Synchronous parallel kinetic Monte Carlo for continuum diffusion-reaction systems

Journal of Computational Physics

Volumn 227, Issue 8, 2008, Pages 3804-3823

  Martinez E ^a,b   Marian, J ^a   Kalos, M H ^a   Perlado, J M ^b  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b INSTITUTO DE FUSIÓN NUCLEAR   (Spain)

Author keywords

Diffusion; Kinetic Monte Carlo; Parallel computing; Scalability

Indexed keywords

KINETICS; MONTE CARLO METHODS; PARALLEL ARCHITECTURES;

ASYMPTOTIC BEHAVIOUR; DIFFUSION PROBLEMS; DIFFUSION-REACTION SYSTEMS; GENERALISATION; KINETIC MONTE CARLO; KINETIC MONTE CARLO METHODS; MASTER EQUATIONS; MONTE CARLO ALGORITHMS; PARALLEL COM- PUTING; PARALLEL PERFORMANCE;

DIFFUSION;

EID: 40249094406     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2007.11.045     Document Type: Article

References (35)

1. M.H. Kalos P.A. Whitlock Monte Carlo Methods 1986 John Wiley & Sons New York
2. D.P. Landau K. Binder Monte Carlo Simulations in Statistical Physics 2000 Cambridge University Press
3. R. Friedberg J.E. Cameron J. Chem. Phys. 52 1970 6049
4. R.H. Swendsen J.S. Wang Phys. Rev. Lett. 57 1986 2607
5. B.D. Lubachevsky Complex Sys. 1 1987 1099
6. B.D. Lubachevsky J. Comput. Phys. 75 1988 103
7. G. Korniss Z. Toroczkai M.A. Novotny P.A. Rikvold Phys. Rev. Lett. 84 2000 1351
8. G. Korniss M.A. Novotny H. Guclu Z. Toroczkai P.A. Rikvold Science 299 2003 677
9. Y. Shim J.G. Amar J. Comput. Phys. 212 2006 305
10. D.R. Jefferson Virtual time ACM Trans. Prog. Lang. Syst. 7 1985 404
11. S.G. Eick A.G. Greenberg B.D. Lubachevsky A. Weiss ACM Trans. Model. Comp. Simul. 3 1993 287
12. B.D. Lubachevsky, A. Weiss, in: Proceedings of the 15th Workshop on Parallel and Distributed Simulations, Lake Arrowhead, CA, 2001, p. 185.
13. Y. Shim J.G. Amar Phys. Rev. B 71 2005 115436
14. M. Merrick K.A. Fichthorn Phys. Rev. E 75 2007 011606
15. Y. Shim J.G. Amar Phys. Rev. B 71 2005 125432
16. A.B. Bortz M.H. Kalos J.L. Lebowitz J. Comput. Phys. 17 1975 10
17. P. Hanusse A. Blanché J. Chem. Phys. 74 1981 6148
18. D. ben-Avraham J. Chem. Phys. 88 1987 941
19. I. Beichl F. Sullivan IEEE Comput. Sci. Eng. 4 1997 91
20. J.G. Amar Comput. Sci. Eng. 8 2006 9
21. M.J. Berger S.H. Bokhari IEEE Trans. Comput. 36 1987 570
22. K. Kang S. Redner Phys. Rev. A 32 1985 435
23. F. Leyvraz S. Redner Phys. Rev. Lett. 66 1991 216
24. T. Oppelstrup V.V. Bulatov G.H. Gilmer M.H. Kalos B. Sadigh Phys. Rev. Lett. 97 2006 230602
25. M.J. Caturla N. Soneda E. Alonso B.D. Wirth T. Díaz de la Rubia J.M. Perlado J. Nucl. Mater. 276 2001 13
26. The LLNL “Zeus” cluster ( http://www.llnl.gov/computing/tutorials/lc_resources/#IntelSystems ) on which all kMC simulations were performed runs version 1 of the MPI libraries, with two-sided communications.
27. D.J. Kerbyson, H.J. Alme, A. Hoisie, F. Petrini, H.J. Wasserman, M. Gittings, in: Proceedings of the ACM/IEEE SC2001 Conference, 2001.
28. S. Goedecker A. Hoisie Performance Optimization of Numerically Intensive Codes 2001 SIAM Philadelphia, PA
29. G. Amdahl, in: AFIPS Conference Proceedings, vol. 30, 1967, pp. 483–485.
30. C.K. Wong M.C. Easton SIAM J. Comput. 9 1980 111
31. D.E. Knuth second ed. The Art of Computer Programming: Sorting and Searching vol. 3 1998 Addison-Wesley Professional
32. I. Beichl F. Sullivan IEEE Comput. Sci. Eng. 3 1996 13
33. D.E. Culler R. Karp D.A. Patterson A. Sahay K.E. Schauser E. Santos R. Subramonian T. von Eicken Commun. ACM 39 1996 78
34. K.W. Cameron R. Ge X.H. Sun IEEE Trans. Comput. 56 2007 314