Parallelization of a molecular dynamics simulation of an ion-surface collision system: Ar-Ni(100)

International Journal of Modern Physics C

Volumn 16, Issue 6, 2005, Pages 969-990

  Atiş, Murat ^a   Özdoǧan, Cem ^b   Güvenç, Ziya B ^b  

^a KIRIKKALE UNIVERSITY   (Turkey)

^b CANKAYA UNIVERSITY   (Turkey)

Author keywords

Ion surface collision; Linear scaling; Molecular dynamics; Parallel; PVM; Sputtering

Indexed keywords

EID: 22944434872     PISSN: 01291831     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0129183105007649     Document Type: Review

References (52)

1. M. P. Allen and D. J. Tildesley, Computer Simulation in Chemical Physics (Kluwer Academic Publishers, Amsterdam, 1993).
2. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Academic Press, San Diego, 1996).
3. J. M. Haile, Molecular Dynamics Simulation: Elementary Methods (Wiley-Interscience, New York, 1992).
4. D. W. Heermann, Computer Simulation Methods in Theoretical Physics (Springer-Verlag, Berlin, 1990).
5. D. C. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge University Press, New York, 1995).
6. N. Laegreid and G. K. Wehner, J. Appl. Phys. 32, 365 (1961).
7. H. Metiu and A. E. DePristo, J. Chem. Phys. 91, 2735 (1989).
8. F. Brugè, Comput. Phys. Commun. 90, 59 (1995).
9. M. Pütz and A. Kolb, Comput. Phys. Commun. 113, 145 (1998).
10. M. Pavese, S. Jang and G. A. Voth, Parallel Computing 26, 1025 (1998).
11. A. Fijany, T. Çaǧin, A. Jaramillo-Botero and W. Goddard, III, Advances in Engineering Software 29, 441 (1998).
12. A. Grama, V. Kumar and A. Sameh, Parallel Computing 24, 797 (1998).
13. R. Murty and D. Okunbur, Parallel Computing 25, 217 (1999).
14. H. Schwichtenberg, G. Winter and H. Wallmeier, Parallel Computing 25, 535 (1999).
15. F. Shimojo, T. J. Campbell, R. K. Kalia, A. Nakano, P. Vashishta, S. Ogata and K. Tsuruta, Future Generation Computer Systems 17, 279 (2000).
16. R. Couturier and C. Chipot, Comput. Phys. Commun. 124, 49 (2000).
17. R. Koradi, M. Billeter and P. Gntert, Comput. Phys. Commun. 124, 139 (2000).
18. V. Zaloj and R. Elber, Comput. Phys. Commun. 128, 118 (2000).
19. G. Heffelfinger, Comput. Phys. Commun. 128, 219 (2000).
20. C. F. Cornwell and L. T. Wille, Comput. Phys. Commun. 128, 477 (2000).
21. W. Andreoni and A. Curioni, Parallel Computing 26, 819 (2000).
22. A. P. Rendell, A. Bliznyuk, T. Huber, R. H. Nobes, E. V. Akhmatskaya, H. A. Früchtl, P. W.-C. Kung, V. Milman and H. Lung, Parallel Computing 26, 887 (2000).
23. C. Özdoǧan, G. Dereli and T. Çaǧin, Comp. Phys. Commun. 148, 188 (2002).
24. W. Gropp, E. Lusk and A. Skejellum, Using MPI Portable Parallel Programming with the Message Passing Interface (MIT Press, Cambridge, MA, 1994), http://www.netlib.org/mpi.
25. A. Geist, A. Beguelin, J. Dongarra, W. Jiang, R. Mancheck and V. Sunderam, PVM: Parallel Virtual Machine. A Users' Guide and Tutorial for Networked Parallel Computing (MIT Press, 1994), http://www.epm.ornl.gov/pvm.
26. M. J. Flynn, IEEE Trans. Comput. C-21, 948 (1972).
27. D. Brown, H. Minoux and B. Maigret, Comput. Phys. Commun. 103, 170 (1997).
28. J. Llnytski and M. R. Wilson, Comput. Phys. Commun. 134, 23 (2001).
29. K. Kadau, T. C. German and P. S. Lomdahl, Int. J. Mod. Phys. C 15, 193 (2004).
30. D. M. Beazley and P. S. Lomdahl, Parallel Computing 20, 173 (1994).
31. B. L. Holian, A. F. Voter, N. J. Wagner, R. J. Ravelo, S. P. Chen, W. G. Hoover, C. G. Hoover, J. E. Hammerberg and T. D. Dantje, Phys. Rev. A 43, 2655 (1991).
32. T. C. German, B. L. Holian, P. S. Lomdahl and R. J. Ravelo, Phys. Rev. Lett. 84, 55351 (2000).
33. R. W. Hamming, Numerical Methods for Scientists and Engineers (McGraw-Hill, New York, 1962).
34. A. F. Voter, Los Alamos Unclassified Technical Report # LA-UR 93, 3901 (1993); and references therein.
35. M. S. Daw and M. I. Baskes, Phys. Rev. Lett. 50, 1285 (1983).
36. Z. B. Güvenç, J. Jellinek and A. F. Voter, Physics and Chemistry of Finite Systems: From Clusters to Crystals, Vol. I, eds. P. Jena, S. N. Khanna and B. K. Rao (Kluwer Academic, Dordrocht, 1992), p. 411-416.
37. Z. B. Güvenç and J. Jellinek, Z. Phys. D 26, 304 (1993).
38. J. Jellinek and Z. B. Güvenç, The Synergy Between Dynamics and Reactivity at Clusters and Surfaces, ed. L. J. Farrugta (Kluwer Academic, Dordrocht, 1995), p. 217-240.
39. W. Eckstein, Computer Simulation of Ion-Solid Interactions (Springer, Berlin, 1991), p. 40.
40. Z. B. Güvenç, Y. Hundur and R. Hippler, Nucl. Instr. and Meth. B 164, 854 (2000).
41. Z. B. Güvenç, R. Hippler and B. Jackson, Thin Solid Films, doi: 10.1016/j.tsf.2004.09.23.
42. D. E. Harrison, Jr., N. S. Levy, J. P. Johnson and H. M. Effron, J. Appl. Phys. 39, 3742 (1968).
43. C. F. Abrams and D. B. Graves, J. IEEE Trans. Plasma Sci. 27, 1426 (1999).
44. U. Hansen, S. Rodgers and K. F. Jensen, J. Phys. Rev. B 62, 2869 (2000).
45. X.-Y. Liu, M. S. Daw, J. D. Kress, D. E. Hanson, V. Arunachalam, D. G. Coronell, C.-L. Liu and A. F. Voter, J. Thin Solid Films 422, 141 (2002).
46. J. D. Kress, D. E. Hanson, A. F. Voter, C.-L. Liu, X.-Y. Liu and D. G. Coronell, J. J. Vac. Sci. Technol. A 17, 2819 (1999).
47. D. E. Hanson, B. C. Stephens, C. Saravanan and J. D. Kress, J. J. Vac. Sci. Technol. A 19, 820 (2001).
48. C. F. Abrams and D. B. Graves, J. J. Appl. Phys. 86, 2263 (1999).
49. C. Doughty, S. M. Gorbatkin and L. A. Berry, J. Appl. Phys. 82, 1868 (1997).
50. Y. Yamamura, N. Matsunami and N. Itoh, Radiat. Eff. Defects Solids 71, 65 (1983).
51. R. V. Stuart and G. K. Wehner, J. Appl. Phys. 33, 2345 (1962).
52. J. S. Colligon and R. W. Bramham, Atomic Collision Phenomena in Solids, eds. D. W. Palmer, M. W. Thompson and P. D. Townsend (North-Holland, Amsterdam, 1970), p. 258.