jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' into exchange-biquadratic

This commit is contained in:
Richard Berger 2020-11-12 10:39:10 -05:00
parent df672fe7d4 b3181a1fa3
commit 724a9978c8
No known key found for this signature in database
GPG Key ID: A9E83994E0BA0CAB
118 changed files with 32328 additions and 1597 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.github/CONTRIBUTING.md vendored
View File

@ -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
View File

@ -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)

4
cmake/Modules/Tools.cmake
View File

@ -50,8 +50,8 @@ if(BUILD_LAMMPS_SHELL)
endif()
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
install(DIRECTORY icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
install(FILES lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
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
View File

@ -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)

12
doc/Makefile
View File

@ -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
View File

@ -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
View File

@ -1,4 +1,4 @@
.TH LAMMPS "22 October 2020" "2020-10-22"
.TH LAMMPS "29 October 2020" "2020-10-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

6
doc/src/Build_development.rst
View File

@ -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
View File

@ -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:

1
doc/src/Errors_warnings.rst
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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

26
doc/src/Manual.rst
View File

@ -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/atc_output.rst
View File

@ -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
View File

@ -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::

2
doc/src/create_atoms.rst
View File

@ -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

2
doc/src/fix_filter_corotate.rst
View File

@ -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.
----------

4
doc/src/fix_rx.rst
View File

@ -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

10
doc/src/molecule.rst
View File

@ -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
@ -484,9 +484,7 @@ 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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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

2
doc/src/pair_srp.rst
View File

@ -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

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
View File

@ -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">

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -2615,7 +2615,6 @@ Ree
refactored
refactoring
reflectionstyle
regoin
Reinders
reinit
relaxbox

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

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
View File

@ -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
28 1 -4.839301125374413 -0.3224292196811998 9.864502598955395 10 1 1 -0.8472 0 0 -1
29 2 -4.437095111731628 0.2761002399087885 -9.442706303026958 10 1 2 0.4236 0 0 0
30 2 -5.723603762893959 0.04632897977241136 9.578203704071562 10 1 3 0.4236 0 0 -1
31 1 0.3575211513985558 0.13924369294039318 -9.96943701619651 11 1 1 -0.8472 0 0 0
32 2 -0.15738037709944985 -0.29662855771206287 -9.231291709389254 11 1 2 0.4236 0 0 0
33 2 -0.20014077429910587 0.1573848647716694 9.200728725585764 11 1 3 0.4236 0 0 -1
34 1 4.945607877161568 0.17822976107332558 -9.663221252242849 12 1 1 -0.8472 0 0 0
35 2 5.686261102802035 -0.4628832126235319 -9.864153208899683 12 1 2 0.4236 0 0 0
36 2 4.368131020036397 0.284653451550206 9.527374461142534 12 1 3 0.4236 0 0 -1
37 1 9.834131265901467 5.002816508870191 -9.652690475186276 13 1 1 -0.8472 -1 0 0
38 2 -9.523525531039581 4.309893511844079 -9.980134556788492 13 1 2 0.4236 0 0 0
39 2 9.689394265138116 5.68728997928573 9.63282503197477 13 1 3 0.4236 -1 0 -1
40 1 -4.896522832471423 4.844697230053857 -9.6633729049121 14 1 1 -0.8472 0 0 0
41 2 -5.719481843054487 5.391203391339132 -9.818408963548082 14 1 2 0.4236 0 0 0
42 2 -4.383995324474091 4.764099378607011 9.481781868460182 14 1 3 0.4236 0 0 -1
43 1 0.08644475731548724 4.625177647828908 -9.986591646424854 15 1 1 -0.8472 0 0 0
44 2 0.483199632298402 5.33056133050579 -9.399236450405876 15 1 2 0.4236 0 0 0
45 2 -0.5696443896138887 5.044261021665302 9.38582809683073 15 1 3 0.4236 0 0 -1
46 1 5.279904505775219 4.8738580855036995 9.767866502301072 16 1 1 -0.8472 0 0 -1
47 2 5.051646557564443 5.834165665231483 9.928098703484146 16 1 2 0.4236 0 0 -1
48 2 4.6684489366603374 4.291976249264819 -9.695965205785217 16 1 3 0.4236 0 0 0
49 1 9.908445669769623 9.636632008310487 -4.912103567014368 17 1 1 -0.8472 -1 -1 0
50 2 -9.305514433129819 -9.862297561377305 -4.550114063115585 17 1 2 0.4236 0 0 0
51 2 9.397068763360195 -9.774334446933182 -5.537782369870047 17 1 3 0.4236 -1 0 0
52 1 -5.201907594124834 -9.68877920222961 -5.102563220356437 18 1 1 -0.8472 0 0 0
53 2 -4.940302726022812 9.565133612451614 -5.714840528272083 18 1 2 0.4236 0 -1 0
54 2 -4.857789679852353 -9.876354410222005 -4.182596251371481 18 1 3 0.4236 0 0 0
55 1 0.37327634941779875 -9.91440084751388 -4.961505484040201 19 1 1 -0.8472 0 0 0
56 2 -0.024482580199505652 9.563262486125167 -5.715772636834634 19 1 2 0.4236 0 -1 0
57 2 -0.34879376921829297 -9.648861638611287 -4.322721879125167 19 1 3 0.4236 0 0 0
58 1 5.099017423466195 9.70150361815792 -4.778099717040957 20 1 1 -0.8472 0 -1 0
59 2 5.136067712418359 9.715462771782358 -5.77729895393951 20 1 2 0.4236 0 -1 0
60 2 4.764914864115446 -9.416966389940278 -4.444601329019534 20 1 3 0.4236 0 0 0
61 1 9.67209962879851 -5.197853819118096 -5.0384641199861475 21 1 1 -0.8472 -1 0 0
62 2 9.738936599885 -4.205377815142725 -4.936039036490629 21 1 2 0.4236 -1 0 0
63 2 -9.41103622868351 -5.5967683657391785 -5.025496843523223 21 1 3 0.4236 0 0 0
64 1 -4.689795490189235 -5.165487837213749 -4.843375565356555 22 1 1 -0.8472 0 0 0
65 2 -4.832160266019467 -5.015491947934958 -5.82174165261749 22 1 2 0.4236 0 0 0
66 2 -5.478044243791298 -4.819020214851294 -4.334882782025955 22 1 3 0.4236 0 0 0
67 1 -0.0615634035841769 -4.677472055633765 -5.200823176306976 23 1 1 -0.8472 0 0 0
68 2 -0.6036354578743581 -5.514703146142694 -5.272716750031286 23 1 2 0.4236 0 0 0
69 2 0.6651988614585344 -4.807824798223541 -4.526460073661738 23 1 3 0.4236 0 0 0
70 1 4.802754604301762 -5.1046044449424395 -5.313522630242427 24 1 1 -0.8472 0 0 0
71 2 4.674742935683063 -5.484552334539641 -4.397433491136363 24 1 2 0.4236 0 0 0
72 2 5.522502460015175 -4.410843220517918 -5.28904387862121 24 1 3 0.4236 0 0 0
73 1 -9.83451039343324 -0.34326467353508094 -4.9458998177338245 25 1 1 -0.8472 0 0 0
74 2 -9.500257580872022 0.5235593797386398 -4.5759568290706625 25 1 2 0.4236 0 0 0
75 2 9.334767974305263 -0.18029470620355853 -5.478143353195513 25 1 3 0.4236 -1 0 0
76 1 -5.307686388170551 -0.09393136703842697 -4.788693917454198 26 1 1 -0.8472 0 0 0
77 2 -5.322666676950796 0.48158209129479823 -5.606328644655405 26 1 2 0.4236 0 0 0
78 2 -4.369646934878654 -0.38765072425637087 -4.604977437890398 26 1 3 0.4236 0 0 0
79 1 0.25915920502631956 0.1183661006970869 -5.258786105415057 27 1 1 -0.8472 0 0 0
80 2 0.4129987454382328 0.060712811699061064 -4.2723905503898125 27 1 2 0.4236 0 0 0
81 2 -0.6721579504645518 -0.17907891239614798 -5.46882334419513 27 1 3 0.4236 0 0 0
82 1 4.645093317547853 -0.032892978577141976 -5.145270693572841 28 1 1 -0.8472 0 0 0
83 2 5.384532151641317 -0.6939822880761514 -5.272384156276919 28 1 2 0.4236 0 0 0
84 2 4.9703745308108305 0.7268752666532926 -4.58234515015024 28 1 3 0.4236 0 0 0
85 1 -9.935887941471492 4.620929536576184 -4.981574381668706 29 1 1 -0.8472 0 0 0
86 2 -9.510577225229298 5.307736013867678 -4.392189656467925 29 1 2 0.4236 0 0 0
87 2 9.44646516670079 5.071334449556138 -5.626235961863369 29 1 3 0.4236 -1 0 0
88 1 -5.008590477951656 4.617494616944972 -5.041953680678674 30 1 1 -0.8472 0 0 0
89 2 -4.783022517847073 5.100600801092718 -4.195966560733896 30 1 2 0.4236 0 0 0
90 2 -5.2083870042012705 5.281904581962309 -5.762079758587429 30 1 3 0.4236 0 0 0
91 1 -0.10236681102215972 4.670575674519795 -5.170718849231903 31 1 1 -0.8472 0 0 0
92 2 0.6714005117953412 5.244086072416178 -5.439673586212998 31 1 2 0.4236 0 0 0
93 2 -0.569033700773181 5.085338253064027 -4.389607564555099 31 1 3 0.4236 0 0 0
94 1 4.793442916655695 4.895053625339889 -4.692648888946219 32 1 1 -0.8472 0 0 0
95 2 5.78790922296981 4.82542619694358 -4.771105779790033 32 1 2 0.4236 0 0 0
96 2 4.418647860374495 5.279520177716531 -5.536245331263747 32 1 3 0.4236 0 0 0
97 1 -9.972346516877309 9.813426641245107 0.3355144443598525 33 1 1 -0.8472 0 -1 0
98 2 9.902394946876838 9.380578255545881 -0.5571889055807204 33 1 2 0.4236 -1 -1 0
99 2 -9.930048429999529 -9.194004896790988 0.22167446122086756 33 1 3 0.4236 0 0 0
100 1 -5.055092848610487 9.62043108608943 -0.032194616393628146 34 1 1 -0.8472 0 -1 0
101 2 -4.242564100118214 -9.944998495531546 0.35627968294091067 34 1 2 0.4236 0 0 0
102 2 -5.702343051271298 -9.675432590557886 -0.3240850665472822 34 1 3 0.4236 0 0 0
103 1 -0.16422105747150104 -9.658585046539034 0.06790839076424156 35 1 1 -0.8472 0 0 0
104 2 0.24178705531724526 9.747651563696497 0.7625803609956086 35 1 2 0.4236 0 -1 0
105 2 -0.07756599784574403 9.910933482842538 -0.8304887517598495 35 1 3 0.4236 0 -1 0
106 1 5.252774480020046 -9.731538918744256 0.11035391158265477 36 1 1 -0.8472 0 0 0
107 2 4.897417222941987 -9.843232415673553 -0.8176614328409508 36 1 2 0.4236 0 0 0
108 2 4.849808297037967 9.57477133441781 0.7073075212582953 36 1 3 0.4236 0 -1 0
109 1 -9.974235357986496 -5.3824393899672485 -0.03493668449344743 37 1 1 -0.8472 0 0 0
110 2 -9.424638978370009 -4.718082489267676 -0.5414348828173003 37 1 2 0.4236 0 0 0
111 2 9.398874336356506 -4.8994781207650755 0.5763715673107472 37 1 3 0.4236 -1 0 0
112 1 -4.9279099757557 -5.3611565776237216 -0.11186255201619967 38 1 1 -0.8472 0 0 0
113 2 -4.312252322613385 -4.791643655121096 0.43273581570979314 38 1 2 0.4236 0 0 0
114 2 -5.759837701630914 -4.847199767255183 -0.3208732636935932 38 1 3 0.4236 0 0 0
115 1 -0.1760601646477313 -4.705054107276162 0.17364911312630318 39 1 1 -0.8472 0 0 0
116 2 -0.5420681618198102 -5.220988302880955 -0.6008292588839926 39 1 2 0.4236 0 0 0
117 2 0.718128326467541 -5.073957589842884 0.42718014575768887 39 1 3 0.4236 0 0 0
118 1 4.903025698266734 -5.298533854737944 0.22275052879544271 40 1 1 -0.8472 0 0 0
119 2 5.616278707356452 -4.629646152095917 0.43209733000991873 40 1 2 0.4236 0 0 0
120 2 4.480695594376815 -5.071819993166138 -0.654847858805361 40 1 3 0.4236 0 0 0
121 1 -9.873572998065784 0.3496117939501917 0.09965983349802573 41 1 1 -0.8472 0 0 0
122 2 -9.29961582738827 -0.39891518603423753 -0.23237513960458678 41 1 2 0.4236 0 0 0
123 2 9.173188825454053 0.049303392084045605 0.1327153061065609 41 1 3 0.4236 -1 0 0
124 1 -4.9726203993223415 0.3762262293330992 0.07647520858768621 42 1 1 -0.8472 0 0 0
125 2 -4.438314607446875 -0.11323391388289276 -0.6126639543332082 42 1 2 0.4236 0 0 0
126 2 -5.589064993230783 -0.2629923154502063 0.5361887457455214 42 1 3 0.4236 0 0 0
127 1 0.18831172963220283 -0.0017827385000351538 -0.33567810477653826 43 1 1 -0.8472 0 0 0
128 2 0.5388694262034436 -0.37110526230565655 0.5249477556788119 43 1 2 0.4236 0 0 0
129 2 -0.7271811558356458 0.37288800080569134 -0.18926965090227335 43 1 3 0.4236 0 0 0
130 1 5.104261929822929 -0.37049035001218517 -0.0032597910127999223 44 1 1 -0.8472 0 0 0
131 2 5.443981207967718 0.31928842752835596 0.6360857704885375 44 1 2 0.4236 0 0 0
132 2 4.451756862209354 0.05120192248382927 -0.632825979475737 44 1 3 0.4236 0 0 0
133 1 -9.716043338324948 4.963029008083921 -0.2571887162126298 45 1 1 -0.8472 0 0 0
134 2 9.633590016729197 4.245448234803103 -0.008054700350535071 45 1 2 0.4236 -1 0 0
135 2 -9.91754667840425 5.7915227571129755 0.2652434165631647 45 1 3 0.4236 0 0 0
136 1 -4.931156721648044 5.071542291899035 -0.37186903500505175 46 1 1 -0.8472 0 0 0
137 2 -4.7201838672715 5.691314393753101 0.38400112142368736 46 1 2 0.4236 0 0 0
138 2 -5.348659411080455 4.237143314347865 -0.01213208641863553 46 1 3 0.4236 0 0 0
139 1 -0.29471440691413636 4.8919898068292405 -0.22275882076466474 47 1 1 -0.8472 0 0 0
140 2 0.47778738080671596 4.311370196843371 0.03431811979582844 47 1 2 0.4236 0 0 0
141 2 -0.1830729738925793 5.796639996327388 0.1884407009688362 47 1 3 0.4236 0 0 0
142 1 5.244491723131163 4.903715118454363 -0.28124241253071613 48 1 1 -0.8472 0 0 0
143 2 5.50417215460746 5.126383429014502 0.6584126273006984 48 1 2 0.4236 0 0 0
144 2 4.251336122261378 4.969901452531135 -0.37717021476998186 48 1 3 0.4236 0 0 0
145 1 -9.75433202641418 9.779421187196018 4.802170503220012 49 1 1 -0.8472 0 -1 0
146 2 -9.650691740312444 -9.238436410716417 4.959083504652068 49 1 2 0.4236 0 0 0
147 2 9.405023766726625 9.4590152235204 5.23874599212792 49 1 3 0.4236 -1 -1 0
148 1 -5.055559152245123 9.796109196537483 5.321692394322919 50 1 1 -0.8472 0 -1 0
149 2 -4.236869822621204 -9.669811657248509 5.110803930818502 50 1 2 0.4236 0 0 0
150 2 -5.707571025133673 9.873702460711026 4.567503674858579 50 1 3 0.4236 0 -1 0
151 1 -0.3144184450941294 9.858810634406513 5.171320985661122 51 1 1 -0.8472 0 -1 0
152 2 0.615199476372441 9.80483357605659 5.535825710129903 51 1 2 0.4236 0 -1 0
153 2 -0.3007810312783112 -9.663644210463103 4.2928533042089745 51 1 3 0.4236 0 0 0
154 1 5.179923035894489 -9.84699214646902 5.303908824505562 52 1 1 -0.8472 0 0 0
155 2 4.677889877415472 9.288179903352757 5.305330541115184 52 1 2 0.4236 0 -1 0
156 2 5.142187086690039 -9.441187756883737 4.390760634379253 52 1 3 0.4236 0 0 0
157 1 -9.76115088009254 -5.067151371069817 5.294255105279205 53 1 1 -0.8472 0 0 0
158 2 9.804521478005048 -5.770185852326005 4.7311665558091125 53 1 2 0.4236 -1 0 0
159 2 9.956629402087492 -4.162662776604179 4.974578338911683 53 1 3 0.4236 -1 0 0
160 1 -4.819922322428162 -5.012318205300016 5.339947889475019 54 1 1 -0.8472 0 0 0
161 2 -4.552065575809134 -4.439732159321751 4.565115855972501 54 1 2 0.4236 0 0 0
162 2 -5.628012101762703 -5.547949635378233 5.094936254552479 54 1 3 0.4236 0 0 0
163 1 0.29966811591104 -5.191175652071799 5.147631859912588 55 1 1 -0.8472 0 0 0
164 2 0.3611846876298095 -4.438894380085313 4.491693374898662 55 1 2 0.4236 0 0 0
165 2 -0.6608528035408491 -5.369929967842888 5.36067476518875 55 1 3 0.4236 0 0 0
166 1 5.3306179671843905 -5.068017854599851 5.184958392430555 56 1 1 -0.8472 0 0 0
167 2 4.476738522756953 -4.77740396721618 5.616699240328971 56 1 2 0.4236 0 0 0
168 2 5.192643510058656 -5.15457817818397 4.198342367240475 56 1 3 0.4236 0 0 0
169 1 9.638387780386097 -0.05547861370703253 4.880404842292622 57 1 1 -0.8472 -1 0 0
170 2 -9.563668781750316 -0.5682641712421934 4.563696871357572 57 1 2 0.4236 0 0 0
171 2 9.925281001364219 0.6237427849492254 5.555898286349805 57 1 3 0.4236 -1 0 0
172 1 -4.92778155001994 -0.37347611049974844 5.058688721816523 58 1 1 -0.8472 0 0 0
173 2 -4.424197210986553 0.3841495388065775 5.4738668593592825 58 1 2 0.4236 0 0 0
174 2 -5.648021238993507 -0.010673428306828894 4.467444418824195 58 1 3 0.4236 0 0 0
175 1 -0.18546503303408043 -0.19411622829904296 4.724199551971681 59 1 1 -0.8472 0 0 0
176 2 0.12350879890318767 -0.5797357237270384 5.593566835013698 59 1 2 0.4236 0 0 0
177 2 0.06195623413089274 0.7738519520260807 4.6822336130146205 59 1 3 0.4236 0 0 0
178 1 5.024542870757014 0.35521327726870416 4.8538307458901455 60 1 1 -0.8472 0 0 0
179 2 4.467087613939382 -0.3858533028483605 4.47962404180805 60 1 2 0.4236 0 0 0
180 2 5.508369515303603 0.030640025579656158 5.666545212301804 60 1 3 0.4236 0 0 0
181 1 -9.847544046825007 4.880766990446809 5.332693473747822 61 1 1 -0.8472 0 0 0
182 2 9.515349627917418 5.644715153580236 5.230490581118248 61 1 2 0.4236 -1 0 0
183 2 -9.667805581092411 4.474517855972955 4.4368159451339295 61 1 3 0.4236 0 0 0
184 1 -4.983147898074708 4.80201241412343 4.670362019482786 62 1 1 -0.8472 0 0 0
185 2 -5.672581470726773 4.677668740177936 5.383935208826349 62 1 2 0.4236 0 0 0
186 2 -4.34427063119852 5.520318845698633 4.945702771690865 62 1 3 0.4236 0 0 0
187 1 0.07042696284035434 4.658502024966576 5.162982979642521 63 1 1 -0.8472 0 0 0
188 2 0.34620602341786555 5.544257758500404 5.536278287889138 63 1 2 0.4236 0 0 0
189 2 -0.41663298625821943 4.79724021653302 4.300738732468342 63 1 3 0.4236 0 0 0
190 1 5.127488702006002 4.733664731038008 5.246893562224226 64 1 1 -0.8472 0 0 0
191 2 4.64413754361587 5.5715868659899 5.500319784901714 64 1 2 0.4236 0 0 0
192 2 5.228373754378127 4.694748402972092 4.25278665287406 64 1 3 0.4236 0 0 0
193 3 -7.5 -7.5 -7.5 65 2 1 0.7 0 0 0
194 4 -7.363090579820503 -8.108207908322568 -8.478232564843351 65 2 2 -0.35 0 0 0
195 4 -7.636909420179497 -6.8917920916774325 -6.521767435156649 65 2 3 -0.35 0 0 0
196 3 -2.5 -7.5 -7.5 66 2 1 0.7 0 0 0
197 4 -1.9890145185459458 -8.507238712895377 -7.764507113303278 66 2 2 -0.35 0 0 0
198 4 -3.010985481454054 -6.492761287104623 -7.235492886696722 66 2 3 -0.35 0 0 0
199 3 2.5 -7.5 -7.5 67 2 1 0.7 0 0 0
200 4 1.3412381615021542 -7.520352744205465 -7.4504342109474795 67 2 2 -0.35 0 0 0
201 4 3.6587618384978455 -7.479647255794535 -7.5495657890525205 67 2 3 -0.35 0 0 0
202 3 7.5 -7.5 -7.5 68 2 1 0.7 0 0 0
203 4 8.30819917176506 -6.684226989986137 -7.33590096011495 68 2 2 -0.35 0 0 0
204 4 6.691800828234942 -8.315773010013862 -7.66409903988505 68 2 3 -0.35 0 0 0
205 3 -7.5 -2.5 -7.5 69 2 1 0.7 0 0 0
206 4 -7.042985934526503 -2.3910630732039384 -8.560599306967347 69 2 2 -0.35 0 0 0
207 4 -7.957014065473497 -2.6089369267960616 -6.4394006930326535 69 2 3 -0.35 0 0 0
208 3 -2.5 -2.5 -7.5 70 2 1 0.7 0 0 0
209 4 -2.463675404493939 -2.5978807004677122 -6.344707875800553 70 2 2 -0.35 0 0 0
210 4 -2.536324595506061 -2.4021192995322878 -8.655292124199448 70 2 3 -0.35 0 0 0
211 3 2.5 -2.5 -7.5 71 2 1 0.7 0 0 0
212 4 3.194913946357355 -2.0817981930843534 -6.670661796460253 71 2 2 -0.35 0 0 0
213 4 1.8050860536426452 -2.9182018069156466 -8.329338203539747 71 2 3 -0.35 0 0 0
214 3 7.5 -2.5 -7.5 72 2 1 0.7 0 0 0
215 4 7.892546142220834 -2.47905949037101 -8.591361086572185 72 2 2 -0.35 0 0 0
216 4 7.107453857779166 -2.52094050962899 -6.408638913427816 72 2 3 -0.35 0 0 0
217 3 -7.5 2.5 -7.5 73 2 1 0.7 0 0 0
218 4 -7.3828346282522315 1.479592808564327 -6.96088828678133 73 2 2 -0.35 0 0 0
219 4 -7.6171653717477685 3.520407191435673 -8.03911171321867 73 2 3 -0.35 0 0 0
220 3 -2.5 2.5 -7.5 74 2 1 0.7 0 0 0
221 4 -2.060468233000571 2.976742396757671 -8.461836011455233 74 2 2 -0.35 0 0 0
222 4 -2.939531766999429 2.023257603242329 -6.538163988544768 74 2 3 -0.35 0 0 0
223 3 2.5 2.5 -7.5 75 2 1 0.7 0 0 0
224 4 2.3501758165742057 3.3407716363704516 -8.28501959818577 75 2 2 -0.35 0 0 0
225 4 2.6498241834257943 1.6592283636295486 -6.71498040181423 75 2 3 -0.35 0 0 0
226 3 7.5 2.5 -7.5 76 2 1 0.7 0 0 0
227 4 6.491384484733663 2.798405737744011 -7.989130614504423 76 2 2 -0.35 0 0 0
228 4 8.508615515266337 2.201594262255989 -7.010869385495577 76 2 3 -0.35 0 0 0
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
278 4 -8.143093600185056 7.538481444597049 -3.4646500919104017 93 2 2 -0.35 0 0 0
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
281 4 -2.8237854486228446 7.809312312718537 -1.429911743611391 94 2 2 -0.35 0 0 0
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
284 4 3.21905026313534 7.538258309964428 -1.5905479557427649 95 2 2 -0.35 0 0 0
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

62
examples/template/h2o.mol Normal file
View File

@ -0,0 +1,62 @@
# 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
examples/template/in.hybrid Normal file
View File

@ -0,0 +1,29 @@
# 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
examples/template/in.mol-data-mix Normal file
View File

@ -0,0 +1,21 @@
# 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
examples/template/in.mol-restart-mix Normal file
View File

@ -0,0 +1,11 @@
# 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
examples/template/in.molecular-mix Normal file
View File

@ -0,0 +1,42 @@
# 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
examples/template/in.template-mix Normal file
View File

@ -0,0 +1,42 @@
# 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
examples/template/in.tmpl-data-mix Normal file
View File

@ -0,0 +1,21 @@
# 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
examples/template/in.tmpl-restart-mix Normal file
View File

@ -0,0 +1,11 @@
# 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
View File

@ -0,0 +1,158 @@
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

158
examples/template/log.22Oct20.hybrid.g++.4 Normal file
View File

@ -0,0 +1,158 @@
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

122
examples/template/log.22Oct20.mol-data-mix.g++.1 Normal file
View File

@ -0,0 +1,122 @@
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

122
examples/template/log.22Oct20.mol-data-mix.g++.4 Normal file
View File

@ -0,0 +1,122 @@
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

106
examples/template/log.22Oct20.mol-restart-mix.g++.1 Normal file
View File

@ -0,0 +1,106 @@
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

107
examples/template/log.22Oct20.mol-restart-mix.g++.4 Normal file
View File

@ -0,0 +1,107 @@
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

174
examples/template/log.22Oct20.molecular-mix.g++.1 Normal file
View File

@ -0,0 +1,174 @@
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

175
examples/template/log.22Oct20.molecular-mix.g++.4 Normal file
View File

@ -0,0 +1,175 @@
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

175
examples/template/log.22Oct20.template-mix.g++.1 Normal file
View File

@ -0,0 +1,175 @@
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

176
examples/template/log.22Oct20.template-mix.g++.4 Normal file
View File

@ -0,0 +1,176 @@
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

105
examples/template/log.22Oct20.tmpl-data-mix.g++.1 Normal file
View File

@ -0,0 +1,105 @@
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

105
examples/template/log.22Oct20.tmpl-data-mix.g++.4 Normal file
View File

@ -0,0 +1,105 @@
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
View File

@ -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
View File

@ -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

17011
examples/template/molecular-mix.data Normal file
View File

File diff suppressed because it is too large Load Diff

7783
examples/template/template-mix.data Normal file
View File

File diff suppressed because it is too large Load Diff

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).

19
src/GRANULAR/pair_granular.cpp
View File

@ -1102,15 +1102,8 @@ 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 +1398,15 @@ 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 +1533,8 @@ 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)

6
src/KOKKOS/comm_kokkos.cpp
View File

@ -394,6 +394,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair)
{
int iswap,n;
MPI_Request request;
DAT::tdual_xfloat_1d k_buf_tmp;
int nsize = pair->comm_forward;
KokkosBase* pairKKBase = dynamic_cast<KokkosBase*>(pair);
@ -441,11 +442,12 @@ void CommKokkos::forward_comm_pair_device(Pair *pair)
k_buf_recv_pair.modify<LMPHostType>();
k_buf_recv_pair.sync<DeviceType>();
}
} else k_buf_recv_pair = k_buf_send_pair;
k_buf_tmp = k_buf_recv_pair;
} else k_buf_tmp = k_buf_send_pair;
// unpack buffer
pairKKBase->unpack_forward_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv_pair);
pairKKBase->unpack_forward_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_tmp);
DeviceType().fence();
}
}

1
src/MISC/fix_deposit.cpp
View File

@ -718,7 +718,6 @@ void FixDeposit::options(int narg, char **arg)
error->all(FLERR,"Illegal fix deposit command");
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
int n = strlen(arg[iarg+1]) + 1;

37
src/MOLECULE/atom_vec_template.cpp
View File

@ -44,7 +44,7 @@ AtomVecTemplate::AtomVecTemplate(LAMMPS *lmp) : AtomVec(lmp)
fields_restart = (char *) "molecule molindex molatom";
fields_create = (char *) "molecule molindex molatom";
fields_data_atom = (char *) "id molecule molindex molatom type x";
fields_data_vel = (char *) "";
fields_data_vel = (char *) "id v";
setup_fields();
}
@ -64,12 +64,6 @@ void AtomVecTemplate::process_args(int narg, char **arg)
onemols = &atom->molecules[imol];
nset = atom->molecules[imol]->nset;
// error check on molecule template fields
for (int i = 0; i < nset; i++)
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Atom style template molecule must have atom types");
// set bonds_allow,angles_allow,etc based on the molecules in template set
// similar to how atom_style bond,angle,full set it
@ -112,6 +106,27 @@ void AtomVecTemplate::create_atom_post(int ilocal)
molatom[ilocal] = -1;
}
/* ----------------------------------------------------------------------
modify values for AtomVec::pack_data() to pack
------------------------------------------------------------------------- */
void AtomVecTemplate::pack_data_pre(int ilocal)
{
molindex[ilocal]++;
molatom[ilocal]++;
}
/* ----------------------------------------------------------------------
unmodify values packed by AtomVec::pack_data()
------------------------------------------------------------------------- */
void AtomVecTemplate::pack_data_post(int ilocal)
{
molindex[ilocal]--;
molatom[ilocal]--;
}
/* ----------------------------------------------------------------------
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
@ -119,11 +134,11 @@ void AtomVecTemplate::create_atom_post(int ilocal)
void AtomVecTemplate::data_atom_post(int ilocal)
{
int molindex_one = molindex[ilocal];
int molatom_one = molatom[ilocal];
int molindex_one = --molindex[ilocal];
int molatom_one = --molatom[ilocal];
if (molindex_one < 0 || molindex_one >= nset)
if ((molindex_one < -1) || (molindex_one >= nset))
error->one(FLERR,"Invalid template index in Atoms section of data file");
if (molatom_one < 0 || molatom_one >= onemols[molindex_one]->natoms)
if ((molatom_one < -1) || ((molindex_one >= 0) && (molatom_one >= onemols[molindex_one]->natoms)))
error->one(FLERR,"Invalid template atom in Atoms section of data file");
}

2
src/MOLECULE/atom_vec_template.h
View File

@ -31,6 +31,8 @@ class AtomVecTemplate : public AtomVec {
void grow_pointers();
void process_args(int, char **);
void create_atom_post(int);
void pack_data_pre(int);
void pack_data_post(int);
void data_atom_post(int);
private:

16
src/RIGID/fix_rigid.cpp
View File

@ -1098,12 +1098,12 @@ void FixRigid::compute_forces_and_torques()
// include Langevin thermostat forces
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
fcm[ibody][0] = all[ibody][0] + fflag[ibody][0]*langextra[ibody][0];
fcm[ibody][1] = all[ibody][1] + fflag[ibody][1]*langextra[ibody][1];
fcm[ibody][2] = all[ibody][2] + fflag[ibody][2]*langextra[ibody][2];
torque[ibody][0] = all[ibody][3] + tflag[ibody][0]*langextra[ibody][3];
torque[ibody][1] = all[ibody][4] + tflag[ibody][1]*langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + tflag[ibody][2]*langextra[ibody][5];
}
// add gravity force to COM of each body
@ -2710,11 +2710,15 @@ double FixRigid::compute_scalar()
void *FixRigid::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"body") == 0) {
if (!setupflag) return nullptr;
dim = 1;
return body;
}
if (strcmp(str,"masstotal") == 0) {
if (!setupflag) return nullptr;
dim = 1;
return masstotal;
}

9
src/RIGID/fix_rigid_small.cpp
View File

@ -875,6 +875,11 @@ void FixRigidSmall::apply_langevin_thermostat()
// convert langevin torques from body frame back to space frame
MathExtra::matvec(ex_space,ey_space,ez_space,tbody,&langextra[ibody][3]);
// enforce 2d motion
if (domain->dimension == 2)
langextra[ibody][2] = langextra[ibody][3] = langextra[ibody][4] = 0.0;
}
}
@ -3419,7 +3424,10 @@ int FixRigidSmall::modify_param(int narg, char **arg)
void *FixRigidSmall::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"body") == 0) {
if (!setupflag) return nullptr;
dim = 1;
return atom2body;
}
@ -3433,6 +3441,7 @@ void *FixRigidSmall::extract(const char *str, int &dim)
// used by granular pair styles, indexed by atom2body
if (strcmp(str,"masstotal") == 0) {
if (!setupflag) return nullptr;
dim = 1;
if (nmax_mass < nmax_body) {

4
src/RIGID/fix_shake.cpp
View File

@ -2536,13 +2536,13 @@ void FixShake::stats()
auto mesg = fmt::format("SHAKE stats (type/ave/delta/count) on step {}\n",
update->ntimestep);
for (i = 1; i < nb; i++) {
const auto bcnt = b_count_all[i];
const auto bcnt = b_count_all[i]/2;
if (bcnt)
mesg += fmt::format("{:>6d} {:<9.6} {:<11.6} {:>8d}\n",i,
b_ave_all[i]/bcnt,b_max_all[i]-b_min_all[i],bcnt);
}
for (i = 1; i < na; i++) {
const auto acnt = a_count_all[i];
const auto acnt = a_count_all[i]/3;
if (acnt)
mesg += fmt::format("{:>6d} {:<9.6} {:<11.6} {:>8d}\n",i,
a_ave_all[i]/acnt,a_max_all[i]-a_min_all[i],acnt);

2
src/USER-NETCDF/dump_netcdf.cpp
View File

@ -183,7 +183,7 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
for (int j = 0; j < DUMP_NC_MAX_DIMS; j++) {
perat[inc].field[j] = -1;
}
strcpy(perat[inc].name, mangled);
strncpy(perat[inc].name, mangled, NC_FIELD_NAME_MAX);
n_perat++;
}

2
src/USER-PLUMED/README
View File

@ -30,7 +30,7 @@ even if PLUMED is not in the path if as long as the input does not contain a fix
plumed command.
If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS. You can
download a tar ball into that directory or you can clone the plumed2 repository from github there. Once you have created a
download a tar ball into that directory or you can clone the plumed2 repository from GitHub there. Once you have created a
directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing
the usual commands. It is worth noting that we have provided a script that will download and build PLUMED for you with
a minimal set of options. To run this script you need to issue the following command:

2
src/atom.cpp
View File

@ -1910,7 +1910,7 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
onemol->avec_body->set_quat(ilocal,onemol->quat_external);
}
if (molecular != 1) return;
if (molecular != Atom::MOLECULAR) return;
// add bond topology info
// for molecular atom styles, but not atom style template

3
src/atom_vec_ellipsoid.cpp
View File

@ -533,8 +533,7 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag
this may create or delete entry in bonus data
------------------------------------------------------------------------- */
void AtomVecEllipsoid::
set_shape(int i, double shapex, double shapey, double shapez)
void AtomVecEllipsoid::set_shape(int i, double shapex, double shapey, double shapez)
{
if (ellipsoid[i] < 0) {
if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) return;

1
src/delete_atoms.cpp
View File

@ -557,6 +557,7 @@ void DeleteAtoms::recount_topology()
for (int i = 0; i < nlocal; i++) {
imol = molindex[i];
iatom = molatom[i];
if (imol < 0) continue;
nbonds += onemols[imol]->num_bond[iatom];
nangles += onemols[imol]->num_angle[iatom];
ndihedrals += onemols[imol]->num_dihedral[iatom];

15
src/domain.cpp
View File

@ -1873,6 +1873,7 @@ void Domain::set_boundary(int narg, char **arg, int flag)
else zperiodic = 0;
// record if we changed a periodic boundary to a non-periodic one
int pflag=0;
if ((periodicity[0] && !xperiodic)
|| (periodicity[1] && !yperiodic)
@ -1889,23 +1890,27 @@ void Domain::set_boundary(int narg, char **arg, int flag)
boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
boundary[2][0] >= 2 || boundary[2][1] >= 2) nonperiodic = 2;
}
// force non-zero image flags to zero for non-periodic dimensions
// keep track if a change was made, so we can print a warning message
if (pflag) {
pflag = 0;
for (int i=0; i < atom->nlocal; ++i) {
int xbox = (atom->image[i] & IMGMASK) - IMGMAX;
int ybox = (atom->image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int zbox = (atom->image[i] >> IMG2BITS) - IMGMAX;
if (!xperiodic) { xbox = 0; pflag = 1; }
if (!yperiodic) { ybox = 0; pflag = 1; }
if (!zperiodic) { zbox = 0; pflag = 1; }
if ((!xperiodic) && (xbox != 0)) { xbox = 0; pflag = 1; }
if ((!yperiodic) && (ybox != 0)) { ybox = 0; pflag = 1; }
if ((!zperiodic) && (zbox != 0)) { zbox = 0; pflag = 1; }
atom->image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
int flag_all;
MPI_Allreduce(&flag,&flag_all, 1, MPI_INT, MPI_SUM, world);
MPI_Allreduce(&pflag,&flag_all, 1, MPI_INT, MPI_SUM, world);
if ((flag_all > 0) && (comm->me == 0))
error->warning(FLERR,"Reset image flags for non-periodic boundary");
error->warning(FLERR,"Resetting image flags for non-periodic dimensions");
}
}

19
src/dump_dcd.cpp
View File

@ -97,16 +97,19 @@ void DumpDCD::init_style()
error->all(FLERR,"Dump dcd requires sorting by atom ID");
// check that dump frequency has not changed and is not a variable
// but only when not being called from the "write_dump" command.
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
if (output->every_dump[idump] == 0)
error->all(FLERR,"Cannot use variable every setting for dump dcd");
if (strcmp(id,"WRITE_DUMP") != 0) {
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
if (output->every_dump[idump] == 0)
error->all(FLERR,"Cannot use variable every setting for dump dcd");
if (nevery_save == 0) nevery_save = output->every_dump[idump];
else if (nevery_save != output->every_dump[idump])
error->all(FLERR,"Cannot change dump_modify every for dump dcd");
if (nevery_save == 0) nevery_save = output->every_dump[idump];
else if (nevery_save != output->every_dump[idump])
error->all(FLERR,"Cannot change dump_modify every for dump dcd");
}
}
/* ---------------------------------------------------------------------- */

6
src/fix_box_relax.cpp
View File

@ -735,12 +735,18 @@ void FixBoxRelax::couple()
p_current[2] = tensor[2];
}
if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2]))
error->all(FLERR,"Non-numeric pressure - simulation unstable");
// switch order from xy-xz-yz to Voigt
if (pstyle == TRICLINIC) {
p_current[3] = tensor[5];
p_current[4] = tensor[4];
p_current[5] = tensor[3];
if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5]))
error->all(FLERR,"Non-numeric pressure - simulation unstable");
}
}

79
src/fmt/chrono.h
View File

@ -72,43 +72,27 @@ FMT_CONSTEXPR To lossless_integral_conversion(const From from, int& ec) {
static_assert(F::is_integer, "From must be integral");
static_assert(T::is_integer, "To must be integral");
if (F::is_signed && !T::is_signed) {
if (detail::const_check(F::is_signed && !T::is_signed)) {
// From may be negative, not allowed!
if (fmt::detail::is_negative(from)) {
ec = 1;
return {};
}
// From is positive. Can it always fit in To?
if (F::digits <= T::digits) {
// yes, From always fits in To.
} else {
// from may not fit in To, we have to do a dynamic check
if (from > static_cast<From>((T::max)())) {
ec = 1;
return {};
}
if (F::digits > T::digits &&
from > static_cast<From>(detail::max_value<To>())) {
ec = 1;
return {};
}
}
if (!F::is_signed && T::is_signed) {
// can from be held in To?
if (F::digits < T::digits) {
// yes, From always fits in To.
} else {
// from may not fit in To, we have to do a dynamic check
if (from > static_cast<From>((T::max)())) {
// outside range.
ec = 1;
return {};
}
}
if (!F::is_signed && T::is_signed && F::digits >= T::digits &&
from > static_cast<From>(detail::max_value<To>())) {
ec = 1;
return {};
}
// reaching here means all is ok for lossless conversion.
return static_cast<To>(from);
} // function
return static_cast<To>(from); // Lossless conversion.
}
template <typename To, typename From,
FMT_ENABLE_IF(std::is_same<From, To>::value)>
@ -190,11 +174,9 @@ To safe_duration_cast(std::chrono::duration<FromRep, FromPeriod> from,
// safe conversion to IntermediateRep
IntermediateRep count =
lossless_integral_conversion<IntermediateRep>(from.count(), ec);
if (ec) {
return {};
}
if (ec) return {};
// multiply with Factor::num without overflow or underflow
if (Factor::num != 1) {
if (detail::const_check(Factor::num != 1)) {
const auto max1 = detail::max_value<IntermediateRep>() / Factor::num;
if (count > max1) {
ec = 1;
@ -209,17 +191,9 @@ To safe_duration_cast(std::chrono::duration<FromRep, FromPeriod> from,
count *= Factor::num;
}
// this can't go wrong, right? den>0 is checked earlier.
if (Factor::den != 1) {
count /= Factor::den;
}
// convert to the to type, safely
using ToRep = typename To::rep;
const ToRep tocount = lossless_integral_conversion<ToRep>(count, ec);
if (ec) {
return {};
}
return To{tocount};
if (detail::const_check(Factor::den != 1)) count /= Factor::den;
auto tocount = lossless_integral_conversion<typename To::rep>(count, ec);
return ec ? To() : To(tocount);
}
/**
@ -351,6 +325,11 @@ inline std::tm localtime(std::time_t time) {
return lt.tm_;
}
inline std::tm localtime(
std::chrono::time_point<std::chrono::system_clock> time_point) {
return localtime(std::chrono::system_clock::to_time_t(time_point));
}
// Thread-safe replacement for std::gmtime
inline std::tm gmtime(std::time_t time) {
struct dispatcher {
@ -387,6 +366,11 @@ inline std::tm gmtime(std::time_t time) {
return gt.tm_;
}
inline std::tm gmtime(
std::chrono::time_point<std::chrono::system_clock> time_point) {
return gmtime(std::chrono::system_clock::to_time_t(time_point));
}
namespace detail {
inline size_t strftime(char* str, size_t count, const char* format,
const std::tm* time) {
@ -399,6 +383,17 @@ inline size_t strftime(wchar_t* str, size_t count, const wchar_t* format,
}
} // namespace detail
template <typename Char>
struct formatter<std::chrono::time_point<std::chrono::system_clock>, Char>
: formatter<std::tm, Char> {
template <typename FormatContext>
auto format(std::chrono::time_point<std::chrono::system_clock> val,
FormatContext& ctx) -> decltype(ctx.out()) {
std::tm time = localtime(val);
return formatter<std::tm, Char>::format(time, ctx);
}
};
template <typename Char> struct formatter<std::tm, Char> {
template <typename ParseContext>
auto parse(ParseContext& ctx) -> decltype(ctx.begin()) {

57
src/fmt/color.h
View File

@ -463,16 +463,16 @@ template <> inline void reset_color<wchar_t>(FILE* stream) FMT_NOEXCEPT {
}
template <typename Char>
inline void reset_color(basic_memory_buffer<Char>& buffer) FMT_NOEXCEPT {
inline void reset_color(buffer<Char>& buffer) FMT_NOEXCEPT {
const char* begin = data::reset_color;
const char* end = begin + sizeof(data::reset_color) - 1;
buffer.append(begin, end);
}
template <typename Char>
void vformat_to(basic_memory_buffer<Char>& buf, const text_style& ts,
void vformat_to(buffer<Char>& buf, const text_style& ts,
basic_string_view<Char> format_str,
basic_format_args<buffer_context<Char>> args) {
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
bool has_style = false;
if (ts.has_emphasis()) {
has_style = true;
@ -496,7 +496,7 @@ void vformat_to(basic_memory_buffer<Char>& buf, const text_style& ts,
template <typename S, typename Char = char_t<S>>
void vprint(std::FILE* f, const text_style& ts, const S& format,
basic_format_args<buffer_context<Char>> args) {
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
basic_memory_buffer<Char> buf;
detail::vformat_to(buf, ts, to_string_view(format), args);
buf.push_back(Char(0));
@ -504,20 +504,22 @@ void vprint(std::FILE* f, const text_style& ts, const S& format,
}
/**
\rst
Formats a string and prints it to the specified file stream using ANSI
escape sequences to specify text formatting.
Example:
**Example**::
fmt::print(fmt::emphasis::bold | fg(fmt::color::red),
"Elapsed time: {0:.2f} seconds", 1.23);
\endrst
*/
template <typename S, typename... Args,
FMT_ENABLE_IF(detail::is_string<S>::value)>
void print(std::FILE* f, const text_style& ts, const S& format_str,
const Args&... args) {
detail::check_format_string<Args...>(format_str);
using context = buffer_context<char_t<S>>;
format_arg_store<context, Args...> as{args...};
vprint(f, ts, format_str, basic_format_args<context>(as));
vprint(f, ts, format_str,
fmt::make_args_checked<Args...>(format_str, args...));
}
/**
@ -558,7 +560,42 @@ template <typename S, typename... Args, typename Char = char_t<S>>
inline std::basic_string<Char> format(const text_style& ts, const S& format_str,
const Args&... args) {
return vformat(ts, to_string_view(format_str),
detail::make_args_checked<Args...>(format_str, args...));
fmt::make_args_checked<Args...>(format_str, args...));
}
/**
Formats a string with the given text_style and writes the output to ``out``.
*/
template <typename OutputIt, typename Char,
FMT_ENABLE_IF(detail::is_output_iterator<OutputIt, Char>::value)>
OutputIt vformat_to(
OutputIt out, const text_style& ts, basic_string_view<Char> format_str,
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
decltype(detail::get_buffer<Char>(out)) buf(detail::get_buffer_init(out));
detail::vformat_to(buf, ts, format_str, args);
return detail::get_iterator(buf);
}
/**
\rst
Formats arguments with the given text_style, writes the result to the output
iterator ``out`` and returns the iterator past the end of the output range.
**Example**::
std::vector<char> out;
fmt::format_to(std::back_inserter(out),
fmt::emphasis::bold | fg(fmt::color::red), "{}", 42);
\endrst
*/
template <typename OutputIt, typename S, typename... Args,
bool enable = detail::is_output_iterator<OutputIt, char_t<S>>::value&&
detail::is_string<S>::value>
inline auto format_to(OutputIt out, const text_style& ts, const S& format_str,
Args&&... args) ->
typename std::enable_if<enable, OutputIt>::type {
return vformat_to(out, ts, to_string_view(format_str),
fmt::make_args_checked<Args...>(format_str, args...));
}
FMT_END_NAMESPACE

82
src/fmt/compile.h
View File

@ -368,7 +368,8 @@ template <typename... Args> struct type_list {};
// Returns a reference to the argument at index N from [first, rest...].
template <int N, typename T, typename... Args>
constexpr const auto& get(const T& first, const Args&... rest) {
constexpr const auto& get([[maybe_unused]] const T& first,
[[maybe_unused]] const Args&... rest) {
static_assert(N < 1 + sizeof...(Args), "index is out of bounds");
if constexpr (N == 0)
return first;
@ -406,6 +407,19 @@ constexpr text<Char> make_text(basic_string_view<Char> s, size_t pos,
return {{&s[pos], size}};
}
template <typename Char> struct code_unit {
Char value;
using char_type = Char;
template <typename OutputIt, typename... Args>
OutputIt format(OutputIt out, const Args&...) const {
return write<Char>(out, value);
}
};
template <typename Char>
struct is_compiled_format<code_unit<Char>> : std::true_type {};
// A replacement field that refers to argument N.
template <typename Char, typename T, int N> struct field {
using char_type = Char;
@ -430,7 +444,9 @@ template <typename Char, typename T, int N> struct spec_field {
OutputIt format(OutputIt out, const Args&... args) const {
// This ensures that the argument type is convertile to `const T&`.
const T& arg = get<N>(args...);
basic_format_context<OutputIt, Char> ctx(out, {});
const auto& vargs =
make_format_args<basic_format_context<OutputIt, Char>>(args...);
basic_format_context<OutputIt, Char> ctx(out, vargs);
return fmt.format(arg, ctx);
}
};
@ -489,16 +505,17 @@ constexpr auto parse_tail(T head, S format_str) {
template <typename T, typename Char> struct parse_specs_result {
formatter<T, Char> fmt;
size_t end;
int next_arg_id;
};
template <typename T, typename Char>
constexpr parse_specs_result<T, Char> parse_specs(basic_string_view<Char> str,
size_t pos) {
size_t pos, int arg_id) {
str.remove_prefix(pos);
auto ctx = basic_format_parse_context<Char>(str);
auto ctx = basic_format_parse_context<Char>(str, {}, arg_id + 1);
auto f = formatter<T, Char>();
auto end = f.parse(ctx);
return {f, pos + (end - str.data()) + 1};
return {f, pos + (end - str.data()) + 1, ctx.next_arg_id()};
}
// Compiles a non-empty format string and returns the compiled representation
@ -518,8 +535,8 @@ constexpr auto compile_format_string(S format_str) {
format_str);
} else if constexpr (str[POS + 1] == ':') {
using type = get_type<ID, Args>;
constexpr auto result = parse_specs<type>(str, POS + 2);
return parse_tail<Args, result.end, ID + 1>(
constexpr auto result = parse_specs<type>(str, POS + 2, ID);
return parse_tail<Args, result.end, result.next_arg_id>(
spec_field<char_type, type, ID>{result.fmt}, format_str);
} else {
return unknown_format();
@ -530,8 +547,13 @@ constexpr auto compile_format_string(S format_str) {
return parse_tail<Args, POS + 2, ID>(make_text(str, POS, 1), format_str);
} else {
constexpr auto end = parse_text(str, POS + 1);
return parse_tail<Args, end, ID>(make_text(str, POS, end - POS),
format_str);
if constexpr (end - POS > 1) {
return parse_tail<Args, end, ID>(make_text(str, POS, end - POS),
format_str);
} else {
return parse_tail<Args, end, ID>(code_unit<char_type>{str[POS]},
format_str);
}
}
}
@ -587,8 +609,7 @@ template <typename CompiledFormat, typename... Args,
FMT_INLINE std::basic_string<Char> format(const CompiledFormat& cf,
const Args&... args) {
basic_memory_buffer<Char> buffer;
detail::buffer<Char>& base = buffer;
cf.format(std::back_inserter(base), args...);
cf.format(detail::buffer_appender<Char>(buffer), args...);
return to_string(buffer);
}
@ -608,8 +629,7 @@ template <typename CompiledFormat, typename... Args,
std::basic_string<Char> format(const CompiledFormat& cf, const Args&... args) {
basic_memory_buffer<Char> buffer;
using context = buffer_context<Char>;
detail::buffer<Char>& base = buffer;
detail::cf::vformat_to<context>(std::back_inserter(base), cf,
detail::cf::vformat_to<context>(detail::buffer_appender<Char>(buffer), cf,
make_format_args<context>(args...));
return to_string(buffer);
}
@ -618,9 +638,13 @@ template <typename S, typename... Args,
FMT_ENABLE_IF(detail::is_compiled_string<S>::value)>
FMT_INLINE std::basic_string<typename S::char_type> format(const S&,
Args&&... args) {
constexpr basic_string_view<typename S::char_type> str = S();
if (str.size() == 2 && str[0] == '{' && str[1] == '}')
return fmt::to_string(detail::first(args...));
#ifdef __cpp_if_constexpr
if constexpr (std::is_same<typename S::char_type, char>::value) {
constexpr basic_string_view<typename S::char_type> str = S();
if (str.size() == 2 && str[0] == '{' && str[1] == '}')
return fmt::to_string(detail::first(args...));
}
#endif
constexpr auto compiled = detail::compile<Args...>(S());
return format(compiled, std::forward<Args>(args)...);
}
@ -643,18 +667,30 @@ OutputIt format_to(OutputIt out, const S&, const Args&... args) {
return format_to(out, compiled, args...);
}
template <
typename OutputIt, typename CompiledFormat, typename... Args,
FMT_ENABLE_IF(detail::is_output_iterator<OutputIt>::value&& std::is_base_of<
detail::basic_compiled_format, CompiledFormat>::value)>
format_to_n_result<OutputIt> format_to_n(OutputIt out, size_t n,
const CompiledFormat& cf,
const Args&... args) {
template <typename OutputIt, typename CompiledFormat, typename... Args>
auto format_to_n(OutputIt out, size_t n, const CompiledFormat& cf,
const Args&... args) ->
typename std::enable_if<
detail::is_output_iterator<OutputIt,
typename CompiledFormat::char_type>::value &&
std::is_base_of<detail::basic_compiled_format,
CompiledFormat>::value,
format_to_n_result<OutputIt>>::type {
auto it =
format_to(detail::truncating_iterator<OutputIt>(out, n), cf, args...);
return {it.base(), it.count()};
}
template <typename OutputIt, typename S, typename... Args,
FMT_ENABLE_IF(detail::is_compiled_string<S>::value)>
format_to_n_result<OutputIt> format_to_n(OutputIt out, size_t n, const S&,
const Args&... args) {
constexpr auto compiled = detail::compile<Args...>(S());
auto it = format_to(detail::truncating_iterator<OutputIt>(out, n), compiled,
args...);
return {it.base(), it.count()};
}
template <typename CompiledFormat, typename... Args>
size_t formatted_size(const CompiledFormat& cf, const Args&... args) {
return format_to(detail::counting_iterator(), cf, args...).count();

448
src/fmt/core.h
View File

@ -18,7 +18,7 @@
#include <vector>
// The fmt library version in the form major * 10000 + minor * 100 + patch.
#define FMT_VERSION 70003
#define FMT_VERSION 70102
#ifdef __clang__
# define FMT_CLANG_VERSION (__clang_major__ * 100 + __clang_minor__)
@ -57,6 +57,7 @@
# define FMT_MSC_VER 0
# define FMT_SUPPRESS_MSC_WARNING(n)
#endif
#ifdef __has_feature
# define FMT_HAS_FEATURE(x) __has_feature(x)
#else
@ -64,7 +65,7 @@
#endif
#if defined(__has_include) && !defined(__INTELLISENSE__) && \
!(FMT_ICC_VERSION && FMT_ICC_VERSION < 1600)
(!FMT_ICC_VERSION || FMT_ICC_VERSION >= 1600)
# define FMT_HAS_INCLUDE(x) __has_include(x)
#else
# define FMT_HAS_INCLUDE(x) 0
@ -99,7 +100,7 @@
#endif
#ifndef FMT_OVERRIDE
# if FMT_HAS_FEATURE(cxx_override) || \
# if FMT_HAS_FEATURE(cxx_override_control) || \
(FMT_GCC_VERSION >= 408 && FMT_HAS_GXX_CXX11) || FMT_MSC_VER >= 1900
# define FMT_OVERRIDE override
# else
@ -152,7 +153,7 @@
# if FMT_HAS_CPP14_ATTRIBUTE(deprecated) || FMT_MSC_VER >= 1900
# define FMT_DEPRECATED [[deprecated]]
# else
# if defined(__GNUC__) || defined(__clang__)
# if (defined(__GNUC__) && !defined(__LCC__)) || defined(__clang__)
# define FMT_DEPRECATED __attribute__((deprecated))
# elif FMT_MSC_VER
# define FMT_DEPRECATED __declspec(deprecated)
@ -177,6 +178,15 @@
# endif
#endif
#ifndef FMT_USE_INLINE_NAMESPACES
# if FMT_HAS_FEATURE(cxx_inline_namespaces) || FMT_GCC_VERSION >= 404 || \
(FMT_MSC_VER >= 1900 && !_MANAGED)
# define FMT_USE_INLINE_NAMESPACES 1
# else
# define FMT_USE_INLINE_NAMESPACES 0
# endif
#endif
// LAMMPS customization
// use 'v7_lmp' namespace instead of 'v7' so that our
// bundled copy does not collide with linking other code
@ -184,8 +194,7 @@
// a different version.
#ifndef FMT_BEGIN_NAMESPACE
# if FMT_HAS_FEATURE(cxx_inline_namespaces) || FMT_GCC_VERSION >= 404 || \
FMT_MSC_VER >= 1900
# if FMT_USE_INLINE_NAMESPACES
# define FMT_INLINE_NAMESPACE inline namespace
# define FMT_END_NAMESPACE \
} \
@ -275,8 +284,7 @@ struct monostate {};
namespace detail {
// A helper function to suppress bogus "conditional expression is constant"
// warnings.
// A helper function to suppress "conditional expression is constant" warnings.
template <typename T> constexpr T const_check(T value) { return value; }
FMT_NORETURN FMT_API void assert_fail(const char* file, int line,
@ -305,7 +313,8 @@ template <typename T> struct std_string_view {};
#ifdef FMT_USE_INT128
// Do nothing.
#elif defined(__SIZEOF_INT128__) && !FMT_NVCC && !(FMT_CLANG_VERSION && FMT_MSC_VER)
#elif defined(__SIZEOF_INT128__) && !FMT_NVCC && \
!(FMT_CLANG_VERSION && FMT_MSC_VER)
# define FMT_USE_INT128 1
using int128_t = __int128_t;
using uint128_t = __uint128_t;
@ -514,6 +523,18 @@ template <typename S> struct char_t_impl<S, enable_if_t<is_string<S>::value>> {
using type = typename result::value_type;
};
// Reports a compile-time error if S is not a valid format string.
template <typename..., typename S, FMT_ENABLE_IF(!is_compile_string<S>::value)>
FMT_INLINE void check_format_string(const S&) {
#ifdef FMT_ENFORCE_COMPILE_STRING
static_assert(is_compile_string<S>::value,
"FMT_ENFORCE_COMPILE_STRING requires all format strings to use "
"FMT_STRING.");
#endif
}
template <typename..., typename S, FMT_ENABLE_IF(is_compile_string<S>::value)>
void check_format_string(S);
struct error_handler {
constexpr error_handler() = default;
constexpr error_handler(const error_handler&) = default;
@ -553,8 +574,9 @@ class basic_format_parse_context : private ErrorHandler {
using iterator = typename basic_string_view<Char>::iterator;
explicit constexpr basic_format_parse_context(
basic_string_view<Char> format_str, ErrorHandler eh = {})
: ErrorHandler(eh), format_str_(format_str), next_arg_id_(0) {}
basic_string_view<Char> format_str, ErrorHandler eh = {},
int next_arg_id = 0)
: ErrorHandler(eh), format_str_(format_str), next_arg_id_(next_arg_id) {}
/**
Returns an iterator to the beginning of the format string range being
@ -624,8 +646,24 @@ template <typename T, typename Context>
using has_formatter =
std::is_constructible<typename Context::template formatter_type<T>>;
// Checks whether T is a container with contiguous storage.
template <typename T> struct is_contiguous : std::false_type {};
template <typename Char>
struct is_contiguous<std::basic_string<Char>> : std::true_type {};
namespace detail {
// Extracts a reference to the container from back_insert_iterator.
template <typename Container>
inline Container& get_container(std::back_insert_iterator<Container> it) {
using bi_iterator = std::back_insert_iterator<Container>;
struct accessor : bi_iterator {
accessor(bi_iterator iter) : bi_iterator(iter) {}
using bi_iterator::container;
};
return *accessor(it).container;
}
/**
\rst
A contiguous memory buffer with an optional growing ability. It is an internal
@ -648,6 +686,8 @@ template <typename T> class buffer {
size_(sz),
capacity_(cap) {}
~buffer() = default;
/** Sets the buffer data and capacity. */
void set(T* buf_data, size_t buf_capacity) FMT_NOEXCEPT {
ptr_ = buf_data;
@ -663,7 +703,6 @@ template <typename T> class buffer {
buffer(const buffer&) = delete;
void operator=(const buffer&) = delete;
virtual ~buffer() = default;
T* begin() FMT_NOEXCEPT { return ptr_; }
T* end() FMT_NOEXCEPT { return ptr_ + size_; }
@ -683,24 +722,26 @@ template <typename T> class buffer {
/** Returns a pointer to the buffer data. */
const T* data() const FMT_NOEXCEPT { return ptr_; }
/**
Resizes the buffer. If T is a POD type new elements may not be initialized.
*/
void resize(size_t new_size) {
reserve(new_size);
size_ = new_size;
}
/** Clears this buffer. */
void clear() { size_ = 0; }
/** Reserves space to store at least *capacity* elements. */
void reserve(size_t new_capacity) {
// Tries resizing the buffer to contain *count* elements. If T is a POD type
// the new elements may not be initialized.
void try_resize(size_t count) {
try_reserve(count);
size_ = count <= capacity_ ? count : capacity_;
}
// Tries increasing the buffer capacity to *new_capacity*. It can increase the
// capacity by a smaller amount than requested but guarantees there is space
// for at least one additional element either by increasing the capacity or by
// flushing the buffer if it is full.
void try_reserve(size_t new_capacity) {
if (new_capacity > capacity_) grow(new_capacity);
}
void push_back(const T& value) {
reserve(size_ + 1);
try_reserve(size_ + 1);
ptr_[size_++] = value;
}
@ -713,32 +754,150 @@ template <typename T> class buffer {
}
};
// A container-backed buffer.
struct buffer_traits {
explicit buffer_traits(size_t) {}
size_t count() const { return 0; }
size_t limit(size_t size) { return size; }
};
class fixed_buffer_traits {
private:
size_t count_ = 0;
size_t limit_;
public:
explicit fixed_buffer_traits(size_t limit) : limit_(limit) {}
size_t count() const { return count_; }
size_t limit(size_t size) {
size_t n = limit_ - count_;
count_ += size;
return size < n ? size : n;
}
};
// A buffer that writes to an output iterator when flushed.
template <typename OutputIt, typename T, typename Traits = buffer_traits>
class iterator_buffer final : public Traits, public buffer<T> {
private:
OutputIt out_;
enum { buffer_size = 256 };
T data_[buffer_size];
protected:
void grow(size_t) final FMT_OVERRIDE {
if (this->size() == buffer_size) flush();
}
void flush();
public:
explicit iterator_buffer(OutputIt out, size_t n = buffer_size)
: Traits(n),
buffer<T>(data_, 0, n < size_t(buffer_size) ? n : size_t(buffer_size)),
out_(out) {}
~iterator_buffer() { flush(); }
OutputIt out() {
flush();
return out_;
}
size_t count() const { return Traits::count() + this->size(); }
};
template <typename T> class iterator_buffer<T*, T> final : public buffer<T> {
protected:
void grow(size_t) final FMT_OVERRIDE {}
public:
explicit iterator_buffer(T* out, size_t = 0) : buffer<T>(out, 0, ~size_t()) {}
T* out() { return &*this->end(); }
};
// A buffer that writes to a container with the contiguous storage.
template <typename Container>
class container_buffer : public buffer<typename Container::value_type> {
class iterator_buffer<std::back_insert_iterator<Container>,
enable_if_t<is_contiguous<Container>::value,
typename Container::value_type>>
final : public buffer<typename Container::value_type> {
private:
Container& container_;
protected:
void grow(size_t capacity) FMT_OVERRIDE {
void grow(size_t capacity) final FMT_OVERRIDE {
container_.resize(capacity);
this->set(&container_[0], capacity);
}
public:
explicit container_buffer(Container& c)
explicit iterator_buffer(Container& c)
: buffer<typename Container::value_type>(c.size()), container_(c) {}
explicit iterator_buffer(std::back_insert_iterator<Container> out, size_t = 0)
: iterator_buffer(get_container(out)) {}
std::back_insert_iterator<Container> out() {
return std::back_inserter(container_);
}
};
// Extracts a reference to the container from back_insert_iterator.
template <typename Container>
inline Container& get_container(std::back_insert_iterator<Container> it) {
using bi_iterator = std::back_insert_iterator<Container>;
struct accessor : bi_iterator {
accessor(bi_iterator iter) : bi_iterator(iter) {}
using bi_iterator::container;
};
return *accessor(it).container;
// A buffer that counts the number of code units written discarding the output.
template <typename T = char> class counting_buffer final : public buffer<T> {
private:
enum { buffer_size = 256 };
T data_[buffer_size];
size_t count_ = 0;
protected:
void grow(size_t) final FMT_OVERRIDE {
if (this->size() != buffer_size) return;
count_ += this->size();
this->clear();
}
public:
counting_buffer() : buffer<T>(data_, 0, buffer_size) {}
size_t count() { return count_ + this->size(); }
};
// An output iterator that appends to the buffer.
// It is used to reduce symbol sizes for the common case.
template <typename T>
class buffer_appender : public std::back_insert_iterator<buffer<T>> {
using base = std::back_insert_iterator<buffer<T>>;
public:
explicit buffer_appender(buffer<T>& buf) : base(buf) {}
buffer_appender(base it) : base(it) {}
buffer_appender& operator++() {
base::operator++();
return *this;
}
buffer_appender operator++(int) {
buffer_appender tmp = *this;
++*this;
return tmp;
}
};
// Maps an output iterator into a buffer.
template <typename T, typename OutputIt>
iterator_buffer<OutputIt, T> get_buffer(OutputIt);
template <typename T> buffer<T>& get_buffer(buffer_appender<T>);
template <typename OutputIt> OutputIt get_buffer_init(OutputIt out) {
return out;
}
template <typename T> buffer<T>& get_buffer_init(buffer_appender<T> out) {
return get_container(out);
}
template <typename Buffer>
auto get_iterator(Buffer& buf) -> decltype(buf.out()) {
return buf.out();
}
template <typename T> buffer_appender<T> get_iterator(buffer<T>& buf) {
return buffer_appender<T>(buf);
}
template <typename T, typename Char = char, typename Enable = void>
@ -767,7 +926,8 @@ template <typename Char> struct named_arg_info {
template <typename T, typename Char, size_t NUM_ARGS, size_t NUM_NAMED_ARGS>
struct arg_data {
// args_[0].named_args points to named_args_ to avoid bloating format_args.
T args_[1 + (NUM_ARGS != 0 ? NUM_ARGS : 1)];
// +1 to workaround a bug in gcc 7.5 that causes duplicated-branches warning.
T args_[1 + (NUM_ARGS != 0 ? NUM_ARGS : +1)];
named_arg_info<Char> named_args_[NUM_NAMED_ARGS];
template <typename... U>
@ -779,7 +939,8 @@ struct arg_data {
template <typename T, typename Char, size_t NUM_ARGS>
struct arg_data<T, Char, NUM_ARGS, 0> {
T args_[NUM_ARGS != 0 ? NUM_ARGS : 1];
// +1 to workaround a bug in gcc 7.5 that causes duplicated-branches warning.
T args_[NUM_ARGS != 0 ? NUM_ARGS : +1];
template <typename... U>
FMT_INLINE arg_data(const U&... init) : args_{init...} {}
@ -967,6 +1128,8 @@ enum { long_short = sizeof(long) == sizeof(int) };
using long_type = conditional_t<long_short, int, long long>;
using ulong_type = conditional_t<long_short, unsigned, unsigned long long>;
struct unformattable {};
// Maps formatting arguments to core types.
template <typename Context> struct arg_mapper {
using char_type = typename Context::char_type;
@ -1075,15 +1238,7 @@ template <typename Context> struct arg_mapper {
return map(val.value);
}
int map(...) {
constexpr bool formattable = sizeof(Context) == 0;
static_assert(
formattable,
"Cannot format argument. To make type T formattable provide a "
"formatter<T> specialization: "
"https://fmt.dev/latest/api.html#formatting-user-defined-types");
return 0;
}
unformattable map(...) { return {}; }
};
// A type constant after applying arg_mapper<Context>.
@ -1207,15 +1362,25 @@ FMT_CONSTEXPR_DECL FMT_INLINE auto visit_format_arg(
return vis(monostate());
}
// Checks whether T is a container with contiguous storage.
template <typename T> struct is_contiguous : std::false_type {};
template <typename Char>
struct is_contiguous<std::basic_string<Char>> : std::true_type {};
template <typename Char>
struct is_contiguous<detail::buffer<Char>> : std::true_type {};
template <typename T> struct formattable : std::false_type {};
namespace detail {
// A workaround for gcc 4.8 to make void_t work in a SFINAE context.
template <typename... Ts> struct void_t_impl { using type = void; };
template <typename... Ts>
using void_t = typename detail::void_t_impl<Ts...>::type;
template <typename It, typename T, typename Enable = void>
struct is_output_iterator : std::false_type {};
template <typename It, typename T>
struct is_output_iterator<
It, T,
void_t<typename std::iterator_traits<It>::iterator_category,
decltype(*std::declval<It>() = std::declval<T>())>>
: std::true_type {};
template <typename OutputIt>
struct is_back_insert_iterator : std::false_type {};
template <typename Container>
@ -1227,6 +1392,9 @@ struct is_contiguous_back_insert_iterator : std::false_type {};
template <typename Container>
struct is_contiguous_back_insert_iterator<std::back_insert_iterator<Container>>
: is_contiguous<Container> {};
template <typename Char>
struct is_contiguous_back_insert_iterator<buffer_appender<Char>>
: std::true_type {};
// A type-erased reference to an std::locale to avoid heavy <locale> include.
class locale_ref {
@ -1258,13 +1426,24 @@ FMT_CONSTEXPR basic_format_arg<Context> make_arg(const T& value) {
return arg;
}
template <typename T> int check(unformattable) {
static_assert(
formattable<T>(),
"Cannot format an argument. To make type T formattable provide a "
"formatter<T> specialization: https://fmt.dev/latest/api.html#udt");
return 0;
}
template <typename T, typename U> inline const U& check(const U& val) {
return val;
}
// The type template parameter is there to avoid an ODR violation when using
// a fallback formatter in one translation unit and an implicit conversion in
// another (not recommended).
template <bool IS_PACKED, typename Context, type, typename T,
FMT_ENABLE_IF(IS_PACKED)>
inline value<Context> make_arg(const T& val) {
return arg_mapper<Context>().map(val);
return check<T>(arg_mapper<Context>().map(val));
}
template <bool IS_PACKED, typename Context, type, typename T,
@ -1364,13 +1543,13 @@ template <typename OutputIt, typename Char> class basic_format_context {
template <typename Char>
using buffer_context =
basic_format_context<std::back_insert_iterator<detail::buffer<Char>>, Char>;
basic_format_context<detail::buffer_appender<Char>, Char>;
using format_context = buffer_context<char>;
using wformat_context = buffer_context<wchar_t>;
// Workaround a bug in gcc: https://stackoverflow.com/q/62767544/471164.
// Workaround an alias issue: https://stackoverflow.com/q/62767544/471164.
#define FMT_BUFFER_CONTEXT(Char) \
basic_format_context<std::back_insert_iterator<detail::buffer<Char>>, Char>
basic_format_context<detail::buffer_appender<Char>, Char>
/**
\rst
@ -1422,7 +1601,7 @@ class format_arg_store
/**
\rst
Constructs an `~fmt::format_arg_store` object that contains references to
Constructs a `~fmt::format_arg_store` object that contains references to
arguments and can be implicitly converted to `~fmt::format_args`. `Context`
can be omitted in which case it defaults to `~fmt::context`.
See `~fmt::arg` for lifetime considerations.
@ -1434,6 +1613,27 @@ inline format_arg_store<Context, Args...> make_format_args(
return {args...};
}
/**
\rst
Constructs a `~fmt::format_arg_store` object that contains references
to arguments and can be implicitly converted to `~fmt::format_args`.
If ``format_str`` is a compile-time string then `make_args_checked` checks
its validity at compile time.
\endrst
*/
template <typename... Args, typename S, typename Char = char_t<S>>
inline auto make_args_checked(const S& format_str,
const remove_reference_t<Args>&... args)
-> format_arg_store<buffer_context<Char>, remove_reference_t<Args>...> {
static_assert(
detail::count<(
std::is_base_of<detail::view, remove_reference_t<Args>>::value &&
std::is_reference<Args>::value)...>() == 0,
"passing views as lvalues is disallowed");
detail::check_format_string<Args...>(format_str);
return {args...};
}
/**
\rst
Returns a named argument to be used in a formatting function. It should only
@ -1737,7 +1937,14 @@ template <typename Context> class basic_format_args {
}
};
/** An alias to ``basic_format_args<context>``. */
#ifdef FMT_ARM_ABI_COMPATIBILITY
/** An alias to ``basic_format_args<format_context>``. */
// Separate types would result in shorter symbols but break ABI compatibility
// between clang and gcc on ARM (#1919).
using format_args = basic_format_args<format_context>;
using wformat_args = basic_format_args<wformat_context>;
#else
// DEPRECATED! These are kept for ABI compatibility.
// It is a separate type rather than an alias to make symbols readable.
struct format_args : basic_format_args<format_context> {
template <typename... Args>
@ -1746,32 +1953,10 @@ struct format_args : basic_format_args<format_context> {
struct wformat_args : basic_format_args<wformat_context> {
using basic_format_args::basic_format_args;
};
#endif
namespace detail {
// Reports a compile-time error if S is not a valid format string.
template <typename..., typename S, FMT_ENABLE_IF(!is_compile_string<S>::value)>
FMT_INLINE void check_format_string(const S&) {
#ifdef FMT_ENFORCE_COMPILE_STRING
static_assert(is_compile_string<S>::value,
"FMT_ENFORCE_COMPILE_STRING requires all format strings to use "
"FMT_STRING.");
#endif
}
template <typename..., typename S, FMT_ENABLE_IF(is_compile_string<S>::value)>
void check_format_string(S);
template <typename... Args, typename S, typename Char = char_t<S>>
inline format_arg_store<buffer_context<Char>, remove_reference_t<Args>...>
make_args_checked(const S& format_str,
const remove_reference_t<Args>&... args) {
static_assert(count<(std::is_base_of<view, remove_reference_t<Args>>::value &&
std::is_reference<Args>::value)...>() == 0,
"passing views as lvalues is disallowed");
check_format_string<Args...>(format_str);
return {args...};
}
template <typename Char, FMT_ENABLE_IF(!std::is_same<Char, char>::value)>
std::basic_string<Char> vformat(
basic_string_view<Char> format_str,
@ -1780,9 +1965,10 @@ std::basic_string<Char> vformat(
FMT_API std::string vformat(string_view format_str, format_args args);
template <typename Char>
typename FMT_BUFFER_CONTEXT(Char)::iterator vformat_to(
void vformat_to(
buffer<Char>& buf, basic_string_view<Char> format_str,
basic_format_args<FMT_BUFFER_CONTEXT(type_identity_t<Char>)> args);
basic_format_args<FMT_BUFFER_CONTEXT(type_identity_t<Char>)> args,
detail::locale_ref loc = {});
template <typename Char, typename Args,
FMT_ENABLE_IF(!std::is_same<Char, char>::value)>
@ -1797,26 +1983,80 @@ inline void vprint_mojibake(std::FILE*, string_view, format_args) {}
/** Formats a string and writes the output to ``out``. */
// GCC 8 and earlier cannot handle std::back_insert_iterator<Container> with
// vformat_to<ArgFormatter>(...) overload, so SFINAE on iterator type instead.
template <
typename OutputIt, typename S, typename Char = char_t<S>,
FMT_ENABLE_IF(detail::is_contiguous_back_insert_iterator<OutputIt>::value)>
OutputIt vformat_to(
OutputIt out, const S& format_str,
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
auto& c = detail::get_container(out);
detail::container_buffer<remove_reference_t<decltype(c)>> buf(c);
template <typename OutputIt, typename S, typename Char = char_t<S>,
bool enable = detail::is_output_iterator<OutputIt, Char>::value>
auto vformat_to(OutputIt out, const S& format_str,
basic_format_args<buffer_context<type_identity_t<Char>>> args)
-> typename std::enable_if<enable, OutputIt>::type {
decltype(detail::get_buffer<Char>(out)) buf(detail::get_buffer_init(out));
detail::vformat_to(buf, to_string_view(format_str), args);
return out;
return detail::get_iterator(buf);
}
template <typename Container, typename S, typename... Args,
FMT_ENABLE_IF(
is_contiguous<Container>::value&& detail::is_string<S>::value)>
inline std::back_insert_iterator<Container> format_to(
std::back_insert_iterator<Container> out, const S& format_str,
Args&&... args) {
return vformat_to(out, to_string_view(format_str),
detail::make_args_checked<Args...>(format_str, args...));
/**
\rst
Formats arguments, writes the result to the output iterator ``out`` and returns
the iterator past the end of the output range.
**Example**::
std::vector<char> out;
fmt::format_to(std::back_inserter(out), "{}", 42);
\endrst
*/
// We cannot use FMT_ENABLE_IF because of a bug in gcc 8.3.
template <typename OutputIt, typename S, typename... Args,
bool enable = detail::is_output_iterator<OutputIt, char_t<S>>::value>
inline auto format_to(OutputIt out, const S& format_str, Args&&... args) ->
typename std::enable_if<enable, OutputIt>::type {
const auto& vargs = fmt::make_args_checked<Args...>(format_str, args...);
return vformat_to(out, to_string_view(format_str), vargs);
}
template <typename OutputIt> struct format_to_n_result {
/** Iterator past the end of the output range. */
OutputIt out;
/** Total (not truncated) output size. */
size_t size;
};
template <typename OutputIt, typename Char, typename... Args,
FMT_ENABLE_IF(detail::is_output_iterator<OutputIt, Char>::value)>
inline format_to_n_result<OutputIt> vformat_to_n(
OutputIt out, size_t n, basic_string_view<Char> format_str,
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
detail::iterator_buffer<OutputIt, Char, detail::fixed_buffer_traits> buf(out,
n);
detail::vformat_to(buf, format_str, args);
return {buf.out(), buf.count()};
}
/**
\rst
Formats arguments, writes up to ``n`` characters of the result to the output
iterator ``out`` and returns the total output size and the iterator past the
end of the output range.
\endrst
*/
template <typename OutputIt, typename S, typename... Args,
bool enable = detail::is_output_iterator<OutputIt, char_t<S>>::value>
inline auto format_to_n(OutputIt out, size_t n, const S& format_str,
const Args&... args) ->
typename std::enable_if<enable, format_to_n_result<OutputIt>>::type {
const auto& vargs = fmt::make_args_checked<Args...>(format_str, args...);
return vformat_to_n(out, n, to_string_view(format_str), vargs);
}
/**
Returns the number of characters in the output of
``format(format_str, args...)``.
*/
template <typename... Args>
inline size_t formatted_size(string_view format_str, Args&&... args) {
const auto& vargs = fmt::make_args_checked<Args...>(format_str, args...);
detail::counting_buffer<> buf;
detail::vformat_to(buf, format_str, vargs);
return buf.count();
}
template <typename S, typename Char = char_t<S>>
@ -1840,7 +2080,7 @@ FMT_INLINE std::basic_string<Char> vformat(
// std::basic_string<char_t<S>> to reduce the symbol size.
template <typename S, typename... Args, typename Char = char_t<S>>
FMT_INLINE std::basic_string<Char> format(const S& format_str, Args&&... args) {
const auto& vargs = detail::make_args_checked<Args...>(format_str, args...);
const auto& vargs = fmt::make_args_checked<Args...>(format_str, args...);
return detail::vformat(to_string_view(format_str), vargs);
}
@ -1860,7 +2100,7 @@ FMT_API void vprint(std::FILE*, string_view, format_args);
*/
template <typename S, typename... Args, typename Char = char_t<S>>
inline void print(std::FILE* f, const S& format_str, Args&&... args) {
const auto& vargs = detail::make_args_checked<Args...>(format_str, args...);
const auto& vargs = fmt::make_args_checked<Args...>(format_str, args...);
return detail::is_unicode<Char>()
? vprint(f, to_string_view(format_str), vargs)
: detail::vprint_mojibake(f, to_string_view(format_str), vargs);
@ -1879,7 +2119,7 @@ inline void print(std::FILE* f, const S& format_str, Args&&... args) {
*/
template <typename S, typename... Args, typename Char = char_t<S>>
inline void print(const S& format_str, Args&&... args) {
const auto& vargs = detail::make_args_checked<Args...>(format_str, args...);
const auto& vargs = fmt::make_args_checked<Args...>(format_str, args...);
return detail::is_unicode<Char>()
? vprint(to_string_view(format_str), vargs)
: detail::vprint_mojibake(stdout, to_string_view(format_str),

1898
src/fmt/format-inl.h
View File

File diff suppressed because it is too large Load Diff

1151
src/fmt/format.h
View File

File diff suppressed because it is too large Load Diff

44
src/fmt/locale.h
View File

@ -15,22 +15,12 @@
FMT_BEGIN_NAMESPACE
namespace detail {
template <typename Char>
typename buffer_context<Char>::iterator vformat_to(
const std::locale& loc, buffer<Char>& buf,
basic_string_view<Char> format_str,
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
using af = arg_formatter<typename buffer_context<Char>::iterator, Char>;
return vformat_to<af>(std::back_inserter(buf), to_string_view(format_str),
args, detail::locale_ref(loc));
}
template <typename Char>
std::basic_string<Char> vformat(
const std::locale& loc, basic_string_view<Char> format_str,
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
basic_memory_buffer<Char> buffer;
detail::vformat_to(loc, buffer, format_str, args);
detail::vformat_to(buffer, format_str, args, detail::locale_ref(loc));
return fmt::to_string(buffer);
}
} // namespace detail
@ -45,32 +35,28 @@ inline std::basic_string<Char> vformat(
template <typename S, typename... Args, typename Char = char_t<S>>
inline std::basic_string<Char> format(const std::locale& loc,
const S& format_str, Args&&... args) {
return detail::vformat(
loc, to_string_view(format_str),
detail::make_args_checked<Args...>(format_str, args...));
return detail::vformat(loc, to_string_view(format_str),
fmt::make_args_checked<Args...>(format_str, args...));
}
template <typename S, typename OutputIt, typename... Args,
typename Char = enable_if_t<
detail::is_output_iterator<OutputIt>::value, char_t<S>>>
typename Char = char_t<S>,
FMT_ENABLE_IF(detail::is_output_iterator<OutputIt, Char>::value)>
inline OutputIt vformat_to(
OutputIt out, const std::locale& loc, const S& format_str,
format_args_t<type_identity_t<OutputIt>, Char> args) {
using af = detail::arg_formatter<OutputIt, Char>;
return vformat_to<af>(out, to_string_view(format_str), args,
detail::locale_ref(loc));
basic_format_args<buffer_context<type_identity_t<Char>>> args) {
decltype(detail::get_buffer<Char>(out)) buf(detail::get_buffer_init(out));
vformat_to(buf, to_string_view(format_str), args, detail::locale_ref(loc));
return detail::get_iterator(buf);
}
template <typename OutputIt, typename S, typename... Args,
FMT_ENABLE_IF(detail::is_output_iterator<OutputIt>::value&&
detail::is_string<S>::value)>
inline OutputIt format_to(OutputIt out, const std::locale& loc,
const S& format_str, Args&&... args) {
detail::check_format_string<Args...>(format_str);
using context = format_context_t<OutputIt, char_t<S>>;
format_arg_store<context, Args...> as{args...};
return vformat_to(out, loc, to_string_view(format_str),
basic_format_args<context>(as));
bool enable = detail::is_output_iterator<OutputIt, char_t<S>>::value>
inline auto format_to(OutputIt out, const std::locale& loc,
const S& format_str, Args&&... args) ->
typename std::enable_if<enable, OutputIt>::type {
const auto& vargs = fmt::make_args_checked<Args...>(format_str, args...);
return vformat_to(out, loc, to_string_view(format_str), vargs);
}
FMT_END_NAMESPACE

106
src/fmt/os.h
View File

@ -29,7 +29,8 @@
#if FMT_HAS_INCLUDE("winapifamily.h")
# include <winapifamily.h>
#endif
#if FMT_HAS_INCLUDE("fcntl.h") && \
#if (FMT_HAS_INCLUDE(<fcntl.h>) || defined(__APPLE__) || \
defined(__linux__)) && \
(!defined(WINAPI_FAMILY) || (WINAPI_FAMILY == WINAPI_FAMILY_DESKTOP_APP))
# include <fcntl.h> // for O_RDONLY
# define FMT_USE_FCNTL 1
@ -278,7 +279,8 @@ class file {
RDONLY = FMT_POSIX(O_RDONLY), // Open for reading only.
WRONLY = FMT_POSIX(O_WRONLY), // Open for writing only.
RDWR = FMT_POSIX(O_RDWR), // Open for reading and writing.
CREATE = FMT_POSIX(O_CREAT) // Create if the file doesn't exist.
CREATE = FMT_POSIX(O_CREAT), // Create if the file doesn't exist.
APPEND = FMT_POSIX(O_APPEND) // Open in append mode.
};
// Constructs a file object which doesn't represent any file.
@ -343,36 +345,69 @@ class file {
// Returns the memory page size.
long getpagesize();
class direct_buffered_file;
namespace detail {
template <typename S, typename... Args>
void print(direct_buffered_file& f, const S& format_str,
const Args&... args);
struct buffer_size {
size_t value = 0;
buffer_size operator=(size_t val) const {
auto bs = buffer_size();
bs.value = val;
return bs;
}
};
// A buffered file with a direct buffer access and no synchronization.
class direct_buffered_file {
struct ostream_params {
int oflag = file::WRONLY | file::CREATE;
size_t buffer_size = BUFSIZ > 32768 ? BUFSIZ : 32768;
ostream_params() {}
template <typename... T>
ostream_params(T... params, int oflag) : ostream_params(params...) {
this->oflag = oflag;
}
template <typename... T>
ostream_params(T... params, detail::buffer_size bs)
: ostream_params(params...) {
this->buffer_size = bs.value;
}
};
} // namespace detail
static constexpr detail::buffer_size buffer_size;
// A fast output stream which is not thread-safe.
class ostream final : private detail::buffer<char> {
private:
file file_;
enum { buffer_size = 4096 };
char buffer_[buffer_size];
int pos_;
void flush() {
if (pos_ == 0) return;
file_.write(buffer_, pos_);
pos_ = 0;
if (size() == 0) return;
file_.write(data(), size());
clear();
}
int free_capacity() const { return buffer_size - pos_; }
void grow(size_t) final;
ostream(cstring_view path, const detail::ostream_params& params)
: file_(path, params.oflag) {
set(new char[params.buffer_size], params.buffer_size);
}
public:
direct_buffered_file(cstring_view path, int oflag)
: file_(path, oflag), pos_(0) {}
~direct_buffered_file() {
flush();
ostream(ostream&& other)
: detail::buffer<char>(other.data(), other.size(), other.capacity()),
file_(std::move(other.file_)) {
other.set(nullptr, 0);
}
~ostream() {
flush();
delete[] data();
}
template <typename... T>
friend ostream output_file(cstring_view path, T... params);
void close() {
flush();
@ -380,25 +415,20 @@ class direct_buffered_file {
}
template <typename S, typename... Args>
friend void print(direct_buffered_file& f, const S& format_str,
const Args&... args) {
// We could avoid double buffering.
auto buf = fmt::memory_buffer();
fmt::format_to(std::back_inserter(buf), format_str, args...);
auto remaining_pos = 0;
auto remaining_size = buf.size();
while (remaining_size > detail::to_unsigned(f.free_capacity())) {
auto size = f.free_capacity();
memcpy(f.buffer_ + f.pos_, buf.data() + remaining_pos, size);
f.pos_ += size;
f.flush();
remaining_pos += size;
remaining_size -= size;
}
memcpy(f.buffer_ + f.pos_, buf.data() + remaining_pos, remaining_size);
f.pos_ += static_cast<int>(remaining_size);
void print(const S& format_str, const Args&... args) {
format_to(detail::buffer_appender<char>(*this), format_str, args...);
}
};
/**
Opens a file for writing. Supported parameters passed in `params`:
* ``<integer>``: Output flags (``file::WRONLY | file::CREATE`` by default)
* ``buffer_size=<integer>``: Output buffer size
*/
template <typename... T>
inline ostream output_file(cstring_view path, T... params) {
return {path, detail::ostream_params(params...)};
}
#endif // FMT_USE_FCNTL
#ifdef FMT_LOCALE

28
src/fmt/ostream.h
View File

@ -49,17 +49,27 @@ template <class Char> class formatbuf : public std::basic_streambuf<Char> {
}
};
struct converter {
template <typename T, FMT_ENABLE_IF(is_integral<T>::value)> converter(T);
};
template <typename Char> struct test_stream : std::basic_ostream<Char> {
private:
// Hide all operator<< from std::basic_ostream<Char>.
void_t<> operator<<(null<>);
void_t<> operator<<(const Char*);
template <typename T, FMT_ENABLE_IF(std::is_convertible<T, int>::value &&
!std::is_enum<T>::value)>
void_t<> operator<<(T);
void_t<> operator<<(converter);
};
// Hide insertion operators for built-in types.
template <typename Char, typename Traits>
void_t<> operator<<(std::basic_ostream<Char, Traits>&, Char);
template <typename Char, typename Traits>
void_t<> operator<<(std::basic_ostream<Char, Traits>&, char);
template <typename Traits>
void_t<> operator<<(std::basic_ostream<char, Traits>&, char);
template <typename Traits>
void_t<> operator<<(std::basic_ostream<char, Traits>&, signed char);
template <typename Traits>
void_t<> operator<<(std::basic_ostream<char, Traits>&, unsigned char);
// Checks if T has a user-defined operator<< (e.g. not a member of
// std::ostream).
template <typename T, typename Char> class is_streamable {
@ -103,7 +113,7 @@ void format_value(buffer<Char>& buf, const T& value,
#endif
output << value;
output.exceptions(std::ios_base::failbit | std::ios_base::badbit);
buf.resize(buf.size());
buf.try_resize(buf.size());
}
// Formats an object of type T that has an overloaded ostream operator<<.
@ -160,7 +170,7 @@ template <typename S, typename... Args,
typename Char = enable_if_t<detail::is_string<S>::value, char_t<S>>>
void print(std::basic_ostream<Char>& os, const S& format_str, Args&&... args) {
vprint(os, to_string_view(format_str),
detail::make_args_checked<Args...>(format_str, args...));
fmt::make_args_checked<Args...>(format_str, args...));
}
FMT_END_NAMESPACE

4
src/fmt/printf.h
View File

@ -181,7 +181,7 @@ template <typename Char> class printf_width_handler {
template <typename Char, typename Context>
void vprintf(buffer<Char>& buf, basic_string_view<Char> format,
basic_format_args<Context> args) {
Context(std::back_inserter(buf), format, args).format();
Context(buffer_appender<Char>(buf), format, args).format();
}
} // namespace detail
@ -598,7 +598,7 @@ OutputIt basic_printf_context<OutputIt, Char>::format() {
template <typename Char>
using basic_printf_context_t =
basic_printf_context<std::back_insert_iterator<detail::buffer<Char>>, Char>;
basic_printf_context<detail::buffer_appender<Char>, Char>;
using printf_context = basic_printf_context_t<char>;
using wprintf_context = basic_printf_context_t<wchar_t>;

19
src/fmt/ranges.h
View File

@ -157,6 +157,9 @@ template <class Tuple, class F> void for_each(Tuple&& tup, F&& f) {
for_each(indexes, std::forward<Tuple>(tup), std::forward<F>(f));
}
template <typename Range>
using value_type = remove_cvref_t<decltype(*std::declval<Range>().begin())>;
template <typename Arg, FMT_ENABLE_IF(!is_like_std_string<
typename std::decay<Arg>::type>::value)>
FMT_CONSTEXPR const char* format_str_quoted(bool add_space, const Arg&) {
@ -182,7 +185,6 @@ FMT_CONSTEXPR const char* format_str_quoted(bool add_space, const char) {
FMT_CONSTEXPR const wchar_t* format_str_quoted(bool add_space, const wchar_t) {
return add_space ? L" '{}'" : L"'{}'";
}
} // namespace detail
template <typename T> struct is_tuple_like {
@ -246,9 +248,15 @@ template <typename T, typename Char> struct is_range {
!std::is_constructible<detail::std_string_view<Char>, T>::value;
};
template <typename RangeT, typename Char>
struct formatter<RangeT, Char,
enable_if_t<fmt::is_range<RangeT, Char>::value>> {
template <typename T, typename Char>
struct formatter<
T, Char,
enable_if_t<fmt::is_range<T, Char>::value
// Workaround a bug in MSVC 2017 and earlier.
#if !FMT_MSC_VER || FMT_MSC_VER >= 1927
&& has_formatter<detail::value_type<T>, format_context>::value
#endif
>> {
formatting_range<Char> formatting;
template <typename ParseContext>
@ -257,8 +265,7 @@ struct formatter<RangeT, Char,
}
template <typename FormatContext>
typename FormatContext::iterator format(const RangeT& values,
FormatContext& ctx) {
typename FormatContext::iterator format(const T& values, FormatContext& ctx) {
auto out = detail::copy(formatting.prefix, ctx.out());
size_t i = 0;
auto it = values.begin();

34
src/fmtlib_format.cpp
View File

@ -23,6 +23,36 @@ int format_float(char* buf, std::size_t size, const char* format, int precision,
return precision < 0 ? snprintf_ptr(buf, size, format, value)
: snprintf_ptr(buf, size, format, precision, value);
}
template dragonbox::decimal_fp<float> dragonbox::to_decimal(float x)
FMT_NOEXCEPT;
template dragonbox::decimal_fp<double> dragonbox::to_decimal(double x)
FMT_NOEXCEPT;
// DEPRECATED! This function exists for ABI compatibility.
template <typename Char>
typename basic_format_context<std::back_insert_iterator<buffer<Char>>,
Char>::iterator
vformat_to(buffer<Char>& buf, basic_string_view<Char> format_str,
basic_format_args<basic_format_context<
std::back_insert_iterator<buffer<type_identity_t<Char>>>,
type_identity_t<Char>>>
args) {
using iterator = std::back_insert_iterator<buffer<char>>;
using context = basic_format_context<
std::back_insert_iterator<buffer<type_identity_t<Char>>>,
type_identity_t<Char>>;
auto out = iterator(buf);
format_handler<iterator, Char, context> h(out, format_str, args, {});
parse_format_string<false>(format_str, h);
return out;
}
template basic_format_context<std::back_insert_iterator<buffer<char>>,
char>::iterator
vformat_to(buffer<char>&, string_view,
basic_format_args<basic_format_context<
std::back_insert_iterator<buffer<type_identity_t<char>>>,
type_identity_t<char>>>);
} // namespace detail
template struct FMT_INSTANTIATION_DEF_API detail::basic_data<void>;
@ -44,9 +74,9 @@ template FMT_API char detail::decimal_point_impl(locale_ref);
template FMT_API void detail::buffer<char>::append(const char*, const char*);
template FMT_API FMT_BUFFER_CONTEXT(char)::iterator detail::vformat_to(
template FMT_API void detail::vformat_to(
detail::buffer<char>&, string_view,
basic_format_args<FMT_BUFFER_CONTEXT(char)>);
basic_format_args<FMT_BUFFER_CONTEXT(char)>, detail::locale_ref);
template FMT_API int detail::snprintf_float(double, int, detail::float_specs,
detail::buffer<char>&);

17
src/fmtlib_os.cpp
View File

@ -62,7 +62,7 @@ using RWResult = int;
inline unsigned convert_rwcount(std::size_t count) {
return count <= UINT_MAX ? static_cast<unsigned>(count) : UINT_MAX;
}
#else
#elif FMT_USE_FCNTL
// Return type of read and write functions.
using RWResult = ssize_t;
@ -124,7 +124,8 @@ void detail::format_windows_error(detail::buffer<char>& out, int error_code,
if (result != 0) {
utf16_to_utf8 utf8_message;
if (utf8_message.convert(system_message) == ERROR_SUCCESS) {
format_to(std::back_inserter(out), "{}: {}", message, utf8_message);
format_to(buffer_appender<char>(out), "{}: {}", message,
utf8_message);
return;
}
break;
@ -288,12 +289,12 @@ void file::pipe(file& read_end, file& write_end) {
}
buffered_file file::fdopen(const char* mode) {
// Don't retry as fdopen doesn't return EINTR.
#if defined(__MINGW32__) && defined(_POSIX_)
// Don't retry as fdopen doesn't return EINTR.
# if defined(__MINGW32__) && defined(_POSIX_)
FILE* f = ::fdopen(fd_, mode);
#else
# else
FILE* f = FMT_POSIX_CALL(fdopen(fd_, mode));
#endif
# endif
if (!f)
FMT_THROW(
system_error(errno, "cannot associate stream with file descriptor"));
@ -313,5 +314,9 @@ long getpagesize() {
return size;
# endif
}
void ostream::grow(size_t) {
if (this->size() == this->capacity()) flush();
}
#endif // FMT_USE_FCNTL
FMT_END_NAMESPACE

Some files were not shown because too many files have changed in this diff Show More