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document updated citation reminder

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This commit is contained in:
Axel Kohlmeyer
2021-01-08 18:29:15 -05:00
parent d3c14dcb51
commit 6428e542db
5 changed files with 43 additions and 23 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>`.

14
doc/src/Modify_contribute.rst
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@ -209,13 +209,13 @@ packages in the src directory for examples. If you are uncertain, please ask.
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.
their input script, this will cause LAMMPS to output a reminder to
cite that reference. 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 in the
documentation page you provide describing your contribution.
Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the

27
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 +221,32 @@ 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 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. Any other option will be taken as a file name to which the detailed
citation info is written and screen and log file output will be short
(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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@ -616,8 +616,8 @@ reset_mol_ids = yes, custom_charges = no, molecule = off
.. _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