Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing
Abstract
Molecular dynamics (MD) is one of the most widely used techniques in computational materials science. By providing fully resolved trajectories, it allows for a natural description of static, thermodynamic, and kinetic properties. A major hurdle that has hampered the use of MD is the fact that the timescales that can be directly simulated are very limited, even when using massively parallel computers. We compare two time-parallelization approaches, parallel replica dynamics (ParRep) and parallel trajectory splicing (ParSplice), that were specifically designed to address this issue for rare event systems by leveraging parallel computing resources. Using simulations of the relaxation of small disordered platinum nanoparticles, a comparative performance analysis of the two methods is presented. Finally, the results show that ParSplice can significantly outperform ParRep in the common case where the trajectory remains trapped for a long time within a region of configuration space but makes rapid structural transitions within this region.
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE National Nuclear Security Administration (NNSA); LANL Laboratory Directed Research and Development (LDRD) Program; China Scholarship Council
- OSTI Identifier:
- 1483553
- Report Number(s):
- LA-UR-18-30994
Journal ID: ISSN 0884-2914
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Materials Research
- Additional Journal Information:
- Journal Volume: 33; Journal Issue: 7; Journal ID: ISSN 0884-2914
- Publisher:
- Materials Research Society
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE; 97 MATHEMATICS AND COMPUTING
Citation Formats
Perez, Danny, Huang, Rao, and Voter, Arthur F. Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing. United States: N. p., 2017.
Web. doi:10.1557/jmr.2017.456.
Perez, Danny, Huang, Rao, & Voter, Arthur F. Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing. United States. https://doi.org/10.1557/jmr.2017.456
Perez, Danny, Huang, Rao, and Voter, Arthur F. Wed .
"Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing". United States. https://doi.org/10.1557/jmr.2017.456. https://www.osti.gov/servlets/purl/1483553.
@article{osti_1483553,
title = {Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing},
author = {Perez, Danny and Huang, Rao and Voter, Arthur F.},
abstractNote = {Molecular dynamics (MD) is one of the most widely used techniques in computational materials science. By providing fully resolved trajectories, it allows for a natural description of static, thermodynamic, and kinetic properties. A major hurdle that has hampered the use of MD is the fact that the timescales that can be directly simulated are very limited, even when using massively parallel computers. We compare two time-parallelization approaches, parallel replica dynamics (ParRep) and parallel trajectory splicing (ParSplice), that were specifically designed to address this issue for rare event systems by leveraging parallel computing resources. Using simulations of the relaxation of small disordered platinum nanoparticles, a comparative performance analysis of the two methods is presented. Finally, the results show that ParSplice can significantly outperform ParRep in the common case where the trajectory remains trapped for a long time within a region of configuration space but makes rapid structural transitions within this region.},
doi = {10.1557/jmr.2017.456},
journal = {Journal of Materials Research},
number = 7,
volume = 33,
place = {United States},
year = {Wed Dec 20 00:00:00 EST 2017},
month = {Wed Dec 20 00:00:00 EST 2017}
}
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Figures / Tables:
Table I: Performance summary for the ParSplice simulations of the relaxation of disordered Pt nanoparticles at different temperatures. Averages are taken over the entire simulations.
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Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.