From 16ab49cff463f94cca446c4d7f48cc76a35bc398 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 23 Sep 2021 11:52:31 -0400 Subject: [PATCH] update citation info with new LAMMPS paper reference and acknowledge it --- doc/src/Developer_parallel.rst | 6 ++++ doc/src/Intro_citing.rst | 58 +++++++++++++++++++++------------- 2 files changed, 42 insertions(+), 22 deletions(-) diff --git a/doc/src/Developer_parallel.rst b/doc/src/Developer_parallel.rst index 84b228280d..0e492772cc 100644 --- a/doc/src/Developer_parallel.rst +++ b/doc/src/Developer_parallel.rst @@ -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 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 `. + .. toctree:: :maxdepth: 1 diff --git a/doc/src/Intro_citing.rst b/doc/src/Intro_citing.rst index 978def9f15..7d63dfc518 100644 --- a/doc/src/Intro_citing.rst +++ b/doc/src/Intro_citing.rst @@ -4,28 +4,40 @@ Citing LAMMPS Core Algorithms ^^^^^^^^^^^^^^^ -Since LAMMPS is a community project, there is not a single one -publication or reference that describes **all** of LAMMPS. -The canonical publication that describes the foundation, that is -the basic spatial decomposition approach, the neighbor finding, -and basic communications algorithms used in LAMMPS is: +Since LAMMPS is a community project there is not one single publication +or reference that describes **all** of LAMMPS. There are publications +describing the core of LAMMPS, but then also publications describing the +algorithms and methods it implements or the software that it has +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). `_ +.. _lammps_paper: -So any project using LAMMPS (or a derivative application using LAMMPS as -a simulation engine) should cite this paper. A new publication -describing the developments and improvements of LAMMPS in the 25 years -since then is currently in preparation. +The canonical publication that describes the basic features, the source +code design, the program structure, the spatial decomposition approach, +the neighbor finding, basic communications algorithms, and how users and +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 `_ + +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). `_ DOI for the LAMMPS code ^^^^^^^^^^^^^^^^^^^^^^^ -LAMMPS developers use the `Zenodo service at CERN -`_ to create digital object identifies (DOI) for -stable releases of the LAMMPS code. There are two types of DOIs for the -LAMMPS source code: the canonical DOI for **all** versions of LAMMPS, -which will always point to the **latest** stable release version is: +LAMMPS developers use the `Zenodo service at CERN `_ +to create digital object identifies (DOI) for stable releases of the +LAMMPS source code. There are two types of DOIs for the 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 `_ @@ -45,11 +57,13 @@ about LAMMPS and its features. Citing contributions ^^^^^^^^^^^^^^^^^^^^ -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 `. Additional references are +LAMMPS has many features that use either previously published methods +and algorithms or novel features. It also includes potential parameter +files 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 `. Additional references are given in the documentation of the :doc:`corresponding commands -` or in the :doc:`Howto tutorials `. +` or in the :doc:`Howto tutorials `. So please +make certain, that you provide the proper acknowledgments and citations +in any published works using LAMMPS.