Skip to main content Accessibility help

Speculation and replication in temperature accelerated dynamics

  • Richard J. Zamora (a1), Danny Perez (a1) and Arthur F. Voter (a1)


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.


Corresponding author

a)Address all correspondence to this author. e-mail:


Hide All

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

Contributing Editor: Enrique Martinez



Hide All
1.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, 17551761 (2006).
2.Germann, T.C. and Kadau, K.: Trillion-atom molecular dynamics becomes a reality. Int. J. Mod. Phys. C 8, 13151319 (2008).
3.Voter, A.F.: A method for accelerating the molecular dynamics simulation of infrequent events. J. Chem. Phys. 106, 46654677 (1997).
4.Voter, A.F.: Parallel replica method for dynamics of infrequent events. Phys. Rev. B 57, R13985 (1998).
5.Perez, D., Uberuaga, B.P., and Voter, A.F.: The parallel replica dynamics method coming of age. Comp. Mater. Sci. 100(Part B), 90103 (2015).
6.Sorensen, M.R. and Voter, A.F.: Temperature-accelerated dynamics for simulation of infrequent events. J. Chem. Phys. 112, 95999606 (2000).
7.Vineyard, G.H.: Frequency factors and isotope effects in solid state rate processes. J. Phys. Chem. Solids 3, 121127 (1957).
8.Zamora, R.J., Uberuaga, B.P., Perez, D., and Voter, A.F.: The modern temperature-accelerated dynamics approach. Annu. Rev. Chem. Biomol. Eng. 7, 87110 (2016).
9.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, 1964719654 (2016).
10.Allen, M.P. and Tildesley, D.J.: Computer Simulation of Liquids (Clarendon Press, New York, NY, 1989).
11.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. 385404.
12.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).
13.Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117, 119 (1995).
14.Perez, D., Cubuk, E.D., Waterland, A., and Kaxiras, E.: Long-time dynamics through parallel trajectory splicing. J. Chem. Theory Comput. 12, 1828 (2016).
15.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, 15:115:26 (2015).
16.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, 10651086 (2016).
17.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, 64436453 (1984).
18.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. 214226.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Journal of Materials Research
  • ISSN: 0884-2914
  • EISSN: 2044-5326
  • URL: /core/journals/journal-of-materials-research
Please enter your name
Please enter a valid email address
Who would you like to send this to? *



Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed