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update citation info with new LAMMPS paper reference and acknowledge it

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Axel Kohlmeyer
2021-09-23 11:52:31 -04:00
parent 5ef4913ebb
commit 16ab49cff4
2 changed files with 42 additions and 22 deletions
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6
doc/src/Developer_parallel.rst
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@ -12,6 +12,12 @@ most of the following illustrations show the 2d simulation case. The
underlying algorithms in those cases, however, apply to both 2d and 3d underlying algorithms in those cases, however, apply to both 2d and 3d
cases equally well. cases equally well.
.. note::
The text and most of the figures in this chapter were adapted
for the manual from the section on parallel algorithms in the
:ref:`new LAMMPS paper <lammps_paper>`.
.. toctree:: .. toctree::
:maxdepth: 1 :maxdepth: 1

58
doc/src/Intro_citing.rst
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@ -4,28 +4,40 @@ Citing LAMMPS
Core Algorithms Core Algorithms
^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^
Since LAMMPS is a community project, there is not a single one Since LAMMPS is a community project there is not one single publication
publication or reference that describes **all** of LAMMPS. or reference that describes **all** of LAMMPS. There are publications
The canonical publication that describes the foundation, that is describing the core of LAMMPS, but then also publications describing the
the basic spatial decomposition approach, the neighbor finding, algorithms and methods it implements or the software that it has
and basic communications algorithms used in LAMMPS is: interfaces to. Please see below for how to cite contributions to
LAMMPS.
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_ .. _lammps_paper:
So any project using LAMMPS (or a derivative application using LAMMPS as The canonical publication that describes the basic features, the source
a simulation engine) should cite this paper. A new publication code design, the program structure, the spatial decomposition approach,
describing the developments and improvements of LAMMPS in the 25 years the neighbor finding, basic communications algorithms, and how users and
since then is currently in preparation. developers have contributed to LAMMPS is:
`LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. (accepted 09/2021), DOI:10.1016/j.cpc.2021.108171 <https://doi.org/10.1016/j.cpc.2021.108171>`_
So any project using LAMMPS or a derivative application that uses LAMMPS
as a simulation engine should cite this paper. The paper is expected to
be published in its final form under the same DOI in the first half of 2022.
The original publication describing LAMMPS in its early implementations is:
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
DOI for the LAMMPS code DOI for the LAMMPS code
^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS developers use the `Zenodo service at CERN LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
<https://zenodo.org/>`_ to create digital object identifies (DOI) for to create digital object identifies (DOI) for stable releases of the
stable releases of the LAMMPS code. There are two types of DOIs for the LAMMPS source code. There are two types of DOIs for the LAMMPS source code.
LAMMPS source code: the canonical DOI for **all** versions of LAMMPS,
which will always point to the **latest** stable release version is: 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>`_
@ -45,11 +57,13 @@ about LAMMPS and its features.
Citing contributions Citing contributions
^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^
LAMMPS has many features and that use either previously published LAMMPS has many features that use either previously published methods
methods and algorithms or novel features. It also includes potential and algorithms or novel features. It also includes potential parameter
parameter filed for specific models. Where available, a reminder about files for specific models. Where available, a reminder about references
references for optional features used in a specific run is printed to for optional features used in a specific run is printed to the screen
the screen and log file. Style and output location can be selected with and log file. Style and output location can be selected with the
the :ref:`-cite command-line switch <cite>`. Additional references are :ref:`-cite command-line switch <cite>`. Additional references are
given in the documentation of the :doc:`corresponding commands given in the documentation of the :doc:`corresponding commands
<Commands_all>` or in the :doc:`Howto tutorials <Howto>`. <Commands_all>` or in the :doc:`Howto tutorials <Howto>`. So please
make certain, that you provide the proper acknowledgments and citations
in any published works using LAMMPS.