Hostname: page-component-84b7d79bbc-g78kv Total loading time: 0 Render date: 2024-07-28T06:13:40.818Z Has data issue: false hasContentIssue false
  • English
  • Français

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
Get access

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
Check for updates
Copyright
Copyright © Materials Research Society 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

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

REFERENCES

Kadau, K., Germann, T.C., and Lomdahl, P.S.: Molecular dynamics comes of age: 320 billion atom simulation on BlueGene/L. Int. J. Mod. Phys. C 17, 1755–1761 (2006).Google Scholar
Germann, T.C. and Kadau, K.: Trillion-atom molecular dynamics becomes a reality. Int. J. Mod. Phys. C 8, 1315–1319 (2008).Google Scholar
Voter, A.F.: A method for accelerating the molecular dynamics simulation of infrequent events. J. Chem. Phys. 106, 4665–4677 (1997).CrossRefGoogle Scholar
Voter, A.F.: Parallel replica method for dynamics of infrequent events. Phys. Rev. B 57, R13985 (1998).Google Scholar
Perez, D., Uberuaga, B.P., and Voter, A.F.: The parallel replica dynamics method coming of age. Comp. Mater. Sci. 100(Part B), 90–103 (2015).CrossRefGoogle Scholar
Sorensen, M.R. and Voter, A.F.: Temperature-accelerated dynamics for simulation of infrequent events. J. Chem. Phys. 112, 9599–9606 (2000).CrossRefGoogle Scholar
Vineyard, G.H.: Frequency factors and isotope effects in solid state rate processes. J. Phys. Chem. Solids 3, 121–127 (1957).Google Scholar
Zamora, R.J., Uberuaga, B.P., Perez, D., and Voter, A.F.: The modern temperature-accelerated dynamics approach. Annu. Rev. Chem. Biomol. Eng. 7, 87–110 (2016).Google Scholar
Zamora, R.J., Voter, A.F., Perriot, R., Perez, D., and Uberuaga, B.P.: The effects of cation-anion clustering on defect migration in MgAl2O4. Phys. Chem. Chem. Phys. 18, 19647–19654 (2016).Google Scholar
Allen, M.P. and Tildesley, D.J.: Computer Simulation of Liquids (Clarendon Press, New York, NY, 1989).Google Scholar
Jonsson, H., Mills, G., and Jacobsen, K.W.: Nudged elastic band method for finding minimum energy paths of transition. In Classical and Quantum Dynamics in Condensed Phase Simulations, Berne, B.J., Ciccotti, G., and Coker, D.F., eds. (World Scientific Publishing, Singapore, 1997), pp. 385–404.Google Scholar
Henkelman, G., Uberuaga, B.P., and Jónsson, H.: A climbing image nudged elastic band method for finding saddle points and minimum energy paths. J. Chem. Phys. 113, 9901 (2000).Google Scholar
Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117, 1–19 (1995).Google Scholar
Perez, D., Cubuk, E.D., Waterland, A., and Kaxiras, E.: Long-time dynamics through parallel trajectory splicing. J. Chem. Theory Comput. 12, 18–28 (2016).Google Scholar
Mniszewski, S.M., Junghans, C., Voter, A.F., Perez, D., and Eidenbenz, S.J.: TADSim: Discrete event-based performance prediction for temperature-accelerated dynamics. ACM Trans. Model. Comput. Simul. 25, 15:1–15:26 (2015).Google Scholar
Zamora, R.J., Voter, A.F., Perez, D., Santhi, N., Mniszewski, S.M., Thulasidasan, S., and Eidenbenz, S.J.: Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics. Simulation 92, 1065–1086 (2016).Google Scholar
Daw, M.S. and Baskes, M.I.: Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals. Phys. Rev. B 29, 6443–6453 (1984).Google Scholar
Voter, A.F.: Simulation of the layer-growth dynamics in silver films: Dynamics of adatom and vacancy clusters on ag (100). In 31st Annual Technical Symposium of the International Society for Optics and Photonics, Jacobson, M.R., ed. (Society of Photo-Optical Instrumentation Engineers, Bellingham, Washington, 1988), pp. 214–226.Google Scholar