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Merge branch 'develop' of github.com:lammps/lammps into triclinic-neighbor-bug

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This commit is contained in:
Stan Gerald Moore
2023-10-16 12:18:04 -06:00
parent dbab5b6931 53d123caa5
commit 51f0c9eac4
409 changed files with 19456 additions and 6575 deletions
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2
.github/workflows/codeql-analysis.yml vendored
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@ -25,7 +25,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 2

2
.github/workflows/compile-msvc.yml vendored
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@ -19,7 +19,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 2

2
.github/workflows/coverity.yml vendored
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@ -16,7 +16,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 2

2
.github/workflows/unittest-macos.yml vendored
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@ -21,7 +21,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 2

11
cmake/CMakeLists.txt
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@ -145,6 +145,7 @@ if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_options(/wd4250)
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
@ -268,7 +269,6 @@ set(STANDARD_PACKAGES
MOFFF
MOLECULE
MOLFILE
MPIIO
NETCDF
ORIENT
PERI
@ -377,7 +377,6 @@ endif()
# "hard" dependencies between packages resulting
# in an error instead of skipping over files
pkg_depends(ML-IAP ML-SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(SCAFACOS MPI)
@ -388,6 +387,7 @@ pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
pkg_depends(MESONT MOLECULE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -579,13 +579,6 @@ foreach(PKG ${STANDARD_PACKAGES})
RegisterPackages(${${PKG}_SOURCES_DIR})
endforeach()
# packages that need defines set
foreach(PKG MPIIO)
if(PKG_${PKG})
target_compile_definitions(lammps PRIVATE -DLMP_${PKG})
endif()
endforeach()
# dedicated check for entire contents of accelerator packages
foreach(PKG ${SUFFIX_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})

12
cmake/Modules/FindClangFormat.cmake
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@ -1,5 +1,7 @@
# Find clang-format
find_program(ClangFormat_EXECUTABLE NAMES clang-format
clang-format-17.0
clang-format-16.0
clang-format-15.0
clang-format-14.0
clang-format-13.0
@ -19,7 +21,7 @@ if(ClangFormat_EXECUTABLE)
OUTPUT_VARIABLE clang_format_version
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*")
# Arch Linux output:
# clang-format version 10.0.0
#
@ -32,9 +34,15 @@ if(ClangFormat_EXECUTABLE)
# Ubuntu 22.04 LTS output:
# Ubuntu clang-format version 14.0.0-1ubuntu1
#
# Debian 11 output:
# Debian clang-format version 11.0.1-2
#
# Debian 12 output:
# Debian clang-format version 14.0.6
#
# Fedora 36 output:
# clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*"
"\\2"
ClangFormat_VERSION
"${clang_format_version}")

1
cmake/Modules/LAMMPSInterfacePlugin.cmake
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@ -28,6 +28,7 @@ if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_options(/wd4250)
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)

4
cmake/Modules/Packages/ML-PACE.cmake
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@ -1,6 +1,6 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)

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cmake/packaging/LAMMPS_DMG_Background.png
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2
cmake/packaging/MacOSXBundleInfo.plist.in
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@ -17,7 +17,7 @@
<key>CFBundleLongVersionString</key>
<string>${MACOSX_BUNDLE_LONG_VERSION_STRING}</string>
<key>CFBundleName</key>
<string>LAMMPS</string>
<string>LAMMPS_GUI</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleShortVersionString</key>

26
cmake/packaging/README.macos
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@ -9,7 +9,7 @@ of the available packages.
The following individual commands are included:
binary2txt lammps-gui lmp msi2lmp phana stl_bin2txt
After copying the lammps-gui folder into your Applications folder, please follow
After copying the LAMMPS_GUI folder into your Applications folder, please follow
these steps:
1. Open the Terminal app
@ -23,7 +23,7 @@ these steps:
3. Add the following lines to the end of the file, save it, and close the editor
LAMMPS_INSTALL_DIR=/Applications/LAMMPS.app/Contents
LAMMPS_INSTALL_DIR=/Applications/LAMMPS_GUI.app/Contents
LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials
LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench
MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files
@ -38,9 +38,9 @@ these steps:
the changes from .zprofile automatically.
Note: the above assumes you use the default shell (zsh) that comes with
MacOS. If you customized MacOS to use a different shell, you'll need to modify
that shell's init file (.cshrc, .bashrc, etc.) instead with appropiate commands
to modify the same environment variables.
MacOS. If you customized MacOS to use a different shell, you'll need to
modify that shell's init file (.cshrc, .bashrc, etc.) instead with
appropiate commands to modify the same environment variables.
5. Try running LAMMPS (which might fail, see step 7)
@ -50,10 +50,10 @@ these steps:
lammps-gui ${LAMMPS_BENCH_DIR}/in.rhodo
Depending on the size and resolution of your screen, the fonts may
be too small to read. This can be adjusted by setting the environment
variable QT_FONT_DPI. The default value would be 72, so to increase
the fonts by a third one can add to the .zprofile file the line
Depending on the size and resolution of your screen, the fonts may be too
small to read. This can be adjusted by setting the environment variable
QT_FONT_DPI. The default value would be 72, so to increase the fonts by a
third, one can add to the .zprofile file the line
export QT_FONT_DPI=96
@ -61,9 +61,9 @@ these steps:
7. Give permission to execute the commands (lmp, lammps-gui, msi2lmp, binary2txt, phana, stl_bin2txt)
MacOS will likely block the initial run of the executables, since they
were downloaded from the internet and are missing a known signature from an
identified developer. Go to "Settings" and search for "Security settings". It
should display a message that an executable like "lmp" was blocked. Press
MacOS will likely block the initial run of the executables, since they were
downloaded from the internet and are missing a known signature from an
identified developer. Go to "Settings" and search for "Security settings".
It should display a message that an executable like "lmp" was blocked. Press
"Open anyway", which might prompt you for your admin credentials. Afterwards
"lmp" and the other executables should work as expected.

4
cmake/packaging/build_linux_tgz.sh
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@ -4,7 +4,7 @@ APP_NAME=lammps-gui
DESTDIR=${PWD}/../LAMMPS_GUI
echo "Delete old files, if they exist"
rm -rf ${DESTDIR} ../LAMMPS-Linux-amd64.tar.gz
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
@ -69,7 +69,7 @@ do \
done
pushd ..
tar -czvvf LAMMPS-Linux-amd64.tar.gz LAMMPS_GUI
tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI
popd
echo "Cleanup dir"

14
cmake/packaging/build_macos_dmg.sh
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@ -3,7 +3,7 @@
APP_NAME=lammps-gui
echo "Delete old files, if they exist"
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS-macOS-multiarch.dmg
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch.dmg
echo "Create initial dmg file with macdeployqt"
macdeployqt lammps-gui.app -dmg
@ -22,8 +22,8 @@ ln -s /Applications .
mv ${APP_NAME}.app/Contents/Resources/README.txt .
mkdir .background
mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png
mv ${APP_NAME}.app LAMMPS.app
cd LAMMPS.app/Contents
mv ${APP_NAME}.app LAMMPS_GUI.app
cd LAMMPS_GUI.app/Contents
echo "Attach icons to LAMMPS console and GUI executables"
echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc
@ -75,7 +75,7 @@ echo '
set statusbar visible to false
set toolbar visible to false
set the bounds to { 100, 40, 868, 640 }
set position of item "'LAMMPS'.app" to { 190, 216 }
set position of item "'LAMMPS_GUI'.app" to { 190, 216 }
set position of item "Applications" to { 576, 216 }
set position of item "README.txt" to { 190, 400 }
end tell
@ -96,12 +96,12 @@ sync
echo "Unmount modified disk image and convert to compressed read-only image"
hdiutil detach "${DEVICE}"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS-macOS-multiarch.dmg"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch.dmg"
echo "Attach icon to .dmg file"
echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
Rez -a icon.rsrc -o LAMMPS-macOS-multiarch.dmg
SetFile -a C LAMMPS-macOS-multiarch.dmg
Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch.dmg
SetFile -a C LAMMPS_GUI-macOS-multiarch.dmg
rm icon.rsrc
echo "Delete temporary disk images"

11
cmake/packaging/build_windows_vs.cmake
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@ -1,7 +1,7 @@
# CMake script to be run post installation to build zipped package
# clean up old zipfile and deployment tree
file(REMOVE LAMMPS-Win10-amd64.zip)
file(REMOVE LAMMPS_GUI-Win10-amd64.zip)
file(REMOVE_RECURSE LAMMPS_GUI)
file(RENAME ${INSTNAME} LAMMPS_GUI)
@ -21,8 +21,15 @@ file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r
execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
file(REMOVE qtdeploy.bat)
# download and uncompress static FFMpeg and gzip binaries
file(DOWNLOAD "https://download.lammps.org/thirdparty/ffmpeg-gzip.zip" ffmpeg-gzip.zip)
file(WRITE unpackzip.ps1 "Expand-Archive -Path ffmpeg-gzip.zip -DestinationPath LAMMPS_GUI")
execute_process(COMMAND powershell -ExecutionPolicy Bypass -File unpackzip.ps1)
file(REMOVE unpackzip.ps1)
file(REMOVE ffmpeg-gzip.zip)
# create zip archive
file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS-Win10-amd64.zip")
file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS_GUI-Win10-amd64.zip")
execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)
file(REMOVE makearchive.ps1)
file(REMOVE_RECURSE LAMMPS_GUI)

3
cmake/packaging/linux_wrapper.sh
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@ -1,6 +1,9 @@
#!/bin/sh
# wrapper for bundled executables
# reset locale to avoid problems with decimal numbers
export LC_ALL=C
BASEDIR=$(dirname "$0")
EXENAME=$(basename "$0")

1
cmake/presets/all_off.cmake
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@ -63,7 +63,6 @@ set(ALL_PACKAGES
MOFFF
MOLECULE
MOLFILE
MPIIO
NETCDF
OPENMP
OPT

1
cmake/presets/all_on.cmake
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@ -65,7 +65,6 @@ set(ALL_PACKAGES
MOFFF
MOLECULE
MOLFILE
MPIIO
NETCDF
OPENMP
OPT

2
cmake/presets/macos-multiarch.cmake
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@ -10,5 +10,3 @@ set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(BUILD_MPI FALSE CACHE BOOL "" FORCE)
set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE)
set(LAMMPS_EXCEPTIONS TRUE CACHE BOOL "" FORCE)

1
cmake/presets/mingw-cross.cmake
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@ -83,7 +83,6 @@ endforeach()
# these two packages require a full MPI implementation
if(BUILD_MPI)
set(PKG_MPIIO ON CACHE BOOL "" FORCE)
set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
endif()

1
cmake/presets/nolib.cmake
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@ -19,7 +19,6 @@ set(PACKAGES_WITH_LIB
ML-PACE
ML-QUIP
MOLFILE
MPIIO
NETCDF
PLUMED
PYTHON

23
doc/src/Build_basics.rst
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@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below.
directory, or ``make`` from the ``src/STUBS`` dir. If the build
fails, you may need to edit the ``STUBS/Makefile`` for your
platform. The stubs library does not provide MPI/IO functions
required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
required by some LAMMPS packages, e.g. ``LATBOLTZ``,
and thus is not compatible with those packages.
.. note::
@ -128,14 +128,13 @@ and adds vectorization support when compiled with compatible compilers,
in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
package can be compiled to include OpenMP threading.
In addition, there are a few commands in LAMMPS that have native
OpenMP support included as well. These are commands in the ``MPIIO``,
``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.
Furthermore, some packages support OpenMP threading indirectly through
the libraries they interface to: e.g. ``KSPACE``, and ``COLVARS``.
See the :doc:`Packages details <Packages_details>` page for more info
on these packages, and the pages for their respective commands for
OpenMP threading info.
In addition, there are a few commands in LAMMPS that have native OpenMP
support included as well. These are commands in the ``ML-SNAP``,
``DIFFRACTION``, and ``DPD-REACT`` packages. Furthermore, some packages
support OpenMP threading indirectly through the libraries they interface
to: e.g. ``KSPACE``, and ``COLVARS``. See the :doc:`Packages details
<Packages_details>` page for more info on these packages, and the pages
for their respective commands for OpenMP threading info.
For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
and turn on their native OpenMP support and turn on their native OpenMP
@ -489,8 +488,9 @@ using CMake or Make.
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default)
-D BUILD_LAMMPS_SHELL=value # yes or no (default)
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-D BUILD_LAMMPS_SHELL=value # yes or no (default). Build lammps-shell
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build lammps-gui
The generated binaries will also become part of the LAMMPS installation
(see below).
@ -504,7 +504,6 @@ using CMake or Make.
make binary2txt # build only binary2txt tool
make chain # build only chain tool
make micelle2d # build only micelle2d tool
make thermo_extract # build only thermo_extract tool
cd lammps/tools/lammps-shell
make # build LAMMPS shell

14
doc/src/Build_cmake.rst
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@ -177,13 +177,13 @@ configuration is selected with the *-C* flag:
ctest -C Debug
The CMake scripts in LAMMPS have basic support for being compiled using a
multi-config build system, but not all of it has been ported. This is in
particular applicable to compiling packages that require additional libraries
that would be downloaded and compiled by CMake. The "windows" preset file
tries to keep track of which packages can be compiled natively with the
MSVC compilers out-of-the box. Not all of those external libraries are
portable to Windows, either.
The CMake scripts in LAMMPS have basic support for being compiled using
a multi-config build system, but not all of it has been ported. This is
in particular applicable to compiling packages that require additional
libraries that would be downloaded and compiled by CMake. The
``windows.cmake`` preset file tries to keep track of which packages can
be compiled natively with the MSVC compilers out-of-the box. Not all of
the external libraries are portable to Windows, either.
Installing CMake

193
doc/src/Build_extras.rst
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@ -722,9 +722,10 @@ This list was last updated for version 4.0.1 of the Kokkos library.
``cmake/presets`` folder, ``kokkos-serial.cmake``,
``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``. They will enable
the KOKKOS package and enable some hardware choice. So to compile
with CUDA device parallelization (for GPUs with CC 5.0 and up)
with some common packages enabled, you can do the following:
the KOKKOS package and enable some hardware choices. For GPU
support those preset files must be customized to match the
hardware used. So to compile with CUDA device parallelization with
some common packages enabled, you can do the following:
.. code-block:: bash
@ -886,6 +887,50 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
----------
.. _machdyn:
MACHDYN package
-------------------------------
To build with this package, you must download the Eigen3 library.
Eigen3 is a template library, so you do not need to build it.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
downloaded and inside the CMake build directory. If the Eigen3
library is already on your system (in a location where CMake
cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
``Eigen3`` include file is in.
.. tab:: Traditional make
You can download the Eigen3 library manually if you prefer; follow
the instructions in ``lib/machdyn/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invokes the ``lib/machdyn/Install.py`` script with the
specified args:
.. code-block:: bash
make lib-machdyn # print help message
make lib-machdyn args="-b" # download to lib/machdyn/eigen3
make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
Note that a symbolic (soft) link named ``includelink`` is created
in ``lib/machdyn`` to point to the Eigen dir. When LAMMPS builds it
will use this link. You should not need to edit the
``lib/machdyn/Makefile.lammps`` file.
----------
.. _mliap:
ML-IAP package
@ -1431,6 +1476,55 @@ ML-POD package
----------
.. _ml-quip:
ML-QUIP package
---------------------------------
To build with this package, you must download and build the QUIP
library. It can be obtained from GitHub. For support of GAP
potentials, additional files with specific licensing conditions need
to be downloaded and configured. The automatic download will from
within CMake will download the non-commercial use version.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git
installed. It will use the same compilers and flags as used for
compiling LAMMPS. Currently this is only supported for the GNU
and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
want to use a previously compiled and installed QUIP library and
CMake cannot find it.
The QUIP library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the QUIP build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make
The download/build procedure for the QUIP library, described in
``lib/quip/README`` file requires setting two environment
variables, ``QUIP_ROOT`` and ``QUIP_ARCH``. These are accessed by
the ``lib/quip/Makefile.lammps`` file which is used when you
compile and link LAMMPS with this package. You should only need
to edit ``Makefile.lammps`` if the LAMMPS build can not use its
settings to successfully build on your system.
----------
.. _plumed:
PLUMED package
@ -1952,55 +2046,6 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
----------
.. _ml-quip:
ML-QUIP package
---------------------------------
To build with this package, you must download and build the QUIP
library. It can be obtained from GitHub. For support of GAP
potentials, additional files with specific licensing conditions need
to be downloaded and configured. The automatic download will from
within CMake will download the non-commercial use version.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git
installed. It will use the same compilers and flags as used for
compiling LAMMPS. Currently this is only supported for the GNU
and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
want to use a previously compiled and installed QUIP library and
CMake cannot find it.
The QUIP library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the QUIP build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make
The download/build procedure for the QUIP library, described in
``lib/quip/README`` file requires setting two environment
variables, ``QUIP_ROOT`` and ``QUIP_ARCH``. These are accessed by
the ``lib/quip/Makefile.lammps`` file which is used when you
compile and link LAMMPS with this package. You should only need
to edit ``Makefile.lammps`` if the LAMMPS build can not use its
settings to successfully build on your system.
----------
.. _scafacos:
SCAFACOS package
@ -2048,50 +2093,6 @@ To build with this package, you must download and build the
----------
.. _machdyn:
MACHDYN package
-------------------------------
To build with this package, you must download the Eigen3 library.
Eigen3 is a template library, so you do not need to build it.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
downloaded and inside the CMake build directory. If the Eigen3
library is already on your system (in a location where CMake
cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
``Eigen3`` include file is in.
.. tab:: Traditional make
You can download the Eigen3 library manually if you prefer; follow
the instructions in ``lib/smd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invokes the ``lib/smd/Install.py`` script with the
specified args:
.. code-block:: bash
make lib-smd # print help message
make lib-smd args="-b" # download to lib/smd/eigen3
make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
Note that a symbolic (soft) link named ``includelink`` is created
in ``lib/smd`` to point to the Eigen dir. When LAMMPS builds it
will use this link. You should not need to edit the
``lib/smd/Makefile.lammps`` file.
----------
.. _vtk:
VTK package

1
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@ -182,6 +182,7 @@ make a copy of one of them and modify it to suit your needs.
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
Presets that have names starting with "windows" are specifically for
compiling LAMMPS :doc:`natively on Windows <Build_windows>` and

1
doc/src/Commands_compute.rst
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@ -91,6 +91,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`composition/atom (k) <compute_composition_atom>`
* :doc:`mliap <compute_mliap>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`

4
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View File

@ -23,17 +23,14 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`
* :doc:`atom/gz <dump>`
* :doc:`atom/mpiio <dump>`
* :doc:`atom/zstd <dump>`
* :doc:`cfg <dump>`
* :doc:`cfg/gz <dump>`
* :doc:`cfg/mpiio <dump>`
* :doc:`cfg/uef <dump_cfg_uef>`
* :doc:`cfg/zstd <dump>`
* :doc:`custom <dump>`
* :doc:`custom/adios <dump_adios>`
* :doc:`custom/gz <dump>`
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`grid <dump>`
@ -51,7 +48,6 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
* :doc:`xtc <dump>`
* :doc:`xyz <dump>`
* :doc:`xyz/gz <dump>`
* :doc:`xyz/mpiio <dump>`
* :doc:`xyz/zstd <dump>`
* :doc:`yaml <dump>`

5
doc/src/Commands_fix.rst
View File

@ -69,7 +69,7 @@ OPT.
* :doc:`drude/transform/inverse <fix_drude_transform>`
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield <fix_efield>`
* :doc:`efield (k) <fix_efield>`
* :doc:`efield/tip4p <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode>`
@ -181,6 +181,7 @@ OPT.
* :doc:`pour <fix_pour>`
* :doc:`precession/spin <fix_precession_spin>`
* :doc:`press/berendsen <fix_press_berendsen>`
* :doc:`press/langevin <fix_press_langevin>`
* :doc:`print <fix_print>`
* :doc:`propel/self <fix_propel_self>`
* :doc:`property/atom (k) <fix_property_atom>`
@ -232,7 +233,7 @@ OPT.
* :doc:`spring <fix_spring>`
* :doc:`spring/chunk <fix_spring_chunk>`
* :doc:`spring/rg <fix_spring_rg>`
* :doc:`spring/self <fix_spring_self>`
* :doc:`spring/self (k) <fix_spring_self>`
* :doc:`srd <fix_srd>`
* :doc:`store/force <fix_store_force>`
* :doc:`store/state <fix_store_state>`

4
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@ -265,7 +265,7 @@ OPT.
* :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (k) <pair_snap>`
* :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`sph/heatconduction <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
@ -305,5 +305,5 @@ OPT.
* :doc:`wf/cut <pair_wf_cut>`
* :doc:`ylz <pair_ylz>`
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`yukawa/colloid (gko) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`

19
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@ -85,6 +85,25 @@ The same functionality is available through
:doc:`bond style mesocnt <bond_mesocnt>` and
:doc:`angle style mesocnt <angle_mesocnt>`.
MPIIO package
-------------
.. deprecated:: TBD
The MPIIO package has been removed from LAMMPS since it was unmaintained
for many years and thus not updated to incorporate required changes that
had been applied to the corresponding non-MPIIO commands. As a
consequence the MPIIO commands had become unreliable and sometimes
crashing LAMMPS or corrupting data. Similar functionality is available
through the :ref:`ADIOS package <PKG-ADIOS>` and the :ref:`NETCDF
package <PKG-NETCDF>`. Also, the :doc:`dump_modify nfile or dump_modify
fileper <dump_modify>` keywords may be used for an efficient way of
writing out dump files when running on large numbers of processors.
Similarly, the "nfile" and "fileper" keywords exist for restarts:
see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
:doc:`write_restart <write_restart>`.
MSCG package
------------

6
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@ -7148,9 +7148,6 @@ keyword to allow for additional bonds to be formed
*Read_dump xyz fields do not have consistent scaling/wrapping*
Self-explanatory.
*Reading from MPI-IO filename when MPIIO package is not installed*
Self-explanatory.
*Reax_defs.h setting for NATDEF is too small*
Edit the setting in the ReaxFF library and re-compile the
library and re-build LAMMPS.
@ -8489,9 +8486,6 @@ keyword to allow for additional bonds to be formed
The write_restart command cannot be used before a read_data,
read_restart, or create_box command.
*Writing to MPI-IO filename when MPIIO package is not installed*
Self-explanatory.
*Zero length rotation vector with displace_atoms*
Self-explanatory.

1
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@ -100,6 +100,7 @@ Tutorials howto
Howto_cmake
Howto_github
Howto_lammps_gui
Howto_pylammps
Howto_wsl

9
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@ -1,10 +1,10 @@
Using CMake with LAMMPS tutorial
================================
Using CMake with LAMMPS
=======================
The support for building LAMMPS with CMake is a recent addition to
LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard
Berger (LANL). One of the key strengths of CMake is that it is not
tied to a specific platform or build system and thus it generates the
tied to a specific platform or build system. Instead it generates the
files necessary to build and develop for different build systems and on
different platforms. Note, that this applies to the build system itself
not the LAMMPS code. In other words, without additional porting effort,
@ -32,7 +32,8 @@ program ``cmake`` (or ``cmake3``), a text mode interactive user
interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user
interface (GUI) program ``cmake-gui``. All of them are portable
software available on all supported platforms and can be used
interchangeably. The minimum required CMake version is 3.16.
interchangeably. As of LAMMPS version 2 August 2023, the minimum
required CMake version is 3.16.
All details about features and settings for CMake are in the `CMake
online documentation <https://cmake.org/documentation/>`_. We focus

700
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@ -0,0 +1,700 @@
Using the LAMMPS GUI
====================
This document describes **LAMMPS GUI version 1.5**.
-----
LAMMPS GUI is a graphical text editor customized for editing LAMMPS
input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
and thus can run LAMMPS directly using the contents of the editor's text
buffer as input. It can retrieve and display information from LAMMPS
while it is running, display visualizations created with the :doc:`dump
image command <dump_image>`, and is adapted specifically for editing
LAMMPS input files through text completion and reformatting, and linking
to the online LAMMPS documentation for known LAMMPS commands and styles.
.. note::
Pre-compiled, ready-to-use LAMMPS GUI executables for Linux (Ubuntu
20.04LTS or later and compatible), macOS (version 11 aka Big Sur or
later), and Windows (version 10 or later) :ref:`are available
<lammps_gui_install>` for download. They may be linked to a
development version of LAMMPS in case they need features not yet
available in a released version. Serial LAMMPS executables of the
same LAMMPS version are included as well. The source code for the
LAMMPS GUI is included in the LAMMPS source code and can be found in
the ``tools/lammps-gui`` folder. It can be compiled alongside LAMMPS
when :doc:`compiling with CMake <Build_cmake>`.
LAMMPS GUI tries to provide an experience similar to what people
traditionally would do to run LAMMPS using a command line window:
- editing inputs with a text editor
- run LAMMPS on the input with selected command line flags
- and then use or extract data from the created files and visualize it
That procedure is quite effective for people proficient in using the
command line, as that allows them to use tools for the individual steps
which they are most comfortable with. It is often required when running
LAMMPS on high-performance computing facilities.
The main benefit of using the LAMMPS GUI application instead is that
many basic tasks can be done directly from the GUI without switching to
a text console window or using external programs, let alone writing
scripts to extract data from the generated output. It also integrates
well with graphical desktop environments.
LAMMPS GUI thus makes it easier for beginners to get started running
simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
since you only need to learn how to use a single program for most tasks
and thus time can be saved and people can focus on learning LAMMPS. It
is also designed to keep the barrier low when you decide to switch to a
full featured, standalone programming editor and more sophisticated
visualization and analysis tools and run LAMMPS from a command line.
The following text provides a detailed tour of the features and
functionality of the LAMMPS GUI.
Suggestions for new features and reports of bugs are always welcome.
You can use the :doc:`the same channels as for LAMMPS itself
<Errors_bugs>` for that purpose.
-----
Main window
-----------
When LAMMPS GUI starts, it will show a main window with either an
empty buffer or the contents of a loaded file. In the latter case it
may look like the following:
.. image:: JPG/lammps-gui-main.png
:align: center
:scale: 50%
There is the typical menu bar at the top, then the main editor buffer,
and a status bar at the bottom. The input file contents are shown
with line numbers on the left and the input is colored according to
the LAMMPS input file syntax. The status bar shows the status of
LAMMPS execution on the left (e.g. "Ready." when idle) and the current
working directory on the right. The name of the current file in the
buffer is shown in the window title; the word `*modified*` is added if
the buffer edits have not yet saved to a file. The size of the main
window will be stored when exiting and restored when starting again.
Opening Files
^^^^^^^^^^^^^
The LAMMPS GUI application will try to open the first command line
argument as a LAMMPS input script, further arguments are ignored.
When no argument is given, LAMMPS GUI will start with an empty buffer.
Files can also be opened via the ``File`` menu or by drag-and-drop of
a file from a graphical file manager into the editor window. Only one
file can be open at a time, so opening a new file with a filled buffer
will close the buffer. If the buffer has unsaved modifications, you
will be asked to either cancel the operation, discard the changes, or
save them.
Running LAMMPS
^^^^^^^^^^^^^^
From within the LAMMPS GUI main window LAMMPS can be started either from
the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by
the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by
clicking on the green "Run" button in the status bar. All of these
operations will cause LAMMPS to process the entire input script, which
may contain multiple :doc:`run <run>` or :doc:`minimize <minimize>`
commands.
LAMMPS runs in a separate thread, so the GUI stays responsive and is
able to interact with the running calculation and access data it
produces. It is important to note that running LAMMPS this way is
using the contents of the input buffer for the run (via the
:cpp:func:`lammps_commands_string()` function of the LAMMPS C-library
interface), and **not** the original file it was read from. Thus, if
there are unsaved changes in the buffer, they *will* be used. As an
alternative, it is also possible to run LAMMPS by reading the contents
of a file from the ``Run LAMMPS from File`` menu entry or with
`Ctrl-Shift-Enter`. This option may be required in some rare cases
where the input uses some functionality that is not compatible with
running LAMMPS from a string buffer. For consistency, any unsaved
changes in the buffer must be either saved to the file or undone
before LAMMPS can be run from a file.
.. image:: JPG/lammps-gui-running.png
:align: center
:scale: 75%
While LAMMPS is running, the contents of the status bar change. On
the left side there is a text indicating that LAMMPS is running, which
will also show the number of active threads, if thread-parallel
acceleration was selected in the ``Preferences`` dialog. On the right
side, a progress bar is shown that displays the estimated progress for
the current :doc:`run command <run>`.
Also, the line number of the currently executed command will be
highlighted in green.
.. image:: JPG/lammps-gui-run-highlight.png
:align: center
:scale: 75%
If an error occurs (in the example below the command :doc:`label
<label>` was incorrectly capitalized as "Label"), an error message
dialog will be shown and the line of the input which triggered the
error will be highlighted. The state of LAMMPS in the status bar will
be set to "Failed." instead of "Ready."
.. image:: JPG/lammps-gui-run-error.png
:align: center
:scale: 75%
Up to three additional windows will open during a run:
- a log window with the captured screen output
- a chart window with a line graph created from the thermodynamic output of the run
- a slide show window with images created by a :doc:`dump image command <dump_image>`
More information on those windows and how to adjust their behavior and
contents is given below.
An active LAMMPS run can be stopped cleanly by using either the ``Stop
LAMMPS`` entry in the ``Run`` menu, the keyboard shortcut `Ctrl-/`
(`Command-/` on macOS), or by clicking on the red button in the status
bar. This will cause the running LAMMPS process to complete the current
timestep (or iteration for energy minimization) and then complete the
processing of the buffer while skipping all run or minimize commands.
This is equivalent to the input script command :doc:`timer timeout 0
<timer>` and is implemented by calling the
:cpp:func:`lammps_force_timeout()` function of the LAMMPS C-library
interface. Please see the corresponding documentation pages to
understand the implications of this operation.
Log Window
----------
By default, when starting a run, a "Log Window" will open that displays
the current screen output of the LAMMPS calculation, that would normally
be seen in the command line window, as shown below.
.. image:: JPG/lammps-gui-log.png
:align: center
:scale: 50%
LAMMPS GUI captures the screen output as it is generated and updates
the log window regularly during a run.
By default, the log window will be replaced each time a run is started.
The runs are counted and the run number for the current run is displayed
in the window title. It is possible to change the behavior of LAMMPS
GUI in the preferences dialog to create a *new* log window for every run
or to not show the current log window. It is also possible to show or
hide the *current* log window from the ``View`` menu.
The text in the log window is read-only and cannot be modified, but
keyboard shortcuts to select and copy all or parts of the text can be
used to transfer text to another program. Also, the keyboard shortcut
`Ctrl-S` (`Command-S` on macOS) is available to save the log buffer to a
file. The "Select All" and "Copy" functions, as well as a "Save Log to
File" option are also available from a context menu by clicking with the
right mouse button into the log window text area.
Chart Window
------------
By default, when starting a run, a "Chart Window" will open that
displays a plot of thermodynamic output of the LAMMPS calculation as
shown below.
.. image:: JPG/lammps-gui-chart.png
:align: center
:scale: 50%
The drop down menu on the top right allows selection of different
properties that are computed and written to thermo output. Only one
property can be shown at a time. The plots will be updated with new
data as the run progresses, so they can be used to visually monitor the
evolution of available properties. The window title will show the
current run number that this chart window corresponds to. Same as
explained for the log window above, by default, the chart window will
be replaced on each new run, but the behavior can be changed in the
preferences dialog.
From the ``File`` menu on the top left, it is possible to save an image
of the currently displayed plot or export the data in either plain text
columns (for use by plotting tools like `gnuplot
<http://www.gnuplot.info/>`_ or `grace
<https://plasma-gate.weizmann.ac.il/Grace/>`_), or as CSV data which can
be imported for further processing with Microsoft Excel or `pandas
<https://pandas.pydata.org/>`_
Thermo output data from successive run commands in the input script will
be combined into a single data set unless the format, number, or names
of output columns are changed with a :doc:`thermo_style <thermo_style>`
or a :doc:`thermo_modify <thermo_modify>` command, or the current time
step is reset with :doc:`reset_timestep <reset_timestep>`, or if a
:doc:`clear <clear>` command is issued.
Image Slide Show
----------------
By default, if the LAMMPS input contains a :doc:`dump image
<dump_image>` command, a "Slide Show" window will open which loads and
displays the images created by LAMMPS as they are written.
.. image:: JPG/lammps-gui-slideshow.png
:align: center
:scale: 50%
The various buttons at the bottom right of the window allow single
stepping through the sequence of images or playing an animation (as a
continuous loop or once from first to last). It is also possible to
zoom in or zoom out of the displayed images, and to export the slide
show animation to a movie file, if `ffmpeg <https://ffmpeg.org/>`_ is
installed.
Variable Info
-------------
During a run, it may be of interest to monitor the value of input script
variables, for example to monitor the progress of loops. This can be
done by enabling the "Variables Window" in the ``View`` menu or by using
the `Ctrl-Shift-W` keyboard shortcut. This will show info similar to
the :doc:`info variables <info>` command in a separate window as shown
below.
.. image:: JPG/lammps-gui-variable-info.png
:align: center
:scale: 75%
Like the log and chart windows, its content is continuously updated
during a run. It will show "(none)" if there are no variables
defined. Note that it is also possible to *set* :doc:`index style
variables <variable>`, that would normally be set via command line
flags, via the "Set Variables..." dialog from the ``Run`` menu.
LAMMPS GUI will automatically set the variable "gui_run" to the
current value of the run counter. That way it would be possible
to automatically record a log for each run attempt by using the
command
.. code-block:: LAMMPS
log logfile-${gui_run}.txt
at the beginning of an input file. That would record logs to files
``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
Viewing Snapshot Images
-----------------------
By selecting the ``Create Image`` entry in the ``Run`` menu, or by
hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
clicking on the "palette" button in the status bar, LAMMPS GUI will send
a custom :doc:`write_dump image <dump_image>` command to LAMMPS and read
the resulting snapshot image with the current state of the system into
an image viewer window. This functionality is not available *during* an
ongoing run. When LAMMPS is not yet initialized, LAMMPS GUI will try to
identify the line with the first run or minimize command and execute all
command up to that line from the input buffer and then add a "run 0"
command. This will initialize the system so an image of the initial
state of the system can be rendered. If there was an error, the
snapshot image viewer will not appear.
When possible, LAMMPS GUI will try to detect which elements the atoms
correspond to (via their mass) and then colorize them in the image
accordingly. Otherwise the default predefined sequence of colors is
assigned to the different atom types.
.. image:: JPG/lammps-gui-image.png
:align: center
:scale: 50%
The default image size, some default image quality settings, the view
style and some colors can be changed in the ``Preferences`` dialog
window. From the image viewer window further adjustments can be made:
actual image size, high-quality (SSAO) rendering, anti-aliasing, view
style, display of box or axes, zoom factor. The view of the system
can be rotated horizontally and vertically. It is also possible to
only display the atoms within a group defined in the input script
(default is "all"). After each change, the image is rendered again
and the display updated. The small palette icon on the top left will
be colored while LAMMPS is running to render the new image; it will be
grayed out when it is finished. When there are many atoms to render
and high quality images with anti-aliasing are requested, re-rendering
may take several seconds. From the ``File`` menu of the image window,
the current image can be saved to a file or copied into the
cut-n-paste buffer for pasting into another application.
Editor Functions
----------------
The editor has most of the usual functionality that similar programs
have: text selection via mouse or with cursor moves while holding the
Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`), Paste (`Ctrl-V`), Undo
(`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All (`Ctrl-A`). When trying
to exit the editor with a modified buffer, a dialog will pop up asking
whether to cancel the exit operation, or to save or not save the buffer
contents to a file.
Context Specific Word Completion
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
By default, LAMMPS GUI will display a small pop-up frame with possible
choices for LAMMPS input script commands or styles after 2 characters of
a word have been typed.
.. image:: JPG/lammps-gui-complete.png
:align: center
:scale: 75%
The word can then be completed through selecting an entry by scrolling
up and down with the cursor keys and selecting with the 'Enter' key or
by clicking on the entry with the mouse. The automatic completion
pop-up can be disabled in the ``Preferences`` dialog, but the completion
can still be requested manually by either hitting the 'Shift-TAB' key or
by right-clicking with the mouse and selecting the option from the
context menu. Most of the completion information is taken from the
LAMMPS instance and thus it will be adjusted to only show available
options that have been enabled while compiling LAMMPS. That, however,
excludes accelerated styles and commands; for improved clarity, only the
non-suffix version of styles are shown.
Line Reformatting
^^^^^^^^^^^^^^^^^
The editor supports reformatting lines according to the syntax in order
to have consistently aligned lines. This primarily means adding
whitespace padding to commands, type specifiers, IDs and names. This
reformatting is performed by default when hitting the 'Enter' key to
start a new line. This feature can be turned on or off in the
``Preferences`` dialog, but it can still be manually performed by
hitting the 'TAB' key. The amount of padding can also be changed in the
``Preferences`` dialog.
Internally this functionality is achieved by splitting the line into
"words" and then putting it back together with padding added where the
context can be detected; otherwise a single space is used between words.
Context Specific Help
^^^^^^^^^^^^^^^^^^^^^
.. image:: JPG/lammps-gui-popup-help.png
:align: center
:scale: 50%
A unique feature of the LAMMPS GUI is the option to look up the
documentation for the command in the current line. This can be done by
either clicking the right mouse button or by using the `Ctrl-?` keyboard
shortcut. When clicking the mouse there are additional entries in the
context menu that will open the corresponding documentation page in the
online LAMMPS documentation. When using the keyboard, the first of
those entries will be chosen directly.
Menu
----
The menu bar has entries ``File``, ``Edit``, ``Run``, ``View``, and
``About``. Instead of using the mouse to click on them, the individual
menus can also be activated by hitting the `Alt` key together with the
corresponding underlined letter, that is `Alt-F` will activate the
``File`` menu. For the corresponding activated sub-menus, the key
corresponding the underlined letters can again be used to select entries
instead of using the mouse.
File
^^^^
The ``File`` menu offers the usual options:
- ``New`` will clear the current buffer and reset the file name to ``*unknown*``
- ``Open`` will open a dialog to select a new file
- ``Save`` will save the current file; if the file name is ``*unknown*``
a dialog will open to select a new file name
- ``Save As`` will open a dialog to select and new file name and save
the buffer to it
- ``Quit`` will exit LAMMPS GUI. If there are unsaved changes, a dialog
will appear to either cancel the operation, or to save or not save the
edited file.
In addition, up to 5 recent file names will be listed after the
``Open`` entry that allows re-opening recent files. This list is
stored when quitting and recovered when starting again.
Edit
^^^^
The ``Edit`` menu offers the usual editor functions like ``Undo``,
``Redo``, ``Cut``, ``Copy``, ``Paste``. It can also open a
``Preferences`` dialog (keyboard shortcut `Ctrl-P`) and allows deletion
of all stored preferences so they will be reset to default values.
Run
^^^
The ``Run`` menu has options to start and stop a LAMMPS process.
Rather than calling the LAMMPS executable as a separate executable,
the LAMMPS GUI is linked to the LAMMPS library and thus can run LAMMPS
internally through the :ref:`LAMMPS C-library interface
<lammps_c_api>`.
Specifically, a LAMMPS instance will be created by calling
:cpp:func:`lammps_open_no_mpi`. The buffer contents then executed by
calling :cpp:func:`lammps_commands_string`. Certain commands and
features are only available after a LAMMPS instance is created. Its
presence is indicated by a small LAMMPS ``L`` logo in the status bar
at the bottom left of the main window. As an alternative, it is also
possible to run LAMMPS using the contents of the edited file by
reading the file. This is mainly provided as a fallback option in
case the input uses some feature that is not available when running
from a string buffer.
The LAMMPS calculation will be run in a concurrent thread so that the
GUI can stay responsive and be updated during the run. This can be
used to tell the running LAMMPS instance to stop at the next timestep.
The ``Stop LAMMPS`` entry will do this by calling
:cpp:func:`lammps_force_timeout`, which is equivalent to a :doc:`timer
timeout 0 <timer>` command.
The ``Set Variables...`` entry will open a dialog box where
:doc:`index style variables <variable>` can be set. Those variables
will be passed to the LAMMPS instance when it is created and are thus
set *before* a run is started.
.. image:: JPG/lammps-gui-variables.png
:align: center
:scale: 75%
The ``Set Variables`` dialog will be pre-populated with entries that
are set as index variables in the input and any variables that are
used but not defined, if the built-in parser can detect them. New
rows for additional variables can be added through the ``Add Row``
button and existing rows can be deleted by clicking on the ``X`` icons
on the right.
The ``Create Image`` entry will send a :doc:`dump image <dump_image>`
command to the LAMMPS instance, read the resulting file, and show it
in an ``Image Viewer`` window.
The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
with a :doc:`data file <write_data>` containing the current state of
the system. This option is only available if the LAMMPS GUI can find
the OVITO executable in the system path.
The ``View in VMD`` entry will launch VMD with a :doc:`data file
<write_data>` containing the current state of the system. This option
is only available if the LAMMPS GUI can find the VMD executable in the
system path.
View
^^^^
The ``View`` menu offers to show or hide additional windows with log
output, charts, slide show, variables, or snapshot images. The
default settings for their visibility can be changed in the
``Preferences dialog``.
About
^^^^^
The ``About`` menu finally offers a couple of dialog windows and an
option to launch the LAMMPS online documentation in a web browser.
The ``About LAMMPS`` entry displays a dialog with a summary of the
configuration settings of the LAMMPS library in use and the version
number of LAMMPS GUI itself. The ``Quick Help`` displays a dialog
with a minimal description of LAMMPS GUI. The ``LAMMPS GUI Howto``
entry will open this documentation page from the online documentation
in a web browser window. The ``LAMMPS Manual`` entry will open the
main page of the LAMMPS documentation in the web browser.
-----
Preferences
-----------
The ``Preferences`` dialog allows customization of the behavior and
look of the LAMMPS GUI application. The settings are grouped and each
group is displayed within a tab.
.. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
:width: 24%
.. |guiprefs2| image:: JPG/lammps-gui-prefs-accel.png
:width: 24%
.. |guiprefs3| image:: JPG/lammps-gui-prefs-image.png
:width: 24%
.. |guiprefs4| image:: JPG/lammps-gui-prefs-editor.png
:width: 24%
|guiprefs1| |guiprefs2| |guiprefs3| |guiprefs4|
General Settings:
^^^^^^^^^^^^^^^^^
- *Echo input to log:* when checked, all input commands, including
variable expansions, will be echoed to the log window. This is
equivalent to using `-echo screen` at the command line. There is no
log *file* produced by default, since LAMMPS GUI uses `-log none`.
- *Include citation details:* when checked full citation info will be
included to the log window. This is equivalent to using `-cite
screen` on the command line.
- *Show log window by default:* when checked, the screen output of a
LAMMPS run will be collected in a log window during the run
- *Show chart window by default:* when checked, the thermodynamic
output of a LAMMPS run will be collected and displayed in a chart
window as line graphs.
- *Show slide show window by default:* when checked, a slide show
window will be shown with images from a dump image command, if
present, in the LAMMPS input.
- *Replace log window on new run:* when checked, an existing log
window will be replaced on a new LAMMPS run, otherwise each run will
create a new log window.
- *Replace chart window on new run:* when checked, an existing chart
window will be replaced on a new LAMMPS run, otherwise each run will
create a new chart window.
- *Replace image window on new render:* when checked, an existing
chart window will be replaced when a new snapshot image is requested,
otherwise each command will create a new image window.
- *Path to LAMMPS Shared Library File:* this option is only visible
when LAMMPS GUI was compiled to load the LAMMPS library at run time
instead of being linked to it directly. With the ``Browse..`` button
or by changing the text, a different shared library file with a
different compilation of LAMMPS with different settings or from a
different version can be loaded. After this setting was changed,
LAMMPS GUI needs to be re-launched.
- *Select Default Font:* Opens a font selection dialog where the type
and size for the default font (used for everything but the editor and
log) of the application can be set.
- *Select Text Font:* Opens a font selection dialog where the type and
size for the text editor and log font of the application can be set.
- *GUI update interval:* Allows to set the time interval between GUI
and data updates during a LAMMPS run in milliseconds. The default is
to update the GUI every 100 milliseconds. This is good for most cases.
For LAMMPS runs that run very fast, however, data may be missed and
through lowering this interval, this can be corrected. However, this
will make the GUI use more resources, which may be a problem on some
computers with slower CPUs. The default value is 100 milliseconds.
Accelerators:
^^^^^^^^^^^^^
This tab enables selection of an accelerator package for LAMMPS to use
and is equivalent to using the `-suffix` and `-package` flags on the
command line. Only settings supported by the LAMMPS library and local
hardware are available. The `Number of threads` field allows setting
the maximum number of threads for the accelerator packages that use
threads.
Snapshot Image:
^^^^^^^^^^^^^^^
This tab allows setting defaults for the snapshot images displayed in
the ``Image Viewer`` window, such as its dimensions and the zoom
factor applied. The *Antialias* switch will render images with twice
the number of pixels for width and height and then smoothly scale the
image back to the requested size. This produces higher quality images
with smoother edges at the expense of requiring more CPU time to
render the image. The *HQ Image mode* option turns on screen space
ambient occlusion (SSAO) mode when rendering images. This is also
more time consuming, but produces a more 'spatial' representation of
the system shading of atoms by their depth. The *VDW Style* checkbox
selects whether atoms are represented by space filling spheres when
checked or by smaller spheres and sticks. Finally there are a couple
of drop down lists to select the background and box colors.
Editor Settings:
^^^^^^^^^^^^^^^^
This tab allows tweaking settings of the editor window. Specifically
the amount of padding to be added to LAMMPS commands, types or type
ranges, IDs (e.g. for fixes), and names (e.g. for groups). The value
set is the minimum width for the text element and it can be chosen in
the range between 1 and 32.
The two settings which follow enable or disable the automatic
reformatting when hitting the 'Enter' key and the automatic display of
the completion pop-up window.
-----------
Keyboard Shortcuts
------------------
Almost all functionality is accessible from the menu of the editor
window or through keyboard shortcuts. The following shortcuts are
available (On macOS use the Command key instead of Ctrl/Control).
.. list-table::
:header-rows: 1
:widths: auto
* - Shortcut
- Function
- Shortcut
- Function
- Shortcut
- Function
* - Ctrl+N
- New File
- Ctrl+Z
- Undo edit
- Ctrl+Enter
- Run Input
* - Ctrl+O
- Open File
- Ctrl+Shift+Z
- Redo edit
- Ctrl+/
- Stop Active Run
* - Ctrl+S
- Save File
- Ctrl+C
- Copy text
- Ctrl+Shift+V
- Set Variables
* - Ctrl+Shift+S
- Save File As
- Ctrl+X
- Cut text
- Ctrl+I
- Snapshot Image
* - Ctrl+Q
- Quit Application
- Ctrl+V
- Paste text
- Ctrl+L
- Slide Show
* - Ctrl+W
- Close Window
- Ctrl+A
- Select All
- Ctrl+P
- Preferences
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS GUI Howto
* - Ctrl+Shift+M
- LAMMPS Manual
- Ctrl+?
- Context Help
- Ctrl+Shift+W
- Show Variables
* - Ctrl+Shift+Enter
- Run File
- TAB
- Reformat line
- Shift+TAB
- Show Completions
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In
case of conflicts the list above takes precedence.
All other windows only support a subset of keyboard shortcuts listed
above. Typically, the shortcuts `Ctrl-/` (Stop Run), `Ctrl-W` (Close
Window), and `Ctrl-Q` (Quit Application) are supported.

2
doc/src/Install_mac.rst
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@ -5,7 +5,7 @@ LAMMPS can be downloaded, built, and configured for macOS with `Homebrew
<homebrew_>`_. (Alternatively, see the installation instructions for
:doc:`downloading an executable via Conda <Install_conda>`.) The
following LAMMPS packages are unavailable at this time because of
additional requirements not yet met: GPU, KOKKOS, MSCG, MPIIO, POEMS,
additional requirements not yet met: GPU, KOKKOS, MSCG, POEMS,
VORONOI.
After installing Homebrew, you can install LAMMPS on your system with

9
doc/src/Install_windows.rst
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@ -18,11 +18,10 @@ needed to run in parallel with MPI.
The LAMMPS binaries contain *all* :doc:`optional packages <Packages>`
included in the source distribution except: ADIOS, H5MD, KIM, ML-PACE,
ML-QUIP, MSCG, NETCDF, PLUMED, QMMM, SCAFACOS, and VTK. The serial
version also does not include the MPIIO and LATBOLTZ packages. The
PYTHON package is only available in the Python installers that bundle a
Python runtime. The GPU package is compiled for OpenCL with mixed
precision kernels.
ML-QUIP, MSCG, NETCDF, QMMM, SCAFACOS, and VTK. The serial version also
does not include the LATBOLTZ package. The PYTHON package is only
available in the Python installers that bundle a Python runtime. The
GPU package is compiled for OpenCL with mixed precision kernels.
The LAMMPS library is compiled as a shared library and the
:doc:`LAMMPS Python module <Python_module>` is installed, so that

14
doc/src/Intro_nonfeatures.rst
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@ -5,7 +5,7 @@ LAMMPS is designed to be a fast, parallel engine for molecular
dynamics (MD) simulations. It provides only a modest amount of
functionality for setting up simulations and analyzing their output.
Specifically, LAMMPS was not conceived and designed for:
Originally, LAMMPS was not conceived and designed for:
* being run through a GUI
* building molecular systems, or building molecular topologies
@ -14,9 +14,10 @@ Specifically, LAMMPS was not conceived and designed for:
* visualize your MD simulation interactively
* plot your output data
Over the years some of these limitations have been reduced or
removed, through features added to LAMMPS or external tools
that either closely interface with LAMMPS or extend LAMMPS.
Over the years many of these limitations have been reduced or
removed. In part through features added to LAMMPS and in part
through external tools that either closely interface with LAMMPS
or extend LAMMPS.
Here are suggestions on how to perform these tasks:
@ -24,8 +25,9 @@ Here are suggestions on how to perform these tasks:
wraps the library interface is provided. Thus, GUI interfaces can be
written in Python or C/C++ that run LAMMPS and visualize or plot its
output. Examples of this are provided in the python directory and
described on the :doc:`Python <Python_head>` doc page. Also, there
are several external wrappers or GUI front ends.
described on the :doc:`Python <Python_head>` doc page. As of version
2 August 2023 :ref:`a GUI tool <lammps_gui>` is included in LAMMPS.
Also, there are several external wrappers or GUI front ends.
* **Builder:** Several pre-processing tools are packaged with LAMMPS.
Some of them convert input files in formats produced by other MD codes
such as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of

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6
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@ -9,6 +9,7 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
- :cpp:func:`lammps_variable_info`
-----------------------
@ -37,6 +38,11 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_variable_info
:project: progguide
-----------------------
.. doxygenenum:: _LMP_DATATYPE_CONST
.. doxygenenum:: _LMP_STYLE_CONST

21
doc/src/Manual.rst
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@ -23,10 +23,23 @@ coordinated.
----------
The content for this manual is part of the LAMMPS distribution. The
online version always corresponds to the latest feature release version.
If needed, you can build a local copy of the manual as HTML pages or a
PDF file by following the steps on the :doc:`Build_manual` page. If you
The content for this manual is part of the LAMMPS distribution in its
doc directory.
* The version of the manual on the LAMMPS website corresponds to the
latest LAMMPS feature release. It is available at:
`https://docs.lammps.org/ <https://docs.lammps.org/>`_.
* A version of the manual corresponding to the latest LAMMPS stable
release (state of the *stable* branch on GitHub) is available online
at: `https://docs.lammps.org/stable/
<https://docs.lammps.org/stable/>`_
* A version of the manual with the features most recently added to
LAMMPS (state of the *develop* branch on GitHub) is available at:
`https://docs.lammps.org/latest/ <https://docs.lammps.org/latest/>`_
If needed, you can build a copy on your local machine of the manual
(HTML pages or PDF file) for the version of LAMMPS you have
downloaded. Follow the steps on the :doc:`Build_manual` page. If you
have difficulties viewing the pages, please :ref:`see this note
<webbrowser>`.

33
doc/src/Packages_details.rst
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@ -87,7 +87,6 @@ page gives those details.
* :ref:`MOFFF <PKG-MOFFF>`
* :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MOLFILE <PKG-MOLFILE>`
* :ref:`MPIIO <PKG-MPIIO>`
* :ref:`NETCDF <PKG-NETCDF>`
* :ref:`OPENMP <PKG-OPENMP>`
* :ref:`OPT <PKG-OPT>`
@ -2033,38 +2032,6 @@ This package has :ref:`specific installation instructions <molfile>` on the :doc
----------
.. _PKG-MPIIO:
MPIIO package
-------------
**Contents:**
Support for parallel output/input of dump and restart files via the
MPIIO library. It adds :doc:`dump styles <dump>` with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
**Install:**
The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
**Supporting info:**
* src/MPIIO: filenames -> commands
* :doc:`dump <dump>`
* :doc:`restart <restart>`
* :doc:`write_restart <write_restart>`
* :doc:`read_restart <read_restart>`
----------
.. _PKG-NETCDF:
NETCDF package

5
doc/src/Packages_list.rst
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@ -333,11 +333,6 @@ whether an extra library is needed to build and use the package:
- :doc:`dump molfile <dump_molfile>`
- n/a
- ext
* - :ref:`MPIIO <PKG-MPIIO>`
- MPI parallel I/O dump and restart
- :doc:`dump <dump>`
- n/a
- no
* - :ref:`NETCDF <PKG-NETCDF>`
- dump output via NetCDF
- :doc:`dump netcdf <dump_netcdf>`

7
doc/src/Speed_kokkos.rst
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@ -18,7 +18,7 @@ package was developed primarily by Christian Trott (Sandia) and Stan
Moore (Sandia) with contributions of various styles by others,
including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
(Sandia). For more information on developing using Kokkos abstractions
see the Kokkos `Wiki <https://github.com/kokkos/kokkos/wiki>`_.
see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
Kokkos currently provides support for 4 modes of execution (per MPI
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
@ -32,8 +32,9 @@ produce an executable compatible with a specific hardware.
Kokkos requires using a compiler that supports the c++17 standard. For
some compilers, it may be necessary to add a flag to enable c++17 support.
For example, the GNU compiler uses the -std=c++17 flag. For a list of
compilers that have been tested with the Kokkos library, see the Kokkos
`Wiki <https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
compilers that have been tested with the Kokkos library, see the
`requirements document of the Kokkos Wiki
<https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
.. admonition:: NVIDIA CUDA support
:class: note

271
doc/src/Tools.rst
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@ -645,106 +645,56 @@ LAMMPS GUI
Overview
^^^^^^^^
LAMMPS GUI is essentially a small graphical text editor that is linked
to the :ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run
LAMMPS directly using the contents of the editor's text buffer as input.
This is similar to what people usually would do using a text editor to
edit the input and then a command line terminal window to run the input
commands. The main benefit is that this integrates very well with
graphical desktop environments and that it is easier to use for
beginners in running computations and thus very suitable for tutorials
on LAMMPS. A small difference is that for the LAMMPS GUI it is not
require to first commit its buffer of the text editor to a file.
LAMMPS GUI is a graphical text editor customized for editing LAMMPS
input files that is linked to the :ref:`LAMMPS C-library <lammps_c_api>`
and thus can run LAMMPS directly using the contents of the editor's text
buffer as input. It can retrieve and display information from LAMMPS
while it is running, display visualizations created with the :doc:`dump
image command <dump_image>`, and is adapted specifically for editing
LAMMPS input files through text completion and reformatting, and linking
to the online LAMMPS documentation for known LAMMPS commands and styles.
This is similar to what people traditionally would do to run LAMMPS:
using a regular text editor to edit the input and run the necessary
commands, possibly including the text editor, too, from a command line
terminal window. This similarity is a design goal. While making it easy
for beginners to start with LAMMPS, it is also the intention to simplify
the transition to workflows like most experienced LAMMPS users do.
All features have been extensively exposed to keyboard shortcuts, so
that there is also appeal for experienced LAMMPS users for prototyping
and testing simulations setups.
Features
^^^^^^^^
The main window of the LAMMPS GUI is a generic text editor window with
line numbers and syntax highlighting set up for LAMMPS input files. It
can be used to edit any kind of text file, though. The output of a run
is captured and displayed in a separate dialog window and *not* sent to
the console or a log file (unless the :doc:`log command <log>` is used
in the input. The log window is regularly updated during the run and a
progress bar for the run command shown at the bottom of the main window.
Starting a new run will open another log windows. The state of LAMMPS
will be reset between two runs. After the simulation is finished, an
image of the simulated system can be created and shown in an image
viewer window. Ongoing runs can be stopped at the next iteration via
triggering a timeout.
A detailed discussion and explanation of all features and functionality
are in the :doc:`Howto_lammps_gui` tutorial Howto page.
When opening a file, the editor will determine the directory where the
file resides and switch its current working directory to the folder of
that file. Many LAMMPS inputs contain commands that read other files,
typically from the folder of the input file. The GUI will always show
the current working directory in the bottom. The editor window can also
receive (entire) files via drag-n-drop from a file manager GUI or a
desktop environment. When exiting the GUI with a modified buffer, a
dialog asking to either cancel, ignore the modifications, or save the
file with show up. Same when attempting to load a new file into a
modified buffer.
Here are a few highlights of LAMMPS GUI
Hotkeys
^^^^^^^
Almost all functionality is accessible from the menu or via hotkeys.
The following hotkeys are available (On macOS use the Command key
instead of Ctrl (aka Control)).
.. list-table::
:header-rows: 1
:widths: auto
* - Hotkey
- Function
- Hotkey
- Function
- Hotkey
- Function
- Hotkey
- Function
* - Ctrl+N
- New File
- Ctrl+Z
- Undo edit
- Ctrl+V
- Paste text
- Ctrl+Q
- Quit (Main Window only)
* - Ctrl+O
- Open File
- Ctrl+Shift+Z
- Redo edit
- Ctrl+Enter
- Run LAMMPS
- Ctrl+W
- Close (Log and Image Window only)
* - CTRL+S
- Save File
- Ctrl+C
- Copy text
- Ctrl+/
- Stop Active Run
- Ctrl+P
- Preferences
* - Ctrl+Shift+S
- Save File As
- Ctrl+X
- Cut text
- Ctrl+I
- Create Snapshot Image
- Ctrl+Shift+/
- Quick Help
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In
case of conflicts the list above takes precedence.
- Text editor with syntax highlighting customized for LAMMPS
- Text editor will switch working directory to folder of file in buffer
- Text editor will remember up to 5 recent files
- Context specific LAMMPS command help via online documentation
- LAMMPS is running in a concurrent thread, so the GUI remains responsive
- Support for most accelerator packages
- Progress bar indicates how far a run command is completed
- LAMMPS can be started and stopped with a hotkey
- Screen output is captured in a Log Window
- Thermodynamic output is captured and displayed as line graph in a Chart Window
- Indicator for currently executed command
- Indicator for line that caused an error
- Visualization of current state in Image Viewer (via :doc:`dump image <dump_image>`)
- Many adjustable settings and preferences that are persistent
- Dialog to set variables from the LAMMPS command line
Parallelization
^^^^^^^^^^^^^^^
Due to its nature as a graphical application, it is not possible to use
the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading is
available and enabled by default.
the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading and GPU
acceleration is available and enabled by default.
Prerequisites and portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -752,63 +702,75 @@ Prerequisites and portability
LAMMPS GUI is programmed in C++ based on the C++11 standard and using
the `Qt GUI framework <https://www.qt.io/product/framework>`_.
Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
recommended Qt 6.x not (yet) supported. Furthermore, CMake version 3.16
is required and LAMMPS must be configured with ``-D
LAMMPS_EXCETIONS=on`` and ``-D BUILD_MPI=off``. It has been successfully
compiled and tested on:
recommended; support for Qt version 6.x is under active development and
thus far only tested with Qt 6.5LTS on Linux. Building LAMMPS with
CMake is required.
The LAMMPS GUI has been successfully compiled and tested on:
- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
.. _lammps_gui_install:
Pre-compiled executables
^^^^^^^^^^^^^^^^^^^^^^^^
Pre-compiled LAMMPS executables including the GUI are currently
available from https://download.lammps.org/static. You can unpack the
archive (or mount the macOS disk image) and run the GUI directly in
place. The folder may also be moved around and added to the ``PATH``
environment variable so the executables will be found automatically. The
LAMMPS GUI executable is called ``lammps-gui`` and takes no arguments or
will interpret the first argument as filename to load.
Pre-compiled LAMMPS executable packages that include the GUI are currently
available from https://download.lammps.org/static or
https://github.com/lammps/lammps/releases. You can unpack the archives
(or mount the macOS disk image) and run the GUI directly in place. The
folder may also be moved around and added to the ``PATH`` environment
variable so the executables will be found automatically. The LAMMPS GUI
executable is called ``lammps-gui`` and either takes no arguments or
attempts to load the first argument as LAMMPS input file.
Compilation
^^^^^^^^^^^
The source for the LAMMPS GUI is included with the LAMMPS source code
distribution in the folder `tools/lammps-gui` and thus it can be can be
built as part of a regular LAMMPS compilation.
:doc:`Using CMake <Howto_cmake>` is required.
To enable its compilation the CMake variable ``-D BUILD_LAMMPS_GUI=on``
must be set when creating the CMake configuration. All other settings
(compiler, flags, compile type) for LAMMPS GUI are then inherited from
the regular LAMMPS build. If the Qt library is packaged for Linux
distributions, then its location is typically auto-detected since the
required CMake configuration files are stored in a location where CMake
can find them without additional help. Otherwise, the location of the
Qt library installation must be indicated by setting
``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to a folder inside
the Qt installation that contains the file ``Qt5Config.cmake``.
distribution in the folder ``tools/lammps-gui`` and thus it can be can
be built as part of a regular LAMMPS compilation. :doc:`Using CMake
<Howto_cmake>` is required. To enable its compilation, the CMake
variable ``-D BUILD_LAMMPS_GUI=on`` must be set when creating the CMake
configuration. All other settings (compiler, flags, compile type) for
LAMMPS GUI are then inherited from the regular LAMMPS build. If the Qt
library is packaged for Linux distributions, then its location is
typically auto-detected since the required CMake configuration files are
stored in a location where CMake can find them without additional help.
Otherwise, the location of the Qt library installation must be indicated
by setting ``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to
a folder inside the Qt installation that contains the file
``Qt5Config.cmake``. Similarly, for Qt6 the location of the Qt library
installation can be indicated by setting ``-D Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``,
if necessary. When both, Qt5 and Qt6 are available, Qt6 will be preferred
unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
It is also possible to build the LAMMPS GUI as a standalone executable
(e.g. when LAMMPS has been compiled with traditional make), then the
CMake configuration needs to be told where to find the LAMMPS headers
and the LAMMPS library, via `-D LAMMPS_SOURCE_DIR=/path/to/lammps/src`.
CMake will try to guess a build folder with the LAMMPS library from that
path, but it can also be set with `-D LAMMPS_LIB_DIR=/path/to/lammps/lib`.
It should be possible to build the LAMMPS GUI as a standalone
compilation (e.g. when LAMMPS has been compiled with traditional make),
then the CMake configuration needs to be told where to find the LAMMPS
headers and the LAMMPS library, via ``-D
LAMMPS_SOURCE_DIR=/path/to/lammps/src``. CMake will try to guess a
build folder with the LAMMPS library from that path, but it can also be
set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader library that will load
the LAMMPS library dynamically at runtime during the start of the GUI
from a shared library; e.g. `liblammps.so` or `liblammps.dylib` or
`liblammps.dll` (depending on the operating system). This has the
from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
``liblammps.dll`` (depending on the operating system). This has the
advantage that the LAMMPS library can be updated LAMMPS without having
to recompile the GUI. The ABI of the LAMMPS C-library interface is very
stable and generally backward compatible. This feature is enabled by
setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then
``-D LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS distribution.
setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
distribution.
Platform notes
^^^^^^^^^^^^^^
@ -818,7 +780,7 @@ macOS
When building on macOS, the build procedure will try to manufacture a
drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
target (i.e. `cmake --build <build dir> --target dmg` or `make dmg`.
target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
To build multi-arch executables that will run on both, arm64 and x86_64
architectures natively, it is necessary to set the CMake variable ``-D
@ -831,29 +793,50 @@ version.
Windows
"""""""
On Windows currently only compilation from within Visual Studio 2022 is
supported and tested. Using CMake and Ninja as build system is
required. Qt needs to be installed, tested was a package downloaded from
https://www.qt.io, into the ``C:\\Qt`` folder. There is a custom
`x64-GUI-MSVC` build configuration provided that will activate building
the `lammps-gui.exe` executable in addition to LAMMPS. When requesting
an installation from the `Build` menu, it will create a compressed zip
file with the executables and required dependent .dll files. This zip
file can be uncompressed and ``lammps-gui.exe`` run directly from there.
The uncompressed folder can be added to the ``PATH`` environment and
LAMMPS and LAMMPS GUI can be launched from anywhere from the command
line.
On Windows either native compilation from within Visual Studio 2022 with
Visual C++ is supported and tested, or compilation with the MinGW / GCC
cross-compiler environment on Fedora Linux.
**Visual Studio**
Using CMake and Ninja as build system are required. Qt needs to be
installed, tested was a binary package downloaded from
https://www.qt.io, which installs into the ``C:\\Qt`` folder by default.
There is a custom `x64-GUI-MSVC` build configuration provided in the
``CMakeSettings.json`` file that Visual Studio uses to store different
compilation settings for project. Choosing this configuration will
activate building the `lammps-gui.exe` executable in addition to LAMMPS
through importing package selection from the ``windows.cmake`` preset
file and enabling building the LAMMPS GUI and disabling building with MPI.
When requesting an installation from the `Build` menu in Visual Studio,
it will create a compressed ``LAMMPS-Win10-amd64.zip`` zip file with the
executables and required dependent .dll files. This zip file can be
uncompressed and ``lammps-gui.exe`` run directly from there. The
uncompressed folder can be added to the ``PATH`` environment and LAMMPS
and LAMMPS GUI can be launched from anywhere from the command line.
**MinGW64 Cross-compiler**
The standard CMake build procedure can be applied and the
``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
command will automatically include a suitable CMake toolset file (the
regular cmake command can be used after that). After building the
libraries and executables, you can build the target 'zip'
(i.e. ``cmake --build <build dir> --target zip`` or ``make zip``
to stage all installed files into a LAMMPS_GUI folder and then
run a script to copy all required dependencies, some other files,
and create a zip file from it.
Linux
"""""
Version 5.12 or later of the Qt library and CMake version 3.16 are
required and those are provided by, e.g., Ubuntu 20.04LTS. Thus older
Linux distributions are not likely to be supported, while more recent
ones will work, even for pre-compiled executables (see above). After
compiling with ``cmake --build <build folder>``, use
``cmake --build <build folder> --target tgz`` or ``make tgz`` to build
a ``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
Version 5.12 or later of the Qt library is required. Those are provided
by, e.g., Ubuntu 20.04LTS. Thus older Linux distributions are not
likely to be supported, while more recent ones will work, even for
pre-compiled executables (see above). After compiling with
``cmake --build <build folder>``, use ``cmake --build <build
folder> --target tgz`` or ``make tgz`` to build a
``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
support libraries.
----------

1
doc/src/compute.rst
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@ -245,6 +245,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
* :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
* :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
* :doc:`composition/atom <compute_composition_atom>` - local composition for each atom
* :doc:`mliap <compute_mliap>` - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials
* :doc:`momentum <compute_momentum>` - translational momentum
* :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms

118
doc/src/compute_composition_atom.rst Normal file
View File

@ -0,0 +1,118 @@
.. index:: compute composition/atom
.. index:: compute composition/atom/kk
compute composition/atom command
================================
Accelerator Variants: *composition/atom/kk*
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID composition/atom keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* composition/atom = style name of this compute command
* one or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *cutoff*
*cutoff* value = distance cutoff
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all composition/atom
compute 1 all composition/atom cutoff 9.0
comm_modify cutoff 9.0
Description
"""""""""""
.. versionadded:: TBD
Define a computation that calculates a local composition vector for each
atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,
composition is defined as the number of atoms of a given type
(including the central atom) divided by (:math:`M+1`). For a given central atom,
the sum of all compositions equals one.
.. note::
This compute uses the number of atom types, not chemical species, assigned in
:doc:`pair_coeff <pair_coeff>` command. If an interatomic potential has two
species (i.e., Cu and Ni) assigned to four different atom types in
:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the compute will
output four fractional values. In those cases, the user may desire an extra
calculation step to consolidate per-type fractions into per-species fractions.
This calculation can be conducted within LAMMPS using another compute such as
:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
post-processing step.
----------
The optional keyword *cutoff* defines the distance cutoff used when
searching for neighbors. The default value is the cutoff specified by
the pair style. If no pair style is defined, then a cutoff must be
defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is
defined), the *comm_modify cutoff* option must also be set to match
that of the *cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
.. note::
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral.
This is the default setting for the :doc:`special_bonds
<special_bonds>` command, and means those pairwise interactions do
not appear in the neighbor list. Because this compute uses the
neighbor list, it also means those pairs will not be included in
the order parameter. This difficulty can be circumvented by
writing a dump file, and using the :doc:`rerun <rerun>` command to
compute the order parameter for snapshots in the dump file. The
rerun script can use a :doc:`special_bonds <special_bonds>` command
that includes all pairs in the neighbor list.
----------
Output info
"""""""""""
This compute calculates a per-atom array with :math:`1 + N` columns, where :math:`N`
is the number of atom types. The first column is a count of the number of atoms
used to calculate composition (including the central atom), and each subsequent
column indicates the fraction of that atom type within the cutoff sphere.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>`
doc page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`comm_modify <comm_modify>`
Default
"""""""
The option defaults are *cutoff* = pair style cutoff.

20
doc/src/compute_property_grid.rst
View File

@ -19,6 +19,7 @@ Syntax
attributes = id, ix, iy, iz, x, y, z, xs, ys, zs, xc, yc, zc, xsc, ysc, zsc
id = ID of grid cell, x fastest, y next, z slowest
proc = processor ID (0 to Nprocs-1) which owns the grid cell
ix,iy,iz = grid indices in each dimension (1 to N inclusive)
x,y,z = coords of lower left corner of grid cell
xs,ys,zs = scaled coords of lower left corner of grid cell (0.0 to 1.0)
@ -30,8 +31,8 @@ Examples
.. code-block:: LAMMPS
compute 1 all property/grid id ix iy iz
compute 1 all property/grid id xc yc zc
compute 1 all property/grid 10 10 20 id ix iy iz
compute 1 all property/grid 100 100 1 id xc yc zc
Description
"""""""""""
@ -53,13 +54,20 @@ to output per-grid values from other computes of fixes, the grid size
specified for this command must be consistent with the grid sizes
used by the other commands.
The *id* attribute stores the grid ID for each grid cell. For a
global grid of size Nx by Ny by Nz (in 3d simulations) the grid IDs
range from 1 to Nx*Ny*Nz. They are ordered with the X index of the 3d
grid varying fastest, then Y, then Z slowest. For 2d grids (in 2d
The *id* attribute is the grid ID for each grid cell. For a global
grid of size Nx by Ny by Nz (in 3d simulations) the grid IDs range
from 1 to Nx*Ny*Nz. They are ordered with the X index of the 3d grid
varying fastest, then Y, then Z slowest. For 2d grids (in 2d
simulations), the grid IDs range from 1 to Nx*Ny, with X varying
fastest and Y slowest.
.. versionadded:: TBD
The *proc* attribute is the ID of the processor which owns the grid
cell. Processor IDs range from 0 to Nprocs - 1, where Nprocs is the
number of processors the simulation is running on. Each grid cell is
owned by a single processor.
The *ix*, *iy*, *iz* attributes are the indices of a grid cell in
each dimension. They range from 1 to Nx inclusive in the X dimension,
and similar for Y and Z.

2
doc/src/compute_stress_atom.rst
View File

@ -223,7 +223,7 @@ result. I.e. the last 2 columns of thermo output will be the same:
system pressure.
The compute stress/atom can be used in a number of ways. Here is an
example to compute a 1-d pressure profile in z-direction across the
example to compute a 1-d pressure profile in x-direction across the
complete simulation box. You will need to adjust the number of bins and the
selections for time averaging to your specific simulation. This assumes
that the dimensions of the simulation cell does not change.

44
doc/src/dump.rst
View File

@ -14,10 +14,6 @@
.. index:: dump custom/gz
.. index:: dump local/gz
.. index:: dump xyz/gz
.. index:: dump atom/mpiio
.. index:: dump cfg/mpiio
.. index:: dump custom/mpiio
.. index:: dump xyz/mpiio
.. index:: dump atom/zstd
.. index:: dump cfg/zstd
.. index:: dump custom/zstd
@ -63,7 +59,7 @@ Syntax
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml*
* N = dump on timesteps which are multiples of N
* file = name of file to write dump info to
* attribute1,attribute2,... = list of attributes for a particular style
@ -74,13 +70,11 @@ Syntax
*atom/adios* attributes = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*atom/gz* attributes = none
*atom/zstd* attributes = none
*atom/mpiio* attributes = none
*cfg* attributes = same as *custom* attributes, see below
*cfg/gz* attributes = same as *custom* attributes, see below
*cfg/zstd* attributes = same as *custom* attributes, see below
*cfg/mpiio* attributes = same as *custom* attributes, see below
*cfg/uef* attributes = same as *custom* attributes, discussed on :doc:`dump cfg/uef <dump_cfg_uef>` page
*custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* attributes = see below
*custom*, *custom/gz*, *custom/zstd* attributes = see below
*custom/adios* attributes = same as *custom* attributes, discussed on :doc:`dump custom/adios <dump_adios>` page
*dcd* attributes = none
*h5md* attributes = discussed on :doc:`dump h5md <dump_h5md>` page
@ -97,10 +91,9 @@ Syntax
*xyz* attributes = none
*xyz/gz* attributes = none
*xyz/zstd* attributes = none
*xyz/mpiio* attributes = none
*yaml* attributes = same as *custom* attributes, see below
* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* attributes:
* *custom* or *custom/gz* or *custom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* attributes:
.. parsed-literal::
@ -179,11 +172,9 @@ Examples
.. code-block:: LAMMPS
dump myDump all atom 100 dump.lammpstrj
dump myDump all atom/mpiio 100 dump.atom.mpiio
dump myDump all atom/gz 100 dump.atom.gz
dump myDump all atom/zstd 100 dump.atom.zst
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom/mpiio 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4a all custom 100 dump.myvel.lammpsbin id type x y z vx vy vz
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
@ -622,27 +613,10 @@ when running on large numbers of processors.
Note that using the "\*" and "%" characters together can produce a
large number of small dump files!
For styles that end with *mpiio* an ".mpiio" must appear somewhere in
the specified filename. These styles write their dump file in
parallel via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Note these styles are identical in command
syntax to the corresponding styles without "mpiio". Likewise, the
dump files produced by these MPI-IO styles are identical in format to
the files produced by their non-MPI-IO style counterparts. This means
you can write a dump file using MPI-IO and use the :doc:`read_dump
<read_dump>` command or perform other post-processing, just as if the
dump file was not written using MPI-IO.
.. deprecated:: TBD
Because MPI-IO dump files are one large file which all processors
write to, you cannot use the "%" wildcard character described above in
the filename. However you can use the ".bin" or ".lammpsbin" suffix
described below. Again, this file will be written in parallel and
have the same binary format as if it were written without MPI-IO.
.. warning::
The MPIIO package within LAMMPS is currently unmaintained and has
become unreliable. Use with caution.
The MPIIO package and the the corresponding "/mpiio" dump styles, except
for the unrelated "netcdf/mpiio" style were removed from LAMMPS.
----------
@ -956,11 +930,6 @@ the COMPRESS package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` page for
more info.
The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles
are part of the MPIIO package. They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
The *xtc*, *dcd*, and *yaml* styles are part of the EXTRA-DUMP package.
They are only enabled if LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
@ -971,6 +940,7 @@ Related commands
:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`,
:doc:`dump cfg/uef <dump_cfg_uef>`, :doc:`dump h5md <dump_h5md>`,
:doc:`dump image <dump_image>`, :doc:`dump molfile <dump_molfile>`,
:doc:`dump netcdf <dump_netcdf>`, :doc:`dump netcdf/mpiio <dump_netcdf>`,
:doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`,
:doc:`write_dump <write_dump>`

53
doc/src/dump_image.rst
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@ -24,7 +24,7 @@ Syntax
* color = atom attribute that determines color of each atom
* diameter = atom attribute that determines size of each atom
* zero or more keyword/value pairs may be appended
* keyword = *atom* or *adiam* or *bond* or *grid* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao*
* keyword = *atom* or *adiam* or *bond* or *grid* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *fsaa* or *ssao*
.. parsed-literal::
@ -85,6 +85,8 @@ Syntax
diam = diameter of subdomain lines as fraction of shortest box length
*shiny* value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
*fsaa* arg = yes/no
yes/no = do or do not apply anti-aliasing
*ssao* value = shading seed dfactor = SSAO depth shading
shading = *yes* or *no* = turn depth shading on/off
seed = random # seed (positive integer)
@ -597,13 +599,47 @@ image will appear. The *sfactor* value must be a value 0.0 <=
*sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface
and *sfactor* = 0 is a rough non-shiny surface.
The *ssao* keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If *yes* is set, then atoms further
away from the viewer are darkened via a randomized process, which is
perceived as depth. The calculation of this effect can increase the
cost of computing the image by roughly 2x. The strength of the effect
can be scaled by the *dfactor* parameter. If *no* is set, no depth
shading is performed.
.. versionadded:: TBD
The *fsaa* keyword can be used with the dump image command to improve
the image quality by enabling full scene anti-aliasing. Internally the
image is rendered at twice the width and height and then scaled down by
computing the average of each 2x2 block of pixels to produce a single
pixel in the final image at the original size. This produces images with
smoother, less ragged edges. The application of this algorithm can
increase the cost of computing the image by about 3x or more.
The *ssao* keyword turns on/off a screen space ambient occlusion (SSAO)
model for depth shading. If *yes* is set, then atoms further away from
the viewer are darkened via a randomized process, which is perceived as
depth. The strength of the effect can be scaled by the *dfactor*
parameter. If *no* is set, no depth shading is performed. The
calculation of this effect can increase the cost of computing the image
substantially by 5x or more, especially with larger images. When used
in combination with the *fsaa* keyword the computational cost of depth
shading is particularly large.
----------
Image Quality Settings
""""""""""""""""""""""
The two keywords *fsaa* and *ssao* can be used to improve the image
quality at the expense of additional computational cost to render the
images. The images below show from left to right the same render with
default settings, with *fsaa* added, with *ssao* added, and with both
keywords added.
.. |imagequality1| image:: JPG/image.default.png
:width: 24%
.. |imagequality2| image:: JPG/image.fsaa.png
:width: 24%
.. |imagequality3| image:: JPG/image.ssao.png
:width: 24%
.. |imagequality4| image:: JPG/image.both.png
:width: 24%
|imagequality1| |imagequality2| |imagequality3| |imagequality4|
----------
@ -1051,6 +1087,7 @@ The defaults for the dump_modify keywords specific to dump image and dump movie
* boxcolor = yellow
* color = 140 color names are pre-defined as listed below
* framerate = 24
* fsaa = no
* gmap = min max cf 0.0 2 min blue max red
----------

46
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@ -124,17 +124,6 @@ Description
Modify the parameters of a previously defined dump command. Not all
parameters are relevant to all dump styles.
As explained on the :doc:`dump <dump>` doc page, the *atom/mpiio*,
*custom/mpiio*, and *xyz/mpiio* dump styles are identical in command
syntax and in the format of the dump files they create, to the
corresponding styles without "mpiio", except the single dump file they
produce is written in parallel via the MPI-IO library. Thus if a
dump_modify option below is valid for the *atom* style, it is also
valid for the *atom/mpiio* style, and similarly for the other styles
which allow for use of MPI-IO.
----------
Unless otherwise noted, the following keywords apply to all the
various dump styles, including the :doc:`dump image <dump_image>` and
:doc:`dump movie <dump_image>` styles.
@ -181,19 +170,20 @@ extra buffering.
.. versionadded:: 4May2022
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, *cfg*, and *local* and their compressed,
ADIOS, and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
for dump styles: *atom*, *custom*, *cfg*, and *local* and their
compressed, ADIOS variants. The setting for *ID string* replaces the
default text with the provided string. *ID* can be a positive integer
when it represents the column number counting from the left, a negative
integer when it represents the column number from the right (i.e. -1 is
the last column/keyword), or a custom dump keyword (or compute, fix,
property, or variable reference) and then it replaces the string for
that specific keyword. For *atom* dump styles only the keywords "id",
"type", "x", "y", "z", "ix", "iy", "iz" can be accessed via string
regardless of whether scaled or unwrapped coordinates were enabled or
disabled, and it always assumes 8 columns for indexing regardless of
whether image flags are enabled or not. For dump style *cfg* only
changes to the "auxiliary" keywords (6th or later keyword) will become
visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
@ -417,10 +407,10 @@ performed with dump style *xtc*\ .
----------
The *format* keyword can be used to change the default numeric format output
by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
options can be used with the *atom* and *xyz* styles.
The *format* keyword can be used to change the default numeric format
output by the text-based dump styles: *atom*, *local*, *custom*, *cfg*,
and *xyz* styles. Only the *line* or *none* options can be used with the
*atom* and *xyz* styles.
All the specified format strings are C-style formats, such as used by
the C/C++ printf() command. The *line* keyword takes a single

1
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@ -333,6 +333,7 @@ accelerated styles exist.
* :doc:`pour <fix_pour>` - pour new atoms/molecules into a granular simulation domain
* :doc:`precession/spin <fix_precession_spin>` - apply a precession torque to each magnetic spin
* :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat
* :doc:`press/langevin <fix_press_langevin>` - pressure control by Langevin barostat
* :doc:`print <fix_print>` - print text and variables during a simulation
* :doc:`propel/self <fix_propel_self>` - model self-propelled particles
* :doc:`property/atom <fix_property_atom>` - add customized per-atom values

7
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View File

@ -1,4 +1,5 @@
.. index:: fix efield
.. index:: fix efield/kk
.. index:: fix efield/tip4p
fix efield command
@ -210,6 +211,12 @@ the iteration count during the minimization.
system (the quantity being minimized), you MUST enable the
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

2
doc/src/fix_plumed.rst
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@ -24,7 +24,7 @@ Examples
.. code-block:: LAMMPS
fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
fix pl all plumed plumedfile plumed.dat outfile p.log
Description
"""""""""""

301
doc/src/fix_press_langevin.rst Normal file
View File

@ -0,0 +1,301 @@
.. index:: fix press/langevin
fix press/langevin command
===========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID press/langevin keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* press/langevin = style name of this fix command
.. parsed-literal::
one or more keyword value pairs may be appended
keyword = *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *xz* or *yz* or *couple* or *dilate* or *modulus* or *temp* or *flip*
*iso* or *aniso* or *tri* values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
*x* or *y* or *z* or *xy* or *xz* or *yz* values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = pressure damping parameter
*flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed
*couple* = *none* or *xyz* or *xy* or *yz* or *xz*
*friction* value = Friction coefficient for the barostat (time units)
*temp* values = Tstart, Tstop, seed
Tstart, Tstop = target temperature used for the barostat at start/end of run
seed = seed of the random number generator
*dilate* value = *all* or *partial*
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all press/langevin iso 0.0 0.0 1000.0 temp 300 300 487374
fix 2 all press/langevin aniso 0.0 0.0 1000.0 temp 100 300 238 dilate partial
Description
"""""""""""
Adjust the pressure of the system by using a Langevin stochastic barostat
:ref:`(Gronbech) <Gronbech>`, which rescales the system volume and
(optionally) the atoms coordinates within the simulation box every
timestep.
The Langevin barostat couple each direction *L* with a pseudo-particle that obeys
the Langevin equation such as:
.. math::
f_P = & \frac{N k_B T_{target}}{V} + \frac{1}{V d}\sum_{i=1}^{N} \vec r_i \cdot \vec f_i - P_{target} \\
Q\ddot{L} + \alpha{}\dot{L} = & f_P + \beta(t)\\
L^{n+1} = & L^{n} + bdt\dot{L}^{n} \frac{bdt^{2}}{2Q} \\
\dot{L}^{n+1} = & \alpha\dot{L}^{n} + \frac{dt}{2Q}\left(a f^{n}_{P} + f^{n+1}_{P}\right) + \frac{b}{Q}\beta^{n+1} \\
a = & \frac{1-\frac{\alpha{}dt}{2Q}}{1+\frac{\alpha{}dt}{2Q}} \\
b = & \frac{1}{1+\frac{\alpha{}dt}{2Q}} \\
\left< \beta(t)\beta(t') \right> = & 2\alpha k_B Tdt
Where :math:`dt` is the timestep :math:`\dot{L}` and :math:`\ddot{L}` the first
and second derivatives of the coupled direction with regard to time,
:math:`\alpha` is a friction coefficient, :math:`\beta` is a random gaussian
variable and :math:`Q` the effective mass of the coupled pseudoparticle. The
two first terms on the right-hand side of the first equation are the virial
expression of the canonical pressure. It is to be noted that the temperature
used to compute the pressure is not based on the atom velocities but rather on
the canonical
target temperature directly. This temperature is specified using the *temp*
keyword parameter and should be close to the expected target temperature of the
system.
Regardless of what atoms are in the fix group, a global pressure is
computed for all atoms. Similarly, when the size of the simulation
box is changed, all atoms are re-scaled to new positions, unless the
keyword *dilate* is specified with a value of *partial*, in which case
only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
.. note::
Unlike the :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` commands which
perform Nose-Hoover barostatting AND time integration, this fix does NOT
perform time integration of the atoms but only of the barostat coupled
coordinate. It then only modifies the box size and atom coordinates to
effect barostatting. Thus you must use a separate time integration fix,
like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` to actually update
the positions and velocities of atoms. This fix can be used in conjunction
with thermostatting fixes to control the temperature, such as :doc:`fix nvt
<fix_nh>` or :doc:`fix langevin <fix_langevin>` or :doc:`fix temp/berendsen
<fix_temp_berendsen>`.
See the :doc:`Howto barostat <Howto_barostat>` page for a
discussion of different ways to perform barostatting.
----------
The barostat is specified using one or more of the *iso*, *aniso*, *tri* *x*,
*y*, *z*, *xy*, *xz*, *yz*, and *couple* keywords. These keywords give you the
ability to specify the 3 diagonal components of an external stress tensor, and
to couple various of these components together so that the dimensions they
represent are varied together during a constant-pressure simulation.
The target pressures for each of the 6 diagonal components of the stress tensor
can be specified independently via the *x*, *y*, *z*, keywords, which
correspond to the 3 simulation box dimensions, and the *xy*, *xz* and *yz*
keywords which corresponds to the 3 simulation box tilt factors. For each
component, the external pressure or tensor component at each timestep is a
ramped value during the run from *Pstart* to *Pstop*\ . If a target pressure is
specified for a component, then the corresponding box dimension will change
during a simulation. For example, if the *y* keyword is used, the y-box length
will change. A box dimension will not change if that component is not
specified, although you have the option to change that dimension via the
:doc:`fix deform <fix_deform>` command.
The *Pdamp* parameter can be seen in the same way as a Nose-Hoover parameter as
it is used to compute the mass of the fictitious particle. Without friction,
the barostat can be compared to a single particle Nose-Hoover barostat and
should follow a similar decay in time. The mass of the barostat is
linked to *Pdamp* by the relation
:math:`Q=(N_{at}+1)\cdot{}k_BT_{target}\cdot{}P_{damp}^2`. Note that *Pdamp*
should be expressed in time units.
.. note::
As for Berendsen barostat, a Langevin barostat will not work well for
arbitrary values of *Pdamp*\ . If *Pdamp* is too small, the pressure and
volume can fluctuate wildly; if it is too large, the pressure will take a
very long time to equilibrate. A good choice for many models is a *Pdamp*
of around 1000 timesteps. However, note that *Pdamp* is specified in time
units, and that timesteps are NOT the same as time units for most
:doc:`units <units>` settings.
----------
The *temp* keyword sets the temperature to use in the equation of motion of the
barostat. This value is used to compute the value of the force :math:`f_P` in
the equation of motion. It is important to note that this value is not the
instantaneous temperature but a target temperature that ramps from *Tstart* to
*Tstop*. Also the required argument *seed* sets the seed for the random
number generator used in the generation of the random forces.
----------
The *couple* keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together. The value specified
with the keyword determines which are coupled. For example, *xz*
means the *Pxx* and *Pzz* components of the stress tensor are coupled.
*Xyz* means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must
be identical. *Couple xyz* can be used for a 2d simulation; the *z*
dimension is simply ignored.
----------
The *iso*, *aniso* and *tri* keywords are simply shortcuts that are
equivalent to specifying several other keywords together.
The keyword *iso* means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
specifying these 4 keywords:
.. parsed-literal::
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple xyz
The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled
independently using the *Pxx*, *Pyy*, and *Pzz* components of the
stress tensor as the driving forces, and the specified scalar external
pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
these 4 keywords:
.. parsed-literal::
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple none
The keyword *tri* is the same as *aniso* but also adds the control on the
shear pressure coupled with the tilt factors.
.. parsed-literal::
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
xy Pstart Pstop Pdamp
xz Pstart Pstop Pdamp
yz Pstart Pstop Pdamp
couple none
----------
The *flip* keyword allows the tilt factors for a triclinic box to
exceed half the distance of the parallel box length, as discussed
below. If the *flip* value is set to *yes*, the bound is enforced by
flipping the box when it is exceeded. If the *flip* value is set to
*no*, the tilt will continue to change without flipping. Note that if
applied stress induces large deformations (e.g. in a liquid), this
means the box shape can tilt dramatically and LAMMPS will run less
efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped subdomain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
----------
The *friction* keyword sets the friction parameter :math:`\alpha` in the
equations of motion of the barostat. For each barostat direction, the value of
:math:`\alpha` depends on both *Pdamp* and *friction*. The value given as a
parameter is the Langevin characteristic time
:math:`\tau_{L}=\frac{Q}{\alpha}` in time units. The langevin time can be understood as a
decorrelation time for the pressure. A long Langevin time value will make the
barostat act as an underdamped oscillator while a short value will make it
act as an overdamped oscillator. The ideal configuration would be to find
the critical parameter of the barostat. Empirically this is observed to
occur for :math:`\tau_{L}\approx{}P_{damp}`. For this reason, if the *friction*
keyword is not used, the default value *Pdamp* is used for each barostat direction.
----------
This fix computes pressure each timestep. To do
this, the fix creates its own computes of style "pressure",
as if this command had been issued:
.. code-block:: LAMMPS
compute fix-ID_press group-ID pressure NULL virial
The kinetic contribution to the pressure is taken as the ensemble value
:math:`\frac{Nk_bT}{V}` and computed by the fix itself.
See the :doc:`compute pressure <compute_pressure>` command for details. Note
that the IDs of the new compute is the fix-ID + underscore + "press" and the
group for the new computes is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see the
:doc:`thermo_style <thermo_style>` command) with ID = *thermo_press*. This
means you can change the attributes of this fix's pressure via the
:doc:`compute_modify <compute_modify>` command or print this temperature or
pressure during thermodynamic output via the :doc:`thermo_style custom
<thermo_style>` command using the appropriate compute-ID. It also means that
changing attributes of *thermo_temp* or *thermo_press* will have no effect on
this fix.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *press* option is
supported by this fix. You can use it to assign a
:doc:`compute <compute>` you have defined to this fix which will be used
in its pressure calculations.
No global or per-atom quantities are stored by this fix for access by
various :doc:`output commands <Howto_output>`.
This fix can ramp its target pressure and temperature over multiple runs, using
the *start* and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this. It is recommended that
the ramped temperature is the same as the effective temperature of the
thermostatted system. That is, if the system's temperature is ramped by other
commands, it is recommended to do the same with this pressure control.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
Any dimension being adjusted by this fix must be periodic.
Related commands
""""""""""""""""
:doc:`fix press/berendsen <fix_press_berendsen>`,
:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix_modify <fix_modify>`
Default
"""""""
The keyword defaults are *dilate* = all, *flip* = yes, and *friction* = *Pdamp*.
----------
.. _Gronbech:
**(Gronbech)** Gronbech-Jensen, Farago, J Chem Phys, 141, 194108 (2014).

7
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@ -1,4 +1,5 @@
.. index:: fix spring/self
.. index:: fix spring/self/kk
fix spring/self command
=======================
@ -80,6 +81,12 @@ invoked by the :doc:`minimize <minimize>` command.
you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for
this fix.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""
none

49
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@ -71,14 +71,15 @@ imbue the SRD particles with fluid-like properties, including an
effective viscosity. Thus simulations with large solute particles can
be run more quickly, to measure solute properties like diffusivity
and viscosity in a background fluid. The usual LAMMPS fixes for such
simulations, such as :doc:`fix deform <fix_deform>`, :doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
simulations, such as :doc:`fix deform <fix_deform>`,
:doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
can be used in conjunction with the SRD model.
For more details on how the SRD model is implemented in LAMMPS, :ref:`this paper <Petersen1>` describes the implementation and usage of pure SRD
fluids. :ref:`This paper <Lechman>`, which is nearly complete, describes
the implementation and usage of mixture systems (solute particles in
an SRD fluid). See the examples/srd directory for sample input
scripts using SRD particles in both settings.
For more details on how the SRD model is implemented in LAMMPS,
:ref:`(Petersen) <Petersen1>` describes the implementation and usage of
pure SRD fluids. See the ``examples/srd`` directory for sample input
scripts using SRD particles for that and for mixture systems (solute
particles in an SRD fluid).
This fix does two things:
@ -357,28 +358,28 @@ These are the 12 quantities. All are values for the current timestep,
except for quantity 5 and the last three, each of which are
cumulative quantities since the beginning of the run.
* (1) # of SRD/big collision checks performed
* (2) # of SRDs which had a collision
* (3) # of SRD/big collisions (including multiple bounces)
* (4) # of SRD particles inside a big particle
* (5) # of SRD particles whose velocity was rescaled to be < Vmax
* (6) # of bins for collision searching
* (7) # of bins for SRD velocity rotation
* (8) # of bins in which SRD temperature was computed
* (9) SRD temperature
* (10) # of SRD particles which have undergone max # of bounces
* (11) max # of bounces any SRD particle has had in a single step
* (12) # of reneighborings due to SRD particles moving too far
(1) # of SRD/big collision checks performed
(2) # of SRDs which had a collision
(3) # of SRD/big collisions (including multiple bounces)
(4) # of SRD particles inside a big particle
(5) # of SRD particles whose velocity was rescaled to be < Vmax
(6) # of bins for collision searching
(7) # of bins for SRD velocity rotation
(8) # of bins in which SRD temperature was computed
(9) SRD temperature
(10) # of SRD particles which have undergone max # of bounces
(11) max # of bounces any SRD particle has had in a single step
(12) # of reneighborings due to SRD particles moving too far
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This command can only be used if LAMMPS was built with the SRD
package. See the :doc:`Build package <Build_package>` doc
page for more info.
This command can only be used if LAMMPS was built with the SRD package.
See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
@ -403,7 +404,3 @@ no, and rescale = yes.
**(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
Chem Phys, 132, 174106 (2010).
.. _Lechman:
**(Lechman)** Lechman, et al, in preparation (2010).

79
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@ -8,7 +8,7 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID vector Nevery value1 value2 ...
fix ID group-ID vector Nevery value1 value2 ... keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* vector = style name of this fix command
@ -25,6 +25,13 @@ Syntax
v_name = value calculated by an equal-style variable with name
v_name[I] = Ith component of vector-style variable with name
* zero or more keyword/args pairs may be appended
* keyword = *nmax*
.. parsed-literal::
*nmax* length = set maximal length of vector to <length>
Examples
""""""""
@ -32,21 +39,26 @@ Examples
fix 1 all vector 100 c_myTemp
fix 1 all vector 5 c_myTemp v_integral
fix 1 all vector 50 c_myTemp nmax 200
Description
"""""""""""
Use one or more global values as inputs every few timesteps, and
simply store them. For a single specified value, the values are
Use one or more global values as inputs every few timesteps, and simply
store them as a sequence. For a single specified value, the values are
stored as a global vector of growing length. For multiple specified
values, they are stored as rows in a global array, whose number of
rows is growing. The resulting vector or array can be used by other
values, they are stored as rows in a global array, whose number of rows
is growing. The resulting vector or array can be used by other
:doc:`output commands <Howto_output>`.
The optional *nmax* keyword can be used to restrict the length of the
vector to the given *length* value. Once the restricted vector is
filled, the oldest entry will be discarded when a entry is added.
One way to to use this command is to accumulate a vector that is
time-integrated using the :doc:`variable trap() <variable>` function.
For example the velocity auto-correlation function (VACF) can be
time-integrated, to yield a diffusion coefficient, as follows:
numerically integrated using the :doc:`variable trap() <variable>`
function. For example, the velocity auto-correlation function (VACF)
can be integrated, to yield a diffusion coefficient, as follows:
.. code-block:: LAMMPS
@ -77,6 +89,15 @@ The *Nevery* argument specifies on what timesteps the input values
will be used in order to be stored. Only timesteps that are a
multiple of *Nevery*, including timestep 0, will contribute values.
.. note::
:class: warning
If *Nevery* is a small number and the simulation runs for many
steps, the accumulated vector or array can become very large and
thus consume a lot of memory. The implementation limit is about
2 billion entries. Using the *nmax* keyword mentioned above can
avoid that by limiting the size of the vector.
Note that if you perform multiple runs, using the "pre no" option of
the :doc:`run <run>` command to avoid initialization on subsequent runs,
then you need to use the *stop* keyword with the first :doc:`run <run>`
@ -94,11 +115,12 @@ calculated by the compute is used.
Note that there is a :doc:`compute reduce <compute_reduce>` command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix vector. Or it can be a compute defined
not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
can thus be accessed by fix vector. Or it can be a compute defined not
in your input script, but by :doc:`thermodynamic output <thermo_style>`
or other fixes such as :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale
<fix_temp_rescale>`. See the doc pages for these commands which give
the IDs of these computes. Users can also write code for their own
compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
@ -108,7 +130,8 @@ calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
Users can also write code for their own fix styles and :doc:`add them to
LAMMPS <Modify>`.
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. An equal-style or
@ -126,8 +149,9 @@ quantities to be stored by fix vector.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix produces a global vector or global array which can be
accessed by various :doc:`output commands <Howto_output>`. The values
@ -144,15 +168,15 @@ the vector are "intensive" or "extensive". If the fix produces an
array, then all elements in the array must be the same, either
"intensive" or "extensive". If a compute or fix provides the value
stored, then the compute or fix determines whether the value is
intensive or extensive; see the page for that compute or fix for
further info. Values produced by a variable are treated as intensive.
intensive or extensive; see the page for that compute or fix for further
info. Values produced by a variable are treated as intensive.
This fix can allocate storage for stored values accumulated over
multiple runs, using the *start* and *stop* keywords of the
:doc:`run <run>` command. See the :doc:`run <run>` command for details of
how to do this. If using the :doc:`run pre no <run>` command option,
this is required to allow the fix to allocate sufficient storage for
stored values.
multiple runs, using the *start* and *stop* keywords of the :doc:`run
<run>` command. See the :doc:`run <run>` command for details of how to
do this. If using the :doc:`run pre no <run>` command option, this is
required to allow the fix to allocate sufficient storage for stored
values.
This fix is not invoked during :doc:`energy minimization <minimize>`.
@ -165,7 +189,10 @@ Related commands
:doc:`compute <compute>`, :doc:`variable <variable>`
Default
"""""""
Defaults
""""""""
none
The default value of *nmax* is deduced from the number of steps
in a run (or multiple runs when using the *start* and *stop*
keywords of the :doc:`run command <run>`) divided by the choice
of *Nevery* plus 1.

12
doc/src/pair_ilp_tmd.rst
View File

@ -22,12 +22,12 @@ Examples
.. code-block:: LAMMPS
pair_style hybrid/overlay ilp/tmd 16.0 1
pair_coeff * * ilp/tmd TMD.ILP Mo S S
pair_coeff * * ilp/tmd MoS2.ILP Mo S S
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
pair_coeff * * ilp/tmd TMD.ILP Mo S S Mo S S
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
Description
"""""""""""
@ -69,7 +69,7 @@ calculating the normals.
each atom `i`, its six nearest neighboring atoms belonging to the same
sub-layer are chosen to define the normal vector `{\bf n}_i`.
The parameter file (e.g. TMD.ILP), is intended for use with *metal*
The parameter file (e.g. MoS2.ILP), is intended for use with *metal*
:doc:`units <units>`, with energies in meV. Two additional parameters,
*S*, and *rcut* are included in the parameter file. *S* is designed to
facilitate scaling of energies. *rcut* is designed to build the neighbor
@ -77,7 +77,7 @@ list for calculating the normals for each atom pair.
.. note::
The parameters presented in the parameter file (e.g. TMD.ILP),
The parameters presented in the parameter file (e.g. MoS2.ILP),
are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
These parameters provide a good description in both short- and long-range
@ -133,10 +133,10 @@ if LAMMPS was built with that package. See the :doc:`Build package
This pair style requires the newton setting to be *on* for pair
interactions.
The TMD.ILP potential file provided with LAMMPS (see the potentials
The MoS2.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your own
custom TMD.ILP potential file with coefficients listed in the appropriate
custom MoS2.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands

16
doc/src/pair_reaxff.rst
View File

@ -43,18 +43,18 @@ Examples
Description
"""""""""""
Style *reaxff* computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
Pair style *reaxff* computes the ReaxFF potential of van Duin, Goddard
and co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper:
:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`. The version integrated
into LAMMPS matches the version of ReaxFF From Summer 2010. For more
technical details about the pair reaxff implementation of ReaxFF, see
the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style was initially
implemented as a stand-alone C code and is now converted to C++ and
integrated into LAMMPS as a package.
:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>` and matches the
version of the reference ReaxFF implementation from Summer 2010. For
more technical details about the implementation of ReaxFF in pair style
*reaxff*, see the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style
was initially implemented as a stand-alone C code and is now converted
to C++ and integrated into LAMMPS as a package.
The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that
is derived from the *reaxff* style. The Kokkos version can run on GPUs

11
doc/src/pair_snap.rst
View File

@ -1,10 +1,11 @@
.. index:: pair_style snap
.. index:: pair_style snap/intel
.. index:: pair_style snap/kk
pair_style snap command
=======================
Accelerator Variants: *snap/kk*
Accelerator Variants: *snap/intel*, *snap/kk*
Syntax
""""""
@ -260,6 +261,14 @@ This style is part of the ML-SNAP package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
The *snap/intel* accelerator variant will *only* be available if LAMMPS
is built with Intel *compilers* and for CPUs with AVX-512 support.
While the INTEL package in general allows multiple floating point
precision modes to be selected, *snap/intel* will currently always use
full double precision regardless of the precision mode selected.
Additionally, the *intel* variant of snap will **NOT** use multiple
threads with OpenMP.
Related commands
""""""""""""""""

9
doc/src/pair_yukawa_colloid.rst
View File

@ -1,11 +1,12 @@
.. index:: pair_style yukawa/colloid
.. index:: pair_style yukawa/colloid/gpu
.. index:: pair_style yukawa/colloid/kk
.. index:: pair_style yukawa/colloid/omp
pair_style yukawa/colloid command
=================================
Accelerator Variants: *yukawa/colloid/gpu*, *yukawa/colloid/omp*
Accelerator Variants: *yukawa/colloid/gpu*, *yukawa/colloid/kk*, *yukawa/colloid/omp*
Syntax
""""""
@ -131,6 +132,12 @@ per-type polydispersity is allowed. This means all particles of the
same type must have the same diameter. Each type can have a different
diameter.
----------
.. include:: accel_styles.rst
----------
Related commands
""""""""""""""""

20
doc/src/read_restart.rst
View File

@ -19,7 +19,6 @@ Examples
read_restart save.10000
read_restart restart.*
read_restart restart.*.mpiio
Description
"""""""""""
@ -120,22 +119,6 @@ different the number of processors in the current LAMMPS simulation.
This can be a fast mode of input on parallel machines that support
parallel I/O.
A restart file can also be read in parallel as one large binary file
via the MPI-IO library, assuming it was also written with MPI-IO.
MPI-IO is part of the MPI standard for versions 2.0 and above. Using
MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g.
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.
----------
Here is the list of information included in a restart file, which
@ -268,8 +251,7 @@ information about these bonds is written to the restart file.
Restrictions
""""""""""""
To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.
none
Related commands
""""""""""""""""

39
doc/src/restart.rst
View File

@ -33,7 +33,6 @@ Examples
restart 0
restart 1000 poly.restart
restart 1000 poly.restart.mpiio
restart 1000 restart.*.equil
restart 10000 poly.%.1 poly.%.2 nfile 10
restart v_mystep poly.restart
@ -81,21 +80,6 @@ of output and subsequent input on parallel machines that support
parallel I/O. The optional *fileper* and *nfile* keywords discussed
below can alter the number of files written.
The restart file can also be written in parallel as one large binary
file via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g.
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.
Restart files are written on timesteps that are a multiple of N but
not on the first timestep of a run or minimization. You can use the
:doc:`write_restart <write_restart>` command to write a restart file
@ -104,15 +88,17 @@ timestep of a run unless it is a multiple of N. A restart file is
written on the last timestep of a minimization if N > 0 and the
minimization converges.
Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v_name, where
name is the variable name. In this case, the variable is evaluated at
the beginning of a run to determine the next timestep at which a
restart file will be written out. On that timestep, the variable will
be evaluated again to determine the next timestep, etc. Thus the
variable should return timestep values. See the stagger() and
logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
this context. Other similar math functions could easily be added as
options for :doc:`equal-style variables <variable>`.
Instead of a numeric value, N can be specified as an :doc:`equal-style
variable <variable>`, which should be specified as v_name, where name is
the variable name. In this case, the variable is evaluated at the
beginning of a run to determine the next timestep at which a restart
file will be written out. On that timestep, the variable will be
evaluated again to determine the next timestep, etc. Thus the variable
should return timestep values. See the stagger() and logfreq() and
stride() math functions for :doc:`equal-style variables <variable>`, as
examples of useful functions to use in this context. Other similar math
functions could easily be added as options for :doc:`equal-style
variables <variable>`.
For example, the following commands will write restart files
every step from 1100 to 1200, and could be useful for debugging
@ -170,8 +156,7 @@ next 3 processors and write it to a restart file.
Restrictions
""""""""""""
To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.
none
Related commands
""""""""""""""""

30
doc/src/write_restart.rst
View File

@ -27,7 +27,6 @@ Examples
.. code-block:: LAMMPS
write_restart restart.equil
write_restart restart.equil.mpiio
write_restart poly.%.* nfile 10
Description
@ -53,32 +52,6 @@ output and subsequent input on parallel machines that support parallel
I/O. The optional *fileper* and *nfile* keywords discussed below can
alter the number of files written.
The restart file can also be written in parallel as one large binary
file via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
cmake . -DPKG_MPIIO=on # enables the MPIIO package in the build folder
cmake --build . # recompiles LAMMPS with the package code included
.. tab:: Traditional make
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.
Restart files can be read by a :doc:`read_restart <read_restart>`
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
@ -128,9 +101,6 @@ before the restart file is written. This means that your system must
be ready to perform a simulation before using this command (force
fields setup, atom masses initialized, etc).
To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.
Related commands
""""""""""""""""

2
doc/utils/requirements.txt
View File

@ -1,4 +1,4 @@
Sphinx >= 5.3.0, <7.2.0
Sphinx >= 5.3.0, <8.0
sphinxcontrib-spelling
sphinxcontrib-jquery
git+https://github.com/akohlmey/sphinx-fortran@parallel-read

8
doc/utils/sphinx-config/false_positives.txt
View File

@ -1195,6 +1195,7 @@ Freitas
Frenkel
Friedrichs
fs
fsaa
fsh
fstyle
fsw
@ -1505,6 +1506,7 @@ Im
imageint
Imageint
Imagemagick
imagename
imd
Impey
impl
@ -2229,6 +2231,7 @@ monolayer
monopole
monovalent
Montalenti
Monterey
Montero
Monti
Mora
@ -2585,6 +2588,7 @@ Nurdin
Nvalue
nvaluelast
Nvalues
nvar
nvc
nvcc
nve
@ -2888,6 +2892,7 @@ pscrozi
pseudocode
Pseudocode
pseudodynamics
pseudoparticle
pseudopotential
psllod
pSp
@ -3621,6 +3626,7 @@ Tk
Tkin
tloop
tlsph
tm
tmax
Tmax
tmd
@ -3637,6 +3643,7 @@ tokyo
tol
tomic
toolchain
toolset
topologies
Toporov
Torder
@ -3749,6 +3756,7 @@ uncomment
uncommented
uncompress
uncompute
underdamped
underprediction
undump
uniaxial

18
examples/ASPHERE/tri/in.tri.srd
View File

@ -2,7 +2,7 @@
units lj
atom_style tri
atom_modify first big
atom_modify first big map yes
read_data data.tri.srd
@ -52,12 +52,12 @@ pair_coeff 1 2 0.0 1.0 0.0
timestep 0.001
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
fix 2 small srd 20 big 1.0 0.25 49894 &
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
fix 2 small srd 20 big 1.0 1.0 49894 &
search 0.2 cubic warn 0.0001 shift yes 49829 &
overlap yes collision noslip
overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
@ -73,8 +73,8 @@ compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step f_1 c_tsmall f_2[9] temp press
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
compute 10 all property/atom corner1x corner1y corner1z &
@ -93,9 +93,9 @@ unfix 3
change_box all triclinic
fix 2 small srd 20 big 1.0 0.25 49894 &
fix 2 small srd 20 big 1.0 1.0 49894 &
search 0.2 cubic warn 0.0001 shift yes 49829 &
overlap yes collision noslip tstat yes
overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type &

812
examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8 Normal file
View File

@ -0,0 +1,812 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big map yes
read_data data.tri.srd
Reading data file ...
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
read_data CPU = 0.007 seconds
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
create_atoms 2 region box
Created 91125 atoms
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
create_atoms CPU = 0.002 seconds
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
Setting atom values ...
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
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 = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 19 19 19
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
create bodies CPU = 0.000 seconds
125 rigid bodies with 1500 atoms
1.8601881 = max distance from body owner to body atom
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -4500
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
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
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 17 17 17
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
SRD per actual grid cell = -3.9971745
SRD viscosity = -34.162587
big/SRD mass density ratio = -3.3753691
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.970837 35.150443
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 16.874681, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/3d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
0 0 1.4401779 0 -0.15917996 0 0
100 0.36662911 1.1475389 0.24585067 1.0290503 1.1382325 18
200 0.73133134 1.0558153 0.49986673 0.73932383 1.049638 34
300 1.1229361 1.0218621 0.82641583 0.7589689 1.0205369 40
400 1.5826262 0.99541508 1.2201293 0.69171726 0.99190857 52
500 1.8834563 0.99351667 1.4778822 1.0147794 1.0005581 63
600 2.4225372 0.98954834 1.8740966 1.1362893 0.99760042 61
700 3.0172772 0.99153625 2.3351502 1.3284877 0.98731355 39
800 3.5307913 1.0012521 2.6477224 1.1404922 0.9846605 52
900 3.757064 0.99743944 2.7220653 1.4078087 0.97538456 55
1000 4.3165268 1.002214 3.055501 1.2252972 0.99123745 63
1100 4.2796945 1.0075233 3.1022956 1.1893685 1.0139864 69
1200 4.3719315 1.0037271 3.0054509 1.3886162 1.002661 64
1300 4.5628012 0.99368316 3.2690604 1.3621012 0.9810568 56
1400 4.6954389 0.99365088 3.1940001 1.8485712 0.99571089 71
1500 5.0270163 0.99455258 3.4120396 1.5992539 0.98294263 77
1600 5.5897797 1.0021621 3.647347 1.7796904 0.98967622 66
1700 5.5330194 1.0130853 3.6407996 1.8005429 1.0068955 62
1800 5.3606928 1.0090284 3.5863618 1.3308757 1.0214092 59
1900 5.6086195 1.0071865 3.7427101 1.5296314 0.99886937 55
2000 5.3726474 1.0064207 3.603621 1.9473142 0.99999816 54
2100 5.836183 1.0124553 3.7321841 1.7889397 1.0188986 59
2200 5.5090061 1.0113832 3.5884963 1.6617781 1.0071583 59
2300 5.4011211 1.0095947 3.520406 1.8937582 0.99689983 61
2400 5.2219281 1.0053246 3.3699458 1.7231672 0.99899754 59
2500 5.7695275 1.0141459 3.6211469 1.7767598 1.0143133 65
2600 5.4206253 1.0182828 3.521774 2.0800518 1.0081603 70
2700 5.1401099 1.0085209 3.4200563 2.4019836 1.0107652 59
2800 6.5420721 1.0159876 4.1996904 1.863842 1.0160738 61
2900 5.9082962 1.0106921 3.7223419 2.0586998 1.0073885 67
3000 5.6556123 1.0099021 3.6768976 1.921987 1.0068962 76
3100 5.2913762 1.0008567 3.4103831 1.9831969 0.99187526 80
3200 5.1032361 0.99756662 3.1967156 2.2448433 0.99743574 93
3300 5.2622386 1.0024934 3.3325614 2.0078097 1.0047789 86
3400 5.1247527 0.99810102 3.1363556 1.8907269 0.98936508 82
3500 4.9424333 1.0009344 3.2153968 1.9002728 0.99161849 71
3600 5.1243735 1.0037377 3.3117313 2.1267438 1.0078943 65
3700 5.5045819 1.0006119 3.5686193 2.3466538 0.99876164 68
3800 5.5355384 1.0022639 3.6701457 2.0383269 1.0008683 76
3900 6.4915796 1.0137733 4.3225864 2.6996933 1.0064787 79
4000 6.6631737 1.0236248 4.3057163 2.6352666 1.0255232 75
4100 6.2999507 1.0263876 4.0101385 2.5479077 1.0168303 79
4200 6.7902489 1.0247392 4.4616158 2.4926177 1.0191403 91
4300 6.505908 1.0182073 4.0675428 2.168754 1.0177101 74
4400 5.9554283 1.0115938 3.5787297 2.9258144 1.0133896 72
4500 6.2276609 1.0202416 3.8211204 2.5308249 1.0174385 74
4600 6.0485727 1.0195757 3.8217434 2.6421797 1.0201441 78
4700 6.511063 1.0220764 3.933486 2.8591093 1.0147269 83
4800 6.9478172 1.0106414 4.345402 3.3257663 1.00469 85
4900 6.7547045 1.0211842 4.1874576 3.6503845 1.022873 94
5000 7.2603949 1.0234313 4.5393985 3.4667806 1.0222306 105
5100 7.1899652 1.0256566 4.5421834 3.8137207 1.0317242 99
5200 7.1960739 1.026746 4.4288606 3.5523675 1.0242269 97
5300 7.1294458 1.017883 4.5799808 3.3917274 1.0145317 99
5400 6.2810892 1.0291953 4.0109229 2.8604571 1.0289438 97
5500 6.15246 1.0288734 3.8714587 3.2760394 1.0210757 89
5600 6.5860526 1.0192882 4.0272883 3.3124298 1.0096258 93
5700 7.0296116 1.0097293 4.2652722 3.6049788 1.012463 82
5800 6.8372302 1.0140065 4.2205065 4.3686183 1.0088542 93
5900 7.8887098 1.0090612 4.9724078 4.457317 1.0045137 92
6000 10.120663 1.0312443 6.3025192 4.72018 1.0374722 91
6100 9.1318265 1.0304199 5.7084296 4.244548 1.0259056 97
6200 8.9758903 1.0295285 5.1842704 4.870955 1.0178851 95
6300 9.0088218 1.022484 5.3742805 5.1554352 1.0138365 101
6400 10.470322 1.0287848 6.4602103 4.5461489 1.0335978 105
6500 11.100779 1.0347405 6.9630121 4.9840664 1.0339044 99
6600 10.139333 1.0476079 6.4284839 4.5523893 1.0433517 104
6700 8.9706766 1.0386262 5.8387485 4.247024 1.0408151 101
6800 7.7799532 1.0362651 4.9946283 4.6093924 1.0274763 102
6900 8.0866551 1.0337743 4.9942769 4.1679939 1.0454805 102
7000 8.0224277 1.0193598 4.9380527 3.9173115 1.0185001 109
7100 7.8361001 1.0211143 4.872673 5.3471479 1.024779 110
7200 7.8542147 1.0057183 4.8666653 4.668317 0.99980296 122
7300 7.9313852 1.0159181 5.0062527 4.1410294 1.0195705 114
7400 7.2769846 1.0155245 4.6349779 4.9138895 1.0005886 119
7500 7.5974523 1.0196295 4.7918247 4.2525935 1.0211412 124
7600 6.7835063 1.0203187 4.2674694 4.9251624 1.0218296 113
7700 6.4039017 1.0119494 4.1086667 5.5240525 1.0078246 118
7800 7.0715134 1.0149015 4.2450776 4.8796778 1.0164737 125
7900 6.3626535 1.02294 4.202778 4.482164 1.0235878 136
8000 6.2423869 1.0212553 4.0460303 5.2753307 1.0124884 132
8100 6.550891 1.0223318 4.2993545 5.2634985 1.0163244 143
8200 6.9122202 1.008347 4.3551124 5.4108909 1.0084913 142
8300 6.9104634 1.0103936 4.4622206 5.6762373 0.99559355 143
8400 6.4918879 1.0084381 4.1050732 5.8389788 1.0036021 135
8500 7.4377218 1.0216662 4.5229841 5.5431311 1.0260799 123
8600 7.572198 1.0228381 4.9058913 7.1028185 1.0015164 116
8700 8.204675 1.03457 5.2231696 6.4790244 1.0214635 132
8800 8.3118914 1.0381333 5.1795799 6.7437722 1.0290086 132
8900 8.2559198 1.0268665 5.218352 7.2191395 1.019804 138
9000 8.0403128 1.0339414 4.9310394 6.4942331 1.041527 156
9100 7.1773079 1.0397062 4.4993688 7.0272109 1.0388012 167
9200 7.1793935 1.0373589 4.3481663 7.4894459 1.0078785 157
9300 8.3705146 1.0248112 5.1036971 8.2173072 1.010168 156
9400 9.4935002 1.0252907 5.7846951 9.7466018 1.028941 170
9500 9.5208037 1.0371093 5.9635099 7.6444933 1.022673 165
9600 8.9992217 1.0292895 5.6224192 8.8071452 1.0101362 169
9700 8.682661 1.0422224 5.3997636 8.6827834 1.0337928 149
9800 7.6191562 1.0350948 4.7198842 8.6125595 1.0300395 151
9900 8.0910913 1.0319432 4.8843183 7.9013334 1.0272495 167
10000 7.4438347 1.0186098 4.7184985 8.999795 0.99762661 177
Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.647 | 64.106 | 79.639 | 169.5 | 39.49
Neigh | 0.30808 | 0.44033 | 0.50863 | 9.8 | 0.27
Comm | 26.611 | 43.438 | 74.998 | 215.7 | 26.76
Output | 0.0072573 | 0.0087791 | 0.0097993 | 0.9 | 0.01
Modify | 53.171 | 54.121 | 55.362 | 12.3 | 33.34
Other | | 0.2104 | | | 0.13
Nlocal: 2033.88 ave 2601 max 1413 min
Histogram: 1 2 0 0 0 0 2 1 1 1
Nghost: 1647.25 ave 1714 max 1617 min
Histogram: 4 0 1 0 0 1 1 0 0 1
Neighs: 12482.8 ave 17009 max 8679 min
Histogram: 1 1 1 0 1 1 2 0 0 1
Total # of neighbors = 99862
Ave neighs/atom = 6.1374224
Neighbor list builds = 562
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 13 13 13
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
SRD per actual grid cell = -2.775698
SRD viscosity = -12.180602
big/SRD mass density ratio = -5.5653033
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.14994 40
ave/max big velocity = 1.6952661 5.2200074
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 13.499745, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton/tri
stencil: half/multi/3d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
10000 7.4438347 1.0189789 4.7184481 7.9505614 0 0
10100 7.0770142 1.0021471 4.4491455 6.606701 1 141
10200 6.7628072 1.002308 4.152988 8.5190386 1 125
10300 6.5333319 1.0007472 4.1295404 8.2341747 1 109
10400 6.3237519 1.0024029 3.8636034 9.4058128 1 95
10500 6.6411054 1.0026261 4.2975997 7.6122304 1 82
10600 5.7470775 1.0004827 3.7959947 7.3091777 1 67
10700 5.9744919 1.0014977 3.6885649 7.5517197 1 59
10800 5.8028731 1.0029627 3.7553961 6.2787087 1 49
10900 5.3755286 1.0019318 3.5334739 7.1318348 1 41
11000 5.3915962 1.001463 3.483172 7.6362496 1 40
11100 5.8683672 1.0022459 3.6697589 6.9711866 1 33
11200 5.4351801 0.99956703 3.4548447 7.0745257 1 29
11300 4.9397513 1.0008287 3.1990325 6.0917337 1 27
11400 4.9159845 1.0017862 3.0005677 7.653817 1 26
11500 4.9243103 1.0013135 3.1799841 7.744414 1 23
11600 5.2036357 1.0017984 3.2963749 7.540477 1 22
11700 4.8991892 1.0020757 3.1773032 8.7218471 1 27
11800 4.9489399 1.003438 3.1679764 7.1605486 1 26
11900 4.82398 1.0019946 3.1939566 7.1397869 1 21
12000 4.3531411 1.000532 2.8321416 7.6672501 1 23
12100 4.8226081 1.0018898 3.0382137 6.8343432 1 25
12200 4.7456418 1.0032116 2.9186038 7.3067818 1 20
12300 4.4280468 1.0005857 2.734593 8.0365684 1 22
12400 4.7311239 1.0000982 2.8898839 7.9231831 1 22
12500 4.7261054 1.0016127 2.9090517 7.6085854 1 24
12600 4.7719025 1.0016702 2.9736761 7.6101796 1 26
12700 4.386248 1.001394 2.8508378 6.4765102 1 28
12800 4.3313538 1.0019737 2.6258221 6.3164681 1 19
12900 4.2219861 1.0007469 2.5345699 7.0901077 1 22
13000 4.1775643 1.0011891 2.5807017 7.3579938 1 25
13100 4.3060837 1.0008671 2.5974066 6.9301328 1 22
13200 4.3529062 0.99996469 2.7571632 6.7806287 1 21
13300 4.2178709 1.000673 2.7819091 7.6449064 1 18
13400 4.2714169 1.0021294 2.7280794 8.0986691 1 18
13500 4.3430969 1.0037732 2.6768429 8.1267941 1 18
13600 4.3664374 1.0016083 2.6470186 6.2797727 1 20
13700 4.4904769 1.0008993 2.7885718 7.7410193 1 22
13800 4.2966193 1.001532 2.73862 7.9651302 1 21
13900 4.4003185 1.0009984 2.7484129 8.7160439 1 24
14000 4.5948292 1.0011748 2.9051777 7.842121 1 22
14100 4.6901122 1.0001265 2.9404111 8.9953816 1 20
14200 4.8517518 0.99998743 2.9647625 6.6450509 1 22
14300 4.889628 1.0018051 3.0891097 7.2671824 1 20
14400 4.578862 1.0010629 2.8239776 6.1317183 1 23
14500 4.0865406 1.0013917 2.5119661 6.864665 1 19
14600 4.30688 1.0009041 2.6817814 6.9007433 1 18
14700 4.1295726 1.002342 2.6032093 7.1441648 1 15
14800 4.2176021 1.0015157 2.7332903 6.8394683 1 16
14900 4.2012664 0.99986345 2.6498409 7.4568241 1 15
15000 4.6124269 1.0014751 2.9584178 7.9341875 1 16
15100 4.947327 1.0010615 3.0784409 7.6241305 1 21
15200 5.253281 1.002095 3.3093754 8.1872718 1 25
15300 5.2642369 1.0017799 3.1511136 7.4668389 1 25
15400 5.1967916 1.0029407 3.247548 8.0840111 1 23
15500 5.7465412 1.001896 3.468834 9.5990471 1 15
15600 6.2245772 1.0021086 3.6127689 7.8242016 1 19
15700 5.5626191 0.99984979 3.3893723 7.8124588 1 20
15800 5.5945727 1.0010291 3.3442448 7.0116922 1 17
15900 5.4450219 1.0006248 3.3132381 8.4803413 1 15
16000 5.7800459 1.001449 3.5002534 8.7989456 1 19
16100 6.1168718 1.0008109 3.8081142 8.0119729 1 18
16200 5.4901649 1.0020643 3.3673653 7.3483134 1 17
16300 5.4051694 1.0015652 3.3560012 7.4641983 1 19
16400 5.4237612 1.0012686 3.3816406 7.3845086 1 14
16500 5.1935593 1.001754 3.3340381 7.8607712 1 16
16600 5.539343 1.0021073 3.4164309 8.1541097 1 12
16700 5.8922923 1.0013792 3.553426 7.5220576 1 14
16800 5.956937 1.0005959 3.7630589 8.7417987 1 13
16900 5.469721 1.0016219 3.5531223 8.6721994 1 13
17000 5.3110154 1.001142 3.4167244 7.4644182 1 15
17100 5.9226035 0.99918238 4.0244287 6.5172028 1 16
17200 5.4897042 0.99981565 3.4350691 5.6840394 1 20
17300 5.4302636 1.0021571 3.421473 6.4317025 1 21
17400 5.5559131 1.0013807 3.4951403 6.874191 1 24
17500 5.4068006 1.0010448 3.4506835 7.7069504 1 22
17600 4.9283792 1.0007628 3.1736308 7.3098058 1 20
17700 4.9319722 0.99935896 3.0956257 8.2120111 1 15
17800 4.6842391 1.00037 2.9602433 7.4116352 1 17
17900 4.7714682 1.0009332 2.9666778 7.5925131 1 17
18000 4.7233188 1.0035687 3.0991778 7.1636357 1 10
18100 4.6487958 1.0020255 3.10781 6.8468658 1 12
18200 4.6284129 1.0012617 3.089724 6.3082275 1 13
18300 4.7136404 0.99962415 3.1261978 7.3359556 1 15
18400 5.0367681 1.0011016 3.2413493 8.3910633 1 14
18500 4.9658104 1.0025407 3.2420827 7.4701216 1 17
18600 4.6100059 1.0014508 3.0216884 6.553483 1 17
18700 4.3246452 1.0016721 2.7810363 6.7450293 1 19
18800 4.9415788 1.0012406 3.1661907 7.5544034 1 18
18900 5.3930915 1.000138 3.2557456 7.350955 1 21
19000 5.1938599 1.0007364 3.2398733 6.5397956 1 22
19100 5.4433048 1.0019191 3.2699245 8.3625772 1 22
19200 6.1303261 1.0004005 3.7823203 8.0537369 1 22
19300 5.5762518 1.0008117 3.5689121 8.3714373 1 22
19400 5.1316743 0.9999834 3.099381 7.405287 1 23
19500 5.2064799 1.0012007 3.3059455 7.3499127 1 25
19600 5.1650099 1.0023314 3.3759492 7.3637616 1 21
19700 5.8316278 1.0023317 3.601564 7.153887 1 19
19800 5.6435147 1.0010657 3.4967581 6.8899334 1 21
19900 5.4071193 0.99961357 3.4977894 6.1068438 1 20
20000 5.5058495 1.000982 3.5185057 8.5657603 1 19
20100 5.6551271 1.0025852 3.5672369 7.8242273 1 20
20200 5.7196886 1.002283 3.6010925 7.1449072 1 22
20300 5.5593553 1.0009987 3.4363398 8.4141755 1 21
20400 5.5550247 1.001081 3.3950874 8.0222131 1 20
20500 5.4510415 0.99997273 3.5505093 7.5243655 1 18
20600 5.8014064 1.0007611 3.8084579 7.6583499 1 18
20700 5.7337315 1.0020309 3.7973684 8.7376766 1 17
20800 5.2512898 0.99901254 3.5027763 7.8902791 1 14
20900 5.3245034 1.0014504 3.3354615 6.7030716 1 17
21000 5.2071731 1.0020459 3.3881369 5.8616999 1 20
21100 5.3187535 1.0010762 3.2845672 8.1422146 1 21
21200 5.5298545 0.99942313 3.4393978 7.1183144 1 22
21300 5.8430744 1.0008652 3.719408 7.8522038 1 20
21400 5.8190457 1.0017046 3.5624252 7.8150165 1 20
21500 6.004585 1.0035276 3.9161914 7.7719377 1 21
21600 6.7202635 0.99970072 3.9642141 8.7934294 1 18
21700 6.8590346 1.0007883 4.4285217 8.9014638 1 20
21800 6.627638 1.0012117 4.1154082 8.3153026 1 22
21900 7.8281047 1.0008299 4.8842343 8.4016227 1 20
22000 7.200038 1.0014681 4.4141419 9.4091956 1 18
22100 7.7442011 1.0018051 4.7850371 8.9885489 1 15
22200 7.4770203 1.0033558 4.7512643 8.4898148 1 17
22300 8.1080801 1.0000019 5.2725185 9.2314625 1 14
22400 7.8068311 1.0020672 4.9055683 8.4064748 1 12
22500 7.4594636 1.0008427 4.6586396 8.5102986 1 11
22600 6.9380609 1.0024634 4.2435619 10.395118 1 16
22700 6.9338066 1.001056 4.3436179 7.9126284 1 18
22800 6.8049493 1.0020052 4.1443407 7.8228868 1 18
22900 6.2280158 1.0021474 3.7695343 7.3179647 1 20
23000 5.649403 1.0017128 3.5941976 7.2964709 1 19
23100 5.3203116 1.001912 3.3807399 6.6454551 1 15
23200 5.8172882 1.0005742 3.6625896 8.4256312 1 15
23300 5.9647182 1.0015466 3.9106019 8.3303303 1 14
23400 5.9784055 1.0034542 3.7229235 7.7934273 1 14
23500 5.377627 1.00192 3.5481778 6.8195124 1 17
23600 5.4807136 1.0014662 3.563123 7.6356376 1 18
23700 5.8896329 1.0013553 3.7990694 8.5513408 1 13
23800 6.3463707 0.9999403 3.9609397 8.5741923 1 11
23900 6.656669 1.0014998 4.1993183 9.0862996 1 13
24000 7.583723 1.0025057 4.7628652 7.5007245 1 20
24100 6.9868359 1.0014089 4.4369841 7.692833 1 25
24200 7.1966062 1.0013149 4.4384528 9.5264821 1 18
24300 6.7765706 1.0007065 4.3500477 9.4974154 1 16
24400 7.0853466 1.0013246 4.409163 9.2215823 1 17
24500 6.9603823 1.0004247 4.4866051 7.7870058 1 20
24600 6.9208291 0.99953329 4.2298144 6.5732392 1 21
24700 6.5005518 1.0026848 4.0003505 7.8094715 1 22
24800 5.8421948 1.0012055 3.6686768 7.6078157 1 26
24900 5.8410604 1.0023428 3.746177 6.8971309 1 22
25000 5.8728511 1.0001747 3.7170134 7.4456816 1 19
25100 6.0217168 1.000624 3.7756108 6.6542452 1 20
25200 6.1939015 1.0017861 3.8943084 9.395821 1 25
25300 6.161998 1.0010373 3.9255122 6.2228884 1 28
25400 5.5850406 1.0018505 3.5129832 7.2551309 1 24
25500 6.0286276 1.0009028 3.8580887 6.8065265 1 24
25600 5.6262228 1.0005097 3.4574446 7.5061246 1 21
25700 6.1348187 1.0009828 3.8073512 7.4818375 1 17
25800 6.09781 1.0026426 3.9585383 9.0915939 1 21
25900 6.2673667 1.0002269 3.8182813 9.2134822 1 21
26000 6.6001776 1.0020444 4.041386 8.0403555 1 18
26100 6.3063025 1.0016633 3.8649839 8.8149734 1 19
26200 6.0046983 1.002332 3.5380766 8.6145656 1 17
26300 5.9627788 1.0005401 3.56864 6.7821213 1 15
26400 5.0547314 0.9998295 3.2106781 9.2935351 1 15
26500 5.256781 1.0013131 3.2946631 8.8590275 1 15
26600 5.6250355 1.0023929 3.5243033 8.8985058 1 17
26700 6.0197165 1.0018323 3.7973947 7.3093402 1 17
26800 5.4556541 1.0015309 3.4295107 8.2342049 1 18
26900 5.420428 1.0024996 3.4374201 7.1444636 1 16
27000 6.165624 1.0019174 3.8726016 8.6588275 1 20
27100 6.7131697 1.0006541 4.266264 8.7063389 1 24
27200 6.4855163 1.0016139 4.2029778 7.667611 1 29
27300 6.0525608 1.000478 3.9169723 7.4515279 1 25
27400 6.1426194 1.0014522 3.9176108 6.8689671 1 24
27500 6.5981349 1.0001143 4.0620686 8.6804552 1 27
27600 6.7827138 1.0016694 4.2764286 9.3912843 1 21
27700 6.6368902 1.0025149 4.1452128 9.1814523 1 24
27800 6.9791025 1.0019486 4.3989933 7.9446882 1 24
27900 6.617142 1.0015736 4.360571 9.3732108 1 26
28000 7.2818263 1.0014101 4.6041512 8.2398587 1 28
28100 7.2543709 1.0007625 4.5724787 7.7373488 1 22
28200 7.0631847 1.0023922 4.4021705 8.3290554 1 29
28300 7.2999952 1.0012593 4.4655563 8.612666 1 27
28400 7.4124538 1.0014043 4.5011335 8.379391 1 29
28500 7.0350937 1.0011392 4.3528091 7.8167375 1 24
28600 7.9659642 1.0031684 4.8732467 8.0661929 1 30
28700 7.2865919 1.0010958 4.6650146 8.0325989 1 32
28800 7.7039529 1.0027912 4.8299888 9.5471747 1 30
28900 8.3288847 1.0012438 5.0785288 8.8964877 1 31
29000 7.9348665 1.0021794 4.9393968 9.5531767 1 31
29100 8.2473389 1.0013795 4.9890359 9.7697184 1 29
29200 8.6383362 1.0018356 4.9856954 7.6402719 1 25
29300 8.2504592 1.0011048 4.9631793 7.9466724 1 24
29400 8.0502922 1.0010516 5.2521065 8.4515028 1 26
29500 7.9475896 1.0012951 4.8584644 9.1225463 1 19
29600 8.5641641 1.0016228 5.4361335 9.2045399 1 23
29700 8.9932021 1.0011848 5.5727205 8.6045729 1 23
29800 8.0320178 1.0019073 5.2837013 8.9335413 1 22
29900 8.2676522 1.0012734 5.2213798 8.8966896 1 24
30000 9.1848984 1.001747 5.9147628 12.096129 1 27
30100 10.184519 0.99977427 6.4260136 11.140491 1 27
30200 9.271472 1.0023983 6.0252189 9.6954338 1 30
30300 9.0751572 1.000851 5.6010295 9.734426 1 28
30400 9.4581261 1.0018449 5.6987258 9.70456 1 34
30500 9.1574751 0.99944001 5.582217 9.300318 1 27
30600 8.619312 1.001388 5.3503985 8.2759155 1 26
30700 7.9370031 1.0026674 5.0702831 8.5368014 1 28
30800 7.9221619 1.0019077 5.1278637 11.046922 1 26
30900 9.9722884 1.0025903 6.4055506 10.167311 1 25
31000 8.8648667 0.99962676 5.4777514 10.142102 1 21
31100 8.576344 1.000906 5.3216342 8.7984921 1 18
31200 7.8480974 1.0010341 4.9584917 9.0696437 1 16
31300 8.3536183 1.0005758 5.208516 9.7971514 1 15
31400 8.5301933 1.0007603 5.2241536 9.0257241 1 17
31500 8.5196226 1.0018215 5.0576064 8.8847294 1 19
31600 8.1470823 1.0023147 4.9182956 9.0205413 1 20
31700 8.1475888 1.0005764 5.1814113 9.0603162 1 16
31800 7.8629717 1.0014194 4.9221218 9.366291 1 16
31900 7.7206559 1.0021082 4.9167636 7.4136735 1 16
32000 7.5152809 1.0004752 4.6330638 8.830959 1 16
32100 8.2693974 1.0011751 4.9094804 9.427636 1 13
32200 8.3067661 0.9997006 4.9036865 9.0374633 1 17
32300 7.2068514 1.0007866 4.3580755 8.6445065 1 17
32400 6.885063 1.0011887 4.1528011 8.1199454 1 16
32500 6.9147014 1.0020825 4.160405 7.5398034 1 19
32600 6.8809668 1.000971 4.3312782 8.2157688 1 16
32700 6.4818892 1.0000885 3.9433899 7.309605 1 22
32800 6.6875555 1.0018674 4.1017504 7.2327183 1 22
32900 7.6118502 0.99975736 4.4498951 8.5072395 1 19
33000 7.7576909 1.0022061 4.7239551 9.2132467 1 22
33100 7.8616235 1.000482 5.0031322 9.349805 1 20
33200 8.2620563 1.0015059 5.2482188 10.286446 1 17
33300 8.0217099 1.0015466 5.1166876 9.1381844 1 20
33400 7.6565746 1.0024855 4.7594208 9.2646824 1 22
33500 7.9633887 1.0010334 4.6754116 9.1085184 1 23
33600 7.9566834 1.0024542 4.6712679 9.2046594 1 25
33700 8.2639384 1.0003021 5.1326892 8.0930215 1 24
33800 8.5648917 1.0000947 5.2099387 8.8127486 1 21
33900 8.3593557 1.0002488 5.1291354 8.5938391 1 25
34000 8.1922068 1.0030011 5.1441189 7.1529563 1 24
34100 8.4260308 1.0004639 5.5876122 9.0450303 1 28
34200 8.3014654 1.0002204 5.1964772 8.4920822 1 33
34300 7.4736545 1.0010306 4.7932244 7.8442244 1 30
34400 7.0023126 1.0024002 4.5665168 8.4702188 1 29
34500 7.3797703 1.000813 4.7224014 8.4098954 1 30
34600 7.7158761 0.99973161 4.7441628 8.5818592 1 29
34700 7.6135895 1.0015768 4.6612844 7.2195952 1 28
34800 7.0458078 0.99992638 4.2805357 7.4162305 1 32
34900 7.6190708 1.0007146 4.8064968 8.2709405 1 27
35000 7.4614294 1.0006051 4.7807207 7.7137359 1 28
35100 7.7008336 1.0008263 4.6823621 7.0208513 1 26
35200 8.1510766 1.000271 5.1781834 7.3231692 1 24
35300 7.5106275 1.0010438 4.6988185 8.9418343 1 25
35400 7.8116652 1.0009688 4.8622216 7.4624002 1 17
35500 7.2159785 1.0027484 4.543984 8.3177043 1 21
35600 7.6978875 1.0004834 4.7021203 8.3706905 1 20
35700 7.7827655 1.0019919 4.775879 8.6083292 1 15
35800 7.8433537 1.001844 4.7506574 7.3250009 1 15
35900 7.9456497 1.0004336 4.7925775 7.9824359 1 18
36000 8.1044513 1.0022261 5.1213755 9.211699 1 16
36100 7.6657532 1.0025661 4.751804 8.9770412 1 19
36200 7.909323 1.0035462 4.8435293 10.232493 1 21
36300 8.4188244 1.0016775 5.4337725 9.2060079 1 24
36400 8.7352689 1.0011274 5.6313351 8.6202832 1 24
36500 8.3459273 1.0005659 5.187336 6.9333716 1 21
36600 7.7118105 1.0018769 4.9293347 8.2789615 1 14
36700 7.8069879 1.0014021 4.7782709 8.4841233 1 15
36800 7.862085 1.0005342 4.8680692 8.1055023 1 16
36900 7.9469362 1.0027815 4.9339095 9.157722 1 16
37000 7.9085375 1.0024851 5.0921374 8.9374239 1 16
37100 8.9464869 1.0005734 5.6837772 8.806998 1 16
37200 8.1482632 1.0021175 5.1266453 8.5772094 1 18
37300 7.7958072 1.0026336 4.788431 8.3233372 1 19
37400 7.3647655 1.0015482 4.4786134 9.6606112 1 23
37500 7.3071882 1.0003912 4.681549 8.6319438 1 17
37600 7.8672509 1.0000478 4.7981944 8.3051478 1 14
37700 7.9306696 0.99923102 4.9316544 9.3672856 1 15
37800 7.7397949 0.99948557 5.1168552 8.5978047 1 17
37900 7.9121039 1.0020122 4.9866234 7.640888 1 14
38000 7.433451 1.0007901 4.6254894 8.0853539 1 14
38100 7.4636908 1.0021552 4.8472833 8.1975615 1 10
38200 7.4453077 1.0010305 4.6910943 7.8192603 1 13
38300 7.0488536 1.0012587 4.5490462 8.190036 1 16
38400 8.0686748 1.0016782 5.0747029 7.7242015 1 15
38500 7.9575875 1.0007137 4.8361776 8.05268 1 15
38600 7.6690498 1.0027522 4.8823286 9.1926516 1 20
38700 7.1567 1.002374 4.5600354 10.098089 1 19
38800 6.9100518 1.0008695 4.4101446 7.8832032 1 19
38900 6.8021882 1.0017647 4.1844125 8.1858761 1 21
39000 8.3996464 1.0010263 4.8183813 8.0997387 1 16
39100 8.4533834 1.0021643 5.074254 11.291904 1 19
39200 8.2406701 1.002062 5.0117425 8.778159 1 24
39300 8.3134114 1.0008218 5.0067136 7.9871787 1 22
39400 7.4307571 1.0014205 4.5858283 8.8596594 1 25
39500 7.1146821 1.0016367 4.5021057 7.4890018 1 22
39600 8.0048978 0.99992107 4.9235747 7.8770845 1 24
39700 8.070853 1.0029024 5.0842957 9.020664 1 21
39800 7.6939108 1.0012543 4.8986595 8.3306129 1 20
39900 7.2915444 1.00267 4.5038291 8.3844384 1 20
40000 7.3023994 1.0020441 4.4960911 8.1023709 1 18
40100 7.0221648 1.0033695 4.6374149 8.3756822 1 24
40200 7.4114756 1.0019246 4.6733475 7.6547258 1 23
40300 7.5323108 1.0005472 4.8284493 8.2820085 1 26
40400 7.3890772 1.0010491 4.6599273 8.9203575 1 19
40500 7.5786764 1.0016114 4.8166885 8.6760107 1 25
40600 8.165763 1.0006961 5.1488995 7.9321524 1 22
40700 8.1277597 0.99933464 5.0441567 10.069551 1 16
40800 8.1050904 1.0024705 5.4408599 8.3244459 1 21
40900 7.805318 1.0022992 4.9965408 9.7193723 1 21
41000 9.0130932 1.0006842 5.7931112 6.1646073 1 20
41100 8.0387975 1.0017359 5.3355655 9.6123191 1 21
41200 8.4484723 1.0014151 5.4461007 8.5146504 1 27
41300 8.6181909 1.0007562 5.2963876 9.1122306 1 30
41400 9.6762899 1.0010931 5.950456 9.2851025 1 25
41500 9.9414226 1.0016186 6.1433384 10.741453 1 24
41600 9.3348435 1.0003483 5.9291766 11.460717 1 20
41700 9.6125587 1.0013661 5.8530052 9.2105722 1 19
41800 11.383056 1.0032034 7.1988684 10.312945 1 22
41900 10.884524 1.0034888 6.9126707 10.775457 1 20
42000 11.071218 1.0026753 7.0004189 10.740627 1 20
42100 11.054304 1.0008347 6.9602414 8.9885498 1 22
42200 22.478691 1.0020466 14.997099 12.72513 1 19
42300 18.303508 1.0027626 11.336523 12.638769 1 18
42400 15.998712 1.0030312 9.4092725 11.070501 1 24
42500 15.034488 1.0024472 9.3543751 11.48052 1 28
42600 14.538257 1.0033153 9.2523745 10.909576 1 27
42700 13.986613 1.001458 8.5544184 10.765136 1 29
42800 13.240256 1.0027899 8.2014429 10.506497 1 32
42900 12.784336 1.0001406 8.0823431 12.258209 1 33
43000 13.374145 1.0012996 8.4207155 10.32817 1 31
43100 13.142334 1.0022503 8.5908808 10.152205 1 32
43200 12.669284 1.0018944 7.8511966 10.580104 1 32
43300 13.155032 1.001144 8.0337768 10.6652 1 39
43400 12.155928 1.0019472 7.5886584 11.234772 1 35
43500 12.385603 1.0007639 7.8865245 9.3868914 1 32
43600 12.236179 1.0027456 7.7521353 10.456701 1 42
43700 11.49535 1.0008758 7.3633144 8.8490079 1 40
43800 11.469157 1.0015845 7.0035577 10.594522 1 41
43900 11.228266 1.0013014 7.0137223 8.0653711 1 38
44000 10.56742 1.0016631 6.6908938 8.1094154 1 35
44100 9.8964699 1.0008351 6.3550438 8.6578181 1 36
44200 9.041539 1.0019541 5.6721401 8.6518043 1 38
44300 9.0767434 1.0034191 5.7446596 8.3838528 1 38
44400 9.2299608 1.0019526 5.7117964 8.3106491 1 37
44500 9.458981 1.0030409 5.7612138 7.7679755 1 37
44600 8.9611997 1.0014848 5.6490756 6.9224078 1 37
44700 8.0853184 1.0018894 5.2288749 8.0910912 1 32
44800 7.9999755 1.0015853 4.8088312 7.1854304 1 30
44900 7.6598023 1.0009751 4.6690664 7.1999858 1 28
45000 7.4939315 1.0010307 4.8119666 7.9615769 1 26
45100 7.4690079 0.99913423 4.9704428 7.6026835 1 32
45200 7.7001199 1.001626 4.9315953 7.4926686 1 25
45300 7.8794405 1.0011648 4.8624857 8.0804457 1 26
45400 7.493909 1.0016257 4.7631808 8.0330626 1 26
45500 7.5963141 1.0005825 4.7220659 7.0971298 1 23
45600 7.9028612 1.0017008 4.9561022 8.440428 1 23
45700 7.2285584 1.0006033 4.5521456 9.385579 1 23
45800 7.5687284 1.0024318 4.8557498 8.3052658 1 23
45900 7.8938604 1.0013937 5.1393944 5.5323667 1 26
46000 8.318466 1.0020803 5.4761811 8.2227801 1 25
46100 7.9169512 1.0024598 5.0406355 8.64365 1 27
46200 7.5535458 1.0016318 4.8010133 9.370726 1 26
46300 7.8926896 1.0001525 5.18463 7.9830196 1 27
46400 7.487145 1.002671 4.7718312 8.300134 1 29
46500 7.3564658 1.0006114 4.6762189 7.34947 1 26
46600 7.2261291 1.0005569 4.4751221 6.5847138 1 27
46700 7.2943203 1.0020164 4.3335327 7.7296507 1 25
46800 8.5849411 1.0014634 5.4501531 9.0933014 1 25
46900 10.176752 1.0023799 6.0456779 9.4050423 1 16
47000 9.1913098 1.0029076 5.7577256 9.1826215 1 22
47100 9.5479771 1.0022102 6.1100973 8.9440056 1 28
47200 9.9944172 1.0004924 6.3649417 9.1507264 1 25
47300 9.3543283 1.0013246 6.0873147 10.41657 1 24
47400 8.594101 1.0020068 5.6864295 9.2388304 1 24
47500 9.3191964 1.002411 6.0537511 9.3506828 1 23
47600 8.1615734 1.001364 5.3757905 10.303962 1 30
47700 8.3615046 1.0003075 5.2727936 9.3162209 1 32
47800 8.3566467 1.0026031 5.4379524 7.7644422 1 33
47900 8.4062556 1.0006471 5.3098736 8.0181121 1 33
48000 8.2233307 1.0012304 4.9650027 9.2644288 1 34
48100 8.4495256 1.000088 4.9940422 10.01023 1 27
48200 8.8068097 1.0014275 5.4732649 8.410093 1 31
48300 8.0008187 1.0017459 4.7732764 9.25726 1 27
48400 7.7242529 1.0026909 4.9084505 8.7147295 1 30
48500 8.3752816 1.001333 5.1071228 8.2267308 1 32
48600 9.0777805 1.0019328 5.7331841 9.6679383 1 29
48700 9.3623061 1.0001767 5.7117062 8.396895 1 25
48800 8.1186637 1.0013185 5.2697427 8.6058372 1 27
48900 7.3685497 1.0007173 4.6097553 7.8047228 1 24
49000 7.1661421 1.0023152 4.5389038 8.8759552 1 22
49100 6.9857144 1.0016394 4.6489319 8.2022359 1 24
49200 6.7160336 1.0018413 4.2488082 8.3393245 1 25
49300 7.9703755 1.0010628 5.2328567 7.968278 1 28
49400 8.2628465 1.0010877 5.2292977 8.0196533 1 27
49500 8.1436558 1.0015175 5.0344712 8.0712037 1 30
49600 8.5182498 1.0021589 5.1029028 8.6869789 1 28
49700 8.3604444 1.0015016 5.0333696 9.4861656 1 25
49800 7.336335 1.0020055 4.6365173 8.7210022 1 30
49900 7.432996 1.0016415 4.7090587 8.7033033 1 29
50000 7.4937053 1.001014 4.7212573 9.0890363 1 29
Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 293.48 | 403.7 | 545.29 | 357.5 | 40.39
Neigh | 2.4176 | 3.2721 | 3.8303 | 25.2 | 0.33
Comm | 163.58 | 305.88 | 419.83 | 416.7 | 30.60
Output | 0.032483 | 0.034794 | 0.040514 | 1.2 | 0.00
Modify | 281.15 | 285.67 | 293.8 | 24.3 | 28.58
Other | | 1.023 | | | 0.10
Nlocal: 2033.88 ave 2657 max 1198 min
Histogram: 2 0 0 0 0 2 1 0 1 2
Nghost: 1628.12 ave 1719 max 1569 min
Histogram: 2 0 1 1 2 1 0 0 0 1
Neighs: 13566 ave 18212 max 8488 min
Histogram: 1 0 0 1 2 1 2 0 0 1
Total # of neighbors = 108528
Ave neighs/atom = 6.6700264
Neighbor list builds = 2447
Dangerous builds = 2
Total wall time: 0:19:22

243
examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8
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@ -1,243 +0,0 @@
LAMMPS (1 Feb 2014)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big
read_data data.tri.srd
orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.35721 1.35721 1.35721
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.368403 0.368403 0.368403
create_atoms 2 region box
Created 91125 atoms
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
125 rigid bodies with 1500 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step f_1 c_tsmall f_2[9] temp press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 67 67 67
SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861
SRD per actual grid cell = 0.0647662
SRD viscosity = -1.09837
big/SRD mass density ratio = 24.668
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.9708 35.1504
ave/max big velocity = 0 0
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
Memory usage per processor = 116.135 Mbytes
Step 1 tsmall 2[9] Temp Press
0 0 1.4405441 0 0 -0.15917996
1000 1.0535509 1.1241378 1.1224038 0 0.15526438
2000 2.4635987 1.0240667 0.94231519 0 0.011069846
3000 3.1093028 1.0070585 1.0176028 0 0.34124888
4000 2.9524179 1.0101774 1.0311733 0 -0.22118101
5000 2.9175438 1.0109144 1.0284445 0 0.1839507
6000 3.3200928 0.99108983 0.95968219 0 1.0229339
7000 3.3020156 0.99661428 0.98000621 0 2.3333851
8000 4.1500999 0.99129645 0.99723707 0 4.3054414
9000 6.537028 1.0074533 1.0251098 0 18.782913
10000 16.233245 1.0145766 1.0219787 0 147.83787
Loop time of 228.558 on 8 procs for 10000 steps with 16271 atoms
Pair time (%) = 145.018 (63.4492)
Neigh time (%) = 32.6283 (14.2757)
Comm time (%) = 43.3283 (18.9572)
Outpt time (%) = 0.000848889 (0.00037141)
Other time (%) = 7.58254 (3.31755)
Nlocal: 2033.88 ave 2092 max 1902 min
Histogram: 1 0 0 0 1 1 0 1 1 3
Nghost: 2805 ave 2855 max 2751 min
Histogram: 1 0 2 1 0 0 0 2 1 1
Neighs: 30026.5 ave 38700 max 24367 min
Histogram: 1 0 2 1 3 0 0 0 0 1
Total # of neighbors = 240212
Ave neighs/atom = 14.7632
Neighbor list builds = 501
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 40 40 40
SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312
SRD per actual grid cell = -1.93929
SRD viscosity = -0.36972
big/SRD mass density ratio = -0.836253
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.0639 40
ave/max big velocity = 2.05735 6.73052
Memory usage per processor = 65.2471 Mbytes
Step 1 tsmall 2[9] Temp Press
10000 16.233245 1.0144194 0 0 146.27032
11000 17.301043 1.0619209 1 0 84.226323
12000 13.481177 1.063945 1 0 80.42834
13000 12.616615 1.0536125 1 0 68.365053
14000 12.16592 1.0581344 1 0 59.709941
15000 10.811557 1.0650453 1 0 59.869798
16000 9.9303081 1.0641012 1 0 59.289126
17000 10.452639 1.0589904 1 0 52.680235
18000 9.2488947 1.0556713 1 0 51.044123
19000 8.7179788 1.0566791 1 0 50.927924
20000 7.8641299 1.0668891 1 0 53.961014
21000 8.4333975 1.0628003 1 0 54.677068
22000 8.554623 1.0591872 1 0 51.784737
23000 7.895462 1.0598512 1 0 53.26885
24000 7.7014869 1.055569 1 0 54.236941
25000 7.508138 1.0581539 1 0 53.297709
26000 8.0707381 1.0586451 1 0 51.411341
27000 8.224223 1.0585509 1 0 52.775784
28000 8.8720461 1.0648837 1 0 49.681447
29000 8.503895 1.0538278 1 0 52.478556
30000 8.2272425 1.0625583 1 0 52.795709
31000 8.4626161 1.0599557 1 0 52.905343
32000 7.7410527 1.0587681 1 0 57.464472
33000 7.2765481 1.0677531 1 0 59.46728
34000 7.036016 1.0640728 1 0 60.636828
35000 8.497203 1.0577458 1 0 55.257312
36000 8.9218761 1.0585038 1 0 55.668201
37000 8.0469115 1.0561193 1 0 58.711565
38000 8.6456966 1.0663818 1 0 53.691658
39000 8.566667 1.0616928 1 0 52.866468
40000 7.7081259 1.0577046 1 0 54.105829
41000 7.4051952 1.0570277 1 0 56.094997
42000 7.331432 1.0632261 1 0 55.661067
43000 7.5587053 1.0602077 1 0 54.30762
44000 7.4521497 1.0594391 1 0 52.993548
45000 7.6234559 1.0641992 1 0 53.352202
46000 8.0659693 1.0609367 1 0 50.302682
47000 7.5227882 1.0563543 1 0 50.43551
48000 8.0798684 1.0628968 1 0 48.419201
49000 7.130784 1.0594143 1 0 50.656081
50000 7.3219268 1.0608236 1 0 54.808358
Loop time of 1651.84 on 8 procs for 40000 steps with 16271 atoms
Pair time (%) = 1232.76 (74.6296)
Neigh time (%) = 171.893 (10.4061)
Comm time (%) = 193.625 (11.7218)
Outpt time (%) = 0.00338289 (0.000204795)
Other time (%) = 53.5578 (3.24231)
Nlocal: 2033.88 ave 2229 max 1953 min
Histogram: 2 1 2 2 0 0 0 0 0 1
Nghost: 2757.88 ave 2810 max 2692 min
Histogram: 1 1 1 0 1 0 0 1 1 2
Neighs: 30098.6 ave 37369 max 25592 min
Histogram: 1 3 0 1 0 1 1 0 0 1
Total # of neighbors = 240789
Ave neighs/atom = 14.7987
Neighbor list builds = 2007
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

1
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -110,6 +110,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(extract_variable);
ADDSYM(extract_variable_datatype);
ADDSYM(set_variable);
ADDSYM(variable_info);
ADDSYM(gather_atoms);
ADDSYM(gather_atoms_concat);

5
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -106,7 +106,7 @@ typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
#endif
#define LAMMPSPLUGIN_ABI_VERSION 1
#define LAMMPSPLUGIN_ABI_VERSION 2
struct _liblammpsplugin {
int abiversion;
int has_exceptions;
@ -127,7 +127,7 @@ struct _liblammpsplugin {
void (*error)(void *, int, const char *);
void (*file)(void *, char *);
void (*file)(void *, const char *);
char *(*command)(void *, const char *);
void (*commands_list)(void *, int, const char **);
void (*commands_string)(void *, const char *);
@ -155,6 +155,7 @@ struct _liblammpsplugin {
void *(*extract_variable)(void *, const char *, char *);
int (*extract_variable_datatype)(void *, const char *);
int (*set_variable)(void *, char *, char *);
int (*variable_info)(void *, int, char *, int);
void (*gather_atoms)(void *, const char *, int, int, void *);
void (*gather_atoms_concat)(void *, const char *, int, int, void *);

2
examples/PACKAGES/hdnnp/in.hdnnp
View File

@ -39,7 +39,7 @@ fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
dump 1 all atom 1 dump.hdnnp
# dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION

53
examples/PACKAGES/hdnnp/in.hybrid Normal file
View File

@ -0,0 +1,53 @@
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
create_box 3 box
mass 1 1.0
read_data ${cfgFile} add append offset 1 0 0 0 0
timestep ${dt}
thermo 1
###############################################################################
# HDNNP
###############################################################################
pair_style hybrid lj/cut 6.0 hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * hdnnp NULL H O
pair_coeff 1 * lj/cut 0.1 3.0
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
#dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}

667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.1 Normal file
View File

@ -0,0 +1,667 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
read_data ${cfgFile}
read_data data.H2O-360mol
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
1 by 1 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.004 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * H O
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
# dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* General citation for n²p² and the LAMMPS interface:
Singraber, A.; Behler, J.; Dellago, C.
Library-Based LAMMPS Implementation of High-Dimensional
Neural Network Potentials.
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
https://doi.org/10.1021/acs.jctc.8b00770
-------------------------------------------------------------------------------
* Additionally, if you use the NNP training features of n²p²:
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
Parallel Multistream Training of High-Dimensional Neural
Network Potentials.
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
https://doi.org/10.1021/acs.jctc.8b01092
-------------------------------------------------------------------------------
* Additionally, if polynomial symmetry functions are used:
Bircher, M. P.; Singraber, A.; Dellago, C.
Improved Description of Atomic Environments Using Low-Cost
Polynomial Functions with Compact Support.
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
https://arxiv.org/abs/2010.14414
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** SETUP: CUTOFF FUNCTIONS ***************************************************
Parameter alpha for inner cutoff: 0.000000
Inner cutoff = Symmetry function cutoff * alpha
Equal cutoff function type for all symmetry functions:
CutoffFunction::CT_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** SETUP: SYMMETRY FUNCTIONS *************************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
Short range atomic symmetry functions element H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
mi ..... Member index.
sfi .... Symmetry function index.
e ...... Recalculate exponential term.
Short range atomic symmetry function groups element H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
----------------------------------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: NEURAL NETWORKS ****************************************************
Normalize neurons (all elements): 0
-------------------------------------------------------------------------------
Atomic short range NN for element H :
Number of weights : 1325
Number of biases : 51
Number of connections: 1376
Architecture 27 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
-------------------------------------------------------------------------------
Atomic short range NN for element O :
Number of weights : 1400
Number of biases : 51
Number of connections: 1451
Architecture 30 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
28 G
29 G
30 G
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
Equal scaling type for all symmetry functions:
Scaling type::ST_SCALECENTER (3)
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
Smin = 0.000000
Smax = 1.000000
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
-------------------------------------------------------------------------------
Abbreviations:
--------------
ind ..... Symmetry function index.
min ..... Minimum symmetry function value.
max ..... Maximum symmetry function value.
mean .... Mean symmetry function value.
sigma ... Standard deviation of symmetry function values.
sf ...... Scaling factor for derivatives.
Smin .... Desired minimum scaled symmetry function value.
Smax .... Desired maximum scaled symmetry function value.
t ....... Scaling type.
Scaling data for symmetry functions element H :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
-------------------------------------------------------------------------------
Scaling data for symmetry functions element O :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
Equal symmetry function statistics for all elements.
Collect min/max/mean/sigma : 0
Collect extrapolation warnings : 1
Write extrapolation warnings immediately to stderr: 0
Halt on any extrapolation warning : 0
*******************************************************************************
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
Short NN weight file name format: hdnnp-data/weights.%03d.data
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
*******************************************************************************
*** SETUP: LAMMPS INTERFACE ***************************************************
Individual extrapolation warnings will not be shown.
Extrapolation warning summary will be shown every 5 timesteps.
The simulation will be stopped when 100 extrapolation warnings are exceeded.
Extrapolation warnings are accumulated over all time steps.
-------------------------------------------------------------------------------
CAUTION: If the LAMMPS unit system differs from the one used
during NN training, appropriate conversion factors
must be provided (see keywords cflength and cfenergy).
Length unit conversion factor: 1.8897261327999999E+00
Energy unit conversion factor: 3.6749325399999998E-02
Checking consistency of cutoff radii (in LAMMPS units):
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
Maximum symmetry function cutoff: 6.350E+00
Cutoff radii are consistent.
-------------------------------------------------------------------------------
Element mapping string from LAMMPS to n2p2: "1:H,2:O"
CAUTION: Please ensure that this mapping between LAMMPS
atom types and NNP elements is consistent:
---------------------------
LAMMPS type | NNP element
---------------------------
1 <-> H ( 1)
2 <-> O ( 8)
---------------------------
NNP setup for LAMMPS completed.
*******************************************************************************
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.36
ghost atom cutoff = 8.36
binsize = 4.18, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hdnnp, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
Per MPI rank memory allocation (min/avg/max) = 4.021 | 4.021 | 4.021 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -750069.48 0 -750069.48 -5297.5537
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
2 30.988787 -750073.91 0 -750069.59 -5023.6945
3 58.859866 -750077.88 0 -750069.67 -4427.8346
4 82.576399 -750081.26 0 -750069.74 -3275.4378
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
5 94.968097 -750083.01 0 -750069.76 -1511.6733
6 93.724286 -750082.8 0 -750069.73 709.20465
7 82.243957 -750081.13 0 -750069.66 3020.5084
8 68.611429 -750079.14 0 -750069.57 4922.5176
9 62.314385 -750078.21 0 -750069.51 5933.1543
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
10 69.501045 -750079.21 0 -750069.52 5761.8646
Loop time of 3.2801 on 1 procs for 10 steps with 1080 atoms
Performance: 0.132 ns/day, 182.228 hours/ns, 3.049 timesteps/s, 3.293 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2794 | 3.2794 | 3.2794 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00030785 | 0.00030785 | 0.00030785 | 0.0 | 0.01
Output | 0.00018531 | 0.00018531 | 0.00018531 | 0.0 | 0.01
Modify | 0.00013118 | 0.00013118 | 0.00013118 | 0.0 | 0.00
Other | | 9.142e-05 | | | 0.00
Nlocal: 1080 ave 1080 max 1080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4536 ave 4536 max 4536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 239270 ave 239270 max 239270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 239270
Ave neighs/atom = 221.5463
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.4 Normal file
View File

@ -0,0 +1,667 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
read_data ${cfgFile}
read_data data.H2O-360mol
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
2 by 2 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.007 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * H O
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
# dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* General citation for n²p² and the LAMMPS interface:
Singraber, A.; Behler, J.; Dellago, C.
Library-Based LAMMPS Implementation of High-Dimensional
Neural Network Potentials.
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
https://doi.org/10.1021/acs.jctc.8b00770
-------------------------------------------------------------------------------
* Additionally, if you use the NNP training features of n²p²:
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
Parallel Multistream Training of High-Dimensional Neural
Network Potentials.
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
https://doi.org/10.1021/acs.jctc.8b01092
-------------------------------------------------------------------------------
* Additionally, if polynomial symmetry functions are used:
Bircher, M. P.; Singraber, A.; Dellago, C.
Improved Description of Atomic Environments Using Low-Cost
Polynomial Functions with Compact Support.
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
https://arxiv.org/abs/2010.14414
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** SETUP: CUTOFF FUNCTIONS ***************************************************
Parameter alpha for inner cutoff: 0.000000
Inner cutoff = Symmetry function cutoff * alpha
Equal cutoff function type for all symmetry functions:
CutoffFunction::CT_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** SETUP: SYMMETRY FUNCTIONS *************************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
Short range atomic symmetry functions element H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
mi ..... Member index.
sfi .... Symmetry function index.
e ...... Recalculate exponential term.
Short range atomic symmetry function groups element H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
----------------------------------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: NEURAL NETWORKS ****************************************************
Normalize neurons (all elements): 0
-------------------------------------------------------------------------------
Atomic short range NN for element H :
Number of weights : 1325
Number of biases : 51
Number of connections: 1376
Architecture 27 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
-------------------------------------------------------------------------------
Atomic short range NN for element O :
Number of weights : 1400
Number of biases : 51
Number of connections: 1451
Architecture 30 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
28 G
29 G
30 G
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
Equal scaling type for all symmetry functions:
Scaling type::ST_SCALECENTER (3)
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
Smin = 0.000000
Smax = 1.000000
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
-------------------------------------------------------------------------------
Abbreviations:
--------------
ind ..... Symmetry function index.
min ..... Minimum symmetry function value.
max ..... Maximum symmetry function value.
mean .... Mean symmetry function value.
sigma ... Standard deviation of symmetry function values.
sf ...... Scaling factor for derivatives.
Smin .... Desired minimum scaled symmetry function value.
Smax .... Desired maximum scaled symmetry function value.
t ....... Scaling type.
Scaling data for symmetry functions element H :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
-------------------------------------------------------------------------------
Scaling data for symmetry functions element O :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
Equal symmetry function statistics for all elements.
Collect min/max/mean/sigma : 0
Collect extrapolation warnings : 1
Write extrapolation warnings immediately to stderr: 0
Halt on any extrapolation warning : 0
*******************************************************************************
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
Short NN weight file name format: hdnnp-data/weights.%03d.data
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
*******************************************************************************
*** SETUP: LAMMPS INTERFACE ***************************************************
Individual extrapolation warnings will not be shown.
Extrapolation warning summary will be shown every 5 timesteps.
The simulation will be stopped when 100 extrapolation warnings are exceeded.
Extrapolation warnings are accumulated over all time steps.
-------------------------------------------------------------------------------
CAUTION: If the LAMMPS unit system differs from the one used
during NN training, appropriate conversion factors
must be provided (see keywords cflength and cfenergy).
Length unit conversion factor: 1.8897261327999999E+00
Energy unit conversion factor: 3.6749325399999998E-02
Checking consistency of cutoff radii (in LAMMPS units):
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
Maximum symmetry function cutoff: 6.350E+00
Cutoff radii are consistent.
-------------------------------------------------------------------------------
Element mapping string from LAMMPS to n2p2: "1:H,2:O"
CAUTION: Please ensure that this mapping between LAMMPS
atom types and NNP elements is consistent:
---------------------------
LAMMPS type | NNP element
---------------------------
1 <-> H ( 1)
2 <-> O ( 8)
---------------------------
NNP setup for LAMMPS completed.
*******************************************************************************
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.36
ghost atom cutoff = 8.36
binsize = 4.18, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hdnnp, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -750069.48 0 -750069.48 -5297.5537
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
2 30.988787 -750073.91 0 -750069.59 -5023.6945
3 58.859866 -750077.88 0 -750069.67 -4427.8346
4 82.576399 -750081.26 0 -750069.74 -3275.4378
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
5 94.968097 -750083.01 0 -750069.76 -1511.6733
6 93.724286 -750082.8 0 -750069.73 709.20465
7 82.243957 -750081.13 0 -750069.66 3020.5084
8 68.611429 -750079.14 0 -750069.57 4922.5176
9 62.314385 -750078.21 0 -750069.51 5933.1543
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
10 69.501045 -750079.21 0 -750069.52 5761.8646
Loop time of 0.930358 on 4 procs for 10 steps with 1080 atoms
Performance: 0.464 ns/day, 51.687 hours/ns, 10.749 timesteps/s, 11.608 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.85419 | 0.89495 | 0.92919 | 3.5 | 96.19
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00075831 | 0.035035 | 0.075822 | 17.5 | 3.77
Output | 0.00018471 | 0.00023973 | 0.00031043 | 0.0 | 0.03
Modify | 4.0258e-05 | 4.2308e-05 | 4.4218e-05 | 0.0 | 0.00
Other | | 9.199e-05 | | | 0.01
Nlocal: 270 ave 278 max 262 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2552 ave 2564 max 2541 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 59817.5 ave 61917 max 57577 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 239270
Ave neighs/atom = 221.5463
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.1 Normal file
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@ -0,0 +1,689 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
create_box 3 box
Created orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
1 by 1 by 1 MPI processor grid
mass 1 1.0
read_data ${cfgFile} add append offset 1 0 0 0 0
read_data data.H2O-360mol add append offset 1 0 0 0 0
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
1 by 1 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.004 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
pair_style hybrid lj/cut 6.0 hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * hdnnp NULL H O
pair_coeff 1 * lj/cut 0.1 3.0
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
#dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* General citation for n²p² and the LAMMPS interface:
Singraber, A.; Behler, J.; Dellago, C.
Library-Based LAMMPS Implementation of High-Dimensional
Neural Network Potentials.
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
https://doi.org/10.1021/acs.jctc.8b00770
-------------------------------------------------------------------------------
* Additionally, if you use the NNP training features of n²p²:
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
Parallel Multistream Training of High-Dimensional Neural
Network Potentials.
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
https://doi.org/10.1021/acs.jctc.8b01092
-------------------------------------------------------------------------------
* Additionally, if polynomial symmetry functions are used:
Bircher, M. P.; Singraber, A.; Dellago, C.
Improved Description of Atomic Environments Using Low-Cost
Polynomial Functions with Compact Support.
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
https://arxiv.org/abs/2010.14414
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** SETUP: CUTOFF FUNCTIONS ***************************************************
Parameter alpha for inner cutoff: 0.000000
Inner cutoff = Symmetry function cutoff * alpha
Equal cutoff function type for all symmetry functions:
CutoffFunction::CT_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** SETUP: SYMMETRY FUNCTIONS *************************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
Short range atomic symmetry functions element H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
mi ..... Member index.
sfi .... Symmetry function index.
e ...... Recalculate exponential term.
Short range atomic symmetry function groups element H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
----------------------------------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: NEURAL NETWORKS ****************************************************
Normalize neurons (all elements): 0
-------------------------------------------------------------------------------
Atomic short range NN for element H :
Number of weights : 1325
Number of biases : 51
Number of connections: 1376
Architecture 27 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
-------------------------------------------------------------------------------
Atomic short range NN for element O :
Number of weights : 1400
Number of biases : 51
Number of connections: 1451
Architecture 30 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
28 G
29 G
30 G
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
Equal scaling type for all symmetry functions:
Scaling type::ST_SCALECENTER (3)
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
Smin = 0.000000
Smax = 1.000000
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
-------------------------------------------------------------------------------
Abbreviations:
--------------
ind ..... Symmetry function index.
min ..... Minimum symmetry function value.
max ..... Maximum symmetry function value.
mean .... Mean symmetry function value.
sigma ... Standard deviation of symmetry function values.
sf ...... Scaling factor for derivatives.
Smin .... Desired minimum scaled symmetry function value.
Smax .... Desired maximum scaled symmetry function value.
t ....... Scaling type.
Scaling data for symmetry functions element H :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
-------------------------------------------------------------------------------
Scaling data for symmetry functions element O :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
Equal symmetry function statistics for all elements.
Collect min/max/mean/sigma : 0
Collect extrapolation warnings : 1
Write extrapolation warnings immediately to stderr: 0
Halt on any extrapolation warning : 0
*******************************************************************************
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
Short NN weight file name format: hdnnp-data/weights.%03d.data
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
*******************************************************************************
*** SETUP: LAMMPS INTERFACE ***************************************************
Individual extrapolation warnings will not be shown.
Extrapolation warning summary will be shown every 5 timesteps.
The simulation will be stopped when 100 extrapolation warnings are exceeded.
Extrapolation warnings are accumulated over all time steps.
-------------------------------------------------------------------------------
CAUTION: If the LAMMPS unit system differs from the one used
during NN training, appropriate conversion factors
must be provided (see keywords cflength and cfenergy).
Length unit conversion factor: 1.8897261327999999E+00
Energy unit conversion factor: 3.6749325399999998E-02
Checking consistency of cutoff radii (in LAMMPS units):
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
Maximum symmetry function cutoff: 6.350E+00
Cutoff radii are consistent.
-------------------------------------------------------------------------------
Element mapping string from LAMMPS to n2p2: "2:H,3:O"
CAUTION: Please ensure that this mapping between LAMMPS
atom types and NNP elements is consistent:
---------------------------
LAMMPS type | NNP element
---------------------------
1 <-> --
2 <-> H ( 1)
3 <-> O ( 8)
---------------------------
NNP setup for LAMMPS completed.
*******************************************************************************
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.36
ghost atom cutoff = 8.36
binsize = 4.18, bins = 6 6 6
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on, cut 8
pair build: skip
stencil: none
bin: none
(2) pair hdnnp, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual, half/full trim from (4)
attributes: half, newton on, cut 8
pair build: halffull/newton/trim
stencil: none
bin: none
(4) neighbor class addition, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
Per MPI rank memory allocation (min/avg/max) = 7.06 | 7.06 | 7.06 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -750069.48 0 -750069.48 -5297.5537
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
2 30.988787 -750073.91 0 -750069.59 -5023.6945
3 58.859866 -750077.88 0 -750069.67 -4427.8346
4 82.576399 -750081.26 0 -750069.74 -3275.4378
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
5 94.968097 -750083.01 0 -750069.76 -1511.6733
6 93.724286 -750082.8 0 -750069.73 709.20465
7 82.243957 -750081.13 0 -750069.66 3020.5084
8 68.611429 -750079.14 0 -750069.57 4922.5176
9 62.314385 -750078.21 0 -750069.51 5933.1543
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
10 69.501045 -750079.21 0 -750069.52 5761.8646
Loop time of 3.32416 on 1 procs for 10 steps with 1080 atoms
Performance: 0.130 ns/day, 184.675 hours/ns, 3.008 timesteps/s, 3.249 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3234 | 3.3234 | 3.3234 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00032742 | 0.00032742 | 0.00032742 | 0.0 | 0.01
Output | 0.00019506 | 0.00019506 | 0.00019506 | 0.0 | 0.01
Modify | 0.00011454 | 0.00011454 | 0.00011454 | 0.0 | 0.00
Other | | 0.0001165 | | | 0.00
Nlocal: 1080 ave 1080 max 1080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4536 ave 4536 max 4536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.4 Normal file
View File

@ -0,0 +1,689 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
create_box 3 box
Created orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
2 by 2 by 1 MPI processor grid
mass 1 1.0
read_data ${cfgFile} add append offset 1 0 0 0 0
read_data data.H2O-360mol add append offset 1 0 0 0 0
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
2 by 2 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.007 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
pair_style hybrid lj/cut 6.0 hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * hdnnp NULL H O
pair_coeff 1 * lj/cut 0.1 3.0
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
#dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* General citation for n²p² and the LAMMPS interface:
Singraber, A.; Behler, J.; Dellago, C.
Library-Based LAMMPS Implementation of High-Dimensional
Neural Network Potentials.
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
https://doi.org/10.1021/acs.jctc.8b00770
-------------------------------------------------------------------------------
* Additionally, if you use the NNP training features of n²p²:
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
Parallel Multistream Training of High-Dimensional Neural
Network Potentials.
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
https://doi.org/10.1021/acs.jctc.8b01092
-------------------------------------------------------------------------------
* Additionally, if polynomial symmetry functions are used:
Bircher, M. P.; Singraber, A.; Dellago, C.
Improved Description of Atomic Environments Using Low-Cost
Polynomial Functions with Compact Support.
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
https://arxiv.org/abs/2010.14414
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** SETUP: CUTOFF FUNCTIONS ***************************************************
Parameter alpha for inner cutoff: 0.000000
Inner cutoff = Symmetry function cutoff * alpha
Equal cutoff function type for all symmetry functions:
CutoffFunction::CT_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** SETUP: SYMMETRY FUNCTIONS *************************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
Short range atomic symmetry functions element H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
mi ..... Member index.
sfi .... Symmetry function index.
e ...... Recalculate exponential term.
Short range atomic symmetry function groups element H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
----------------------------------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: NEURAL NETWORKS ****************************************************
Normalize neurons (all elements): 0
-------------------------------------------------------------------------------
Atomic short range NN for element H :
Number of weights : 1325
Number of biases : 51
Number of connections: 1376
Architecture 27 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
-------------------------------------------------------------------------------
Atomic short range NN for element O :
Number of weights : 1400
Number of biases : 51
Number of connections: 1451
Architecture 30 25 25 1
-------------------------------------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 G t t
15 G t t
16 G t t
17 G t t
18 G t t
19 G t t
20 G t t
21 G t t
22 G t t
23 G t t
24 G t t
25 G t t
26 G
27 G
28 G
29 G
30 G
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
Equal scaling type for all symmetry functions:
Scaling type::ST_SCALECENTER (3)
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
Smin = 0.000000
Smax = 1.000000
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
-------------------------------------------------------------------------------
Abbreviations:
--------------
ind ..... Symmetry function index.
min ..... Minimum symmetry function value.
max ..... Maximum symmetry function value.
mean .... Mean symmetry function value.
sigma ... Standard deviation of symmetry function values.
sf ...... Scaling factor for derivatives.
Smin .... Desired minimum scaled symmetry function value.
Smax .... Desired maximum scaled symmetry function value.
t ....... Scaling type.
Scaling data for symmetry functions element H :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
-------------------------------------------------------------------------------
Scaling data for symmetry functions element O :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
-------------------------------------------------------------------------------
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
Equal symmetry function statistics for all elements.
Collect min/max/mean/sigma : 0
Collect extrapolation warnings : 1
Write extrapolation warnings immediately to stderr: 0
Halt on any extrapolation warning : 0
*******************************************************************************
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
Short NN weight file name format: hdnnp-data/weights.%03d.data
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
*******************************************************************************
*** SETUP: LAMMPS INTERFACE ***************************************************
Individual extrapolation warnings will not be shown.
Extrapolation warning summary will be shown every 5 timesteps.
The simulation will be stopped when 100 extrapolation warnings are exceeded.
Extrapolation warnings are accumulated over all time steps.
-------------------------------------------------------------------------------
CAUTION: If the LAMMPS unit system differs from the one used
during NN training, appropriate conversion factors
must be provided (see keywords cflength and cfenergy).
Length unit conversion factor: 1.8897261327999999E+00
Energy unit conversion factor: 3.6749325399999998E-02
Checking consistency of cutoff radii (in LAMMPS units):
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
Maximum symmetry function cutoff: 6.350E+00
Cutoff radii are consistent.
-------------------------------------------------------------------------------
Element mapping string from LAMMPS to n2p2: "2:H,3:O"
CAUTION: Please ensure that this mapping between LAMMPS
atom types and NNP elements is consistent:
---------------------------
LAMMPS type | NNP element
---------------------------
1 <-> --
2 <-> H ( 1)
3 <-> O ( 8)
---------------------------
NNP setup for LAMMPS completed.
*******************************************************************************
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.36
ghost atom cutoff = 8.36
binsize = 4.18, bins = 6 6 6
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on, cut 8
pair build: skip
stencil: none
bin: none
(2) pair hdnnp, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual, half/full trim from (4)
attributes: half, newton on, cut 8
pair build: halffull/newton/trim
stencil: none
bin: none
(4) neighbor class addition, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -750069.48 0 -750069.48 -5297.5537
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
2 30.988787 -750073.91 0 -750069.59 -5023.6945
3 58.859866 -750077.88 0 -750069.67 -4427.8346
4 82.576399 -750081.26 0 -750069.74 -3275.4378
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
5 94.968097 -750083.01 0 -750069.76 -1511.6733
6 93.724286 -750082.8 0 -750069.73 709.20465
7 82.243957 -750081.13 0 -750069.66 3020.5084
8 68.611429 -750079.14 0 -750069.57 4922.5176
9 62.314385 -750078.21 0 -750069.51 5933.1543
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
10 69.501045 -750079.21 0 -750069.52 5761.8646
Loop time of 0.936871 on 4 procs for 10 steps with 1080 atoms
Performance: 0.461 ns/day, 52.048 hours/ns, 10.674 timesteps/s, 11.528 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.86567 | 0.89891 | 0.93611 | 3.1 | 95.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00035446 | 0.037585 | 0.070835 | 15.3 | 4.01
Output | 0.00018528 | 0.00023648 | 0.00030553 | 0.0 | 0.03
Modify | 4.2224e-05 | 4.4078e-05 | 4.6256e-05 | 0.0 | 0.00
Other | | 9.307e-05 | | | 0.01
Nlocal: 270 ave 278 max 262 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2552 ave 2564 max 2541 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

1
examples/plugins/CMakeLists.txt
View File

@ -35,6 +35,7 @@ else()
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_options(/wd4250)
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)

1
lib/colvars/colvar.cpp
View File

@ -30,6 +30,7 @@ colvar::colvar()
after_restart = false;
kinetic_energy = 0.0;
potential_energy = 0.0;
period = 0.0;
#ifdef LEPTON
dev_null = 0.0;

3
lib/gpu/lal_dpd.cu
View File

@ -301,9 +301,10 @@ __kernel void k_dpd_fast(const __global numtyp4 *restrict x_,
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4)
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
}

10
lib/machdyn/Install.py
View File

@ -31,8 +31,8 @@ checksums = { \
# help message
HELP = """
Syntax from src dir: make lib-smd args="-b"
or: make lib-smd args="-p /usr/include/eigen3"
Syntax from src dir: make lib-machdyn args="-b"
or: make lib-machdyn args="-p /usr/include/eigen3"
Syntax from lib dir: python Install.py -b
or: python Install.py -p /usr/include/eigen3"
@ -40,8 +40,8 @@ Syntax from lib dir: python Install.py -b
Example:
make lib-smd args="-b" # download/build in default lib/smd/eigen-eigen-*
make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
make lib-machdyn args="-b" # download/build in default lib/machdyn/eigen-eigen-*
make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
"""
pgroup = parser.add_mutually_exclusive_group()
@ -105,7 +105,7 @@ if buildflag:
edir = os.path.join(homepath, "eigen-%s" % version)
os.rename(edir, eigenpath)
# create link in lib/smd to Eigen src dir
# create link in lib/machdyn to Eigen src dir
print("Creating link to Eigen include folder")
if os.path.isfile("includelink") or os.path.islink("includelink"):

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