LAMMPS

Summary

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories.[1] LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License.[1]

Large-scale Atomic/Molecular Massively Parallel Simulator
Original author(s)Steve Plimpton, Aidan Thompson, Stan Moore, Axel Kohlmeyer, Richard Berger
Developer(s)Sandia National Laboratories
Temple University
Initial release1995; 29 years ago (1995)
Stable release
2August2023 / August 2, 2023; 11 months ago (2023-08-02)
Repositorygithub.com/lammps/lammps
Written inC++
Operating systemCross-platform: Linux, macOS, Windows, FreeBSD, Solaris
Platformx86, x86-64, ARM, POWER9
Size534 MB
Available inEnglish
TypeMolecular dynamics
LicenseGNU General Public License
Websitewww.lammps.org

LAMMPS was originally developed under a Cooperative Research and Development Agreement between two laboratories from United States Department of Energy and three other laboratories from private sector firms.[1] As of 2016, it is maintained and distributed by researchers at the Sandia National Laboratories and Temple University.[1]

Features

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For computing efficiency, LAMMPS uses neighbor lists (Verlet lists) to keep track of nearby particles. The lists are optimized for systems with particles that repel at short distances, so that the local density of particles never grows too large.[2]

On parallel computers, LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3D sub-domains, one of which is assigned to each processor. Processors communicate and store ghost atom information for atoms that border their subdomain. LAMMPS is most efficient (in a parallel computing sense) for systems whose particles fill a 3D rectangular box with approximately uniform density. Lots of accelerators are supported by LAMMPS, including GPU (CUDA, OpenCL, HIP, SYCL), Intel Xeon Phi, and OpenMP, due to its integration with Trilinos.

LAMMPS also allows for coupled spin and molecular dynamics in an accelerated fashion.[3]

LAMMPS is coupled to many analysis tools and engines as well.[4][5][6] LAMMPS also can be coupled with free energy calculators, such as PLUMED and Colvar.[7][8]

See also

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References

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  1. ^ a b c d "LAMMPS Molecular Dynamics Simulator". Sandia National Laboratories. Retrieved 2022-07-13.
  2. ^ Plimpton, S. (1993-05-01). "Fast parallel algorithms for short-range molecular dynamics". doi:10.2172/10176421. {{cite journal}}: Cite journal requires |journal= (help)
  3. ^ Tranchida, Julien Guy; Wood, Mitchell; Moore, Stan Gerald (2018-09-01). "Coupled Magnetic Spin Dynamics and Molecular Dynamics in a Massively Parallel Framework: LDRD Final Report". doi:10.2172/1493836. OSTI 1493836. S2CID 127973739. {{cite journal}}: Cite journal requires |journal= (help)
  4. ^ Stukowski, Alexander (2009-12-15). "Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool". Modelling and Simulation in Materials Science and Engineering. 18 (1): 015012. doi:10.1088/0965-0393/18/1/015012. ISSN 0965-0393. S2CID 42073422.
  5. ^ Goswami, Rohit; Goswami, Amrita; Singh, Jayant K. (2019). "dSEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations". Journal of Chemical Information and Modeling. arXiv:1909.09830. doi:10.1021/acs.jcim.0c00031.s001.
  6. ^ McGibbon, Robert T; Beauchamp, Kyle A; Schwantes, Christian R; Wang, Lee-Ping; Hernández, Carlos X; Harrigan, Matthew P; Lane, Thomas J; Swails, Jason M; Pande, Vijay S (2014-09-09). "MDTraj: a modern, open library for the analysis of molecular dynamics trajectories". Biophysical Journal. 109 (8): 1528–32. bioRxiv 10.1101/008896. doi:10.1016/j.bpj.2015.08.015. PMC 4623899. PMID 26488642.
  7. ^ Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni (2014-02-01). "PLUMED 2: New feathers for an old bird". Computer Physics Communications. 185 (2): 604–613. arXiv:1310.0980. doi:10.1016/j.cpc.2013.09.018. ISSN 0010-4655. S2CID 17904052.
  8. ^ Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme (December 2013). "Using collective variables to drive molecular dynamics simulations". Molecular Physics. 111 (22–23): 3345–3362. doi:10.1080/00268976.2013.813594. ISSN 0026-8976.
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  • Official website