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Merge pull request #2545 from akohlmey/citation-refactor

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Refactor citation handling in LAMMPS
This commit is contained in:
Axel Kohlmeyer
2021-02-10 18:19:21 -05:00
committed by GitHub
parent 6adcb4f5b9 f8a5991416
commit 11d99d9513
11 changed files with 190 additions and 69 deletions
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19
doc/src/Intro_citing.rst
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@ -38,17 +38,18 @@ In addition there are DOIs for individual stable releases. Currently there are:
Home page
^^^^^^^^^
The LAMMPS website at `https://lammps.sandia.gov/ <https://lammps.sandia.gov>`_ is the canonical
location for information about LAMMPS and more detailed lists of publications
using LAMMPS and contributing features.
The LAMMPS website at `https://lammps.sandia.gov/
<https://lammps.sandia.gov>`_ is the canonical location for information
about LAMMPS and its features.
Citing contributions
^^^^^^^^^^^^^^^^^^^^
LAMMPS has many features and uses previously published methods and
algorithms or novel features. It also includes potential parameter
filed for specific models. You can look up relevant publications either
in the LAMMPS output to the screen, the ``log.cite`` file (which is
populated with references to relevant papers through embedding them into
the source code) and in the documentation of the :doc:`corresponding commands
LAMMPS has many features and that use either previously published
methods and algorithms or novel features. It also includes potential
parameter filed for specific models. Where available, a reminder about
references for optional features used in a specific run is printed to
the screen and log file. Style and output location can be selected with
the :ref:`-cite command-line switch <cite>`. Additional references are
given in the documentation of the :doc:`corresponding commands
<Commands_all>` or in the :doc:`Howto tutorials <Howto>`.

26
doc/src/Modify_contribute.rst
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@ -206,16 +206,22 @@ packages in the src directory for examples. If you are uncertain, please ask.
algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the \*.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the
constructor of the class. Whenever a user invokes your feature from
their input script, this will cause LAMMPS to output the citation to a
log.cite file and prompt the user to examine the file. Note that you
should only use this for a paper you or your group authored.
E.g. adding a cite in the code for a paper by Nose and Hoover if you
write a fix that implements their integrator is not the intended
usage. That kind of citation should just be in the doc page you
provide.
A LaTeX citation is stored in a variable at the top of the file and
a single line of code registering this variable is added to the
constructor of the class. If there is additional functionality (which
may have been added later) described in a different publication,
additional citation descriptions may be added for as long as they
are only registered when the corresponding keyword activating this
functionality is used. With these options it is possible to have
LAMMPS output a specific citation reminder whenever a user invokes
your feature from their input script. Note that you should only use
this for the most relevant paper for a feature and a publication that
you or your group authored. E.g. adding a citation in the code for
a paper by Nose and Hoover if you write a fix that implements their
integrator is not the intended usage. That kind of citation should
just be included in the documentation page you provide describing
your contribution. If you are not sure what the best option would
be, please contact the LAMMPS developers for advice.
Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the

26
doc/src/Run_options.rst
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@ -11,6 +11,7 @@ letter abbreviation can be used:
* :ref:`-k or -kokkos <run-kokkos>`
* :ref:`-l or -log <log>`
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
* :ref:`-pk or -package <package>`
* :ref:`-p or -partition <partition>`
@ -220,14 +221,31 @@ links with from the lib/message directory. See the
----------
.. _cite:
**-cite style or file name**
Select how and where to output a reminder about citing contributions
to the LAMMPS code that were used during the run. Available styles are
"both", "none", "screen", or "log". Any flag will be considered a file
name to write the detailed citation info to. Default is the "log" style
where there is a short summary in the screen output and detailed citations
in BibTeX format in the logfile. The option "both" selects the detailed
output for both, "none", the short output for both, and "screen" will
write the detailed info to the screen and the short version to the log
file. If a dedicated citation info file is requested, the screen and
log file output will be in the short format (same as with "none").
See the :doc:`citation page <Intro_citing>` for more details on
how to correctly reference and cite LAMMPS.
----------
.. _nocite:
**-nocite**
Disable writing the log.cite file which is normally written to list
references for specific cite-able features used during a LAMMPS run.
See the `citation page <https://lammps.sandia.gov/cite.html>`_ for more
details.
Disable generating a citation reminder (see above) at all.
----------

4
doc/src/fix_bond_react.rst
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@ -650,8 +650,8 @@ reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
.. _Gissinger:
**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
**(Gissinger2017)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
.. _Gissinger2020:
**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
**(Gissinger2020)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).

2
doc/src/kim_commands.rst
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@ -1286,7 +1286,7 @@ to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`, KIM API
in addition to the relevant scientific references for the IM.
The citation format for an IM is displayed on its page on
`OpenKIM <https://openkim.org>`_ along with the corresponding BibTex file,
and is automatically added to the LAMMPS *log.cite* file.
and is automatically added to the LAMMPS citation reminder.
Citing the IM software (KIM infrastructure and specific PM or SM codes)
used in the simulation gives credit to the researchers who developed them