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update some formulations as suggested by @sjplimp

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Axel Kohlmeyer
2021-09-23 13:17:43 -04:00
parent 16ab49cff4
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doc/src/Developer_parallel.rst
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@ -1,16 +1,16 @@
Parallel algorithms
-------------------
LAMMPS is from ground up designed to be running in parallel using the
MPI standard with distributed data via domain decomposition. The
parallelization has to be efficient to enable good strong scaling (=
good speedup for the same system) and good weak scaling (= the
computational cost of enlarging the system is proportional to the system
size). Additional parallelization using GPUs or OpenMP can then be
applied within the sub-domain assigned to an MPI process. For clarity,
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.
LAMMPS is designed to enable running simulations in parallel using the
MPI parallel communication standard with distributed data via domain
decomposition. The parallelization aims to be efficient result in good
strong scaling (= good speedup for the same system) and good weak
scaling (= the computational cost of enlarging the system is
proportional to the system size). Additional parallelization using GPUs
or OpenMP can also be applied within the sub-domain assigned to an MPI
process. For clarity, 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::

26
doc/src/Intro_citing.rst
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@ -4,27 +4,27 @@ Citing LAMMPS
Core Algorithms
^^^^^^^^^^^^^^^
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.
The paper mentioned below is the best overview of LAMMPS, but there are
also publications describing particular models or algorithms implemented
in LAMMPS or complementary software that is has interfaces to. Please
see below for how to cite contributions to LAMMPS.
.. _lammps_paper:
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:
The latest 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 <https://doi.org/10.1016/j.cpc.2021.108171>`_
So any project using LAMMPS or a derivative application that uses LAMMPS
So a 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.
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:
The original publication describing the parallel algorithms used in the
initial versions of LAMMPS 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>`_