update some formulations as suggested by @sjplimp

This commit is contained in:
Axel Kohlmeyer
2021-09-23 13:17:43 -04:00
parent 16ab49cff4
commit 46f331095a
2 changed files with 23 additions and 23 deletions

View File

@ -1,16 +1,16 @@
Parallel algorithms Parallel algorithms
------------------- -------------------
LAMMPS is from ground up designed to be running in parallel using the LAMMPS is designed to enable running simulations in parallel using the
MPI standard with distributed data via domain decomposition. The MPI parallel communication standard with distributed data via domain
parallelization has to be efficient to enable good strong scaling (= decomposition. The parallelization aims to be efficient result in good
good speedup for the same system) and good weak scaling (= the strong scaling (= good speedup for the same system) and good weak
computational cost of enlarging the system is proportional to the system scaling (= the computational cost of enlarging the system is
size). Additional parallelization using GPUs or OpenMP can then be proportional to the system size). Additional parallelization using GPUs
applied within the sub-domain assigned to an MPI process. For clarity, or OpenMP can also be applied within the sub-domain assigned to an MPI
most of the following illustrations show the 2d simulation case. The process. For clarity, most of the following illustrations show the 2d
underlying algorithms in those cases, however, apply to both 2d and 3d simulation case. The underlying algorithms in those cases, however,
cases equally well. apply to both 2d and 3d cases equally well.
.. note:: .. note::

View File

@ -4,27 +4,27 @@ Citing LAMMPS
Core Algorithms Core Algorithms
^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^
Since LAMMPS is a community project there is not one single publication The paper mentioned below is the best overview of LAMMPS, but there are
or reference that describes **all** of LAMMPS. There are publications also publications describing particular models or algorithms implemented
describing the core of LAMMPS, but then also publications describing the in LAMMPS or complementary software that is has interfaces to. Please
algorithms and methods it implements or the software that it has see below for how to cite contributions to LAMMPS.
interfaces to. Please see below for how to cite contributions to
LAMMPS.
.. _lammps_paper: .. _lammps_paper:
The canonical publication that describes the basic features, the source The latest canonical publication that describes the basic features, the
code design, the program structure, the spatial decomposition approach, source code design, the program structure, the spatial decomposition
the neighbor finding, basic communications algorithms, and how users and approach, the neighbor finding, basic communications algorithms, and how
developers have contributed to LAMMPS is: 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>`_ `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 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>`_ `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>`_