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Title: Parallel algorithms for hyperdynamics and local hyperdynamics

Abstract

Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In [Kim, Perez, Voter, J Chem Phys, 139:144110, 2013)1, a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. In this paper, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost 3-5x that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clusteringmore » of Pt adatoms on a large patch of Pt(100) surface for 80 and 160 μs.« less

Authors:
ORCiD logo [1];  [2]; ORCiD logo [2]
+ Show Author Affiliations
  1. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC)
OSTI Identifier:
1668355
Alternate Identifier(s):
OSTI ID: 1645148
Report Number(s):
SAND-2020-4952J
Journal ID: ISSN 0021-9606; 686012; TRN: US2203691
Grant/Contract Number:  
AC04-94AL85000; 17-SC-20-SC; ACO2-06CH11357; 89233218NCA000001
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 153; Journal Issue: 5; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; accelerated molecular dynamics; hyperdynamics; parallel algorithms; LAMMPS

Citation Formats

Plimpton, Steven J., Perez, Danny, and Voter, Arthur F. Parallel algorithms for hyperdynamics and local hyperdynamics. United States: N. p., 2020. Web. doi:10.1063/5.0014448.
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Plimpton, Steven J., Perez, Danny, & Voter, Arthur F. Parallel algorithms for hyperdynamics and local hyperdynamics. United States. https://doi.org/10.1063/5.0014448
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Plimpton, Steven J., Perez, Danny, and Voter, Arthur F. Wed . "Parallel algorithms for hyperdynamics and local hyperdynamics". United States. https://doi.org/10.1063/5.0014448. https://www.osti.gov/servlets/purl/1668355.
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@article{osti_1668355,
title = {Parallel algorithms for hyperdynamics and local hyperdynamics},
author = {Plimpton, Steven J. and Perez, Danny and Voter, Arthur F.},
abstractNote = {Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In [Kim, Perez, Voter, J Chem Phys, 139:144110, 2013)1, a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. In this paper, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost 3-5x that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clustering of Pt adatoms on a large patch of Pt(100) surface for 80 and 160 μs.},
doi = {10.1063/5.0014448},
journal = {Journal of Chemical Physics},
number = 5,
volume = 153,
place = {United States},
year = {Wed Aug 05 00:00:00 EDT 2020},
month = {Wed Aug 05 00:00:00 EDT 2020}
}
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https://doi.org/10.1063/5.0014448
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