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Merge branch 'master' into bond_gaussian

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Axel Kohlmeyer
2020-11-25 15:50:54 -05:00
parent af179f9901 7cb644b425
commit abdfcceab2
303 changed files with 39068 additions and 5556 deletions
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2
.github/CONTRIBUTING.md vendored
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@ -108,7 +108,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit).
Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit).
You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.

10
cmake/Modules/Documentation.cmake
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@ -57,20 +57,14 @@ if(BUILD_DOC)
# download mathjax distribution and unpack to folder "mathjax"
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
endif()
# for increased browser compatibility
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
"${DOC_BUILD_STATIC_DIR}/polyfill.js")
endif()
# set up doxygen and add targets to run it
file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})
file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)

13
cmake/Modules/Tools.cmake
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@ -34,13 +34,24 @@ if(BUILD_LAMMPS_SHELL)
if(NOT LAMMPS_EXCEPTIONS)
message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
endif()
add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp)
# include resource compiler to embed icons into the executable on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
enable_language(RC)
set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
endif()
add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
# workaround for broken readline pkg-config file on FreeBSD
if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD)
target_include_directories(lammps-shell PRIVATE /usr/local/include)
endif()
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
endif()

32
cmake/Modules/YAML.cmake Normal file
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@ -0,0 +1,32 @@
message(STATUS "Downloading and building YAML library")
include(ExternalProject)
set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
mark_as_advanced(YAML_URL)
ExternalProject_Add(libyaml
URL ${YAML_URL}
URL_MD5 bb15429d8fb787e7d3f1c83ae129a999
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
CXX=${CMAKE_CXX_COMPILER}
CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
TEST_COMMAND "")
ExternalProject_Get_Property(libyaml INSTALL_DIR)
set(YAML_INCLUDE_DIR ${INSTALL_DIR}/include)
set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a)
add_library(Yaml::Yaml UNKNOWN IMPORTED)
set_target_properties(Yaml::Yaml PROPERTIES
IMPORTED_LOCATION ${YAML_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${YAML_INCLUDE_DIR})
add_dependencies(Yaml::Yaml libyaml)

9
cmake/Modules/generate_lmpgitversion.cmake
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@ -7,17 +7,20 @@ set(temp_git_info "false")
message(STATUS "Git Directory: ${LAMMPS_DIR}/.git")
if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
set(temp_git_info "true")
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse HEAD
execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
OUTPUT_VARIABLE temp_git_commit
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse --abbrev-ref HEAD
execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
OUTPUT_VARIABLE temp_git_branch
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} describe --dirty=-modified
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()

12
doc/Makefile
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@ -14,7 +14,6 @@ TXT2RST = $(VENV)/bin/txt2rst
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
POLYFILL = $(SPHINXCONFIG)/_static/polyfill.js
PYTHON = $(shell which python3)
DOXYGEN = $(shell which doxygen)
@ -81,7 +80,7 @@ help:
# ------------------------------------------
clean-all: clean
rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(POLYFILL) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
clean: clean-spelling
rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py
@ -95,7 +94,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
-e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
-e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@$(MAKE) $(MFLAGS) -C graphviz all
@(\
@ -237,13 +236,6 @@ $(VENV):
$(MATHJAX):
@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
# fall back to using wget and/or unencrypted download, if curl fails
$(POLYFILL): $(MATHJAX)
@curl -s -o $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \
curl -s -o $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \
wget -O $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \
wget -O $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1
$(TXT2RST) $(ANCHORCHECK): $(VENV)
@( \
. $(VENV)/bin/activate; \

2
doc/github-development-workflow.md
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@ -95,7 +95,7 @@ on the pull request discussion page on GitHub, so that other developers
can later review the entire discussion after the fact and understand the
rationale behind choices made. Exceptions to this policy are technical
discussions, that are centered on tools or policies themselves
(git, github, c++) rather than on the content of the pull request.
(git, GitHub, c++) rather than on the content of the pull request.
### Checklist for Pull Requests

2
doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "9 October 2020" "2020-10-09"
.TH LAMMPS "29 October 2020" "2020-10-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

6
doc/src/Build_development.rst
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@ -111,8 +111,10 @@ error margin). The status of this automated testing can be viewed on
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `PyYAML <http://pyyaml.org/>`_ library and development
headers to compile and will download and compile a recent version of the
It requires the `YAML <http://pyyaml.org/>`_ library and development
headers (if not found locally a recent version will be downloaded
and compiled transparently) to compile and will download and compile
a specific recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.

4
doc/src/Build_manual.rst
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@ -73,8 +73,8 @@ after the documentation folder is returned to a pristine state with
For the documentation build a python virtual environment is set up in
the folder ``doc/docenv`` and various python packages are installed into
that virtual environment via the ``pip`` tool. For rendering embedded
LaTeX code also the `MathJax <https://www.mathjax.org/>`_ and the
`Polyfill <https://polyfill.io/>`_ JavaScript engines need to be downloaded.
LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
engine needs to be downloaded.
The actual translation is then done via ``make`` commands in the doc
folder. The following ``make`` commands are available:

2
doc/src/Commands_fix.rst
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@ -195,7 +195,7 @@ OPT.
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`shake <fix_shake>`
* :doc:`shake (k) <fix_shake>`
* :doc:`shardlow (k) <fix_shardlow>`
* :doc:`smd <fix_smd>`
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>`

1
doc/src/Commands_pair.rst
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@ -241,6 +241,7 @@ OPT.
* :doc:`spin/dipole/long <pair_spin_dipole>`
* :doc:`spin/dmi <pair_spin_dmi>`
* :doc:`spin/exchange <pair_spin_exchange>`
* :doc:`spin/exchange/biquadratic <pair_spin_exchange>`
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`

1
doc/src/Errors_warnings.rst
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@ -119,7 +119,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
Since LAMMPS stores topology data with individual atoms, all atoms
comprising a bond, angle, dihedral or improper must be present on any
sub-domain that "owns" the atom with the information, either as a

4
doc/src/Howto_github.rst
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@ -72,7 +72,7 @@ explained in more detail here: `feature branch workflow <https://www.atlassian.c
**Feature branches**
First of all, create a clone of your version on github on your local
First of all, create a clone of your version on GitHub on your local
machine via HTTPS:
.. code-block:: bash
@ -155,7 +155,7 @@ useful message that explains the change.
.. code-block:: bash
$ git commit -m 'Finally updated the github tutorial'
$ git commit -m 'Finally updated the GitHub tutorial'
After the commit, the changes can be pushed to the same branch on GitHub:

2
doc/src/Howto_walls.rst
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@ -67,5 +67,5 @@ rotate.
The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the :doc:`fix wall/gran <fix_wall_gran>`
command. At some point we plan to allow regoin surfaces to be used as
command. At some point we plan to allow region surfaces to be used as
frictional walls, as well as triangulated surfaces.

12
doc/src/Intro_citing.rst
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@ -24,13 +24,15 @@ DOI for the LAMMPS code
LAMMPS developers use the `Zenodo service at CERN
<https://zenodo.org/>`_ to create digital object identifies (DOI) for
stable releases of the LAMMPS code. There are two types of DOIs for the
LAMMPS source code: 1) the canonical DOI for **all** versions of LAMMPS,
which will always point to the latest stable release version is:
LAMMPS source code: the canonical DOI for **all** versions of LAMMPS,
which will always point to the **latest** stable release version is:
`DOI: 10.5281/zenodo.3726416 <https://dx.doi/org/10.5281/zenodo.3726416>`_
- DOI: `10.5281/zenodo.3726416 <https://dx.doi.org/10.5281/zenodo.3726416>`_
In addition there are DOIs for individual stable releases starting with
the `3 March 2020 version, DOI:10.5281/zenodo.3726417 <https://dx.doi/org/10.5281/zenodo.3726416>`_
In addition there are DOIs for individual stable releases. Currently there are:
- 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
- 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
Home page

11
doc/src/Library_create.rst
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@ -9,7 +9,6 @@ This section documents the following functions:
- :cpp:func:`lammps_close`
- :cpp:func:`lammps_mpi_init`
- :cpp:func:`lammps_mpi_finalize`
- :cpp:func:`lammps_free`
--------------------
@ -75,11 +74,6 @@ that may only be called once. See :cpp:func:`lammps_mpi_finalize` for
an alternative to invoking ``MPI_Finalize()`` explicitly from the
calling program.
The :cpp:func:`lammps_free` function is a clean-up
function to free memory that the library allocated previously
via other function calls. See below for notes in the descriptions
of the individual commands where such memory buffers were allocated.
-----------------------
.. doxygenfunction:: lammps_open
@ -109,8 +103,3 @@ of the individual commands where such memory buffers were allocated.
.. doxygenfunction:: lammps_mpi_finalize
:project: progguide
-----------------------
.. doxygenfunction:: lammps_free
:project: progguide

12
doc/src/Library_utility.rst
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@ -9,11 +9,18 @@ functions. They do not directly call the LAMMPS library.
- :cpp:func:`lammps_set_fix_external_callback`
- :cpp:func:`lammps_fix_external_set_energy_global`
- :cpp:func:`lammps_fix_external_set_virial_global`
- :cpp:func:`lammps_free`
- :cpp:func:`lammps_is_running`
- :cpp:func:`lammps_force_timeout`
- :cpp:func:`lammps_has_error`
- :cpp:func:`lammps_get_last_error_message`
The :cpp:func:`lammps_free` function is a clean-up function to free
memory that the library had allocated previously via other function
calls. Look for notes in the descriptions of the individual commands
where such memory buffers were allocated that require the use of
:cpp:func:`lammps_free`.
-----------------------
.. doxygenfunction:: lammps_encode_image_flags
@ -41,6 +48,11 @@ functions. They do not directly call the LAMMPS library.
-----------------------
.. doxygenfunction:: lammps_free
:project: progguide
-----------------------
.. doxygenfunction:: lammps_is_running
:project: progguide

26
doc/src/Manual.rst
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@ -21,10 +21,16 @@ where all LAMMPS development is coordinated.
----------
The content for this manual is part of the LAMMPS distribution. 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. The manual is
organized in two parts:
The content for this manual is part of the LAMMPS distribution. The
online version always corresponds to the latest development version.
If needed, you can download or 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 have difficulties viewing the pages
please :ref:`see this note <webbrowser>`.
-----------
The manual is organized in two parts:
1) the :ref:`User Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different
@ -107,3 +113,15 @@ Indices and tables
* :ref:`genindex`
* :ref:`search`
.. _webbrowser:
.. admonition:: Web Browser Compatibility
The HTML version of the manual makes use of advanced features present
int "modern" web browsers. This can lead to incompatibilities with older
web browsers (released more than 4 years ago) and specific vendor browsers
(e.g. Internet Explorer on Windows; Microsoft Edge works well though)
where parts of the pages are not rendered as expected (e.g. the layout is
broken or mathematical expressions not typeset). In that case we
recommend to install/use a different/newer web browser or use
the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_.

2
doc/src/Packages_details.rst
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@ -1036,9 +1036,11 @@ the usual manner via MD. Various pair, fix, and compute styles.
* :doc:`pair_style spin/dipole/long <pair_spin_dipole>`
* :doc:`pair_style spin/dmi <pair_spin_dmi>`
* :doc:`pair_style spin/exchange <pair_spin_exchange>`
* :doc:`pair_style spin/exchange/biquadratic <pair_spin_exchange>`
* :doc:`pair_style spin/magelec <pair_spin_magelec>`
* :doc:`pair_style spin/neel <pair_spin_neel>`
* :doc:`fix nve/spin <fix_nve_spin>`
* :doc:`fix langevin/spin <fix_langevin_spin>`
* :doc:`fix precession/spin <fix_precession_spin>`
* :doc:`compute spin <compute_spin>`
* :doc:`neb/spin <neb_spin>`

19
doc/src/Run_options.rst
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@ -62,15 +62,18 @@ used.
**-in file**
Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its script from standard input, typically from a script
via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
also work in parallel, but if it does not (in the unlikely case that
an MPI implementation does not support it), then use the -in flag.
Specify a file to use as an input script. This is an optional but
recommended switch when running LAMMPS in one-partition mode. If it
is not specified, LAMMPS reads its script from standard input, typically
from a script via I/O redirection; e.g. lmp_linux < in.run.
With many MPI implementations I/O redirection also works in parallel,
but using the -in flag will always work.
Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.
stdin concurrently. The file name may be "none" for starting
multi-partition calculations without reading an initial input file
from the library interface.
----------
@ -296,7 +299,7 @@ command-line option.
**-pscreen file**
Specify the base name for the partition screen file, so partition N
writes screen information to file.N. If file is none, then no
writes screen information to file.N. If file is "none", then no
partition screen files are created. This overrides the filename
specified in the -screen command-line option. This option is useful
when working with large numbers of partitions, allowing the partition

2
doc/src/atc_output.rst
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@ -14,7 +14,7 @@ Syntax
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
* *output* or *output index* = name of the AtC sub-command
* filename_prefix = prefix for data files (for *output*)
* frequency = frequency of output in time-steps (for *output*)
* frequency = frequency of output in timesteps (for *output*)
* optional keywords for *output*:
- text = creates text output of index, step and nodal variable values for unique nodes

3
doc/src/atom_style.rst
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@ -42,6 +42,7 @@ Examples
atom_style hybrid charge body nparticle 2 5
atom_style spin
atom_style template myMols
atom_style hybrid template twomols charge
atom_style tdpd 2
Description
@ -239,6 +240,8 @@ can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
can be advantageous for large-scale coarse-grained systems.
The ``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::

236
doc/src/compute_stress_atom.rst
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@ -33,32 +33,31 @@ Examples
Description
"""""""""""
Define a computation that computes per-atom stress
tensor for each atom in a group. In case of compute *stress/atom*,
the tensor for each atom is symmetric with 6
components and is stored as a 6-element vector in the following order:
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
In case of compute *centroid/stress/atom*,
the tensor for each atom is asymmetric with 9 components
and is stored as a 9-element vector in the following order:
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`,
:math:`yx`, :math:`zx`, :math:`zy`.
See the :doc:`compute pressure <compute_pressure>` command if you want the stress tensor
Define a computation that computes per-atom stress tensor for each
atom in a group. In case of compute *stress/atom*, the tensor for
each atom is symmetric with 6 components and is stored as a 6-element
vector in the following order: :math:`xx`, :math:`yy`, :math:`zz`,
:math:`xy`, :math:`xz`, :math:`yz`. In case of compute
*centroid/stress/atom*, the tensor for each atom is asymmetric with 9
components and is stored as a 9-element vector in the following order:
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`, :math:`yx`, :math:`zx`, :math:`zy`. See the :doc:`compute
pressure <compute_pressure>` command if you want the stress tensor
(pressure) of the entire system.
The stress tensor for atom :math:`I` is given by the following formula,
where :math:`a` and :math:`b` take on values :math:`x`, :math:`y`, :math:`z`
to generate the components of the tensor:
The stress tensor for atom :math:`I` is given by the following
formula, where :math:`a` and :math:`b` take on values :math:`x`,
:math:`y`, :math:`z` to generate the components of the tensor:
.. math::
S_{ab} = - m v_a v_b - W_{ab}
The first term is a kinetic energy contribution for atom :math:`I`. See
details below on how the specified *temp-ID* can affect the velocities
used in this calculation. The second term is the virial
contribution due to intra and intermolecular interactions,
where the exact computation details are determined by the compute style.
The first term is a kinetic energy contribution for atom :math:`I`.
See details below on how the specified *temp-ID* can affect the
velocities used in this calculation. The second term is the virial
contribution due to intra and intermolecular interactions, where the
exact computation details are determined by the compute style.
In case of compute *stress/atom*, the virial contribution is:
@ -68,29 +67,26 @@ In case of compute *stress/atom*, the virial contribution is:
& + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
& + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
The first term is a pairwise energy
contribution where :math:`n` loops over the :math:`N_p`
neighbors of atom :math:`I`, :math:`\mathbf{r}_1` and :math:`\mathbf{r}_2`
are the positions of the 2 atoms in the pairwise interaction,
and :math:`\mathbf{F}_1` and :math:`\mathbf{F}_2` are the forces
on the 2 atoms resulting from the pairwise interaction.
The second term is a bond contribution of
similar form for the :math:`N_b` bonds which atom :math:`I` is part of.
There are similar terms for the :math:`N_a` angle, :math:`N_d` dihedral,
and :math:`N_i` improper interactions atom :math:`I` is part of.
There is also a term for the KSpace
contribution from long-range Coulombic interactions, if defined.
Finally, there is a term for the :math:`N_f` :doc:`fixes <fix>` that apply
internal constraint forces to atom :math:`I`. Currently, only the
:doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>` commands
contribute to this term.
As the coefficients in the formula imply, a virial contribution
produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
atoms in a Tersoff 3-body interaction) is assigned in equal portions
to each atom in the set. E.g. 1/4 of the dihedral virial to each of
the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
to atoms in a water molecule via the :doc:`fix shake <fix_shake>`
command.
The first term is a pairwise energy contribution where :math:`n` loops
over the :math:`N_p` neighbors of atom :math:`I`, :math:`\mathbf{r}_1`
and :math:`\mathbf{r}_2` are the positions of the 2 atoms in the
pairwise interaction, and :math:`\mathbf{F}_1` and
:math:`\mathbf{F}_2` are the forces on the 2 atoms resulting from the
pairwise interaction. The second term is a bond contribution of
similar form for the :math:`N_b` bonds which atom :math:`I` is part
of. There are similar terms for the :math:`N_a` angle, :math:`N_d`
dihedral, and :math:`N_i` improper interactions atom :math:`I` is part
of. There is also a term for the KSpace contribution from long-range
Coulombic interactions, if defined. Finally, there is a term for the
:math:`N_f` :doc:`fixes <fix>` that apply internal constraint forces
to atom :math:`I`. Currently, only the :doc:`fix shake <fix_shake>`
and :doc:`fix rigid <fix_rigid>` commands contribute to this term. As
the coefficients in the formula imply, a virial contribution produced
by a small set of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a
Tersoff 3-body interaction) is assigned in equal portions to each atom
in the set. E.g. 1/4 of the dihedral virial to each of the 4 atoms,
or 1/3 of the fix virial due to SHAKE constraints applied to atoms in
a water molecule via the :doc:`fix shake <fix_shake>` command.
In case of compute *centroid/stress/atom*, the virial contribution is:
@ -99,71 +95,69 @@ In case of compute *centroid/stress/atom*, the virial contribution is:
W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
& + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
As with compute *stress/atom*, the first, second, third, fourth and fifth terms
are pairwise, bond, angle, dihedral and improper contributions,
but instead of assigning the virial contribution equally to each atom,
only the force :math:`\mathbf{F}_I` acting on atom :math:`I`
due to the interaction and the relative
position :math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
of the interacting atoms, i.e. centroid, is used.
As the geometric center is different
for each interaction, the :math:`\mathbf{r}_{I0}` also differs.
The sixth and seventh terms, Kspace and :doc:`fix <fix>` contribution
respectively, are computed identical to compute *stress/atom*.
Although the total system virial is the same as compute *stress/atom*,
compute *centroid/stress/atom* is know to result in more consistent
heat flux values for angle, dihedrals and improper contributions
when computed via :doc:`compute heat/flux <compute_heat_flux>`.
As with compute *stress/atom*, the first, second, third, fourth and
fifth terms are pairwise, bond, angle, dihedral and improper
contributions, but instead of assigning the virial contribution
equally to each atom, only the force :math:`\mathbf{F}_I` acting on
atom :math:`I` due to the interaction and the relative position
:math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
of the interacting atoms, i.e. centroid, is used. As the geometric
center is different for each interaction, the :math:`\mathbf{r}_{I0}`
also differs. The sixth and seventh terms, Kspace and :doc:`fix
<fix>` contribution respectively, are computed identical to compute
*stress/atom*. Although the total system virial is the same as
compute *stress/atom*, compute *centroid/stress/atom* is know to
result in more consistent heat flux values for angle, dihedrals and
improper contributions when computed via :doc:`compute heat/flux
<compute_heat_flux>`.
If no extra keywords are listed, the kinetic contribution
all of the virial contribution terms are
included in the per-atom stress tensor. If any extra keywords are
listed, only those terms are summed to compute the tensor. The
*virial* keyword means include all terms except the kinetic energy
*ke*\ .
If no extra keywords are listed, the kinetic contribution all of the
virial contribution terms are included in the per-atom stress tensor.
If any extra keywords are listed, only those terms are summed to
compute the tensor. The *virial* keyword means include all terms
except the kinetic energy *ke*\ .
Note that the stress for each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.
Details of how compute *stress/atom* obtains the virial for individual atoms for
either pairwise or many-body potentials, and including the effects of
periodic boundary conditions is discussed in :ref:`(Thompson) <Thompson2>`.
The basic idea for many-body potentials is to treat each component of
the force computation between a small cluster of atoms in the same
manner as in the formula above for bond, angle, dihedral, etc
interactions. Namely the quantity :math:`\mathbf{r} \cdot \mathbf{F}`
is summed over the atoms in
the interaction, with the :math:`r` vectors unwrapped by periodic boundaries
so that the cluster of atoms is close together. The total
Details of how compute *stress/atom* obtains the virial for individual
atoms for either pairwise or many-body potentials, and including the
effects of periodic boundary conditions is discussed in
:ref:`(Thompson) <Thompson2>`. The basic idea for many-body
potentials is to treat each component of the force computation between
a small cluster of atoms in the same manner as in the formula above
for bond, angle, dihedral, etc interactions. Namely the quantity
:math:`\mathbf{r} \cdot \mathbf{F}` is summed over the atoms in the
interaction, with the :math:`r` vectors unwrapped by periodic
boundaries so that the cluster of atoms is close together. The total
contribution for the cluster interaction is divided evenly among those
atoms. Details of how compute *centroid/stress/atom* obtains
the virial for individual atoms
is given in :ref:`(Surblys) <Surblys1>`,
where the idea is that the virial of the atom :math:`I`
is the result of only the force :math:`\mathbf{F}_I` on the atom due
to the interaction
and its positional vector :math:`\mathbf{r}_{I0}`,
relative to the geometric center of the
interacting atoms, regardless of the number of participating atoms.
The periodic boundary treatment is identical to
atoms.
Details of how compute *centroid/stress/atom* obtains the virial for
individual atoms is given in :ref:`(Surblys) <Surblys1>`, where the
idea is that the virial of the atom :math:`I` is the result of only
the force :math:`\mathbf{F}_I` on the atom due to the interaction and
its positional vector :math:`\mathbf{r}_{I0}`, relative to the
geometric center of the interacting atoms, regardless of the number of
participating atoms. The periodic boundary treatment is identical to
that of compute *stress/atom*, and both of them reduce to identical
expressions for two-body interactions,
i.e. computed values for contributions from bonds and two-body pair styles,
such as :doc:`Lennard-Jones <pair_lj>`, will be the same,
while contributions from angles, dihedrals and impropers will be different.
expressions for two-body interactions, i.e. computed values for
contributions from bonds and two-body pair styles, such as
:doc:`Lennard-Jones <pair_lj>`, will be the same, while contributions
from angles, dihedrals and impropers will be different.
The :doc:`dihedral_style charmm <dihedral_charmm>` style calculates
pairwise interactions between 1-4 atoms. The virial contribution of
these terms is included in the pair virial, not the dihedral virial.
The KSpace contribution is calculated using the method in
:ref:`(Heyes) <Heyes2>` for the Ewald method and by the methodology described
in :ref:`(Sirk) <Sirk1>` for PPPM. The choice of KSpace solver is specified
by the :doc:`kspace_style pppm <kspace_style>` command. Note that for
PPPM, the calculation requires 6 extra FFTs each timestep that
per-atom stress is calculated. Thus it can significantly increase the
cost of the PPPM calculation if it is needed on a large fraction of
the simulation timesteps.
:ref:`(Heyes) <Heyes2>` for the Ewald method and by the methodology
described in :ref:`(Sirk) <Sirk1>` for PPPM. The choice of KSpace
solver is specified by the :doc:`kspace_style pppm <kspace_style>`
command. Note that for PPPM, the calculation requires 6 extra FFTs
each timestep that per-atom stress is calculated. Thus it can
significantly increase the cost of the PPPM calculation if it is
needed on a large fraction of the simulation timesteps.
The *temp-ID* argument can be used to affect the per-atom velocities
used in the kinetic energy contribution to the total stress. If the
@ -189,10 +183,10 @@ See the :doc:`compute voronoi/atom <compute_voronoi_atom>` command for
one possible way to estimate a per-atom volume.
Thus, if the diagonal components of the per-atom stress tensor are
summed for all atoms in the system and the sum is divided by :math:`dV`, where
:math:`d` = dimension and :math:`V` is the volume of the system,
the result should be :math:`-P`, where :math:`P`
is the total pressure of the system.
summed for all atoms in the system and the sum is divided by
:math:`dV`, where :math:`d` = dimension and :math:`V` is the volume of
the system, the result should be :math:`-P`, where :math:`P` is the
total pressure of the system.
These lines in an input script for a 3d system should yield that
result. I.e. the last 2 columns of thermo output will be the same:
@ -207,33 +201,43 @@ result. I.e. the last 2 columns of thermo output will be the same:
.. note::
The per-atom stress does not include any Lennard-Jones tail
corrections to the pressure added by the :doc:`pair_modify tail yes <pair_modify>` command, since those are contributions to the
global system pressure.
corrections to the pressure added by the :doc:`pair_modify tail yes
<pair_modify>` command, since those are contributions to the global
system pressure.
Output info
"""""""""""
This compute *stress/atom* calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input.
The compute *centroid/stress/atom* produces a per-atom array with 9 columns,
but otherwise can be used in an identical manner to compute *stress/atom*.
See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
Compute *stress/atom* calculates a per-atom array with 6 columns,
which can be accessed by indices 1-6 by any command that uses per-atom
values from a compute as input. Compute *centroid/stress/atom*
produces a per-atom array with 9 columns, but otherwise can be used in
an identical manner to compute *stress/atom*. See the :doc:`Howto
output <Howto_output>` doc page for an overview of LAMMPS output
options.
The per-atom array values will be in pressure\*volume
:doc:`units <units>` as discussed above.
The per-atom array values will be in pressure\*volume :doc:`units
<units>` as discussed above.
Restrictions
""""""""""""
Currently (Spring 2020), compute *centroid/stress/atom* does not support
pair styles with many-body interactions, such as :doc:`Tersoff
<pair_tersoff>`, or pair styles with long-range Coulomb interactions.
LAMMPS will generate an error in such cases. In principal, equivalent
formulation to that of angle, dihedral and improper contributions in the
virial :math:`W_{ab}` formula can also be applied to the many-body pair
styles, and is planned in the future.
Currently, compute *centroid/stress/atom* does not support pair styles
with many-body interactions (:doc:`EAM <pair_eam>` is an exception,
since its computations are performed pairwise), nor granular pair
styles with pairwise forces which are not aligned with the vector
between the pair of particles. All bond styles are supported. All
angle, dihedral, improper styles are supported with the exception of
USER-INTEL and KOKKOS variants of specific styles. It also does not
support models with long-range Coulombic or dispersion forces,
i.e. the kspace_style command in LAMMPS. It also does not support the
following fixes which add rigid-body constraints: :doc:`fix shake
<fix_shake>`, :doc:`fix rattle <fix_rattle>`, :doc:`fix rigid
<fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`.
LAMMPS will generate an error if one of these options is included in
your model. Extension of centroid stress calculations to these force
and fix styles is planned for the futre.
Related commands
""""""""""""""""

2
doc/src/create_atoms.rst
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@ -28,7 +28,7 @@ Syntax
* zero or more keyword/value pairs may be appended
* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units*
.. code-block:: LAMMPS
.. parsed-literal::
*mol* value = template-ID seed
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command

43
doc/src/fix_bond_react.rst
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@ -174,10 +174,12 @@ integer.
Three physical conditions must be met for a reaction to occur. First,
a bonding atom pair must be identified within the reaction distance
cutoffs. Second, the topology surrounding the bonding atom pair must
match the topology of the pre-reaction template. Finally, any reaction
constraints listed in the map file (see below) must be satisfied. If
all of these conditions are met, the reaction site is eligible to be
modified to match the post-reaction template.
match the topology of the pre-reaction template. Only atom types and
bond connectivity are used to identify a valid reaction site (not bond
types, etc.). Finally, any reaction constraints listed in the map file
(see below) must be satisfied. If all of these conditions are met, the
reaction site is eligible to be modified to match the post-reaction
template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms I,J within the specified react-group-ID of type
@ -192,19 +194,26 @@ be a function of the reaction conversion using the following commands:
fix myrxn all bond/react react myrxn1 all 1 0 v_rmax mol1 mol2 map_file.txt
variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count
It is possible that multiple bonding atom pairs are identified: if the
bonding atoms in the pre-reacted template are 1-2 neighbors, i.e.
directly bonded, the farthest bonding atom partner is set as its
bonding partner; otherwise, the closest potential partner is chosen.
Then, if both an atom I and atom J have each other as their bonding
partners, these two atoms are identified as the bonding atom pair of
the reaction site. Once this unique bonding atom pair is identified
for each reaction, there could two or more reactions that involve a
given atom on the same timestep. If this is the case, only one such
reaction is permitted to occur. This reaction is chosen randomly from
all potential reactions. This capability allows e.g. for different
reaction pathways to proceed from identical reaction sites with
user-specified probabilities.
The following criteria are used if multiple candidate bonding atom
pairs are identified within the cutoff distance: 1) If the bonding
atoms in the pre-reaction template are not 1-2 neighbors (i.e. not
directly bonded) the closest potential partner is chosen. 2)
Otherwise, if the bonding atoms in the pre-reaction template are 1-2
neighbors (i.e. directly bonded) the farthest potential partner is
chosen. 3) Then, if both an atom I and atom J have each other as their
bonding partners, these two atoms are identified as the bonding atom
pair of the reaction site. Note that it can be helpful to select
unique atom types for the bonding atoms: if a bonding atom pair is
identified, as described in the previous steps, but does not
correspond to the same pair specified in the pre-reaction template, an
otherwise eligible reaction could be prevented from occurring. Once
this unique bonding atom pair is identified for each reaction, there
could be two or more reactions that involve the same atom on the same
timestep. If this is the case, only one such reaction is permitted to
occur. This reaction is chosen randomly from all potential reactions
involving the overlapping atom. This capability allows e.g. for
different reaction pathways to proceed from identical reaction sites
with user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its

2
doc/src/fix_filter_corotate.rst
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@ -56,7 +56,7 @@ is slightly modified only for the computation of long-range forces. A
good cluster decomposition constitutes in building clusters which
contain the fastest covalent bonds inside clusters.
If the clusters are chosen suitably, the :doc:`run_style respa <run_style>` is stable for outer time-steps of at least 8fs.
If the clusters are chosen suitably, the :doc:`run_style respa <run_style>` is stable for outer timesteps of at least 8fs.
----------

2
doc/src/fix_precession_spin.rst
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@ -62,7 +62,7 @@ with:
The field value in Tesla is multiplied by the gyromagnetic
ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in
rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`).
rad.THz (in metal units and with :math:`\mu_B = 5.788\cdot 10^{-5}` eV/T).
As a comparison, the figure below displays the simulation of a
single spin (of norm :math:`\mu_i = 1.0`) submitted to an external

4
doc/src/fix_rx.rst
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@ -90,10 +90,10 @@ accepted, *h* is increased by a proportional amount, and the next ODE step is be
Otherwise, *h* is shrunk and the ODE step is repeated.
Run-time diagnostics are available for the rkf45 ODE solver. The frequency
(in time-steps) that diagnostics are reported is controlled by the last (optional)
(in timesteps) that diagnostics are reported is controlled by the last (optional)
12th argument. A negative frequency means that diagnostics are reported once at the
end of each run. A positive value N means that the diagnostics are reported once
per N time-steps.
per N timesteps.
The diagnostics report the average # of integrator steps and RHS function evaluations
and run-time per ODE as well as the average/RMS/min/max per process. If the

3
doc/src/fix_shake.rst
View File

@ -1,9 +1,12 @@
.. index:: fix shake
.. index:: fix shake/kk
.. index:: fix rattle
fix shake command
=================
Accelerator Variants: *shake/kk*
fix rattle command
==================

21
doc/src/molecule.rst
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@ -79,9 +79,9 @@ make it easy to use the same molecule file in different molecule
templates or in different simulations. You can specify the same file
multiple times with different optional keywords.
The *offset*\ , *toff*\ , *aoff*\ , *doff*\ , *ioff* keywords add the
specified offset values to the atom types, bond types, angle types,
dihedral types, and/or improper types as they are read from the
The *offset*\ , *toff*\ , *boff*\ , *aoff*\ , *doff*\ , *ioff* keywords
add the specified offset values to the atom types, bond types, angle
types, dihedral types, and/or improper types as they are read from the
molecule file. E.g. if *toff* = 2, and the file uses atom types
1,2,3, then each created molecule will have atom types 3,4,5. For the
*offset* keyword, all five offset values must be specified, but
@ -201,11 +201,12 @@ bonds between nuclear cores and Drude electrons in a different manner.
Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for whether it can appear in the data file. In each
case the ID is ignored; it is simply included for readability, and
should be a number from 1 to Nlines for the section, indicating which
atom (or bond, etc) the entry applies to. The lines are assumed to be
listed in order from 1 to Nlines, but LAMMPS does not check for this.
rules (if any) for whether it can appear in the data file. For per-
atom sections, entries should be numbered from 1 to Natoms (where
Natoms is the number of atoms in the template), indicating which atom
(or bond, etc) the entry applies to. Per-atom sections need to
include a setting for every atom, but the atoms can be listed in any
order.
----------
@ -484,9 +485,7 @@ of SHAKE clusters.
Restrictions
""""""""""""
This command must come after the simulation box is define by a
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <create_box>` command.
None
Related commands
""""""""""""""""

2
doc/src/pair_atm.rst
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@ -143,7 +143,7 @@ combinations, else an error will result.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles do not support the :doc:`pair_modify <pair_modify>`
This pair style do not support the :doc:`pair_modify <pair_modify>`
mix, shift, table, and tail options.
This pair style writes its information to :doc:`binary restart files

2
doc/src/pair_buck_long.rst
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@ -117,7 +117,7 @@ global Coulombic cutoff is allowed.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles does not support mixing. Thus, coefficients for all
This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style supports the :doc:`pair_modify <pair_modify>` shift

2
doc/src/pair_gayberne.rst
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@ -160,7 +160,7 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is *geometric*\ . See the "pair_modify" command for details.
This pair styles supports the :doc:`pair_modify <pair_modify>` shift
This pair style supports the :doc:`pair_modify <pair_modify>` shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic

9
doc/src/pair_lcbop.rst
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@ -75,14 +75,15 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This pair styles is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.
This pair potential requires the :doc:`newton <newton>` setting to be
"on" for pair interactions.
The C.lcbop potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal :doc:`units <units>`. You can use
The ``C.lcbop`` potential file provided with LAMMPS (see the potentials
directory) is parameterized for :doc:`metal units <units>`. You can use
the LCBOP potential with any LAMMPS units, but you would need to
create your own LCBOP potential file with coefficients listed in the
appropriate units if your simulation does not use "metal" units.

2
doc/src/pair_polymorphic.rst
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@ -298,7 +298,7 @@ described above. For each of the F functions, nx values are listed.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles does not support the :doc:`pair_modify <pair_modify>`
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write their information to :doc:`binary restart

2
doc/src/pair_resquared.rst
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@ -173,7 +173,7 @@ equation for the Hamaker constant presented here. Mixing of sigma and
epsilon followed by calculation of the energy prefactors using the
equations above is recommended.
This pair styles supports the :doc:`pair_modify <pair_modify>` shift
This pair style supports the :doc:`pair_modify <pair_modify>` shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic

161
doc/src/pair_spin_exchange.rst
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@ -1,14 +1,19 @@
.. index:: pair_style spin/exchange
.. index:: pair_style spin/exchange/biquadratic
pair_style spin/exchange command
================================
pair_style spin/exchange/biquadratic command
============================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style spin/exchange cutoff
pair_style spin/exchange/biquadratic cutoff
* cutoff = global cutoff pair (distance in metal units)
@ -19,7 +24,11 @@ Examples
pair_style spin/exchange 4.0
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 offset yes
pair_style spin/exchange/biquadratic 4.0
pair_coeff * * biquadratic 4.0 0.05 0.03 1.48 0.05 0.03 1.48 offset no
pair_coeff 1 2 biquadratic 6.0 -0.01 0.0 1.9 0.0 0.1 19
Description
"""""""""""
@ -31,69 +40,163 @@ pairs of magnetic spins:
H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j
where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles,
:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance between the two
particles. The summation is over pairs of nearest neighbors.
:math:`J(r_{ij})` is a function defining the intensity and the sign of the exchange
interaction for different neighboring shells. This function is defined as:
where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two unit vectors representing
the magnetic spins of two particles (usually atoms), and
:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance
between those two particles. The summation is over pairs of nearest neighbors.
:math:`J(r_{ij})` is a function defining the intensity and the sign of the
exchange interaction for different neighboring shells.
Style *spin/exchange/biquadratic* computes a biquadratic exchange interaction
between pairs of magnetic spins:
.. math::
{J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
H_{bi} = -\sum_{i, j}^{N} {J}_{ij} \left(r_{ij} \right)\,
\vec{s}_{i}\cdot \vec{s}_{j}
-\sum_{i, j}^{N} {K}_{ij} \left(r_{ij} \right)\,
\left(\vec{s}_{i}\cdot
\vec{s}_{j}\right)^2
where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the associated
"pair_coeff" command, and :math:`R_c` is the radius cutoff associated to
the pair interaction (see below for more explanations).
where :math:`\vec{s}_i`, :math:`\vec{s}_j`, :math:`r_{ij}` and
:math:`J(r_{ij})` have the same definitions as above, and :math:`K(r_{ij})` is
a second function, defining the intensity and the sign of the biquadratic term.
The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with
the value of the exchange interaction for the :math:`N` neighbor shells taken into account.
Examples and more explanations about this function and its parameterization are reported
in :ref:`(Tranchida) <Tranchida3>`.
The interatomic dependence of :math:`J(r_{ij})` and :math:`K(r_{ij})` in both
interactions above is defined by the following function:
.. math::
{f}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2
\left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right)
e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients
defined in the associated "pair_coeff" command, and :math:`R_c` is the radius
cutoff associated to the pair interaction (see below for more explanations).
The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that
the function above matches with the value of the exchange interaction for the
:math:`N` neighbor shells taken into account.
Examples and more explanations about this function and its parameterization
are reported in :ref:`(Tranchida) <Tranchida3>`.
When a *spin/exchange/biquadratic* pair style is defined, six coefficients
(three for :math:`J(r_{ij})`, and three for :math:`K(r_{ij})`) have to be
fitted.
From this exchange interaction, each spin :math:`i` will be submitted
to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
such as:
to a magnetic torque :math:`\vec{\omega}_{i}`, and its associated atom can be
submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see
:doc:`fix nve/spin <fix_nve_spin>`), such as:
.. math::
\vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
\left(r_{ij} \right)\,\vec{s}_{j}
~~{\rm and}~~
\vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
\vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
\partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij} = \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij}
= \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
vector between sites :math:`i` and :math:`j`.
Equivalent forces and magnetic torques are generated for the biquadratic term
when a *spin/exchange/biquadratic* pair style is defined.
More details about the derivation of these torques/forces are reported in
:ref:`(Tranchida) <Tranchida3>`.
For the *spin/exchange* pair style, the following coefficients must be defined
for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in
the examples above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands, and
set in the following order:
For the *spin/exchange* and *spin/exchange/biquadratic* pair styles, the
following coefficients must be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data
file or restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands, and set in the following order:
* :math:`R_c` (distance units)
* :math:`a` (energy units)
* :math:`b` (adim parameter)
* :math:`d` (distance units)
Note that :math:`R_c` is the radius cutoff of the considered exchange interaction,
and :math:`a`, :math:`b` and :math:`d` are the three coefficients performing the parameterization
of the function :math:`J(r_{ij})` defined above.
for the *spin/exchange* pair style, and:
* :math:`R_c` (distance units)
* :math:`a_j` (energy units)
* :math:`b_j` (adim parameter)
* :math:`d_j` (distance units)
* :math:`a_k` (energy units)
* :math:`b_k` (adim parameter)
* :math:`d_k` (distance units)
for the *spin/exchange/biquadratic* pair style.
Note that :math:`R_c` is the radius cutoff of the considered exchange
interaction, and :math:`a`, :math:`b` and :math:`d` are the three coefficients
performing the parameterization of the function :math:`J(r_{ij})` defined
above (in the *biquadratic* style, :math:`a_j`, :math:`b_j`, :math:`d_j` and
:math:`a_k`, :math:`b_k`, :math:`d_k` are the coefficients of :math:`J(r_{ij})`
and :math:`K(r_{ij})` respectively).
None of those coefficients is optional. If not specified, the
*spin/exchange* pair style cannot be used.
----------
**Offsetting magnetic forces and energies**\ :
For spin-lattice simulation, it can be useful to offset the
mechanical forces and energies generated by the exchange
interaction.
The *offset* keyword allows to apply this offset.
By setting *offset* to *yes*, the energy definitions above are
replaced by:
.. math::
H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,[ \vec{s}_i \cdot \vec{s}_j-1 ]
for the *spin/exchange* pair style, and:
.. math::
H_{bi} = -\sum_{i, j}^{N} {J}_{ij} \left(r_{ij} \right)\,
[ \vec{s}_{i}\cdot \vec{s}_{j} -1 ]
-\sum_{i, j}^{N} {K}_{ij} \left(r_{ij} \right)\,
[ \left(\vec{s}_{i}\cdot
\vec{s}_{j}\right)^2 -1]
for the *spin/exchange/biquadratic* pair style.
Note that this offset only affects the calculation of the energy
and mechanical forces. It does not modify the calculation of the
precession vectors (and thus does no impact the purely magnetic
properties).
This ensures that when all spins are aligned, the magnetic energy
and the associated mechanical forces (and thus the pressure
generated by the magnetic potential) are null.
.. note::
This offset term can be very important when calculations such as
equations of state (energy vs volume, or energy vs pressure) are
being performed. Indeed, setting the *offset* term ensures that
at the ground state of the crystal and at the equilibrium magnetic
configuration (typically ferromagnetic), the pressure is null,
as expected.
Otherwise, magnetic forces could generate a residual pressure.
When the *offset* option is set to *no*, no offset is applied
(also corresponding to the default option).
----------
Restrictions
""""""""""""
All the *pair/spin* styles are part of the SPIN package. These styles
are only enabled if LAMMPS was built with this package, and if the
atom_style "spin" was declared. See the :doc:`Build package <Build_package>` doc page for more info.
atom_style "spin" was declared.
See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
@ -105,7 +208,7 @@ Default
"""""""
none
The default *offset* keyword value is *no*.
----------

2
doc/src/pair_srp.rst
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@ -124,7 +124,7 @@ at the cutoff distance :math:`r_c`.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles does not support mixing.
This pair style does not support mixing.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift option for the energy of the pair interaction. Note that as

1
doc/src/pair_style.rst
View File

@ -305,6 +305,7 @@ accelerated styles exist.
* :doc:`spin/dipole/long <pair_spin_dipole>` -
* :doc:`spin/dmi <pair_spin_dmi>` -
* :doc:`spin/exchange <pair_spin_exchange>` -
* :doc:`spin/exchange/biquadratic <pair_spin_exchange>` -
* :doc:`spin/magelec <pair_spin_magelec>` -
* :doc:`spin/neel <pair_spin_neel>` -
* :doc:`srp <pair_srp>` -

8
doc/src/read_data.rst
View File

@ -618,7 +618,7 @@ of analysis.
* - tdpd
- atom-ID atom-type x y z cc1 cc2 ... ccNspecies
* - template
- atom-ID molecule-ID template-index template-atom atom-type x y z
- atom-ID atom-type molecule-ID template-index template-atom x y z
* - tri
- atom-ID molecule-ID atom-type triangleflag density x y z
* - wavepacket
@ -695,9 +695,9 @@ triangle, or body in the corresponding *Ellipsoids*\ , *Lines*\ ,
The *template-index* and *template-atom* are only defined used by
:doc:`atom_style template <atom_style>`. In this case the
:doc:`molecule <molecule>` command is used to define a molecule template
which contains one or more molecules. If an atom belongs to one of
those molecules, its *template-index* and *template-atom* are both set
to positive integers; if not the values are both 0. The
which contains one or more molecules (as separate files). If an atom
belongs to one of those molecules, its *template-index* and *template-atom*
are both set to positive integers; if not the values are both 0. The
*template-index* is which molecule (1 to Nmols) the atom belongs to.
The *template-atom* is which atom (1 to Natoms) within the molecule
the atom is.

2
doc/src/read_dump.rst
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@ -370,6 +370,8 @@ needed to generate absolute, unscaled coordinates.
Restrictions
""""""""""""
The *native* dump file reader does not support binary .bin dump files.
To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
doc page for details.

29
doc/src/rerun.rst
View File

@ -99,14 +99,15 @@ files do not match the specified output frequency.
----------
If more than one dump file is specified, the dump files are read one
after the other. It is assumed that snapshot timesteps will be in
ascending order. If a snapshot is encountered that is not in
ascending order, it will skip the snapshot until it reads one that is.
after the other in the order specified. It is assumed that snapshot
timesteps will be in ascending order. If a snapshot is encountered that
is not in ascending order, it will skip the snapshot until it reads one
that is.
This allows skipping of a duplicate snapshot (same timestep),
e.g. that appeared at the end of one file and beginning of the next.
However if you specify a series of dump files in an incorrect order
(with respect to the timesteps they contain), you may skip large
numbers of snapshots
numbers of snapshots.
Note that the dump files specified as part of the *dump* keyword can be
parallel files, i.e. written as multiple files either per processor
@ -118,17 +119,24 @@ and write parallel dump files.
The *first*\ , *last*\ , *every*\ , *skip* keywords determine which
snapshots are read from the dump file(s). Snapshots are skipped until
they have a timestamp >= *Nfirst*\ . When a snapshot with a timestamp >
*Nlast* is encountered, the rerun command finishes. Note below that
they have a timestep >= *Nfirst*\ . When a snapshot with a timestep >
*Nlast* is encountered, the rerun command finishes. Note that
the defaults for *first* and *last* are to read all snapshots. If the
*every* keyword is set to a value > 0, then only snapshots with
timestamps that are a multiple of *Nevery* are read (the first
timesteps that are a multiple of *Nevery* are read (the first
snapshot is always read). If *Nevery* = 0, then this criterion is
ignored, i.e. every snapshot is read that meets the other criteria.
If the *skip* keyword is used, then after the first snapshot is read,
every Nth snapshot is read, where N = *Nskip*\ . E.g. if *Nskip* = 3,
then only 1 out of every 3 snapshots is read, assuming the snapshot
timestamp is also consistent with the other criteria.
timestep is also consistent with the other criteria.
.. note::
Not all dump formats contain the timestep and not all dump readers
support reading it. In that case individual snapshots are assigned
consecutive timestep numbers starting at 1.
The *start* and *stop* keywords do not affect which snapshots are read
from the dump file(s). Rather, they have the same meaning that they
@ -205,9 +213,8 @@ thermodynamic output or new dump file output.
Restrictions
""""""""""""
To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
doc page for details.
The *rerun* command is subject to all restrictions of
the :doc:`read_dump <read_dump>` command.
Related commands
""""""""""""""""

10
doc/utils/sphinx-config/_themes/lammps_theme/layout.html
View File

@ -48,6 +48,10 @@
<!--[if lt IE 9]>
<script src="{{ pathto('_static/js/html5shiv.min.js', 1) }}"></script>
<![endif]-->
{# Keep modernizr in head - http://modernizr.com/docs/#installing #}
<script src="{{ pathto('_static/js/modernizr.min.js', 1) }}"></script>
{%- if not embedded %}
{# XXX Sphinx 1.8.0 made this an external js-file, quick fix until we refactor the template to inherert more blocks directly from sphinx #}
{% if sphinx_version >= "1.8.0" %}
@ -103,12 +107,6 @@
{%- endif %}
{%- endblock %}
{%- block extrahead %} {% endblock %}
{# Keep modernizr in head - http://modernizr.com/docs/#installing #}
<script src="{{ pathto('_static/js/modernizr.min.js', 1) }}"></script>
{# for improved browser compatibility #}
<script src="{{ pathto('_static/polyfill.js', 1) }}"></script>
</head>
<body class="wy-body-for-nav">

4
doc/utils/sphinx-config/false_positives.txt
View File

@ -240,6 +240,7 @@ bigint
Bij
bilayer
bilayers
biquadratic
binsize
binstyle
binutils
@ -2619,7 +2620,6 @@ Ree
refactored
refactoring
reflectionstyle
regoin
Reinders
reinit
relaxbox
@ -2985,6 +2985,8 @@ Subclassed
subcutoff
subcycle
subcycling
subhi
sublo
Subramaniyan
subscripted
subscripting

1
examples/README
View File

@ -111,6 +111,7 @@ srd: stochastic rotation dynamics (SRD) particles as solvent
steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
streitz: Streitz-Mintmire potential for Al2O3
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
template: examples for using atom_style template and comparing to atom style molecular
threebody: regression test input for a variety of manybody potentials
vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command

2
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
View File

@ -26,7 +26,7 @@ velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
pair_coeff * * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.0645 offset yes
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
neighbor 0.1 bin

2
examples/SPIN/iron/in.spin.iron
View File

@ -25,7 +25,7 @@ velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 offset yes
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20

4
examples/SPIN/iron/in.spin.iron_cubic
View File

@ -21,9 +21,9 @@ mass 1 55.845
set group all spin 2.2 -1.0 0.0 0.0
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
pair_style hybrid/overlay eam/alloy spin/exchange/biquadratic 3.5
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
pair_coeff * * spin/exchange/biquadratic biquadratic 3.4 0.02726 0.2171 1.841 0.0 0.0 2.0 offset yes
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20

20
examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
View File

@ -6,9 +6,17 @@ import matplotlib.pyplot as plt
import mpmath as mp
hbar=0.658212 # Planck's constant (eV.fs/rad)
J0=0.05 # per-neighbor exchange interaction (eV)
# J0=0.05 # per-neighbor exchange interaction (eV)
# exchange interaction parameters
J1 = 11.254 # in eV
J2 = 0.0 # adim
J3 = 1.0 # in Ang.
# initial spins
S1 = np.array([1.0, 0.0, 0.0])
S2 = np.array([0.0, 1.0, 0.0])
alpha=0.01 # damping coefficient
pi=math.pi
@ -30,6 +38,14 @@ def rotation_matrix(axis, theta):
[2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
[2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
#Definition of the Bethe-Slater function
def func_BS(x,a,b,c):
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
#Definition of the derivative of the Bethe-Slater function
def func_dBS(x,a,b,c):
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
# calculating precession field of spin Sr
def calc_rot_vector(Sr,Sf):
rot = (J0/hbar)*(Sf-alpha*np.cross(Sf,Sr))/(1.0+alpha**2)
@ -65,6 +81,6 @@ for t in range (0,N):
# calc. average magnetization
Sm = (S1+S2)*0.5
# calc. energy
en = -2.0*J0*(np.dot(S1,S2))
en = -J0*(np.dot(S1,S2))
# print res. in ps for comparison with LAMMPS
print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en)

4
examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
View File

@ -13,7 +13,7 @@ en="$(echo "$en-$in" | bc -l)"
tail -n +$in log.lammps | head -n $en > res_lammps.dat
# compute Langevin
python3 -m llg_exchange.py > res_llg.dat
python3 llg_exchange.py > res_llg.dat
# plot results
python3 -m plot_precession.py res_lammps.dat res_llg.dat
python3 plot_precession.py res_lammps.dat res_llg.dat

23
examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in
View File

@ -5,22 +5,24 @@ atom_style spin
atom_modify map array
boundary f f f
read_data two_spins.data
atom_modify map array
lattice sc 3.0
region box block 0 2 0 1 0 1
create_box 1 box
create_atoms 1 box
mass 1 55.845
set atom 1 spin 2.0 1.0 0.0 0.0
set atom 2 spin 2.0 0.0 1.0 0.0
pair_style spin/exchange 3.1
pair_coeff * * exchange 3.1 11.254 0.0 1.0
group bead type 1
variable H equal 0.0
variable Kan equal 0.0
variable Temperature equal 0.0
variable RUN equal 30000
fix 1 all nve/spin lattice no
fix 2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
fix_modify 2 energy yes
fix 3 all langevin/spin ${Temperature} 0.01 12345
fix 1 all nve/spin lattice frozen
fix 2 all langevin/spin ${Temperature} 0.01 12345
compute out_mag all spin
compute out_pe all pe
@ -34,6 +36,9 @@ variable emag equal c_out_mag[5]
thermo_style custom step time v_magx v_magy v_magz v_emag pe etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 10 dump.data type x y z c_outsp[1] c_outsp[2] c_outsp[3] fx fy fz
timestep 0.0001
run ${RUN}

22
examples/SPIN/test_problems/validation_damped_exchange/two_spins.data
View File

@ -1,22 +0,0 @@
LAMMPS data file via write_data, version 19 Sep 2019, timestep = 0
2 atoms
1 atom types
0.0 6.0 xlo xhi
0.0 3.0 ylo yhi
0.0 3.0 zlo zhi
Masses
1 1
Atoms # spin
1 1 2.0 0.0 0.0 0.0 1.0 0.0 0.0 0 0 0
2 1 2.0 3.0 0.0 0.0 0.0 1.0 0.0 0 0 0
Velocities
1 0.0 0.0 0.0
2 0.0 0.0 0.0

2
examples/SPIN/test_problems/validation_nve/run-test-nve.sh
View File

@ -13,4 +13,4 @@ en="$(echo "$en-$in" | bc -l)"
tail -n +$in log.lammps | head -n $en > res_lammps.dat
# plot results
python3 -m plot_nve.py res_lammps.dat res_llg.dat
python3 plot_nve.py res_lammps.dat res_llg.dat

2
examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice
View File

@ -30,7 +30,7 @@ neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin 200.0 200.0 10.0 48279
fix 2 all langevin 200.0 200.0 1.0 48279
fix 3 all langevin/spin 0.0 0.00001 321
fix 4 all nve/spin lattice moving
timestep 0.001

2
examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin
View File

@ -29,7 +29,7 @@ neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 200.0 0.1 321
fix 2 all langevin/spin 200.0 0.01 321
fix 3 all nve/spin lattice moving
timestep 0.001

2
examples/SPIN/test_problems/validation_nvt/plot_nvt.py
View File

@ -39,5 +39,5 @@ plt.xlabel('Time (in ps)')
plt.legend()
plt.show()
fig.savefig(os.path.join(os.getcwd(), "nve_spin_lattice.pdf"), bbox_inches="tight")
fig.savefig(os.path.join(os.getcwd(), "nvt_spin_lattice.pdf"), bbox_inches="tight")
plt.close(fig)

4
examples/gcmc/data.spce
View File

@ -28,8 +28,8 @@ LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.8 o
Masses
1 1.007940 # 1
2 15.999400 # 2
1 15.999400 # 1
2 1.007940 # 2
Atoms # full

111
examples/granular/in.pour.drum
View File

@ -2,99 +2,98 @@
# 'turn' cylinder by changing direction of gravity, then rotate it.
# This simulates a rotating drum powder characterization experiment.
variable name string rotating_drum_two_types
variable name string rotating_drum_two_types
atom_style sphere
units lj
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable drum_rad equal ${boxx}*0.5
variable drum_height equal 20
variable drum_rad equal ${boxx}*0.5
variable drum_height equal 20
variable xc equal 0.5*${boxx}
variable yc equal 0.5*${boxx}
variable zc equal 0.5*${boxz}
variable xc equal 0.5*${boxx}
variable yc equal 0.5*${boxx}
variable zc equal 0.5*${boxz}
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable dens equal 1.0
variable dens equal 1.0
variable skin equal 0.4*${rhi}
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
comm_modify vel yes
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
variable theta equal 0
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
variable theta equal 0
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
comm_modify vel yes
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
comm_modify vel yes
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
timestep 0.001
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
group delgroup dynamic all var zmax every 10000
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
group delgroup dynamic all var zmax every 10000
run 2000
run 2000
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
delete_atoms group delgroup
#Add top lid
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
variable theta equal 2*PI*elapsed/20000.0
run 3000

76
examples/granular/in.pour.flatwall
View File

@ -1,67 +1,65 @@
# pour two types of particles (cohesive and non-cohesive) on flat wall
variable name string pour_two_types
variable name string pour_two_types
atom_style sphere
units lj
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable xc1 equal 0.3*${boxx}
variable xc2 equal 0.7*${boxx}
variable yc equal 0.5*${boxy}
variable xc1 equal 0.3*${boxx}
variable xc2 equal 0.7*${boxx}
variable yc equal 0.5*${boxy}
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable dens equal 1.0
variable dens equal 1.0
variable skin equal 0.3*${rhi}
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
comm_modify vel yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
comm_modify vel yes
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
comm_modify vel yes
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
thermo_style custom step cpu atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
run 5000

150
examples/granular/log.29Mar19.pour.drum.g++.1 → examples/granular/log.29Oct20.pour.drum.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
@ -55,10 +54,14 @@ region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (30 30 50)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
comm_modify vel yes
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
variable theta equal 0
@ -104,10 +107,6 @@ neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
@ -117,8 +116,7 @@ thermo 100
timestep 0.001
dump 1 all custom 100 ${name}.dump id type radius mass x y z
dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
@ -140,7 +138,7 @@ Neighbor list info ...
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.02 | 13.02 | 13.02 Mbytes
Per MPI rank memory allocation (min/avg/max) = 13.03 | 13.03 | 13.03 Mbytes
Step Atoms KinEng v_theta
0 0 -0 0
100 4000 -0 0
@ -163,32 +161,32 @@ Step Atoms KinEng v_theta
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 3.54461 on 1 procs for 2000 steps with 4000 atoms
Loop time of 10.5178 on 1 procs for 2000 steps with 4000 atoms
Performance: 48750.057 tau/day, 564.237 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 16429.309 tau/day, 190.154 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.61949 | 0.61949 | 0.61949 | 0.0 | 17.48
Neigh | 1.2492 | 1.2492 | 1.2492 | 0.0 | 35.24
Comm | 0.046404 | 0.046404 | 0.046404 | 0.0 | 1.31
Output | 0.15901 | 0.15901 | 0.15901 | 0.0 | 4.49
Modify | 1.4165 | 1.4165 | 1.4165 | 0.0 | 39.96
Other | | 0.05391 | | | 1.52
Pair | 1.0701 | 1.0701 | 1.0701 | 0.0 | 10.17
Neigh | 4.2135 | 4.2135 | 4.2135 | 0.0 | 40.06
Comm | 0.38276 | 0.38276 | 0.38276 | 0.0 | 3.64
Output | 0.0013647 | 0.0013647 | 0.0013647 | 0.0 | 0.01
Modify | 4.7076 | 4.7076 | 4.7076 | 0.0 | 44.76
Other | | 0.1424 | | | 1.35
Nlocal: 4000 ave 4000 max 4000 min
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 166 ave 166 max 166 min
Nghost: 171.000 ave 171 max 171 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8195 ave 8195 max 8195 min
Neighs: 8093.00 ave 8093 max 8093 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8195
Ave neighs/atom = 2.04875
Total # of neighbors = 8093
Ave neighs/atom = 2.0232500
Neighbor list builds = 1004
Dangerous builds = 3
Dangerous builds = 4
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
@ -205,67 +203,69 @@ fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindl
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Per MPI rank memory allocation (min/avg/max) = 24.81 | 24.81 | 24.81 Mbytes
Per MPI rank memory allocation (min/avg/max) = 19.37 | 19.37 | 19.37 Mbytes
Step Atoms KinEng v_theta
2000 4000 64.333531 0
2100 4000 106.69182 0.031415927
2200 4000 121.8461 0.062831853
2300 4000 88.767952 0.09424778
2400 4000 82.850721 0.12566371
2500 4000 91.683284 0.15707963
2600 4000 31.56344 0.18849556
2700 4000 4.5697672 0.21991149
2800 4000 3.9879051 0.25132741
2900 4000 4.4394235 0.28274334
3000 4000 5.1212931 0.31415927
3100 4000 5.8608892 0.34557519
3200 4000 6.600714 0.37699112
3300 4000 7.3497851 0.40840704
3400 4000 8.0490988 0.43982297
3500 4000 8.6712396 0.4712389
3600 4000 9.1328667 0.50265482
3700 4000 9.4683561 0.53407075
3800 4000 9.5878145 0.56548668
3900 4000 9.387745 0.5969026
4000 4000 8.9117631 0.62831853
4100 4000 8.2344368 0.65973446
4200 4000 7.5335088 0.69115038
4300 4000 6.8426179 0.72256631
4400 4000 6.0567247 0.75398224
4500 4000 5.4166132 0.78539816
4600 4000 4.6012409 0.81681409
4700 4000 3.8314982 0.84823002
4800 4000 3.1916415 0.87964594
4900 4000 2.7833964 0.91106187
5000 4000 2.5051362 0.9424778
Loop time of 11.9545 on 1 procs for 3000 steps with 4000 atoms
2000 4000 65.647582 0
2100 4000 105.60001 0.031415927
2200 4000 112.27573 0.062831853
2300 4000 92.758671 0.09424778
2400 4000 88.925835 0.12566371
2500 4000 81.369163 0.15707963
2600 4000 32.046943 0.18849556
2700 4000 4.1926368 0.21991149
2800 4000 3.9933453 0.25132741
2900 4000 4.5062193 0.28274334
3000 4000 5.3409521 0.31415927
3100 4000 6.0165991 0.34557519
3200 4000 6.606767 0.37699112
3300 4000 7.3997751 0.40840704
3400 4000 8.1098807 0.43982297
3500 4000 8.6552424 0.4712389
3600 4000 9.8445204 0.50265482
3700 4000 10.098753 0.53407075
3800 4000 10.039489 0.56548668
3900 4000 9.6376278 0.5969026
4000 4000 9.2598836 0.62831853
4100 4000 8.7116037 0.65973446
4200 4000 8.1274117 0.69115038
4300 4000 7.1487627 0.72256631
4400 4000 6.2253778 0.75398224
4500 4000 5.3061398 0.78539816
4600 4000 4.4319316 0.81681409
4700 4000 4.205607 0.84823002
4800 4000 3.2112987 0.87964594
4900 4000 2.6449777 0.91106187
5000 4000 2.3475497 0.9424778
Loop time of 32.4926 on 1 procs for 3000 steps with 4000 atoms
Performance: 21682.142 tau/day, 250.951 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 7977.205 tau/day, 92.329 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8291 | 4.8291 | 4.8291 | 0.0 | 40.40
Neigh | 2.7489 | 2.7489 | 2.7489 | 0.0 | 22.99
Comm | 0.071249 | 0.071249 | 0.071249 | 0.0 | 0.60
Output | 0.20547 | 0.20547 | 0.20547 | 0.0 | 1.72
Modify | 4.0179 | 4.0179 | 4.0179 | 0.0 | 33.61
Other | | 0.0819 | | | 0.69
Pair | 8.0124 | 8.0124 | 8.0124 | 0.0 | 24.66
Neigh | 10.993 | 10.993 | 10.993 | 0.0 | 33.83
Comm | 0.86697 | 0.86697 | 0.86697 | 0.0 | 2.67
Output | 0.0021827 | 0.0021827 | 0.0021827 | 0.0 | 0.01
Modify | 12.367 | 12.367 | 12.367 | 0.0 | 38.06
Other | | 0.2515 | | | 0.77
Nlocal: 4000 ave 4000 max 4000 min
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 322 ave 322 max 322 min
Nghost: 318.000 ave 318 max 318 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14849 ave 14849 max 14849 min
Neighs: 14807.0 ave 14807 max 14807 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14849
Ave neighs/atom = 3.71225
Neighbor list builds = 1290
Dangerous builds = 672
Total wall time: 0:00:15
Total # of neighbors = 14807
Ave neighs/atom = 3.7017500
Neighbor list builds = 2189
Dangerous builds = 1536
Total wall time: 0:00:43

156
examples/granular/log.29Mar19.pour.drum.g++.4 → examples/granular/log.29Oct20.pour.drum.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
@ -55,10 +54,14 @@ region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (30 30 50)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
comm_modify vel yes
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
variable theta equal 0
@ -104,10 +107,6 @@ neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
@ -117,8 +116,7 @@ thermo 100
timestep 0.001
dump 1 all custom 100 ${name}.dump id type radius mass x y z
dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
@ -163,32 +161,32 @@ Step Atoms KinEng v_theta
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 2.0709 on 4 procs for 2000 steps with 4000 atoms
Loop time of 3.86825 on 4 procs for 2000 steps with 4000 atoms
Performance: 83442.024 tau/day, 965.764 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 44671.398 tau/day, 517.030 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24679 | 0.26336 | 0.28853 | 3.0 | 12.72
Neigh | 0.52279 | 0.5332 | 0.53858 | 0.9 | 25.75
Comm | 0.17418 | 0.20253 | 0.23266 | 4.7 | 9.78
Output | 0.092897 | 0.093531 | 0.09515 | 0.3 | 4.52
Modify | 0.88151 | 0.89571 | 0.90582 | 0.9 | 43.25
Other | | 0.08257 | | | 3.99
Pair | 0.26114 | 0.27918 | 0.28728 | 2.0 | 7.22
Neigh | 1.2044 | 1.2414 | 1.3105 | 3.7 | 32.09
Comm | 0.38592 | 0.47065 | 0.51052 | 7.4 | 12.17
Output | 0.0007236 | 0.0013456 | 0.0024846 | 1.8 | 0.03
Modify | 1.6217 | 1.6723 | 1.7801 | 5.0 | 43.23
Other | | 0.2034 | | | 5.26
Nlocal: 1000 ave 1001 max 999 min
Nlocal: 1000.00 ave 1012 max 988 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 267.75 ave 276 max 262 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 2031.5 ave 2091 max 1958 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 269.250 ave 278 max 256 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 2060.50 ave 2156 max 1921 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8126
Ave neighs/atom = 2.0315
Total # of neighbors = 8242
Ave neighs/atom = 2.0605000
Neighbor list builds = 1004
Dangerous builds = 3
Dangerous builds = 4
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
@ -205,67 +203,69 @@ fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindl
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Per MPI rank memory allocation (min/avg/max) = 21.6 | 22.6 | 23.82 Mbytes
Per MPI rank memory allocation (min/avg/max) = 18.55 | 18.55 | 18.55 Mbytes
Step Atoms KinEng v_theta
2000 4000 64.255821 0
2100 4000 106.47082 0.031415927
2200 4000 121.52634 0.062831853
2300 4000 87.748818 0.09424778
2400 4000 82.712784 0.12566371
2500 4000 90.618713 0.15707963
2600 4000 30.096031 0.18849556
2700 4000 4.0838611 0.21991149
2800 4000 3.7485959 0.25132741
2900 4000 4.2159774 0.28274334
3000 4000 4.8730048 0.31415927
3100 4000 5.6109465 0.34557519
3200 4000 6.4290528 0.37699112
3300 4000 7.2699677 0.40840704
3400 4000 8.0895944 0.43982297
3500 4000 8.7222781 0.4712389
3600 4000 9.133205 0.50265482
3700 4000 9.3404584 0.53407075
3800 4000 9.3359844 0.56548668
3900 4000 9.0916854 0.5969026
4000 4000 8.5596424 0.62831853
4100 4000 7.9734883 0.65973446
4200 4000 7.2154383 0.69115038
4300 4000 6.7039232 0.72256631
4400 4000 6.1542738 0.75398224
4500 4000 5.4049454 0.78539816
4600 4000 4.4603192 0.81681409
4700 4000 3.6197985 0.84823002
4800 4000 2.9895571 0.87964594
4900 4000 2.5314553 0.91106187
5000 4000 2.2645533 0.9424778
Loop time of 6.64209 on 4 procs for 3000 steps with 4000 atoms
2000 4000 65.819213 0
2100 4000 105.02389 0.031415927
2200 4000 112.02469 0.062831853
2300 4000 92.271262 0.09424778
2400 4000 89.369506 0.12566371
2500 4000 80.910925 0.15707963
2600 4000 31.620722 0.18849556
2700 4000 4.3019937 0.21991149
2800 4000 3.9913967 0.25132741
2900 4000 4.5203726 0.28274334
3000 4000 5.484886 0.31415927
3100 4000 6.1085958 0.34557519
3200 4000 6.7085635 0.37699112
3300 4000 7.4787777 0.40840704
3400 4000 8.2116413 0.43982297
3500 4000 8.7979302 0.4712389
3600 4000 9.871649 0.50265482
3700 4000 10.012426 0.53407075
3800 4000 9.9067754 0.56548668
3900 4000 9.725458 0.5969026
4000 4000 9.3350056 0.62831853
4100 4000 8.8337295 0.65973446
4200 4000 8.2712493 0.69115038
4300 4000 6.9609934 0.72256631
4400 4000 6.0120294 0.75398224
4500 4000 5.0490036 0.78539816
4600 4000 4.2796544 0.81681409
4700 4000 4.1736483 0.84823002
4800 4000 3.0860106 0.87964594
4900 4000 2.6670909 0.91106187
5000 4000 2.2901814 0.9424778
Loop time of 10.7627 on 4 procs for 3000 steps with 4000 atoms
Performance: 39023.861 tau/day, 451.665 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 24083.252 tau/day, 278.741 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8376 | 2.126 | 2.3131 | 12.6 | 32.01
Neigh | 0.97762 | 1.0518 | 1.1337 | 5.4 | 15.84
Comm | 0.53699 | 0.84265 | 1.2325 | 27.6 | 12.69
Output | 0.13922 | 0.14159 | 0.14388 | 0.4 | 2.13
Modify | 1.8815 | 2.1026 | 2.3368 | 11.2 | 31.66
Other | | 0.3774 | | | 5.68
Pair | 1.6731 | 2.0701 | 2.3327 | 18.9 | 19.23
Neigh | 2.7389 | 3.1706 | 3.5146 | 15.7 | 29.46
Comm | 0.93507 | 1.5441 | 2.1182 | 39.1 | 14.35
Output | 0.0021682 | 0.0044412 | 0.006026 | 2.2 | 0.04
Modify | 3.0031 | 3.4223 | 3.9262 | 18.3 | 31.80
Other | | 0.5511 | | | 5.12
Nlocal: 1000 ave 1256 max 744 min
Nlocal: 1000.00 ave 1277 max 723 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 579.5 ave 789 max 498 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 3696.25 ave 4853 max 2590 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 569.750 ave 809 max 454 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Neighs: 3690.50 ave 4937 max 2426 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 14785
Ave neighs/atom = 3.69625
Neighbor list builds = 1230
Dangerous builds = 676
Total wall time: 0:00:08
Total # of neighbors = 14762
Ave neighs/atom = 3.6905000
Neighbor list builds = 2187
Dangerous builds = 1610
Total wall time: 0:00:14

120
examples/granular/log.29Mar19.pour.flatwall.g++.1 → examples/granular/log.29Oct20.pour.flatwall.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) on flat wall
@ -45,9 +44,14 @@ region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (20 20 30)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
@ -75,19 +79,13 @@ fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step cpu atoms ke
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
@ -109,26 +107,82 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
100 3.8153191 855 -0
200 4.195287 855 -0
300 4.5890362 855 -0
400 10.636087 1500 -0
500 11.306909 1500 -0
600 11.968198 1500 -0
700 22.631892 2288 -0
800 23.711387 2288 -0
900 24.754344 2288 -0
1000 25.811778 2288 -0
1100 35.368869 2845 -0
1200 37.149843 2845 -0
1300 39.026458 2845 -0
1400 41.757583 3000 -0
1500 45.155503 3000 -0
1600 48.570241 3000 -0
1700 52.839322 3000 -0
1800 59.772697 3000 -0
1900 69.493305 3000 -0
2000 114.61886 3000 -0
2100 152.89232 3000 -0
Step Atoms KinEng
0 0 -0
100 926 -0
200 926 -0
300 926 -0
400 1498 -0
500 1498 -0
600 1498 -0
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 24.3889 on 1 procs for 5000 steps with 3000 atoms
Performance: 17713.003 tau/day, 205.012 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.362 | 14.362 | 14.362 | 0.0 | 58.89
Neigh | 3.3483 | 3.3483 | 3.3483 | 0.0 | 13.73
Comm | 0.42893 | 0.42893 | 0.42893 | 0.0 | 1.76
Output | 0.0025065 | 0.0025065 | 0.0025065 | 0.0 | 0.01
Modify | 6.059 | 6.059 | 6.059 | 0.0 | 24.84
Other | | 0.1876 | | | 0.77
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 462.000 ave 462 max 462 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 17694.0 ave 17694 max 17694 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17694
Ave neighs/atom = 5.8980000
Neighbor list builds = 1133
Dangerous builds = 0
Total wall time: 0:00:24

161
examples/granular/log.29Mar19.pour.flatwall.g++.4 → examples/granular/log.29Oct20.pour.flatwall.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) on flat wall
@ -45,9 +44,14 @@ region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (20 20 30)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
@ -75,26 +79,19 @@ fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step cpu atoms ke
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
dump 1 all custom 100 ${name}.dump id type radius mass x y z
dump 1 all custom 100 pour_two_types.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
Neighbor list info ...
@ -110,82 +107,82 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
100 0.11584234 855 -0
200 0.12743592 855 -0
300 0.13925815 855 -0
400 0.35203671 1500 -0
500 0.37055922 1500 -0
600 0.38671875 1500 -0
700 0.71736908 2288 -0
800 0.74506783 2288 -0
900 0.77112222 2288 -0
1000 0.79632139 2288 -0
1100 1.0384252 2845 -0
1200 1.08093 2845 -0
1300 1.1224561 2845 -0
1400 1.1811485 3000 -0
1500 1.2414908 3000 -0
1600 1.3105879 3000 -0
1700 1.390928 3000 -0
1800 1.4869275 3000 -0
1900 1.5958266 3000 -0
2000 1.7172487 3000 -0
2100 1.851155 3000 -0
2200 1.9957182 3000 -0
2300 2.1593764 3000 -0
2400 2.3433132 3000 -0
2500 2.532742 3000 -0
2600 2.7376895 3000 -0
2700 2.9463468 3000 -0
2800 3.1645725 3000 -0
2900 3.3879526 3000 -0
3000 3.6152103 3000 -0
3100 3.8467371 3000 -0
3200 4.0787683 3000 -0
3300 4.3097105 3000 -0
3400 4.5423617 3000 -0
3500 4.7773693 3000 -0
3600 5.0127218 3000 -0
3700 5.2519271 3000 -0
3800 5.4951298 3000 -0
3900 5.7210469 3000 -0
4000 5.9432652 3000 -0
4100 6.1687591 3000 -0
4200 6.3942792 3000 -0
4300 6.6331475 3000 -0
4400 6.8632154 3000 -0
4500 7.0979366 3000 -0
4600 7.3305347 3000 -0
4700 7.5670528 3000 -0
4800 7.8086057 3000 -0
4900 8.0407174 3000 -0
5000 8.2765219 3000 -0
Loop time of 8.27669 on 4 procs for 5000 steps with 3000 atoms
Step Atoms KinEng
0 0 -0
100 926 -0
200 926 -0
300 926 -0
400 1498 -0
500 1498 -0
600 1498 -0
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 12.1982 on 4 procs for 5000 steps with 3000 atoms
Performance: 52194.788 tau/day, 604.106 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 35414.923 tau/day, 409.895 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6106 | 3.4073 | 5.4191 | 95.7 | 41.17
Neigh | 0.51456 | 0.64572 | 0.81542 | 16.6 | 7.80
Comm | 0.2808 | 2.5222 | 4.4998 | 121.9 | 30.47
Output | 0.15695 | 0.15919 | 0.16502 | 0.8 | 1.92
Modify | 1.3517 | 1.4192 | 1.4904 | 4.9 | 17.15
Other | | 0.123 | | | 1.49
Pair | 1.7141 | 3.8131 | 6.2143 | 107.3 | 31.26
Neigh | 0.77648 | 0.96585 | 1.1892 | 18.3 | 7.92
Comm | 0.7427 | 3.5566 | 5.9731 | 128.4 | 29.16
Output | 0.0067544 | 0.0086352 | 0.011408 | 1.8 | 0.07
Modify | 3.3476 | 3.5826 | 3.8235 | 11.5 | 29.37
Other | | 0.2715 | | | 2.23
Nlocal: 750 ave 1036 max 482 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 429.75 ave 475 max 386 min
Nlocal: 750.000 ave 1033 max 463 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 435.000 ave 492 max 378 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4434.50 ave 7028 max 1967 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4051.75 ave 6274 max 2057 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 16207
Ave neighs/atom = 5.40233
Neighbor list builds = 1165
Total # of neighbors = 17738
Ave neighs/atom = 5.9126667
Neighbor list builds = 1139
Dangerous builds = 0
Total wall time: 0:00:08
Total wall time: 0:00:12

63
examples/template/co2.mol Normal file
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@ -0,0 +1,63 @@
# CO2 molecule file. TraPPE model.
3 atoms
2 bonds
1 angles
Coords
1 0.0 0.0 0.0
2 -1.16 0.0 0.0
3 1.16 0.0 0.0
Types
1 1
2 2
3 2
Charges
1 0.7
2 -0.35
3 -0.35
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2
Shake Flags
1 0
2 0
3 0
Shake Atoms
1
2
3
Shake Bond Types
1
2
3

68
examples/template/cyclohexane.mol Normal file
View File

@ -0,0 +1,68 @@
LAMMPS molecule file. Cyclohexane(UA)
6 atoms
6 bonds
6 angles
6 dihedrals
Coords
1 0.000000 0.000000 0.000000
2 0.000000 0.000000 1.536000
3 1.431000 0.000000 2.094000
4 2.247000 1.176000 1.536000
5 2.247000 1.176000 0.000000
6 0.815000 1.176000 -0.557000
Types
1 1
2 1
3 1
4 1
5 1
6 1
Bonds
1 1 1 6
2 1 1 2
3 1 2 3
4 1 3 4
5 1 4 5
6 1 5 6
Angles
1 1 2 1 6
2 1 1 2 3
3 1 2 3 4
4 1 3 4 5
5 1 4 5 6
6 1 1 6 5
Dihedrals
1 1 2 1 6 5
2 1 6 1 2 3
3 1 1 2 3 4
4 1 2 3 4 5
5 1 3 4 5 6
6 1 4 5 6 1
Special Bond Counts
1 2 2 1
2 2 2 1
3 2 2 1
4 2 2 1
5 2 2 1
6 2 2 1
Special Bonds
1 2 6 3 5 4
2 3 1 4 6 5
3 4 2 5 1 6
4 5 3 6 2 1
5 6 4 1 3 2
6 1 5 2 4 3

428
examples/template/h2o-co2.data Normal file
View File

@ -0,0 +1,428 @@
LAMMPS data file via write_data, version 22 Oct 2020, timestep = 0
384 atoms
4 atom types
2 bond types
2 angle types
-10.0 10.0 xlo xhi
-10.0 10.0 ylo yhi
-10.0 10.0 zlo zhi
Masses
1 15.9994
2 1
3 12.0107
4 15.9994
PairIJ Coeffs # lj/cut/coul/cut
1 1 0.15535 3.166 14
1 2 0 0 14
1 3 0.0912928 2.983 14
1 4 0.156159 3.108 14
2 2 0 0 14
2 3 0 1.4 14
2 4 0 1.525 14
3 3 0.053649 2.8 14
3 4 0.0917684 2.925 14
4 4 0.156973 3.05 14
Bond Coeffs # harmonic
1 1000 1
2 1000 1.16
Angle Coeffs # harmonic
1 100 109.47
2 100 180
Atoms # hybrid
1 1 -9.915603425183674 9.642074614047225 9.886373806057632 1 1 1 -0.8472 0 -1 -1
2 2 -9.955077256991814 9.952071397945474 -9.163725932085827 1 1 2 0.4236 0 -1 0
3 2 9.870680682175488 -9.594146011992699 9.277352126028195 1 1 3 0.4236 -1 0 -1
4 1 -5.377413308169694 -9.975845367284359 9.928445655374531 2 1 1 -0.8472 0 0 -1
5 2 -4.868089392205772 9.173804835517629 -9.939414010387674 2 1 2 0.4236 0 -1 0
6 2 -4.754497299624534 -9.19795946823327 -9.989031644986857 2 1 3 0.4236 0 0 0
7 1 0.2862645369165933 -9.834750023705109 9.802796207089045 3 1 1 -0.8472 0 0 -1
8 2 -0.20506315473823142 -9.416615546409432 -9.433183272761259 3 1 2 0.4236 0 0 0
9 2 -0.08120138217836187 9.25136557011454 9.630387065672213 3 1 3 0.4236 0 -1 -1
10 1 4.954244542709665 9.733846444128554 9.725750116636055 4 1 1 -0.8472 0 -1 -1
11 2 5.314186858355006 9.562011307112279 -9.357254293410282 4 1 2 0.4236 0 -1 0
12 2 4.731568598935329 -9.295857751240833 9.631504176774227 4 1 3 0.4236 0 0 -1
13 1 -9.885042196263848 -5.366646729833796 -9.977658232783796 5 1 1 -0.8472 0 0 0
14 2 -9.499988310087788 -4.607821917003056 -9.452410572081622 5 1 2 0.4236 0 0 0
15 2 9.385030506351637 -5.025531353163147 9.430068804865417 5 1 3 0.4236 -1 0 -1
16 1 -5.3381930384891545 -4.817187821023332 -9.98130637447481 6 1 1 -0.8472 0 0 0
17 2 -4.814226078866727 -5.143876565241305 -9.194731656774504 6 1 2 0.4236 0 0 0
18 2 -4.8475808826441185 -5.038935613735363 9.176038031249314 6 1 3 0.4236 0 0 -1
19 1 -0.17437585816420464 -5.00267209015634 -9.656881659301497 7 1 1 -0.8472 0 0 0
20 2 0.5142734508723548 -5.661488493390246 -9.959684850984493 7 1 2 0.4236 0 0 0
21 2 -0.3398975927081498 -4.335839416453415 9.61656651028599 7 1 3 0.4236 0 0 -1
22 1 5.027007160081784 -5.376778433628809 -9.926156239555816 8 1 1 -0.8472 0 0 0
23 2 5.040872603784614 -4.651165711374701 -9.238216835484566 8 1 2 0.4236 0 0 0
24 2 4.932120236133603 -4.97205585499649 9.164373075040384 8 1 3 0.4236 0 0 -1
25 1 -9.774983021942727 -0.11627625671956153 9.710187185567547 9 1 1 -0.8472 0 0 -1
26 2 -9.547719336441409 -0.18624762678535645 -9.31851372479864 9 1 2 0.4236 0 0 0
27 2 9.322702358384136 0.30252388350491777 9.608326539231093 9 1 3 0.4236 -1 0 -1
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229 3 -7.5 7.5 -7.5 77 2 1 0.7 0 0 0
230 4 -8.223742289003038 8.374984745462024 -7.26293715112359 77 2 2 -0.35 0 0 0
231 4 -6.776257710996962 6.625015254537976 -7.73706284887641 77 2 3 -0.35 0 0 0
232 3 -2.5 7.5 -7.5 78 2 1 0.7 0 0 0
233 4 -3.61460324665069 7.680615494066614 -7.7657774366999845 78 2 2 -0.35 0 0 0
234 4 -1.3853967533493103 7.319384505933386 -7.2342225633000155 78 2 3 -0.35 0 0 0
235 3 2.5 7.5 -7.5 79 2 1 0.7 0 0 0
236 4 2.7768699697291033 8.100687316711076 -6.547047867201792 79 2 2 -0.35 0 0 0
237 4 2.2231300302708967 6.899312683288924 -8.452952132798208 79 2 3 -0.35 0 0 0
238 3 7.5 7.5 -7.5 80 2 1 0.7 0 0 0
239 4 7.16783620529347 7.207818725743377 -6.4276673480398285 80 2 2 -0.35 0 0 0
240 4 7.83216379470653 7.792181274256623 -8.57233265196017 80 2 3 -0.35 0 0 0
241 3 -7.5 -7.5 -2.5 81 2 1 0.7 0 0 0
242 4 -6.904167548557492 -8.34992426129338 -1.9821076947154799 81 2 2 -0.35 0 0 0
243 4 -8.095832451442508 -6.6500757387066205 -3.01789230528452 81 2 3 -0.35 0 0 0
244 3 -2.5 -7.5 -2.5 82 2 1 0.7 0 0 0
245 4 -3.342504009848425 -6.73061486491979 -2.7093645321130886 82 2 2 -0.35 0 0 0
246 4 -1.6574959901515751 -8.26938513508021 -2.2906354678869114 82 2 3 -0.35 0 0 0
247 3 2.5 -7.5 -2.5 83 2 1 0.7 0 0 0
248 4 2.1689944159865804 -6.498569494779038 -2.0171208778950747 83 2 2 -0.35 0 0 0
249 4 2.8310055840134196 -8.501430505220963 -2.9828791221049253 83 2 3 -0.35 0 0 0
250 3 7.5 -7.5 -2.5 84 2 1 0.7 0 0 0
251 4 7.672524274844629 -6.627256087060682 -1.7555851714153565 84 2 2 -0.35 0 0 0
252 4 7.327475725155371 -8.372743912939317 -3.2444148285846435 84 2 3 -0.35 0 0 0
253 3 -7.5 -2.5 -2.5 85 2 1 0.7 0 0 0
254 4 -7.9562680998953565 -2.81558187201847 -1.4812618083770501 85 2 2 -0.35 0 0 0
255 4 -7.0437319001046435 -2.18441812798153 -3.51873819162295 85 2 3 -0.35 0 0 0
256 3 -2.5 -2.5 -2.5 86 2 1 0.7 0 0 0
257 4 -3.655855156414235 -2.500158391730412 -2.597973630649695 86 2 2 -0.35 0 0 0
258 4 -1.3441448435857646 -2.499841608269588 -2.402026369350305 86 2 3 -0.35 0 0 0
259 3 2.5 -2.5 -2.5 87 2 1 0.7 0 0 0
260 4 2.3492190747015416 -2.0985959396284857 -3.577840383769045 87 2 2 -0.35 0 0 0
261 4 2.6507809252984584 -2.9014040603715143 -1.422159616230955 87 2 3 -0.35 0 0 0
262 3 7.5 -2.5 -2.5 88 2 1 0.7 0 0 0
263 4 6.369167808148362 -2.680475446720884 -2.685059901121005 88 2 2 -0.35 0 0 0
264 4 8.630832191851638 -2.319524553279116 -2.314940098878995 88 2 3 -0.35 0 0 0
265 3 -7.5 2.5 -2.5 89 2 1 0.7 0 0 0
266 4 -8.653001820685228 2.600334495702883 -2.5782290896572104 89 2 2 -0.35 0 0 0
267 4 -6.346998179314771 2.399665504297117 -2.4217709103427896 89 2 3 -0.35 0 0 0
268 3 -2.5 2.5 -2.5 90 2 1 0.7 0 0 0
269 4 -2.4389431621625337 2.9182920508772057 -1.4197667739204507 90 2 2 -0.35 0 0 0
270 4 -2.5610568378374663 2.0817079491227943 -3.5802332260795495 90 2 3 -0.35 0 0 0
271 3 2.5 2.5 -2.5 91 2 1 0.7 0 0 0
272 4 1.7245732398737652 2.522972739967341 -1.637569948982224 91 2 2 -0.35 0 0 0
273 4 3.275426760126235 2.477027260032659 -3.362430051017776 91 2 3 -0.35 0 0 0
274 3 7.5 2.5 -2.5 92 2 1 0.7 0 0 0
275 4 6.354214677495708 2.528966092667298 -2.6787091497638675 92 2 2 -0.35 0 0 0
276 4 8.645785322504292 2.471033907332702 -2.3212908502361325 92 2 3 -0.35 0 0 0
277 3 -7.5 7.5 -2.5 93 2 1 0.7 0 0 0
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279 4 -6.856906399814943 7.461518555402951 -1.535349908089598 93 2 3 -0.35 0 0 0
280 3 -2.5 7.5 -2.5 94 2 1 0.7 0 0 0
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282 4 -2.1762145513771554 7.190687687281463 -3.570088256388609 94 2 3 -0.35 0 0 0
283 3 2.5 7.5 -2.5 95 2 1 0.7 0 0 0
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285 4 1.78094973686466 7.461741690035572 -3.409452044257235 95 2 3 -0.35 0 0 0
286 3 7.5 7.5 -2.5 96 2 1 0.7 0 0 0
287 4 7.739558757849892 7.897562136690081 -3.563087930985878 96 2 2 -0.35 0 0 0
288 4 7.260441242150108 7.102437863309919 -1.436912069014122 96 2 3 -0.35 0 0 0
289 3 -7.5 -7.5 2.5 97 2 1 0.7 0 0 0
290 4 -7.4900021089395485 -6.340045447267127 2.5023404633351993 97 2 2 -0.35 0 0 0
291 4 -7.5099978910604515 -8.659954552732874 2.4976595366648007 97 2 3 -0.35 0 0 0
292 3 -2.5 -7.5 2.5 98 2 1 0.7 0 0 0
293 4 -3.106830756206168 -6.511472531062921 2.5130336671395352 98 2 2 -0.35 0 0 0
294 4 -1.8931692437938321 -8.488527468937079 2.4869663328604648 98 2 3 -0.35 0 0 0
295 3 2.5 -7.5 2.5 99 2 1 0.7 0 0 0
296 4 1.3541840293569891 -7.32995582507702 2.4384310143483083 99 2 2 -0.35 0 0 0
297 4 3.645815970643011 -7.67004417492298 2.5615689856516917 99 2 3 -0.35 0 0 0
298 3 7.5 -7.5 2.5 100 2 1 0.7 0 0 0
299 4 6.890528994434403 -6.53074739493991 2.6862645456309138 100 2 2 -0.35 0 0 0
300 4 8.109471005565597 -8.46925260506009 2.3137354543690862 100 2 3 -0.35 0 0 0
301 3 -7.5 -2.5 2.5 101 2 1 0.7 0 0 0
302 4 -8.402413809003143 -1.9960963670464098 1.9733782704667298 101 2 2 -0.35 0 0 0
303 4 -6.597586190996857 -3.00390363295359 3.0266217295332702 101 2 3 -0.35 0 0 0
304 3 -2.5 -2.5 2.5 102 2 1 0.7 0 0 0
305 4 -3.1146628699497816 -3.0155291909493633 1.6621341338948146 102 2 2 -0.35 0 0 0
306 4 -1.8853371300502184 -1.9844708090506367 3.3378658661051857 102 2 3 -0.35 0 0 0
307 3 2.5 -2.5 2.5 103 2 1 0.7 0 0 0
308 4 1.7091896213819626 -3.348636804240857 2.505875334702054 103 2 2 -0.35 0 0 0
309 4 3.2908103786180374 -1.651363195759143 2.494124665297946 103 2 3 -0.35 0 0 0
310 3 7.5 -2.5 2.5 104 2 1 0.7 0 0 0
311 4 7.846121450678692 -1.863352310559478 1.5941966764743452 104 2 2 -0.35 0 0 0
312 4 7.153878549321308 -3.136647689440522 3.405803323525655 104 2 3 -0.35 0 0 0
313 3 -7.5 2.5 2.5 105 2 1 0.7 0 0 0
314 4 -7.415505185247761 1.3693275996894718 2.2549682684711767 105 2 2 -0.35 0 0 0
315 4 -7.584494814752239 3.6306724003105284 2.7450317315288233 105 2 3 -0.35 0 0 0
316 3 -2.5 2.5 2.5 106 2 1 0.7 0 0 0
317 4 -1.6566227058869707 3.061399569140947 3.0649294323567706 106 2 2 -0.35 0 0 0
318 4 -3.3433772941130293 1.938600430859053 1.9350705676432294 106 2 3 -0.35 0 0 0
319 3 2.5 2.5 2.5 107 2 1 0.7 0 0 0
320 4 1.8018606440593001 1.6504313913225857 2.1306294288432994 107 2 2 -0.35 0 0 0
321 4 3.1981393559407 3.3495686086774143 2.8693705711567006 107 2 3 -0.35 0 0 0
322 3 7.5 2.5 2.5 108 2 1 0.7 0 0 0
323 4 7.454398927291544 1.350628262336051 2.3501162089244056 108 2 2 -0.35 0 0 0
324 4 7.545601072708456 3.649371737663949 2.6498837910755944 108 2 3 -0.35 0 0 0
325 3 -7.5 7.5 2.5 109 2 1 0.7 0 0 0
326 4 -7.639487922633921 8.47694083419964 1.8903035788914426 109 2 2 -0.35 0 0 0
327 4 -7.360512077366079 6.523059165800359 3.1096964211085574 109 2 3 -0.35 0 0 0
328 3 -2.5 7.5 2.5 110 2 1 0.7 0 0 0
329 4 -3.653132322293053 7.551646962835361 2.385028531744119 110 2 2 -0.35 0 0 0
330 4 -1.3468676777069468 7.448353037164639 2.614971468255881 110 2 3 -0.35 0 0 0
331 3 2.5 7.5 2.5 111 2 1 0.7 0 0 0
332 4 2.8364898316331035 7.678145325449636 3.595736663723528 111 2 2 -0.35 0 0 0
333 4 2.1635101683668965 7.321854674550364 1.4042633362764718 111 2 3 -0.35 0 0 0
334 3 7.5 7.5 2.5 112 2 1 0.7 0 0 0
335 4 6.479552888446932 7.807048742079671 2.958267130078399 112 2 2 -0.35 0 0 0
336 4 8.520447111553068 7.192951257920329 2.041732869921601 112 2 3 -0.35 0 0 0
337 3 -7.5 -7.5 7.5 113 2 1 0.7 0 0 0
338 4 -7.6197834102650095 -6.871306065029082 8.46746879575316 113 2 2 -0.35 0 0 0
339 4 -7.3802165897349905 -8.128693934970917 6.53253120424684 113 2 3 -0.35 0 0 0
340 3 -2.5 -7.5 7.5 114 2 1 0.7 0 0 0
341 4 -3.6462582687736766 -7.5580642653980155 7.6682870237177 114 2 2 -0.35 0 0 0
342 4 -1.3537417312263231 -7.4419357346019845 7.3317129762823 114 2 3 -0.35 0 0 0
343 3 2.5 -7.5 7.5 115 2 1 0.7 0 0 0
344 4 1.3734554259918312 -7.525081897193473 7.224558134616524 115 2 2 -0.35 0 0 0
345 4 3.626544574008169 -7.474918102806527 7.775441865383476 115 2 3 -0.35 0 0 0
346 3 7.5 -7.5 7.5 116 2 1 0.7 0 0 0
347 4 8.414658305507071 -7.215850731078148 8.154415294089395 116 2 2 -0.35 0 0 0
348 4 6.585341694492928 -7.784149268921852 6.845584705910605 116 2 3 -0.35 0 0 0
349 3 -7.5 -2.5 7.5 117 2 1 0.7 0 0 0
350 4 -8.645413670915179 -2.6453055222059496 7.611865221123771 117 2 2 -0.35 0 0 0
351 4 -6.354586329084821 -2.3546944777940504 7.388134778876229 117 2 3 -0.35 0 0 0
352 3 -2.5 -2.5 7.5 118 2 1 0.7 0 0 0
353 4 -2.601509341816184 -1.9084001398846042 8.492625538174135 118 2 2 -0.35 0 0 0
354 4 -2.398490658183816 -3.091599860115396 6.507374461825866 118 2 3 -0.35 0 0 0
355 3 2.5 -2.5 7.5 119 2 1 0.7 0 0 0
356 4 2.2485924178438 -2.364925227008703 8.624343823452472 119 2 2 -0.35 0 0 0
357 4 2.7514075821562 -2.635074772991297 6.375656176547529 119 2 3 -0.35 0 0 0
358 3 7.5 -2.5 7.5 120 2 1 0.7 0 0 0
359 4 6.784038999809617 -1.8413110953985297 8.13176639128819 120 2 2 -0.35 0 0 0
360 4 8.215961000190383 -3.1586889046014703 6.86823360871181 120 2 3 -0.35 0 0 0
361 3 -7.5 2.5 7.5 121 2 1 0.7 0 0 0
362 4 -7.537548740040521 3.6593910439642627 7.49841908354891 121 2 2 -0.35 0 0 0
363 4 -7.462451259959479 1.340608956035737 7.50158091645109 121 2 3 -0.35 0 0 0
364 3 -2.5 2.5 7.5 122 2 1 0.7 0 0 0
365 4 -1.649121019955475 1.7301813803117607 7.3297523741731405 122 2 2 -0.35 0 0 0
366 4 -3.350878980044525 3.2698186196882393 7.6702476258268595 122 2 3 -0.35 0 0 0
367 3 2.5 2.5 7.5 123 2 1 0.7 0 0 0
368 4 3.2379752354871414 1.771831388509018 6.979651054534562 123 2 2 -0.35 0 0 0
369 4 1.7620247645128586 3.228168611490982 8.020348945465438 123 2 3 -0.35 0 0 0
370 3 7.5 2.5 7.5 124 2 1 0.7 0 0 0
371 4 7.334452984137467 1.3548227605993108 7.582239138478142 124 2 2 -0.35 0 0 0
372 4 7.665547015862533 3.645177239400689 7.417760861521858 124 2 3 -0.35 0 0 0
373 3 -7.5 7.5 7.5 125 2 1 0.7 0 0 0
374 4 -8.324913544328572 8.31456508779972 7.459982977108372 125 2 2 -0.35 0 0 0
375 4 -6.675086455671429 6.6854349122002805 7.540017022891628 125 2 3 -0.35 0 0 0
376 3 -2.5 7.5 7.5 126 2 1 0.7 0 0 0
377 4 -2.8359455597090397 6.421926623286971 7.76551530150699 126 2 2 -0.35 0 0 0
378 4 -2.1640544402909603 8.578073376713029 7.23448469849301 126 2 3 -0.35 0 0 0
379 3 2.5 7.5 7.5 127 2 1 0.7 0 0 0
380 4 1.4186788873677927 7.288670506833647 7.862883585594468 127 2 2 -0.35 0 0 0
381 4 3.5813211126322075 7.711329493166353 7.137116414405532 127 2 3 -0.35 0 0 0
382 3 7.5 7.5 7.5 128 2 1 0.7 0 0 0
383 4 6.9664096100856385 6.501410755376355 7.247609793547735 128 2 2 -0.35 0 0 0
384 4 8.03359038991436 8.498589244623645 7.752390206452265 128 2 3 -0.35 0 0 0

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examples/template/h2o.mol Normal file
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# Water molecule. SPC/E model.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 1
2 2
3 2
Charges
1 -0.8472
2 0.4236
3 0.4236
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2

29
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# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
units real
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
atom_style hybrid template twomols charge
boundary p p p
pair_style lj/cut/coul/long 12
pair_modify mix arithmetic tail yes
kspace_style pppm 0.0001
pair_style lj/cut/coul/long 12
bond_style harmonic
angle_style harmonic
read_data h2o-co2.data
group h2o type 1 2
group co2 type 3 4
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
timestep 1.0
velocity all create 300.0 34672
thermo 100
fix 1 all nve
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
run 2500

21
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# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data molecular-mix.data
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

11
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# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
read_restart molecular-mix.restart
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

42
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# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 &
extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
create_atoms 0 box mol cychex 734594
create_atoms 2 random 800 495437 box
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
#write_data molecular-mix.data
#write_restart molecular-mix.restart

42
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# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
create_atoms 0 box mol cychex 734594
create_atoms 2 random 800 495437 box
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
#write_data template-mix.data
#write_restart template-mix.restart

21
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# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data template-mix.data
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

11
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# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
read_restart template-mix.restart
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

158
examples/template/log.22Oct20.hybrid.g++.1 Normal file
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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
units real
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
Read molecule template twomols:
1 molecules
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
Read molecule template twomols:
1 molecules
3 atoms with max type 4
2 bonds with max type 2
1 angles with max type 2
0 dihedrals with max type 0
0 impropers with max type 0
atom_style hybrid template twomols charge
boundary p p p
pair_style lj/cut/coul/long 12
pair_modify mix arithmetic tail yes
kspace_style pppm 0.0001
pair_style lj/cut/coul/long 12
bond_style harmonic
angle_style harmonic
read_data h2o-co2.data
Reading data file ...
orthogonal box = (-10.000000 -10.000000 -10.000000) to (10.000000 10.000000 10.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
256 template bonds
128 template angles
read_data CPU = 0.003 seconds
group h2o type 1 2
192 atoms in group h2o
group co2 type 3 4
192 atoms in group co2
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
timestep 1.0
velocity all create 300.0 34672
thermo 100
fix 1 all nve
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
WARNING: Molecule template for fix shake has multiple molecules (src/RIGID/fix_shake.cpp:174)
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
64 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
run 2500
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.21452218
grid = 8 8 8
stencil order = 5
estimated absolute RMS force accuracy = 0.0237525
estimated relative force accuracy = 7.1529949e-05
using double precision FFTW3
3d grid and FFT values/proc = 2197 512
Neighbor list info ...
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15
ghost atom cutoff = 15
binsize = 7.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
1 1.99995 1.29379e-05 192
1 328.411 6.25278e-13 64
Per MPI rank memory allocation (min/avg/max) = 5.625 | 5.625 | 5.625 Mbytes
Step Temp E_pair E_mol TotEng Press
0 360.18809 -173.24472 3.5527137e-13 169.25036 2429.6019
100 363.1919 -274.40147 44.351072 115.30094 -883.3694
200 427.79493 -329.78833 38.354106 115.34674 1523.3792
300 465.88637 -350.56147 22.604289 115.04411 385.4719
400 436.9596 -357.24661 57.161471 115.41032 2307.0158
SHAKE stats (type/ave/delta/count) on step 500
1 2.00000 4.02911e-07 192
1 328.410 5.78944e-05 64
500 480.93508 -378.08914 36.26854 115.49018 2822.245
600 457.38119 -381.9922 62.73272 115.65441 -387.65281
700 488.20843 -393.89334 45.144546 115.47805 3086.293
800 463.52123 -384.28537 59.827245 116.2942 3310.9672
900 500.42748 -424.29715 64.614956 116.16348 -612.56056
SHAKE stats (type/ave/delta/count) on step 1000
1 2.00000 8.23271e-07 192
1 328.410 5.98754e-05 64
1000 522.46734 -424.93564 44.24152 116.1088 3948.9908
1100 470.79532 -398.30875 66.721422 116.08177 2480.4521
1200 515.87076 -433.25982 58.802584 116.07313 1913.2295
1300 517.25521 -425.5203 49.308433 115.63494 3343.755
1400 515.28471 -427.75141 53.078285 115.29997 2755.9048
SHAKE stats (type/ave/delta/count) on step 1500
1 2.00000 8.95165e-07 192
1 328.410 7.19288e-05 64
1500 514.22181 -421.99736 48.624007 115.58906 2400.1515
1600 533.9392 -430.89564 38.263047 115.07866 4331.2167
1700 529.29154 -424.02106 35.673551 114.94439 2973.3181
1800 535.52166 -438.41572 43.952454 114.75272 1799.8588
1900 519.40791 -413.30717 34.399008 114.9856 4270.415
SHAKE stats (type/ave/delta/count) on step 2000
1 2.00000 8.04353e-07 192
1 328.410 7.97925e-05 64
2000 553.26572 -446.67936 35.423618 114.83268 1729.4708
2100 546.58793 -448.39367 43.475288 114.82028 1266.9778
2200 536.17021 -442.03485 46.968579 114.76641 2419.0965
2300 556.29724 -457.19766 43.217115 114.99049 1122.5796
2400 529.02178 -437.66639 49.530498 114.89949 1714.4747
SHAKE stats (type/ave/delta/count) on step 2500
1 2.00000 6.70601e-07 192
1 328.410 6.39002e-05 64
2500 500.56024 -423.00108 62.368402 115.33925 3750.7564
Loop time of 6.4485 on 1 procs for 2500 steps with 384 atoms
Performance: 33.496 ns/day, 0.717 hours/ns, 387.687 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.9332 | 4.9332 | 4.9332 | 0.0 | 76.50
Bond | 0.013685 | 0.013685 | 0.013685 | 0.0 | 0.21
Kspace | 0.33226 | 0.33226 | 0.33226 | 0.0 | 5.15
Neigh | 1.0663 | 1.0663 | 1.0663 | 0.0 | 16.54
Comm | 0.062471 | 0.062471 | 0.062471 | 0.0 | 0.97
Output | 0.00048861 | 0.00048861 | 0.00048861 | 0.0 | 0.01
Modify | 0.030447 | 0.030447 | 0.030447 | 0.0 | 0.47
Other | | 0.009605 | | | 0.15
Nlocal: 384.000 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5594.00 ave 5594 max 5594 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 129739.0 ave 129739 max 129739 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 129739
Ave neighs/atom = 337.86198
Ave special neighs/atom = 2.0000000
Neighbor list builds = 320
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
units real
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
Read molecule template twomols:
1 molecules
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
Read molecule template twomols:
1 molecules
3 atoms with max type 4
2 bonds with max type 2
1 angles with max type 2
0 dihedrals with max type 0
0 impropers with max type 0
atom_style hybrid template twomols charge
boundary p p p
pair_style lj/cut/coul/long 12
pair_modify mix arithmetic tail yes
kspace_style pppm 0.0001
pair_style lj/cut/coul/long 12
bond_style harmonic
angle_style harmonic
read_data h2o-co2.data
Reading data file ...
orthogonal box = (-10.000000 -10.000000 -10.000000) to (10.000000 10.000000 10.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
256 template bonds
128 template angles
read_data CPU = 0.002 seconds
group h2o type 1 2
192 atoms in group h2o
group co2 type 3 4
192 atoms in group co2
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
timestep 1.0
velocity all create 300.0 34672
thermo 100
fix 1 all nve
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
WARNING: Molecule template for fix shake has multiple molecules (src/RIGID/fix_shake.cpp:174)
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
64 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
run 2500
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.21452218
grid = 8 8 8
stencil order = 5
estimated absolute RMS force accuracy = 0.0237525
estimated relative force accuracy = 7.1529949e-05
using double precision FFTW3
3d grid and FFT values/proc = 1053 128
Neighbor list info ...
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15
ghost atom cutoff = 15
binsize = 7.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
1 1.99995 1.29379e-05 192
1 328.411 6.25278e-13 64
Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes
Step Temp E_pair E_mol TotEng Press
0 360.18809 -173.24472 3.5527137e-13 169.25036 2429.6019
100 363.1919 -274.40147 44.351072 115.30094 -883.3694
200 427.79493 -329.78833 38.354106 115.34674 1523.3792
300 465.88637 -350.56147 22.60429 115.0441 385.47189
400 436.9596 -357.24661 57.161471 115.41032 2307.0158
SHAKE stats (type/ave/delta/count) on step 500
1 2.00000 4.02911e-07 192
1 328.410 5.78945e-05 64
500 480.93505 -378.08914 36.268541 115.49016 2822.245
600 457.38144 -381.99241 62.732739 115.65446 -387.65505
700 488.20801 -393.89265 45.144482 115.47829 3086.2987
800 463.5234 -384.28682 59.826927 116.2945 3310.9691
900 500.48024 -424.35693 64.621298 116.16022 -612.4406
SHAKE stats (type/ave/delta/count) on step 1000
1 2.00000 8.21157e-07 192
1 328.410 5.79572e-05 64
1000 522.3905 -424.85292 44.232122 116.10905 3948.1535
1100 466.7856 -395.03916 67.204265 116.02145 2555.2069
1200 505.58079 -424.30563 59.681049 116.12127 1919.2701
1300 510.78441 -418.28838 48.398524 115.804 3476.7443
1400 494.39282 -407.60176 52.9665 115.47219 2343.5129
SHAKE stats (type/ave/delta/count) on step 1500
1 2.00000 7.21617e-07 192
1 328.410 8.01168e-05 64
1500 533.48096 -444.9571 53.263393 115.58182 1055.8053
1600 548.84084 -449.81134 43.134527 115.20409 3084.0678
1700 522.65205 -419.10648 37.279839 115.1519 1813.2589
1800 497.72839 -403.88156 45.774501 115.17212 1822.8113
1900 535.04509 -434.52042 40.685094 114.9275 4216.4353
SHAKE stats (type/ave/delta/count) on step 2000
1 2.00000 1.03652e-06 192
1 328.410 5.49305e-05 64
2000 540.42903 -436.41996 37.284032 114.74637 1422.0078
2100 534.80707 -439.51681 46.068646 115.08833 1460.2864
2200 507.8413 -419.62464 51.912776 115.18345 3790.8003
2300 553.37305 -456.23124 45.592723 115.55197 515.72888
2400 538.60716 -447.65657 51.130476 115.62382 2087.6217
SHAKE stats (type/ave/delta/count) on step 2500
1 2.00000 6.38759e-07 192
1 328.410 5.54712e-05 64
2500 507.38323 -436.58125 69.949293 115.8278 3313.9095
Loop time of 2.62759 on 4 procs for 2500 steps with 384 atoms
Performance: 82.205 ns/day, 0.292 hours/ns, 951.443 timesteps/s
93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1769 | 1.3595 | 1.5961 | 13.1 | 51.74
Bond | 0.0040634 | 0.0042451 | 0.0044163 | 0.2 | 0.16
Kspace | 0.37643 | 0.62177 | 0.8124 | 20.0 | 23.66
Neigh | 0.35517 | 0.35603 | 0.35688 | 0.1 | 13.55
Comm | 0.15521 | 0.16781 | 0.18101 | 2.8 | 6.39
Output | 0.00039921 | 0.00083364 | 0.0018058 | 0.0 | 0.03
Modify | 0.081231 | 0.095032 | 0.10957 | 3.5 | 3.62
Other | | 0.02238 | | | 0.85
Nlocal: 96.0000 ave 105 max 84 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 3764.00 ave 3776 max 3755 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 32527.2 ave 34260 max 29030 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 130109
Ave neighs/atom = 338.82552
Ave special neighs/atom = 2.0000000
Neighbor list builds = 321
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data molecular-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
scanning dihedrals ...
2 = max dihedrals/atom
reading bonds ...
3072 bonds
reading angles ...
3072 angles
reading dihedrals ...
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.74 | 10.74 | 10.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
Loop time of 15.6807 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.020 ns/day, 2.178 hours/ns, 127.545 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.196 | 14.196 | 14.196 | 0.0 | 90.53
Bond | 0.58712 | 0.58712 | 0.58712 | 0.0 | 3.74
Neigh | 0.6978 | 0.6978 | 0.6978 | 0.0 | 4.45
Comm | 0.082724 | 0.082724 | 0.082724 | 0.0 | 0.53
Output | 0.00052338 | 0.00052338 | 0.00052338 | 0.0 | 0.00
Modify | 0.078892 | 0.078892 | 0.078892 | 0.0 | 0.50
Other | | 0.0374 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11633.0 ave 11633 max 11633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770365.0 ave 770365 max 770365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770365
Ave neighs/atom = 198.95790
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data molecular-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
scanning dihedrals ...
2 = max dihedrals/atom
reading bonds ...
3072 bonds
reading angles ...
3072 angles
reading dihedrals ...
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.039 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.101 | 8.197 | 8.483 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
400 302 -4951.4895 1664.5419 197.74463 10784.638
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
Loop time of 4.33662 on 4 procs for 2000 steps with 3872 atoms
Performance: 39.847 ns/day, 0.602 hours/ns, 461.188 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6239 | 3.6669 | 3.7143 | 1.8 | 84.56
Bond | 0.14954 | 0.15355 | 0.15614 | 0.7 | 3.54
Neigh | 0.17931 | 0.17933 | 0.17934 | 0.0 | 4.14
Comm | 0.23604 | 0.28181 | 0.32663 | 6.5 | 6.50
Output | 0.00034802 | 0.00069388 | 0.0017292 | 0.0 | 0.02
Modify | 0.029915 | 0.036141 | 0.039601 | 1.9 | 0.83
Other | | 0.01821 | | | 0.42
Nlocal: 968.000 ave 979 max 948 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6321.25 ave 6336 max 6309 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 192540.0 ave 195406 max 187182 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 770161
Ave neighs/atom = 198.90522
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
restoring atom style molecular from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.008 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.74 | 10.74 | 10.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
Loop time of 15.5879 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.086 ns/day, 2.165 hours/ns, 128.305 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.116 | 14.116 | 14.116 | 0.0 | 90.56
Bond | 0.58742 | 0.58742 | 0.58742 | 0.0 | 3.77
Neigh | 0.68543 | 0.68543 | 0.68543 | 0.0 | 4.40
Comm | 0.082574 | 0.082574 | 0.082574 | 0.0 | 0.53
Output | 0.00054698 | 0.00054698 | 0.00054698 | 0.0 | 0.00
Modify | 0.078446 | 0.078446 | 0.078446 | 0.0 | 0.50
Other | | 0.03761 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11633.0 ave 11633 max 11633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770365.0 ave 770365 max 770365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770365
Ave neighs/atom = 198.95790
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:697)
restoring atom style molecular from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_restart CPU = 0.031 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.101 | 8.197 | 8.483 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
400 302 -4951.4895 1664.5419 197.74463 10784.638
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
Loop time of 5.2142 on 4 procs for 2000 steps with 3872 atoms
Performance: 33.140 ns/day, 0.724 hours/ns, 383.568 timesteps/s
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5706 | 3.6724 | 3.7809 | 4.9 | 70.43
Bond | 0.14654 | 0.1524 | 0.15708 | 1.2 | 2.92
Neigh | 0.18217 | 0.1822 | 0.18221 | 0.0 | 3.49
Comm | 0.74346 | 0.8715 | 0.9808 | 10.9 | 16.71
Output | 0.00034776 | 0.00084716 | 0.0023413 | 0.0 | 0.02
Modify | 0.12457 | 0.18985 | 0.31013 | 17.4 | 3.64
Other | | 0.145 | | | 2.78
Nlocal: 968.000 ave 979 max 948 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6321.25 ave 6336 max 6309 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 192540.0 ave 195406 max 187182 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 770161
Ave neighs/atom = 198.90522
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.003 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
100 0 -4351.8383 516.49891 -3835.3394 11635.037
190 0 -6191.8175 457.61209 -5734.2054 4365.373
Loop time of 3.46057 on 1 procs for 190 steps with 3872 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
43897850768892.8 -5729.17187196146 -5734.20542785978
Force two-norm initial, final = 1.1080994e+15 72.746805
Force max component initial, final = 4.6607099e+14 17.394645
Final line search alpha, max atom move = 0.0041634525 0.072421779
Iterations, force evaluations = 190 297
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0573 | 3.0573 | 3.0573 | 0.0 | 88.35
Bond | 0.10271 | 0.10271 | 0.10271 | 0.0 | 2.97
Neigh | 0.26654 | 0.26654 | 0.26654 | 0.0 | 7.70
Comm | 0.013532 | 0.013532 | 0.013532 | 0.0 | 0.39
Output | 3.3796e-05 | 3.3796e-05 | 3.3796e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02041 | | | 0.59
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12122.0 ave 12122 max 12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 774375.0 ave 774375 max 774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6191.8175 457.61209 -4580.3339 4842.3161
100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039
200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994
300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162
400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751
500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441
600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853
700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226
800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079
900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364
1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001
1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527
1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591
1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876
1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713
1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559
1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277
1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124
1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491
1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722
2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769
2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807
2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183
2300 278.05084 -5053.818 1495.944 -349.52438 10299.97
2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877
2500 302.37248 -4957.687 1700.6563 231.95939 10617.134
Loop time of 18.6761 on 1 procs for 2500 steps with 3872 atoms
Performance: 11.566 ns/day, 2.075 hours/ns, 133.861 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.06 | 17.06 | 17.06 | 0.0 | 91.35
Bond | 0.73068 | 0.73068 | 0.73068 | 0.0 | 3.91
Neigh | 0.63671 | 0.63671 | 0.63671 | 0.0 | 3.41
Comm | 0.10272 | 0.10272 | 0.10272 | 0.0 | 0.55
Output | 0.00064976 | 0.00064976 | 0.00064976 | 0.0 | 0.00
Modify | 0.098028 | 0.098028 | 0.098028 | 0.0 | 0.52
Other | | 0.04742 | | | 0.25
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11793.0 ave 11793 max 11793 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770411.0 ave 770411 max 770411 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770411
Ave neighs/atom = 198.96978
Ave special neighs/atom = 3.9669421
Neighbor list builds = 33
Dangerous builds = 0
write_data molecular-mix.data
System init for write_data ...
Total wall time: 0:00:22

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.011 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
100 0 -3410.6986 572.28283 -2838.4158 14603.831
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
204 0 -6137.0238 483.14639 -5653.8774 4952.4081
Loop time of 1.10481 on 4 procs for 204 steps with 3872 atoms
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.54300441078755e+16 -5648.75822692028 -5653.87742448419
Force two-norm initial, final = 8.7430661e+18 74.636845
Force max component initial, final = 4.1468626e+18 8.6800755
Final line search alpha, max atom move = 0.0032186736 0.02793833
Iterations, force evaluations = 204 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.89902 | 0.90561 | 0.90821 | 0.4 | 81.97
Bond | 0.029749 | 0.030411 | 0.031345 | 0.4 | 2.75
Neigh | 0.088655 | 0.088662 | 0.088666 | 0.0 | 8.03
Comm | 0.063187 | 0.068096 | 0.070678 | 1.1 | 6.16
Output | 4.8304e-05 | 0.00011426 | 0.00031124 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01191 | | | 1.08
Nlocal: 968.000 ave 980 max 954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 6630.00 ave 6644 max 6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 193550.0 ave 195957 max 191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6137.0238 483.14639 -4500.0059 5429.3513
100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924
200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637
300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525
400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877
500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965
600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406
700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188
800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425
900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018
1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688
1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754
1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58
1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311
1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773
1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161
1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26
1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606
1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089
1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027
2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833
2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961
2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443
2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176
2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
Loop time of 5.954 on 4 procs for 2500 steps with 3872 atoms
Performance: 36.278 ns/day, 0.662 hours/ns, 419.886 timesteps/s
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4642 | 4.6298 | 4.8946 | 7.5 | 77.76
Bond | 0.18992 | 0.19849 | 0.20566 | 1.3 | 3.33
Neigh | 0.18926 | 0.18928 | 0.18929 | 0.0 | 3.18
Comm | 0.56456 | 0.82727 | 1.0096 | 17.9 | 13.89
Output | 0.00044023 | 0.00092791 | 0.0020343 | 0.0 | 0.02
Modify | 0.077974 | 0.080378 | 0.082874 | 0.8 | 1.35
Other | | 0.02782 | | | 0.47
Nlocal: 968.000 ave 989 max 944 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 6381.50 ave 6416 max 6351 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 192557.0 ave 197456 max 188754 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 770229
Ave neighs/atom = 198.92278
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
write_data molecular-mix.data
System init for write_data ...
Total wall time: 0:00:07

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.001 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.050 | 8.050 | 8.050 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
100 0 -4351.8383 516.49891 -3835.3394 11635.037
190 0 -6191.8175 457.61209 -5734.2054 4365.373
Loop time of 3.4619 on 1 procs for 190 steps with 3872 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
43897850768892.8 -5729.17187196146 -5734.20542785978
Force two-norm initial, final = 1.1080994e+15 72.746805
Force max component initial, final = 4.6607099e+14 17.394645
Final line search alpha, max atom move = 0.0041634525 0.072421779
Iterations, force evaluations = 190 297
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0549 | 3.0549 | 3.0549 | 0.0 | 88.24
Bond | 0.10344 | 0.10344 | 0.10344 | 0.0 | 2.99
Neigh | 0.2695 | 0.2695 | 0.2695 | 0.0 | 7.78
Comm | 0.013772 | 0.013772 | 0.013772 | 0.0 | 0.40
Output | 3.3707e-05 | 3.3707e-05 | 3.3707e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02027 | | | 0.59
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12122.0 ave 12122 max 12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 774375.0 ave 774375 max 774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6191.8175 457.61209 -4580.3339 4842.3161
100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039
200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994
300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162
400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751
500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441
600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853
700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226
800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079
900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364
1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001
1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527
1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591
1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876
1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713
1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559
1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277
1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124
1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491
1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722
2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769
2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807
2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183
2300 278.05084 -5053.818 1495.944 -349.52438 10299.97
2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877
2500 302.37248 -4957.687 1700.6563 231.95939 10617.134
Loop time of 18.7845 on 1 procs for 2500 steps with 3872 atoms
Performance: 11.499 ns/day, 2.087 hours/ns, 133.089 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.14 | 17.14 | 17.14 | 0.0 | 91.25
Bond | 0.74217 | 0.74217 | 0.74217 | 0.0 | 3.95
Neigh | 0.65005 | 0.65005 | 0.65005 | 0.0 | 3.46
Comm | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.55
Output | 0.0006739 | 0.0006739 | 0.0006739 | 0.0 | 0.00
Modify | 0.099647 | 0.099647 | 0.099647 | 0.0 | 0.53
Other | | 0.04816 | | | 0.26
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11793.0 ave 11793 max 11793 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770411.0 ave 770411 max 770411 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770411
Ave neighs/atom = 198.96978
Ave special neighs/atom = 3.9669421
Neighbor list builds = 33
Dangerous builds = 0
write_data template-mix.data
System init for write_data ...
Total wall time: 0:00:22

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.001 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.345 | 5.441 | 5.728 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
100 0 -3410.6986 572.28283 -2838.4158 14603.831
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
204 0 -6137.0238 483.14639 -5653.8774 4952.4081
Loop time of 1.08919 on 4 procs for 204 steps with 3872 atoms
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.54300441078755e+16 -5648.75822692028 -5653.87742448419
Force two-norm initial, final = 8.7430661e+18 74.636845
Force max component initial, final = 4.1468626e+18 8.6800755
Final line search alpha, max atom move = 0.0032186736 0.02793833
Iterations, force evaluations = 204 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.8748 | 0.88765 | 0.9004 | 1.2 | 81.50
Bond | 0.029354 | 0.029865 | 0.030434 | 0.2 | 2.74
Neigh | 0.07699 | 0.077483 | 0.077966 | 0.2 | 7.11
Comm | 0.072926 | 0.084481 | 0.097433 | 3.8 | 7.76
Output | 4.7316e-05 | 0.00010999 | 0.00029778 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009602 | | | 0.88
Nlocal: 968.000 ave 980 max 954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 6630.00 ave 6644 max 6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 193550.0 ave 195957 max 191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 4.220 | 4.507 | 4.603 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6137.0238 483.14639 -4500.0059 5429.3513
100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924
200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637
300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525
400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877
500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965
600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406
700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188
800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425
900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018
1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688
1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754
1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58
1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311
1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773
1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161
1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26
1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606
1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089
1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027
2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833
2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961
2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443
2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176
2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
Loop time of 5.70106 on 4 procs for 2500 steps with 3872 atoms
Performance: 37.888 ns/day, 0.633 hours/ns, 438.515 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4476 | 4.5874 | 4.9593 | 10.1 | 80.47
Bond | 0.18485 | 0.19038 | 0.19543 | 0.9 | 3.34
Neigh | 0.18057 | 0.18059 | 0.18062 | 0.0 | 3.17
Comm | 0.30256 | 0.67081 | 0.81456 | 26.1 | 11.77
Output | 0.00042399 | 0.00053327 | 0.00085633 | 0.0 | 0.01
Modify | 0.035251 | 0.043755 | 0.052209 | 4.0 | 0.77
Other | | 0.02758 | | | 0.48
Nlocal: 968.000 ave 989 max 944 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 6381.50 ave 6416 max 6351 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 192557.0 ave 197456 max 188754 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 770229
Ave neighs/atom = 198.92278
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
write_data template-mix.data
System init for write_data ...
Total wall time: 0:00:06

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data template-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
3072 template bonds
3072 template angles
3072 template dihedrals
read_data CPU = 0.016 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.879 | 6.879 | 6.879 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
Loop time of 15.3795 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.236 ns/day, 2.136 hours/ns, 130.043 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.905 | 13.905 | 13.905 | 0.0 | 90.41
Bond | 0.58069 | 0.58069 | 0.58069 | 0.0 | 3.78
Neigh | 0.69766 | 0.69766 | 0.69766 | 0.0 | 4.54
Comm | 0.08196 | 0.08196 | 0.08196 | 0.0 | 0.53
Output | 0.00052444 | 0.00052444 | 0.00052444 | 0.0 | 0.00
Modify | 0.077644 | 0.077644 | 0.077644 | 0.0 | 0.50
Other | | 0.03568 | | | 0.23
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11633.0 ave 11633 max 11633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770365.0 ave 770365 max 770365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770365
Ave neighs/atom = 198.95790
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data template-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
3072 template bonds
3072 template angles
3072 template dihedrals
read_data CPU = 0.022 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.193 | 4.289 | 4.575 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
400 302 -4951.4895 1664.5419 197.74463 10784.638
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
Loop time of 4.67813 on 4 procs for 2000 steps with 3872 atoms
Performance: 36.938 ns/day, 0.650 hours/ns, 427.522 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5547 | 3.689 | 3.8706 | 5.9 | 78.86
Bond | 0.14554 | 0.15424 | 0.1658 | 2.0 | 3.30
Neigh | 0.19598 | 0.19599 | 0.19599 | 0.0 | 4.19
Comm | 0.39992 | 0.57068 | 0.7172 | 14.9 | 12.20
Output | 0.00034507 | 0.00063055 | 0.0014842 | 0.0 | 0.01
Modify | 0.036995 | 0.043513 | 0.048096 | 2.0 | 0.93
Other | | 0.02411 | | | 0.52
Nlocal: 968.000 ave 979 max 948 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6321.25 ave 6336 max 6309 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 192540.0 ave 195406 max 187182 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 770161
Ave neighs/atom = 198.90522
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:04

102
examples/template/log.22Oct20.tmpl-restart-mix.g++.1 Normal file
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@ -0,0 +1,102 @@
LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:697)
restoring atom style template from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.002 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.879 | 6.879 | 6.879 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
2600 303.69861 -4872.1658 1620.5986 252.72467 8824.1501
2700 304.64827 -4885.5903 1747.1956 376.85504 11560.748
2800 298.79617 -4851.2752 1644.5913 241.04014 9198.1133
2900 302.323 -4949.4247 1661.0637 200.05824 10788.039
3000 302.8192 -4983.7441 1617.1412 127.5418 9606.2027
3100 305.27495 -4999.5335 1589.7081 112.65547 9258.8096
3200 294.9932 -4960.8253 1650.5396 93.556955 11103.25
3300 299.8705 -4896.6757 1711.6029 275.0477 8404.2758
3400 308.43113 -5035.583 1732.7837 256.09989 11520.651
3500 302.54 -4887.2016 1770.4336 374.15506 8359.8351
3600 294.00064 -5011.409 1768.0298 149.01058 11257.53
3700 303.26654 -4942.0636 1690.4493 247.69209 8749.4281
3800 294.7064 -5009.5839 1638.6276 29.577045 10460.396
3900 300.34826 -5011.778 1699.4384 153.29355 9558.3891
4000 298.76709 -5014.8089 1613.1902 45.769836 9254.1067
4100 297.77294 -4978.3228 1736.8967 194.49122 10810.757
4200 302.14768 -5049.4356 1713.0187 149.97929 8258.5093
4300 295.1467 -5094.2287 1757.8215 69.206733 11022.023
4400 305.24677 -4967.1951 1762.3252 317.28577 8423.2256
4500 305.53119 -5047.7285 1775.2795 252.98852 11178.338
Loop time of 15.3536 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.255 ns/day, 2.132 hours/ns, 130.263 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.88 | 13.88 | 13.88 | 0.0 | 90.40
Bond | 0.58065 | 0.58065 | 0.58065 | 0.0 | 3.78
Neigh | 0.69518 | 0.69518 | 0.69518 | 0.0 | 4.53
Comm | 0.0826 | 0.0826 | 0.0826 | 0.0 | 0.54
Output | 0.00053438 | 0.00053438 | 0.00053438 | 0.0 | 0.00
Modify | 0.07779 | 0.07779 | 0.07779 | 0.0 | 0.51
Other | | 0.03687 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11670.0 ave 11670 max 11670 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770032.0 ave 770032 max 770032 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770032
Ave neighs/atom = 198.87190
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

101
examples/template/log.22Oct20.tmpl-restart-mix.g++.4 Normal file
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@ -0,0 +1,101 @@
LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
restoring atom style template from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.006 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.193 | 4.289 | 4.575 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
2600 303.6986 -4872.1658 1620.5986 252.72458 8824.1501
2700 296.80713 -4884.3012 1753.5243 293.99628 11523.482
2800 298.88856 -4849.1995 1639.5709 239.1615 9214.1261
2900 297.12578 -4949.9958 1657.7582 136.2123 10727.69
3000 298.19234 -4984.9797 1618.0356 73.812582 9576.9074
3100 301.54182 -4999.9775 1588.997 68.424766 9225.9502
3200 294.07259 -4962.8351 1646.3012 76.686125 11080.923
3300 303.55697 -4900.0696 1721.4077 323.99573 8433.7992
3400 297.80636 -5036.3758 1735.0734 135.00054 11440.101
3500 303.96121 -4882.4297 1757.4268 382.31908 8497.7685
3600 298.21153 -5006.6599 1759.9584 194.27658 11184.938
3700 300.77921 -4941.495 1688.3988 217.50964 8820.5666
3800 294.33206 -5011.7746 1653.7511 38.190478 10418.208
3900 304.38175 -5004.4071 1719.9139 227.68132 9632.0557
4000 302.44152 -5029.0544 1610.1577 70.889929 9237.6379
4100 298.82638 -4971.4109 1755.8272 232.48883 10814.056
4200 297.77273 -5040.0028 1718.5112 114.42322 8287.605
4300 300.50984 -5082.4128 1742.354 127.43881 11003.298
4400 310.02885 -4971.4191 1749.1209 355.03646 8502.7004
4500 302.62639 -5033.3284 1753.488 212.07956 11150.514
Loop time of 4.39645 on 4 procs for 2000 steps with 3872 atoms
Performance: 39.304 ns/day, 0.611 hours/ns, 454.913 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6185 | 3.6709 | 3.7028 | 1.7 | 83.50
Bond | 0.14772 | 0.15338 | 0.1621 | 1.5 | 3.49
Neigh | 0.17739 | 0.17747 | 0.17756 | 0.0 | 4.04
Comm | 0.29637 | 0.33265 | 0.39131 | 6.7 | 7.57
Output | 0.00034028 | 0.0006627 | 0.0016284 | 0.0 | 0.02
Modify | 0.039076 | 0.041988 | 0.043469 | 0.9 | 0.96
Other | | 0.01937 | | | 0.44
Nlocal: 968.000 ave 977 max 956 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 6322.75 ave 6345 max 6308 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 192555.0 ave 195249 max 188636 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 770221
Ave neighs/atom = 198.92071
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
Total wall time: 0:00:04

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examples/template/molecular-mix.data Normal file
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4
lib/kokkos/README.md
View File

@ -18,7 +18,7 @@ profiling and debugging tools (https://github.com/kokkos/kokkos-tools).
A programming guide can be found on the Wiki, the API reference is under development.
For questions find us on Slack: https://kokkosteam.slack.com or open a github issue.
For questions find us on Slack: https://kokkosteam.slack.com or open a GitHub issue.
For non-public questions send an email to
crtrott(at)sandia.gov
@ -44,7 +44,7 @@ To learn more about Kokkos consider watching one of our presentations:
We are open and try to encourage contributions from external developers.
To do so please first open an issue describing the contribution and then issue
a pull request against the develop branch. For larger features it may be good
to get guidance from the core development team first through the github issue.
to get guidance from the core development team first through the GitHub issue.
Note that Kokkos Core is licensed under standard 3-clause BSD terms of use.
Which means contributing to Kokkos allows anyone else to use your contributions

2
lib/quip/README
View File

@ -17,7 +17,7 @@ Building LAMMPS with QUIP support:
1) Building QUIP
1.1) Obtaining QUIP
The most current release of QUIP can be obtained from github:
The most current release of QUIP can be obtained from GitHub:
$ git clone https://github.com/libAtoms/QUIP.git QUIP

2
lib/scafacos/README
View File

@ -3,7 +3,7 @@ is required to use the KSPACE scafacos and its kspace_style
scafacos command in a LAMMPS input script.
The ScaFaCoS library is available at http://scafacos.de or
on github at https://github.com/scafacos, the library was
on GitHub at https://github.com/scafacos, the library was
developed by a consortium of different universities in
Germany (Bonn, Chemnitz, Stuttgart, Wuppertal) and
the Research Centre Juelich (Juelich Supercomputing Centre).

2
src/CLASS2/pair_lj_class2.cpp
View File

@ -35,7 +35,7 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
writedata = 1;
centroidstressflag = 1;
centroidstressflag = CENTROID_SAME;
}
/* ---------------------------------------------------------------------- */

2
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -33,7 +33,7 @@ using namespace MathConst;
PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
centroidstressflag = 1;
centroidstressflag = CENTROID_SAME;
}
/* ---------------------------------------------------------------------- */

1
src/Depend.sh
View File

@ -107,6 +107,7 @@ if (test $1 = "PERI") then
fi
if (test $1 = "RIGID") then
depend KOKKOS
depend USER-OMP
depend USER-SDPD
fi

2
src/GRANULAR/pair_gran_hooke_history.cpp
View File

@ -34,7 +34,6 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -43,6 +42,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 1;
no_virial_fdotr_compute = 1;
centroidstressflag = CENTROID_NOTAVAIL;
history = 1;
size_history = 3;

20
src/GRANULAR/pair_granular.cpp
View File

@ -66,6 +66,7 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 1;
no_virial_fdotr_compute = 1;
centroidstressflag = CENTROID_NOTAVAIL;
single_extra = 12;
svector = new double[single_extra];
@ -1102,15 +1103,8 @@ void PairGranular::init_style()
// this is so its order in the fix list is preserved
if (use_history && fix_history == nullptr) {
char dnumstr[16];
sprintf(dnumstr,"%d",size_history);
char **fixarg = new char*[4];
fixarg[0] = (char *) "NEIGH_HISTORY_GRANULAR";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "NEIGH_HISTORY";
fixarg[3] = dnumstr;
modify->replace_fix("NEIGH_HISTORY_GRANULAR_DUMMY",4,fixarg,1);
delete [] fixarg;
modify->replace_fix("NEIGH_HISTORY_GRANULAR_DUMMY","NEIGH_HISTORY_GRANULAR"
" all NEIGH_HISTORY " + std::to_string(size_history),1);
int ifix = modify->find_fix("NEIGH_HISTORY_GRANULAR");
fix_history = (FixNeighHistory *) modify->fix[ifix];
fix_history->pair = this;
@ -1405,11 +1399,15 @@ double PairGranular::single(int i, int j, int itype, int jtype,
int *jlist;
double *history,*allhistory;
int nall = atom->nlocal + atom->nghost;
if ((i >= nall) || (j >= nall))
error->all(FLERR,"Not enough atoms for pair granular single function");
double *radius = atom->radius;
radi = radius[i];
radj = radius[j];
radsum = radi + radj;
Reff = radi*radj/radsum;
Reff = (radsum > 0.0) ? radi*radj/radsum : 0.0;
bool touchflag;
E = normal_coeffs[itype][jtype][0];
@ -1536,6 +1534,8 @@ double PairGranular::single(int i, int j, int itype, int jtype,
jlist = list->firstneigh[i];
if (use_history) {
if ((fix_history == nullptr) || (fix_history->firstvalue == nullptr))
error->one(FLERR,"Pair granular single computation needs history");
allhistory = fix_history->firstvalue[i];
for (int jj = 0; jj < jnum; jj++) {
neighprev++;

6
src/KIM/kim_interactions.cpp
View File

@ -185,6 +185,9 @@ void KimInteractions::do_setup(int narg, char **arg)
KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel,i,&sim_lines,&sim_field);
if (0 == strcmp(sim_field,"model-defn")) {
if (domain->periodicity[0]&&domain->periodicity[1]&&domain->periodicity[2]) input->one("variable kim_periodic equal 1");
else if (domain->periodicity[0]&&domain->periodicity[1]&&!domain->periodicity[2]) input->one("variable kim_periodic equal 2");
else input->one("variable kim_periodic equal 0");
sim_model_idx = i;
for (int j=0; j < sim_lines; ++j) {
KIM_SimulatorModel_GetSimulatorFieldLine(
@ -276,7 +279,6 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
ptr = line;
nocomment = line[0] != '#';
if(nocomment) {
@ -286,7 +288,7 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con
for (int ib = ia; ib < atom->ntypes; ++ib)
if (((species[ia] == words[0]) && (species[ib] == words[1]))
|| ((species[ib] == words[0]) && (species[ia] == words[1])))
input->one(fmt::format("pair_coeff {} {} {}",ia+1,ib+1,words[2]));
input->one(fmt::format("pair_coeff {} {} {}",ia+1,ib+1,fmt::join(words.begin()+2,words.end()," ")));
}
} else if (key == "charge") {
for (int ia = 0; ia < atom->ntypes; ++ia)

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