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Title: 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:
 [1];  [1];  [1]
  1. 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) (SC-22); 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. doi: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. doi: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 = {2017},
month = {12}
}

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Figures / Tables:

Table I 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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