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Merge branch 'develop' into patch-4

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Axel Kohlmeyer
2025-02-26 10:40:41 -05:00
parent ea973e1d6c 7ceb8c461f
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327
.github/release_steps.md vendored
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@ -1,42 +1,54 @@
# LAMMPS Release Steps
The following notes chronicle the current steps for preparing and publishing LAMMPS releases. For
definitions of LAMMPS versions and releases mean, please refer to [the corresponding section in the
LAMMPS manual](https://docs.lammps.org/Manual_version.html).
The following notes chronicle the current steps for preparing and
publishing LAMMPS releases. For definitions of LAMMPS versions and
releases, please refer to [the corresponding section in the LAMMPS
manual](https://docs.lammps.org/Manual_version.html).
## LAMMPS Feature Release
A LAMMPS feature release is currently prepared after about 500 to 750 commits to the 'develop'
branch or after a period of four weeks up to two months. This is not a fixed rule, though, since
external circumstances can cause delays in preparing a release, or pull requests that are desired to
be merged for the release are not yet completed.
A LAMMPS feature release is currently prepared after about 500 to 750
commits to the 'develop' branch or after a period of four weeks up to
two months. This is not a fixed rule, though, since external
circumstances can cause delays in preparing a release, or pull requests
that are desired to be merged for the release are not yet completed.
### Preparing a 'next\_release' branch
Create a 'next\_release' branch off 'develop' and make the following changes:
- set the LAMMPS\_VERSION define to the planned release date in src/version.h in the format
"D Mmm YYYY" or "DD Mmm YYYY"
- set the LAMMPS\_VERSION define to the planned release date in
src/version.h in the format "D Mmm YYYY" or "DD Mmm YYYY"
- remove the LAMMPS\_UPDATE define in src/version.h
- update the release date in doc/lammps.1
- update all TBD arguments for ..versionadded::, ..versionchanged:: ..deprecated:: to the
planned release date in the format "DMmmYYYY" or "DDMmmYYYY"
- check release notes for merged new features and check if ..versionadded:: or ..versionchanged::
are missing and need to be added
Submit this pull request, rebase if needed. This is the last pull request merged for the release
and should not contain any other changes. (Exceptions: this document, last minute trivial(!) changes).
- update all TBD arguments for ..versionadded::, ..versionchanged::
..deprecated:: to the planned release date in the format "DMmmYYYY" or
"DDMmmYYYY"
- check release notes for merged new features and check if
..versionadded:: or ..versionchanged:: are missing and need to be
added
This PR shall not be merged before **all** pending tests have completed and cleared. If needed, a
bugfix pull request should be created and merged to clear all tests.
Submit this pull request. This is the last pull request merged for the
release and should not contain any other changes. (Exceptions: this
document, last minute trivial(!) changes).
This PR shall not be merged before **all** pending tests have completed
and cleared. We currently use a mix of automated tests running on
either Temple's Jenkins cluster or GitHub workflows. Those include time
consuming tests not run on pull requests. If needed, a bug-fix pull
request should be created and merged to clear all tests.
### Create release on GitHub
When all pending pull requests for the release are merged and have cleared testing, the
'next\_release' branch is merged into 'develop'.
When all pending pull requests for the release are merged and have
cleared testing, the 'next\_release' branch is merged into 'develop'.
Check out 'develop' locally, pull the latest changes, merge them into 'release', apply a suitable
release tag (for historical reasons the tag starts with "patch_" followed by the date, and finally
push everything back to GitHub. Example:
Check out or update the 'develop' branch locally, pull the latest
changes, merge them into 'release' with a fast forward(!) merge, and
apply a suitable release tag (for historical reasons the tag starts with
"patch_" followed by the date, and finally push everything back to
GitHub. There should be no commits made to 'release' but only
fast forward merges. Example:
```
git checkout develop
@ -44,62 +56,271 @@ git pull
git checkout release
git pull
git merge --ff-only develop
git tag -s -m "LAMMPS feature release 19 November 2024" patch_19Nov2024
git tag -s -m "LAMMPS feature release 4 February 2025" patch_4Feb2025
git push git@github.com:lammps/lammps.git --tags develop release
```
Go to https://github.com/lammps/lammps/releases and create a new (draft) release page or check the
existing draft for any necessary changes from pull requests that were merged but are not listed.
Then select the applied tag for the release in the "Choose a tag" dropdown list. Go to the bottom of
the list and select the "Set as pre-release" checkbox. The "Set as the latest release" button is
Applying this tag will trigger two actions on the Temple Jenkins cluster:
- The online manual at https://docs.lammps.org/ will be updated to the
state of the 'release' branch. Merges to the 'develop' branch will
trigger updating https://docs.lammps.org/latest/ so by reviewing the
version of the manual under the "latest" URL, it is possible to preview
what the updated release documentation will look like.
- A downloadable tar archive of the LAMMPS distribution that includes the
html format documentation and a PDF of the manual will be created and
uploaded to the download server at https://download.lammps.org/tars
Note that the file is added, but the `index.html` file is not updated,
so it is not yet publicly visible.
Go to https://github.com/lammps/lammps/releases and create a new (draft)
release page with a summary of all the changes included and references
to the pull requests they were merged from or check the existing draft
for any necessary changes from pull requests that were merged but are
not listed. Then select the applied tag for the release in the "Choose
a tag" drop-down list. Go to the bottom of the list and select the "Set
as pre-release" checkbox. The "Set as the latest release" button is
reserved for stable releases and updates to them.
If everything is in order, you can click on the "Publish release" button. Otherwise, click on "Save
draft" and finish pending tasks until you can return to edit the release page and publish it.
If everything is in order, you can click on the "Publish release"
button. Otherwise, click on "Save draft" and finish pending tasks until
you can return to edit the release page and publish it.
### Update download website, prepare pre-compiled packages, update packages to GitHub
### Prepare pre-compiled packages, update packages to GitHub
Publishing the release on GitHub will trigger the Temple Jenkins cluster to update
the https://docs.lammps.org/ website with the documentation for the new feature release
and it will create a tarball for download (which contains the translated manual).
A suitable build environment is provided with the
https://download.lammps.org/static/fedora41_musl_mingw.sif container
image. The corresponding container build definition file is maintained
in the tools/singularity folder of the LAMMPS source distribution.
Build a fully static LAMMPS installation using a musl-libc cross-compiler, install into a
lammps-static folder, and create a tarball called lammps-linux-x86_64-19Nov2024.tar.gz (or using a
corresponding date with a future release) from the lammps-static folder and upload it to GitHub
#### Fully portable static Linux x86_64 non-MPI binaries
The following commands use the Fedora container to build a fully static
LAMMPS installation using a musl-libc cross-compiler, install it into a
`lammps-static` folder, and create a tarball called
`lammps-linux-x86_64-4Feb2025.tar.gz` (or using a corresponding date
with a future release) from the `lammps-static` folder.
``` sh
rm -rf release-packages
mkdir release-packages
cd release-packages
wget https://download.lammps.org/static/fedora41_musl.sif
apptainer shell fedora41_musl.sif
git clone -b release --depth 10 https://github.com/lammps/lammps.git lammps-release
cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
cmake --build build-release --target all
cmake --build build-release --target install
/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
exit # fedora 41 container
cd ..
```
The resulting tar archive can be uploaded to the GitHub release page with:
``` sh
gh release upload patch_4Feb2025 lammps-linux-x86_64-4Feb2025.tar.gz
```
#### Linux x86_64 Flatpak bundle with GUI included
Make sure you have the `flatpak` and `flatpak-builder` packages
installed locally (they require binaries that run with elevated
privileges and thus cannot be used from the container) and build a
LAMMPS and LAMMPS-GUI flatpak bundle in the `release-packages` folder
with:
```
gh release upload patch_19Nov2024 ~/Downloads/lammps-linux-x86_64-19Nov2024.tar.gz
``` sh
cd release-packages
flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
flatpak-builder --force-clean --verbose --repo=$PWD/flatpak-repo --install-deps-from=flathub --state-dir=$PWD --user --ccache --default-branch=release flatpak-build lammps-release/tools/lammps-gui/org.lammps.lammps-gui.yml
flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo --verbose $PWD/flatpak-repo ../LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak org.lammps.lammps-gui release
cd ..
```
The resulting flatpak bundle file can be uploaded to the GitHub release page with:
``` sh
gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak
```
#### LAMMPS Source tarball
The container for the static binary can also be used to prepare the source
tarball including the HTML and PDF manual (this is currently done automatically
when the releases is created and the tarball uploaded to https://download.lammps.org/tars/).
The steps are as follows:
``` sh
cd release-packages
apptainer shell fedora41_musl_mingw.sif
cd lammps-release
rm -f ../release.tar*
git archive --output=../release.tar --prefix=lammps-4Feb2025/ HEAD
cd doc
make clean-all
make html pdf
tar -rf ../../release.tar --transform 's,^,lammps-4Feb2025/doc/,' html Manual.pdf
gzip -9v ../../release.tar
mv ../../release.tar.gz ../../lammps-src-4Feb2025.tar.gz
exit # fedora41 container
cd ..
```
The resulting source tarball can be uploaded to the GitHub release page with:
``` sh
gh release upload patch_4Feb2025 lammps-src-4Feb2025.tar.gz
```
#### Build Windows Installer Packages with MinGW Linux-to-Windows Cross-compiler
The various Windows installer packages can also be built with
apptainer container image.
``` sh
cd release-packages
apptainer shell fedora41_musl_mingw.sif
git clone --depth 10 https://github.com/lammps/lammps-packages.git lammps-packages
cd lammps-packages/mingw-cross
ln -sf ../../lammps-release lammps
./buildall.sh release >& mk.log & less +F mk.log
```
The installer with the GUI included can be uploaded to the GitHub release page with:
``` sh
ln -sf LAMMPS-64bit-GUI-4Feb2025.exe LAMMPS-Win10-64bit-GUI-4Feb2025.exe
gh release upload patch_4Feb2025 LAMMPS-Win10-64bit-GUI-4Feb2025.exe
```
The symbolic link is used to have a consistent naming scheme for the packages
attached to the GitHub release page.
#### Clean up:
``` sh
cd ..
rm -r release-packages
```
#### Build Multi-arch App-bundle for macOS
Building app-bundles for macOS is not as easily automated and portable
as some of the other steps. It requires a machine actually running
macOS. In that machine the Xcode compiler package needs to be
installed. This also includes tools for building and manipulating disk
images. This compiler supports building executables for both, the
x86_64 and the arm64 architectures. This requires building with CMake
and using the CMake settings:
``` sh
-D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
-D CMAKE_OSX_DEPLOYMENT_TARGER=11.0
```
This will add the compiler flags `-arch arm64 -arch x86_64
-mmacosx-version-min=11.0` and thus produce object for both
architectures and support for macOS versions back to version 11 (aka Big
Sur). With these settings the following libraries should be compiled
and installed (e.g. to `$HOME/.local`) as static libraries only:
- libomp taken from the LLVM/Clang source distribution (to support OpenMP)
- jpeg
- zlib
- png
- Qt (for LAMMPS-GUI)
When configuring LAMMPS the `cmake/presets/clang.cmake` should be used
and as many packages as possible enabled. For LAMMPS-GUI, MPI should be
disabled with `-D BUILD_MPI=OFF` and LAMMPS-GUI enabled with
`-D BUILD_LAMMPS_GUI=ON`. If the CMake configuration is successful,
settings for building a macOS app-bundle are enabled and with `cmake
--build build --target dmg` extra steps will be executed that will build
a macOS application installer image under the name
`LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg`
The application image can be uploaded to the GitHub release page with:
``` sh
ln -sf LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
gh release upload patch_4Feb2025 LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
```
The symbolic link is used to have a consistent naming scheme for the packages
attached to the GitHub release page.
We are currently building the application images on macOS 12 (aka Monterey).
#### Build Linux x86_64 binary tarball on Ubuntu 20.04LTS
While the flatpak Linux version uses portable runtime libraries provided
by the flatpak environment, we also build regular Linux executables that
use a wrapper script and matching shared libraries in a tarball. To be
compatible with many Linux distributions, one has to build this on a
very old Linux distribution, since most Linux system libraries are
usually backward compatible but not forward compatible. This is
currently done on an Ubuntu 20.04LTS system. Once LAMMPS moves to
require CMake 3.20 and C++17, we will have to move to Ubuntu 22.04LTS.
This installation (either on a real or a virtual machine) should have
the packages installed that are indicated in
`tools/singularity/ubuntu20.04.def` plus Qt version 5.x with development
headers, so that LAMMPS-GUI can be compiled.
Also the building of the binary tarball and setup of the bundled
libraries and wrapper scripts is automated and can executed with `cmake
--build build --target tgz`. This should produce a file
`LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz` which can be uploaded to the
GitHub release page with:
``` sh
ln -sf LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
```
### Update download page on LAMMPS website
Check out the LAMMPS website repo
https://github.com/lammps/lammps-website.git and edit the file
`src/download.txt` for the new release. Test translation with `make
html` and review `html/download.html` Then add and commit to git and
push the changes to GitHub. The Temple Jenkis cluster will
automatically update https://www.lammps.org/download.html accordingly.
Also notify Steve of the release so he can update `src/bug.txt` on the
website from the available release notes.
## LAMMPS Stable Release
A LAMMPS stable release is prepared about once per year in the months July, August, or September.
One (or two, if needed) feature releases before the stable release shall contain only bug fixes
or minor feature updates in optional packages. Also substantial changes to the core of the code
shall be applied rather toward the beginning of a development cycle between two stable releases
than toward the end. The intention is to stablilize significant change to the core and have
outside users and developers try them out during the development cycle; the sooner the changes
are included, the better chances for spotting peripheral bugs and issues.
A LAMMPS stable release is prepared about once per year in the months
July, August, or September. One (or two, if needed) feature releases
before the stable release shall contain only bug fixes or minor feature
updates in optional packages. Also substantial changes to the core of
the code shall be applied rather toward the beginning of a development
cycle between two stable releases than toward the end. The intention is
to stablilize significant change to the core and have outside users and
developers try them out during the development cycle; the sooner the
changes are included, the better chances for spotting peripheral bugs
and issues.
### Prerequesites
Before making a stable release all remaining backported bugfixes shall be released as a (final)
stable update release (see below).
Before making a stable release all remaining backported bugfixes shall
be released as a (final) stable update release (see below).
A LAMMPS stable release process starts like a feature release (see above), only that this feature
release is called a "Stable Release Candidate" and no assets are uploaded to GitHub.
A LAMMPS stable release process starts like a feature release (see
above), only that this feature release is called a "Stable Release
Candidate" and no assets are uploaded to GitHub.
### Synchronize 'maintenance' branch with 'release'
The state of the 'release' branch is then transferred to the 'maintenance' branch (which will
have diverged significantly from 'release' due to the selectively backported bug fixes).
The state of the 'release' branch is then transferred to the
'maintenance' branch (which will have diverged significantly from
'release' due to the selectively backported bug fixes).
### Fast-forward merge of 'maintenance' into 'stable' and apply tag
At this point it should be possible to do a fast-forward merge of 'maintenance' to 'stable'
and then apply the stable\_DMmmYYYY tag.
At this point it should be possible to do a fast-forward merge of
'maintenance' to 'stable' and then apply the stable\_DMmmYYYY tag.
### Push branches and tags

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.github/workflows/check-vla.yml vendored
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@ -77,7 +77,7 @@ jobs:
-D PKG_MDI=on \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=off \
-D PKG_ML-RANN=on \
-D PKG_MOLFILE=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \

15
README
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@ -23,17 +23,20 @@ more information about the code and its uses.
The LAMMPS distribution includes the following files and directories:
README this file
LICENSE the GNU General Public License (GPL)
bench benchmark problems
LICENSE the GNU General Public License (GPLv2)
CITATION.cff Citation information for LAMMPS in CFF format
bench benchmark inputs
cmake CMake build files
doc documentation
examples simple test problems
fortran Fortran wrapper for LAMMPS
examples example inputs for many LAMMPS commands
fortran Fortran 2003 module for LAMMPS
lib additional provided or external libraries
potentials interatomic potential files
python Python wrappers for LAMMPS
python Python module for LAMMPS
src source files
tools pre- and post-processing tools
unittest test programs for use with CTest
.github Git and GitHub related files and tools
Point your browser at any of these files to get started:
@ -42,6 +45,8 @@ https://docs.lammps.org/Intro.html hi-level introduction
https://docs.lammps.org/Build.html how to build LAMMPS
https://docs.lammps.org/Run_head.html how to run LAMMPS
https://docs.lammps.org/Commands_all.html Table of available commands
https://docs.lammps.org/Howto.html Short tutorials and HowTo discussions
https://docs.lammps.org/Errors.html How to interpret and debug errors
https://docs.lammps.org/Library.html LAMMPS library interfaces
https://docs.lammps.org/Modify.html how to modify and extend LAMMPS
https://docs.lammps.org/Developer.html LAMMPS developer info

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cmake/CMakeLists.txt
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@ -209,7 +209,7 @@ endif()
########################################################################
# User input options #
########################################################################
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
# backward compatibility with older LAMMPS documentation
if (PYTHON_EXECUTABLE)
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
endif()
@ -225,6 +225,12 @@ if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
" Setting Python interpreter to: ${Python_EXECUTABLE}")
endif()
find_package(Python COMPONENTS Interpreter QUIET)
# NOTE: RHEL 8.0 and Ubuntu 18.04LTS ship with Python 3.6, Python 3.8 was EOL in 2024
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "LAMMPS requires Python 3.6 or later")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)
@ -930,7 +936,7 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
find_package(ClangFormat 11.0)
find_package(ClangFormat 11.0 QUIET)
if(ClangFormat_FOUND)
add_custom_target(format-src

120
cmake/Modules/CodeCoverage.cmake
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@ -7,76 +7,76 @@
# For Python coverage the coverage package needs to be installed
###############################################################################
if(ENABLE_COVERAGE)
find_program(GCOVR_BINARY gcovr)
find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
find_program(GCOVR_BINARY gcovr)
find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
find_program(COVERAGE_BINARY coverage)
find_package_handle_standard_args(COVERAGE DEFAULT_MSG COVERAGE_BINARY)
find_program(COVERAGE_BINARY coverage)
find_package_handle_standard_args(COVERAGE DEFAULT_MSG COVERAGE_BINARY)
if(GCOVR_FOUND)
get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
if(GCOVR_FOUND)
get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
add_custom_target(
gen_coverage_xml
COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating XML coverage report..."
)
add_custom_target(
gen_coverage_xml
COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating XML coverage report..."
)
set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
add_custom_target(coverage_html_folder
COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
add_custom_target(coverage_html_folder
COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
add_custom_target(
gen_coverage_html
COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating HTML coverage report..."
)
add_dependencies(gen_coverage_html coverage_html_folder)
add_custom_target(
gen_coverage_html
COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating HTML coverage report..."
)
add_dependencies(gen_coverage_html coverage_html_folder)
add_custom_target(clean_coverage_html
${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
COMMENT "Deleting HTML coverage report..."
)
add_custom_target(clean_coverage_html
${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
COMMENT "Deleting HTML coverage report..."
)
add_custom_target(reset_coverage
${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
*/*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Deleting coverage data files..."
)
add_dependencies(reset_coverage clean_coverage_html)
endif()
add_custom_target(reset_coverage
${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
*/*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Deleting coverage data files..."
)
add_dependencies(reset_coverage clean_coverage_html)
endif()
if(COVERAGE_FOUND)
set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
if(COVERAGE_FOUND)
set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
add_custom_command(
OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
COMMAND ${COVERAGE_BINARY} combine
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Combine Python coverage files..."
)
add_custom_command(
OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
COMMAND ${COVERAGE_BINARY} combine
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Combine Python coverage files..."
)
add_custom_target(
gen_python_coverage_html
COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating HTML Python coverage report..."
)
add_custom_target(
gen_python_coverage_html
COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating HTML Python coverage report..."
)
add_custom_target(
gen_python_coverage_xml
COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating XML Python coverage report..."
)
endif()
add_custom_target(
gen_python_coverage_xml
COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating XML Python coverage report..."
)
endif()
endif()

67
cmake/Modules/CodingStandard.cmake
View File

@ -1,40 +1,39 @@
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
# use default (or custom) Python executable.
# Python version check is in main CMakeLists.txt file
if(Python_EXECUTABLE)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 COMPONENTS Interpreter)
if(Python3_EXECUTABLE)
if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
add_custom_target(
check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for permission errors")
add_custom_target(
fix-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix permission errors")
endif()
add_custom_target(
check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for permission errors")
add_custom_target(
fix-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix permission errors")
endif()

6
cmake/Modules/Documentation.cmake
View File

@ -13,7 +13,7 @@ if(BUILD_DOC)
endif()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.8)
message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
message(FATAL_ERROR "Python 3.8 and up is required to build the LAMMPS HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
@ -65,8 +65,8 @@ if(BUILD_DOC)
find_package(Sphinx)
endif()
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.2.2.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "08dd6ef33ca08870220d9aade2a62845" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL)
GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)

22
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -34,8 +34,26 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# C++11 is required
set(CMAKE_CXX_STANDARD 11)
if(NOT CMAKE_CXX_STANDARD)
if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
set(CMAKE_CXX_STANDARD 17)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(CMAKE_CXX_STANDARD LESS 17)
message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
# turn off C++17 check in lmptype.h
if(LAMMPS_CXX11)
add_compile_definitions(LAMMPS_CXX11)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers

4
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -24,9 +24,7 @@ if(MLIAP_ENABLE_PYTHON)
if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif()
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
# Python version check is in main CMakeLists.txt file
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)

2
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -37,7 +37,7 @@ if(DOWNLOAD_QUIP)
endforeach()
# Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
set(temp "${temp} -L/_DUMMY_PATH_\n")
set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
set(temp "${temp}PYTHON=${Python_EXECUTABLE}\nPIP=pip\nEXTRA_LINKOPTS=\n")
set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")

11
cmake/Modules/Packages/PLUMED.cmake
View File

@ -40,6 +40,13 @@ mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
# adjust C++ standard support for self-compiled Plumed2
if(CMAKE_CXX_STANDARD GREATER 11)
set(PLUMED_CXX_STANDARD 14)
else()
set(PLUMED_CXX_STANDARD 11)
endif()
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
set(CROSS_CONFIGURE mingw64-configure)
@ -55,7 +62,7 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
URL_MD5 ${PLUMED_MD5}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
--disable-python --enable-cxx=11
--disable-python --enable-cxx=${PLUMED_CXX_STANDARD}
--enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
${PLUMED_CONFIG_OMP}
${PLUMED_CONFIG_MPI}
@ -142,7 +149,7 @@ else()
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
--enable-cxx=11
--enable-cxx=${PLUMED_CXX_STANDARD}
--disable-python
${PLUMED_CONFIG_MPI}
${PLUMED_CONFIG_OMP}

2
cmake/Modules/Packages/PYTHON.cmake
View File

@ -1,6 +1,6 @@
if(NOT Python_INTERPRETER)
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
# backward compatibility with older LAMMPS documentation
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()

20
doc/README
View File

@ -22,12 +22,12 @@ doxygen-warn.log logfile with warnings from running doxygen
and:
github-development-workflow.md notes on the LAMMPS development workflow
include-file-conventions.md notes on LAMMPS' include file conventions
documentation_conventions.md notes on writing documentation for LAMMPS
If you downloaded a LAMMPS tarball from www.lammps.org, then the html
folder and the PDF manual should be included. If you downloaded LAMMPS
from GitHub then you either need to build them.
using GitHub then you either need to build them yourself or read the
online version at https://docs.lammps.org/
You can build the HTML and PDF files yourself, by typing "make html"
or by "make pdf", respectively. This requires various tools and files.
@ -39,10 +39,10 @@ environment and local folders.
Installing prerequisites for the documentation build
To run the HTML documention build toolchain, python 3.x, doxygen, git,
and the venv python module have to be installed if not already available.
Also internet access is initially required to download external files
and tools.
To run the HTML documention build toolchain, python 3.8 or later,
doxygen 1.8.10 or later, git, and the venv python module have to be
installed if not already available. Also internet access is initially
required to download external files and tools.
Building the PDF format manual requires in addition a compatible LaTeX
installation with support for PDFLaTeX and several add-on LaTeX packages
@ -52,16 +52,24 @@ installed. This includes:
- babel
- capt-of
- cmap
- dvipng
- ellipse
- fncychap
- fontawesom
- framed
- geometry
- gyre
- hyperref
- hypcap
- needspace
- pict2e
- times
- tabulary
- titlesec
- upquote
- wrapfig
- xindy
Also the latexmk script is required to run PDFLaTeX and related tools.
the required number of times to have self-consistent output and include
updated bibliography and indices.

6
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "19 November 2024" "2024-11-19"
.TH LAMMPS "1" "4 February 2025" "2025-02-04"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 19 November 2024
\- Molecular Dynamics Simulator. Version 4 February 2025
.SH SYNOPSIS
.B lmp
@ -311,7 +311,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2024 Sandia Corporation
© 2003--2025 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

23
doc/src/Build.rst
View File

@ -14,6 +14,29 @@ As an alternative, you can download a package with pre-built executables
or automated build trees, as described in the :doc:`Install <Install>`
section of the manual.
Prerequisites
-------------
Which software you need to compile and use LAMMPS strongly depends on
which :doc:`features and settings <Build_settings>` and which
:doc:`optional packages <Packages_list>` you are trying to include.
Common to all is that you need a C++ and C compiler, where the C++
compiler has to support at least the C++11 standard (note that some
compilers require command-line flag to activate C++11 support).
Furthermore, if you are building with CMake, you need at least CMake
version 3.20 and a compatible build tool (make or ninja-build); if you
are building the the legacy GNU make based build system you need GNU
make (other make variants are not going to work since the build system
uses features unique to GNU make) and a Unix-like build environment with
a Bourne shell, and shell tools like "sed", "grep", "touch", "test",
"tr", "cp", "mv", "rm", "ln", "diff" and so on. Parts of LAMMPS
interface with or use Python version 3.6 or later.
The LAMMPS developers aim to keep LAMMPS very portable and usable -
at least in parts - on most operating systems commonly used for
running MD simulations. Please see the :doc:`section on portablility
<Intro_portability>` for more details.
.. toctree::
:maxdepth: 1

6
doc/src/Build_cmake.rst
View File

@ -52,9 +52,9 @@ software or for people that want to modify or extend LAMMPS.
compilers can be configured and built concurrently from the same
source tree.
- Simplified packaging of LAMMPS for Linux distributions, environment
modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
- Integration of automated unit and regression testing (the LAMMPS side
of this is still under active development).
modules, or automated build tools like `Spack <https://spack.io>`_
or `Homebrew <https://brew.sh/>`_.
- Integration of automated unit and regression testing.
.. _cmake_build:

11
doc/src/Build_extras.rst
View File

@ -1139,11 +1139,10 @@ POEMS package
PYTHON package
---------------------------
Building with the PYTHON package requires you have a the Python development
headers and library available on your system, which needs to be a Python 2.7
version or a Python 3.x version. Since support for Python 2.x has ended,
using Python 3.x is strongly recommended. See ``lib/python/README`` for
additional details.
Building with the PYTHON package requires you have a the Python
development headers and library available on your system, which
needs to be Python version 3.6 or later. See ``lib/python/README``
for additional details.
.. tabs::
@ -1159,7 +1158,7 @@ additional details.
set the Python_EXECUTABLE variable to specify which Python
interpreter should be used. Note note that you will also need to
have the development headers installed for this version,
e.g. python2-devel.
e.g. python3-devel.
.. tab:: Traditional make

6
doc/src/Build_make.rst
View File

@ -30,9 +30,9 @@ additional tools to be available and functioning.
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* Python (optional, required for ``make lib-<pkg>`` in the ``src``
folder). Python scripts are currently tested with python 2.7 and
3.6 to 3.11. The procedure for :doc:`building the documentation
<Build_manual>` *requires* Python 3.5 or later.
folder). Python scripts are currently tested with 3.6 to 3.11.
The procedure for :doc:`building the documentation <Build_manual>`
*requires* Python 3.8 or later.
Getting started
^^^^^^^^^^^^^^^

45
doc/src/Build_manual.rst
View File

@ -116,9 +116,9 @@ environment variable.
Prerequisites for HTML
----------------------
To run the HTML documentation build toolchain, python 3, git, doxygen,
and virtualenv have to be installed locally. Here are instructions for
common setups:
To run the HTML documentation build toolchain, Python 3.8 or later, git,
doxygen, and virtualenv have to be installed locally. Here are
instructions for common setups:
.. tabs::
@ -128,13 +128,7 @@ common setups:
sudo apt-get install git doxygen
.. tab:: RHEL or CentOS (Version 7.x)
.. code-block:: bash
sudo yum install git doxygen
.. tab:: Fedora or RHEL/CentOS (8.x or later)
.. tab:: Fedora or RHEL/AlmaLinux/RockyLinux (8.x or later)
.. code-block:: bash
@ -154,7 +148,36 @@ Prerequisites for PDF
In addition to the tools needed for building the HTML format manual,
a working LaTeX installation with support for PDFLaTeX and a selection
of LaTeX styles/packages are required. To run the PDFLaTeX translation
of LaTeX styles/packages are required. Apart from LaTeX packages that
are usually installed by default, the following packages are required:
.. table_from_list::
:columns: 11
- amsmath
- anysize
- babel
- capt-of
- cmap
- dvipng
- ellipse
- fncychap
- fontawesome
- framed
- geometry
- gyre
- hyperref
- hypcap
- needspace
- pict2e
- times
- tabulary
- titlesec
- upquote
- wrapfig
- xindy
To run the PDFLaTeX translation
the ``latexmk`` script needs to be installed as well.
Prerequisites for ePUB and MOBI

28
doc/src/Build_settings.rst
View File

@ -8,7 +8,7 @@ Optional build settings
LAMMPS can be built with several optional settings. Each subsection
explains how to do this for building both with CMake and make.
* `C++11 standard compliance`_ when building all of LAMMPS
* `C++11 and C++17 standard compliance`_ when building all of LAMMPS
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
* `Size of LAMMPS integer types and size limits`_
* `Read or write compressed files`_
@ -23,14 +23,15 @@ explains how to do this for building both with CMake and make.
.. _cxx11:
C++11 standard compliance
-------------------------
C++11 and C++17 standard compliance
-----------------------------------
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
LAMMPS version 3 March 2020 is the last version compatible with the previous
C++98 standard for the core code and most packages. Most currently used
C++ compilers are compatible with C++11, but some older ones may need extra
flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
A C++11 standard compatible compiler is currently the minimum
requirement for compiling LAMMPS. LAMMPS version 3 March 2020 is the
last version compatible with the previous C++98 standard for the core
code and most packages. Most currently used C++ compilers are compatible
with C++11, but some older ones may need extra flags to enable C++11
compliance. Example for GNU c++ 4.8.x:
.. code-block:: make
@ -40,6 +41,17 @@ Individual packages may require compliance with a later C++ standard
like C++14 or C++17. These requirements will be documented with the
:doc:`individual packages <Packages_details>`.
.. versionchanged:: 4Feb2025
Starting with LAMMPS version 4 February 2025 we are starting a
transition to require the C++17 standard. Most current compilers are
compatible and if the C++17 standard is available by default, LAMMPS
will enable C++17 and will compile normally. If the chosen compiler is
not compatible with C++17, but only supports C++11, then the define
-DLAMMPS_CXX11 is required to fall back to compiling with a C++11
compiler. After the next stable release of LAMMPS in summer 2025, the
LAMMPS development branch and future releases will require C++17.
----------
.. _fft:

1
doc/src/Commands_all.rst
View File

@ -140,6 +140,7 @@ additional letter in parenthesis: k = KOKKOS.
* :doc:`plugin <plugin>`
* :doc:`prd <prd>`
* :doc:`python <python>`
* :doc:`region2vmd <region2vmd>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`
* :doc:`temper/grem <temper_grem>`

1
doc/src/Commands_compute.rst
View File

@ -178,6 +178,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ti <compute_ti>`
* :doc:`torque/chunk <compute_torque_chunk>`
* :doc:`vacf <compute_vacf>`
* :doc:`vacf/chunk <compute_vacf_chunk>`
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`viscosity/cos <compute_viscosity_cos>`
* :doc:`voronoi/atom <compute_voronoi_atom>`

2
doc/src/Commands_removed.rst
View File

@ -87,7 +87,7 @@ Minimize style fire/old
.. deprecated:: 8Feb2023
Minimize style *fire/old* has been removed. Its functionality can be
reproduced with *fire* with specific options. Please see the
reproduced with style *fire* with specific options. Please see the
:doc:`min_modify command <min_modify>` documentation for details.
Pair style mesont/tpm, compute style mesont, atom style mesont

5
doc/src/Developer_notes.rst
View File

@ -270,7 +270,10 @@ There are multiple "signatures" that can be called:
- ``Error::all(FLERR, idx, "Error message")``: this is for argument
parsing where "idx" is the index (starting at 0) of the argument for a
LAMMPS command that is causing the failure (use -1 for the command
itself). The output may also include the last input line *before* and
itself). For index 0, you need to use the constant ``Error::ARGZERO``
to work around the inability of some compilers to disambiguate between
a NULL pointer and an integer constant 0, even with an added type cast.
The output may also include the last input line *before* and
*after*, if they differ due to substituting variables. A textual
indicator is pointing to the specific word that failed. Using the
constant ``Error::NOPOINTER`` in place of the *idx* argument will

89
doc/src/Errors_details.rst
View File

@ -12,9 +12,12 @@ following are discussions of such cases.
- :ref:`Incorrect format in ... section of data file <err0002>`
- :ref:`Illegal variable command: expected X arguments but found Y <err0003>`
- :ref:`Out of range atoms - cannot compute ... <err0004>`
- :ref:`Cannot use neighbor bins - box size \<\< cutoff <err0005>`
- :ref:`Too many neighbor bins <err0006>`
- :ref:`Domain too large for neighbor bins <err0007>`
- :ref:`Too many neighbor bins <err0009>`
- :ref:`Cannot use neighbor bins - box size \<\< cutoff <err0015>`
- :ref:`Domain too large for neighbor bins <err0017>`
- :ref:`Molecule topology/atom exceeds system topology/atom <err0024>`
- :ref:`Molecule topology type exceeds system topology type <err0025>`
- :ref:`Molecule attributes do not match system attributes <err0026>`
------
@ -276,7 +279,19 @@ 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:
.. _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.
.. _err0015:
Cannot use neighbor bins - box size \<\< cutoff
-----------------------------------------------
@ -290,19 +305,7 @@ fill space. This error can be avoided using the generally slower
:doc:`nsq neighbor style <neighbor>` or by increasing the size of the
smallest box lengths.
.. _err0006:
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 shrinkwrap
boundaries or when a fix (like fix deform or a barostat) excessively
grows the simulation box.
.. _err0007:
.. _err0017:
Domain too large for neighbor bins
----------------------------------
@ -312,3 +315,55 @@ 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
excessively grown the simulation box.
.. _err0024:
Molecule topology/atom exceeds system topology/atom
---------------------------------------------------
LAMMPS uses :doc:`domain decomposition <Developer_par_part>` 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 <special_bonds>`.
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 <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
avoid the error, one or more of the `extra/XXX/per/atom` keywords are
required to extend the corresponding storage. It is no problem to
choose those numbers generously and have more storage reserved than
actually needed, but having these numbers set too small will lead to an
error.
.. _err0025:
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
through either the :doc:`create_box <create_box>`, the :doc:`read_data
<read_data>`, or the :doc:`read_restart <read_restart>` command. After
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
extend the maximum number of the individual types.
.. _err0026:
Molecule attributes do not match system attributes
--------------------------------------------------
Choosing an :doc:`atom_style <atom_style>` in LAMMPS determines which
per-atom properties are available. In a :doc:`molecule file
<molecule>`, however, it is possible to add sections (for example Masses
or Charges) that are not supported by the atom style. Masses for
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.

8
doc/src/Fortran.rst
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@ -1470,7 +1470,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
LAMMPS equal style variable string, evaluates it and returns the resulting
scalar value as a floating-point number.
.. versionadded:: TBD
.. versionadded:: 4Feb2025
:p character(len=\*) expr: string to be evaluated
:to: :cpp:func:`lammps_eval`
@ -1482,7 +1482,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
Clear whether a compute has been invoked
.. versionadded:: TBD
.. versionadded:: 4Feb2025
:to: :cpp:func:`lammps_clearstep_compute`
@ -1493,7 +1493,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
Add timestep to list of future compute invocations
if the compute has been invoked on the current timestep
.. versionadded:: TBD
.. versionadded:: 4Feb2025
overloaded for 32-bit and 64-bit integer arguments
@ -1506,7 +1506,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
Add timestep to list of future compute invocations
.. versionadded:: TBD
.. versionadded:: 4Feb2025
overloaded for 32-bit and 64-bit integer arguments

14
doc/src/Intro_portability.rst
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@ -13,10 +13,14 @@ Programming language standards
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 3.5 or later or
Python 2.7. Some Python scripts *require* Python 3 and a few others
still need to be ported from Python 2 to Python 3.
the Python code is written to be compatible with Python 3.6 or later.
.. deprecated:: TBD
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
some part of the LAMMPS distribution that is not (yet) compatible with
Python 3, please notify the LAMMPS developers.
Build systems
^^^^^^^^^^^^^
@ -24,8 +28,8 @@ Build systems
LAMMPS can be compiled from source code using a (traditional) build
system based on shell scripts, a few shell utilities (grep, sed, cat,
tr) and the GNU make program. This requires running within a Bourne
shell (``/bin/sh``). Alternatively, a build system with different back ends
can be created using CMake. CMake must be at least version 3.16.
shell (``/bin/sh``). Alternatively, a build system with different back
ends can be created using CMake. CMake must be at least version 3.16.
Operating systems
^^^^^^^^^^^^^^^^^

6
doc/src/Modify_requirements.rst
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@ -189,10 +189,8 @@ of the contribution. As of January 2023, all previously included
Fortran code for the LAMMPS executable has been replaced by equivalent
C++ code.
Python code must be compatible with Python 3.5 and later. Large parts
of LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
compatible with Python 2.7. Compatibility with Python 2.7 is desirable,
but compatibility with Python 3.5 is **required**.
Python code currently must be compatible with Python 3.6. If a later
version or Python is required, it needs to be documented.
Compatibility with older programming language standards is very
important to maintain portability and availability of LAMMPS on many

2
doc/src/Packages_details.rst
View File

@ -2428,7 +2428,7 @@ ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python development
environment (headers and libraries) available on your system, which needs
to be either Python version 2.7 or Python 3.5 and later.
to be Python version 3.6 or later.
**Install:**

19
doc/src/Python_install.rst
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@ -7,6 +7,10 @@ LAMMPS shared library through the Python `ctypes <ctypes_>`_
module. Because of the dynamic loading, it is required that LAMMPS is
compiled in :ref:`"shared" mode <exe>`.
.. versionchanged:: TBD
LAMMPS currently only supports Python version 3.6 or later.
Two components are necessary for Python to be able to invoke LAMMPS code:
* The LAMMPS Python Package (``lammps``) from the ``python`` folder
@ -136,11 +140,6 @@ folder that the dynamic loader searches or inside of the installed
# create virtual environment in folder $HOME/myenv
python3 -m venv $HOME/myenv
For Python versions prior 3.3 you can use `virtualenv
<https://packaging.python.org/en/latest/key_projects/#virtualenv>`_
command instead of "python3 -m venv". This step has to be done
only once.
To activate the virtual environment type:
.. code-block:: bash
@ -245,14 +244,14 @@ make MPI calls directly from Python in your script, if you desire.
We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
(aka mpi4py) and you will find installation instruction for it below.
Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
Installation of mpi4py (version 4.0.1 as of Feb 2025) can be done as
follows:
- Via ``pip`` into a local user folder with:
.. code-block:: bash
pip install --user mpi4py
python3 -m pip install --user mpi4py
- Via ``dnf`` into a system folder for RedHat/Fedora systems:
@ -261,20 +260,20 @@ follows:
# for use with OpenMPI
sudo dnf install python3-mpi4py-openmpi
# for use with MPICH
sudo dnf install python3-mpi4py-openmpi
sudo dnf install python3-mpi4py-mpich
- Via ``pip`` into a virtual environment (see above):
.. code-block:: console
$ source $HOME/myenv/activate
(myenv)$ pip install mpi4py
(myenv)$ python -m pip install mpi4py
- Via ``pip`` into a system folder (not recommended):
.. code-block:: bash
sudo pip install mpi4py
sudo python3 -m pip install mpi4py
For more detailed installation instructions and additional options,
please see the `mpi4py installation <https://mpi4py.readthedocs.io/en/stable/install.html>`_ page.

14
doc/src/Python_overview.rst
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@ -44,15 +44,11 @@ Below is an example output for Python version 3.8.5.
.. warning::
The options described in this section of the manual for using Python
with LAMMPS currently support either Python 2 or 3. Specifically
version 2.7 or later and 3.6 or later. Since the Python community no
longer maintains Python 2 (see `this notice
<https://www.python.org/doc/sunset-python-2/>`_), we recommend use of
Python 3 with LAMMPS. While Python 2 code should continue to work,
that is not something we can guarantee long-term. If you notice
Python code in the LAMMPS distribution that is not compatible with
Python 3, please contact the LAMMPS developers or submit `and issue
on GitHub <https://github.com/lammps/lammps/issues>`_
with LAMMPS support only Python 3.6 or later. For use with Python
2.x you will need to use an older LAMMPS version like 29 Aug 2024
or older. If you notice Python code in the LAMMPS distribution that
is not compatible with Python 3, please contact the LAMMPS developers
or submit `and issue on GitHub <https://github.com/lammps/lammps/issues>`_
---------

21
doc/src/Run_output.rst
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@ -117,14 +117,19 @@ number of histogram counts is equal to the number of processors.
----------
The last section gives aggregate statistics (across all processors)
for pairwise neighbors and special neighbors that LAMMPS keeps track
of (see the :doc:`special_bonds <special_bonds>` command). The number
of times neighbor lists were rebuilt is tallied, as is the number of
potentially *dangerous* rebuilds. If atom movement triggered neighbor
list rebuilding (see the :doc:`neigh_modify <neigh_modify>` command),
then dangerous reneighborings are those that were triggered on the
first timestep atom movement was checked for. If this count is
The last section gives aggregate statistics (across all processors) for
pairwise neighbors and special neighbors that LAMMPS keeps track of (see
the :doc:`special_bonds <special_bonds>` command). This section will
not always contain data, for example when there has not been a neighbor
rebuild, or the neighbor list was constructed on the GPU or when a
hybrid pair style was used and LAMMPS cannot determine a suitable (base)
neighbor list to draw the statistics from.
The number of times neighbor lists were rebuilt is tallied, as is the
number of potentially *dangerous* rebuilds. If atom movement triggered
neighbor list rebuilding (see the :doc:`neigh_modify <neigh_modify>`
command), then dangerous reneighborings are those that were triggered on
the first timestep atom movement was checked for. If this count is
non-zero you may wish to reduce the delay factor to ensure no force
interactions are missed by atoms moving beyond the neighbor skin
distance before a rebuild takes place.

2
doc/src/angle_mwlc.rst
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@ -21,7 +21,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 4Feb2025
The *mwlc* angle style models a meltable wormlike chain and can be used
to model non-linear bending elasticity of polymers, e.g. DNA. *mwlc*

2
doc/src/bond_bpm_spring.rst
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@ -123,7 +123,7 @@ heuristic maximum strain used by typical non-bpm bond styles. Similar behavior
to *break no* can also be attained by setting an arbitrarily high value of
:math:`\epsilon_c`. One cannot use *break no* with *smooth yes*.
.. versionadded:: TBD
.. versionadded:: 4Feb2025
The *volume/factor* keyword toggles whether an additional multibody
contribution is added to he force using the formulation in

36
doc/src/comm_modify.rst
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@ -15,15 +15,12 @@ Syntax
.. parsed-literal::
*mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances
*mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
*cutoff* value = Rcut (distance units) = communicate atoms from this far away
*cutoff/multi* collection value
collection = atom collection or collection range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style
*cutoff/multi/old* type value
type = atom type or type range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*group* value = group-ID = only communicate atoms in the group
*vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms
@ -66,19 +63,16 @@ subdomain. The distance is by default the maximum of the neighbor
cutoff across all atom type pairs.
For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
be faster. In *multi*, each atom is assigned to a collection which should
correspond to a set of atoms with similar interaction cutoffs.
See the :doc:`neighbor <neighbor>` command for a detailed description of collections.
In this case, each atom collection is assigned its own distance
cutoff for communication purposes, and fewer atoms will be
communicated. in *multi/old*, a similar technique is used but atoms
are grouped by atom type. See the :doc:`neighbor multi <neighbor>` and
:doc:`neighbor multi/old <neighbor>` commands for
widely varying cutoffs for different type pairs, the *multi* mode can be
faster. In *multi*, each atom is assigned to a collection which should
correspond to a set of atoms with similar interaction cutoffs. See the
:doc:`neighbor <neighbor>` command for a detailed description of
collections. In this case, each atom collection is assigned its own
distance cutoff for communication purposes, and fewer atoms will be
communicated. See the :doc:`neighbor multi <neighbor>` command for
neighbor list construction options that may also be beneficial for
simulations of this kind. The *multi* communication mode is only compatible
with the *multi* neighbor style. The *multi/old* communication mode is comparable
with both the *multi* and *multi/old* neighbor styles.
simulations of this kind. The *multi* communication mode is only
compatible with the *multi* neighbor style.
The *cutoff* keyword allows you to extend the ghost cutoff distance
for communication mode *single*, which is the distance from the borders
@ -108,14 +102,12 @@ simulation to account for potential changes in the number of
collections. Custom cutoffs are preserved between runs but if
collections are redefined, one may want to re-specify the communication
cutoffs. For granular pair styles,the default cutoff is set to the sum
of the current maximum atomic radii for each collection. The
*cutoff/multi/old* option is similar to *cutoff/multi* except it
operates on atom types as opposed to collections.
of the current maximum atomic radii for each collection.
The *reduce/multi* option applies to *multi* and sets the communication
cutoff for a particle equal to the maximum interaction distance between particles
in the same collection. This reduces the number of
ghost atoms that need to be communicated. This method is only compatible with the
cutoff for a particle equal to the maximum interaction distance between
particles in the same collection. This reduces the number of ghost atoms
that need to be communicated. This method is only compatible with the
*multi* neighbor style and requires a half neighbor list and Newton on.
See the :doc:`neighbor multi <neighbor>` command for more information.

1
doc/src/commands_list.rst
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@ -82,6 +82,7 @@ Commands
read_dump
read_restart
region
region2vmd
replicate
rerun
reset_atoms

1
doc/src/compute.rst
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@ -356,6 +356,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`ti <compute_ti>` - thermodynamic integration free energy values
* :doc:`torque/chunk <compute_torque_chunk>` - torque applied on each chunk
* :doc:`vacf <compute_vacf>` - velocity auto-correlation function of group of atoms
* :doc:`vacf/chunk <compute_vacf_chunk>` - velocity auto-correlation for the center of mass velocities of chunks of atoms
* :doc:`vcm/chunk <compute_vcm_chunk>` - velocity of center-of-mass for each chunk
* :doc:`viscosity/cos <compute_viscosity_cos>` - velocity profile under cosine-shaped acceleration
* :doc:`voronoi/atom <compute_voronoi_atom>` - Voronoi volume and neighbors for each atom

2
doc/src/compute_gaussian_grid_local.rst
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@ -30,7 +30,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 4Feb2025
Define a computation that calculates a Gaussian representation of the ionic
structure. This representation is used for the efficient evaluation

4
doc/src/compute_msd.rst
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@ -116,7 +116,9 @@ Compute *msd* cannot be used with a dynamic group.
Related commands
""""""""""""""""
:doc:`compute msd/nongauss <compute_msd_nongauss>`, :doc:`compute displace_atom <compute_displace_atom>`, :doc:`fix store/state <fix_store_state>`, :doc:`compute msd/chunk <compute_msd_chunk>`
:doc:`compute msd/nongauss <compute_msd_nongauss>`,
:doc:`compute displace_atom <compute_displace_atom>`, :doc:`fix store/state <fix_store_state>`,
:doc:`compute msd/chunk <compute_msd_chunk>`
Default
"""""""

2
doc/src/compute_msd_chunk.rst
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@ -131,7 +131,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute msd <compute_msd>`
:doc:`compute msd <compute_msd>`, :doc:`compute vacf/chunk <compute_vacf_chunk>`
Default
"""""""

2
doc/src/compute_reduce.rst
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@ -87,7 +87,7 @@ values in the vector. The *sumsq* option sums the square of the
values in the vector into a global total. The *avesq* setting does
the same as *sumsq*, then divides the sum of squares by the number of
values. The last two options can be useful for calculating the
variance of some quantity (e.g., variance = sumsq :math:`-` ave\
variance of some quantity (e.g., variance = *avesq* :math:`-` *ave*\
:math:`^2`). The *sumabs* option sums the absolute values in the
vector into a global total. The *aveabs* setting does the same as
*sumabs*, then divides the sum of absolute values by the number of

2
doc/src/compute_vacf.rst
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@ -76,7 +76,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute msd <compute_msd>`
:doc:`compute msd <compute_msd>`, :doc:`compute vacf/chunk <compute_vacf_chunk>`
Default
"""""""

124
doc/src/compute_vacf_chunk.rst Normal file
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@ -0,0 +1,124 @@
.. index:: compute vacf/chunk
compute vacf/chunk command
==========================
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID vacf/chunk chunkID
* ID, group-ID are documented in :doc:`compute <compute>` command
* vacf/chunk = style name of this compute command
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all vacf/chunk molchunk
Description
"""""""""""
.. versionadded:: TBD
Define a computation that calculates the velocity auto-correlation
function (VACF) for multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
single chunk (or no chunk). The ID for this command is specified as
chunkID. For example, a single chunk could be the atoms in a molecule
or atoms in a spatial bin. See the :doc:`compute chunk/atom
<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
details of how chunks can be defined and examples of how they can be
used to measure properties of a system.
Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the product of the initial center of mass
velocity (VCM) for each chunk in *x*, *y*, and *z* direction with the
current center of mass velocity in the same direction. The fourth
component is the total VACF, i.e. the sum of the three components.
Note that only atoms in the specified group contribute to the
calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
defines its own group; atoms will have a chunk ID = 0 if they are not in
that group, signifying they are not assigned to a chunk, and will thus
also not contribute to this calculation. You can specify the "all"
group for this command if you simply want to include atoms with non-zero
chunk IDs.
The integral of the VACF versus time is proportional to the diffusion
coefficient of the diffusing chunks.
.. note::
The number of chunks *Nchunk* calculated by the
:doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant
each time this compute is invoked, so that the dot product for each chunk
from its original position can be computed consistently. If *Nchunk*
does not remain constant, an error will be generated. If needed, you
can enforce a constant *Nchunk* by using the *nchunk once* or *ids once*
options when specifying the :doc:`compute chunk/atom <compute_chunk_atom>`
command.
.. note::
This compute stores the original center-of-mass velocities of each
chunk. When a VACF is calculated on a later timestep, it is assumed
that the same atoms are assigned to the same chunk ID. However
LAMMPS has no simple way to ensure this is the case, though you can
use the *ids once* option when specifying the :doc:`compute
chunk/atom <compute_chunk_atom>` command. Note that if this is not
the case, the VACF calculation does not have a sensible meaning.
.. note::
If you want the quantities calculated by this compute to be
continuous when running from a :doc:`restart file <read_restart>`, then
you should use the same ID for this compute, as in the original run.
This is so that the fix this compute creates to store per-chunk
quantities will also have the same ID, and thus be initialized
correctly with chunk reference positions from the restart file.
The simplest way to output the results of the compute vacf/chunk
calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example:
.. code-block:: LAMMPS
compute cc1 all chunk/atom molecule
compute myChunk all vacf/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
Output info
"""""""""""
This compute calculates a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified :doc:`compute
chunk/atom <compute_chunk_atom>` command. The number of columns = 4 for
the *x*, *y*, *z*, component and the total VACF. These values can be
accessed by any command that uses global array values from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an overview
of LAMMPS output options.
The array values are "intensive". The array values will be in
distance\ :math:`^2` divided by time\ :math:`^2` :doc:`units <units>`.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`compute vacf <compute_vacf>`, :doc:`compute msd/chunk <compute_msd_chunk>`
Default
"""""""
none

2
doc/src/fix_efield_lepton.rst
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@ -40,7 +40,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 4Feb2025
Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,

2
doc/src/fix_imd.rst
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@ -120,7 +120,7 @@ with different units or as a measure to tweak the forces generated by
the manipulation of the IMD client, this option allows to make
adjustments.
.. versionadded:: TBD
.. versionadded:: 4Feb2025
In `IMDv3 <IMDv3_>`_, the IMD protocol has been extended to allow for
the transmission of simulation time, box dimensions, atomic coordinates,

14
doc/src/min_modify.rst
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@ -84,10 +84,10 @@ energy after) and that difference may be smaller than machine epsilon
even if atoms could move in the gradient direction to reduce forces
further.
The choice of a norm can be modified for the min styles *cg*, *sd*\
, *quickmin*, *fire*, *fire/old*, *spin*, *spin/cg* and
*spin/lbfgs* using the *norm* keyword. The default *two* norm computes
the 2-norm (Euclidean length) of the global force vector:
The choice of a norm can be modified for the min styles *cg*, *sd*,
*quickmin*, *fire*, *spin*, *spin/cg*, and *spin/lbfgs* using the
*norm* keyword. The default *two* norm computes the 2-norm
(Euclidean length) of the global force vector:
.. math::
|| \vec{F} ||_{2} = \sqrt{\vec{F}_1^2+ \cdots + \vec{F}_N^2}
@ -160,9 +160,9 @@ that modifies the bias and scaling of the velocities of the atoms during
the mixing step :ref:`(Echeverri Restrepo) <EcheverriRestrepo>`. This
can lead to faster convergence of the minimizer.
The :doc:`min_style <min_style>` *fire* is an optimized implementation of
:doc:`min_style <min_style>` *fire/old*. It can however behave similarly
to the *fire/old* style by using the following set of parameters:
The :doc:`min_style <min_style>` *fire* is an optimized implementation.
It can behave similarly to the previous version by using the following
set of parameters:
.. code-block:: LAMMPS

4
doc/src/minimize.rst
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@ -89,8 +89,8 @@ be more robust than previous line searches we have tried. The
backtracking method is described in Nocedal and Wright's Numerical
Optimization (Procedure 3.1 on p 41).
The :doc:`minimization styles <min_style>` *quickmin*, *fire* and
*fire/old* perform damped dynamics using an Euler integration step. Thus
The :doc:`minimization styles <min_style>` *quickmin* and *fire*
perform damped dynamics using an Euler integration step. Thus
they require a :doc:`timestep <timestep>` be defined.
.. note::

12
doc/src/neighbor.rst
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@ -11,7 +11,7 @@ Syntax
neighbor skin style
* skin = extra distance beyond force cutoff (distance units)
* style = *bin* or *nsq* or *multi* or *multi/old*
* style = *bin* or *nsq* or *multi*
Examples
""""""""
@ -83,16 +83,6 @@ is customized or not, also see the :doc:`comm_modify mode multi
<comm_modify>` command for communication options that further improve
performance in a manner consistent with neighbor style multi.
An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
cutoff distance and multiple sets of bins are defined to search over for
different atom types. This algorithm used to be the default *multi*
algorithm in LAMMPS but was found to be significantly slower than the new
approach. For the dense binary system, computational costs still grew as
:math:`\lambda^{2d}` at large enough :math:`\lambda`. This is equivalent
to the default style, albeit with a smaller prefactor. For now we are
keeping the old option in case there are use cases where multi/old
outperforms the new multi style.
.. note::
If there are multiple sub-styles in a :doc:`hybrid/overlay pair style

2
doc/src/pair_bpm_spring.rst
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@ -85,7 +85,7 @@ commands, or by mixing as described below:
* :math:`r_c` (distance units)
* :math:`\gamma` (force/velocity units)
.. versionadded:: TBD
.. versionadded:: 4Feb2025
Additionally, if *anharmonic* is set to *yes*, a fourth coefficient
must be provided:

2
doc/src/pair_dispersion_d3.rst
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@ -26,7 +26,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 4Feb2025
Style *dispersion/d3* computes the dispersion energy-correction used in
the DFT-D3 method of Grimme :ref:`(Grimme1) <Grimme1>`. It would

2
doc/src/pair_hbond_dreiding.rst
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@ -111,7 +111,7 @@ potential for the Donor-Acceptor interactions. :ref:`(Liu) <Liu>` showed
that the Morse form gives improved results for Dendrimer simulations,
when n = 2.
.. versionadded:: TBD
.. versionadded:: 4Feb2025
The style variants *hbond/dreiding/lj/angleoffset* and
*hbond/dreiding/lj/angleoffset* take the equilibrium angle of the AHD as

8
doc/src/region.rst
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@ -46,6 +46,7 @@ Syntax
xy = distance to tilt y in x direction (distance units)
xz = distance to tilt z in x direction (distance units)
yz = distance to tilt z in y direction (distance units)
xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz can be a variable (see below)
*sphere* args = x y z radius
x,y,z = center of sphere (distance units)
radius = radius of sphere (distance units)
@ -211,9 +212,10 @@ and *ellipsoid* the x-, y-, and z- coordinates of the center of the
sphere/ellipsoid can be specified as an equal-style variable. And for
style *cylinder* the two center positions c1 and c2 for the location of
the cylinder axes can be specified as a equal-style variable. For styles
*cone* and *plane* all properties can be defined via equal-style variables.
For style *plane*, the components of the direction vector normal to plane
should be either all constants or all defined by equal-style variables.
*cone*, *prism*, and *plane* all properties can be defined via
equal-style variables. For style *plane*, the components of the direction
vector normal to plane should be either all constants or all defined by
equal-style variables.
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be

179
doc/src/region2vmd.rst Normal file
View File

@ -0,0 +1,179 @@
.. index:: region2vmd
region2vmd command
==================
Syntax
""""""
.. code-block:: LAMMPS
region2vmd file keyword arg ...
* filename = name of file to write VMD script commands to
* zero or more keyword/arg pairs may be appended
* keyword = *region* or *color* or *material* or *command*
.. parsed-literal::
*region* region-ID = name of region to translate to VMD graphics
*color* color-name = set color for following visualized objects
*material* material-name = set material for following visualized objects
*command* string = string with custom VMD script command (in quotes)
Examples
""""""""
.. code-block:: LAMMPS
region2vmd regions.vmd material Opaque color red region c1 color green region c2
region2vmd vizbox.vmd command "mol new system.lammpstrj waitfor all" region box
region2vmd regdefs.vmd region upper region lower region hole
Description
"""""""""""
.. versionadded:: TBD
Write a `VMD <https:://ks.uiuc.edu/Research/vmd/>`_ Tcl script file with
commands that aim to create a visualization of :doc:`regions <region>`.
There may be multiple region visualizations stored in a single file.
The visualization is implemented by creating a new (and empty) "VMD
molecule" and then assigning a sequence of VMD graphics primitives to
represent the region in VMD. Each region will be stored in a separate
"VMD molecule" with the name "LAMMPS region <region ID>".
The *region2vmd* command is following by the filename for the resulting
VMD script and an arbitrary number of keyword argument pairs to either
write out a new *region* visualization, change the *color* or *material*
setting, or to insert arbitrary VMD script *command*\ s. The keywords
and arguments are processed in sequence.
The *region* keyword must be followed by a previously defined LAMMPS
:doc:`region <region>`. Only a limited set region styles and region
settings are currently supported. See **Restrictions** below.
Unsupported region styles or regions with unsupported settings will be
skipped and a corresponding message is printed.
The *color* keyword must be followed by a color name that is defined in
VMD. This color will be used by all following region visualizations.
The default setting is 'silver'. VMD has the following colors
pre-defined:
.. table_from_list::
:columns: 11
* blue
* red
* gray
* orange
* yellow
* tan
* silver
* green
* white
* pink
* cyan
* purple
* lime
* mauve
* ochre
* iceblue
* black
* yellow2
* yellow3
* green2
* green3
* cyan2
* cyan3
* blue2
* blue3
* violet
* violet2
* magenta
* magenta2
* red2
* red3
* orange2
* orange3
The *material* keyword must be followed by a material name that is defined in
VMD. This material will be used by all following visualizations. The
default setting is 'Transparent'. VMD has the following materials
pre-defined:
.. table_from_list::
:columns: 8
* Opaque
* Transparent
* BrushedMetal
* Diffuse
* Ghost
* Glass1
* Glass2
* Glass3
* Glossy
* HardPlastic
* MetallicPastel
* Steel
* Translucent
* Edgy
* EdgyShiny
* EdgyGlass
* Goodsell
* AOShiny
* AOChalky
* AOEdgy
* BlownGlass
* GlassBubble
* RTChrome
The *command* keyword must be followed by a VMD script command as a
single string in quotes. This VMD command will be directly inserted
into the created VMD script.
The created file can be loaded into VMD either from the command line
with the '-e' flag, or from the command prompt with 'play <script
file>', or from the File menu via "Load VMD visualization state".
.. admonition:: Setting the "top" molecule in VMD
:class: note
It is usually desirable to have the "molecule" with the LAMMPS
trajectory set at "top" molecule in VMD and not one of the "region
molecules". The VMD script generated by this region2vmd assumes that
this molecule is already loaded and set as the current "top"
molecule. Thus at the beginning of the script the index of the top
molecule is stored in the VMD variable 'oldtop' and at the end of the
script, that "top" molecule is restored. If no molecule is loaded,
this can be inserted into the script with a custom command. The
molecule index to this new molecules should be assigned to the oldtop
variable. This can be done with e.g. ``set oldtop [mol new
{regions.vmd} waitfor all]``
----------
Restrictions
""""""""""""
This command is part of the EXTRA-COMMAND package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Only the following region styles are currently supported: *block*,
*cone*, *cylinder*, *ellipsoid*, *prism*, and *sphere*. Regions formed
from unions or intersections of other regions are not supported.
Rotating regions are currently not supported.
Related commands
""""""""""""""""
:doc:`region <region>`
Defaults
""""""""
*color* = silver, *material* = Transparent

20
doc/utils/sphinx-config/false_positives.txt
View File

@ -99,6 +99,7 @@ AMD
amino
Amirjalayer
Amit
amsmath
amu
Amzallag
analytical
@ -128,6 +129,7 @@ Antisymmetrized
antisymmetry
anton
Antonelli
anysize
api
apolar
Apoorva
@ -613,6 +615,7 @@ Courant
covalent
covalently
covariance
cp
cpp
cpu
cradius
@ -905,6 +908,7 @@ dUs
Duval
dV
dvector
dvipng
dVx
dW
dx
@ -1215,12 +1219,14 @@ fmz
fN
Fn
fname
fncychap
fno
Fnudge
foces
Fock
Fogarty
Foiles
fontawesome
fopenmp
forceclear
forestgreen
@ -1353,6 +1359,7 @@ Goga
Goldfarb
Gompper
Gonzalez-Melchor
Goodsell
googlemail
googletest
Gordan
@ -1406,6 +1413,7 @@ Gunsteren
Gunzenmuller
Guo
gw
gyre
gyromagnetic
gz
gzip
@ -1531,10 +1539,12 @@ hydrostatically
hydroxyl
Hynninen
Hyoungki
hypcap
hyperdynamics
hyperparameters
hyperplane
hyperradius
hyperref
hyperspherical
hysteretic
hz
@ -1544,6 +1554,7 @@ Ibanez
ibar
ibm
icc
iceblue
ico
icosahedral
idealgas
@ -2512,6 +2523,7 @@ Ndof
Ndouble
ndx
neb
needspace
neel
Neel
Neelov
@ -2724,6 +2736,7 @@ nylo
nz
Nz
nzlo
ochre
ocl
octahedral
octants
@ -2738,6 +2751,7 @@ Okazaki
O'Keefe
OKeefe
oldlace
oldtop
olecular
Oleinik
Olfason
@ -2914,6 +2928,7 @@ picogram
picograms
picosecond
picoseconds
pict
pid
piecewise
Pieniazek
@ -3685,6 +3700,7 @@ Sz
Tabbernor
tabinner
tabstyle
tabulary
Tadmor
Tafipolsky
tagID
@ -3782,6 +3798,7 @@ timestamps
timestep
timestepping
timesteps
titlesec
TiN
TiO
Tirado
@ -3958,6 +3975,7 @@ untilted
Unwin
uparrow
upenn
upquote
upto
Urbakh
Urbana
@ -4144,6 +4162,7 @@ Workum
Worley
wormlike
wpbe
wrapfig
Wriggers
writedata
Wuppertal
@ -4174,6 +4193,7 @@ Xia
Xiaohu
Xiaowang
Xie
xindy
xk
xlat
xlattice

4
examples/PACKAGES/eff/Auger-Adamantane/in.adamantane_ionized.nve
View File

@ -16,7 +16,7 @@ comm_modify vel yes
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp press
thermo_style custom step pe temp etotal press
thermo_modify temp effTemp
# Minimization
@ -36,7 +36,7 @@ undump 2
#velocity all create 300.0 4928459 dist uniform
# NVE
timestep 0.001
timestep 0.0001
fix 1 all nve/eff
dump 1 all xyz 1000 ${sname}.nve.xyz

367
examples/PACKAGES/eff/Auger-Adamantane/log.31Jan25.adamantane_ionized.nve.g++.1 Normal file
View File

@ -0,0 +1,367 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index adamantane_ionized
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
read_data data.adamantane_ionized
Reading data file ...
orthogonal box = (-50 -50 -50) to (50 50 50)
1 by 1 by 1 MPI processor grid
reading atoms ...
101 atoms
read_data CPU = 0.038 seconds
pair_style eff/cut 100.0
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp etotal press
thermo_modify temp effTemp
# Minimization
min_style cg
dump 1 all xyz 500 ${sname}.min.xyz
dump 1 all xyz 500 adamantane_ionized.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
min_modify line quadratic
minimize 0.0 1.0e-5 10000 100000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
@Article{Jaramillo-Botero11,
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
journal = {J.~Comp.\ Chem.},
year = 2011,
volume = 32,
number = 3,
pages = {497--512}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 102
ghost atom cutoff = 102
binsize = 51, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.222 | 5.222 | 5.222 Mbytes
Step PotEng Temp TotEng Press
0 -320.50186 0 -320.50186 -45590269
571 -324.30072 0 -324.30072 21193099
Loop time of 2.61846 on 1 procs for 571 steps with 101 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-320.501859657303 -324.30071870307 -324.30071870307
Force two-norm initial, final = 2.8135352 2.2777398
Force max component initial, final = 1.7194878 2.093044
Final line search alpha, max atom move = 2.2781994e-09 4.7683716e-09
Iterations, force evaluations = 571 5621
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.602 | 2.602 | 2.602 | 0.0 | 99.37
Neigh | 2.5097e-05 | 2.5097e-05 | 2.5097e-05 | 0.0 | 0.00
Comm | 0.00046417 | 0.00046417 | 0.00046417 | 0.0 | 0.02
Output | 0.00029579 | 0.00029579 | 0.00029579 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0157 | | | 0.60
Nlocal: 101 ave 101 max 101 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: 5050 ave 5050 max 5050 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 1
Dangerous builds = 0
undump 1
undump 2
#restart timestep
# set velocities for nve
#velocity all create 300.0 4928459 dist uniform
# NVE
timestep 0.0001
fix 1 all nve/eff
dump 1 all xyz 1000 ${sname}.nve.xyz
dump 1 all xyz 1000 adamantane_ionized.nve.xyz
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
run 200000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.097 | 4.097 Mbytes
Step PotEng Temp TotEng Press
571 -324.30072 0 -324.30072 21193099
1000 -324.00833 75606.318 -315.02966 1.9184325e+08
2000 -322.45879 62558.11 -315.02966 1.4564261e+08
3000 -322.01495 58820.681 -315.02966 1.3051251e+08
4000 -321.3178 52950.225 -315.02966 75989118
5000 -320.89488 49388.959 -315.02966 55413771
6000 -320.97564 50069.086 -315.02966 67105302
7000 -320.9772 50082.172 -315.02966 90728737
8000 -320.76927 48331.305 -315.02966 1.1054849e+08
9000 -320.40821 45290.936 -315.02966 1.1325434e+08
10000 -320.10216 42713.788 -315.02966 1.0766253e+08
11000 -320.00263 41875.679 -315.02966 1.0831982e+08
12000 -319.92006 41180.36 -315.02966 1.0888686e+08
13000 -319.85913 40667.331 -315.02966 1.0763265e+08
14000 -319.86056 40679.317 -315.02966 1.1159571e+08
15000 -319.79071 40091.129 -315.02966 1.1261281e+08
16000 -319.7393 39658.231 -315.02966 1.0983394e+08
17000 -319.74963 39745.211 -315.02966 1.12573e+08
18000 -319.70347 39356.518 -315.02966 1.1249278e+08
19000 -319.68924 39236.684 -315.02966 1.084432e+08
20000 -319.74747 39727.04 -315.02966 1.109151e+08
21000 -319.76264 39854.793 -315.02966 1.0990745e+08
22000 -319.7997 40166.86 -315.02966 1.0446598e+08
23000 -319.91061 41100.771 -315.02966 1.0605289e+08
24000 -319.98762 41749.299 -315.02966 1.0312843e+08
25000 -320.06842 42429.669 -315.02966 96790253
26000 -320.2321 43807.92 -315.02966 98941422
27000 -320.43008 45475.083 -315.02966 99172853
28000 -320.75368 48199.998 -315.02966 1.0304506e+08
29000 -321.43727 53956.239 -315.02966 1.2359013e+08
30000 -322.86003 65936.838 -315.02966 1.6426506e+08
31000 -325.85698 91173.108 -315.02966 2.3460809e+08
32000 -323.96663 75255.122 -315.02967 1.4386254e+08
33000 -324.31173 78161.078 -315.02966 1.9611146e+08
34000 -321.81048 57098.954 -315.02966 1.3183304e+08
35000 -321.11553 51247.011 -315.02966 1.1860383e+08
36000 -320.7006 47753.061 -315.02966 1.0988072e+08
37000 -320.42875 45463.834 -315.02966 1.0486186e+08
38000 -320.37522 45013.139 -315.02966 1.0667734e+08
39000 -320.16625 43253.419 -315.02966 1.0141734e+08
40000 -320.09034 42614.247 -315.02966 1.0082579e+08
41000 -320.21558 43668.822 -315.02966 1.0548768e+08
42000 -320.19431 43489.747 -315.02966 1.0242614e+08
43000 -320.35932 44879.232 -315.02966 1.0646487e+08
44000 -320.67457 47533.878 -315.02966 1.1366565e+08
45000 -320.83512 48885.757 -315.02966 1.111537e+08
46000 -321.16647 51675.946 -315.02966 1.1302624e+08
47000 -321.38122 53484.331 -315.02966 1.0507686e+08
48000 -321.06774 50844.617 -315.02966 74672082
49000 -322.49756 62884.615 -315.02966 1.044115e+08
50000 -325.97731 92186.422 -315.02966 2.2498335e+08
51000 -320.66106 47420.072 -315.02966 34605338
52000 -323.2278 69033.706 -315.02966 1.4817693e+08
53000 -322.82489 65640.939 -315.02966 1.6065307e+08
54000 -321.95574 58322.133 -315.02966 1.3860454e+08
55000 -321.41375 53758.198 -315.02966 1.1831887e+08
56000 -320.82121 48768.626 -315.02966 97374067
57000 -320.39876 45211.333 -315.02966 85881342
58000 -320.26394 44076.088 -315.02966 80873235
59000 -320.06828 42428.515 -315.02966 75885502
60000 -320.12912 42940.809 -315.02966 83005858
61000 -320.34086 44723.765 -315.02966 90748569
62000 -320.3942 45172.977 -315.02966 93992240
63000 -320.63122 47168.811 -315.02966 1.0726441e+08
64000 -320.86235 49115.084 -315.02966 1.1515294e+08
65000 -320.95075 49859.439 -315.02966 1.1705259e+08
66000 -321.28995 52715.744 -315.02966 1.3144493e+08
67000 -321.69035 56087.363 -315.02966 1.4188253e+08
68000 -322.28755 61116.149 -315.02966 1.5220904e+08
69000 -323.31574 69774.213 -315.02966 1.5914511e+08
70000 -322.98352 66976.685 -315.02966 1.0382488e+08
71000 -323.42006 70652.696 -315.02966 1.1257889e+08
72000 -322.38839 61965.354 -315.02966 1.213394e+08
73000 -321.62733 55556.719 -315.02966 1.2062207e+08
74000 -321.10333 51144.304 -315.02966 1.0628135e+08
75000 -320.84916 49004.001 -315.02966 1.0188029e+08
76000 -320.51651 46202.858 -315.02966 94118114
77000 -320.47427 45847.17 -315.02966 91437540
78000 -320.52773 46297.312 -315.02966 95165197
79000 -320.43972 45556.265 -315.02966 95366722
80000 -320.58645 46791.792 -315.02966 1.0182068e+08
81000 -320.75509 48211.862 -315.02966 1.0907204e+08
82000 -320.77091 48345.056 -315.02966 1.1257336e+08
83000 -321.02219 50461.057 -315.02966 1.2376776e+08
84000 -321.20064 51963.656 -315.02966 1.2909546e+08
85000 -321.2856 52679.138 -315.02966 1.3104703e+08
86000 -321.67229 55935.33 -315.02966 1.4072532e+08
87000 -322.11917 59698.307 -315.02966 1.4404812e+08
88000 -324.23523 77516.896 -315.02966 1.9731217e+08
89000 -320.62579 47123.095 -315.02966 75893884
90000 -324.35107 78492.385 -315.02966 2.1044355e+08
91000 -322.47803 62720.127 -315.02966 1.5538903e+08
92000 -321.71623 56305.3 -315.02966 1.3227964e+08
93000 -321.22259 52148.564 -315.02966 1.1511464e+08
94000 -320.89326 49375.312 -315.02966 1.0320494e+08
95000 -320.60652 46960.796 -315.02966 93163389
96000 -320.42504 45432.671 -315.02966 82638699
97000 -320.35025 44802.889 -315.02966 77728012
98000 -320.38016 45054.714 -315.02966 76753988
99000 -320.64823 47312.019 -315.02966 79089183
100000 -321.20665 52014.291 -315.02966 90654215
101000 -322.45176 62498.949 -315.02966 1.1671692e+08
102000 -325.27551 86276.757 -315.02966 1.7450838e+08
103000 -324.86597 82828.164 -315.02967 1.5358223e+08
104000 -323.50288 71350.092 -315.02966 1.3914499e+08
105000 -321.83206 57280.642 -315.02966 1.1374062e+08
106000 -321.23029 52213.369 -315.02966 1.0154377e+08
107000 -320.79552 48552.352 -315.02966 93581739
108000 -320.85374 49042.571 -315.02966 1.0230141e+08
109000 -320.711 47840.638 -315.02966 98035102
110000 -320.92927 49678.547 -315.02966 1.0291687e+08
111000 -321.37088 53397.184 -315.02966 1.161465e+08
112000 -321.64623 55715.825 -315.02966 1.2178973e+08
113000 -323.29623 69609.916 -315.02966 1.5738912e+08
114000 -326.43458 96036.881 -315.02966 2.2117147e+08
115000 -326.29249 94840.366 -315.02967 2.1727072e+08
116000 -323.49398 71275.138 -315.02966 1.6236371e+08
117000 -321.69956 56164.918 -315.02966 1.2248665e+08
118000 -321.03061 50531.902 -315.02966 1.114646e+08
119000 -320.58664 46793.421 -315.02966 1.0201646e+08
120000 -320.31068 44469.633 -315.02966 92788900
121000 -320.33764 44696.673 -315.02966 96573809
122000 -320.29533 44340.406 -315.02966 96276795
123000 -320.48178 45910.447 -315.02966 96702563
124000 -320.99926 50267.91 -315.02966 1.1042709e+08
125000 -321.72882 56411.316 -315.02966 1.2653574e+08
126000 -323.76935 73593.887 -315.02966 1.6411768e+08
127000 -323.84136 74200.288 -315.02967 1.2684596e+08
128000 -325.27771 86295.322 -315.02966 1.7908195e+08
129000 -322.44151 62412.6 -315.02966 1.2334056e+08
130000 -321.33424 53088.672 -315.02966 1.0110915e+08
131000 -320.74694 48143.276 -315.02966 87343006
132000 -320.58456 46775.879 -315.02966 84619630
133000 -320.42884 45464.64 -315.02966 80256772
134000 -320.41844 45377.068 -315.02966 79998095
135000 -320.67167 47509.417 -315.02966 88059739
136000 -320.94223 49787.695 -315.02966 94538899
137000 -321.61703 55469.964 -315.02966 1.1016475e+08
138000 -323.12933 68204.503 -315.02966 1.4202379e+08
139000 -326.08028 93053.485 -315.02966 1.894649e+08
140000 -326.22688 94287.865 -315.02967 1.9082785e+08
141000 -323.43485 70777.215 -315.02966 1.4698731e+08
142000 -321.79035 56929.435 -315.02966 1.1785802e+08
143000 -321.17113 51715.2 -315.02966 1.0630317e+08
144000 -320.72407 47950.681 -315.02966 94302254
145000 -320.53771 46381.4 -315.02966 89962864
146000 -320.57538 46698.572 -315.02966 90769921
147000 -320.65873 47400.459 -315.02966 88297290
148000 -321.05389 50727.942 -315.02966 95860956
149000 -321.86647 57570.413 -315.02966 1.1210695e+08
150000 -323.71338 73122.627 -315.02966 1.4277977e+08
151000 -325.52965 88416.746 -315.02967 1.7216009e+08
152000 -325.82817 90930.57 -315.02966 1.8312663e+08
153000 -322.5891 63655.44 -315.02966 1.2089115e+08
154000 -321.32957 53049.334 -315.02966 96494848
155000 -320.66612 47462.65 -315.02966 81236441
156000 -320.47196 45827.713 -315.02966 78679995
157000 -320.33169 44646.581 -315.02966 75407967
158000 -320.42358 45420.371 -315.02966 76161171
159000 -320.79103 48514.483 -315.02966 84173108
160000 -321.27968 52629.281 -315.02966 92130817
161000 -322.50401 62938.95 -315.02966 1.138272e+08
162000 -325.40267 87347.575 -315.02966 1.6576028e+08
163000 -323.59983 72166.432 -315.02967 1.1072655e+08
164000 -324.04378 75904.823 -315.02966 1.4709858e+08
165000 -322.01605 58829.972 -315.02966 1.0400742e+08
166000 -321.15747 51600.213 -315.02966 82397014
167000 -320.8409 48934.422 -315.02966 73988066
168000 -320.58861 46810.029 -315.02966 64925698
169000 -320.54312 46426.959 -315.02966 61942158
170000 -320.68604 47630.438 -315.02966 64309567
171000 -320.77008 48338.134 -315.02966 63324927
172000 -321.08474 50987.727 -315.02966 69721832
173000 -321.6134 55439.431 -315.02966 80485473
174000 -322.41904 62223.44 -315.02966 94329801
175000 -324.95819 83604.705 -315.02966 1.5681125e+08
176000 -321.71907 56329.278 -315.02966 45217519
177000 -324.24577 77605.673 -315.02966 1.5164385e+08
178000 -322.34082 61564.766 -315.02966 1.0677988e+08
179000 -321.3229 52993.228 -315.02966 80528491
180000 -320.91614 49567.992 -315.02966 70928167
181000 -320.79771 48570.793 -315.02966 70105356
182000 -320.43289 45498.72 -315.02966 62263793
183000 -320.59821 46890.81 -315.02966 67986358
184000 -320.64879 47316.739 -315.02966 70175355
185000 -320.52287 46256.459 -315.02966 68704646
186000 -320.94252 49790.187 -315.02966 81368769
187000 -321.10174 51130.914 -315.02966 84251825
188000 -321.38014 53475.167 -315.02966 91376642
189000 -322.14722 59934.547 -315.02966 1.1198813e+08
190000 -322.9004 66276.794 -315.02966 1.2823518e+08
191000 -323.63455 72458.807 -315.02966 1.6144592e+08
192000 -324.3348 78355.338 -315.02966 1.5544396e+08
193000 -321.63344 55608.185 -315.02966 85813641
194000 -323.54261 71684.651 -315.02966 1.4340251e+08
195000 -323.1577 68443.449 -315.02966 1.5089288e+08
196000 -322.90055 66278.083 -315.02966 1.4392954e+08
197000 -322.45751 62547.374 -315.02966 1.2607137e+08
198000 -322.18257 60232.201 -315.02966 1.137101e+08
199000 -322.24297 60740.76 -315.02966 1.0950975e+08
200000 -322.47749 62715.575 -315.02966 1.070732e+08
200571 -323.24897 69211.97 -315.02966 1.1694375e+08
Loop time of 86.0986 on 1 procs for 200000 steps with 101 atoms
Performance: 20070.020 fs/day, 0.001 hours/fs, 2322.919 timesteps/s, 234.615 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 | 85.691 | 85.691 | 85.691 | 0.0 | 99.53
Neigh | 0.0010104 | 0.0010104 | 0.0010104 | 0.0 | 0.00
Comm | 0.016762 | 0.016762 | 0.016762 | 0.0 | 0.02
Output | 0.061098 | 0.061098 | 0.061098 | 0.0 | 0.07
Modify | 0.22948 | 0.22948 | 0.22948 | 0.0 | 0.27
Other | | 0.09905 | | | 0.12
Nlocal: 101 ave 101 max 101 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: 5050 ave 5050 max 5050 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 46
Dangerous builds = 0
unfix 1
undump 1
undump 2
Total wall time: 0:01:28

367
examples/PACKAGES/eff/Auger-Adamantane/log.31Jan25.adamantane_ionized.nve.g++.4 Normal file
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@ -0,0 +1,367 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index adamantane_ionized
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
read_data data.adamantane_ionized
Reading data file ...
orthogonal box = (-50 -50 -50) to (50 50 50)
1 by 2 by 2 MPI processor grid
reading atoms ...
101 atoms
read_data CPU = 0.001 seconds
pair_style eff/cut 100.0
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp etotal press
thermo_modify temp effTemp
# Minimization
min_style cg
dump 1 all xyz 500 ${sname}.min.xyz
dump 1 all xyz 500 adamantane_ionized.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
min_modify line quadratic
minimize 0.0 1.0e-5 10000 100000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
@Article{Jaramillo-Botero11,
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
journal = {J.~Comp.\ Chem.},
year = 2011,
volume = 32,
number = 3,
pages = {497--512}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 102
ghost atom cutoff = 102
binsize = 51, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.253 | 5.253 | 5.253 Mbytes
Step PotEng Temp TotEng Press
0 -320.50186 0 -320.50186 -45590269
493 -324.31743 0 -324.31743 20971271
Loop time of 0.883439 on 4 procs for 493 steps with 101 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-320.501859657306 -324.317430790588 -324.317430790588
Force two-norm initial, final = 2.8135352 1.2148731
Force max component initial, final = 1.7194878 1.1232786
Final line search alpha, max atom move = 4.245048e-09 4.7683716e-09
Iterations, force evaluations = 493 3804
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24614 | 0.45831 | 0.84299 | 34.7 | 51.88
Neigh | 1.1159e-05 | 1.2751e-05 | 1.5479e-05 | 0.0 | 0.00
Comm | 0.019423 | 0.40607 | 0.62032 | 37.1 | 45.97
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01905 | | | 2.16
Nlocal: 25.25 ave 30 max 17 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 75.75 ave 84 max 71 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 1262.5 ave 2394 max 663 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 1
Dangerous builds = 0
undump 1
undump 2
#restart timestep
# set velocities for nve
#velocity all create 300.0 4928459 dist uniform
# NVE
timestep 0.0001
fix 1 all nve/eff
dump 1 all xyz 1000 ${sname}.nve.xyz
dump 1 all xyz 1000 adamantane_ionized.nve.xyz
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
run 200000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.128 | 4.128 | 4.128 Mbytes
Step PotEng Temp TotEng Press
493 -324.31743 0 -324.31743 20971271
1000 -324.2963 3994.2535 -323.82196 29875505
2000 -324.14448 2715.8412 -323.82196 24005899
3000 -323.9446 1032.7299 -323.82196 16224812
4000 -323.83425 103.47941 -323.82196 11886177
5000 -323.87559 451.59681 -323.82196 13395168
6000 -324.05446 1957.8271 -323.82196 20034811
7000 -324.24814 3588.7467 -323.82196 28092249
8000 -324.3149 4150.7958 -323.82197 31632418
9000 -324.25366 3635.1689 -323.82196 27760974
10000 -324.05069 1926.0777 -323.82196 19436396
11000 -323.88484 529.46541 -323.82196 13264080
12000 -323.86286 344.37477 -323.82196 12741952
13000 -324.00393 1532.3029 -323.82196 17720089
14000 -324.20987 3266.4109 -323.82196 25528615
15000 -324.34308 4388.1934 -323.82196 30700580
16000 -324.30475 4065.4216 -323.82196 29168176
17000 -324.12375 2541.2612 -323.82196 21928164
18000 -323.93619 961.92262 -323.82196 14363951
19000 -323.87105 413.39974 -323.82196 11446320
20000 -323.9713 1257.5055 -323.82196 15118972
21000 -324.16564 2894.0212 -323.82196 22749979
22000 -324.32073 4199.9228 -323.82196 29044099
23000 -324.34614 4413.8921 -323.82196 29514541
24000 -324.20431 3219.6717 -323.82196 23595226
25000 -324.01211 1601.1964 -323.82196 15812197
26000 -323.90577 705.76969 -323.82196 11992491
27000 -323.95668 1134.4631 -323.82196 14679820
28000 -324.12645 2564.0146 -323.82196 21299092
29000 -324.29158 3954.5234 -323.82196 28120074
30000 -324.32731 4255.3405 -323.82196 31311574
31000 -324.27771 3837.6901 -323.82196 28270491
32000 -324.09259 2278.8862 -323.82196 21338356
33000 -323.95465 1117.2898 -323.82196 15833338
34000 -323.95469 1117.6477 -323.82196 16034624
35000 -324.08796 2239.9037 -323.82196 22076527
36000 -324.26866 3761.5323 -323.82196 29147703
37000 -324.3502 4448.1533 -323.82196 33380564
38000 -324.29459 3979.8076 -323.82196 31533851
39000 -324.1694 2925.6774 -323.82196 25161011
40000 -324.01365 1614.1815 -323.82196 19145060
41000 -323.97015 1247.8234 -323.82196 16994462
42000 -324.04755 1899.62 -323.82196 19654332
43000 -324.22071 3357.7354 -323.82196 25666317
44000 -324.35528 4490.9023 -323.82196 30318540
45000 -324.35807 4514.3651 -323.82196 30645986
46000 -324.24462 3559.0921 -323.82196 25690532
47000 -324.09319 2283.909 -323.82196 18529309
48000 -324.00266 1521.597 -323.82196 14177383
49000 -324.04261 1858.0104 -323.82196 15780869
50000 -324.19619 3151.2862 -323.82196 21070555
51000 -324.32727 4255.0227 -323.82196 26451705
52000 -324.3917 4797.6094 -323.82196 28066000
53000 -324.30169 4039.6086 -323.82196 24214730
54000 -324.14884 2752.5491 -323.82196 17848175
55000 -324.02946 1747.258 -323.82196 13686029
56000 -324.05031 1922.825 -323.82196 14113758
57000 -324.16944 2925.9624 -323.82196 18723794
58000 -324.30745 4088.1772 -323.82196 24387592
59000 -324.36463 4569.6324 -323.82196 27059420
60000 -324.32147 4206.1707 -323.82196 25012812
61000 -324.18133 3026.1579 -323.82196 19500659
62000 -324.07027 2090.9001 -323.82196 14626096
63000 -324.04536 1881.129 -323.82196 13606034
64000 -324.14417 2713.2333 -323.82196 17524492
65000 -324.28817 3925.7771 -323.82196 23261363
66000 -324.37816 4683.5409 -323.82196 26852878
67000 -324.34311 4388.4452 -323.82196 25854003
68000 -324.24346 3549.2763 -323.82196 20818195
69000 -324.1067 2397.6992 -323.82196 15550338
70000 -324.05471 1959.908 -323.82196 13178617
71000 -324.12382 2541.8769 -323.82196 15655087
72000 -324.25986 3687.3615 -323.82196 20831733
73000 -324.37345 4643.9165 -323.82196 25082640
74000 -324.38407 4733.3013 -323.82196 25377064
75000 -324.28752 3920.3485 -323.82196 21185087
76000 -324.14479 2718.409 -323.82196 15093238
77000 -324.06273 2027.4447 -323.82196 11357895
78000 -324.1027 2363.9918 -323.82196 12682184
79000 -324.24431 3556.4784 -323.82196 17923460
80000 -324.37329 4642.461 -323.82197 22977159
81000 -324.40875 4941.1418 -323.82196 24175202
82000 -324.33677 4334.993 -323.82196 20418362
83000 -324.18471 3054.6117 -323.82196 14173787
84000 -324.08262 2194.902 -323.82196 10107358
85000 -324.07536 2133.7765 -323.82196 9748952.1
86000 -324.18707 3074.432 -323.82196 13462472
87000 -324.32091 4201.5211 -323.82196 19096674
88000 -324.44557 5251.2038 -323.82196 22573960
89000 -324.39988 4866.4678 -323.82196 21348490
90000 -324.25685 3662.0864 -323.82196 15903121
91000 -324.0755 2135.0001 -323.82196 10233161
92000 -324.06354 2034.2765 -323.82196 7509452
93000 -324.15185 2777.9236 -323.82196 9750370.3
94000 -324.30478 4065.6146 -323.82196 15561885
95000 -324.42696 5094.5186 -323.82196 20667693
96000 -324.44094 5212.1846 -323.82196 21153174
97000 -324.33283 4301.8232 -323.82196 16435314
98000 -324.1883 3084.8099 -323.82196 10336860
99000 -324.09656 2312.304 -323.82196 6808669.9
100000 -324.13298 2619.0245 -323.82196 7675912.4
101000 -324.25984 3687.2237 -323.82196 11868042
102000 -324.40322 4894.6055 -323.82196 17007266
103000 -324.44333 5232.3546 -323.82196 19025190
104000 -324.39727 4844.4421 -323.82196 15980570
105000 -324.25 3604.3886 -323.82196 9668044.1
106000 -324.08507 2215.5839 -323.82196 4405958.8
107000 -324.11835 2495.8211 -323.82196 3436936.2
108000 -324.21008 3268.2404 -323.82196 6028268.3
109000 -324.34118 4372.1743 -323.82196 10939013
110000 -324.40282 4891.1987 -323.82196 14333667
111000 -324.45353 5318.1927 -323.82196 13380345
112000 -324.33795 4344.9374 -323.82196 7923709.9
113000 -324.19654 3154.2192 -323.82196 1970263.7
114000 -324.12867 2582.7343 -323.82196 -1481413.1
115000 -324.17132 2941.8126 -323.82196 -290956.43
116000 -324.33613 4329.6247 -323.82196 5245770.9
117000 -324.41548 4997.8222 -323.82196 10354303
118000 -324.48518 5584.7558 -323.82196 11795673
119000 -324.41046 4955.5092 -323.82196 8031391.3
120000 -324.24749 3583.2536 -323.82196 1845177.6
121000 -324.14124 2688.5331 -323.82196 -2784584.1
122000 -324.14467 2717.4458 -323.82196 -2261498.4
123000 -324.28472 3896.7771 -323.82196 3080452.1
124000 -324.43687 5177.9121 -323.82196 9819540.9
125000 -324.51452 5831.8132 -323.82196 13180239
126000 -324.47691 5515.0823 -323.82196 11018721
127000 -324.31812 4178.0163 -323.82196 4976672.9
128000 -324.16884 2920.9366 -323.82196 -186371.44
129000 -324.13025 2596.0395 -323.82196 -1883126.3
130000 -324.22275 3374.922 -323.82196 1526423.1
131000 -324.41343 4980.5335 -323.82196 8415685
132000 -324.45089 5296.046 -323.82196 13250300
133000 -324.51148 5806.2229 -323.82196 12827560
134000 -324.39463 4822.239 -323.82196 7049805.8
135000 -324.20254 3204.6979 -323.82196 -187723.51
136000 -324.1379 2660.4388 -323.82196 -3970679.9
137000 -324.18473 3054.7443 -323.82196 -2351010.9
138000 -324.35172 4460.9406 -323.82196 3024494.5
139000 -324.48743 5603.6722 -323.82196 8652609.2
140000 -324.53668 6018.4343 -323.82196 9612584.9
141000 -324.43638 5173.8016 -323.82196 4805500.8
142000 -324.28353 3886.746 -323.82196 -2740880.4
143000 -324.14169 2692.2995 -323.82196 -8310197.6
144000 -324.13063 2599.1788 -323.82196 -9603391.1
145000 -324.27459 3811.4423 -323.82196 -5690559.8
146000 -324.4342 5155.4519 -323.82196 431484.28
147000 -324.55834 6200.7798 -323.82196 4166801.6
148000 -324.51567 5841.5105 -323.82196 2299540.9
149000 -324.34424 4397.967 -323.82196 -4487220.6
150000 -324.20348 3212.6032 -323.82196 -10852097
151000 -324.13211 2611.6979 -323.82196 -12942852
152000 -324.20634 3236.7635 -323.82196 -10732036
153000 -324.35827 4516.0788 -323.82196 -4665668.3
154000 -324.5074 5771.8121 -323.82196 1703175.2
155000 -324.51881 5867.9505 -323.82196 2959605.5
156000 -324.44762 5268.4581 -323.82196 -1706620
157000 -324.25179 3619.4025 -323.82196 -8511782.3
158000 -324.13478 2634.1695 -323.82196 -11767435
159000 -324.17085 2937.9043 -323.82196 -10356431
160000 -324.28946 3936.6179 -323.82196 -5252437.9
161000 -324.47596 5507.0864 -323.82196 1737812.2
162000 -324.52686 5935.7476 -323.82196 5782720.9
163000 -324.5121 5811.4236 -323.82196 4273238.8
164000 -324.35265 4468.7315 -323.82196 -1590319.8
165000 -324.19582 3148.1193 -323.82196 -6770200.2
166000 -324.15306 2788.0507 -323.82196 -8385908.5
167000 -324.24186 3535.8588 -323.82196 -4776412.5
168000 -324.4 4867.4913 -323.82196 2207883.7
169000 -324.52732 5939.6216 -323.82196 7770368.9
170000 -324.53787 6028.4604 -323.82196 8163057.7
171000 -324.42167 5049.9129 -323.82196 2893037
172000 -324.25784 3670.3642 -323.82196 -4020286
173000 -324.16815 2915.1362 -323.82196 -7461767.8
174000 -324.21774 3332.737 -323.82196 -5214520.3
175000 -324.37502 4657.1185 -323.82196 -81968.156
176000 -324.5128 5817.2882 -323.82196 5130806.8
177000 -324.4983 5695.2281 -323.82196 6394017.7
178000 -324.47309 5482.9629 -323.82196 2466372.3
179000 -324.31526 4153.8777 -323.82196 -4378953.5
180000 -324.2046 3222.0434 -323.82196 -9221400.9
181000 -324.21978 3349.8648 -323.82196 -9338327.2
182000 -324.33867 4351.0162 -323.82196 -5586765.2
183000 -324.44483 5244.9523 -323.82196 -706564.21
184000 -324.54787 6112.6128 -323.82196 1971109.1
185000 -324.49436 5662.0508 -323.82196 -1239.0449
186000 -324.38425 4734.8404 -323.82196 -5595239.9
187000 -324.25734 3666.1954 -323.82196 -10793981
188000 -324.21303 3293.0496 -323.82196 -11574584
189000 -324.28662 3912.7067 -323.82196 -8579023.4
190000 -324.4316 5133.5815 -323.82196 -2888022.8
191000 -324.51735 5855.6722 -323.82196 1558206.4
192000 -324.55207 6147.9783 -323.82196 1897782.9
193000 -324.43491 5161.4381 -323.82196 -1998628.2
194000 -324.28751 3920.2514 -323.82196 -6841627.4
195000 -324.24114 3529.7564 -323.82196 -8565471.5
196000 -324.30158 4038.6851 -323.82196 -5634096.8
197000 -324.44261 5226.2386 -323.82196 443851.89
198000 -324.53354 5991.9831 -323.82196 5993350.1
199000 -324.5697 6296.4193 -323.82196 7393255.8
200000 -324.46863 5445.3485 -323.82196 4272906.2
200493 -324.39372 4814.6196 -323.82196 1812660.2
Loop time of 42.6156 on 4 procs for 200000 steps with 101 atoms
Performance: 40548.540 fs/day, 0.001 hours/fs, 4693.118 timesteps/s, 474.005 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.576 | 22.615 | 40.956 | 235.7 | 53.07
Neigh | 1.9114e-05 | 2.3629e-05 | 2.5892e-05 | 0.0 | 0.00
Comm | 0.99241 | 19.433 | 30.581 | 255.9 | 45.60
Output | 0.03344 | 0.035732 | 0.037864 | 0.8 | 0.08
Modify | 0.066393 | 0.082377 | 0.09318 | 3.4 | 0.19
Other | | 0.4486 | | | 1.05
Nlocal: 25.25 ave 31 max 21 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 75.75 ave 80 max 70 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1262.5 ave 2143 max 476 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 2
Dangerous builds = 0
unfix 1
undump 1
undump 2
Total wall time: 0:00:43

90
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Be-solid
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.Be-solid
Reading data file ...
orthogonal box = (0 0 0) to (64.288 63.628618 63.225)
2 by 2 by 1 MPI processor grid
reading atoms ...
20160 atoms
read_data CPU = 0.060 seconds
pair_style eff/cut 31.6125
pair_coeff * *
comm_modify vel yes
neigh_modify one 10000 page 100000
compute effTemp all temp/eff
thermo 10
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
compute 1 all property/atom spin eradius
dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z c_1[1] c_1[2]
dump 1 all custom 1 Be-solid.spe.lammpstrj id type x y z c_1[1] c_1[2]
fix 1 all nve/eff
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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: 10000, page size: 100000
master list distance cutoff = 33.6125
ghost atom cutoff = 33.6125
binsize = 16.80625, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 152.2 | 157 | 161.7 Mbytes
Step TotEng PotEng KinEng Temp Press
0 -49308.807 -49308.807 0 0 1.7906684e+11
Loop time of 2.49575e-06 on 4 procs for 0 steps with 20160 atoms
140.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.496e-06 | | |100.00
Nlocal: 5040 ave 5040 max 5040 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 97370 ave 97370 max 97370 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.11643e+07 ave 3.241e+07 max 2.99372e+07 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 1.2465734e+08
Ave neighs/atom = 6183.4
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

118
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index SiC
variable nstep equal 100
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.SiC
Reading data file ...
orthogonal box = (0 0 0) to (41.1 41.1 41.1)
1 by 2 by 2 MPI processor grid
reading atoms ...
5000 atoms
read_data CPU = 0.016 seconds
pair_style eff/cut 20.0 limit/eradius pressure/evirials ecp 1 Si 2 C
pair_coeff * *
pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 2 p 22.721015 0.728733 1.103199 17.695345 6.693621
comm_modify vel yes
neigh_modify one 4000 page 40000
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable ecoul equal c_energies[3]
variable erres equal c_energies[4]
variable etotalnew equal c_energies[1]+c_energies[2]+c_energies[3]+c_energies[4]
thermo ${nstep}
thermo 100
thermo_style custom step etotal pe ke v_etotalnew v_eke v_epauli v_ecoul v_erres
thermo_modify format float %16.8f
thermo_modify lost warn norm yes flush yes
# Minimization
min_style cg
dump 1 all xyz ${nstep} ${sname}.min.xyz
dump 1 all xyz 100 ${sname}.min.xyz
dump 1 all xyz 100 SiC.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom ${nstep} ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 100 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 100 SiC.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 3 all custom ${nstep} ${sname}.data.restart id type q c_1[1] c_1[2] x y z
dump 3 all custom 100 ${sname}.data.restart id type q c_1[1] c_1[2] x y z
dump 3 all custom 100 SiC.data.restart id type q c_1[1] c_1[2] x y z
min_modify line quadratic
minimize 0 1e-8 100000 1000000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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: 4000, page size: 40000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 20.12 | 20.7 | 21.34 Mbytes
Step TotEng PotEng KinEng v_etotalnew v_eke v_epauli v_ecoul v_erres
0 -0.61266585 -0.61266585 0.00000000 -3063.32924433 2666.66666667 2055.59661323 -7785.59252422 0.00000000
27 -0.87995767 -0.87995767 0.00000000 -4399.78836066 2569.46885777 446.25650389 -7415.51372232 0.00000000
Loop time of 7.78522 on 4 procs for 27 steps with 5000 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-0.612665848866385 -0.879957672127075 -0.879957672129693
Force two-norm initial, final = 254.76567 6.2598998e-09
Force max component initial, final = 2.9077051 3.4450958e-10
Final line search alpha, max atom move = 1 3.4450958e-10
Iterations, force evaluations = 27 37
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.976 | 7.3573 | 7.6627 | 10.1 | 94.50
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11037 | 0.41578 | 0.79718 | 42.4 | 5.34
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0121 | | | 0.16
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 25192 ave 25192 max 25192 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.9985e+06 ave 2.14947e+06 max 1.84582e+06 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 7994000
Ave neighs/atom = 1598.8
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:08

11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.ang.g++.4 Normal file
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@ -0,0 +1,11 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2011-01-07
# General parameters
variable sname index SiH4.ang
log ${sname}.log
log SiH4.ang.log

11
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@ -0,0 +1,11 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2011-01-07
# General parameters
variable sname index SiH4
log ${sname}.log
log SiH4.log

95
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@ -0,0 +1,95 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h_atom.ang
units real
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h_atom.ang
Reading data file ...
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 2 by 2 MPI processor grid
reading atoms ...
4 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 0.529177249
pair_coeff * *
comm_modify vel yes
timestep 0.0001
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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 = 2.5291772
ghost atom cutoff = 2.5291772
binsize = 1.2645886, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
Per MPI rank memory allocation (min/avg/max) = 4.35 | 4.35 | 4.35 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 367.03102 367.03102 0 1882.5288 389.88475 -1905.3825 0 0 29191582 29191582
Loop time of 2.124e-06 on 4 procs for 0 steps with 4 atoms
70.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.124e-06 | | |100.00
Nlocal: 1 ave 4 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 549 ave 550 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 121.5 ave 486 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 486
Ave neighs/atom = 121.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

94
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@ -0,0 +1,94 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h_atom.bohr
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h_atom.bohr
Reading data file ...
orthogonal box = (-1 -1 -1) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
2 atoms
read_data CPU = 0.001 seconds
pair_style eff/cut 1.0
pair_coeff * *
comm_modify vel yes
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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 = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
Per MPI rank memory allocation (min/avg/max) = 4.301 | 4.301 | 4.301 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -0.095769122 -0.095769122 0 1.5 0 -1.5957691 0 0 0 0
Loop time of 2.4135e-06 on 4 procs for 0 steps with 2 atoms
0.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.414e-06 | | |100.00
Nlocal: 0.5 ave 2 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 159.5 ave 160 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 9.25 ave 37 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 37
Ave neighs/atom = 18.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

381
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@ -0,0 +1,381 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2
Reading data file ...
orthogonal box = (0 0 0) to (12.895936 12.895936 12.895936)
1 by 2 by 2 MPI processor grid
reading atoms ...
128 atoms
read_data CPU = 0.001 seconds
pair_style eff/cut 6.447968 pressure/evirials
pair_coeff * *
comm_modify vel yes
min_style cg
min_modify line quadratic
minimize 0 1.0e-6 1000 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 8.447968
ghost atom cutoff = 8.447968
binsize = 4.223984, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -25.681592 0 -25.681592 4.1596728e+10
43 0 -29.402735 0 -29.402735 5.8094784e+10
Loop time of 0.00763171 on 4 procs for 43 steps with 128 atoms
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-25.6815917951629 -29.4027346945036 -29.4027347455099
Force two-norm initial, final = 0.90233034 1.9851971e-07
Force max component initial, final = 0.10428109 2.0171202e-08
Final line search alpha, max atom move = 1 2.0171202e-08
Iterations, force evaluations = 43 49
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0027162 | 0.0036134 | 0.0039713 | 0.9 | 47.35
Neigh | 4.3664e-05 | 4.9777e-05 | 5.6567e-05 | 0.0 | 0.65
Comm | 0.0030668 | 0.0034209 | 0.004339 | 0.9 | 44.82
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0005477 | | | 7.18
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 2416 ave 2579 max 2253 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 9664
Ave neighs/atom = 75.5
Neighbor list builds = 1
Dangerous builds = 0
region part block INF 2.0 INF 2.0 INF 5.0 units box
group sub id < 32
31 atoms in group sub
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute regionT sub temp/region/eff part
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 100
thermo_style custom step etotal pe ke temp press v_press c_regionT
thermo_modify temp effTemp press effPress
#velocity all create 300.0 4928459 rot yes dist gaussian
fix 3 all temp/rescale/eff 10 0.0 300.0 0.02 1.0
fix 1 all nve/eff
run 10000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.723 | 4.723 | 4.723 Mbytes
Step TotEng PotEng KinEng Temp Press v_press c_regionT
43 -29.402735 -29.402735 0 0 5.8094784e+10 5.8094784e+10 0
100 -29.402222 -29.402734 0.00051174152 1.71 5.811788e+10 5.8115522e+10 0.84298014
200 -29.401297 -29.402706 0.0014095337 4.71 5.8200069e+10 5.8193571e+10 2.2642129
300 -29.400299 -29.402606 0.0023073258 7.71 5.8313355e+10 5.8302716e+10 3.5188104
400 -29.399185 -29.40239 0.003205118 10.71 5.8450303e+10 5.8435537e+10 4.4975076
500 -29.397917 -29.40202 0.0041029101 13.71 5.8606915e+10 5.8588085e+10 5.0938111
600 -29.396468 -29.401468 0.0050007023 16.71 5.8780191e+10 5.8757458e+10 5.214099
700 -29.394823 -29.400721 0.0058984944 19.71 5.8967293e+10 5.8940983e+10 4.7987742
800 -29.392986 -29.399782 0.0067962866 22.71 5.9165038e+10 5.9135736e+10 3.8586623
900 -29.390985 -29.398679 0.0076940787 25.71 5.936952e+10 5.9338162e+10 2.5267164
1000 -29.388873 -29.397465 0.0085918709 28.71 5.9575808e+10 5.9543743e+10 1.1129096
1100 -29.386732 -29.396221 0.009489663 31.71 5.9777799e+10 5.9746754e+10 0.12904766
1200 -29.38466 -29.395047 0.010387455 34.71 5.9968346e+10 5.9940231e+10 0.23254239
1300 -29.382761 -29.394047 0.011285247 37.71 6.0139768e+10 6.0116306e+10 2.0555958
1400 -29.381123 -29.393306 0.012183039 40.71 6.0284712e+10 6.0267009e+10 5.9623931
1500 -29.379789 -29.39287 0.013080832 43.71 6.0397168e+10 6.0385416e+10 11.867131
1600 -29.378749 -29.392728 0.013978624 46.71 6.0473266e+10 6.0466731e+10 19.241519
1700 -29.377937 -29.392813 0.014876416 49.71 6.051158e+10 6.0508871e+10 27.309028
1800 -29.377239 -29.393013 0.015774208 52.71 6.0512895e+10 6.0512343e+10 35.292057
1900 -29.376517 -29.393189 0.016672 55.71 6.0479626e+10 6.0479611e+10 42.576307
2000 -29.375623 -29.393193 0.017569792 58.71 6.0415141e+10 6.0414287e+10 48.751559
2100 -29.374415 -29.392882 0.018467585 61.71 6.0323201e+10 6.0320436e+10 53.567423
2200 -29.372763 -29.392128 0.019365377 64.71 6.0207563e+10 6.0202104e+10 56.859803
2300 -29.370562 -29.390825 0.020263169 67.71 6.0071772e+10 6.0063077e+10 58.484447
2400 -29.367733 -29.388894 0.021160961 70.71 5.9919081e+10 5.9906793e+10 58.272649
2500 -29.36423 -29.386289 0.022058753 73.71 5.9752468e+10 5.9736389e+10 56.015194
2600 -29.360049 -29.383005 0.022956545 76.71 5.9574736e+10 5.9554816e+10 51.483979
2700 -29.355237 -29.379092 0.023854337 79.71 5.9388664e+10 5.9365044e+10 44.512157
2800 -29.349911 -29.374664 0.02475213 82.71 5.9197231e+10 5.9170319e+10 35.165882
2900 -29.344268 -29.369918 0.025649922 85.71 5.9003898e+10 5.8974484e+10 24.034217
3000 -29.338593 -29.365141 0.026547714 88.71 5.8812903e+10 5.8782274e+10 12.596437
3100 -29.333256 -29.360702 0.027445506 91.71 5.8629493e+10 5.8599437e+10 3.4545231
3200 -29.328661 -29.357004 0.028343298 94.71 5.8459894e+10 5.8432478e+10 0.016534267
3300 -29.325167 -29.354408 0.02924109 97.71 5.8310843e+10 5.828792e+10 5.3243002
3400 -29.322991 -29.35313 0.030138882 100.71 5.8188646e+10 5.8171288e+10 20.462635
3500 -29.322131 -29.353168 0.031036675 103.71 5.8098076e+10 5.8086277e+10 43.783703
3600 -29.322365 -29.3543 0.031934467 106.71 5.8041579e+10 5.8034437e+10 71.730426
3700 -29.323314 -29.356147 0.032832259 109.71 5.8019147e+10 5.8015336e+10 100.55288
3800 -29.32453 -29.35826 0.033730051 112.71 5.8028749e+10 5.8026989e+10 127.58755
3900 -29.325571 -29.360199 0.034627843 115.71 5.8067003e+10 5.8066317e+10 151.55747
4000 -29.326051 -29.361577 0.035525635 118.71 5.8129753e+10 5.8129529e+10 172.22883
4100 -29.325653 -29.362076 0.036423427 121.71 5.8212438e+10 5.8212365e+10 189.92431
4200 -29.324129 -29.36145 0.03732122 124.71 5.8310227e+10 5.8310175e+10 205.15122
4300 -29.321298 -29.359517 0.038219012 127.71 5.8417974e+10 5.8417851e+10 218.38021
4400 -29.317038 -29.356155 0.039116804 130.71 5.853006e+10 5.8529625e+10 229.92521
4500 -29.311285 -29.3513 0.040014596 133.71 5.8640135e+10 5.8638756e+10 239.8628
4600 -29.304036 -29.344948 0.040912388 136.71 5.8740796e+10 5.8737084e+10 247.94642
4700 -29.295358 -29.337168 0.04181018 139.71 5.8823225e+10 5.8814498e+10 253.48762
4800 -29.285407 -29.328115 0.042707973 142.71 5.8876834e+10 5.8858342e+10 255.20199
4900 -29.274456 -29.318062 0.043605765 145.71 5.8889029e+10 5.8852994e+10 251.07158
5000 -29.262921 -29.307424 0.044503557 148.71 5.8845331e+10 5.8780052e+10 238.3896
5100 -29.251383 -29.296784 0.045401349 151.71 5.8730207e+10 5.8619991e+10 214.32208
5200 -29.240581 -29.286881 0.046299141 154.71 5.8529067e+10 5.8356259e+10 177.37505
5300 -29.231338 -29.278535 0.047196933 157.71 5.8231557e+10 5.7981728e+10 129.63824
5400 -29.2244 -29.272495 0.048094725 160.71 5.783545e+10 5.7504658e+10 78.320218
5500 -29.220236 -29.269228 0.048992518 163.71 5.734924e+10 5.6948969e+10 34.221251
5600 -29.218882 -29.268773 0.04989031 166.71 5.6791455e+10 5.6346643e+10 6.9175951
5700 -29.219941 -29.270729 0.050788102 169.71 5.6186504e+10 5.5727327e+10 0.29716744
5800 -29.222711 -29.274397 0.051685894 172.71 5.5559255e+10 5.5112403e+10 12.070047
5900 -29.226384 -29.278968 0.052583686 175.71 5.4930986e+10 5.4515116e+10 36.620819
6000 -29.230194 -29.283676 0.053481478 178.71 5.4317798e+10 5.394343e+10 68.124786
6100 -29.233502 -29.287881 0.05437927 181.71 5.373093e+10 5.3402599e+10 102.15151
6200 -29.235817 -29.291094 0.055277063 184.71 5.317797e+10 5.2896659e+10 135.88236
6300 -29.236796 -29.29297 0.056174855 187.71 5.266419e+10 5.2429163e+10 167.68481
6400 -29.236229 -29.293302 0.057072647 190.71 5.2193678e+10 5.2003557e+10 196.5624
6500 -29.234036 -29.292006 0.057970439 193.71 5.1770207e+10 5.1623395e+10 221.67578
6600 -29.230262 -29.28913 0.058868231 196.71 5.1397868e+10 5.1292425e+10 241.95867
6700 -29.225101 -29.284867 0.059766023 199.71 5.1081526e+10 5.1014513e+10 255.81687
6800 -29.218918 -29.279582 0.060663816 202.71 5.0827088e+10 5.0793357e+10 260.95381
6900 -29.212279 -29.27384 0.061561608 205.71 5.0641515e+10 5.0632006e+10 254.493
7000 -29.20597 -29.26843 0.0624594 208.71 5.0532428e+10 5.0532428e+10 233.71509
7100 -29.200973 -29.264331 0.063357192 211.71 5.0507114e+10 5.0495687e+10 197.6792
7200 -29.198346 -29.262601 0.064254984 214.71 5.0570894e+10 5.0523214e+10 149.34022
7300 -29.199011 -29.264163 0.065152776 217.71 5.0725246e+10 5.061858e+10 96.508036
7400 -29.203489 -29.26954 0.066050568 220.71 5.0966567e+10 5.0787531e+10 49.67303
7500 -29.211725 -29.278674 0.066948361 223.71 5.1286493e+10 5.103478e+10 17.246635
7600 -29.223104 -29.29095 0.067846153 226.71 5.167383e+10 5.1359868e+10 1.9485991
7700 -29.236642 -29.305386 0.068743945 229.71 5.2117092e+10 5.1756034e+10 1.0837556
7800 -29.251244 -29.320885 0.069641737 232.71 5.2606457e+10 5.2212741e+10 9.4375813
7900 -29.265892 -29.336432 0.070539529 235.71 5.3134616e+10 5.2719209e+10 21.964752
8000 -29.279741 -29.351178 0.071437321 238.71 5.3696722e+10 5.3266678e+10 34.999087
8100 -29.292137 -29.364472 0.072335113 241.71 5.4289899e+10 5.3849048e+10 46.31642
8200 -29.3026 -29.375833 0.073232906 244.71 5.4912636e+10 5.4462542e+10 54.747327
8300 -29.310798 -29.384928 0.074130698 247.71 5.5564256e+10 5.510506e+10 59.766256
8400 -29.316514 -29.391542 0.07502849 250.71 5.6244467e+10 5.5775533e+10 61.201976
8500 -29.319632 -29.395559 0.075926282 253.71 5.6952997e+10 5.6473403e+10 59.079366
8600 -29.32013 -29.396954 0.076824074 256.71 5.7689238e+10 5.719821e+10 53.567555
8700 -29.318072 -29.395794 0.077721866 259.71 5.845187e+10 5.7949231e+10 45.014327
8800 -29.313622 -29.392241 0.078619658 262.71 5.923839e+10 5.8725125e+10 34.059265
8900 -29.307054 -29.386572 0.079517451 265.71 6.0044529e+10 5.9523495e+10 21.822776
9000 -29.298773 -29.379188 0.080415243 268.71 6.0863509e+10 6.0340317e+10 10.151211
9100 -29.289324 -29.370637 0.081313035 271.71 6.1685216e+10 6.1169112e+10 1.8420489
9200 -29.279397 -29.361608 0.082210827 274.71 6.2495436e+10 6.1999812e+10 0.66834686
9300 -29.269795 -29.352904 0.083108619 277.71 6.3275527e+10 6.2817393e+10 10.912705
9400 -29.261351 -29.345358 0.084006411 280.71 6.400305e+10 6.3600785e+10 36.169722
9500 -29.254801 -29.339705 0.084904204 283.71 6.4653796e+10 6.4323113e+10 77.605603
9600 -29.250616 -29.336418 0.085801996 286.71 6.520517e+10 6.4954574e+10 132.59334
9700 -29.248872 -29.335572 0.086699788 289.71 6.5640092e+10 6.5468097e+10 194.91905
9800 -29.249212 -29.33681 0.08759758 292.71 6.59499e+10 6.5845645e+10 256.81628
9900 -29.250911 -29.339406 0.088495372 295.71 6.6135085e+10 6.6081884e+10 311.59173
10000 -29.253024 -29.342417 0.089393164 298.71 6.6203807e+10 6.6183517e+10 355.23319
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
Loop time of 1.04131 on 4 procs for 10000 steps with 128 atoms
Performance: 829720.937 fs/day, 0.000 hours/fs, 9603.252 timesteps/s, 1.229 Matom-step/s
90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.43097 | 0.51117 | 0.59532 | 10.4 | 49.09
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.40178 | 0.48688 | 0.56619 | 10.6 | 46.76
Output | 0.0046624 | 0.0047434 | 0.0049664 | 0.2 | 0.46
Modify | 0.0074002 | 0.007613 | 0.0078044 | 0.2 | 0.73
Other | | 0.0309 | | | 2.97
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 2480 ave 2645 max 2315 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 9920
Ave neighs/atom = 77.5
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
#compute 1 all property/atom spin eradius
#fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 drag 0.5
#dump 1 all custom 100 dump.file id type q c_1[1] c_1[2] x y z
#fix 1 all nve/eff
run 10000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes
Step TotEng PotEng KinEng Temp Press v_press c_regionT
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
10100 -29.253759 -29.344838 0.091079452 304.34478 6.6176296e+10 6.6172538e+10 389.80019
10200 -29.253759 -29.345711 0.091951632 307.2592 6.6052925e+10 6.6052773e+10 409.04715
10300 -29.253759 -29.344222 0.09046268 302.28382 6.5835973e+10 6.5829924e+10 406.94188
10400 -29.253759 -29.339884 0.086124587 287.78795 6.5537696e+10 6.5519727e+10 382.65817
10500 -29.253759 -29.33263 0.078870586 263.54848 6.5173326e+10 6.5140691e+10 337.96709
10600 -29.253759 -29.32285 0.069091456 230.87122 6.476052e+10 6.4713236e+10 277.25232
10700 -29.253759 -29.311365 0.057605907 192.4919 6.4318542e+10 6.4258684e+10 207.17514
10800 -29.253759 -29.299325 0.045566125 152.26061 6.3867235e+10 6.379814e+10 136.00177
10900 -29.253759 -29.288069 0.034309769 114.64714 6.3425834e+10 6.3351345e+10 72.65992
11000 -29.253759 -29.278938 0.025178778 84.135657 6.3011735e+10 6.2935563e+10 25.640652
11100 -29.253759 -29.273091 0.01933168 64.597401 6.2639343e+10 6.2564598e+10 1.8969587
11200 -29.253759 -29.271337 0.01757805 58.737592 6.2319122e+10 6.224804e+10 5.9017765
11300 -29.253759 -29.27402 0.02026083 67.702184 6.2056961e+10 6.1990807e+10 39.010867
11400 -29.253759 -29.280964 0.02720461 90.905038 6.1853928e+10 6.1793041e+10 99.231156
11500 -29.253759 -29.291496 0.037737065 126.09956 6.1706426e+10 6.1650353e+10 181.43067
11600 -29.253759 -29.304538 0.050778773 169.67883 6.1606742e+10 6.1554398e+10 277.95525
11700 -29.253759 -29.318745 0.064985916 217.15243 6.1543891e+10 6.1493702e+10 379.55439
11800 -29.253759 -29.332682 0.078922995 263.72361 6.1504653e+10 6.1454647e+10 476.47604
11900 -29.253759 -29.344999 0.091239641 304.88006 6.1474696e+10 6.1422513e+10 559.5746
12000 -29.253759 -29.354586 0.10082711 336.91689 6.1439645e+10 6.1382484e+10 621.28769
12100 -29.253759 -29.360694 0.10693515 357.32707 6.1386022e+10 6.1320551e+10 656.36975
12200 -29.253759 -29.362996 0.10923714 365.01925 6.1301987e+10 6.1224243e+10 662.31507
12300 -29.253759 -29.361599 0.10783979 360.34996 6.1177837e+10 6.1083188e+10 639.45046
12400 -29.253759 -29.357 0.10324072 344.98202 6.1006282e+10 6.0889481e+10 590.72007
12500 -29.253759 -29.350003 0.096243698 321.60127 6.0782503e+10 6.0637874e+10 521.21754
12600 -29.253759 -29.341604 0.087845122 293.53717 6.0504033e+10 6.032581e+10 437.54122
12700 -29.253759 -29.332866 0.079107181 264.33907 6.017052e+10 5.995332e+10 347.0566
12800 -29.253759 -29.324792 0.071033241 237.35975 5.9783407e+10 5.9522812e+10 257.14865
12900 -29.253759 -29.318218 0.064459023 215.3918 5.9345591e+10 5.9038771e+10 174.53724
13000 -29.253759 -29.313729 0.059970255 200.39245 5.8861097e+10 5.8507403e+10 104.71393
13100 -29.253759 -29.311613 0.057853612 193.31962 5.8334792e+10 5.7936245e+10 51.540581
13200 -29.253759 -29.311843 0.05808372 194.08853 5.777218e+10 5.7333762e+10 17.031706
13300 -29.253759 -29.314104 0.060345047 201.64482 5.7179263e+10 5.6708972e+10 1.3240561
13400 -29.253759 -29.317843 0.064084089 214.13895 5.6562484e+10 5.6071106e+10 2.82093
13500 -29.253759 -29.322344 0.068584649 229.17771 5.5928737e+10 5.542933e+10 18.484961
13600 -29.253759 -29.326816 0.073057273 244.12312 5.528542e+10 5.4792545e+10 44.242832
13700 -29.253759 -29.330492 0.076733214 256.40639 5.4640519e+10 5.4169259e+10 75.458518
13800 -29.253759 -29.332712 0.07895342 263.82528 5.4002682e+10 5.3567542e+10 107.42845
13900 -29.253759 -29.333003 0.079244028 264.79635 5.3381274e+10 5.2995036e+10 135.85235
14000 -29.253759 -29.33113 0.077371384 258.53885 5.2786371e+10 5.2459011e+10 157.23725
14100 -29.253759 -29.327131 0.073371666 245.17367 5.2228695e+10 5.196645e+10 169.19917
14200 -29.253759 -29.321311 0.06755247 225.72865 5.1719461e+10 5.1524114e+10 170.63669
14300 -29.253759 -29.314225 0.060466227 202.04975 5.1270133e+10 5.1138601e+10 161.76275
14400 -29.253759 -29.306617 0.052857773 176.62587 5.089211e+10 5.0816349e+10 143.99448
14500 -29.253759 -29.29935 0.045590774 152.34297 5.059633e+10 5.0563589e+10 119.71531
14600 -29.253759 -29.293319 0.039559773 132.1902 5.0392837e+10 5.0386251e+10 91.93698
14700 -29.253759 -29.289355 0.035596197 118.94579 5.029032e+10 5.0289808e+10 63.900552
14800 -29.253759 -29.288137 0.034377629 114.8739 5.029568e+10 5.0279104e+10 38.66315
14900 -29.253759 -29.290109 0.036349691 121.46361 5.0413636e+10 5.0358148e+10 18.71998
15000 -29.253759 -29.295428 0.041669069 139.23847 5.0646422e+10 5.0529927e+10 5.7077538
15100 -29.253759 -29.303933 0.050174363 167.65917 5.099359e+10 5.079623e+10 0.22655448
15200 -29.253759 -29.315148 0.061388837 205.13268 5.1451944e+10 5.1157502e+10 1.802684
15300 -29.253759 -29.328315 0.074555888 249.13079 5.2015605e+10 5.1612742e+10 8.997261
15400 -29.253759 -29.342464 0.088704628 296.40923 5.2676201e+10 5.2159429e+10 19.646426
15500 -29.253759 -29.356499 0.10273965 343.30769 5.3423173e+10 5.2793473e+10 31.201748
15600 -29.253759 -29.369305 0.11554633 386.10162 5.4244166e+10 5.3509204e+10 41.12616
15700 -29.253759 -29.37986 0.1261011 421.37071 5.5125447e+10 5.429932e+10 47.293231
15800 -29.253759 -29.387334 0.13357524 446.34577 5.6052334e+10 5.5154866e+10 48.336756
15900 -29.253759 -29.39118 0.13742108 459.19674 5.7009617e+10 5.6065206e+10 43.903332
16000 -29.253759 -29.39119 0.13743084 459.22936 5.798194e+10 5.7018034e+10 34.771959
16100 -29.253759 -29.38752 0.13376082 446.96588 5.8954112e+10 5.7999411e+10 22.820321
16200 -29.253759 -29.380676 0.12691686 424.09659 5.9911355e+10 5.8993881e+10 10.835339
16300 -29.253759 -29.37146 0.11770099 393.30145 6.083948e+10 5.9984681e+10 2.1841693
16400 -29.253759 -29.360882 0.10712336 357.956 6.1725019e+10 6.095406e+10 0.37905177
16500 -29.253759 -29.350047 0.096287961 321.74918 6.255531e+10 6.1883732e+10 8.5837627
16600 -29.253759 -29.340023 0.086263871 288.25337 6.3318582e+10 6.2755451e+10 29.119377
16700 -29.253759 -29.331716 0.077957034 260.49582 6.4004055e+10 6.3551677e+10 63.031437
16800 -29.253759 -29.325757 0.071998194 240.58417 6.460208e+10 6.4256316e+10 109.77858
16900 -29.253759 -29.322421 0.06866219 229.43681 6.5104343e+10 6.4855474e+10 167.09379
17000 -29.253759 -29.32159 0.067830842 226.65884 6.5504142e+10 6.5338169e+10 231.05378
17100 -29.253759 -29.322766 0.06900694 230.58881 6.5796723e+10 6.5696949e+10 296.37046
17200 -29.253759 -29.325139 0.071380489 238.52009 6.5979662e+10 6.5928378e+10 356.89258
17300 -29.253759 -29.3277 0.073941262 247.07699 6.6053264e+10 6.6033329e+10 406.27733
17400 -29.253759 -29.329384 0.075624794 252.70257 6.6020907e+10 6.6017081e+10 438.765
17500 -29.253759 -29.329232 0.075473164 252.19589 6.5889298e+10 6.5889197e+10 449.9672
17600 -29.253759 -29.326547 0.072788435 243.22479 6.5668557e+10 6.566317e+10 437.56505
17700 -29.253759 -29.321015 0.067255999 224.73798 6.537209e+10 6.5355863e+10 401.81223
17800 -29.253759 -29.312777 0.059017856 197.20998 6.5016192e+10 6.4986737e+10 345.75083
17900 -29.253759 -29.302441 0.048681923 162.67214 6.461938e+10 6.4576898e+10 275.07707
18000 -29.253759 -29.291021 0.037262252 124.51296 6.4201459e+10 6.4148001e+10 197.63846
18100 -29.253759 -29.279814 0.026055453 87.065095 6.3782375e+10 6.3721066e+10 122.59764
18200 -29.253759 -29.270228 0.016469061 55.031873 6.3380961e+10 6.3315275e+10 59.354773
18300 -29.253759 -29.263585 0.009826229 32.834645 6.3013664e+10 6.2946844e+10 16.367993
18400 -29.253759 -29.260935 0.0071761426 23.9793 6.2693422e+10 6.2628079e+10 0.04021999
18500 -29.253759 -29.262899 0.0091396789 30.540517 6.2428791e+10 6.2366686e+10 13.840884
18600 -29.253759 -29.269574 0.01581463 52.84507 6.2223448e+10 6.2165441e+10 57.800802
18700 -29.253759 -29.280514 0.026755117 89.403044 6.2076104e+10 6.2022224e+10 128.46082
18800 -29.253759 -29.294786 0.041027472 137.09456 6.1980858e+10 6.1930427e+10 219.28144
18900 -29.253759 -29.311091 0.057332365 191.57786 6.1927902e+10 6.1879682e+10 321.44654
19000 -29.253759 -29.327932 0.074172828 247.85078 6.1904521e+10 6.1856811e+10 424.935
19100 -29.253759 -29.343801 0.090041852 300.87761 6.1896231e+10 6.1846902e+10 519.70032
19200 -29.253759 -29.357361 0.10360217 346.18982 6.1887942e+10 6.1834406e+10 596.79434
19300 -29.253759 -29.367593 0.11383425 380.38063 6.1865031e+10 6.1804149e+10 649.29447
19400 -29.253759 -29.373894 0.12013535 401.43594 6.1814231e+10 6.1742208e+10 672.93539
19500 -29.253759 -29.37612 0.12236075 408.87221 6.1724294e+10 6.1636603e+10 666.39687
19600 -29.253759 -29.374566 0.12080701 403.68034 6.1586396e+10 6.1477781e+10 631.24827
19700 -29.253759 -29.369903 0.11614425 388.09956 6.1394308e+10 6.1258917e+10 571.59167
19800 -29.253759 -29.363069 0.10931013 365.26317 6.1144351e+10 6.0976023e+10 493.47418
19900 -29.253759 -29.35514 0.10138144 338.76918 6.0835203e+10 6.0627905e+10 404.15587
20000 -29.253759 -29.347199 0.093439728 312.23172 6.0467587e+10 6.0215993e+10 311.32317
20043 -29.253759 -29.344026 0.090267282 301.63089 6.0292085e+10 6.002012e+10 272.18496
Loop time of 1.02899 on 4 procs for 10000 steps with 128 atoms
Performance: 839654.865 fs/day, 0.000 hours/fs, 9718.228 timesteps/s, 1.244 Matom-step/s
91.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.42341 | 0.50618 | 0.59534 | 10.4 | 49.19
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.39233 | 0.48231 | 0.56438 | 10.7 | 46.87
Output | 0.0047128 | 0.0048033 | 0.0050386 | 0.2 | 0.47
Modify | 0.0052563 | 0.0055253 | 0.0058241 | 0.3 | 0.54
Other | | 0.03018 | | | 2.93
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 2416 ave 2582 max 2250 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 9664
Ave neighs/atom = 75.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

161
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@ -0,0 +1,161 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2bulk
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2bulk
Reading data file ...
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
1 by 2 by 2 MPI processor grid
reading atoms ...
13718 atoms
read_data CPU = 0.048 seconds
pair_style eff/cut 30.627847
pair_coeff * *
neigh_modify one 20000 page 200000
comm_modify vel yes
compute effTemp all temp/eff
thermo 100
thermo_style custom step pe temp press vol
thermo_modify temp effTemp
# structure minimization
dump 1 all xyz 1 ${sname}.min.xyz
dump 1 all xyz 1 h2bulk.min.xyz
min_style cg
minimize 0 1.0e-4 1 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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: 20000, page size: 200000
master list distance cutoff = 32.627847
ghost atom cutoff = 32.627847
binsize = 16.313924, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 87.11 | 93.61 | 100.1 Mbytes
Step PotEng Temp Press Volume
0 -2871.4801 0 2.8596879e+10 229847.29
1 -2872.8077 0 2.8046824e+10 229847.29
Loop time of 1.02378 on 4 procs for 1 steps with 13718 atoms
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2871.48013813359 -2871.48013813359 -2872.8076730722
Force two-norm initial, final = 5.4264823 5.0563616
Force max component initial, final = 0.21424475 0.19518835
Final line search alpha, max atom move = 0.046675588 0.0091105311
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.7704 | 0.89228 | 1.0165 | 11.0 | 87.16
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0028288 | 0.12705 | 0.24891 | 29.2 | 12.41
Output | 0.0037898 | 0.0038794 | 0.0039584 | 0.1 | 0.38
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0005774 | | | 0.06
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 65600.5 ave 67122 max 64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 59740807
Ave neighs/atom = 4354.9211
Neighbor list builds = 0
Dangerous builds = 0
undump 1
# create initial velocities according to temp, w/out e radial dof
velocity all create 20000.0 4928459 rot yes dist gaussian
# npt
fix 1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
variable density equal 11.2058851*mass(all)
thermo_style custom step pe temp press vol v_density
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify temp effTemp
dump 2 all xyz 10000 ${sname}.npt.xyz
dump 2 all xyz 10000 h2bulk.npt.xyz
compute 1 all property/atom spin eradius
dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
dump 3 all custom 10000 h2bulk.npt.lammpstrj id type x y z c_1[1] c_1[2]
thermo 1
run 10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 79.61 | 86.11 | 92.6 Mbytes
Step PotEng Temp Press Volume v_density
1 -2872.8077 40002.916 1.392533e+11 229847.29 154332.61
2 -2872.8075 40002.808 1.3925254e+11 229847.72 154332.61
3 -2872.8072 40002.493 1.3925022e+11 229849.01 154332.61
4 -2872.8068 40001.97 1.3924633e+11 229851.15 154332.61
5 -2872.8064 40001.241 1.3924088e+11 229854.15 154332.61
6 -2872.8058 40000.304 1.3923386e+11 229858.01 154332.61
7 -2872.8052 39999.161 1.3922528e+11 229862.72 154332.61
8 -2872.8045 39997.81 1.3921514e+11 229868.29 154332.61
9 -2872.8037 39996.253 1.3920343e+11 229874.72 154332.61
10 -2872.8028 39994.488 1.3919016e+11 229882.01 154332.61
11 -2872.8018 39992.517 1.3917533e+11 229890.15 154332.61
Loop time of 10.5538 on 4 procs for 10 steps with 13718 atoms
Performance: 81.866 fs/day, 0.293 hours/fs, 0.948 timesteps/s, 12.998 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.6596 | 9.2995 | 10.519 | 24.8 | 88.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.029706 | 1.2492 | 1.8893 | 67.7 | 11.84
Output | 0.00056676 | 0.00059312 | 0.00063847 | 0.0 | 0.01
Modify | 0.0017284 | 0.0019179 | 0.0020891 | 0.4 | 0.02
Other | | 0.002503 | | | 0.02
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 65600.5 ave 67122 max 64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 1.49356e+07 ave 1.64691e+07 max 1.33702e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 59742327
Ave neighs/atom = 4355.0319
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
undump 2
undump 3
Total wall time: 0:00:14

161
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@ -0,0 +1,161 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2bulk.ang
units real
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2bulk.ang
Reading data file ...
orthogonal box = (0 0 0) to (32.41512 32.41512 32.41512)
1 by 2 by 2 MPI processor grid
reading atoms ...
13718 atoms
read_data CPU = 0.039 seconds
pair_style eff/cut 16.207559818252903 limit/eradius pressure/evirials
pair_coeff * *
neigh_modify one 10000 page 100000
comm_modify vel yes
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable ecoul equal c_energies[3]
variable erres equal c_energies[4]
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
thermo_modify temp effTemp press effPress flush yes
# structure minimization
min_style cg
minimize 0 1.0e-4 10 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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: 10000, page size: 100000
master list distance cutoff = 18.20756
ghost atom cutoff = 18.20756
binsize = 9.1037799, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 99.9 | 106.9 | 113.6 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
0 -1801882.2 -1801882.2 0 1941449.2 111650.99 -3854982.4 0 169191.44 169191.44 0
10 -1812982.2 -1812982.2 0 2023531 93131.746 -3929644.9 0 204251.79 204251.79 0
Loop time of 11.8971 on 4 procs for 10 steps with 13718 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-1801882.20439777 -1811783.39715666 -1812982.21160594
Force two-norm initial, final = 4976.0965 945.50616
Force max component initial, final = 134.44103 23.528388
Final line search alpha, max atom move = 0.0010624281 0.024997221
Iterations, force evaluations = 10 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.9682 | 10.823 | 11.655 | 22.1 | 90.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.23254 | 1.0651 | 1.9201 | 70.3 | 8.95
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009102 | | | 0.08
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 75372.5 ave 75724 max 75002 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1.74322e+07 ave 1.91106e+07 max 1.57195e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 69728955
Ave neighs/atom = 5083.0263
Neighbor list builds = 0
Dangerous builds = 0
timestep 0.001
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
# nve
fix 1 all nve/eff
#fix 2 all imd 8888 trate 1 unwrap on nowait on
compute peatom all pe/atom
compute keatom all ke/atom/eff
dump 2 all xyz 1000 ${sname}.nve.xyz
dump 2 all xyz 1000 h2bulk.ang.nve.xyz
compute 1 all property/atom spin eradius
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
dump 3 all custom 1000 h2bulk.ang.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
run 10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 101 | 105.7 | 110.5 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
10 -995226.78 -1812982.2 817755.43 2023531 93131.746 -3929644.9 0 1301774.2 1301774.2 40002.916
20 -995226.78 -1812951.8 817725.06 2023530.9 93136.224 -3929618.9 0 1301757.1 1301757.1 40001.431
Loop time of 9.29954 on 4 procs for 10 steps with 13718 atoms
Performance: 0.000 ns/day, 258320.521 hours/ns, 1.075 timesteps/s, 14.751 katom-step/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.5126 | 8.8333 | 9.1491 | 9.5 | 94.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.14252 | 0.45853 | 0.77938 | 41.7 | 4.93
Output | 0.0046943 | 0.0047097 | 0.0047198 | 0.0 | 0.05
Modify | 0.00051144 | 0.00055804 | 0.00059726 | 0.0 | 0.01
Other | | 0.002462 | | | 0.03
Nlocal: 3429.5 ave 3610 max 3249 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 75372.5 ave 75553 max 75192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.74471e+07 ave 1.82017e+07 max 1.66315e+07 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 69788395
Ave neighs/atom = 5087.3593
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
#unfix 2
undump 2
undump 3
Total wall time: 0:00:24

150
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.g++.4 Normal file
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@ -0,0 +1,150 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2bulk
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2bulk
Reading data file ...
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
1 by 2 by 2 MPI processor grid
reading atoms ...
13718 atoms
read_data CPU = 0.036 seconds
pair_style eff/cut 30.627847
pair_coeff * *
neigh_modify one 10000 page 100000
comm_modify vel yes
compute effTemp all temp/eff
thermo 10
thermo_style custom step pe temp press
thermo_modify temp effTemp
# structure minimization
min_style cg
minimize 0 1.0e-4 10 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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: 10000, page size: 100000
master list distance cutoff = 32.627847
ghost atom cutoff = 32.627847
binsize = 16.313924, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 86.33 | 92.54 | 98.55 Mbytes
Step PotEng Temp Press
0 -2871.4801 0 2.8596879e+10
10 -2882.3401 0 2.1869586e+10
Loop time of 11.6123 on 4 procs for 10 steps with 13718 atoms
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2871.48013813359 -2881.24844591398 -2882.34005034714
Force two-norm initial, final = 5.4264823 1.3218657
Force max component initial, final = 0.21424475 0.025681865
Final line search alpha, max atom move = 0.4402147 0.011305535
Iterations, force evaluations = 10 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.2083 | 10.221 | 11.528 | 31.2 | 88.02
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.07895 | 1.3856 | 2.3982 | 84.8 | 11.93
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005564 | | | 0.05
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 65600.5 ave 67122 max 64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 59740807
Ave neighs/atom = 4354.9211
Neighbor list builds = 0
Dangerous builds = 0
timestep 0.001
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
# nve
fix 1 all nve/eff
#fix 2 all imd 8888 trate 1 unwrap on nowait on
compute peatom all pe/atom
compute keatom all ke/atom/eff
dump 2 all xyz 1000 ${sname}.nve.xyz
dump 2 all xyz 1000 h2bulk.nve.xyz
compute 1 all property/atom spin eradius
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
dump 3 all custom 1000 h2bulk.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
run 10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 82.52 | 87.21 | 91.69 Mbytes
Step PotEng Temp Press
10 -2882.3401 40002.916 1.3307606e+11
20 -2882.2908 40001.405 1.3306905e+11
Loop time of 9.25154 on 4 procs for 10 steps with 13718 atoms
Performance: 93.390 fs/day, 0.257 hours/fs, 1.081 timesteps/s, 14.828 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.2948 | 8.675 | 8.9946 | 10.1 | 93.77
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.2531 | 0.57292 | 0.9531 | 39.5 | 6.19
Output | 3.7757e-05 | 5.7819e-05 | 7.5679e-05 | 0.0 | 0.00
Modify | 0.0005098 | 0.0005357 | 0.00055895 | 0.0 | 0.01
Other | | 0.002988 | | | 0.03
Nlocal: 3429.5 ave 3610 max 3249 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 65600.5 ave 66951 max 64250 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.49409e+07 ave 1.56765e+07 max 1.41457e+07 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 59763523
Ave neighs/atom = 4356.577
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
#unfix 2
undump 2
undump 3
Total wall time: 0:00:23

111
examples/PACKAGES/eff/Li-dendritic/log.01Feb25.Li-dendritic.min.g++.4 Normal file
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@ -0,0 +1,111 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li-dendritic
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.Li-dendritic
Reading data file ...
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
1 by 2 by 2 MPI processor grid
reading atoms ...
3456 atoms
read_data CPU = 0.023 seconds
#read_restart ${sname}.min.restart2
pair_style eff/cut 50.112
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
thermo 10
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
compute 1 all property/atom spin eradius
dump 1 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
dump 1 all custom 10 Li-dendritic.min.lammpstrj id type q c_1[1] c_1[2] x y z
dump 2 all xyz 10 ${sname}.min.xyz
dump 2 all xyz 10 Li-dendritic.min.xyz
restart 10 ${sname}.nve.restart1 ${sname}.nve.restart2
restart 10 Li-dendritic.nve.restart1 ${sname}.nve.restart2
restart 10 Li-dendritic.nve.restart1 Li-dendritic.nve.restart2
#min_style cg
#min_modify line quadratic dmax 2.0
#minimize 0.0 1.0e-5 10000 100000
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all nve/eff
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 52.112
ghost atom cutoff = 52.112
binsize = 26.056, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.4 | 11.59 | 11.78 Mbytes
Step TotEng PotEng KinEng Temp Press
0 -5167.408 -5172.3316 4.9236061 1201.0429 -1.5761339e+09
10 -5167.408 -5172.3292 4.9211748 1200.4498 -1.5762759e+09
20 -5167.408 -5172.3219 4.9139105 1198.6778 -1.5767007e+09
30 -5167.408 -5172.3099 4.9019017 1195.7484 -1.5774041e+09
40 -5167.408 -5172.2933 4.885295 1191.6974 -1.5783794e+09
50 -5167.408 -5172.2723 4.8642936 1186.5744 -1.5796171e+09
60 -5167.408 -5172.2471 4.839155 1180.4422 -1.5811053e+09
70 -5167.408 -5172.2182 4.8101883 1173.3762 -1.5828297e+09
80 -5167.408 -5172.1857 4.7777514 1165.4637 -1.5847737e+09
90 -5167.408 -5172.1502 4.7422469 1156.8029 -1.5869184e+09
100 -5167.408 -5172.1121 4.7041183 1147.502 -1.5892434e+09
Loop time of 9.14099 on 4 procs for 100 steps with 3456 atoms
Performance: 945.193 fs/day, 0.025 hours/fs, 10.940 timesteps/s, 37.808 katom-step/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 | 7.0683 | 7.7216 | 8.7585 | 22.7 | 84.47
Neigh | 0.24686 | 0.25299 | 0.2618 | 1.2 | 2.77
Comm | 0.079533 | 1.1252 | 1.784 | 60.0 | 12.31
Output | 0.035036 | 0.03505 | 0.03506 | 0.0 | 0.38
Modify | 0.0014139 | 0.0014999 | 0.0015446 | 0.1 | 0.02
Other | | 0.004642 | | | 0.05
Nlocal: 864 ave 888 max 851 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 17185 ave 17198 max 17161 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 890568 ave 965810 max 799750 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 3562272
Ave neighs/atom = 1030.75
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:09

178
examples/PACKAGES/eff/Li-dendritic/log.01Feb25.Li-dendritic.nvt.g++.4 Normal file
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@ -0,0 +1,178 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li-dendritic
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.Li-dendritic
Reading data file ...
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
1 by 2 by 2 MPI processor grid
reading atoms ...
3456 atoms
read_data CPU = 0.016 seconds
#read_restart ${sname}.min.restart
pair_style eff/cut 50.112
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 10
thermo_style custom step pe temp press
thermo_modify temp effTemp press effPress
print "Starting minimizer"
Starting minimizer
min_style cg
compute 1 all property/atom spin eradius
#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
#dump 2 all xyz 100 ${sname}.min.xyz
min_modify line quadratic dmax 0.05
minimize 0 1.0e-7 100 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 52.112
ghost atom cutoff = 52.112
binsize = 26.056, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 14.88 | 15.07 | 15.26 Mbytes
Step PotEng Temp Press
0 -5172.3316 0 -1.6720594e+09
10 -5199.5494 0 -1.6721099e+09
20 -5220.9343 0 -1.6720299e+09
30 -5238.4037 0 -1.6694987e+09
40 -5252.5928 0 -1.6515154e+09
50 -5263.7845 0 -1.5851579e+09
60 -5271.8051 0 -1.4304709e+09
70 -5275.1692 0 -1.2764647e+09
80 -5276.9804 0 -1.1135845e+09
87 -5277.5186 0 -1.0157231e+09
Loop time of 9.1237 on 4 procs for 87 steps with 3456 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-5172.33158699748 -5277.50851484438 -5277.51857905665
Force two-norm initial, final = 10.47944 0.61719987
Force max component initial, final = 0.33333431 0.020508985
Final line search alpha, max atom move = 0.48148149 0.0098746969
Iterations, force evaluations = 87 101
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.2296 | 8.0451 | 8.9943 | 23.5 | 88.18
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11943 | 1.0682 | 1.8834 | 64.3 | 11.71
Output | 0.00021247 | 0.00022521 | 0.00026234 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01011 | | | 0.11
Nlocal: 864 ave 864 max 864 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 17185 ave 17185 max 17185 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 890568 ave 968400 max 812736 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 3562272
Ave neighs/atom = 1030.75
Neighbor list builds = 0
Dangerous builds = 0
write_restart ${sname}.min.restart
write_restart Li-dendritic.min.restart
System init for write_restart ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
#undump 1
#undump 2
# NVT
reset_timestep 0
timestep 0.005
print "Starting nvt"
Starting nvt
fix 1 all nvt/eff temp 300.0 300.0 0.1
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
dump 1 all custom 100 Li-dendritic.nvt.lammpstrj id type x y z c_1[1] c_1[2]
dump 2 all xyz 100 ${sname}.nvt.xyz
dump 2 all xyz 100 Li-dendritic.nvt.xyz
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
restart 100 Li-dendritic.nvt.restart1 ${sname}.nvt.restart2
restart 100 Li-dendritic.nvt.restart1 Li-dendritic.nvt.restart2
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.9 | 12.09 | 12.28 Mbytes
Step PotEng Temp Press
0 -5277.5186 0 -1.0157231e+09
10 -5277.5187 0.028803274 -1.0157155e+09
20 -5277.519 0.12372272 -1.0156917e+09
30 -5277.5195 0.29618333 -1.0156507e+09
40 -5277.5201 0.55263617 -1.0155924e+09
50 -5277.5206 0.8932531 -1.0155176e+09
60 -5277.521 1.3127021 -1.015428e+09
70 -5277.5211 1.8037418 -1.0153251e+09
80 -5277.5208 2.3644081 -1.0152094e+09
90 -5277.52 3.0093875 -1.0150781e+09
100 -5277.5187 3.7858675 -1.0149239e+09
Loop time of 8.47644 on 4 procs for 100 steps with 3456 atoms
Performance: 5096.477 fs/day, 0.005 hours/fs, 11.797 timesteps/s, 40.772 katom-step/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 | 6.8234 | 7.537 | 8.2853 | 24.1 | 88.92
Neigh | 0.023585 | 0.024246 | 0.024867 | 0.4 | 0.29
Comm | 0.15595 | 0.90456 | 1.6184 | 69.6 | 10.67
Output | 0.0032476 | 0.0032612 | 0.0032984 | 0.0 | 0.04
Modify | 0.0036078 | 0.0037554 | 0.0039448 | 0.2 | 0.04
Other | | 0.003634 | | | 0.04
Nlocal: 864 ave 881 max 834 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 17185 ave 17215 max 17168 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Neighs: 890568 ave 976912 max 789323 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 3562272
Ave neighs/atom = 1030.75
Neighbor list builds = 1
Dangerous builds = 0
undump 1
undump 2
Total wall time: 0:00:17

155
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.ang.g++.4 Normal file
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@ -0,0 +1,155 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li.ang
units real
newton on
boundary p p p
dielectric 1.0
atom_style electron
read_data data.${sname}
read_data data.Li.ang
Reading data file ...
orthogonal box = (0 0 0) to (22.098442 22.098442 22.098442)
1 by 2 by 2 MPI processor grid
reading atoms ...
2000 atoms
read_data CPU = 0.014 seconds
#read_restart ${sname}.min.restart
pair_style eff/cut 11.049221 limit/eradius pressure/evirials
pair_coeff * *
comm_modify vel yes
neigh_modify one 2000 page 20000
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable ecoul equal c_energies[3]
variable erres equal c_energies[4]
thermo 100
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
thermo_modify temp effTemp press effPress flush yes
#min_style cg
#minimize 0 1e-6 100 1000
#write_restart ${sname}.min.restart
timestep 0.005
velocity all create 10.0 4928459 rot yes mom yes dist gaussian
fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
fix 1 all nve/eff
run 200
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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: 20000
master list distance cutoff = 13.049221
ghost atom cutoff = 13.049221
binsize = 6.5246105, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.772 | 6.887 | 7.001 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
0 -1934872.7 -1934932.3 59.586393 1973239.1 9338.8528 -3917510.2 0 119790.47 119790.47 40.06012
100 -1932300.8 -1934539.4 2238.5734 1864086.1 9857.8379 -3808483.3 0 -100104.15 -105089 1505
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
Loop time of 6.61662 on 4 procs for 200 steps with 2000 atoms
Performance: 0.013 ns/day, 1837.949 hours/ns, 30.227 timesteps/s, 60.454 katom-step/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.572 | 5.9389 | 6.2372 | 9.8 | 89.76
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.37051 | 0.66886 | 1.0359 | 29.2 | 10.11
Output | 0.00076947 | 0.00078111 | 0.00081552 | 0.0 | 0.01
Modify | 0.0035517 | 0.0038042 | 0.0040517 | 0.4 | 0.06
Other | | 0.004249 | | | 0.06
Nlocal: 500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 10252 ave 10252 max 10252 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 424625 ave 448237 max 400021 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 1698500
Ave neighs/atom = 849.25
Neighbor list builds = 0
Dangerous builds = 0
unfix 0
unfix 1
fix 1 all nvt/eff temp 3000.0 3000.0 100.0
compute 1 all property/atom spin eradius ervel
dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
dump 1 all custom 500 Li.ang.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
run 500
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.522 | 7.656 | 7.751 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
300 -1929902.8 -1934223.4 4320.5724 2031898.3 11427.685 -3977549.4 0 268725.75 262717.84 2904.7345
400 -1929360.3 -1935088.8 5728.4403 1850892.1 13473.172 -3799454 0 -105609.57 -118457.31 3851.2485
500 -1929066.1 -1935648.1 6581.9291 1901305.5 14887.365 -3851840.9 0 7045.2102 -9644.887 4425.0518
600 -1929593.6 -1934406.5 4812.986 2003446.8 16194.971 -3954048.4 0 221662.39 211620.13 3235.7857
700 -1930061.3 -1933572.3 3510.9499 1811788.7 18436.004 -3763797 0 -182749.21 -186750.23 2360.4227
Loop time of 16.6082 on 4 procs for 500 steps with 2000 atoms
Performance: 0.013 ns/day, 1845.351 hours/ns, 30.106 timesteps/s, 60.211 katom-step/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 | 12.79 | 14.632 | 16.232 | 32.8 | 88.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.35155 | 1.9504 | 3.7924 | 89.8 | 11.74
Output | 0.0034195 | 0.0035878 | 0.0038027 | 0.3 | 0.02
Modify | 0.01108 | 0.011237 | 0.0114 | 0.1 | 0.07
Other | | 0.01046 | | | 0.06
Nlocal: 500 ave 520 max 480 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 10252 ave 10272 max 10232 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 426287 ave 457559 max 396571 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 1705148
Ave neighs/atom = 852.574
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:23

166
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.bohr.g++.4 Normal file
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@ -0,0 +1,166 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li.bohr
units electron
newton off
boundary p p p
dielectric 1.0
atom_style electron
read_data data.${sname}
read_data data.Li.bohr
Reading data file ...
orthogonal box = (0 0 0) to (41.76 41.76 41.76)
2 by 1 by 2 MPI processor grid
reading atoms ...
2000 atoms
read_data CPU = 0.006 seconds
pair_style eff/cut 20.88 limit/eradius pressure/evirials
pair_coeff * *
comm_modify vel yes
neigh_modify one 2000 page 20000
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain press v_press temp
thermo_modify temp effTemp press effPress
min_style cg
minimize 0 1e-6 100 200
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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: 20000
master list distance cutoff = 22.88
ghost atom cutoff = 22.88
binsize = 11.44, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton off
pair build: half/bin/atomonly/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.51 | 9.51 | 9.51 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
0 -3083.509 -3083.509 0 3144.5578 14.882406 -6242.9492 0 1.2112606e+10 1.2112606e+10 0
10 -3085.4657 -3085.4657 0 3062.6201 21.113244 -6169.199 0 1.797769e+09 1.797769e+09 0
20 -3085.9152 -3085.9152 0 3063.3218 21.843788 -6171.0808 0 1.9306772e+09 1.9306772e+09 0
30 -3086.103 -3086.103 0 3065.4937 21.7953 -6173.392 0 2.1693045e+09 2.1693045e+09 0
40 -3086.2065 -3086.2065 0 3062.3955 22.002457 -6170.6045 0 1.7527596e+09 1.7527596e+09 0
50 -3086.2558 -3086.2558 0 3059.7162 22.165243 -6168.1372 0 1.4005967e+09 1.4005967e+09 0
60 -3086.2823 -3086.2823 0 3061.7509 22.016476 -6170.0497 0 1.6419693e+09 1.6419693e+09 0
70 -3086.3068 -3086.3068 0 3063.1496 22.125331 -6171.5817 0 1.8371954e+09 1.8371954e+09 0
80 -3086.3286 -3086.3286 0 3063.4058 22.112083 -6171.8465 0 1.8595352e+09 1.8595352e+09 0
90 -3086.342 -3086.342 0 3062.6876 22.145517 -6171.1752 0 1.761838e+09 1.761838e+09 0
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
Loop time of 9.51021 on 4 procs for 100 steps with 2000 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-3083.5089570212 -3086.34842671529 -3086.34926128553
Force two-norm initial, final = 3.4238461 0.15353209
Force max component initial, final = 0.15119069 0.017560878
Final line search alpha, max atom move = 0.75419179 0.01324427
Iterations, force evaluations = 100 191
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.8842 | 9.0722 | 9.2808 | 5.4 | 95.39
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.04463 | 0.04473 | 0.04481 | 0.0 | 0.47
Output | 0.00071317 | 0.00073223 | 0.0007793 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.3926 | | | 4.13
Nlocal: 500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 10252 ave 10252 max 10252 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 648158 ave 648158 max 648158 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2592632
Ave neighs/atom = 1296.316
Neighbor list builds = 0
Dangerous builds = 0
fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
compute 1 all property/atom spin eradius
dump 1 all custom 100 ${sname}.spe.lammpstrj id type q c_1[1] c_1[2] x y z
dump 1 all custom 100 Li.bohr.spe.lammpstrj id type q c_1[1] c_1[2] x y z
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.76 | 8.76 | 8.76 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
110 -3085.709 -3086.35 0.64098668 3062.5195 22.168933 -6171.0384 0 1.9130428e+09 1.8610249e+09 270.41729
120 -3084.995 -3086.3497 1.3546418 3064.69 22.151949 -6173.1916 0 2.3968054e+09 2.2869572e+09 571.49172
130 -3084.2774 -3086.3449 2.0675114 3067.5683 22.125927 -6176.0391 0 2.9762332e+09 2.8088108e+09 872.23471
140 -3083.5543 -3086.3327 2.7783319 3071.0091 22.090343 -6179.4321 0 3.6318905e+09 3.4073653e+09 1172.1133
150 -3082.8209 -3086.3101 3.4891918 3074.9323 22.044189 -6183.2866 0 4.3538347e+09 4.0726292e+09 1472.0085
160 -3082.0735 -3086.274 4.2005492 3079.2855 21.986186 -6187.5458 0 5.1353281e+09 4.7979569e+09 1772.1135
170 -3081.3099 -3086.2215 4.911672 3084.0302 21.914874 -6192.1667 0 5.9710184e+09 5.5781934e+09 2072.1196
180 -3080.5276 -3086.1495 5.6218934 3089.1358 21.828679 -6197.1139 0 6.8564778e+09 6.4091119e+09 2371.7454
190 -3079.7237 -3086.0546 6.330928 3094.5768 21.725972 -6202.3574 0 7.787914e+09 7.2871001e+09 2670.8705
200 -3078.895 -3085.9337 7.0387107 3100.3318 21.605131 -6207.8707 0 8.7619059e+09 8.2089091e+09 2969.4675
Loop time of 5.34836 on 4 procs for 100 steps with 2000 atoms
Performance: 1615.450 fs/day, 0.015 hours/fs, 18.697 timesteps/s, 37.395 katom-step/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8621 | 5.065 | 5.2272 | 5.9 | 94.70
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.02486 | 0.025085 | 0.025316 | 0.1 | 0.47
Output | 0.0016755 | 0.0018282 | 0.0019368 | 0.2 | 0.03
Modify | 0.092978 | 0.25534 | 0.4584 | 26.2 | 4.77
Other | | 0.00111 | | | 0.02
Nlocal: 500 ave 518 max 484 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 10252 ave 10268 max 10234 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 621113 ave 642857 max 604509 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 2484453
Ave neighs/atom = 1242.2265
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:15

1165
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158
examples/PACKAGES/eff/fixed-core/C2H6/log.01Feb25.C2H6fc.bohr.g++.4 Normal file
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@ -0,0 +1,158 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2010-12-13
# General parameters
variable sname index C2H6fc.bohr
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
read_data data.C2H6fc.bohr
Reading data file ...
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
1 by 2 by 2 MPI processor grid
reading atoms ...
22 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 1000.0
pair_coeff * *
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
comm_modify vel yes
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
# Minimization
min_style cg
dump 1 all xyz 10 ${sname}.min.xyz
dump 1 all xyz 10 C2H6fc.bohr.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 10 C2H6fc.bohr.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 3 all custom 10 data.${sname}.restart id type q c_1[1] c_1[2] x y z
dump 3 all custom 10 data.C2H6fc.bohr.restart id type q c_1[1] c_1[2] x y z
min_modify line quadratic
minimize 0 1e-6 1000 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 1002
ghost atom cutoff = 1002
binsize = 501, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.129 | 6.129 | 6.129 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -67.202286 -67.202286 0 65.187662 2.0185521 -134.4085 0 0 15.150502 15.150502
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005462 -0.00017005462
Loop time of 0.00261219 on 4 procs for 48 steps with 22 atoms
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-67.202286382145 -67.2023415752272 -67.2023415752273
Force two-norm initial, final = 0.0096326869 5.0767445e-07
Force max component initial, final = 0.0062811481 1.588169e-07
Final line search alpha, max atom move = 1 1.588169e-07
Iterations, force evaluations = 48 94
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00010749 | 0.00066682 | 0.0010722 | 0.0 | 25.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0005904 | 0.0010031 | 0.0015945 | 1.2 | 38.40
Output | 0.00029404 | 0.00030533 | 0.0003226 | 0.0 | 11.69
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0006369 | | | 24.38
Nlocal: 5.5 ave 6 max 5 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 16.5 ave 17 max 16 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 57.75 ave 92 max 13 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 231
Ave neighs/atom = 10.5
Neighbor list builds = 0
Dangerous builds = 0
undump 1
undump 2
undump 3
fix 1 all nvt/eff temp 1 2000 1.0
dump 2 all custom 10 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 10 C2H6fc.bohr.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
run 10000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.738 | 5.738 | 5.738 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005463 -0.00017005463
10048 -67.202342 -67.202342 1.2683664e-08 65.186455 2.0144921 -134.40329 0 0.00038144568 -0.070540027 -0.070540735
Loop time of 0.194625 on 4 procs for 10000 steps with 22 atoms
Performance: 4439300.953 fs/day, 0.000 hours/fs, 51380.798 timesteps/s, 1.130 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0161 | 0.064789 | 0.10999 | 14.0 | 33.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.031236 | 0.07675 | 0.12576 | 13.2 | 39.43
Output | 0.01923 | 0.021471 | 0.025663 | 1.7 | 11.03
Modify | 0.011945 | 0.014438 | 0.017136 | 1.6 | 7.42
Other | | 0.01718 | | | 8.83
Nlocal: 5.5 ave 7 max 4 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 16.5 ave 18 max 15 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 57.75 ave 98 max 16 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 231
Ave neighs/atom = 10.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

40165
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.ang.g++.4 Normal file
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File diff suppressed because it is too large Load Diff

4166
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.bohr.g++.4 Normal file
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File diff suppressed because it is too large Load Diff

100
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.spe.ang.g++.4 Normal file
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@ -0,0 +1,100 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2010-11-28
# General parameters
variable sname index CH4fc.ang
units real
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.CH4fc.ang
Reading data file ...
orthogonal box = (-529.17725 -529.17725 -529.17725) to (529.17725 529.17725 529.17725)
2 by 1 by 2 MPI processor grid
reading atoms ...
13 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
pair_coeff * *
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
comm_modify vel yes
timestep 0.0001
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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 = 1002
ghost atom cutoff = 1002
binsize = 501, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.387 | 4.387 | 4.387 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -17700.537 -17700.537 0 20676.282 6270.6707 -44647.489 0 0 0.21737096 0.21737096
Loop time of 2.41775e-06 on 4 procs for 0 steps with 13 atoms
113.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.418e-06 | | |100.00
Nlocal: 3.25 ave 4 max 3 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 152.75 ave 153 max 152 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 19.5 ave 33 max 6 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 78
Ave neighs/atom = 6
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

99
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.spe.bohr.g++.4 Normal file
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@ -0,0 +1,99 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2010-11-28
# General parameters
variable sname index CH4fc.bohr
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.CH4fc.bohr
Reading data file ...
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
1 by 2 by 2 MPI processor grid
reading atoms ...
13 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
pair_coeff * *
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
comm_modify vel yes
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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 = 1002
ghost atom cutoff = 1002
binsize = 501, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.388 | 4.388 | 4.388 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -28.207572 -28.207572 0 32.949786 9.9929585 -71.150317 0 0 22025.158 22025.158
Loop time of 2.353e-06 on 4 procs for 0 steps with 13 atoms
53.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.353e-06 | | |100.00
Nlocal: 3.25 ave 4 max 3 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 152.75 ave 153 max 152 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 19.5 ave 31 max 10 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 78
Ave neighs/atom = 6
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

27
examples/reaxff/RDX/log.30Nov23.RDX.g++.1 → examples/reaxff/RDX/log.1Feb25.RDX.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
@ -13,7 +12,7 @@ Reading data file ...
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
read_data CPU = 0.012 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.rdx H C O N
@ -70,7 +69,7 @@ Neighbor list info ...
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
pair build: half/bin/ghost/newtoff
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
@ -111,20 +110,20 @@ Per MPI rank memory allocation (min/avg/max) = 16.3 | 16.3 | 16.3 Mbytes
2800 481.73908 -10082.193 0 -9932.852 -27.838881
2900 487.56555 -10082.752 0 -9931.6045 1772.2131
3000 510.30601 -10091.368 0 -9933.1706 1273.0501
Loop time of 5.35022 on 1 procs for 3000 steps with 105 atoms
Loop time of 3.73297 on 1 procs for 3000 steps with 105 atoms
Performance: 12.112 ns/day, 1.982 hours/ns, 560.725 timesteps/s, 58.876 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 17.359 ns/day, 1.383 hours/ns, 803.649 timesteps/s, 84.383 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 | 4.7927 | 4.7927 | 4.7927 | 0.0 | 89.58
Neigh | 0.15169 | 0.15169 | 0.15169 | 0.0 | 2.84
Comm | 0.011036 | 0.011036 | 0.011036 | 0.0 | 0.21
Output | 0.00080628 | 0.00080628 | 0.00080628 | 0.0 | 0.02
Modify | 0.3906 | 0.3906 | 0.3906 | 0.0 | 7.30
Other | | 0.003436 | | | 0.06
Pair | 3.323 | 3.323 | 3.323 | 0.0 | 89.02
Neigh | 0.098934 | 0.098934 | 0.098934 | 0.0 | 2.65
Comm | 0.0060071 | 0.0060071 | 0.0060071 | 0.0 | 0.16
Output | 0.00048946 | 0.00048946 | 0.00048946 | 0.0 | 0.01
Modify | 0.30295 | 0.30295 | 0.30295 | 0.0 | 8.12
Other | | 0.001559 | | | 0.04
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -137,4 +136,4 @@ Total # of neighbors = 3065
Ave neighs/atom = 29.190476
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:05
Total wall time: 0:00:03

139
examples/reaxff/RDX/log.1Feb25.RDX.g++.4 Normal file
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@ -0,0 +1,139 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
units real
atom_style charge
read_data data.RDX
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.rdx H C O N
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.rdx
run 3000
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}
}
- fix qeq/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,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
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 qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.78 | 11.56 | 12.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
100 47.478568 -10176.425 0 -10161.706 633.00869
200 166.95267 -10181.513 0 -10129.757 -27.201454
300 142.53607 -10148.039 0 -10103.852 5120.6542
400 322.68532 -10178.868 0 -10078.834 2342.957
500 193.81485 -10117.984 0 -10057.901 8412.6921
600 300.27212 -10134.473 0 -10041.388 -2801.7705
700 272.6339 -10110.146 0 -10025.628 10749.262
800 339.99701 -10114.123 0 -10008.723 5123.3071
900 231.65605 -10068.587 0 -9996.7728 5306.5428
1000 329.93457 -10088.778 0 -9986.4964 3190.7822
1100 376.61097 -10092.399 0 -9975.6475 2921.8154
1200 361.98407 -10076.598 0 -9964.3813 3613.8142
1300 358.66787 -10069.369 0 -9958.1801 4341.836
1400 470.15712 -10098.554 0 -9952.8032 -146.37541
1500 509.64688 -10106.577 0 -9948.5846 2355.8342
1600 417.94216 -10075.288 0 -9945.7246 1758.8486
1700 453.28944 -10084.351 0 -9943.8294 -570.98573
1800 472.90567 -10087.824 0 -9941.2211 1541.9022
1900 507.19643 -10096.443 0 -9939.2104 -441.97035
2000 443.66882 -10076.87 0 -9939.3312 -131.88097
2100 485.44927 -10088.414 0 -9937.9225 -632.00796
2200 507.55973 -10095.16 0 -9937.8139 1222.9997
2300 496.62243 -10089.722 0 -9935.7672 42.209939
2400 455.56537 -10077.338 0 -9936.1111 1335.7712
2500 512.89536 -10094.239 0 -9935.2396 -593.65834
2600 440.18205 -10070.5 0 -9934.0422 613.18152
2700 501.65067 -10088.403 0 -9932.8889 430.74811
2800 485.3846 -10083.269 0 -9932.7982 715.15642
2900 489.47747 -10083.355 0 -9931.6151 1845.1781
3000 501.34719 -10088.58 0 -9933.1605 2209.09
Loop time of 1.90582 on 4 procs for 3000 steps with 105 atoms
Performance: 34.001 ns/day, 0.706 hours/ns, 1574.129 timesteps/s, 165.284 katom-step/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3982 | 1.4628 | 1.4959 | 3.2 | 76.75
Neigh | 0.048259 | 0.056611 | 0.066179 | 2.7 | 2.97
Comm | 0.059452 | 0.092743 | 0.15695 | 12.5 | 4.87
Output | 0.00028355 | 0.00033432 | 0.00048015 | 0.0 | 0.02
Modify | 0.28239 | 0.29189 | 0.30051 | 1.2 | 15.32
Other | | 0.001446 | | | 0.08
Nlocal: 26.25 ave 46 max 8 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 399.5 ave 512 max 288 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1011.75 ave 1820 max 420 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4047
Ave neighs/atom = 38.542857
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:01

140
examples/reaxff/RDX/log.30Nov23.RDX.g++.4
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@ -1,140 +0,0 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
units real
atom_style charge
read_data data.RDX
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.rdx H C O N
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.rdx
run 3000
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}
}
- fix qeq/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,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.78 | 11.56 | 12.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
100 47.47852 -10176.425 0 -10161.706 632.97359
200 166.95287 -10181.513 0 -10129.757 -27.146803
300 142.53582 -10148.039 0 -10103.852 5120.6397
400 322.68523 -10178.868 0 -10078.834 2342.7187
500 193.81484 -10117.984 0 -10057.901 8412.4559
600 300.27165 -10134.473 0 -10041.388 -2801.9143
700 272.63408 -10110.146 0 -10025.629 10749.2
800 339.99669 -10114.123 0 -10008.723 5123.2489
900 231.65632 -10068.587 0 -9996.7729 5306.0392
1000 329.93324 -10088.777 0 -9986.4967 3190.4707
1100 376.60924 -10092.398 0 -9975.6478 2920.8475
1200 361.98231 -10076.598 0 -9964.3816 3612.0573
1300 358.6599 -10069.366 0 -9958.1803 4341.9871
1400 470.14856 -10098.552 0 -9952.8036 -146.9069
1500 509.6454 -10106.577 0 -9948.5847 2355.4022
1600 417.9276 -10075.284 0 -9945.7249 1749.565
1700 453.25817 -10084.343 0 -9943.8306 -570.48011
1800 472.9517 -10087.84 0 -9941.2226 1532.6424
1900 507.14171 -10096.428 0 -9939.212 -404.84948
2000 443.62843 -10076.86 0 -9939.3329 -132.17302
2100 485.441 -10088.414 0 -9937.925 -609.75758
2200 507.23914 -10095.067 0 -9937.8209 1288.5372
2300 499.64956 -10090.665 0 -9935.7719 149.06622
2400 457.97848 -10078.107 0 -9936.1317 2065.2075
2500 510.58254 -10093.537 0 -9935.2543 -559.75965
2600 440.97503 -10070.865 0 -9934.1605 1164.1078
2700 500.4945 -10088.165 0 -9933.0096 1051.9016
2800 485.77814 -10083.543 0 -9932.9498 294.64404
2900 487.73983 -10082.939 0 -9931.7373 2208.263
3000 504.69717 -10089.803 0 -9933.3447 1723.6386
Loop time of 2.81192 on 4 procs for 3000 steps with 105 atoms
Performance: 23.045 ns/day, 1.041 hours/ns, 1066.887 timesteps/s, 112.023 katom-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 | 2.0513 | 2.1567 | 2.2232 | 4.3 | 76.70
Neigh | 0.072125 | 0.087048 | 0.10214 | 3.7 | 3.10
Comm | 0.086792 | 0.15326 | 0.25749 | 16.2 | 5.45
Output | 0.00058533 | 0.00064027 | 0.00080207 | 0.0 | 0.02
Modify | 0.39587 | 0.41124 | 0.42647 | 1.7 | 14.62
Other | | 0.003062 | | | 0.11
Nlocal: 26.25 ave 46 max 8 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 399.5 ave 512 max 288 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1011.25 ave 1819 max 420 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4045
Ave neighs/atom = 38.52381
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:02

144
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@ -0,0 +1,144 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.000 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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 = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.86 | 13.86 | 13.86 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79932 0 168.88397 12
10 1288.6114 -1989.6644 -1912.8422 -19456.349 -2734.6769 -15.607218 0.20177961 0 54.629555 3.1252297 -77.7067 0 14.933901 -5.810854 843.92074 -180.43322 0 107.75935 8
20 538.95852 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.9078343 0.077926704 0 81.610044 0.22951937 -57.557105 0 30.331203 -10.178049 878.99016 -159.69263 0 89.316862 7
30 463.09515 -1933.5765 -1905.9685 -33255.499 -2749.8591 -8.0154635 0.02762867 0 81.627413 0.1197239 -50.262272 0 20.82032 -9.632703 851.88721 -149.49497 0 79.205707 8
40 885.49689 -1958.9125 -1906.1226 -4814.6325 -2795.644 9.1505916 0.13747481 0 70.948074 0.24360544 -57.862695 0 19.076518 -11.14121 873.73893 -159.9939 0 92.434061 11
50 861.16008 -1954.4602 -1903.1211 -1896.648 -2784.8451 3.8269988 0.1579331 0 79.851597 3.349208 -78.066133 0 32.628942 -7.9565363 872.8186 -190.98572 0 114.76001 10
60 1167.7831 -1971.8435 -1902.2247 -3482.927 -2705.8639 -17.121541 0.22749081 0 44.507721 7.8559737 -74.789039 0 16.2565 -4.6046718 835.8307 -188.33687 0 114.19412 10
70 1439.9897 -1989.3024 -1903.4557 23845.83 -2890.7894 31.958658 0.26671716 0 85.758318 3.1804201 -71.002959 0 24.35723 -10.31128 905.86819 -175.38505 0 106.79678 10
80 502.39931 -1930.7551 -1900.804 -20356.375 -2703.8109 -18.66274 0.1128617 0 99.80351 2.0329611 -76.171312 0 19.236815 -6.2786426 826.47424 -166.03148 0 92.539616 9
90 749.08601 -1946.984 -1902.3264 17798.716 -2863.7585 42.068606 0.24338046 0 96.181674 0.96183581 -69.955564 0 24.615514 -11.582742 903.68878 -190.13822 0 120.69121 11
100 1109.6946 -1968.588 -1902.4322 -4490.4001 -2755.899 -7.1224954 0.21757676 0 61.805955 7.0825894 -75.645488 0 20.115437 -6.2372635 863.56481 -198.56946 0 122.09935 10
Loop time of 0.0692709 on 1 procs for 100 steps with 21 atoms
Performance: 124.728 ns/day, 0.192 hours/ns, 1443.607 timesteps/s, 30.316 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 | 0.060491 | 0.060491 | 0.060491 | 0.0 | 87.33
Neigh | 0.0031331 | 0.0031331 | 0.0031331 | 0.0 | 4.52
Comm | 0.00016256 | 0.00016256 | 0.00016256 | 0.0 | 0.23
Output | 0.00014098 | 0.00014098 | 0.00014098 | 0.0 | 0.20
Modify | 0.0052841 | 0.0052841 | 0.0052841 | 0.0 | 7.63
Other | | 5.873e-05 | | | 0.08
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1306 ave 1306 max 1306 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1306
Ave neighs/atom = 62.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

144
examples/reaxff/log.1Feb25.reaxff.rdx-shielded.g++.4 Normal file
View File

@ -0,0 +1,144 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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 = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.856 | 11.02 | 12.23 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79963 0 168.88428 12
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
20 538.95831 -1942.7037 -1910.5731 -10725.628 -2803.7395 7.9078316 0.077926725 0 81.610046 0.22951948 -57.55711 0 30.331206 -10.178049 878.99011 -159.68964 0 89.313879 6
30 463.09528 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.015479 0.027628772 0 81.627413 0.11972402 -50.262283 0 20.82031 -9.6327014 851.88714 -149.49498 0 79.205717 8
40 885.49492 -1958.9125 -1906.1227 -4814.6646 -2795.6439 9.1506063 0.13747482 0 70.948055 0.2436053 -57.862686 0 19.076515 -11.141211 873.73888 -159.99391 0 92.434067 11
50 861.15982 -1954.4602 -1903.1212 -1896.7209 -2784.845 3.8269674 0.15793308 0 79.851587 3.3492059 -78.06613 0 32.628933 -7.9565341 872.81849 -190.9857 0 114.75999 10
60 1167.7827 -1971.8436 -1902.2248 -3482.8501 -2705.8641 -17.121497 0.22749093 0 44.507698 7.8559911 -74.78902 0 16.256511 -4.6046743 835.83081 -188.33692 0 114.19416 10
70 1439.9904 -1989.3026 -1903.4558 23846.02 -2890.7894 31.95863 0.26671716 0 85.758232 3.1804311 -71.002978 0 24.357223 -10.311272 905.86809 -175.38506 0 106.79678 10
80 502.39774 -1930.7552 -1900.8041 -20356.27 -2703.8119 -18.66246 0.11286127 0 99.803504 2.0329528 -76.171312 0 19.236983 -6.278675 826.47474 -166.03143 0 92.539573 9
90 749.07673 -1946.984 -1902.3269 17798.497 -2863.7581 42.06868 0.24338043 0 96.181508 0.9618341 -69.955454 0 24.615416 -11.582759 903.68853 -190.13817 0 120.69116 11
100 1109.6909 -1968.5881 -1902.4325 -4490.3603 -2755.8994 -7.1223998 0.21757662 0 61.805909 7.0826145 -75.645472 0 20.115466 -6.2372802 863.565 -198.56948 0 122.09938 10
Loop time of 0.0643048 on 4 procs for 100 steps with 21 atoms
Performance: 134.360 ns/day, 0.179 hours/ns, 1555.095 timesteps/s, 32.657 katom-step/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.023311 | 0.03235 | 0.044316 | 4.2 | 50.31
Neigh | 0.0013612 | 0.0019412 | 0.002633 | 1.0 | 3.02
Comm | 0.0010934 | 0.013057 | 0.022095 | 6.7 | 20.31
Output | 0.00014529 | 0.00015387 | 0.00016787 | 0.0 | 0.24
Modify | 0.016042 | 0.016754 | 0.017353 | 0.4 | 26.05
Other | | 4.816e-05 | | | 0.07
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 326.5 ave 927 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1306
Ave neighs/atom = 62.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.1Feb25.reaxff.rdx.g++.1 Normal file
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@ -0,0 +1,154 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.000 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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}
}
- fix qeq/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,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
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 qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.36 | 13.36 | 13.36 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79947 0 168.88412 12
10 1288.6115 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629555 3.1252295 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43321 0 107.75934 8
20 538.95838 -1942.7037 -1910.5731 -10725.629 -2803.7395 7.9078326 0.07792674 0 81.610044 0.22951951 -57.557111 0 30.331206 -10.178049 878.99011 -159.6897 0 89.31394 6.5
30 463.09527 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.0154824 0.027628758 0 81.627415 0.11972401 -50.262282 0 20.82031 -9.6327011 851.88713 -149.49499 0 79.205722 8
40 885.49524 -1958.9125 -1906.1227 -4814.6579 -2795.6439 9.1505958 0.13747478 0 70.948066 0.24360531 -57.862686 0 19.076518 -11.141211 873.73887 -159.9939 0 92.434064 11
50 861.1608 -1954.4602 -1903.121 -1896.6931 -2784.8449 3.8269759 0.15793298 0 79.851634 3.349206 -78.06613 0 32.628956 -7.9565349 872.81845 -190.98568 0 114.75998 10
60 1167.7834 -1971.8435 -1902.2247 -3482.8529 -2705.8639 -17.121541 0.2274908 0 44.507704 7.8559998 -74.789016 0 16.256511 -4.60467 835.83072 -188.33689 0 114.19413 10
70 1439.9911 -1989.3024 -1903.4556 23845.704 -2890.7894 31.958692 0.2667172 0 85.758357 3.1804062 -71.002958 0 24.3572 -10.311286 905.86808 -175.385 0 106.79674 10
80 502.3988 -1930.755 -1900.8039 -20356.389 -2703.8108 -18.662751 0.11286169 0 99.803574 2.032954 -76.171326 0 19.236814 -6.2786428 826.47419 -166.03149 0 92.539626 9
90 749.08532 -1946.9839 -1902.3263 17798.667 -2863.7584 42.06871 0.24338047 0 96.181692 0.96182992 -69.955524 0 24.615455 -11.582756 903.68873 -190.13825 0 120.69125 11
100 1109.6964 -1968.5879 -1902.432 -4490.4599 -2755.8982 -7.1227208 0.21757669 0 61.806042 7.082597 -75.645484 0 20.115271 -6.2372452 863.56435 -198.56945 0 122.09933 10.5
Loop time of 0.0666662 on 1 procs for 100 steps with 21 atoms
Performance: 129.601 ns/day, 0.185 hours/ns, 1500.011 timesteps/s, 31.500 katom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.060081 | 0.060081 | 0.060081 | 0.0 | 90.12
Neigh | 0.0029204 | 0.0029204 | 0.0029204 | 0.0 | 4.38
Comm | 0.000161 | 0.000161 | 0.000161 | 0.0 | 0.24
Output | 0.00014497 | 0.00014497 | 0.00014497 | 0.0 | 0.22
Modify | 0.0033107 | 0.0033107 | 0.0033107 | 0.0 | 4.97
Other | | 4.861e-05 | | | 0.07
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.1Feb25.reaxff.rdx.g++.4 Normal file
View File

@ -0,0 +1,154 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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}
}
- fix qeq/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,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
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 qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.353 | 10.52 | 11.73 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.182 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79916 0 168.88381 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.60722 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95827 -1942.7037 -1910.5731 -10725.675 -2803.7395 7.9078297 0.077926636 0 81.610054 0.22951925 -57.557099 0 30.331205 -10.178049 878.99014 -159.69256 0 89.316794 7
30 463.09513 -1933.5765 -1905.9686 -33255.526 -2749.8591 -8.0154533 0.027628873 0 81.62739 0.11972403 -50.262284 0 20.820312 -9.6327039 851.88722 -149.49494 0 79.205672 8
40 885.49116 -1958.9126 -1906.123 -4814.6959 -2795.6441 9.1506835 0.13747507 0 70.947963 0.24360514 -57.862673 0 19.076493 -11.141218 873.73898 -159.99394 0 92.434099 11
50 861.1691 -1954.4598 -1903.1202 -1896.8779 -2784.8448 3.8270203 0.1579326 0 79.851903 3.3492208 -78.066129 0 32.629013 -7.9565355 872.81826 -190.98566 0 114.75994 10
60 1167.7861 -1971.8427 -1902.2238 -3482.6559 -2705.8627 -17.121772 0.22749069 0 44.507644 7.8561147 -74.788923 0 16.256476 -4.6046327 835.83036 -188.33691 0 114.19412 10
70 1440.0001 -1989.3024 -1903.4551 23845.322 -2890.7895 31.958913 0.26671723 0 85.758826 3.1803176 -71.002871 0 24.357078 -10.311326 905.8676 -175.38455 0 106.79634 10
80 502.39424 -1930.7541 -1900.8033 -20356.365 -2703.8112 -18.662536 0.11285996 0 99.804396 2.032884 -76.171335 0 19.237003 -6.2786875 826.47433 -166.03121 0 92.539366 9
90 749.08858 -1946.9836 -1902.3258 17798.514 -2863.7575 42.068829 0.24338073 0 96.181699 0.9618465 -69.955421 0 24.615236 -11.582776 903.6881 -190.13852 0 120.69151 11
100 1109.7005 -1968.5871 -1902.431 -4490.1423 -2755.8949 -7.1235131 0.21757701 0 61.80622 7.0827961 -75.645322 0 20.114715 -6.2371564 863.56266 -198.56982 0 122.09964 10.5
Loop time of 0.0666879 on 4 procs for 100 steps with 21 atoms
Performance: 129.559 ns/day, 0.185 hours/ns, 1499.522 timesteps/s, 31.490 katom-step/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.023807 | 0.033573 | 0.04688 | 4.6 | 50.34
Neigh | 0.0013829 | 0.001879 | 0.0024761 | 0.9 | 2.82
Comm | 0.0015767 | 0.014898 | 0.024673 | 6.9 | 22.34
Output | 0.00015887 | 0.00016828 | 0.00018839 | 0.0 | 0.25
Modify | 0.015511 | 0.01612 | 0.016628 | 0.3 | 24.17
Other | | 4.966e-05 | | | 0.07
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.904762
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

143
examples/reaxff/log.1Feb25.reaxff.tatb-shielded.g++.1 Normal file
View File

@ -0,0 +1,143 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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 = 5 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 141.8 | 141.8 | 141.8 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7813 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6412 0 6391.0292 31
5 0.61603967 -44761.698 -44760.994 8934.6348 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.191 0 6388.6671 9
10 2.3525554 -44763.227 -44760.541 12288.592 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9738 0 6381.7115 10
15 4.9013248 -44766.36 -44760.764 17716.966 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2495 0 6370.4158 11
20 7.8294647 -44769.686 -44760.747 25205.601 -61089.006 490.21315 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.498 0 6355.2493 10
25 10.697903 -44772.904 -44760.691 34232.795 -61069.308 490.25888 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3636 0 6336.8444 8
Loop time of 1.38877 on 1 procs for 25 steps with 384 atoms
Performance: 0.097 ns/day, 246.892 hours/ns, 18.002 timesteps/s, 6.913 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 | 0.84541 | 0.84541 | 0.84541 | 0.0 | 60.87
Neigh | 0.18596 | 0.18596 | 0.18596 | 0.0 | 13.39
Comm | 0.00085484 | 0.00085484 | 0.00085484 | 0.0 | 0.06
Output | 0.00015065 | 0.00015065 | 0.00015065 | 0.0 | 0.01
Modify | 0.35629 | 0.35629 | 0.35629 | 0.0 | 25.66
Other | | 0.0001081 | | | 0.01
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 336304 ave 336304 max 336304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.79167
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:01

143
examples/reaxff/log.1Feb25.reaxff.tatb-shielded.g++.4 Normal file
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@ -0,0 +1,143 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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 = 5 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 95.02 | 95.02 | 95.02 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7867 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 31
5 0.61603966 -44761.698 -44760.994 8934.6345 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
10 2.3525551 -44763.227 -44760.541 12288.585 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139 10
15 4.9013353 -44766.36 -44760.764 17716.927 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2618 0 6370.428 9
20 7.8294728 -44769.686 -44760.747 25205.533 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.5246 0 6355.2758 9
25 10.697909 -44772.904 -44760.691 34232.903 -61069.308 490.25887 4.7163736 0 1570.7397 20.181346 -251.91376 -1582.3261 253.82253 -653.53184 18791.975 -8684.3314 0 6336.8122 9
Loop time of 0.788795 on 4 procs for 25 steps with 384 atoms
Performance: 0.171 ns/day, 140.230 hours/ns, 31.694 timesteps/s, 12.170 katom-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 | 0.56139 | 0.56526 | 0.56947 | 0.5 | 71.66
Neigh | 0.10336 | 0.10367 | 0.10413 | 0.1 | 13.14
Comm | 0.0032435 | 0.0074406 | 0.011341 | 4.5 | 0.94
Output | 0.00018108 | 0.0012272 | 0.0015806 | 1.7 | 0.16
Modify | 0.11024 | 0.11106 | 0.11251 | 0.3 | 14.08
Other | | 0.0001416 | | | 0.02
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 84076 ave 84076 max 84076 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.79167
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

159
examples/reaxff/log.1Feb25.reaxff.tatb.g++.1 Normal file
View File

@ -0,0 +1,159 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
compute bonds all reaxff/atom bonds yes
variable nqeq equal f_2
# dumps out the local bond information
dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3]
# dumps out the peratom bond information
dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*]
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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}
}
- fix qeq/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,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 5 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
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 qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 148.7 | 148.7 | 148.7 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7886 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6392 0 6391.0272 31.5
5 0.61603945 -44761.698 -44760.994 8934.6263 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1931 0 6388.6691 10.5
10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9689 0 6381.7066 8.5
15 4.9013324 -44766.36 -44760.764 17716.909 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56848 -1566.3829 252.95174 -654.96611 18835.777 -8719.2637 0 6370.4299 9
20 7.8294652 -44769.686 -44760.747 25205.631 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4897 0 6355.241 10
25 10.697902 -44772.904 -44760.691 34232.78 -61069.308 490.25885 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.364 0 6336.8448 10
Loop time of 1.24712 on 1 procs for 25 steps with 384 atoms
Performance: 0.108 ns/day, 221.710 hours/ns, 20.046 timesteps/s, 7.698 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 | 0.87392 | 0.87392 | 0.87392 | 0.0 | 70.07
Neigh | 0.1672 | 0.1672 | 0.1672 | 0.0 | 13.41
Comm | 0.0010267 | 0.0010267 | 0.0010267 | 0.0 | 0.08
Output | 0.0031358 | 0.0031358 | 0.0031358 | 0.0 | 0.25
Modify | 0.20171 | 0.20171 | 0.20171 | 0.0 | 16.17
Other | | 0.0001369 | | | 0.01
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.94792
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:01

159
examples/reaxff/log.1Feb25.reaxff.tatb.g++.4 Normal file
View File

@ -0,0 +1,159 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
compute bonds all reaxff/atom bonds yes
variable nqeq equal f_2
# dumps out the local bond information
dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3]
# dumps out the peratom bond information
dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*]
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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}
}
- fix qeq/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,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 5 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
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 qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 99.8 | 99.8 | 99.8 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277 31
5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 8.5
10 2.352554 -44763.227 -44760.541 12288.582 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139 10
15 4.9013231 -44766.36 -44760.764 17716.979 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2473 0 6370.4136 7
20 7.8294566 -44769.686 -44760.747 25205.638 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4803 0 6355.2315 8.5
25 10.6979 -44772.904 -44760.691 34232.844 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3433 0 6336.8241 9.5
Loop time of 0.771261 on 4 procs for 25 steps with 384 atoms
Performance: 0.175 ns/day, 137.113 hours/ns, 32.414 timesteps/s, 12.447 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 | 0.56965 | 0.57597 | 0.58104 | 0.5 | 74.68
Neigh | 0.097254 | 0.097483 | 0.097832 | 0.1 | 12.64
Comm | 0.003347 | 0.0083916 | 0.014749 | 4.5 | 1.09
Output | 0.00131 | 0.0022935 | 0.0026708 | 1.2 | 0.30
Modify | 0.086284 | 0.086988 | 0.088382 | 0.3 | 11.28
Other | | 0.0001324 | | | 0.02
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.77083
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

144
examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.1
View File

@ -1,144 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.86 | 13.86 | 13.86 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79932 0 168.88397 12
10 1288.6114 -1989.6644 -1912.8422 -19456.349 -2734.6769 -15.607218 0.20177961 0 54.629555 3.1252297 -77.7067 0 14.933901 -5.810854 843.92074 -180.43322 0 107.75935 8
20 538.95852 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.9078343 0.077926704 0 81.610044 0.22951937 -57.557105 0 30.331203 -10.178049 878.99016 -159.69263 0 89.316862 7
30 463.09515 -1933.5765 -1905.9685 -33255.499 -2749.8591 -8.0154635 0.02762867 0 81.627413 0.1197239 -50.262272 0 20.82032 -9.632703 851.88721 -149.49497 0 79.205707 8
40 885.49689 -1958.9125 -1906.1226 -4814.6325 -2795.644 9.1505916 0.13747481 0 70.948074 0.24360544 -57.862695 0 19.076518 -11.14121 873.73893 -159.9939 0 92.434061 11
50 861.16008 -1954.4602 -1903.1211 -1896.648 -2784.8451 3.8269988 0.1579331 0 79.851597 3.349208 -78.066133 0 32.628942 -7.9565363 872.8186 -190.98572 0 114.76001 10
60 1167.7831 -1971.8435 -1902.2247 -3482.927 -2705.8639 -17.121541 0.22749081 0 44.507721 7.8559737 -74.789039 0 16.2565 -4.6046718 835.8307 -188.33687 0 114.19412 10
70 1439.9897 -1989.3024 -1903.4557 23845.83 -2890.7894 31.958658 0.26671716 0 85.758318 3.1804201 -71.002959 0 24.35723 -10.31128 905.86819 -175.38505 0 106.79678 10
80 502.39931 -1930.7551 -1900.804 -20356.375 -2703.8109 -18.66274 0.1128617 0 99.80351 2.0329611 -76.171312 0 19.236815 -6.2786426 826.47424 -166.03148 0 92.539616 9
90 749.08601 -1946.984 -1902.3264 17798.716 -2863.7585 42.068606 0.24338046 0 96.181674 0.96183581 -69.955564 0 24.615514 -11.582742 903.68878 -190.13822 0 120.69121 11
100 1109.6946 -1968.588 -1902.4322 -4490.4001 -2755.899 -7.1224954 0.21757676 0 61.805955 7.0825894 -75.645488 0 20.115437 -6.2372635 863.56481 -198.56946 0 122.09935 10
Loop time of 0.23792 on 1 procs for 100 steps with 21 atoms
Performance: 36.315 ns/day, 0.661 hours/ns, 420.310 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 | 0.21046 | 0.21046 | 0.21046 | 0.0 | 88.46
Neigh | 0.010947 | 0.010947 | 0.010947 | 0.0 | 4.60
Comm | 0.00060345 | 0.00060345 | 0.00060345 | 0.0 | 0.25
Output | 0.00071705 | 0.00071705 | 0.00071705 | 0.0 | 0.30
Modify | 0.014873 | 0.014873 | 0.014873 | 0.0 | 6.25
Other | | 0.0003213 | | | 0.14
Nlocal: 21.0000 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546.000 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1306.00 ave 1306 max 1306 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1306
Ave neighs/atom = 62.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

144
examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.4
View File

@ -1,144 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.003 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.856 | 11.02 | 12.23 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79963 0 168.88428 12
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
20 538.95831 -1942.7037 -1910.5731 -10725.628 -2803.7395 7.9078316 0.077926725 0 81.610046 0.22951948 -57.55711 0 30.331206 -10.178049 878.99011 -159.68964 0 89.313879 6
30 463.09528 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.015479 0.027628772 0 81.627413 0.11972402 -50.262283 0 20.82031 -9.6327014 851.88714 -149.49498 0 79.205717 8
40 885.49492 -1958.9125 -1906.1227 -4814.6646 -2795.6439 9.1506063 0.13747482 0 70.948055 0.2436053 -57.862686 0 19.076515 -11.141211 873.73888 -159.99391 0 92.434067 11
50 861.15982 -1954.4602 -1903.1212 -1896.7209 -2784.845 3.8269674 0.15793308 0 79.851587 3.3492059 -78.06613 0 32.628933 -7.9565341 872.81849 -190.9857 0 114.75999 10
60 1167.7827 -1971.8436 -1902.2248 -3482.8501 -2705.8641 -17.121497 0.22749093 0 44.507698 7.8559911 -74.78902 0 16.256511 -4.6046743 835.83081 -188.33692 0 114.19416 10
70 1439.9904 -1989.3026 -1903.4558 23846.02 -2890.7894 31.95863 0.26671716 0 85.758232 3.1804311 -71.002978 0 24.357223 -10.311272 905.86809 -175.38506 0 106.79678 10
80 502.39774 -1930.7552 -1900.8041 -20356.27 -2703.8119 -18.66246 0.11286127 0 99.803504 2.0329528 -76.171312 0 19.236983 -6.278675 826.47474 -166.03143 0 92.539573 9
90 749.07673 -1946.984 -1902.3269 17798.497 -2863.7581 42.06868 0.24338043 0 96.181508 0.9618341 -69.955454 0 24.615416 -11.582759 903.68853 -190.13817 0 120.69116 11
100 1109.6909 -1968.5881 -1902.4325 -4490.3603 -2755.8994 -7.1223998 0.21757662 0 61.805909 7.0826145 -75.645472 0 20.115466 -6.2372802 863.565 -198.56948 0 122.09938 10
Loop time of 0.427646 on 4 procs for 100 steps with 21 atoms
Performance: 20.204 ns/day, 1.188 hours/ns, 233.838 timesteps/s
88.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1373 | 0.20047 | 0.27938 | 11.8 | 46.88
Neigh | 0.0067 | 0.009334 | 0.01249 | 2.1 | 2.18
Comm | 0.057132 | 0.13685 | 0.19972 | 14.4 | 32.00
Output | 0.00078935 | 0.0013884 | 0.0031266 | 2.7 | 0.32
Modify | 0.075213 | 0.079164 | 0.082556 | 0.9 | 18.51
Other | | 0.0004359 | | | 0.10
Nlocal: 5.25000 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.500 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.750 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 326.500 ave 927 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1306
Ave neighs/atom = 62.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Jul21.reaxff.rdx.g++.1
View File

@ -1,154 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.36 | 13.36 | 13.36 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.231802 on 1 procs for 100 steps with 21 atoms
Performance: 37.273 ns/day, 0.644 hours/ns, 431.402 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20857 | 0.20857 | 0.20857 | 0.0 | 89.98
Neigh | 0.010489 | 0.010489 | 0.010489 | 0.0 | 4.52
Comm | 0.00059632 | 0.00059632 | 0.00059632 | 0.0 | 0.26
Output | 0.00067498 | 0.00067498 | 0.00067498 | 0.0 | 0.29
Modify | 0.011161 | 0.011161 | 0.011161 | 0.0 | 4.82
Other | | 0.000307 | | | 0.13
Nlocal: 21.0000 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546.000 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Jul21.reaxff.rdx.g++.4
View File

@ -1,154 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.001 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#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
run 100
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.353 | 10.52 | 11.73 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418 12
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252292 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
20 538.95847 -1942.7037 -1910.5731 -10725.668 -2803.7395 7.9078328 0.077926688 0 81.610045 0.22951933 -57.557103 0 30.331203 -10.178049 878.99015 -159.69262 0 89.316856 7
30 463.09521 -1933.5765 -1905.9685 -33255.503 -2749.8591 -8.0154614 0.027628708 0 81.627408 0.11972393 -50.262275 0 20.820319 -9.6327031 851.88721 -149.49497 0 79.205707 8
40 885.49559 -1958.9126 -1906.1227 -4814.661 -2795.644 9.1506103 0.13747486 0 70.948058 0.24360549 -57.862693 0 19.076514 -11.141211 873.73894 -159.9939 0 92.434063 11
50 861.16222 -1954.4601 -1903.1209 -1896.7328 -2784.8449 3.8269573 0.15793301 0 79.851661 3.3492101 -78.066131 0 32.628939 -7.9565311 872.81847 -190.9857 0 114.75999 10
60 1167.7838 -1971.8434 -1902.2246 -3482.8253 -2705.8639 -17.121553 0.22749078 0 44.507707 7.8560156 -74.789002 0 16.256509 -4.6046674 835.83076 -188.33689 0 114.19413 10
70 1439.9922 -1989.3024 -1903.4556 23845.682 -2890.7894 31.958742 0.26671722 0 85.758402 3.1803955 -71.002937 0 24.357176 -10.311293 905.86805 -175.38494 0 106.79668 10
80 502.39847 -1930.7549 -1900.8038 -20356.357 -2703.8111 -18.662668 0.11286141 0 99.803668 2.0329484 -76.17132 0 19.236866 -6.2786536 826.47435 -166.03145 0 92.539587 9
90 749.0857 -1946.984 -1902.3263 17798.657 -2863.7584 42.068704 0.24338054 0 96.181666 0.96183837 -69.955527 0 24.615445 -11.58275 903.68864 -190.13828 0 120.69127 11
100 1109.695 -1968.5879 -1902.4321 -4490.3441 -2755.8984 -7.1226574 0.21757683 0 61.806014 7.0826278 -75.645456 0 20.115306 -6.2372466 863.56451 -198.56953 0 122.09941 10.5
Loop time of 0.371707 on 4 procs for 100 steps with 21 atoms
Performance: 23.244 ns/day, 1.033 hours/ns, 269.029 timesteps/s
91.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13518 | 0.19123 | 0.24947 | 9.7 | 51.45
Neigh | 0.0073075 | 0.0096968 | 0.012228 | 1.8 | 2.61
Comm | 0.034511 | 0.093329 | 0.14912 | 14.0 | 25.11
Output | 0.00081416 | 0.0011345 | 0.0019655 | 1.4 | 0.31
Modify | 0.073177 | 0.075449 | 0.078618 | 0.7 | 20.30
Other | | 0.0008711 | | | 0.23
Nlocal: 5.25000 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.500 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.750 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.904762
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

142
examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.1
View File

@ -1,142 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.002 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 141.3 | 141.3 | 141.3 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275 31
5 0.61603968 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665 8
10 2.3525543 -44763.227 -44760.541 12288.589 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714 10
15 4.9013256 -44766.36 -44760.764 17716.957 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2536 0 6370.4198 9
20 7.8294699 -44769.686 -44760.747 25205.552 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5055 0 6355.2567 8
25 10.697916 -44772.904 -44760.691 34232.955 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.308 0 6336.7889 7
Loop time of 3.31728 on 1 procs for 25 steps with 384 atoms
Performance: 0.041 ns/day, 589.738 hours/ns, 7.536 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9321 | 1.9321 | 1.9321 | 0.0 | 58.24
Neigh | 0.6452 | 0.6452 | 0.6452 | 0.0 | 19.45
Comm | 0.0020122 | 0.0020122 | 0.0020122 | 0.0 | 0.06
Output | 0.00030173 | 0.00030173 | 0.00030173 | 0.0 | 0.01
Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 22.22
Other | | 0.0003829 | | | 0.01
Nlocal: 384.000 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559.00 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828.0 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 336304.0 ave 336304 max 336304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.79167
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:03

142
examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.4
View File

@ -1,142 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.004 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 94.50 | 94.50 | 94.50 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7865 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0278 31
5 0.61603964 -44761.698 -44760.994 8934.6344 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
10 2.3525559 -44763.227 -44760.541 12288.611 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9712 0 6381.7089 11
15 4.9013319 -44766.36 -44760.764 17716.965 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2514 0 6370.4176 9
20 7.8294706 -44769.686 -44760.747 25205.511 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5196 0 6355.2708 7
25 10.69792 -44772.904 -44760.691 34232.831 -61069.308 490.25885 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.353 0 6336.8339 11
Loop time of 2.66226 on 4 procs for 25 steps with 384 atoms
Performance: 0.051 ns/day, 473.290 hours/ns, 9.391 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7311 | 1.7619 | 1.794 | 2.0 | 66.18
Neigh | 0.46483 | 0.46901 | 0.47348 | 0.5 | 17.62
Comm | 0.039253 | 0.073989 | 0.10705 | 10.7 | 2.78
Output | 0.0012206 | 0.0080282 | 0.010299 | 4.4 | 0.30
Modify | 0.34359 | 0.3488 | 0.36264 | 1.4 | 13.10
Other | | 0.0005529 | | | 0.02
Nlocal: 96.0000 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118.00 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754.0 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 84076.0 ave 84076 max 84076 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.79167
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:03

151
examples/reaxff/log.21Jul21.reaxff.tatb.g++.1
View File

@ -1,151 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.008 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 148.1 | 148.1 | 148.1 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7878 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 31.5
5 0.61603968 -44761.698 -44760.994 8934.6346 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
10 2.3525552 -44763.227 -44760.541 12288.581 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9765 0 6381.7142 10.5
15 4.9013309 -44766.36 -44760.764 17716.918 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2622 0 6370.4284 9.5
20 7.829469 -44769.686 -44760.747 25205.568 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.5126 0 6355.2639 8
25 10.697899 -44772.904 -44760.691 34232.788 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3619 0 6336.8427 11
Loop time of 2.91659 on 1 procs for 25 steps with 384 atoms
Performance: 0.046 ns/day, 518.504 hours/ns, 8.572 timesteps/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 | 1.9139 | 1.9139 | 1.9139 | 0.0 | 65.62
Neigh | 0.5948 | 0.5948 | 0.5948 | 0.0 | 20.39
Comm | 0.0020205 | 0.0020205 | 0.0020205 | 0.0 | 0.07
Output | 0.00031287 | 0.00031287 | 0.00031287 | 0.0 | 0.01
Modify | 0.40513 | 0.40513 | 0.40513 | 0.0 | 13.89
Other | | 0.0003856 | | | 0.01
Nlocal: 384.000 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559.00 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828.0 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.94792
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:03

151
examples/reaxff/log.21Jul21.reaxff.tatb.g++.4
View File

@ -1,151 +0,0 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.002 seconds
pair_style reaxff control.reax_c.tatb
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 99.27 | 99.27 | 99.27 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 31
5 0.61603941 -44761.698 -44760.994 8934.6279 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 10
10 2.352555 -44763.227 -44760.541 12288.61 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9686 0 6381.7064 9
15 4.9013339 -44766.36 -44760.764 17716.995 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2413 0 6370.4076 10.5
20 7.8294636 -44769.686 -44760.747 25205.611 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4966 0 6355.2478 10
25 10.6979 -44772.904 -44760.691 34232.798 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3574 0 6336.8382 10.5
Loop time of 2.53633 on 4 procs for 25 steps with 384 atoms
Performance: 0.053 ns/day, 450.902 hours/ns, 9.857 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7343 | 1.7637 | 1.815 | 2.4 | 69.54
Neigh | 0.44441 | 0.44869 | 0.45403 | 0.6 | 17.69
Comm | 0.025287 | 0.074702 | 0.10592 | 11.9 | 2.95
Output | 0.0016916 | 0.0080527 | 0.010178 | 4.1 | 0.32
Modify | 0.23126 | 0.24065 | 0.25706 | 2.1 | 9.49
Other | | 0.000566 | | | 0.02
Nlocal: 96.0000 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118.00 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754.0 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.77083
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:02

124
examples/reaxff/water/log.13Oct21.reaxff.water-acks2.g++.4
View File

@ -1,124 +0,0 @@
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.013 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
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) 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 * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
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 acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
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/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 271.9 | 273.6 | 275.1 Mbytes
Step Temp Press Density Volume
0 300 1572.3807 1 29915.273
10 300.6152 8252.4834 1 29915.273
20 294.73868 2502.5661 1 29915.273
Loop time of 11.1133 on 4 procs for 20 steps with 3000 atoms
Performance: 0.078 ns/day, 308.702 hours/ns, 1.800 timesteps/s
92.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3609 | 4.7715 | 5.4812 | 19.5 | 42.94
Neigh | 0.15797 | 0.17176 | 0.19405 | 3.5 | 1.55
Comm | 0.21014 | 0.922 | 1.3353 | 44.6 | 8.30
Output | 8.815e-05 | 0.0002 | 0.00030501 | 0.0 | 0.00
Modify | 5.2267 | 5.2468 | 5.2584 | 0.5 | 47.21
Other | | 0.001074 | | | 0.01
Nlocal: 750.000 ave 760 max 735 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 6231.50 ave 6255 max 6192 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 277006.0 ave 280567 max 271394 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 1108026
Ave neighs/atom = 369.34200
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:12

128
examples/reaxff/water/log.13Oct21.reaxff.water-qeq-field.g++.1
View File

@ -1,128 +0,0 @@
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.010 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
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
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 (../reaxff_ffield.cpp:296)
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 qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
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/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 332.3 | 332.3 | 332.3 Mbytes
Step Temp Press Density Volume
0 300 25015.837 0.99996859 29916.212
10 348.83356 31131.298 0.99964273 29925.965
20 414.67243 27564.999 0.99979791 29921.32
Loop time of 15.4107 on 1 procs for 20 steps with 3000 atoms
Performance: 0.056 ns/day, 428.074 hours/ns, 1.298 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.413 | 11.413 | 11.413 | 0.0 | 74.06
Neigh | 0.57486 | 0.57486 | 0.57486 | 0.0 | 3.73
Comm | 0.0019709 | 0.0019709 | 0.0019709 | 0.0 | 0.01
Output | 0.00013211 | 0.00013211 | 0.00013211 | 0.0 | 0.00
Modify | 3.4192 | 3.4192 | 3.4192 | 0.0 | 22.19
Other | | 0.001104 | | | 0.01
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5439.00 ave 5439 max 5439 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 786591.0 ave 786591 max 786591 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 786591
Ave neighs/atom = 262.19700
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:16

128
examples/reaxff/water/log.13Oct21.reaxff.water-qeq-field.g++.4
View File

@ -1,128 +0,0 @@
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.017 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
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
2 by 1 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 (../reaxff_ffield.cpp:296)
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 qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
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/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 188.9 | 189.5 | 190.1 Mbytes
Step Temp Press Density Volume
0 300 25015.837 0.99996859 29916.212
10 348.83356 31131.298 0.99964273 29925.965
20 414.67243 27564.999 0.99979791 29921.32
Loop time of 5.71549 on 4 procs for 20 steps with 3000 atoms
Performance: 0.151 ns/day, 158.764 hours/ns, 3.499 timesteps/s
94.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6678 | 3.8126 | 4.1402 | 9.8 | 66.71
Neigh | 0.31449 | 0.34639 | 0.38898 | 5.5 | 6.06
Comm | 0.032125 | 0.35935 | 0.50408 | 31.9 | 6.29
Output | 7.643e-05 | 0.00015959 | 0.00039876 | 0.0 | 0.00
Modify | 1.1534 | 1.1959 | 1.2283 | 3.0 | 20.92
Other | | 0.001099 | | | 0.02
Nlocal: 750.000 ave 757 max 738 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 4219.00 ave 4232 max 4198 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 230549.0 ave 233374 max 225849 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 922196
Ave neighs/atom = 307.39867
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:06

123
examples/reaxff/water/log.13Oct21.reaxff.water-qeq.g++.1
View File

@ -1,123 +0,0 @@
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 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
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) 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 (../reaxff_ffield.cpp:296)
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 qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
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/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
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 5433.7415 1 29915.273
20 297.90652 1572.6111 1 29915.273
Loop time of 17.5765 on 1 procs for 20 steps with 3000 atoms
Performance: 0.049 ns/day, 488.237 hours/ns, 1.138 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.806 | 13.806 | 13.806 | 0.0 | 78.55
Neigh | 0.34211 | 0.34211 | 0.34211 | 0.0 | 1.95
Comm | 0.0028155 | 0.0028155 | 0.0028155 | 0.0 | 0.02
Output | 0.00012279 | 0.00012279 | 0.00012279 | 0.0 | 0.00
Modify | 3.4248 | 3.4248 | 3.4248 | 0.0 | 19.49
Other | | 0.001008 | | | 0.01
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11077.0 ave 11077 max 11077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 971826.0 ave 971826 max 971826 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 971826
Ave neighs/atom = 323.94200
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:18

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