Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing

Perez, Danny; Huang, Rao; Voter, Arthur F.

doi:10.1557/jmr.2017.456

Title: Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing

Journal Article · Wed Dec 20 00:00:00 EST 2017 · Journal of Materials Research

DOI:https://doi.org/10.1557/jmr.2017.456· OSTI ID:1483553

Perez, Danny ^[1]; Huang, Rao ^[1]; Voter, Arthur F. ^[1]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: 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

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1483553

Report Number(s):: LA-UR-18-30994

Journal Information:: Journal of Materials Research, Vol. 33, Issue 7; ISSN 0884-2914

Publisher:: Materials Research SocietyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 13 works

Citation information provided by
Web of Science

References (20)

Temperature-accelerated dynamics for simulation of infrequent events So/rensen, Mads R.; Voter, Arthur F. The Journal of Chemical Physics, Vol. 112, Issue 21 https://doi.org/10.1063/1.481576	journal	June 2000
Icosahedral Short-Range Order in Deeply Undercooled Metallic Melts Schenk, T.; Holland-Moritz, D.; Simonet, V. Physical Review Letters, Vol. 89, Issue 7 https://doi.org/10.1103/PhysRevLett.89.075507	journal	July 2002
The parallel replica dynamics method – Coming of age Perez, Danny; Uberuaga, Blas P.; Voter, Arthur F. Computational Materials Science, Vol. 100 https://doi.org/10.1016/j.commatsci.2014.12.011	journal	April 2015
Accurate Interatomic Potentials for Ni, Al and Ni3Al Voter, Arthur F.; Chen, Shao Ping MRS Proceedings, Vol. 82 https://doi.org/10.1557/PROC-82-175	journal	January 1986
The Modern Temperature-Accelerated Dynamics Approach Zamora, Richard J.; Uberuaga, Blas P.; Perez, Danny Annual Review of Chemical and Biomolecular Engineering, Vol. 7, Issue 1 https://doi.org/10.1146/annurev-chembioeng-080615-033608	journal	June 2016
A local superbasin kinetic Monte Carlo method Fichthorn, Kristen A.; Lin, Yangzheng The Journal of Chemical Physics, Vol. 138, Issue 16 https://doi.org/10.1063/1.4801869	journal	April 2013
Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles Huang, Rao; Lo, Li-Ta; Wen, Yuhua The Journal of Chemical Physics, Vol. 147, Issue 15 https://doi.org/10.1063/1.4996922	journal	October 2017
Amorphization Mechanism of Icosahedral Metal Nanoclusters Aprà, E.; Baletto, F.; Ferrando, R. Physical Review Letters, Vol. 93, Issue 6 https://doi.org/10.1103/PhysRevLett.93.065502	journal	August 2004
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events Voter, Arthur F. Physical Review Letters, Vol. 78, Issue 20 https://doi.org/10.1103/PhysRevLett.78.3908	journal	May 1997
Observation of five-fold local symmetry in liquid lead Reichert, H.; Klein, O.; Dosch, H. Nature, Vol. 408, Issue 6814 https://doi.org/10.1038/35048537	journal	December 2000
Robust Perron cluster analysis in conformation dynamics Deuflhard, Peter; Weber, Marcus Linear Algebra and its Applications, Vol. 398 https://doi.org/10.1016/j.laa.2004.10.026	journal	March 2005
A mathematical formalization of the parallel replica dynamics Le Bris, Claude; Lelièvre, Tony; Luskin, Mitchell Monte Carlo Methods and Applications, Vol. 18, Issue 2 https://doi.org/10.1515/mcma-2012-0003	journal	January 2012
Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table Henkelman, Graeme; Jónsson, Hannes The Journal of Chemical Physics, Vol. 115, Issue 21 https://doi.org/10.1063/1.1415500	journal	December 2001
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants Chatterjee, Abhijit; Voter, Arthur F. The Journal of Chemical Physics, Vol. 132, Issue 19 https://doi.org/10.1063/1.3409606	journal	May 2010
Long-Time Dynamics through Parallel Trajectory Splicing Perez, Danny; Cubuk, Ekin D.; Waterland, Amos Journal of Chemical Theory and Computation, Vol. 12, Issue 1 https://doi.org/10.1021/acs.jctc.5b00916	journal	December 2015
The double-funnel energy landscape of the 38-atom Lennard-Jones cluster Doye, Jonathan P. K.; Miller, Mark A.; Wales, David J. The Journal of Chemical Physics, Vol. 110, Issue 14 https://doi.org/10.1063/1.478595	journal	April 1999
Structural changes accompanying densification of random hard-sphere packings Clarke, Andrew S.; Jónsson, Hannes Physical Review E, Vol. 47, Issue 6 https://doi.org/10.1103/physreve.47.3975	journal	June 1993
A mathematical formalization of the parallel replica dynamics Bris, C. Le; Lelièvre, T.; Luskin, M. arXiv https://doi.org/10.48550/arxiv.1105.4636	preprint	January 2011
The double-funnel energy landscape of the 38-atom Lennard-Jones cluster Doye, Jonathan; Miller, Mark; Wales, David arXiv https://doi.org/10.48550/arxiv.cond-mat/9808265	text	January 1998