Fuzzy clustering approach to hierarchical molecular dynamics simulation of multiscale materials phenomena

Computer Physics Communications

Volumn 105, Issue 2-3, 1997, Pages 139-150

  Nakano, Aiichiro ^a  

^a Louisiana State University   (United States)

Author keywords

Fuzzy clustering; Implicit integration; Molecular dynamics; Multiscale algorithm; Normal mode analysis; Parallel computing; Rigid body dynamics

Indexed keywords

ALGORITHMS; CONFORMATIONS; CRYSTAL ATOMIC STRUCTURE; FUZZY SETS; INTEGRATION; MOLECULAR DYNAMICS; NANOSTRUCTURED MATERIALS; PARALLEL PROCESSING SYSTEMS;

FUZZY CLUSTERING; GLOBAL CONFORMATIONAL CHANGES; IMPLICIT INTEGRATION; MULTIPLE LEVEL OF ABSTRACTION; MULTISCALE ALGORITHM; NEWTON EQUATIONS; NORMAL MODE ANALYSIS; RIGID BODY DYNAMICS;

COMPUTER SIMULATION;

EID: 0031246399     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/s0010-4655(97)00044-1     Document Type: Article

References (58)

1. W.E. King et al., Mat. Sci. Eng. A 191 (1995) 1.
2. Research and Development of Synergy Ceramics (New Energy and Industrial Technology Development Organization, Tokyo, 1994).
3. R.K. Kalia, A. Nakano, K. Tsuruta and P. Vashishta, Phys. Rev. Lett. 78 (1997) 689; R.K. Kalia, A. Nakano, A. Omeltchenko, K. Tsuruta and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2144.
4. R.K. Kalia, A. Nakano, K. Tsuruta and P. Vashishta, Phys. Rev. Lett. 78 (1997) 689; R.K. Kalia, A. Nakano, A. Omeltchenko, K. Tsuruta and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2144.
5. R.W. Siegel, in: Atomic-Level Properties of Interface Materials, D. Wolf and S. Yip, eds. (Chapman and Hall, London, 1992).
6. H. Gleiter, Nanostructured Mat. 1 (1992) 1.
7. M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids (Oxford Univ. Press, Oxford, 1987).
8. R.K. Kalia, S.W. de Leeuw, A. Nakano and P. Vashishta, Comput. Phys. Commun. 74 (1993) 316; A. Nakano, P. Vashishta and R.K. Kalia, Comput. Phys. Commun. 77 (1993) 303; A. Nakano, R.K. Kalia and P. Vashishta, Comput. Phys. Commun. 83 (1994) 197.
9. R.K. Kalia, S.W. de Leeuw, A. Nakano and P. Vashishta, Comput. Phys. Commun. 74 (1993) 316; A. Nakano, P. Vashishta and R.K. Kalia, Comput. Phys. Commun. 77 (1993) 303; A. Nakano, R.K. Kalia and P. Vashishta, Comput. Phys. Commun. 83 (1994) 197.
10. R.K. Kalia, S.W. de Leeuw, A. Nakano and P. Vashishta, Comput. Phys. Commun. 74 (1993) 316; A. Nakano, P. Vashishta and R.K. Kalia, Comput. Phys. Commun. 77 (1993) 303; A. Nakano, R.K. Kalia and P. Vashishta, Comput. Phys. Commun. 83 (1994) 197.
11. F.F. Abraham, D. Brodbeck, R.A. Rafey and W.E. Rudge, Phys. Rev. Lett. 73 (1994) 272; F.F. Abraham, Phys. Rev. Lett. 77 (1996) 869.
12. F.F. Abraham, D. Brodbeck, R.A. Rafey and W.E. Rudge, Phys. Rev. Lett. 73 (1994) 272; F.F. Abraham, Phys. Rev. Lett. 77 (1996) 869.
13. S.J. Zhou, D.M. Beazley, P.S. Lomdahl and B.L. Holian, Phys. Rev. Lett. 78 (1997) 479.
14. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
15. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
16. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
17. G.W. Scherer, Sol-Gel Science (Academic Press, San Diego, 1990).
18. A.C. Hindmarsh and L.R. Petzold, Comput. Phys. 9(2) (1995) 148.
19. G. Zhang and T. Schlick, J. Comput. Chem. 14 (1993) 1212.
20. M.E. Tuckeman, D. Marx, M.L. Klein and M. Parrinello, J. Chem. Phys. 104 (1996) 5579.
21. K.D. Hammonds, M.T. Dove, A.P. Giddy and V. Heine, Am. Mineralog. 79 (1994) 1207.
22. J. Wisdom and M. Holman, Astron. J. 102 (1991) 1528.
23. J.-P. Ryckaert, G. Ciccotti and J.C. Berendsen, J. Comput. Phys. 23 (1977) 327.
24. H.C. Andersen, J. Comput. Phys. 52 (1983) 24.
25. B. Space, H. Rabitz and A. Askar, J. Chem. Phys. 99 (1993) 9070.
26. W.B. Streett, D.J. Tildesley and G. Saville, Mol. Phys. 35 (1978) 639.
27. M.E. Tuckeman, B.J. Berne and G.J. Martyna, J. Chem. Phys. 94 (1991) 6811.
28. H. Grubmuller, H. Heller, A. Windemuth and K. Schulten, Mol. Sim. 6 (1991) 121.
29. R.D. Skeel, G. Zhang and T. Schlick, SIAM J. Sci. Comput. 18 (1997) 203.
30. V.I. Arnold, Mathematical Methods of Classical Mechanics (Springer-Verlag, Berlin, 1989).
31. A. Jain, N. Vaidehi and G. Rodriguez, J. Comput. Phys. 106 (1993) 258; M. Mathiowetz, A. Jain, N. Karasawa and W.A. Goddard, Proteins 20 (1994) 227.
32. A. Jain, N. Vaidehi and G. Rodriguez, J. Comput. Phys. 106 (1993) 258; M. Mathiowetz, A. Jain, N. Karasawa and W.A. Goddard, Proteins 20 (1994) 227.
33. E.B. Tadmor, R. Phillips and M. Ortiz, Langmuir 12 (1996) 4529; M.I. Baskes, Langmuir 12 (1996) 4535.
34. E.B. Tadmor, R. Phillips and M. Ortiz, Langmuir 12 (1996) 4529; M.I. Baskes, Langmuir 12 (1996) 4535.
35. A. Madhukar, W. Yu, R. Viswanathan and P. Chen, Mat. Res. Soc. Symp. Proc. 408 (1996) 413.
36. T. Schlick and A. Brandt, IEEE Comput. Sci. & Eng. 3(3) (1996) 78; T. Schlick and A. Brandt, Multigrid Tutorials with Applications to Molecular Dynamics, A. Brandt and T. Schlick, eds. (Oct. 10-12, 1995, Rehovot, Israel).
37. T. Schlick and A. Brandt, IEEE Comput. Sci. & Eng. 3(3) (1996) 78; T. Schlick and A. Brandt, Multigrid Tutorials with Applications to Molecular Dynamics, A. Brandt and T. Schlick, eds. (Oct. 10-12, 1995, Rehovot, Israel).
38. The quantum-mechanical/molecular-mechanical (QMMM) approach embeds a quantum-mechanical description of charge-transfer and chemical reactions in a classical description of environmental atoms, see M.J. Field, P.A. Bash and M. Karplus, J. Comput. Chem. 11 (1990) 700; C.S. Carmer, B. Weiner and M. Frenklach, J. Chem. Phys. 99 (1993) 1356; F. Maseras and K. Morokuma, J. Comput. Chem. 16 (1995) 1170. The QMMM method is included in software packages such as GAMESS [M.W. Schmidt et al., J. Comput. Chem. 14 (1993) 1347].
39. The quantum-mechanical/molecular-mechanical (QMMM) approach embeds a quantum-mechanical description of charge-transfer and chemical reactions in a classical description of environmental atoms, see M.J. Field, P.A. Bash and M. Karplus, J. Comput. Chem. 11 (1990) 700; C.S. Carmer, B. Weiner and M. Frenklach, J. Chem. Phys. 99 (1993) 1356; F. Maseras and K. Morokuma, J. Comput. Chem. 16 (1995) 1170. The QMMM method is included in software packages such as GAMESS [M.W. Schmidt et al., J. Comput. Chem. 14 (1993) 1347].
40. The quantum-mechanical/molecular-mechanical (QMMM) approach embeds a quantum-mechanical description of charge-transfer and chemical reactions in a classical description of environmental atoms, see M.J. Field, P.A. Bash and M. Karplus, J. Comput. Chem. 11 (1990) 700; C.S. Carmer, B. Weiner and M. Frenklach, J. Chem. Phys. 99 (1993) 1356; F. Maseras and K. Morokuma, J. Comput. Chem. 16 (1995) 1170. The QMMM method is included in software packages such as GAMESS [M.W. Schmidt et al., J. Comput. Chem. 14 (1993) 1347].
41. Macro-atomistic-ab initio-dynamics (MAAD) coalition has been formed by F. Abraham, J. Broughton, H. Gao, E. Kaxiras, R. Phillips and X. Xu, see F.F. Abraham, Phys. Today 50(2) (1997) 15.
42. D.J. Evans and S. Murad, Mol. Phys. 34 (1977) 327.
43. J.C. Dunn, J. Cybern. 3 (1974) 32.
44. J.C. Bezdek, Pattern Recognition with Fuzzy Objective Function Algorithms (Plenum, New York, 1981); J.C. Bezdek and R.J. Hathaway, IEEE Trans. Neural Network 3 (1992) 787.
45. J.C. Bezdek, Pattern Recognition with Fuzzy Objective Function Algorithms (Plenum, New York, 1981); J.C. Bezdek and R.J. Hathaway, IEEE Trans. Neural Network 3 (1992) 787.
46. K. Rose, E. Gurewitz and G.C. Fox, Phys. Rev. Lett. 65 (1990) 945.
47. E. Trauwaert, L. Kaufman and P. Rousseeuw, Fuzzy Sets Sys. 42 (1991) 42; P. Rousseeuw, L. Kaufman and E. Trauwaert, Comput. Stat. Data Anal. 23 (1996) 135.
48. E. Trauwaert, L. Kaufman and P. Rousseeuw, Fuzzy Sets Sys. 42 (1991) 42; P. Rousseeuw, L. Kaufman and E. Trauwaert, Comput. Stat. Data Anal. 23 (1996) 135.
49. M.-S. Yang, Math. Comput. Model. 18 (1993) 1.
50. Recent works on fuzzy clustering can be found in: Proc. 5th Int. Conf. Fuzzy Sys., F.E. Petry and D.H. Kraft, eds. (IEEE, Piscataway, 1996).
51. L.A. Zadeh, Inform. Contr. 8 (1965) 338.
52. K. Tsuruta, A. Omeltchenko, R.K. Kalia and P. Vashishta, Europhys. Lett. 33 (1996) 441.
53. H. Zhu and R.S. Averback, Mater. Sci. & Eng. A 204 (1995) 96.
54. P. Vashishta, R.K. Kalia, J.P. Rino and I. Ebbsjö, Phys. Rev. B 41 (1990) 12197.
55. W. Gropp, E. Lusk and A. Skjellum, Using MPI (MIT Press, Cambridge, 1994).
56. M. Snir. S. Otto, S. Huss-Lederman, D. Walker and J. Dongarra, MPI: The Complete Reference (MIT Press, Cambridge, 1996).
57. X.-H. Sun and J. Gustafson, Parall. Comput. 17 (1991) 1093.
58. V. Kumar, A. Grama, A. Gupta and G. Karypis, Introduction to Parallel Computing (Benjamin/Cummings, Redwood City, 1994).