update some formulations as suggested by @sjplimp
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Parallel algorithms
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Parallel algorithms
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-------------------
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LAMMPS is from ground up designed to be running in parallel using the
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LAMMPS is designed to enable running simulations in parallel using the
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MPI standard with distributed data via domain decomposition. The
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MPI parallel communication standard with distributed data via domain
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parallelization has to be efficient to enable good strong scaling (=
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decomposition. The parallelization aims to be efficient result in good
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good speedup for the same system) and good weak scaling (= the
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strong scaling (= good speedup for the same system) and good weak
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computational cost of enlarging the system is proportional to the system
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scaling (= the computational cost of enlarging the system is
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size). Additional parallelization using GPUs or OpenMP can then be
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proportional to the system size). Additional parallelization using GPUs
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applied within the sub-domain assigned to an MPI process. For clarity,
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or OpenMP can also be applied within the sub-domain assigned to an MPI
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most of the following illustrations show the 2d simulation case. The
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process. For clarity, most of the following illustrations show the 2d
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underlying algorithms in those cases, however, apply to both 2d and 3d
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simulation case. The underlying algorithms in those cases, however,
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cases equally well.
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apply to both 2d and 3d cases equally well.
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.. note::
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.. note::
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@ -4,27 +4,27 @@ Citing LAMMPS
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Core Algorithms
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Core Algorithms
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^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^
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Since LAMMPS is a community project there is not one single publication
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The paper mentioned below is the best overview of LAMMPS, but there are
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or reference that describes **all** of LAMMPS. There are publications
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also publications describing particular models or algorithms implemented
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describing the core of LAMMPS, but then also publications describing the
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in LAMMPS or complementary software that is has interfaces to. Please
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algorithms and methods it implements or the software that it has
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see below for how to cite contributions to LAMMPS.
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interfaces to. Please see below for how to cite contributions to
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LAMMPS.
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.. _lammps_paper:
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.. _lammps_paper:
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The canonical publication that describes the basic features, the source
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The latest canonical publication that describes the basic features, the
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code design, the program structure, the spatial decomposition approach,
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source code design, the program structure, the spatial decomposition
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the neighbor finding, basic communications algorithms, and how users and
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approach, the neighbor finding, basic communications algorithms, and how
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developers have contributed to LAMMPS is:
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users and developers have contributed to LAMMPS is:
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`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>`_
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`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>`_
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So any project using LAMMPS or a derivative application that uses LAMMPS
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So a project using LAMMPS or a derivative application that uses LAMMPS
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as a simulation engine should cite this paper. The paper is expected to
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as a simulation engine should cite this paper. The paper is expected to
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be published in its final form under the same DOI in the first half of 2022.
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be published in its final form under the same DOI in the first half
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of 2022.
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The original publication describing LAMMPS in its early implementations is:
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The original publication describing the parallel algorithms used in the
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initial versions of LAMMPS is:
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`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>`_
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`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>`_
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