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

Published online by Cambridge University Press:  20 December 2017

Danny Perez ,
Rao Huang  and
Arthur F. Voter
Danny Perez*
Affiliation:
Theoretical Division T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Rao Huang
Affiliation:
Theoretical Division T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Arthur F. Voter
Affiliation:
Theoretical Division T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
*
a)Address all correspondence to this author. e-mail: danny_perez@lanl.gov
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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. In this study, 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. 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.

Keywords

simulationnanoscale
Type
Article
Information
Journal of Materials Research , Volume 33 , Issue 7: Focus Issue: Advanced Atomistic Algorithms in Materials Science , 13 April 2018 , pp. 813 - 822
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Copyright
Copyright © Materials Research Society 2017 

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Footnotes

b)

This author was an editor of this journal during the review and decision stage. For the JMR policy on review and publication of manuscripts authored by editors, please refer to http://www.mrs.org/editor-manuscripts/.

c)

Permanent address: Department of Physics, Xiamen University, Xiamen 361005, China.

Contributing Editor: Vikram Gavini

References

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