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Speculation and replication in temperature accelerated dynamics

Published online by Cambridge University Press:  12 February 2018

Richard J. Zamora Open the ORCID record for Richard J. Zamora [Opens in a new window] ,
Danny Perez  and
Arthur F. Voter
Richard J. Zamora
Affiliation:
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Danny Perez
Affiliation:
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Arthur F. Voter*
Affiliation:
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
*
a)Address all correspondence to this author. e-mail: afv@lanl.gov
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Abstract

Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. Here, we compare the performance of speculative parallelism with a replica-based technique, similar to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.

Keywords

simulationdefects
Type
Article
Information
Journal of Materials Research , Volume 33 , Issue 7: Focus Issue: Advanced Atomistic Algorithms in Materials Science , 13 April 2018 , pp. 823 - 834
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Copyright
Copyright © Materials Research Society 2018 

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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/.

Contributing Editor: Enrique Martinez

References

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