Software:LAMMPS
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| Original author(s) | Steve Plimpton, Aidan Thompson, Stan Moore, Axel Kohlmeyer, Richard Berger |
|---|---|
| Developer(s) | Sandia National Laboratories Temple University |
| Initial release | 1995 |
| Stable release | 2August2023
/ August 2, 2023 |
| Repository | github |
| Written in | C++ |
| Operating system | Cross-platform: Linux, macOS, Windows, FreeBSD, Solaris |
| Platform | x86, x86-64, ARM, POWER9 |
| Size | 534 MB |
| Available in | English |
| Type | Molecular dynamics |
| License | GNU General Public License |
| Website | www |
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]
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
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, for example, GPU (CUDA, OpenCL, HIP, SYCL), Intel Xeon Phi, and OpenMP support for many code features.
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
- Parallel computing
- Comparison of software for molecular mechanics modeling
- Molecular design software
- List of free and open-source software packages
References
- ↑ 1.0 1.1 1.2 1.3 "LAMMPS Molecular Dynamics Simulator". Sandia National Laboratories. https://www.lammps.org/. Retrieved 2022-07-13.
- ↑ Plimpton, S. (1993-05-01). Fast parallel algorithms for short-range molecular dynamics. doi:10.2172/10176421. https://digital.library.unt.edu/ark:/67531/metadc1389173/.
- ↑ 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. https://www.osti.gov/biblio/1493836.
- ↑ 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. https://iopscience.iop.org/article/10.1088/0965-0393/18/1/015012.
- ↑ Goswami, Rohit; Goswami, Amrita; Singh, Jayant K. (2019). "dSEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations". Journal of Chemical Information and Modeling. doi:10.1021/acs.jcim.0c00031.s001.
- ↑ McGibbon, Robert T; Beauchamp, Kyle A; Schwantes, Christian R; Wang, Lee-Ping; Hernández, Carlos X; Harrigan, Matthew P; Lane, Thomas J; Swails, Jason M et al. (2014-09-09). "MDTraj: a modern, open library for the analysis of molecular dynamics trajectories". Biophysical Journal 109 (8): 1528–32. doi:10.1016/j.bpj.2015.08.015. PMID 26488642.
- ↑ 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. doi:10.1016/j.cpc.2013.09.018. ISSN 0010-4655. https://www.sciencedirect.com/science/article/pii/S0010465513003196.
- ↑ Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme (December 2013). "Using collective variables to drive molecular dynamics simulations" (in en). Molecular Physics 111 (22–23): 3345–3362. doi:10.1080/00268976.2013.813594. ISSN 0026-8976.
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