/examples/granular/log.18Feb25.sync_verlet.g++.1 b/examples/granular/log.18Feb25.sync_verlet.g++.1 new file mode 100644 index 0000000000..4fa1b8f5b3 --- /dev/null +++ b/examples/granular/log.18Feb25.sync_verlet.g++.1 @@ -0,0 +1,186 @@ +LAMMPS (19 Nov 2024 - Development - patch_5May2020-20901-g8641486249-modified) +# Example problem demonstrating the use of synchronized_verlet +# Refer https://doi.org/10.1016/j.cpc.2025.109524 for further details + +units si +atom_style sphere +newton off + +boundary p p f +read_data 3ps.dat +Reading data file ... + orthogonal box = (-0.03 -0.02 -0.02) to (0.03 0.02 0.02) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + reading velocities ... + 3 velocities + read_data CPU = 0.003 seconds + +group ps type 1 +2 atoms in group ps +group fine type 2 +1 atoms in group fine + +pair_style granular +pair_coeff * * hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution synchronized_verlet +# pair_coeff * * hertz/material 5e8 0.5 0.3 tangential mindlin NULL 0.0 0.5 damping coeff_restitution #synchronized_verlet + +timestep 1e-6 +fix frz ps freeze +fix g fine gravity 9.81 vector 0 0 -1 +fix 1 fine nve/sphere +fix 2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane $(zlo) $(zhi) +fix 2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane -0.020000000000000000416 $(zhi) +fix 2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane -0.020000000000000000416 0.020000000000000000416 + +dump 1 all custom 3000 op.dump id x y z vx vy vz type diameter + +comm_modify vel yes + +thermo 3000 +thermo_style custom step ke +run_style verlet +run 300000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.011 + ghost atom cutoff = 0.011 + binsize = 0.0055, bins = 11 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/atomonly/newtoff + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.34 | 10.34 | 10.34 Mbytes + Step KinEng + 0 0 + 3000 7.7090573e-16 + 6000 3.11122e-15 + 9000 7.1189829e-15 + 12000 1.2962539e-14 + 15000 2.0887458e-14 + 18000 3.1226589e-14 + 21000 4.4413694e-14 + 24000 6.1001238e-14 + 27000 8.1683111e-14 + 30000 1.0732325e-13 + 33000 1.3899142e-13 + 36000 1.7800759e-13 + 39000 2.2599689e-13 + 42000 2.849574e-13 + 45000 3.5734355e-13 + 48000 4.4616861e-13 + 51000 5.5513052e-13 + 54000 6.8876606e-13 + 57000 8.5263971e-13 + 60000 1.0535747e-12 + 63000 1.2999356e-12 + 66000 1.6019734e-12 + 69000 1.9722472e-12 + 72000 2.4261384e-12 + 75000 2.9824767e-12 + 78000 3.6643038e-12 + 81000 4.4997992e-12 + 84000 5.5234053e-12 + 87000 6.7771879e-12 + 90000 8.3124767e-12 + 93000 1.0191838e-11 + 96000 1.2491433e-11 + 99000 1.5303816e-11 + 102000 1.8741238e-11 + 105000 2.2939491e-11 + 108000 2.8062329e-11 + 111000 3.4306457e-11 + 114000 4.1907005e-11 + 117000 5.114332e-11 + 120000 6.2344723e-11 + 123000 7.5895667e-11 + 126000 9.2239362e-11 + 129000 1.118785e-10 + 132000 1.3537107e-10 + 135000 1.6331855e-10 + 138000 1.96343e-10 + 141000 2.3504868e-10 + 144000 2.799638e-10 + 147000 4.4767299e-10 + 150000 8.5696526e-10 + 153000 1.4079769e-09 + 156000 2.1007079e-09 + 159000 2.9351582e-09 + 162000 3.9113279e-09 + 165000 5.029217e-09 + 168000 6.2888254e-09 + 171000 7.6901531e-09 + 174000 9.2332002e-09 + 177000 1.0917967e-08 + 180000 1.2744453e-08 + 183000 1.4712658e-08 + 186000 1.6822582e-08 + 189000 1.9074226e-08 + 192000 2.1467589e-08 + 195000 2.4002672e-08 + 198000 2.6679474e-08 + 201000 2.9497995e-08 + 204000 3.2458236e-08 + 207000 6.543991e-09 + 210000 5.3049419e-09 + 213000 4.2076122e-09 + 216000 3.2520018e-09 + 219000 2.4381108e-09 + 222000 1.7659392e-09 + 225000 1.2354868e-09 + 228000 8.4675389e-10 + 231000 5.997403e-10 + 234000 4.9444606e-10 + 237000 5.3087117e-10 + 240000 7.0901564e-10 + 243000 1.0288795e-09 + 246000 1.4904626e-09 + 249000 2.0937652e-09 + 252000 2.8387871e-09 + 255000 3.7255283e-09 + 258000 4.7539889e-09 + 261000 5.9241689e-09 + 264000 7.2360682e-09 + 267000 1.6704365e-09 + 270000 1.161387e-09 + 273000 7.9405678e-10 + 276000 5.6844595e-10 + 279000 4.8455448e-10 + 282000 5.4238236e-10 + 285000 7.419296e-10 + 288000 1.0831962e-09 + 291000 1.5661821e-09 + 294000 8.41555e-10 + 297000 5.7599278e-10 + 300000 4.5214992e-10 +Loop time of 0.193539 on 1 procs for 300000 steps with 3 atoms + +98.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.064036 | 0.064036 | 0.064036 | 0.0 | 33.09 +Neigh | 0.00015725 | 0.00015725 | 0.00015725 | 0.0 | 0.08 +Comm | 0.027944 | 0.027944 | 0.027944 | 0.0 | 14.44 +Output | 0.002992 | 0.002992 | 0.002992 | 0.0 | 1.55 +Modify | 0.059704 | 0.059704 | 0.059704 | 0.0 | 30.85 +Other | | 0.03871 | | | 20.00 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1 +Ave neighs/atom = 0.33333333 +Neighbor list builds = 70 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/melt/in.melt b/examples/melt/in.melt index f169dc2ffc..6b67bfb774 100644 --- a/examples/melt/in.melt +++ b/examples/melt/in.melt @@ -1,33 +1,33 @@ # 3d Lennard-Jones melt -units lj -atom_style atomic +units lj +atom_style atomic -lattice fcc 0.8442 -region box block 0 10 0 10 0 10 -create_box 1 box -create_atoms 1 box -mass 1 1.0 +lattice fcc 0.8442 +region box block 0 10 0 10 0 10 +create_box 1 box +create_atoms 1 box +mass 1 1.0 -velocity all create 3.0 87287 loop geom +velocity all create 3.0 87287 loop geom -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 +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 +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no -fix 1 all nve +fix 1 all nve -#dump id all atom 50 dump.melt +#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 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 +#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 +thermo 50 +run 250 diff --git a/examples/peptide/in.peptide b/examples/peptide/in.peptide index 1a4bc6df31..fc74ec4161 100644 --- a/examples/peptide/in.peptide +++ b/examples/peptide/in.peptide @@ -1,42 +1,42 @@ # Solvated 5-mer peptide -units real -atom_style full +units real +atom_style full -pair_style lj/charmm/coul/long 8.0 10.0 10.0 +pair_style lj/charmm/coul/long 8.0 10.0 10.0 bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic -kspace_style pppm 0.0001 +kspace_style pppm 0.0001 -read_data data.peptide +read_data data.peptide -neighbor 2.0 bin -neigh_modify delay 5 +neighbor 2.0 bin +neigh_modify delay 5 -timestep 2.0 +timestep 2.0 -thermo_style multi -thermo 50 +thermo_style multi +thermo 50 -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 -fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 -group peptide type <= 12 +group peptide type <= 12 -#dump 1 peptide atom 10 dump.peptide +#dump 1 peptide atom 10 dump.peptide -#dump 2 peptide image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 -#dump_modify 2 pad 3 +#dump 2 peptide image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 2 pad 3 -#dump 3 peptide movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 -#dump_modify 3 pad 3 +#dump 3 peptide movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 3 pad 3 -#compute bnd all property/local btype batom1 batom2 -#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] +#compute bnd all property/local btype batom1 batom2 +#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] -run 300 +run 300 diff --git a/examples/plugins/LAMMPSInterfaceCXX.cmake b/examples/plugins/LAMMPSInterfaceCXX.cmake index d1f8faec22..4cd4510a61 100644 --- a/examples/plugins/LAMMPSInterfaceCXX.cmake +++ b/examples/plugins/LAMMPSInterfaceCXX.cmake @@ -131,8 +131,8 @@ endif() ################ # integer size selection -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(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") +set(LAMMPS_SIZES_VALUES smallbig bigbig) set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) diff --git a/examples/reaxff/water/in.water.qeqr b/examples/reaxff/water/in.water.qeqr new file mode 100644 index 0000000000..6debe0b895 --- /dev/null +++ b/examples/reaxff/water/in.water.qeqr @@ -0,0 +1,29 @@ +# Water with QEqR + +boundary p p p +units real +atom_style charge + +read_data data.water + +variable x index 1 +variable y index 1 +variable z index 1 + +replicate $x $y $z + +pair_style reaxff NULL safezone 3.0 mincap 150 +pair_coeff * * qeq_ff.water O H +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +velocity all create 300.0 4928459 rot yes dist gaussian + +fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt +fix 2 all nvt temp 300 300 50.0 + +timestep 0.5 +thermo 10 +thermo_style custom step temp press density vol + +run 20 diff --git a/examples/reaxff/water/in.water.qeqr.field b/examples/reaxff/water/in.water.qeqr.field new file mode 100644 index 0000000000..9c61477ff7 --- /dev/null +++ b/examples/reaxff/water/in.water.qeqr.field @@ -0,0 +1,30 @@ +# Water with QEqR + +boundary p p p +units real +atom_style charge + +read_data data.water + +variable x index 1 +variable y index 1 +variable z index 1 + +replicate $x $y $z + +pair_style reaxff NULL safezone 3.0 mincap 150 +pair_coeff * * qeq_ff.water O H +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +velocity all create 300.0 4928459 rot yes dist gaussian + +fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt +fix 2 all nvt temp 300 300 50.0 +fix 3 all efield 0.0 0.0 0.05 + +timestep 0.5 +thermo 10 +thermo_style custom step temp press density vol + +run 20 diff --git a/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr-field.g++.1 b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr-field.g++.1 new file mode 100644 index 0000000000..7f4c84d0f0 --- /dev/null +++ b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr-field.g++.1 @@ -0,0 +1,115 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-444-gbb8b6590d5-modified) + using 1 OpenMP thread(s) per MPI task +# Water with QEqR + +boundary p p p +units real +atom_style charge + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3000 atoms + read_data CPU = 0.053 seconds + +variable x index 1 +variable y index 1 +variable z index 1 + +replicate $x $y $z +replicate 1 $y $z +replicate 1 1 $z +replicate 1 1 1 +Replication is creating a 1x1x1 = 1 times larger system... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 1 by 1 MPI processor grid + 3000 atoms + replicate CPU = 0.001 seconds + +pair_style reaxff NULL safezone 3.0 mincap 150 +pair_coeff * * qeq_ff.water O H +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:300) +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +velocity all create 300.0 4928459 rot yes dist gaussian + +fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt +fix 2 all nvt temp 300 300 50.0 +fix 3 all efield 0.0 0.0 0.05 + +timestep 0.5 +thermo 10 +thermo_style custom step temp press density vol + +run 20 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: doi:10.1016/j.parco.2011.08.005 + +@Article{Aktulga12, + author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, + title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + number = {4--5}, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/ghost/newtoff + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeqr/reaxff, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes + Step Temp Press Density Volume + 0 300 778.75601 1 29915.273 + 10 301.42845 5423.6612 1 29915.273 + 20 298.24707 1549.2257 1 29915.273 +Loop time of 10.6859 on 1 procs for 20 steps with 3000 atoms + +Performance: 0.081 ns/day, 296.830 hours/ns, 1.872 timesteps/s, 5.615 katom-step/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 | 4.7595 | 4.7595 | 4.7595 | 0.0 | 44.54 +Neigh | 0.17605 | 0.17605 | 0.17605 | 0.0 | 1.65 +Comm | 0.0017511 | 0.0017511 | 0.0017511 | 0.0 | 0.02 +Output | 8.3809e-05 | 8.3809e-05 | 8.3809e-05 | 0.0 | 0.00 +Modify | 5.748 | 5.748 | 5.748 | 0.0 | 53.79 +Other | | 0.0005279 | | | 0.00 + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11075 ave 11075 max 11075 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 971785 ave 971785 max 971785 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 971785 +Ave neighs/atom = 323.92833 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:12 diff --git a/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr-field.g++.4 b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr-field.g++.4 new file mode 100644 index 0000000000..722609d9bf --- /dev/null +++ b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr-field.g++.4 @@ -0,0 +1,115 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-444-gbb8b6590d5-modified) + using 1 OpenMP thread(s) per MPI task +# Water with QEqR + +boundary p p p +units real +atom_style charge + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3000 atoms + read_data CPU = 0.053 seconds + +variable x index 1 +variable y index 1 +variable z index 1 + +replicate $x $y $z +replicate 1 $y $z +replicate 1 1 $z +replicate 1 1 1 +Replication is creating a 1x1x1 = 1 times larger system... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 2 by 2 MPI processor grid + 3000 atoms + replicate CPU = 0.002 seconds + +pair_style reaxff NULL safezone 3.0 mincap 150 +pair_coeff * * qeq_ff.water O H +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:300) +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +velocity all create 300.0 4928459 rot yes dist gaussian + +fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt +fix 2 all nvt temp 300 300 50.0 +fix 3 all efield 0.0 0.0 0.05 + +timestep 0.5 +thermo 10 +thermo_style custom step temp press density vol + +run 20 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: doi:10.1016/j.parco.2011.08.005 + +@Article{Aktulga12, + author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, + title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + number = {4--5}, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/ghost/newtoff + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeqr/reaxff, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes + Step Temp Press Density Volume + 0 300 778.75601 1 29915.273 + 10 301.42845 5423.6623 1 29915.273 + 20 298.24708 1549.2264 1 29915.273 +Loop time of 3.10467 on 4 procs for 20 steps with 3000 atoms + +Performance: 0.278 ns/day, 86.241 hours/ns, 6.442 timesteps/s, 19.326 katom-step/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.668 | 1.6843 | 1.7266 | 1.9 | 54.25 +Neigh | 0.08549 | 0.086004 | 0.086638 | 0.2 | 2.77 +Comm | 0.0135 | 0.055821 | 0.072105 | 10.4 | 1.80 +Output | 4.9632e-05 | 5.4515e-05 | 6.8384e-05 | 0.0 | 0.00 +Modify | 1.2774 | 1.2781 | 1.2786 | 0.0 | 41.17 +Other | | 0.000458 | | | 0.01 + +Nlocal: 750 ave 760 max 735 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Nghost: 6230.75 ave 6255 max 6191 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 276996 ave 280553 max 271385 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 1107985 +Ave neighs/atom = 369.32833 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr.g++.1 b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr.g++.1 new file mode 100644 index 0000000000..9710c81bcb --- /dev/null +++ b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr.g++.1 @@ -0,0 +1,116 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-444-gbb8b6590d5-modified) + using 1 OpenMP thread(s) per MPI task +# Water with QEqR + +boundary p p p +units real +atom_style charge + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3000 atoms + read_data CPU = 0.055 seconds + +variable x index 1 +variable y index 1 +variable z index 1 + +replicate $x $y $z +replicate 1 $y $z +replicate 1 1 $z +replicate 1 1 1 +Replication is creating a 1x1x1 = 1 times larger system... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 1 by 1 MPI processor grid + 3000 atoms + replicate CPU = 0.001 seconds + +pair_style reaxff NULL safezone 3.0 mincap 150 +pair_coeff * * qeq_ff.water O H +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:300) +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +velocity all create 300.0 4928459 rot yes dist gaussian + +fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt +fix 2 all nvt temp 300 300 50.0 + +timestep 0.5 +thermo 10 +thermo_style custom step temp press density vol + +run 20 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: doi:10.1016/j.parco.2011.08.005 + +@Article{Aktulga12, + author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, + title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + number = {4--5}, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: Use fix qeq/reaxff instead of fix qeqr/reaxff when not using fix efield + (src/REAXFF/fix_qtpie_reaxff.cpp:493) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/ghost/newtoff + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeqr/reaxff, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes + Step Temp Press Density Volume + 0 300 780.33989 1 29915.273 + 10 301.29205 5433.7414 1 29915.273 + 20 297.90652 1572.6111 1 29915.273 +Loop time of 6.87447 on 1 procs for 20 steps with 3000 atoms + +Performance: 0.126 ns/day, 190.957 hours/ns, 2.909 timesteps/s, 8.728 katom-step/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 | 4.8461 | 4.8461 | 4.8461 | 0.0 | 70.49 +Neigh | 0.17595 | 0.17595 | 0.17595 | 0.0 | 2.56 +Comm | 0.001787 | 0.001787 | 0.001787 | 0.0 | 0.03 +Output | 8.5794e-05 | 8.5794e-05 | 8.5794e-05 | 0.0 | 0.00 +Modify | 1.8501 | 1.8501 | 1.8501 | 0.0 | 26.91 +Other | | 0.0004811 | | | 0.01 + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11077 ave 11077 max 11077 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 971826 ave 971826 max 971826 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 971826 +Ave neighs/atom = 323.942 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr.g++.4 b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr.g++.4 new file mode 100644 index 0000000000..e6182bf53a --- /dev/null +++ b/examples/reaxff/water/log.20Mar25.reaxff.water-qeqr.g++.4 @@ -0,0 +1,116 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-444-gbb8b6590d5-modified) + using 1 OpenMP thread(s) per MPI task +# Water with QEqR + +boundary p p p +units real +atom_style charge + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3000 atoms + read_data CPU = 0.082 seconds + +variable x index 1 +variable y index 1 +variable z index 1 + +replicate $x $y $z +replicate 1 $y $z +replicate 1 1 $z +replicate 1 1 1 +Replication is creating a 1x1x1 = 1 times larger system... + orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) + 1 by 2 by 2 MPI processor grid + 3000 atoms + replicate CPU = 0.002 seconds + +pair_style reaxff NULL safezone 3.0 mincap 150 +pair_coeff * * qeq_ff.water O H +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:300) +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +velocity all create 300.0 4928459 rot yes dist gaussian + +fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt +fix 2 all nvt temp 300 300 50.0 + +timestep 0.5 +thermo 10 +thermo_style custom step temp press density vol + +run 20 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair reaxff command: doi:10.1016/j.parco.2011.08.005 + +@Article{Aktulga12, + author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, + title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, + journal = {Parallel Computing}, + year = 2012, + volume = 38, + number = {4--5}, + pages = {245--259} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: Use fix qeq/reaxff instead of fix qeqr/reaxff when not using fix efield + (src/REAXFF/fix_qtpie_reaxff.cpp:493) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reaxff, perpetual + attributes: half, newton off, ghost + pair build: half/bin/ghost/newtoff + stencil: full/ghost/bin/3d + bin: standard + (2) fix qeqr/reaxff, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes + Step Temp Press Density Volume + 0 300 780.34006 1 29915.273 + 10 301.29205 5433.7414 1 29915.273 + 20 297.90652 1572.6112 1 29915.273 +Loop time of 2.52349 on 4 procs for 20 steps with 3000 atoms + +Performance: 0.342 ns/day, 70.097 hours/ns, 7.926 timesteps/s, 23.777 katom-step/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.7081 | 1.7518 | 1.7812 | 2.3 | 69.42 +Neigh | 0.10017 | 0.10116 | 0.10315 | 0.4 | 4.01 +Comm | 0.014848 | 0.044256 | 0.087941 | 14.7 | 1.75 +Output | 5.1199e-05 | 5.663e-05 | 7.1837e-05 | 0.0 | 0.00 +Modify | 0.62379 | 0.62575 | 0.62671 | 0.1 | 24.80 +Other | | 0.000504 | | | 0.02 + +Nlocal: 750 ave 759 max 735 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 6230.5 ave 6256 max 6190 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 277008 ave 280943 max 271394 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 1108032 +Ave neighs/atom = 369.344 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/rerun/in.rdf.first b/examples/rerun/in.rdf.first index f9d1ecf55e..a72eae975a 100644 --- a/examples/rerun/in.rdf.first +++ b/examples/rerun/in.rdf.first @@ -27,7 +27,7 @@ neigh_modify delay 0 every 20 check no fix 1 all nve -dump 1 all custom 100 lj.dump id type x y z +dump 1 all custom 100 lj.dump id type x y z vx vy vz compute myRDF all rdf 50 cutoff 2.5 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector diff --git a/fortran/lammps.f90 b/fortran/lammps.f90 index 2cfd4422b0..fdd10167bf 100644 --- a/fortran/lammps.f90 +++ b/fortran/lammps.f90 @@ -248,6 +248,7 @@ MODULE LIBLAMMPS PROCEDURE :: force_timeout => lmp_force_timeout PROCEDURE :: has_error => lmp_has_error PROCEDURE :: get_last_error_message => lmp_get_last_error_message + PROCEDURE :: set_show_error => lmp_set_show_error END TYPE lammps INTERFACE lammps @@ -334,14 +335,6 @@ MODULE LIBLAMMPS ! Interface templates for fix external callbacks ABSTRACT INTERFACE - SUBROUTINE external_callback_smallsmall(caller, timestep, ids, x, fexternal) - IMPORT :: c_int, c_double - CLASS(*), INTENT(INOUT) :: caller - INTEGER(c_int), INTENT(IN) :: timestep - INTEGER(c_int), DIMENSION(:), INTENT(IN) :: ids - REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x - REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal - END SUBROUTINE external_callback_smallsmall SUBROUTINE external_callback_smallbig(caller, timestep, ids, x, fexternal) IMPORT :: c_int, c_double, c_int64_t CLASS(*), INTENT(INOUT) :: caller @@ -363,8 +356,6 @@ MODULE LIBLAMMPS ! Derived type for fix external callback data TYPE fix_external_data CHARACTER(LEN=:), ALLOCATABLE :: id - PROCEDURE(external_callback_smallsmall), NOPASS, POINTER :: & - callback_smallsmall => NULL() PROCEDURE(external_callback_smallbig), NOPASS, POINTER :: & callback_smallbig => NULL() PROCEDURE(external_callback_bigbig), NOPASS, POINTER :: & @@ -1051,6 +1042,13 @@ MODULE LIBLAMMPS INTEGER(c_int), VALUE :: buf_size END FUNCTION lammps_get_last_error_message + INTEGER(c_int) FUNCTION lammps_set_show_error(handle,flag) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle + INTEGER(c_int), VALUE :: flag + END FUNCTION lammps_set_show_error + !--------------------------------------------------------------------- ! Utility functions imported for convenience (not in library.h) !--------------------------------------------------------------------- @@ -2262,7 +2260,7 @@ CONTAINS CALL lammps_free(Cname) END SUBROUTINE lmp_scatter_atoms_subset_double - ! equivalent function to lammps_gather_bonds (LAMMPS_SMALLSMALL or SMALLBIG) + ! equivalent function to lammps_gather_bonds (LAMMPS_SMALLBIG) SUBROUTINE lmp_gather_bonds_small(self, data) CLASS(lammps), INTENT(IN) :: self INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data @@ -2304,7 +2302,7 @@ CONTAINS CALL lammps_gather_bonds(self%handle, Cdata) END SUBROUTINE lmp_gather_bonds_big - ! equivalent function to lammps_gather_angles (LAMMPS_SMALLSMALL or SMALLBIG) + ! equivalent function to lammps_gather_angles (LAMMPS_SMALLBIG) SUBROUTINE lmp_gather_angles_small(self, data) CLASS(lammps), INTENT(IN) :: self INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data @@ -2346,7 +2344,7 @@ CONTAINS CALL lammps_gather_angles(self%handle, Cdata) END SUBROUTINE lmp_gather_angles_big - ! equivalent function to lammps_gather_dihedrals (LAMMPS_SMALLSMALL or SMALLBIG) + ! equivalent function to lammps_gather_dihedrals (LAMMPS_SMALLBIG) SUBROUTINE lmp_gather_dihedrals_small(self, data) CLASS(lammps), INTENT(IN) :: self INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data @@ -2388,7 +2386,7 @@ CONTAINS CALL lammps_gather_dihedrals(self%handle, Cdata) END SUBROUTINE lmp_gather_dihedrals_big - ! equivalent function to lammps_gather_impropers (LAMMPS_SMALLSMALL or SMALLBIG) + ! equivalent function to lammps_gather_impropers (LAMMPS_SMALLBIG) SUBROUTINE lmp_gather_impropers_small(self, data) CLASS(lammps), INTENT(IN) :: self INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data @@ -2763,7 +2761,7 @@ CONTAINS IF (tagint_size /= 4_c_int .AND. (PRESENT(id) .OR. PRESENT(image))) THEN CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & 'Unable to create_atoms; your id/image array types are incompatible& - & with LAMMPS_SMALLBIG and LAMMPS_SMALLSMALL [Fortran/create_atoms]') + & with LAMMPS_SMALLBIG [Fortran/create_atoms]') END IF n = SIZE(type, KIND=c_int) IF (PRESENT(bexpand)) THEN @@ -3360,7 +3358,7 @@ CONTAINS construct_fix_external_data%id = ' ' END FUNCTION construct_fix_external_data - ! equivalent function to lammps_set_fix_external_callback for -DSMALLSMALL + ! equivalent function to lammps_set_fix_external_callback ! note that "caller" is wrapped into a fix_external_data derived type along ! with the fix id and the Fortran calling function. SUBROUTINE lmp_set_fix_external_callback(self, id, callback, caller) @@ -3394,11 +3392,7 @@ CONTAINS ext_data(this_fix)%id = id ext_data(this_fix)%lammps_instance => self - IF (SIZE_TAGINT == 4_c_int .AND. SIZE_BIGINT == 4_c_int) THEN - ! -DSMALLSMALL - c_callback = C_FUNLOC(callback_wrapper_smallsmall) - CALL set_fix_external_callback_smallsmall(this_fix, callback) - ELSE IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN + IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN ! -DBIGBIG c_callback = C_FUNLOC(callback_wrapper_bigbig) CALL set_fix_external_callback_bigbig(this_fix, callback) @@ -3420,12 +3414,6 @@ CONTAINS END SUBROUTINE lmp_set_fix_external_callback ! Wrappers to assign callback pointers with explicit interfaces - SUBROUTINE set_fix_external_callback_smallsmall(id, callback) - INTEGER, INTENT(IN) :: id - PROCEDURE(external_callback_smallsmall) :: callback - - ext_data(id)%callback_smallsmall => callback - END SUBROUTINE set_fix_external_callback_smallsmall SUBROUTINE set_fix_external_callback_smallbig(id, callback) INTEGER, INTENT(IN) :: id @@ -3450,9 +3438,7 @@ CONTAINS DO i = 1, SIZE(ext_data) - 1 c_id = f2c_string(ext_data(i)%id) c_caller = C_LOC(ext_data(i)) - IF (SIZE_TAGINT == 4_c_int .AND. SIZE_BIGINT == 4_c_int) THEN - c_callback = C_FUNLOC(callback_wrapper_smallsmall) - ELSE IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN + IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN c_callback = C_FUNLOC(callback_wrapper_bigbig) ELSE c_callback = C_FUNLOC(callback_wrapper_smallbig) @@ -3464,34 +3450,6 @@ CONTAINS END SUBROUTINE rebind_external_callback_data ! companions to lmp_set_fix_external_callback to change interface - SUBROUTINE callback_wrapper_smallsmall(caller, timestep, nlocal, ids, x, & - fexternal) BIND(C) - TYPE(c_ptr), INTENT(IN), VALUE :: caller - INTEGER(c_int), INTENT(IN), VALUE :: timestep - INTEGER(c_int), INTENT(IN), VALUE :: nlocal - TYPE(c_ptr), INTENT(IN), VALUE :: ids, x, fexternal - TYPE(c_ptr), DIMENSION(:), POINTER :: x0, f0 - INTEGER(c_int), DIMENSION(:), POINTER :: f_ids => NULL() - REAL(c_double), DIMENSION(:,:), POINTER :: f_x => NULL(), & - f_fexternal => NULL() - TYPE(fix_external_data), POINTER :: f_caller => NULL() - - CALL C_F_POINTER(ids, f_ids, [nlocal]) - CALL C_F_POINTER(x, x0, [nlocal]) - CALL C_F_POINTER(x0(1), f_x, [3, nlocal]) - CALL C_F_POINTER(fexternal, f0, [nlocal]) - CALL C_F_POINTER(f0(1), f_fexternal, [3, nlocal]) - IF (C_ASSOCIATED(caller)) THEN - CALL C_F_POINTER(caller, f_caller) - CALL f_caller%callback_smallsmall(f_caller%caller, timestep, f_ids, & - f_x, f_fexternal) - ELSE - CALL lmp_error(f_caller%lammps_instance, & - LMP_ERROR_ALL + LMP_ERROR_WORLD, & - 'Got null pointer from "caller"; this should never happen;& - & please report a bug') - END IF - END SUBROUTINE callback_wrapper_smallsmall SUBROUTINE callback_wrapper_smallbig(caller, timestep, nlocal, ids, x, & fexternal) BIND(C) @@ -3716,6 +3674,14 @@ CONTAINS END IF END SUBROUTINE lmp_get_last_error_message + ! equivalent function to lammps_set_show_error + INTEGER FUNCTION lmp_set_show_error(self, flag) + CLASS(lammps), INTENT(IN) :: self + INTEGER, INTENT(IN) :: flag + + lmp_set_show_error = lammps_set_show_error(self%handle, flag) + END FUNCTION lmp_set_show_error + ! ---------------------------------------------------------------------- ! functions to assign user-space pointers to LAMMPS data ! ---------------------------------------------------------------------- diff --git a/lib/gpu/Makefile.aurora b/lib/gpu/Makefile.aurora index c343e061ee..1f6c9b646a 100644 --- a/lib/gpu/Makefile.aurora +++ b/lib/gpu/Makefile.aurora @@ -11,8 +11,8 @@ EXTRAMAKE = Makefile.lammps.opencl # OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.cuda b/lib/gpu/Makefile.cuda index 75428c9513..d7552d267c 100644 --- a/lib/gpu/Makefile.cuda +++ b/lib/gpu/Makefile.cuda @@ -11,8 +11,8 @@ ifeq ($(CUDA_HOME),) CUDA_HOME = /usr/local/cuda endif -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.cuda_mps b/lib/gpu/Makefile.cuda_mps index 22a34c105c..4063de92e7 100644 --- a/lib/gpu/Makefile.cuda_mps +++ b/lib/gpu/Makefile.cuda_mps @@ -11,8 +11,8 @@ ifeq ($(CUDA_HOME),) CUDA_HOME = /usr/local/cuda endif -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.hip b/lib/gpu/Makefile.hip index 0350c841c4..54085523bf 100644 --- a/lib/gpu/Makefile.hip +++ b/lib/gpu/Makefile.hip @@ -7,8 +7,8 @@ # - change HIP_ARCH for your GPU # ------------------------------------------------------------------------- */ -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux index e02413f3ba..6b7122ea6b 100644 --- a/lib/gpu/Makefile.linux +++ b/lib/gpu/Makefile.linux @@ -51,8 +51,8 @@ CUDA_ARCH = -arch=sm_60 # Hopper hardware #CUDA_ARCH = -arch=sm_90 -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.linux_multi b/lib/gpu/Makefile.linux_multi index e3a76d9934..3fac7030ea 100644 --- a/lib/gpu/Makefile.linux_multi +++ b/lib/gpu/Makefile.linux_multi @@ -51,8 +51,8 @@ CUDA_CODE = -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compu CUDA_ARCH += $(CUDA_CODE) -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.linux_opencl b/lib/gpu/Makefile.linux_opencl index b4b25544ee..1ad4ceba96 100644 --- a/lib/gpu/Makefile.linux_opencl +++ b/lib/gpu/Makefile.linux_opencl @@ -6,8 +6,8 @@ EXTRAMAKE = Makefile.lammps.opencl -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.oneapi b/lib/gpu/Makefile.oneapi index e67f4bb082..79e52482c7 100644 --- a/lib/gpu/Makefile.oneapi +++ b/lib/gpu/Makefile.oneapi @@ -6,8 +6,8 @@ EXTRAMAKE = Makefile.lammps.opencl -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.oneapi_prof b/lib/gpu/Makefile.oneapi_prof index 58a03392e2..160b2f0d33 100644 --- a/lib/gpu/Makefile.oneapi_prof +++ b/lib/gpu/Makefile.oneapi_prof @@ -6,8 +6,8 @@ EXTRAMAKE = Makefile.lammps.opencl -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/Makefile.serial b/lib/gpu/Makefile.serial index 67d2ce927d..43541ef019 100644 --- a/lib/gpu/Makefile.serial +++ b/lib/gpu/Makefile.serial @@ -45,8 +45,8 @@ CUDA_ARCH = -arch=sm_60 #CUDA_ARCH = -arch=sm_80 #CUDA_ARCH = -arch=sm_86 -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL +# this setting should match the LAMMPS Makefile +# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG LMP_INC = -DLAMMPS_SMALLBIG diff --git a/lib/gpu/README b/lib/gpu/README index b720aa65cb..7cc1aea8fb 100644 --- a/lib/gpu/README +++ b/lib/gpu/README @@ -136,10 +136,10 @@ IMPORTANT: If you re-build the library, e.g. for a different precision Makefile.linux clean, to ensure all previous derived files are removed before the new build is done. -NOTE: The system-specific setting LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG, - or LAMMPS_SMALLSMALL if specified when building LAMMPS (i.e. in - src/MAKE/Makefile.foo) should be consistent with that specified - when building libgpu.a (i.e. by LMP_INC in the lib/gpu/Makefile.bar). +NOTE: The system-specific setting LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG + - if specified when building LAMMPS (i.e. in src/MAKE/Makefile.foo) - + should be consistent with that specified when building libgpu.a (i.e. + by LMP_INC in the lib/gpu/Makefile.bar). ------------------------------------------------------------------------------ diff --git a/lib/gpu/lal_amoeba.cu b/lib/gpu/lal_amoeba.cu index a92509f06d..14d1d3e5de 100644 --- a/lib/gpu/lal_amoeba.cu +++ b/lib/gpu/lal_amoeba.cu @@ -23,9 +23,6 @@ #include "inttypes.h" #define tagint int64_t #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #ifndef _DOUBLE_DOUBLE _texture( pos_tex,float4); _texture( q_tex,float); @@ -43,9 +40,6 @@ _texture( q_tex,int2); #ifdef LAMMPS_BIGBIG #define tagint long #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #endif // defined(NV_KERNEL) || defined(USE_HIP) diff --git a/lib/gpu/lal_dpd_coul_slater_long.cu b/lib/gpu/lal_dpd_coul_slater_long.cu index 4835b8777b..44931195ee 100644 --- a/lib/gpu/lal_dpd_coul_slater_long.cu +++ b/lib/gpu/lal_dpd_coul_slater_long.cu @@ -287,16 +287,16 @@ __kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_, // apply Slater electrostatic force if distance below Slater cutoff // and the two species have a slater coeff - // cutsq[mtype].z -> Coulombic squared cutoff - if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){ + // cutsq[mtype].z -> Slater cutoff + // extra[j].x -> q[j] ; particle j charge + if ( rsq < cutsq[mtype].z ){ numtyp r2inv=ucl_recip(rsq); numtyp _erfc; numtyp grij = g_ewald * r; numtyp expm2 = ucl_exp(-grij*grij); numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; - numtyp prefactor = extra[j].x; - prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r; + numtyp prefactor = qqrd2e * extra[j].x * qtmp / r; numtyp rlamdainv = r * lamdainv; numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv); numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv))); @@ -306,9 +306,9 @@ __kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_, if (EVFLAG && eflag) { numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv; - numtyp e = prefactor*(_erfc-e_slater); - if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater); - e_coul += e; + numtyp e_sf = prefactor*(_erfc-e_slater); + if (factor_coul > (numtyp)0) e_sf -= factor_coul*prefactor*((numtyp)1.0 - e_slater); + e_coul += e_sf; } } // if cut_coulsq @@ -471,16 +471,16 @@ __kernel void k_dpd_coul_slater_long_fast(const __global numtyp4 *restrict x_, // apply Slater electrostatic force if distance below Slater cutoff // and the two species have a slater coeff - // cutsq[mtype].z -> Coulombic squared cutoff - if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){ + // cutsq[mtype].z -> Slater cutoff + // extra[j].x -> q[j] ; particle j charge + if ( rsq < cutsq[mtype].z ){ numtyp r2inv=ucl_recip(rsq); numtyp _erfc; numtyp grij = g_ewald * r; numtyp expm2 = ucl_exp(-grij*grij); numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; - numtyp prefactor = extra[j].x; - prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r; + numtyp prefactor = qqrd2e * extra[j].x * qtmp / r; numtyp rlamdainv = r * lamdainv; numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv); numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv))); diff --git a/lib/gpu/lal_dpd_coul_slater_long.h b/lib/gpu/lal_dpd_coul_slater_long.h index 1870255998..007e7a2e00 100644 --- a/lib/gpu/lal_dpd_coul_slater_long.h +++ b/lib/gpu/lal_dpd_coul_slater_long.h @@ -65,7 +65,7 @@ class DPDCoulSlaterLong : public BaseDPD { /// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd UCL_D_Vec coeff; - /// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.w = cut_slatersq + /// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.z = cut_slatersq UCL_D_Vec cutsq; /// Special LJ values diff --git a/lib/gpu/lal_hippo.cu b/lib/gpu/lal_hippo.cu index 01ad8e753a..3ae1e5ff21 100644 --- a/lib/gpu/lal_hippo.cu +++ b/lib/gpu/lal_hippo.cu @@ -23,9 +23,6 @@ #include "inttypes.h" #define tagint int64_t #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #ifndef _DOUBLE_DOUBLE _texture( pos_tex,float4); _texture( q_tex,float); @@ -43,9 +40,6 @@ _texture( q_tex,int2); #ifdef LAMMPS_BIGBIG #define tagint long #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #endif // defined(NV_KERNEL) || defined(USE_HIP) diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu index 26ceb38538..46a47d7710 100644 --- a/lib/gpu/lal_lj_tip4p_long.cu +++ b/lib/gpu/lal_lj_tip4p_long.cu @@ -27,9 +27,6 @@ #define tagint int64_t #endif #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #ifndef _DOUBLE_DOUBLE _texture( pos_tex,float4); _texture( q_tex,float); @@ -50,9 +47,6 @@ _texture( q_tex,int2); #define tagint int64_t #endif #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #define pos_tex x_ #define q_tex q_ #endif diff --git a/lib/gpu/lal_neighbor_gpu.cu b/lib/gpu/lal_neighbor_gpu.cu index 7d0941ccd5..a0fa26b7e4 100644 --- a/lib/gpu/lal_neighbor_gpu.cu +++ b/lib/gpu/lal_neighbor_gpu.cu @@ -28,9 +28,6 @@ #define tagint int64_t #endif #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #ifndef _DOUBLE_DOUBLE _texture( pos_tex,float4); #else @@ -140,9 +137,6 @@ __kernel void kernel_calc_cell_counts(const unsigned *restrict cell_id, #ifdef LAMMPS_BIGBIG #define tagint long #endif -#ifdef LAMMPS_SMALLSMALL -#define tagint int -#endif #endif __kernel void transpose(__global tagint *restrict out, diff --git a/lib/gpu/lal_precision.h b/lib/gpu/lal_precision.h index 85e009e96b..f0df796b49 100644 --- a/lib/gpu/lal_precision.h +++ b/lib/gpu/lal_precision.h @@ -150,8 +150,7 @@ enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE}; // default to 32-bit smallint and other ints, 64-bit bigint: // same as defined in src/lmptype.h -#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && \ - !defined(LAMMPS_SMALLBIG) +#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) #define LAMMPS_SMALLBIG #endif @@ -164,9 +163,5 @@ typedef int tagint; typedef int64_t tagint; #define OCL_INT_TYPE "-DLAMMPS_BIGBIG" #endif -#ifdef LAMMPS_SMALLSMALL -typedef int tagint; -#define OCL_INT_TYPE "-DLAMMPS_SMALLSMALL" -#endif #endif // LAL_PRECISION_H diff --git a/lib/gpu/lal_preprocessor.h b/lib/gpu/lal_preprocessor.h index 93d6936f38..d7f7c700c5 100644 --- a/lib/gpu/lal_preprocessor.h +++ b/lib/gpu/lal_preprocessor.h @@ -406,7 +406,6 @@ ucl_inline int sbmask15(int j) { return j >> SBBITS15 & 7; }; // default to 32-bit smallint and other ints, 64-bit bigint: // same as defined in src/lmptype.h -#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && \ - !defined(LAMMPS_SMALLBIG) +#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) #define LAMMPS_SMALLBIG #endif diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index 84bbd03585..7d39bd36ae 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,72 @@ # CHANGELOG +## 4.6.00 + +[Full Changelog](https://github.com/kokkos/kokkos/compare/4.5.01...4.6.00) + +### Features: + +* Kokkos::Graph: Allow adding tasks to the graph via a `then`-node [\#7629](https://github.com/kokkos/kokkos/pull/7629) +* Kokkos::Graph: Allow construction from CUDA/HIP graph [\#7664](https://github.com/kokkos/kokkos/pull/7664) +* HIP: Add experimental support for using multiple GPUs from one process [\#7130](https://github.com/kokkos/kokkos/pull/7130) + +### Backend and Architecture Enhancements: + +#### CUDA: +* Improved reduction performance, in particular on H100 and newer [\#7823](https://github.com/kokkos/kokkos/pull/7823) + +#### HIP: +* Change block size deduction to prefer smaller blocks/teams [\#7509](https://github.com/kokkos/kokkos/pull/7509) +* Allocate memory with stream ordered semantics (i.e. use `hipMallocAsync`) [\#7659](https://github.com/kokkos/kokkos/pull/7659) +* Fix a segfault when a virtual function called inside a kernel requires too many registers[\#7660](https://github.com/kokkos/kokkos/pull/7660) + +#### SYCL: +* Improve sorting performance for non-contiguous views [\#7502](https://github.com/kokkos/kokkos/pull/7502) + +#### Serial: +* Reduce fences overhead when using `Kokkos_ENABLE_ATOMICS_BYPASS` [\#7821](https://github.com/kokkos/kokkos/pull/7821) + +### General Enhancements +* Allow use of `kokkos_check` in `Config.cmake` without warnings [\#7669](https://github.com/kokkos/kokkos/pull/7669) +* Add simd compound assignments and update simd reductions [\#7486](https://github.com/kokkos/kokkos/pull/7486) +* Improve performance of the `inclusive_scan` algorithm with Cuda and HIP [\#7542](https://github.com/kokkos/kokkos/pull/7542) +* Reduce tooling interface overhead (don't pay for what you don't use) [\#7817](https://github.com/kokkos/kokkos/pull/7817) +* Avoid storing the view in `RandomAccessIterator` to increase performance [\#7304](https://github.com/kokkos/kokkos/pull/7304) +* Make `RandomAccessIterator` fulfill `std::random_access_iterator concept` [\#7451](https://github.com/kokkos/kokkos/pull/7451) +* Include information about support for system allocated memory in `print_configuration` (Cuda and HIP) [\#7673](https://github.com/kokkos/kokkos/pull/7673) + +### Build System Changes +* Add support for Zen 4 AMD microarchitecture [\#7550](https://github.com/kokkos/kokkos/pull/7550) +* Enable NVIDIA Grace architecture with NVHPC [\#7858](https://github.com/kokkos/kokkos/pull/7858) +* Support static library builds when using CUDA as CMake language [\#7830](https://github.com/kokkos/kokkos/pull/7830) + +### Incompatibilities (i.e. breaking changes) +* Change SIMD comparison operator to return `simd_mask` instead of `bool` [\#7781](https://github.com/kokkos/kokkos/pull/7781) +* Remove classic Intel compiler (icpc) support [\#7737](https://github.com/kokkos/kokkos/pull/7737) +* Remove `operator[]` overloads of Kokkos `basic_simd` and `basic_simd_mask` that return a reference [\#7630](https://github.com/kokkos/kokkos/pull/7630) + +### Deprecations +* Deprecate `StaticCrsGraph` and move it to Kokkos Kernels into `KokkosSparse::` [\#7516](https://github.com/kokkos/kokkos/pull/7516) +* Deprecate `native_simd` and hide `simd_abi` [\#7472](https://github.com/kokkos/kokkos/pull/7472) +* Deprecate Makefile support [\#7613](https://github.com/kokkos/kokkos/pull/7613) +* DualView: Deprecate direct access to d_view and h_view [\#7716](https://github.com/kokkos/kokkos/pull/7716) + +### Bug Fixes +* Fix performance bug affecting `atomic_fetch_{add,sub,min,max,and,or,xor}` on integral types `long` and `unsigned long` with HIP [\#7816](https://github.com/kokkos/kokkos/pull/7816) +* Fix execution of ranges with more than 2B elements [\#7797](https://github.com/kokkos/kokkos/pull/7797) +* Fix clean target when embedding Kokkos in another project [\#7557](https://github.com/kokkos/kokkos/pull/7557) +* Fix Zen3 flag for NVHPC [\#7558](https://github.com/kokkos/kokkos/pull/7558) +* graph: nodes must be stored by the graph [\#7619](https://github.com/kokkos/kokkos/pull/7619) +* Make sure lock arrays are on device before launching a graph [\#7685](https://github.com/kokkos/kokkos/pull/7685) +* Performance bug in `RangePolicy`: construct error message if and only if the precondition is violated [\#7809](https://github.com/kokkos/kokkos/pull/7809) +* simd: fix a bug in scalar min/max [\#7813](https://github.com/kokkos/kokkos/pull/7813) +* simd: fix a bug in non-masked reductions [\#7845](https://github.com/kokkos/kokkos/pull/7845) +* Cuda: fix incorrect iteration in `MDRangePolicy` of rank > 4 for high iteration counts [\#7724](https://github.com/kokkos/kokkos/pull/7724) +* Cuda: ignore gcc assembler options in `nvcc-wrapper` [\#7492](https://github.com/kokkos/kokkos/pull/7492) +* Build system: hint to `ARCH_NATIVE` if ARMv9 Grace arch is not explicitly supported by the compiler [\#7862](https://github.com/kokkos/kokkos/pull/7862) +* Use right arch for MI300A in makefiles [\#7786](https://github.com/kokkos/kokkos/pull/7786) +* Fix compiling BasicView on MSVC [\#7751](https://github.com/kokkos/kokkos/pull/7751) + ## 4.5.01 [Full Changelog](https://github.com/kokkos/kokkos/compare/4.5.00...4.5.01) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index 6a70bea149..7a4dc73444 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -148,8 +148,8 @@ elseif(NOT CMAKE_SIZEOF_VOID_P EQUAL 8) endif() set(Kokkos_VERSION_MAJOR 4) -set(Kokkos_VERSION_MINOR 5) -set(Kokkos_VERSION_PATCH 1) +set(Kokkos_VERSION_MINOR 6) +set(Kokkos_VERSION_PATCH 0) set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}") message(STATUS "Kokkos version: ${Kokkos_VERSION}") math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}") diff --git a/lib/kokkos/CTestConfig.cmake b/lib/kokkos/CTestConfig.cmake new file mode 100644 index 0000000000..deb80ab76a --- /dev/null +++ b/lib/kokkos/CTestConfig.cmake @@ -0,0 +1,4 @@ +set(CTEST_PROJECT_NAME Kokkos) +set(CTEST_NIGHTLY_START_TIME 01:00:00 UTC) +set(CTEST_SUBMIT_URL https://my.cdash.org/submit.php?project=Kokkos) +set(CTEST_DROP_SITE_CDASH TRUE) diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index abdfb7a316..65c576bb8d 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -1,18 +1,26 @@ # Default settings common options. -#SPARTA specific settings: +#LAMMPS specific settings: + +KOKKOS_USE_DEPRECATED_MAKEFILES=1 + ifndef KOKKOS_PATH KOKKOS_PATH=../../lib/kokkos endif CXXFLAGS=$(CCFLAGS) ifeq ($(mode),shared) -CXXFLAGS += $(SHFLAGS) + CXXFLAGS += $(SHFLAGS) +endif + + +ifneq ($(KOKKOS_USE_DEPRECATED_MAKEFILES), 1) + $(error Makefile support is deprecated. Only CMake builds will be supported from Kokkos 5 on. Set KOKKOS_USE_DEPRECATED_MAKEFILES=1 to silence this error.) endif KOKKOS_VERSION_MAJOR = 4 -KOKKOS_VERSION_MINOR = 5 -KOKKOS_VERSION_PATCH = 1 +KOKKOS_VERSION_MINOR = 6 +KOKKOS_VERSION_PATCH = 0 KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc) # Options: Cuda,HIP,SYCL,OpenMPTarget,OpenMP,Threads,Serial @@ -24,7 +32,7 @@ KOKKOS_DEVICES ?= "OpenMP" # ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX,ARMv9-Grace # IBM: Power8,Power9 # AMD-GPUS: AMD_GFX906,AMD_GFX908,AMD_GFX90A,AMD_GFX940,AMD_GFX942,AMD_GFX942_APU,AMD_GFX1030,AMD_GFX1100,AMD_GFX1103 -# AMD-CPUS: AMDAVX,Zen,Zen2,Zen3 +# AMD-CPUS: AMDAVX,Zen,Zen2,Zen3,Zen4 # Intel-GPUs: Intel_Gen,Intel_Gen9,Intel_Gen11,Intel_Gen12LP,Intel_DG1,Intel_XeHP,Intel_PVC KOKKOS_ARCH ?= "" # Options: yes,no @@ -442,11 +450,14 @@ 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_ZEN4 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen4) KOKKOS_INTERNAL_USE_ARCH_ZEN3 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen3) KOKKOS_INTERNAL_USE_ARCH_ZEN2 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen2) -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN3), 0) - ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN2), 0) - KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN4), 0) + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN3), 0) + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN2), 0) + KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen) + endif endif endif @@ -463,8 +474,10 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX90A), 0) KOKKOS_INTERNAL_USE_ARCH_AMD_GFX90A := $(call kokkos_has_string,$(KOKKOS_ARCH),VEGA90A) endif KOKKOS_INTERNAL_USE_ARCH_AMD_GFX940 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX940) -KOKKOS_INTERNAL_USE_ARCH_AMD_GFX942 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX942) KOKKOS_INTERNAL_USE_ARCH_AMD_GFX942_APU := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX942_APU) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX942_APU), 0) + KOKKOS_INTERNAL_USE_ARCH_AMD_GFX942 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX942) +endif KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1030 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX1030) ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1030), 0) KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1030 := $(call kokkos_has_string,$(KOKKOS_ARCH),NAVI1030) @@ -857,6 +870,19 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN3), 1) endif endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN4), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_ZEN4") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX512XEON") + + ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) + KOKKOS_CXXFLAGS += -xCORE-AVX512 + KOKKOS_LDFLAGS += -xCORE-AVX512 + else + KOKKOS_CXXFLAGS += -march=znver4 -mtune=znver4 + KOKKOS_LDFLAGS += -march=znver4 -mtune=znver4 + endif +endif + ifeq ($(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") diff --git a/lib/kokkos/README.md b/lib/kokkos/README.md index 56159b35c2..13d99c0bad 100644 --- a/lib/kokkos/README.md +++ b/lib/kokkos/README.md @@ -18,24 +18,24 @@ Kokkos is a [Linux Foundation](https://linuxfoundation.org) project. To start learning about Kokkos: -- [Kokkos Lectures](https://kokkos.org/kokkos-core-wiki/videolectures.html): they contain a mix of lecture videos and hands-on exercises covering all the important capabilities. +- [Kokkos Lectures](https://kokkos.org/kokkos-core-wiki/tutorials-and-examples/video-lectures.html): they contain a mix of lecture videos and hands-on exercises covering all the important capabilities. - [Programming guide](https://kokkos.org/kokkos-core-wiki/programmingguide.html): contains in "narrative" form a technical description of the programming model, machine model, and the main building blocks like the Views and parallel dispatch. - [API reference](https://kokkos.org/kokkos-core-wiki/): organized by category, i.e., [core](https://kokkos.org/kokkos-core-wiki/API/core-index.html), [algorithms](https://kokkos.org/kokkos-core-wiki/API/algorithms-index.html) and [containers](https://kokkos.org/kokkos-core-wiki/API/containers-index.html) or, if you prefer, in [alphabetical order](https://kokkos.org/kokkos-core-wiki/API/alphabetical.html). -- [Use cases and Examples](https://kokkos.org/kokkos-core-wiki/usecases.html): a serie of examples ranging from how to use Kokkos with MPI to Fortran interoperability. +- [Use cases and Examples](https://kokkos.org/kokkos-core-wiki/tutorials-and-examples/use-cases-and-examples.html): a serie of examples ranging from how to use Kokkos with MPI to Fortran interoperability. ## Obtaining Kokkos The latest release of Kokkos can be obtained from the [GitHub releases page](https://github.com/kokkos/kokkos/releases/latest). -The current release is [4.5.01](https://github.com/kokkos/kokkos/releases/tag/4.5.01). +The current release is [4.6.00](https://github.com/kokkos/kokkos/releases/tag/4.6.00). ```bash -curl -OJ -L https://github.com/kokkos/kokkos/releases/download/4.5.01/kokkos-4.5.01.tar.gz +curl -OJ -L https://github.com/kokkos/kokkos/releases/download/4.6.00/kokkos-4.6.00.tar.gz # Or with wget -wget https://github.com/kokkos/kokkos/releases/download/4.5.01/kokkos-4.5.01.tar.gz +wget https://github.com/kokkos/kokkos/releases/download/4.6.00/kokkos-4.6.00.tar.gz ``` To clone the latest development version of Kokkos from GitHub: @@ -47,7 +47,7 @@ git clone -b develop https://github.com/kokkos/kokkos.git ### Building Kokkos To build Kokkos, you will need to have a C++ compiler that supports C++17 or later. -All requirements including minimum and primary tested compiler versions can be found [here](https://kokkos.org/kokkos-core-wiki/requirements.html). +All requirements including minimum and primary tested compiler versions can be found [here](https://kokkos.org/kokkos-core-wiki/get-started/requirements.html). Building and installation instructions are described [here](https://kokkos.org/kokkos-core-wiki/building.html). diff --git a/lib/kokkos/algorithms/CMakeLists.txt b/lib/kokkos/algorithms/CMakeLists.txt index 73ce9f7ec5..e257e4ccce 100644 --- a/lib/kokkos/algorithms/CMakeLists.txt +++ b/lib/kokkos/algorithms/CMakeLists.txt @@ -5,3 +5,7 @@ endif() if(NOT ((KOKKOS_ENABLE_OPENMPTARGET AND KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC) OR KOKKOS_ENABLE_OPENACC)) kokkos_add_test_directories(unit_tests) endif() + +if(Kokkos_ENABLE_BENCHMARKS) + add_subdirectory(perf_test) +endif() diff --git a/lib/kokkos/algorithms/perf_test/CMakeLists.txt b/lib/kokkos/algorithms/perf_test/CMakeLists.txt new file mode 100644 index 0000000000..a41d3f891b --- /dev/null +++ b/lib/kokkos/algorithms/perf_test/CMakeLists.txt @@ -0,0 +1,63 @@ +# FIXME: The following logic should be moved from here and also from `core/perf_test/CMakeLists.txt` to +# the root `CMakeLists.txt` in the form of a macro +# Find or download google/benchmark library +find_package(benchmark QUIET 1.5.6) +if(benchmark_FOUND) + message(STATUS "Using google benchmark found in ${benchmark_DIR}") +else() + message(STATUS "No installed google benchmark found, fetching from GitHub") + include(FetchContent) + set(BENCHMARK_ENABLE_TESTING OFF) + + list(APPEND CMAKE_MESSAGE_INDENT "[benchmark] ") + FetchContent_Declare( + googlebenchmark + DOWNLOAD_EXTRACT_TIMESTAMP FALSE + URL https://github.com/google/benchmark/archive/refs/tags/v1.7.1.tar.gz + URL_HASH MD5=0459a6c530df9851bee6504c3e37c2e7 + ) + FetchContent_MakeAvailable(googlebenchmark) + list(POP_BACK CMAKE_MESSAGE_INDENT) + + # Suppress clang-tidy diagnostics on code that we do not have control over + if(CMAKE_CXX_CLANG_TIDY) + set_target_properties(benchmark PROPERTIES CXX_CLANG_TIDY "") + endif() + + # FIXME: Check whether the following target_compile_options are needed. + # If so, clarify why. + target_compile_options(benchmark PRIVATE -w) + target_compile_options(benchmark_main PRIVATE -w) +endif() + +# FIXME: This function should be moved from here and also from `core/perf_test/CMakeLists.txt` to +# the root `CMakeLists.txt` +# FIXME: Could NAME be a one_value_keyword specified in cmake_parse_arguments? +function(KOKKOS_ADD_BENCHMARK NAME) + cmake_parse_arguments(BENCHMARK "" "" "SOURCES" ${ARGN}) + if(DEFINED BENCHMARK_UNPARSED_ARGUMENTS) + message(WARNING "Unexpected arguments when adding a benchmark: " ${BENCHMARK_UNPARSED_ARGUMENTS}) + endif() + + set(BENCHMARK_NAME Kokkos_${NAME}) + # FIXME: BenchmarkMain.cpp and Benchmark_Context.cpp should be moved to a common location from which + # they can be used by all performance tests. + list(APPEND BENCHMARK_SOURCES ../../core/perf_test/BenchmarkMain.cpp ../../core/perf_test/Benchmark_Context.cpp) + + add_executable(${BENCHMARK_NAME} ${BENCHMARK_SOURCES}) + target_link_libraries(${BENCHMARK_NAME} PRIVATE benchmark::benchmark Kokkos::kokkos impl_git_version) + target_include_directories(${BENCHMARK_NAME} SYSTEM PRIVATE ${benchmark_SOURCE_DIR}/include) + + # FIXME: This alone will not work. It might need an architecture and standard which need to be defined on target level. + # It will potentially go away with #7582. + foreach(SOURCE_FILE ${BENCHMARK_SOURCES}) + set_source_files_properties(${SOURCE_FILE} PROPERTIES LANGUAGE ${KOKKOS_COMPILE_LANGUAGE}) + endforeach() + + string(TIMESTAMP BENCHMARK_TIME "%Y-%m-%d_T%H-%M-%S" UTC) + set(BENCHMARK_ARGS --benchmark_counters_tabular=true --benchmark_out=${BENCHMARK_NAME}_${BENCHMARK_TIME}.json) + + add_test(NAME ${BENCHMARK_NAME} COMMAND ${BENCHMARK_NAME} ${BENCHMARK_ARGS}) +endfunction() + +kokkos_add_benchmark(PerformanceTest_InclusiveScan SOURCES test_inclusive_scan.cpp) diff --git a/lib/kokkos/algorithms/perf_test/test_inclusive_scan.cpp b/lib/kokkos/algorithms/perf_test/test_inclusive_scan.cpp new file mode 100644 index 0000000000..a0a5de6b07 --- /dev/null +++ b/lib/kokkos/algorithms/perf_test/test_inclusive_scan.cpp @@ -0,0 +1,191 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 4.0 +// Copyright (2022) 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. +// +// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions. +// See https://kokkos.org/LICENSE for license information. +// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception +// +//@HEADER + +#include +#include +#include +#include + +#include + +#include +#include +#include +// FIXME: Benchmark_Context.hpp should be moved to a common location +#include "../../core/perf_test/Benchmark_Context.hpp" + +namespace { + +namespace KE = Kokkos::Experimental; + +using ExecSpace = Kokkos::DefaultExecutionSpace; +using HostExecSpace = Kokkos::DefaultHostExecutionSpace; + +// A tag struct to identify when inclusive scan with the implicit sum +// based binary operation needs to be called. +template +struct ImpSumBinOp; + +template +struct SumFunctor { + KOKKOS_FUNCTION + ValueType operator()(const ValueType& a, const ValueType& b) const { + return (a + b); + } +}; + +template +struct MaxFunctor { + KOKKOS_FUNCTION + ValueType operator()(const ValueType& a, const ValueType& b) const { + if (a > b) + return a; + else + return b; + } +}; + +// Helper to obtain last element of a view +template +T obtain_last_elem(const Kokkos::View& v) { + T last_element; + Kokkos::deep_copy(last_element, Kokkos::subview(v, v.extent(0) - 1)); + return last_element; +} + +// Helper to allocate input and output views +template +auto prepare_views(const std::size_t kProbSize) { + Kokkos::View in{"input", kProbSize}; + Kokkos::View out{"output", kProbSize}; + + auto h_in = Kokkos::create_mirror_view(in); + + for (std::size_t i = 0; i < kProbSize; ++i) { + h_in(i) = i; + } + + Kokkos::deep_copy(in, h_in); + + return std::make_tuple(in, out, h_in); +} + +// Perform scan with a reference implementation +template > +T ref_scan(const ViewType& h_in, ScanFunctor scan_functor = ScanFunctor()) { + std::size_t view_size = h_in.extent(0); + + Kokkos::View h_out("output", view_size); + + // FIXME: We have GCC 8.4.0 based check in our ORNL Jenkins CI. + // std::inclusive_scan is available only from GCC 9.3. Since, GCC 9.1 + // std::inclusive_scan that takes execution policy is available. However, + // there is error with header before GCC 10.1. + h_out(0) = h_in(0); + + for (std::size_t i = 1; i < view_size; ++i) { + h_out(i) = scan_functor(h_in(i), h_out(i - 1)); + } + + return h_out(view_size - 1); +} + +// Inclusive Scan with default binary operation (sum) or user provided functor +// Note: The nature of the functor must be compatible with the +// elements in the input and output views +template class ScanFunctor = ImpSumBinOp> +auto inclusive_scan(const Kokkos::View& in, + const Kokkos::View& out, T res_check) { + ExecSpace().fence(); + Kokkos::Timer timer; + + if constexpr (std::is_same_v, ImpSumBinOp>) { + KE::inclusive_scan("Default scan", ExecSpace(), KE::cbegin(in), + KE::cend(in), KE::begin(out)); + } else { + KE::inclusive_scan("Scan using a functor", ExecSpace(), KE::cbegin(in), + KE::cend(in), KE::begin(out), ScanFunctor()); + } + + ExecSpace().fence(); + double time_scan = timer.seconds(); + + T res_scan = obtain_last_elem(out); + bool passed = (res_check == res_scan); + + return std::make_tuple(time_scan, passed); +} + +// Benchmark: Inclusive Scan with default binary operation (sum) +// or user provided functor +template class ScanFunctor = ImpSumBinOp> +void BM_inclusive_scan(benchmark::State& state) { + const std::size_t kProbSize = state.range(0); + + auto [in, out, h_in] = prepare_views(kProbSize); + + T res_check; + + if constexpr (std::is_same_v, ImpSumBinOp>) { + res_check = ref_scan(h_in); + } else { + res_check = ref_scan(h_in, ScanFunctor()); + } + + double time_scan = 0.; + bool passed = false; + + for (auto _ : state) { + if constexpr (std::is_same_v, ImpSumBinOp>) { + std::tie(time_scan, passed) = inclusive_scan(in, out, res_check); + } else { + std::tie(time_scan, passed) = + inclusive_scan(in, out, res_check); + } + + KokkosBenchmark::report_results(state, in, 2, time_scan); + state.counters["Passed"] = passed; + } +} + +constexpr std::size_t PROB_SIZE = 100'000'000; + +} // anonymous namespace + +// FIXME: Add logic to pass min. warm-up time. Also, the value should be set +// by the user. Say, via the environment variable BENCHMARK_MIN_WARMUP_TIME. + +BENCHMARK(BM_inclusive_scan)->Arg(PROB_SIZE)->UseManualTime(); +BENCHMARK(BM_inclusive_scan)->Arg(PROB_SIZE)->UseManualTime(); +BENCHMARK(BM_inclusive_scan)->Arg(PROB_SIZE)->UseManualTime(); +BENCHMARK(BM_inclusive_scan) + ->Arg(PROB_SIZE) + ->UseManualTime(); +BENCHMARK(BM_inclusive_scan) + ->Arg(PROB_SIZE) + ->UseManualTime(); +BENCHMARK(BM_inclusive_scan) + ->Arg(PROB_SIZE) + ->UseManualTime(); +BENCHMARK(BM_inclusive_scan) + ->Arg(PROB_SIZE) + ->UseManualTime(); +BENCHMARK(BM_inclusive_scan) + ->Arg(PROB_SIZE) + ->UseManualTime(); +BENCHMARK(BM_inclusive_scan) + ->Arg(PROB_SIZE) + ->UseManualTime(); diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index b28ea4c2ca..54a853fa55 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -587,11 +587,13 @@ struct Random_XorShift1024_State { int state_idx) : state_(&v(state_idx, 0)), stride_(v.stride_1()) {} + // NOLINTBEGIN(bugprone-implicit-widening-of-multiplication-result) KOKKOS_FUNCTION uint64_t operator[](const int i) const { return state_[i * stride_]; } KOKKOS_FUNCTION uint64_t& operator[](const int i) { return state_[i * stride_]; } + // NOLINTEND(bugprone-implicit-widening-of-multiplication-result) }; template @@ -670,7 +672,12 @@ struct Random_UniqueIndex> { View>; KOKKOS_FUNCTION static int get_state_idx(const locks_view_type& locks_) { +#if defined(KOKKOS_COMPILER_INTEL_LLVM) && \ + KOKKOS_COMPILER_INTEL_LLVM >= 20250000 + auto item = sycl::ext::oneapi::this_work_item::get_nd_item<3>(); +#else auto item = sycl::ext::oneapi::experimental::this_nd_item<3>(); +#endif std::size_t threadIdx[3] = {item.get_local_id(2), item.get_local_id(1), item.get_local_id(0)}; std::size_t blockIdx[3] = {item.get_group(2), item.get_group(1), diff --git a/lib/kokkos/algorithms/src/sorting/Kokkos_BinOpsPublicAPI.hpp b/lib/kokkos/algorithms/src/sorting/Kokkos_BinOpsPublicAPI.hpp index 8e7de32a07..b093b72ad6 100644 --- a/lib/kokkos/algorithms/src/sorting/Kokkos_BinOpsPublicAPI.hpp +++ b/lib/kokkos/algorithms/src/sorting/Kokkos_BinOpsPublicAPI.hpp @@ -45,7 +45,7 @@ struct BinOp1D { // For integral types the number of bins may be larger than the range // in which case we can exactly have one unique value per bin // and then don't need to sort bins. - if (std::is_integral::value && + if (std::is_integral_v && (static_cast(max) - static_cast(min)) <= static_cast(max_bins)) { mul_ = 1.; diff --git a/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp b/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp index 20026c77e4..308e9e3a00 100644 --- a/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp +++ b/lib/kokkos/algorithms/src/sorting/Kokkos_SortPublicAPI.hpp @@ -53,13 +53,9 @@ void sort(const ExecutionSpace& exec, if constexpr (Impl::better_off_calling_std_sort_v) { exec.fence("Kokkos::sort without comparator use std::sort"); - if (view.span_is_contiguous()) { - std::sort(view.data(), view.data() + view.size()); - } else { - auto first = ::Kokkos::Experimental::begin(view); - auto last = ::Kokkos::Experimental::end(view); - std::sort(first, last); - } + auto first = ::Kokkos::Experimental::begin(view); + auto last = ::Kokkos::Experimental::end(view); + std::sort(first, last); } else { Impl::sort_device_view_without_comparator(exec, view); } @@ -111,13 +107,9 @@ void sort(const ExecutionSpace& exec, if constexpr (Impl::better_off_calling_std_sort_v) { exec.fence("Kokkos::sort with comparator use std::sort"); - if (view.span_is_contiguous()) { - std::sort(view.data(), view.data() + view.size(), comparator); - } else { - auto first = ::Kokkos::Experimental::begin(view); - auto last = ::Kokkos::Experimental::end(view); - std::sort(first, last, comparator); - } + auto first = ::Kokkos::Experimental::begin(view); + auto last = ::Kokkos::Experimental::end(view); + std::sort(first, last, comparator); } else { Impl::sort_device_view_with_comparator(exec, view, comparator); } diff --git a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp index 2a8f761d9b..f17d254b0b 100644 --- a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp +++ b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp @@ -47,6 +47,7 @@ #ifdef _CubLog #undef _CubLog #endif +// NOLINTNEXTLINE(bugprone-reserved-identifier) #define _CubLog #include #include @@ -65,12 +66,24 @@ #include #endif -#if defined(KOKKOS_ENABLE_ONEDPL) && \ - (ONEDPL_VERSION_MAJOR > 2022 || \ - (ONEDPL_VERSION_MAJOR == 2022 && ONEDPL_VERSION_MINOR >= 2)) -#define KOKKOS_ONEDPL_HAS_SORT_BY_KEY +#ifdef KOKKOS_ENABLE_ONEDPL +#define KOKKOS_IMPL_ONEDPL_VERSION \ + ONEDPL_VERSION_MAJOR * 10000 + ONEDPL_VERSION_MINOR * 100 + \ + ONEDPL_VERSION_PATCH +#define KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(MAJOR, MINOR, PATCH) \ + (KOKKOS_IMPL_ONEDPL_VERSION >= ((MAJOR)*10000 + (MINOR)*100 + (PATCH))) + +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 2, 0) +#define KOKKOS_IMPL_ONEDPL_HAS_SORT_BY_KEY +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" +#pragma GCC diagnostic ignored "-Wunused-local-typedef" +#pragma GCC diagnostic ignored "-Wunused-parameter" +#pragma GCC diagnostic ignored "-Wunused-variable" #include #include +#pragma GCC diagnostic pop +#endif #endif namespace Kokkos::Impl { @@ -141,12 +154,18 @@ void sort_by_key_rocthrust( #endif #if defined(KOKKOS_ENABLE_ONEDPL) + +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) +template +inline constexpr bool sort_on_device_v = true; +#else template inline constexpr bool sort_on_device_v = std::is_same_v || std::is_same_v; +#endif -#ifdef KOKKOS_ONEDPL_HAS_SORT_BY_KEY +#ifdef KOKKOS_IMPL_ONEDPL_HAS_SORT_BY_KEY template void sort_by_key_onedpl( @@ -154,6 +173,14 @@ void sort_by_key_onedpl( const Kokkos::View& keys, const Kokkos::View& values, MaybeComparator&&... maybeComparator) { + auto queue = exec.sycl_queue(); + auto policy = oneapi::dpl::execution::make_device_policy(queue); +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) + oneapi::dpl::sort_by_key(policy, ::Kokkos::Experimental::begin(keys), + ::Kokkos::Experimental::end(keys), + ::Kokkos::Experimental::begin(values), + std::forward(maybeComparator)...); +#else if (keys.stride(0) != 1 && values.stride(0) != 1) { Kokkos::abort( "SYCL sort_by_key only supports rank-1 Views with stride(0) = 1."); @@ -161,11 +188,10 @@ void sort_by_key_onedpl( // Can't use Experimental::begin/end here since the oneDPL then assumes that // the data is on the host. - auto queue = exec.sycl_queue(); - auto policy = oneapi::dpl::execution::make_device_policy(queue); const int n = keys.extent(0); oneapi::dpl::sort_by_key(policy, keys.data(), keys.data() + n, values.data(), std::forward(maybeComparator)...); +#endif } #endif #endif @@ -336,12 +362,18 @@ void sort_by_key_device_view_without_comparator( const Kokkos::SYCL& exec, const Kokkos::View& keys, const Kokkos::View& values) { -#ifdef KOKKOS_ONEDPL_HAS_SORT_BY_KEY +#ifdef KOKKOS_IMPL_ONEDPL_HAS_SORT_BY_KEY +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) + sort_by_key_onedpl(exec, keys, values); +#else if (keys.stride(0) == 1 && values.stride(0) == 1) sort_by_key_onedpl(exec, keys, values); else -#endif sort_by_key_via_sort(exec, keys, values); +#endif +#else + sort_by_key_via_sort(exec, keys, values); +#endif } #endif @@ -394,12 +426,18 @@ void sort_by_key_device_view_with_comparator( const Kokkos::View& keys, const Kokkos::View& values, const ComparatorType& comparator) { -#ifdef KOKKOS_ONEDPL_HAS_SORT_BY_KEY +#ifdef KOKKOS_IMPL_ONEDPL_HAS_SORT_BY_KEY +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) + sort_by_key_onedpl(exec, keys, values, comparator); +#else if (keys.stride(0) == 1 && values.stride(0) == 1) sort_by_key_onedpl(exec, keys, values, comparator); else -#endif sort_by_key_via_sort(exec, keys, values, comparator); +#endif +#else + sort_by_key_via_sort(exec, keys, values, comparator); +#endif } #endif @@ -416,7 +454,9 @@ sort_by_key_device_view_with_comparator( sort_by_key_via_sort(exec, keys, values, comparator); } -#undef KOKKOS_ONEDPL_HAS_SORT_BY_KEY +#undef KOKKOS_IMPL_ONEDPL_HAS_SORT_BY_KEY } // namespace Kokkos::Impl +#undef KOKKOS_IMPL_ONEDPL_VERSION +#undef KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL #endif diff --git a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp index 734ce450f6..fa7c28b4d0 100644 --- a/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp +++ b/lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortImpl.hpp @@ -51,6 +51,7 @@ #ifdef _CubLog #undef _CubLog #endif +// NOLINTNEXTLINE(bugprone-reserved-identifier) #define _CubLog #include #include @@ -70,8 +71,20 @@ #endif #if defined(KOKKOS_ENABLE_ONEDPL) +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" +#pragma GCC diagnostic ignored "-Wunused-local-typedef" +#pragma GCC diagnostic ignored "-Wunused-parameter" +#pragma GCC diagnostic ignored "-Wunused-variable" #include #include +#pragma GCC diagnostic pop + +#define KOKKOS_IMPL_ONEDPL_VERSION \ + ONEDPL_VERSION_MAJOR * 10000 + ONEDPL_VERSION_MINOR * 100 + \ + ONEDPL_VERSION_PATCH +#define KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(MAJOR, MINOR, PATCH) \ + (KOKKOS_IMPL_ONEDPL_VERSION >= ((MAJOR)*10000 + (MINOR)*100 + (PATCH))) #endif namespace Kokkos { @@ -221,6 +234,10 @@ void sort_onedpl(const Kokkos::SYCL& space, "SYCL execution space is not able to access the memory space " "of the View argument!"); +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) + static_assert(ViewType::rank == 1, + "Kokkos::sort currently only supports rank-1 Views."); +#else static_assert( (ViewType::rank == 1) && (std::is_same_v || @@ -234,18 +251,26 @@ void sort_onedpl(const Kokkos::SYCL& space, if (view.stride(0) != 1) { Kokkos::abort("SYCL sort only supports rank-1 Views with stride(0) = 1."); } +#endif if (view.extent(0) <= 1) { return; } - // Can't use Experimental::begin/end here since the oneDPL then assumes that - // the data is on the host. auto queue = space.sycl_queue(); auto policy = oneapi::dpl::execution::make_device_policy(queue); + +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) + oneapi::dpl::sort(policy, ::Kokkos::Experimental::begin(view), + ::Kokkos::Experimental::end(view), + std::forward(maybeComparator)...); +#else + // Can't use Experimental::begin/end here since the oneDPL then assumes that + // the data is on the host. const int n = view.extent(0); oneapi::dpl::sort(policy, view.data(), view.data() + n, std::forward(maybeComparator)...); +#endif } #endif @@ -269,29 +294,19 @@ void copy_to_host_run_stdsort_copy_back( KE::copy(exec, view, view_dc); // run sort on the mirror of view_dc - auto mv_h = create_mirror_view_and_copy(Kokkos::HostSpace(), view_dc); - if (view.span_is_contiguous()) { - std::sort(mv_h.data(), mv_h.data() + mv_h.size(), - std::forward(maybeComparator)...); - } else { - auto first = KE::begin(mv_h); - auto last = KE::end(mv_h); - std::sort(first, last, std::forward(maybeComparator)...); - } + auto mv_h = create_mirror_view_and_copy(Kokkos::HostSpace(), view_dc); + auto first = KE::begin(mv_h); + auto last = KE::end(mv_h); + std::sort(first, last, std::forward(maybeComparator)...); Kokkos::deep_copy(exec, view_dc, mv_h); // copy back to argument view KE::copy(exec, KE::cbegin(view_dc), KE::cend(view_dc), KE::begin(view)); } else { auto view_h = create_mirror_view_and_copy(Kokkos::HostSpace(), view); - if (view.span_is_contiguous()) { - std::sort(view_h.data(), view_h.data() + view_h.size(), - std::forward(maybeComparator)...); - } else { - auto first = KE::begin(view_h); - auto last = KE::end(view_h); - std::sort(first, last, std::forward(maybeComparator)...); - } + auto first = KE::begin(view_h); + auto last = KE::end(view_h); + std::sort(first, last, std::forward(maybeComparator)...); Kokkos::deep_copy(exec, view, view_h); } } @@ -332,11 +347,15 @@ void sort_device_view_without_comparator( "sort_device_view_without_comparator: supports rank-1 Views " "with LayoutLeft, LayoutRight or LayoutStride"); +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) + sort_onedpl(exec, view); +#else if (view.stride(0) == 1) { sort_onedpl(exec, view); } else { copy_to_host_run_stdsort_copy_back(exec, view); } +#endif } #endif @@ -387,11 +406,15 @@ void sort_device_view_with_comparator( "sort_device_view_with_comparator: supports rank-1 Views " "with LayoutLeft, LayoutRight or LayoutStride"); +#if KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL(2022, 7, 1) + sort_onedpl(exec, view, comparator); +#else if (view.stride(0) == 1) { sort_onedpl(exec, view, comparator); } else { copy_to_host_run_stdsort_copy_back(exec, view, comparator); } +#endif } #endif @@ -423,4 +446,7 @@ sort_device_view_with_comparator( } // namespace Impl } // namespace Kokkos + +#undef KOKKOS_IMPL_ONEDPL_VERSION +#undef KOKKOS_IMPL_ONEDPL_VERSION_GREATER_EQUAL #endif diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Constraints.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Constraints.hpp index da16141f5a..2e73ace8d5 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Constraints.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Constraints.hpp @@ -238,12 +238,9 @@ KOKKOS_INLINE_FUNCTION void expect_no_overlap( [[maybe_unused]] IteratorType2 s_first) { if constexpr (is_kokkos_iterator_v && is_kokkos_iterator_v) { - auto const view1 = first.view(); - auto const view2 = s_first.view(); - - std::size_t stride1 = view1.stride(0); - std::size_t stride2 = view2.stride(0); - ptrdiff_t first_diff = view1.data() - view2.data(); + std::size_t stride1 = first.stride(); + std::size_t stride2 = s_first.stride(); + ptrdiff_t first_diff = first.data() - s_first.data(); // FIXME If strides are not identical, checks may not be made // with the cost of O(1) @@ -251,8 +248,8 @@ KOKKOS_INLINE_FUNCTION void expect_no_overlap( // If first_diff == 0, there is already an overlap if (stride1 == stride2 || first_diff == 0) { [[maybe_unused]] bool is_no_overlap = (first_diff % stride1); - auto* first_pointer1 = view1.data(); - auto* first_pointer2 = view2.data(); + auto* first_pointer1 = first.data(); + auto* first_pointer2 = s_first.data(); [[maybe_unused]] auto* last_pointer1 = first_pointer1 + (last - first); [[maybe_unused]] auto* last_pointer2 = first_pointer2 + (last - first); KOKKOS_EXPECTS(first_pointer1 >= last_pointer2 || diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_CopyIf.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_CopyIf.hpp index ad7b8bb8ca..ef39be6366 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_CopyIf.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_CopyIf.hpp @@ -150,9 +150,8 @@ KOKKOS_FUNCTION OutputIterator copy_if_team_impl( return d_first + count; } -#if defined KOKKOS_COMPILER_INTEL || \ - (defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ - !defined(KOKKOS_COMPILER_MSVC)) +#if defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ + !defined(KOKKOS_COMPILER_MSVC) __builtin_unreachable(); #endif } diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ExclusiveScan.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ExclusiveScan.hpp index 6da992b4bb..08e04810f6 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ExclusiveScan.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ExclusiveScan.hpp @@ -103,7 +103,7 @@ OutputIteratorType exclusive_scan_custom_op_exespace_impl( // aliases using index_type = typename InputIteratorType::difference_type; - using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; + using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; using func_type = TransformExclusiveScanFunctorWithValueWrapper< ExecutionSpace, index_type, ValueType, InputIteratorType, OutputIteratorType, BinaryOpType, unary_op_type>; @@ -177,7 +177,7 @@ KOKKOS_FUNCTION OutputIteratorType exclusive_scan_custom_op_team_impl( // aliases using exe_space = typename TeamHandleType::execution_space; - using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; + using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; using index_type = typename InputIteratorType::difference_type; using func_type = TransformExclusiveScanFunctorWithoutValueWrapper< exe_space, index_type, ValueType, InputIteratorType, OutputIteratorType, diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_IdentityReferenceUnaryFunctor.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_IdentityReferenceUnaryFunctor.hpp index 252511c5d0..928508fdfb 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_IdentityReferenceUnaryFunctor.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_IdentityReferenceUnaryFunctor.hpp @@ -23,10 +23,11 @@ namespace Kokkos { namespace Experimental { namespace Impl { -template struct StdNumericScanIdentityReferenceUnaryFunctor { - KOKKOS_FUNCTION - constexpr const ValueType& operator()(const ValueType& a) const { return a; } + template + KOKKOS_FUNCTION constexpr T&& operator()(T&& t) const { + return static_cast(t); + } }; } // namespace Impl diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_InclusiveScan.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_InclusiveScan.hpp index 0b4acec0fe..867d0b0266 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_InclusiveScan.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_InclusiveScan.hpp @@ -18,12 +18,60 @@ #define KOKKOS_STD_ALGORITHMS_INCLUSIVE_SCAN_IMPL_HPP #include +#include #include "Kokkos_Constraints.hpp" #include "Kokkos_HelperPredicates.hpp" #include #include #include +#if defined(KOKKOS_ENABLE_CUDA) + +// Workaround for `Instruction 'shfl' without '.sync' is not supported on +// .target sm_70 and higher from PTX ISA version 6.4`. +// Also see https://github.com/NVIDIA/cub/pull/170. +#if !defined(CUB_USE_COOPERATIVE_GROUPS) +#define CUB_USE_COOPERATIVE_GROUPS +#endif + +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wshadow" +#pragma GCC diagnostic ignored "-Wsuggest-override" + +#if defined(KOKKOS_COMPILER_CLANG) +// Some versions of Clang fail to compile Thrust, failing with errors like +// this: +// /thrust/system/cuda/detail/core/agent_launcher.h:557:11: +// error: use of undeclared identifier 'va_printf' +// The exact combination of versions for Clang and Thrust (or CUDA) for this +// failure was not investigated, however even very recent version combination +// (Clang 10.0.0 and Cuda 10.0) demonstrated failure. +// +// Defining _CubLog here locally allows us to avoid that code path, however +// disabling some debugging diagnostics +#pragma push_macro("_CubLog") +#ifdef _CubLog +#undef _CubLog +#endif +// NOLINTNEXTLINE(bugprone-reserved-identifier) +#define _CubLog +#include +#include +#pragma pop_macro("_CubLog") +#else +#include +#include +#endif + +#pragma GCC diagnostic pop + +#endif + +#if defined(KOKKOS_ENABLE_ROCTHRUST) +#include +#include +#endif + namespace Kokkos { namespace Experimental { namespace Impl { @@ -101,9 +149,48 @@ struct InclusiveScanDefaultFunctor { } }; -// -// exespace impl -// +// ------------------------------------------------------------- +// inclusive_scan_default_op_exespace_impl +// ------------------------------------------------------------- + +#if defined(KOKKOS_ENABLE_CUDA) +template +OutputIteratorType inclusive_scan_default_op_exespace_impl( + const std::string& label, const Cuda& ex, InputIteratorType first_from, + InputIteratorType last_from, OutputIteratorType first_dest) { + const auto thrust_ex = thrust::cuda::par.on(ex.cuda_stream()); + + Kokkos::Profiling::pushRegion(label + " via thrust::inclusive_scan"); + + thrust::inclusive_scan(thrust_ex, first_from, last_from, first_dest); + + Kokkos::Profiling::popRegion(); + + const auto num_elements = thrust::distance(first_from, last_from); + + return first_dest + num_elements; +} +#endif + +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +OutputIteratorType inclusive_scan_default_op_exespace_impl( + const std::string& label, const HIP& ex, InputIteratorType first_from, + InputIteratorType last_from, OutputIteratorType first_dest) { + const auto thrust_ex = thrust::hip::par.on(ex.hip_stream()); + + Kokkos::Profiling::pushRegion(label + " via thrust::inclusive_scan"); + + thrust::inclusive_scan(thrust_ex, first_from, last_from, first_dest); + + Kokkos::Profiling::popRegion(); + + const auto num_elements = thrust::distance(first_from, last_from); + + return first_dest + num_elements; +} +#endif + template OutputIteratorType inclusive_scan_default_op_exespace_impl( @@ -132,11 +219,16 @@ OutputIteratorType inclusive_scan_default_op_exespace_impl( // run const auto num_elements = Kokkos::Experimental::distance(first_from, last_from); + + Kokkos::Profiling::pushRegion(label + " via Kokkos::parallel_scan"); + ::Kokkos::parallel_scan(label, RangePolicy(ex, 0, num_elements), func_type(first_from, first_dest)); ex.fence("Kokkos::inclusive_scan_default_op: fence after operation"); + Kokkos::Profiling::popRegion(); + // return return first_dest + num_elements; } @@ -144,6 +236,49 @@ OutputIteratorType inclusive_scan_default_op_exespace_impl( // ------------------------------------------------------------- // inclusive_scan_custom_binary_op_impl // ------------------------------------------------------------- + +#if defined(KOKKOS_ENABLE_CUDA) +template +OutputIteratorType inclusive_scan_custom_binary_op_exespace_impl( + const std::string& label, const Cuda& ex, InputIteratorType first_from, + InputIteratorType last_from, OutputIteratorType first_dest, + BinaryOpType binary_op) { + const auto thrust_ex = thrust::cuda::par.on(ex.cuda_stream()); + + Kokkos::Profiling::pushRegion(label + " via thrust::inclusive_scan"); + + thrust::inclusive_scan(thrust_ex, first_from, last_from, first_dest, + binary_op); + + Kokkos::Profiling::popRegion(); + + const auto num_elements = thrust::distance(first_from, last_from); + + return first_dest + num_elements; +} +#endif + +#if defined(KOKKOS_ENABLE_ROCTHRUST) +template +OutputIteratorType inclusive_scan_custom_binary_op_exespace_impl( + const std::string& label, const HIP& ex, InputIteratorType first_from, + InputIteratorType last_from, OutputIteratorType first_dest, + BinaryOpType binary_op) { + const auto thrust_ex = thrust::hip::par.on(ex.hip_stream()); + + Kokkos::Profiling::pushRegion(label + " via thrust::inclusive_scan"); + + thrust::inclusive_scan(thrust_ex, first_from, last_from, first_dest, + binary_op); + + Kokkos::Profiling::popRegion(); + + const auto num_elements = thrust::distance(first_from, last_from); + + return first_dest + num_elements; +} +#endif + template OutputIteratorType inclusive_scan_custom_binary_op_exespace_impl( @@ -160,7 +295,7 @@ OutputIteratorType inclusive_scan_custom_binary_op_exespace_impl( using index_type = typename InputIteratorType::difference_type; using value_type = std::remove_const_t; - using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; + using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; using func_type = ExeSpaceTransformInclusiveScanNoInitValueFunctor< ExecutionSpace, index_type, value_type, InputIteratorType, OutputIteratorType, BinaryOpType, unary_op_type>; @@ -168,11 +303,16 @@ OutputIteratorType inclusive_scan_custom_binary_op_exespace_impl( // run const auto num_elements = Kokkos::Experimental::distance(first_from, last_from); + + Kokkos::Profiling::pushRegion(label + " via Kokkos::parallel_scan"); + ::Kokkos::parallel_scan( label, RangePolicy(ex, 0, num_elements), func_type(first_from, first_dest, binary_op, unary_op_type())); ex.fence("Kokkos::inclusive_scan_custom_binary_op: fence after operation"); + Kokkos::Profiling::popRegion(); + // return return first_dest + num_elements; } @@ -195,7 +335,7 @@ OutputIteratorType inclusive_scan_custom_binary_op_exespace_impl( // aliases using index_type = typename InputIteratorType::difference_type; - using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; + using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; using func_type = ExeSpaceTransformInclusiveScanWithInitValueFunctor< ExecutionSpace, index_type, ValueType, InputIteratorType, OutputIteratorType, BinaryOpType, unary_op_type>; @@ -203,12 +343,17 @@ OutputIteratorType inclusive_scan_custom_binary_op_exespace_impl( // run const auto num_elements = Kokkos::Experimental::distance(first_from, last_from); + + Kokkos::Profiling::pushRegion(label + " via Kokkos::parallel_scan"); + ::Kokkos::parallel_scan(label, RangePolicy(ex, 0, num_elements), func_type(first_from, first_dest, binary_op, unary_op_type(), std::move(init_value))); ex.fence("Kokkos::inclusive_scan_custom_binary_op: fence after operation"); + Kokkos::Profiling::popRegion(); + // return return first_dest + num_elements; } @@ -283,7 +428,7 @@ KOKKOS_FUNCTION OutputIteratorType inclusive_scan_custom_binary_op_team_impl( // aliases using exe_space = typename TeamHandleType::execution_space; - using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; + using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; using func_type = TeamTransformInclusiveScanNoInitValueFunctor< exe_space, value_type, InputIteratorType, OutputIteratorType, BinaryOpType, unary_op_type>; @@ -291,7 +436,6 @@ KOKKOS_FUNCTION OutputIteratorType inclusive_scan_custom_binary_op_team_impl( // run const auto num_elements = Kokkos::Experimental::distance(first_from, last_from); - ::Kokkos::parallel_scan( TeamThreadRange(teamHandle, 0, num_elements), func_type(first_from, first_dest, binary_op, unary_op_type())); @@ -325,7 +469,7 @@ KOKKOS_FUNCTION OutputIteratorType inclusive_scan_custom_binary_op_team_impl( // aliases using exe_space = typename TeamHandleType::execution_space; - using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; + using unary_op_type = StdNumericScanIdentityReferenceUnaryFunctor; using func_type = TeamTransformInclusiveScanWithInitValueFunctor< exe_space, ValueType, InputIteratorType, OutputIteratorType, BinaryOpType, unary_op_type>; diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RandomAccessIterator.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RandomAccessIterator.hpp index e8c638c94c..c504673c3d 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RandomAccessIterator.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RandomAccessIterator.hpp @@ -18,6 +18,7 @@ #define KOKKOS_RANDOM_ACCESS_ITERATOR_IMPL_HPP #include +#include // declval #include #include #include "Kokkos_Constraints.hpp" @@ -29,8 +30,29 @@ namespace Impl { template class RandomAccessIterator; +namespace { + +template +struct is_always_strided { + static_assert(is_view_v); + + constexpr static bool value = +#ifdef KOKKOS_ENABLE_IMPL_MDSPAN + decltype(std::declval().to_mdspan())::is_always_strided(); +#else + (std::is_same_v || + std::is_same_v || + std::is_same_v); +#endif +}; + +} // namespace + template -class RandomAccessIterator< ::Kokkos::View > { +class RandomAccessIterator<::Kokkos::View> { public: using view_type = ::Kokkos::View; using iterator_type = RandomAccessIterator; @@ -41,30 +63,31 @@ class RandomAccessIterator< ::Kokkos::View > { using pointer = typename view_type::pointer_type; using reference = typename view_type::reference_type; +// oneDPL needs this alias in order not to assume the data is on the host but on +// the device, see +// https://github.com/uxlfoundation/oneDPL/blob/a045eac689f9107f50ba7b42235e9e927118e483/include/oneapi/dpl/pstl/hetero/dpcpp/utils_ranges_sycl.h#L210-L214 +#ifdef KOKKOS_ENABLE_ONEDPL + using is_passed_directly = std::true_type; +#endif + static_assert(view_type::rank == 1 && - (std::is_same_v || - std::is_same_v || - std::is_same_v), - "RandomAccessIterator only supports 1D Views with LayoutLeft, " - "LayoutRight, LayoutStride."); + is_always_strided<::Kokkos::View>::value); KOKKOS_DEFAULTED_FUNCTION RandomAccessIterator() = default; explicit KOKKOS_FUNCTION RandomAccessIterator(const view_type view) - : m_view(view) {} + : m_data(view.data()), m_stride(view.stride_0()) {} explicit KOKKOS_FUNCTION RandomAccessIterator(const view_type view, ptrdiff_t current_index) - : m_view(view), m_current_index(current_index) {} + : m_data(view.data() + current_index * view.stride_0()), + m_stride(view.stride_0()) {} #ifndef KOKKOS_ENABLE_CXX17 // C++20 and beyond template requires(std::is_constructible_v) KOKKOS_FUNCTION explicit(!std::is_convertible_v) RandomAccessIterator(const RandomAccessIterator& other) - : m_view(other.m_view), m_current_index(other.m_current_index) {} + : m_data(other.m_data), m_stride(other.m_stride) {} #else template < class OtherViewType, @@ -73,19 +96,22 @@ class RandomAccessIterator< ::Kokkos::View > { int> = 0> KOKKOS_FUNCTION explicit RandomAccessIterator( const RandomAccessIterator& other) - : m_view(other.m_view), m_current_index(other.m_current_index) {} + : m_data(other.m_data), m_stride(other.m_stride) {} template , int> = 0> KOKKOS_FUNCTION RandomAccessIterator( const RandomAccessIterator& other) - : m_view(other.m_view), m_current_index(other.m_current_index) {} + : m_data(other.m_data), m_stride(other.m_stride) {} #endif KOKKOS_FUNCTION iterator_type& operator++() { - ++m_current_index; + if constexpr (is_always_contiguous) + m_data++; + else + m_data += m_stride; return *this; } @@ -98,7 +124,10 @@ class RandomAccessIterator< ::Kokkos::View > { KOKKOS_FUNCTION iterator_type& operator--() { - --m_current_index; + if constexpr (is_always_contiguous) + m_data--; + else + m_data -= m_stride; return *this; } @@ -111,77 +140,95 @@ class RandomAccessIterator< ::Kokkos::View > { KOKKOS_FUNCTION reference operator[](difference_type n) const { - return m_view(m_current_index + n); + if constexpr (is_always_contiguous) + return *(m_data + n); + else + return *(m_data + n * m_stride); } KOKKOS_FUNCTION iterator_type& operator+=(difference_type n) { - m_current_index += n; + if constexpr (is_always_contiguous) + m_data += n; + else + m_data += n * m_stride; return *this; } KOKKOS_FUNCTION iterator_type& operator-=(difference_type n) { - m_current_index -= n; + if constexpr (is_always_contiguous) + m_data -= n; + else + m_data -= n * m_stride; return *this; } KOKKOS_FUNCTION iterator_type operator+(difference_type n) const { - return iterator_type(m_view, m_current_index + n); + auto it = *this; + it += n; + return it; + } + + friend iterator_type operator+(difference_type n, iterator_type other) { + return other + n; } KOKKOS_FUNCTION iterator_type operator-(difference_type n) const { - return iterator_type(m_view, m_current_index - n); + auto it = *this; + it -= n; + return it; } KOKKOS_FUNCTION difference_type operator-(iterator_type it) const { - return m_current_index - it.m_current_index; + if constexpr (is_always_contiguous) + return m_data - it.m_data; + else + return (m_data - it.m_data) / m_stride; } KOKKOS_FUNCTION bool operator==(iterator_type other) const { - return m_current_index == other.m_current_index && - m_view.data() == other.m_view.data(); + return m_data == other.m_data && m_stride == other.m_stride; } KOKKOS_FUNCTION bool operator!=(iterator_type other) const { - return m_current_index != other.m_current_index || - m_view.data() != other.m_view.data(); + return m_data != other.m_data || m_stride != other.m_stride; } KOKKOS_FUNCTION - bool operator<(iterator_type other) const { - return m_current_index < other.m_current_index; - } + bool operator<(iterator_type other) const { return m_data < other.m_data; } KOKKOS_FUNCTION - bool operator<=(iterator_type other) const { - return m_current_index <= other.m_current_index; - } + bool operator<=(iterator_type other) const { return m_data <= other.m_data; } KOKKOS_FUNCTION - bool operator>(iterator_type other) const { - return m_current_index > other.m_current_index; - } + bool operator>(iterator_type other) const { return m_data > other.m_data; } KOKKOS_FUNCTION - bool operator>=(iterator_type other) const { - return m_current_index >= other.m_current_index; - } + bool operator>=(iterator_type other) const { return m_data >= other.m_data; } KOKKOS_FUNCTION - reference operator*() const { return m_view(m_current_index); } + reference operator*() const { return *m_data; } KOKKOS_FUNCTION - view_type view() const { return m_view; } + pointer data() const { return m_data; } + + KOKKOS_FUNCTION + int stride() const { return m_stride; } private: - view_type m_view; - ptrdiff_t m_current_index = 0; + pointer m_data; + int m_stride; + static constexpr bool is_always_contiguous = + (std::is_same_v || + std::is_same_v); // Needed for the converting constructor accepting another iterator template @@ -192,4 +239,10 @@ class RandomAccessIterator< ::Kokkos::View > { } // namespace Experimental } // namespace Kokkos +#ifdef KOKKOS_ENABLE_SYCL +template +struct sycl::is_device_copyable< + Kokkos::Experimental::Impl::RandomAccessIterator> : std::true_type {}; +#endif + #endif diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp index 2863582458..75f3315473 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Unique.hpp @@ -52,13 +52,10 @@ struct StdUniqueFunctor { auto& val_i = m_first_from[i]; const auto& val_ip1 = m_first_from[i + 1]; - if (final_pass) { - if (!m_pred(val_i, val_ip1)) { + if (!m_pred(val_i, val_ip1)) { + if (final_pass) { m_first_dest[update] = std::move(val_i); } - } - - if (!m_pred(val_i, val_ip1)) { update += 1; } } @@ -188,6 +185,7 @@ KOKKOS_FUNCTION IteratorType unique_team_impl(const TeamHandleType& teamHandle, IteratorType result = first; IteratorType lfirst = first; while (++lfirst != last) { + // NOLINTNEXTLINE(bugprone-inc-dec-in-conditions) if (!pred(*result, *lfirst) && ++result != lfirst) { *result = std::move(*lfirst); } diff --git a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_UniqueCopy.hpp b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_UniqueCopy.hpp index 710d04805d..226fd49d16 100644 --- a/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_UniqueCopy.hpp +++ b/lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_UniqueCopy.hpp @@ -175,9 +175,8 @@ KOKKOS_FUNCTION OutputIterator unique_copy_team_impl( d_first + count); } -#if defined KOKKOS_COMPILER_INTEL || \ - (defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ - !defined(KOKKOS_COMPILER_MSVC)) +#if defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ + !defined(KOKKOS_COMPILER_MSVC) __builtin_unreachable(); #endif } diff --git a/lib/kokkos/algorithms/unit_tests/Makefile b/lib/kokkos/algorithms/unit_tests/Makefile index d3946c149b..eaf616c5d6 100644 --- a/lib/kokkos/algorithms/unit_tests/Makefile +++ b/lib/kokkos/algorithms/unit_tests/Makefile @@ -18,6 +18,8 @@ LINK ?= $(CXX) LDFLAGS ?= override LDFLAGS += -lpthread +KOKKOS_USE_DEPRECATED_MAKEFILES=1 + include $(KOKKOS_PATH)/Makefile.kokkos KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/algorithms/unit_tests -I${KOKKOS_PATH}/core/unit_test/category_files diff --git a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp index 6960b912d0..ed9c2610b6 100644 --- a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp @@ -281,7 +281,7 @@ struct test_random_scalar { double covariance_eps = result.covariance / num_draws / 2 / variance_expect; #if defined(KOKKOS_BHALF_T_IS_FLOAT) && !KOKKOS_BHALF_T_IS_FLOAT - if (!std::is_same::value) { + if (!std::is_same_v) { #endif EXPECT_LT(std::abs(mean_eps), tolerance); EXPECT_LT(std::abs(variance_eps), 1.5 * tolerance); @@ -312,7 +312,7 @@ struct test_random_scalar { (result.covariance / HIST_DIM1D - covariance_expect) / mean_expect; #if defined(KOKKOS_HALF_T_IS_FLOAT) && !KOKKOS_HALF_T_IS_FLOAT - if (std::is_same::value) { + if (std::is_same_v) { mean_eps_expect = 0.0003; variance_eps_expect = 1.0; covariance_eps_expect = 5.0e4; @@ -320,7 +320,7 @@ struct test_random_scalar { #endif #if defined(KOKKOS_BHALF_T_IS_FLOAT) && !KOKKOS_BHALF_T_IS_FLOAT - if (!std::is_same::value) { + if (!std::is_same_v) { #endif EXPECT_LT(std::abs(mean_eps), mean_eps_expect); EXPECT_LT(std::abs(variance_eps), variance_eps_expect); @@ -358,13 +358,13 @@ struct test_random_scalar { (result.covariance / HIST_DIM1D - covariance_expect) / mean_expect; #if defined(KOKKOS_HALF_T_IS_FLOAT) && !KOKKOS_HALF_T_IS_FLOAT - if (std::is_same::value) { + if (std::is_same_v) { variance_factor = 7; } #endif #if defined(KOKKOS_BHALF_T_IS_FLOAT) && !KOKKOS_BHALF_T_IS_FLOAT - if (!std::is_same::value) { + if (!std::is_same_v) { #endif EXPECT_LT(std::abs(mean_eps), tolerance); EXPECT_LT(std::abs(variance_eps), variance_factor); diff --git a/lib/kokkos/algorithms/unit_tests/TestRandomAccessIterator.cpp b/lib/kokkos/algorithms/unit_tests/TestRandomAccessIterator.cpp index 5ab348cb19..65e45ebb96 100644 --- a/lib/kokkos/algorithms/unit_tests/TestRandomAccessIterator.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestRandomAccessIterator.cpp @@ -37,12 +37,18 @@ struct random_access_iterator_test : std_algorithms_test { TEST_F(random_access_iterator_test, constructor) { // just tests that constructor works - auto it1 = KE::Impl::RandomAccessIterator(m_static_view); - auto it2 = KE::Impl::RandomAccessIterator(m_dynamic_view); - auto it3 = KE::Impl::RandomAccessIterator(m_strided_view); - auto it4 = KE::Impl::RandomAccessIterator(m_static_view, 3); - auto it5 = KE::Impl::RandomAccessIterator(m_dynamic_view, 3); - auto it6 = KE::Impl::RandomAccessIterator(m_strided_view, 3); + [[maybe_unused]] auto it1 = + KE::Impl::RandomAccessIterator(m_static_view); + [[maybe_unused]] auto it2 = + KE::Impl::RandomAccessIterator(m_dynamic_view); + [[maybe_unused]] auto it3 = + KE::Impl::RandomAccessIterator(m_strided_view); + [[maybe_unused]] auto it4 = + KE::Impl::RandomAccessIterator(m_static_view, 3); + [[maybe_unused]] auto it5 = + KE::Impl::RandomAccessIterator(m_dynamic_view, 3); + [[maybe_unused]] auto it6 = + KE::Impl::RandomAccessIterator(m_strided_view, 3); EXPECT_TRUE(true); } diff --git a/lib/kokkos/algorithms/unit_tests/TestSort.hpp b/lib/kokkos/algorithms/unit_tests/TestSort.hpp index 5ea88ae5d6..562ff97e42 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSort.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSort.hpp @@ -99,6 +99,7 @@ void test_dynamic_view_sort_impl(unsigned int n) { Kokkos::Experimental::DynamicView; using KeyViewType = Kokkos::View; + // NOLINTNEXTLINE(bugprone-implicit-widening-of-multiplication-result) const size_t upper_bound = 2 * n; const size_t min_chunk_size = 1024; diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp index dadce2d474..d8a68f768a 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCommon.hpp @@ -198,9 +198,8 @@ auto create_deep_copyable_compatible_view_with_same_extent(ViewType view) { // this is needed for intel to avoid // error #1011: missing return statement at end of non-void function -#if defined KOKKOS_COMPILER_INTEL || \ - (defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ - !defined(KOKKOS_COMPILER_MSVC)) +#if defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \ + !defined(KOKKOS_COMPILER_MSVC) __builtin_unreachable(); #endif } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCompileOnly.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCompileOnly.cpp index 9324db12f2..ddb7dc2a68 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCompileOnly.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsCompileOnly.cpp @@ -507,6 +507,20 @@ struct TestStruct { } }; +#ifndef KOKKOS_ENABLE_CXX17 +template +constexpr bool +test_kokkos_iterator_satify_std_random_access_iterator_concept() { + return std::random_access_iterator< + Kokkos::Experimental::Impl::RandomAccessIterator>; +} + +static_assert(test_kokkos_iterator_satify_std_random_access_iterator_concept< + Kokkos::View>()); +static_assert(test_kokkos_iterator_satify_std_random_access_iterator_concept< + Kokkos::View>()); +#endif + } // namespace compileonly } // namespace stdalgos } // namespace Test diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsConstraints.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsConstraints.cpp index 923ea970f9..67d21dd740 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsConstraints.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsConstraints.cpp @@ -173,6 +173,7 @@ TEST(std_algorithms_DeathTest, expect_no_overlap) { KE::Impl::expect_no_overlap(sub_first_d0, sub_last_d0, sub_first_d1); + // NOLINTNEXTLINE(bugprone-implicit-widening-of-multiplication-result) Kokkos::LayoutStride layout2d{2, 3, extent0, 2 * 3}; Kokkos::View strided_view_2d{ "std-algo-test-2d-contiguous-view-strided", layout2d}; diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp index a85e63fe34..1a81991c35 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsExclusiveScan.cpp @@ -171,7 +171,7 @@ struct VerifyData { create_mirror_view_and_copy(Kokkos::HostSpace(), test_view_dc); if (test_view_h.extent(0) > 0) { for (std::size_t i = 0; i < test_view_h.extent(0); ++i) { - if (std::is_same::value) { + if (std::is_same_v) { ASSERT_EQ(gold_h(i), test_view_h(i)); } else { const auto error = diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp index b4f40b4651..c8ecc137e2 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsInclusiveScan.cpp @@ -184,7 +184,7 @@ struct VerifyData { const auto ext = test_view_h.extent(0); if (ext > 0) { for (std::size_t i = 0; i < ext; ++i) { - if (std::is_same::value) { + if (std::is_same_v) { ASSERT_EQ(gold_h(i), test_view_h(i)); } else { const auto error = diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp index 8327bfe13c..9e30630f07 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsIsSortedUntil.cpp @@ -153,12 +153,13 @@ void run_single_scenario(const InfoType& scenario_info) { #if !defined KOKKOS_ENABLE_OPENMPTARGET CustomLessThanComparator comp; - auto r5 = + [[maybe_unused]] auto r5 = KE::is_sorted_until(exespace(), KE::cbegin(view), KE::cend(view), comp); - auto r6 = KE::is_sorted_until("label", exespace(), KE::cbegin(view), - KE::cend(view), comp); - auto r7 = KE::is_sorted_until(exespace(), view, comp); - auto r8 = KE::is_sorted_until("label", exespace(), view, comp); + [[maybe_unused]] auto r6 = KE::is_sorted_until( + "label", exespace(), KE::cbegin(view), KE::cend(view), comp); + [[maybe_unused]] auto r7 = KE::is_sorted_until(exespace(), view, comp); + [[maybe_unused]] auto r8 = + KE::is_sorted_until("label", exespace(), view, comp); #endif ASSERT_EQ(r1, gold) << name << ", " << view_tag_to_string(Tag{}); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp index 6918185bc0..1fbeab3d9d 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsModOps.cpp @@ -53,13 +53,13 @@ TEST(std_algorithms_mod_ops_test, move) { // move constr MyMovableType b(std::move(a)); ASSERT_EQ(b.m_value, 11); - ASSERT_EQ(a.m_value, -2); + ASSERT_EQ(a.m_value, -2); // NOLINT(bugprone-use-after-move) // move assign MyMovableType c; c = std::move(b); ASSERT_EQ(c.m_value, 11); - ASSERT_EQ(b.m_value, -4); + ASSERT_EQ(b.m_value, -4); // NOLINT(bugprone-use-after-move) } template @@ -70,7 +70,7 @@ struct StdAlgoModSeqOpsTestMove { void operator()(const int index) const { typename ViewType::value_type a{11}; using move_t = decltype(std::move(a)); - static_assert(std::is_rvalue_reference::value); + static_assert(std::is_rvalue_reference_v); m_view(index) = std::move(a); } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsNumerics.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsNumerics.cpp index 0933c4e135..a3d7df533b 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsNumerics.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsNumerics.cpp @@ -243,16 +243,15 @@ void run_and_check_transform_reduce_overloadA(ViewType1 first_view, ViewType2 second_view, ValueType init_value, ValueType result_value, - Args&&... args) { + Args const&... args) { // trivial cases const auto r1 = KE::transform_reduce( ExecutionSpace(), KE::cbegin(first_view), KE::cbegin(first_view), - KE::cbegin(second_view), init_value, std::forward(args)...); + KE::cbegin(second_view), init_value, args...); - const auto r2 = - KE::transform_reduce("MYLABEL", ExecutionSpace(), KE::cbegin(first_view), - KE::cbegin(first_view), KE::cbegin(second_view), - init_value, std::forward(args)...); + const auto r2 = KE::transform_reduce( + "MYLABEL", ExecutionSpace(), KE::cbegin(first_view), + KE::cbegin(first_view), KE::cbegin(second_view), init_value, args...); ASSERT_EQ(r1, init_value); ASSERT_EQ(r2, init_value); @@ -260,18 +259,16 @@ void run_and_check_transform_reduce_overloadA(ViewType1 first_view, // non trivial cases const auto r3 = KE::transform_reduce( ExecutionSpace(), KE::cbegin(first_view), KE::cend(first_view), - KE::cbegin(second_view), init_value, std::forward(args)...); + KE::cbegin(second_view), init_value, args...); const auto r4 = KE::transform_reduce( "MYLABEL", ExecutionSpace(), KE::cbegin(first_view), KE::cend(first_view), - KE::cbegin(second_view), init_value, std::forward(args)...); + KE::cbegin(second_view), init_value, args...); - const auto r5 = - KE::transform_reduce(ExecutionSpace(), first_view, second_view, - init_value, std::forward(args)...); - const auto r6 = - KE::transform_reduce("MYLABEL", ExecutionSpace(), first_view, second_view, - init_value, std::forward(args)...); + const auto r5 = KE::transform_reduce(ExecutionSpace(), first_view, + second_view, init_value, args...); + const auto r6 = KE::transform_reduce("MYLABEL", ExecutionSpace(), first_view, + second_view, init_value, args...); ASSERT_EQ(r3, result_value); ASSERT_EQ(r4, result_value); @@ -363,32 +360,30 @@ template void run_and_check_transform_reduce_overloadB(ViewType view, ValueType init_value, ValueType result_value, - Args&&... args) { + Args const&... args) { // trivial - const auto r1 = - KE::transform_reduce(ExecutionSpace(), KE::cbegin(view), KE::cbegin(view), - init_value, std::forward(args)...); + const auto r1 = KE::transform_reduce(ExecutionSpace(), KE::cbegin(view), + KE::cbegin(view), init_value, args...); - const auto r2 = KE::transform_reduce("MYLABEL", ExecutionSpace(), - KE::cbegin(view), KE::cbegin(view), - init_value, std::forward(args)...); + const auto r2 = + KE::transform_reduce("MYLABEL", ExecutionSpace(), KE::cbegin(view), + KE::cbegin(view), init_value, args...); ASSERT_EQ(r1, init_value); ASSERT_EQ(r2, init_value); // non trivial - const auto r3 = - KE::transform_reduce(ExecutionSpace(), KE::cbegin(view), KE::cend(view), - init_value, std::forward(args)...); + const auto r3 = KE::transform_reduce(ExecutionSpace(), KE::cbegin(view), + KE::cend(view), init_value, args...); - const auto r4 = KE::transform_reduce("MYLABEL", ExecutionSpace(), - KE::cbegin(view), KE::cend(view), - init_value, std::forward(args)...); - const auto r5 = KE::transform_reduce(ExecutionSpace(), view, init_value, - std::forward(args)...); + const auto r4 = + KE::transform_reduce("MYLABEL", ExecutionSpace(), KE::cbegin(view), + KE::cend(view), init_value, args...); + const auto r5 = + KE::transform_reduce(ExecutionSpace(), view, init_value, args...); const auto r6 = KE::transform_reduce("MYLABEL", ExecutionSpace(), view, - init_value, std::forward(args)...); + init_value, args...); ASSERT_EQ(r3, result_value); ASSERT_EQ(r4, result_value); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsRotate.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsRotate.cpp index bf5c2ee782..b9545e8b2e 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsRotate.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsRotate.cpp @@ -196,7 +196,7 @@ void run_single_scenario(const InfoType& scenario_info, // create host copy BEFORE rotate or view will be modified auto view_h = create_host_space_copy(view); auto rit = KE::rotate(exespace(), view, rotation_point); - // verify_data(rit, view, view_h, rotation_point); + verify_data(rit, view, view_h, rotation_point); } { diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentDifference.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentDifference.cpp index 5a2c046939..1dfdcfd568 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentDifference.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentDifference.cpp @@ -191,6 +191,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { ASSERT_EQ(stdDistance, distancesView_h(i)); break; } + default: Kokkos::abort("unreachable"); } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentFind.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentFind.cpp index 95f2934e01..88fc649a9b 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentFind.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamAdjacentFind.cpp @@ -217,6 +217,7 @@ void test_A(const bool ensureAdjacentFindCanFind, std::size_t numTeams, break; } + default: Kokkos::abort("unreachable"); } } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamEqual.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamEqual.cpp index 82cce0b384..592bb4c864 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamEqual.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamEqual.cpp @@ -244,6 +244,7 @@ void test_A(const bool viewsAreEqual, std::size_t numTeams, std::size_t numCols, break; } + default: Kokkos::abort("unreachable"); } } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp index 0c35c5e599..0c9f1e1bd2 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamExclusiveScan.cpp @@ -224,6 +224,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { break; } #endif + default: Kokkos::abort("unreachable"); } #undef exclusive_scan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindEnd.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindEnd.cpp index d350bc62cd..21a905be56 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindEnd.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindEnd.cpp @@ -227,6 +227,7 @@ void test_A(const bool sequencesExist, std::size_t numTeams, break; } + default: Kokkos::abort("unreachable"); } if (sequencesExist) { diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindFirstOf.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindFirstOf.cpp index e992882e91..ad1043362e 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindFirstOf.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindFirstOf.cpp @@ -244,6 +244,7 @@ void test_A(const bool sequencesExist, std::size_t numTeams, break; } + default: Kokkos::abort("unreachable"); } } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIf.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIf.cpp index 70f2be77f6..f21f947e97 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIf.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIf.cpp @@ -57,14 +57,7 @@ struct TestFunctorA { const auto myRowIndex = member.league_rank(); auto myRowViewFrom = Kokkos::subview(m_dataView, myRowIndex, Kokkos::ALL()); const auto val = m_greaterThanValuesView(myRowIndex); - // FIXME_INTEL -#if defined(KOKKOS_COMPILER_INTEL) && (1900 == KOKKOS_COMPILER_INTEL) - GreaterEqualFunctor< - typename GreaterThanValuesViewType::non_const_value_type> - unaryPred{val}; -#else GreaterEqualFunctor unaryPred{val}; -#endif ptrdiff_t resultDist = 0; switch (m_apiPick) { @@ -185,12 +178,7 @@ void test_A(const bool predicatesReturnTrue, std::size_t numTeams, const auto rowFromBegin = KE::cbegin(rowFrom); const auto rowFromEnd = KE::cend(rowFrom); const auto val = greaterEqualValuesView_h(i); - // FIXME_INTEL -#if defined(KOKKOS_COMPILER_INTEL) && (1900 == KOKKOS_COMPILER_INTEL) - const GreaterEqualFunctor unaryPred{val}; -#else const GreaterEqualFunctor unaryPred{val}; -#endif auto it = std::find_if(rowFromBegin, rowFromEnd, unaryPred); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIfNot.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIfNot.cpp index 873e8faf4c..0794dc0a79 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIfNot.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamFindIfNot.cpp @@ -57,14 +57,7 @@ struct TestFunctorA { const auto myRowIndex = member.league_rank(); auto myRowViewFrom = Kokkos::subview(m_dataView, myRowIndex, Kokkos::ALL()); const auto val = m_greaterThanValuesView(myRowIndex); - // FIXME_INTEL -#if defined(KOKKOS_COMPILER_INTEL) && (1900 == KOKKOS_COMPILER_INTEL) - GreaterEqualFunctor< - typename GreaterThanValuesViewType::non_const_value_type> - unaryPred{val}; -#else GreaterEqualFunctor unaryPred{val}; -#endif ptrdiff_t resultDist = 0; switch (m_apiPick) { @@ -180,12 +173,7 @@ void test_A(const bool predicatesReturnTrue, std::size_t numTeams, const auto rowFromBegin = KE::cbegin(rowFrom); const auto rowFromEnd = KE::cend(rowFrom); const auto val = greaterEqualValuesView_h(i); - // FIXME_INTEL -#if defined(KOKKOS_COMPILER_INTEL) && (1900 == KOKKOS_COMPILER_INTEL) - const GreaterEqualFunctor unaryPred{val}; -#else const GreaterEqualFunctor unaryPred{val}; -#endif auto it = std::find_if_not(rowFromBegin, rowFromEnd, unaryPred); diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp index b5f4cdd612..4c77eff9c4 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamInclusiveScan.cpp @@ -253,6 +253,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { break; } + default: Kokkos::abort("unreachable"); } #undef inclusive_scan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamLexicographicalCompare.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamLexicographicalCompare.cpp index c377b9fec8..9d2d2721c6 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamLexicographicalCompare.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamLexicographicalCompare.cpp @@ -245,6 +245,7 @@ void test_A(const TestCaseType testCase, std::size_t numTeams, break; } + default: Kokkos::abort("unreachable"); } } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamMismatch.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamMismatch.cpp index 84269511d8..9b245508e3 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamMismatch.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamMismatch.cpp @@ -249,6 +249,7 @@ void test_A(const bool viewsAreEqual, std::size_t numTeams, std::size_t numCols, break; } + default: Kokkos::abort("unreachable"); } } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReduce.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReduce.cpp index eb00d9e083..88264b45c0 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReduce.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamReduce.cpp @@ -242,6 +242,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { break; } + default: Kokkos::abort("unreachable"); } #undef reduce diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearch.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearch.cpp index 039db4095d..1f0f4b6c1b 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearch.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearch.cpp @@ -243,6 +243,7 @@ void test_A(const bool sequencesExist, std::size_t numTeams, break; } + default: Kokkos::abort("unreachable"); } } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearchN.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearchN.cpp index 25cd1471e0..6d8a34e842 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearchN.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamSearchN.cpp @@ -258,6 +258,7 @@ void test_A(const bool sequencesExist, std::size_t numTeams, break; } + default: Kokkos::abort("unreachable"); } } } diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp index 1c43854381..60e199a350 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformExclusiveScan.cpp @@ -203,6 +203,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { ASSERT_EQ(stdDistance, distancesView_h(i)); break; } + default: Kokkos::abort("unreachable"); } #undef transform_exclusive_scan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp index 78a21c4430..0dc3e68b1d 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformInclusiveScan.cpp @@ -240,6 +240,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { break; } + default: Kokkos::abort("unreachable"); } } #undef transform_inclusive_scan diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformReduce.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformReduce.cpp index 17ded226aa..3ad0b5b354 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformReduce.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTeamTransformReduce.cpp @@ -293,6 +293,7 @@ void test_A(std::size_t numTeams, std::size_t numCols, int apiId) { break; } + default: Kokkos::abort("unreachable"); } #undef transform_reduce diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp index 365ca21688..e3114daeae 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformExclusiveScan.cpp @@ -344,8 +344,7 @@ TEST(std_algorithms_numeric_ops_test, transform_exclusive_scan_functor) { using view_type = Kokkos::View; view_type dummy_view("dummy_view", 0); using unary_op_type = - Kokkos::Experimental::Impl::StdNumericScanIdentityReferenceUnaryFunctor< - int>; + Kokkos::Experimental::Impl::StdNumericScanIdentityReferenceUnaryFunctor; using functor_type = Kokkos::Experimental::Impl::TransformExclusiveScanFunctorWithValueWrapper< exespace, int, int, view_type, view_type, MultiplyFunctor, diff --git a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp index cc87262147..2dda12e22d 100644 --- a/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestStdAlgorithmsTransformInclusiveScan.cpp @@ -390,8 +390,7 @@ TEST(std_algorithms_numeric_ops_test, transform_inclusive_scan_functor) { int dummy = 0; using view_type = Kokkos::View; view_type dummy_view("dummy_view", 0); - using unary_op_type = - KE::Impl::StdNumericScanIdentityReferenceUnaryFunctor; + using unary_op_type = KE::Impl::StdNumericScanIdentityReferenceUnaryFunctor; { using functor_type = KE::Impl::ExeSpaceTransformInclusiveScanNoInitValueFunctor< diff --git a/lib/kokkos/benchmarks/atomic/Makefile b/lib/kokkos/benchmarks/atomic/Makefile index 636c0ad4ab..c59de75ce8 100644 --- a/lib/kokkos/benchmarks/atomic/Makefile +++ b/lib/kokkos/benchmarks/atomic/Makefile @@ -2,6 +2,7 @@ KOKKOS_DEVICES=Cuda KOKKOS_CUDA_OPTIONS=enable_lambda KOKKOS_ARCH = "SNB,Volta70" +KOKKOS_USE_DEPRECATED_MAKEFILES=1 MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) diff --git a/lib/kokkos/benchmarks/bytes_and_flops/Makefile b/lib/kokkos/benchmarks/bytes_and_flops/Makefile index 1aa4edddcd..4b6f084d20 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/Makefile +++ b/lib/kokkos/benchmarks/bytes_and_flops/Makefile @@ -2,6 +2,7 @@ KOKKOS_DEVICES=Cuda KOKKOS_CUDA_OPTIONS=enable_lambda KOKKOS_ARCH = "SNB,Volta70" +KOKKOS_USE_DEPRECATED_MAKEFILES=1 MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) diff --git a/lib/kokkos/benchmarks/gather/Makefile b/lib/kokkos/benchmarks/gather/Makefile index 6827995bed..e1bfce21a6 100644 --- a/lib/kokkos/benchmarks/gather/Makefile +++ b/lib/kokkos/benchmarks/gather/Makefile @@ -2,6 +2,7 @@ KOKKOS_DEVICES=Cuda KOKKOS_CUDA_OPTIONS=enable_lambda KOKKOS_ARCH = "SNB,Volta70" +KOKKOS_USE_DEPRECATED_MAKEFILES=1 MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) diff --git a/lib/kokkos/benchmarks/launch_latency/launch_latency.cpp b/lib/kokkos/benchmarks/launch_latency/launch_latency.cpp index 156c29af09..0935706ee8 100644 --- a/lib/kokkos/benchmarks/launch_latency/launch_latency.cpp +++ b/lib/kokkos/benchmarks/launch_latency/launch_latency.cpp @@ -37,7 +37,7 @@ template struct TestFunctor { - double values[V]; + double values[V] = {}; Kokkos::View a; int K; TestFunctor(Kokkos::View a_, int K_) : a(a_), K(K_) {} @@ -50,7 +50,7 @@ struct TestFunctor { template struct TestRFunctor { - double values[V]; + double values[V] = {}; Kokkos::View a; int K; TestRFunctor(Kokkos::View a_, int K_) : a(a_), K(K_) {} @@ -247,12 +247,15 @@ int main(int argc, char* argv[]) { // anything that doesn't start with -- if (arg.size() < 2 || (arg.size() >= 2 && arg[0] != '-' && arg[1] != '-')) { + // signing off that arg.data() is null terminated + // NOLINTBEGIN(bugprone-suspicious-stringview-data-usage) if (i == 1) N = atoi(arg.data()); else if (i == 2) M = atoi(arg.data()); else if (i == 3) K = atoi(arg.data()); + // NOLINTEND(bugprone-suspicious-stringview-data-usage) else { Kokkos::abort("unexpected argument!"); } diff --git a/lib/kokkos/benchmarks/policy_performance/Makefile b/lib/kokkos/benchmarks/policy_performance/Makefile index f50aea720e..21365f36c6 100644 --- a/lib/kokkos/benchmarks/policy_performance/Makefile +++ b/lib/kokkos/benchmarks/policy_performance/Makefile @@ -2,6 +2,7 @@ KOKKOS_DEVICES=Cuda KOKKOS_CUDA_OPTIONS=enable_lambda KOKKOS_ARCH = "SNB,Volta70" +KOKKOS_USE_DEPRECATED_MAKEFILES=1 MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) diff --git a/lib/kokkos/benchmarks/policy_performance/main.cpp b/lib/kokkos/benchmarks/policy_performance/main.cpp index 0983a3d535..dd61ba6502 100644 --- a/lib/kokkos/benchmarks/policy_performance/main.cpp +++ b/lib/kokkos/benchmarks/policy_performance/main.cpp @@ -120,11 +120,12 @@ int main(int argc, char* argv[]) { // view appropriately for test and should obey first-touch etc Second call to // test is the one we actually care about and time view_type_1d v_1(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_1"), - team_range * team_size); + static_cast(team_range) * team_size); view_type_2d v_2(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_2"), - team_range * team_size, thread_range); + static_cast(team_range) * team_size, thread_range); view_type_3d v_3(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_3"), - team_range * team_size, thread_range, vector_range); + static_cast(team_range) * team_size, thread_range, + vector_range); double result_computed = 0.0; double result_expect = 0.0; diff --git a/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp b/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp index 0e23d221f6..8a874e0139 100644 --- a/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp +++ b/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp @@ -367,7 +367,7 @@ void test_policy(int team_range, int thread_range, int vector_range, // parallel_for RangePolicy: range = team_size*team_range if (test_type == 300) { Kokkos::parallel_for( - "300 outer for", team_size * team_range, + "300 outer for", static_cast(team_size) * team_range, KOKKOS_LAMBDA(const int idx) { v1(idx) = idx; // prevent compiler from optimizing away the loop @@ -376,14 +376,15 @@ void test_policy(int team_range, int thread_range, int vector_range, // parallel_reduce RangePolicy: range = team_size*team_range if (test_type == 400) { Kokkos::parallel_reduce( - "400 outer reduce", team_size * team_range, + "400 outer reduce", static_cast(team_size) * team_range, KOKKOS_LAMBDA(const int idx, double& val) { val += idx; }, result); result_expect = 0.5 * (team_size * team_range) * (team_size * team_range - 1); } // parallel_scan RangePolicy: range = team_size*team_range if (test_type == 500) { - Kokkos::parallel_scan("500 outer scan", team_size * team_range, + Kokkos::parallel_scan("500 outer scan", + static_cast(team_size) * team_range, ParallelScanFunctor(v1) #if 0 // This does not compile with pre Cuda 8.0 - see Github Issue #913 for explanation diff --git a/lib/kokkos/benchmarks/stream/Makefile b/lib/kokkos/benchmarks/stream/Makefile index 47a13838a4..529e789247 100644 --- a/lib/kokkos/benchmarks/stream/Makefile +++ b/lib/kokkos/benchmarks/stream/Makefile @@ -2,6 +2,7 @@ KOKKOS_DEVICES=Cuda KOKKOS_CUDA_OPTIONS=enable_lambda KOKKOS_ARCH = "SNB,Volta70" +KOKKOS_USE_DEPRECATED_MAKEFILES=1 MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) diff --git a/lib/kokkos/benchmarks/view_copy_constructor/Makefile b/lib/kokkos/benchmarks/view_copy_constructor/Makefile index 70c6d517e0..77845a22b1 100644 --- a/lib/kokkos/benchmarks/view_copy_constructor/Makefile +++ b/lib/kokkos/benchmarks/view_copy_constructor/Makefile @@ -1,6 +1,7 @@ KOKKOS_DEVICES=Serial KOKKOS_ARCH = "" +KOKKOS_USE_DEPRECATED_MAKEFILES=1 MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) diff --git a/lib/kokkos/bin/nvcc_wrapper b/lib/kokkos/bin/nvcc_wrapper index d58645f98a..8d3dbf1c75 100755 --- a/lib/kokkos/bin/nvcc_wrapper +++ b/lib/kokkos/bin/nvcc_wrapper @@ -317,7 +317,7 @@ do # End of Werror handling #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" + fallback_std_flag="-std=c++17" # this is hopefully just occurring in a downstream project during CMake feature tests # we really have no choice here but to accept the flag and change to an accepted C++ standard echo "nvcc_wrapper does not accept standard flags $1 since partial standard flags and standards after C++17 are not supported. nvcc_wrapper will use $fallback_std_flag instead. It is undefined behavior to use this flag. This should only be occurring during CMake configuration." @@ -346,35 +346,17 @@ do # NVCC only has C++20 from version 12 on cuda_main_version=$([[ $(${nvcc_compiler} --version) =~ V([0-9]+) ]] && echo ${BASH_REMATCH[1]}) if [ ${cuda_main_version} -lt 12 ]; then - fallback_std_flag="-std=c++14" + fallback_std_flag="-std=c++17" # this is hopefully just occurring in a downstream project during CMake feature tests # we really have no choice here but to accept the flag and change to an accepted C++ standard - echo "nvcc_wrapper does not accept standard flags $1 since partial standard flags and standards after C++14 are not supported. nvcc_wrapper will use $fallback_std_flag instead. It is undefined behavior to use this flag. This should only be occurring during CMake configuration." + echo "nvcc_wrapper does not accept standard flags $1 since partial standard flags and standards after C++17 are not supported. nvcc_wrapper will use $fallback_std_flag instead. It is undefined behavior to use this flag. This should only be occurring during CMake configuration." std_flag=$fallback_std_flag else std_flag=$1 fi shared_args="$shared_args $std_flag" ;; - --std=c++17|-std=c++17) - if [ -n "$std_flag" ]; then - warn_std_flag - shared_args=${shared_args/ $std_flag/} - fi - # NVCC only has C++17 from version 11 on - cuda_main_version=$([[ $(${nvcc_compiler} --version) =~ V([0-9]+) ]] && echo ${BASH_REMATCH[1]}) - if [ ${cuda_main_version} -lt 11 ]; then - fallback_std_flag="-std=c++14" - # this is hopefully just occurring in a downstream project during CMake feature tests - # we really have no choice here but to accept the flag and change to an accepted C++ standard - echo "nvcc_wrapper does not accept standard flags $1 since partial standard flags and standards after C++14 are not supported. nvcc_wrapper will use $fallback_std_flag instead. It is undefined behavior to use this flag. This should only be occurring during CMake configuration." - std_flag=$fallback_std_flag - else - std_flag=$1 - fi - shared_args="$shared_args $std_flag" - ;; - --std=c++11|-std=c++11|--std=c++14|-std=c++14) + --std=c++11|-std=c++11|--std=c++14|-std=c++14|--std=c++17|-std=c++17) if [ -n "$std_flag" ]; then warn_std_flag shared_args=${shared_args/ $std_flag/} @@ -500,6 +482,20 @@ do xlinker_args="$xlinker_args -Xlinker ${1:4:${#1}}" host_linker_args="$host_linker_args ${1:4:${#1}}" ;; + #Handle host assembler options + -Wa,*) + #To pass the -Wa options to the host compiler via -Xcompiler it is necessary + #to use '\\,' for each comma in the options. As users might already add escapes + #to the comma by themselves, the escapes are first removed and then only the + #required number of \ are added back. + xcompiler_args_wa=$(echo -e "$1" | sed -E 's/\\\+,/,/g' | sed -E 's/,/\\\\\\\,/g') + if [ $first_xcompiler_arg -eq 1 ]; then + xcompiler_args="$xcompiler_args_wa" + first_xcompiler_arg=0 + else + xcompiler_args="$xcompiler_args,$xcompiler_args_wa" + fi + ;; #Handle object files: -x cu applies to all input files, so give them to linker, except if only linking *.a|*.so|*.o|*.obj) object_files="$object_files $1" diff --git a/lib/kokkos/cmake/KokkosConfig.cmake.in b/lib/kokkos/cmake/KokkosConfig.cmake.in index 1b6d1b66ff..aed9f1060c 100644 --- a/lib/kokkos/cmake/KokkosConfig.cmake.in +++ b/lib/kokkos/cmake/KokkosConfig.cmake.in @@ -2,65 +2,71 @@ # loaded by include() and find_package() commands except when invoked with # the NO_POLICY_SCOPE option # CMP0057 + NEW -> IN_LIST operator in IF(...) -CMAKE_POLICY(SET CMP0057 NEW) +cmake_policy(SET CMP0057 NEW) # Compute paths @PACKAGE_INIT@ #Find dependencies -INCLUDE(CMakeFindDependencyMacro) +include(CMakeFindDependencyMacro) #This needs to go above the KokkosTargets in case #the Kokkos targets depend in some way on the TPL imports @KOKKOS_TPL_EXPORTS@ -GET_FILENAME_COMPONENT(Kokkos_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) -INCLUDE("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake") -INCLUDE("${Kokkos_CMAKE_DIR}/KokkosConfigCommon.cmake") -UNSET(Kokkos_CMAKE_DIR) +get_filename_component(Kokkos_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) +include("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake") +include("${Kokkos_CMAKE_DIR}/KokkosConfigCommon.cmake") +unset(Kokkos_CMAKE_DIR) # 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 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 - # +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) + 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 @KOKKOS_COMPILE_LANGUAGE@ STREQUAL CUDA - AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) - # - # if CUDA was enabled, the compilation language was not set to CUDA, and separable compilation was not - # specified, 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 - # +elseif(@Kokkos_ENABLE_CUDA@ AND NOT @KOKKOS_COMPILE_LANGUAGE@ STREQUAL CUDA AND NOT "separable_compilation" IN_LIST + Kokkos_FIND_COMPONENTS +) + # + # if CUDA was enabled, the compilation language was not set to CUDA, and separable compilation was not + # specified, 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}) + # run test to see if CMAKE_CXX_COMPILER=nvcc_wrapper + kokkos_compiler_is_nvcc(IS_NVCC ${CMAKE_CXX_COMPILER}) - # 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() + # 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() - # be mindful of the environment, pollution is bad - UNSET(IS_NVCC) -ENDIF() + # be mindful of the environment, pollution is bad + unset(IS_NVCC) +endif() set(Kokkos_COMPILE_LANGUAGE @KOKKOS_COMPILE_LANGUAGE@) diff --git a/lib/kokkos/cmake/KokkosConfigCommon.cmake.in b/lib/kokkos/cmake/KokkosConfigCommon.cmake.in index d3ac39ffa3..769dff6b10 100644 --- a/lib/kokkos/cmake/KokkosConfigCommon.cmake.in +++ b/lib/kokkos/cmake/KokkosConfigCommon.cmake.in @@ -1,67 +1,67 @@ -SET(Kokkos_DEVICES @KOKKOS_ENABLED_DEVICES@) -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@") -SET(Kokkos_CXX_COMPILER_VERSION "@KOKKOS_CXX_COMPILER_VERSION@") -SET(Kokkos_CXX_STANDARD @KOKKOS_CXX_STANDARD@) +set(Kokkos_DEVICES @KOKKOS_ENABLED_DEVICES@) +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@") +set(Kokkos_CXX_COMPILER_VERSION "@KOKKOS_CXX_COMPILER_VERSION@") +set(Kokkos_CXX_STANDARD @KOKKOS_CXX_STANDARD@) # Required to be a TriBITS-compliant external package -IF(NOT TARGET Kokkos::all_libs) +if(NOT TARGET Kokkos::all_libs) # CMake Error at /lib/cmake/Kokkos/KokkosConfigCommon.cmake:10 (ADD_LIBRARY): # ADD_LIBRARY cannot create ALIAS target "Kokkos::all_libs" because target # "Kokkos::kokkos" is imported but not globally visible. - IF(CMAKE_VERSION VERSION_LESS "3.18") - SET_TARGET_PROPERTIES(Kokkos::kokkos PROPERTIES IMPORTED_GLOBAL ON) - ENDIF() - ADD_LIBRARY(Kokkos::all_libs ALIAS Kokkos::kokkos) -ENDIF() + if(CMAKE_VERSION VERSION_LESS "3.18") + set_target_properties(Kokkos::kokkos PROPERTIES IMPORTED_GLOBAL ON) + endif() + add_library(Kokkos::all_libs ALIAS Kokkos::kokkos) +endif() # Export Kokkos_ENABLE_ for each backend that was enabled. # NOTE: "Devices" is a little bit of a misnomer here. These are really # backends, e.g. Kokkos_ENABLE_OPENMP, Kokkos_ENABLE_CUDA, Kokkos_ENABLE_HIP, # or Kokkos_ENABLE_SYCL. -FOREACH(DEV ${Kokkos_DEVICES}) - SET(Kokkos_ENABLE_${DEV} ON) -ENDFOREACH() +foreach(DEV ${Kokkos_DEVICES}) + set(Kokkos_ENABLE_${DEV} ON) +endforeach() # Export relevant Kokkos_ENABLE