Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics

Computer Physics Communications

Volumn 104, Issue 1-3, 1997, Pages 59-69

  Nakano, Aiichiro ^a  

^a Louisiana State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; COMPUTATIONAL METHODS; COMPUTER SIMULATION; CONVERGENCE OF NUMERICAL METHODS; ELECTROSTATICS; MATRIX ALGEBRA; PARALLEL PROCESSING SYSTEMS;

COULOMB INTERACTION MATRIX; PRECONDITIONED CONJUGATE GRADIENT METHOD;

MOLECULAR DYNAMICS;

EID: 0031212250     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/s0010-4655(97)00041-6     Document Type: Article

References (47)

1. 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.
2. 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.
3. S.J. Zhou, P.S. Lomdahl, R. Thomson and B.L. Holian, Phys. Rev. Lett. 76 (1996) 2318; S.J. Zhou, D.M. Beazley, P.S. Lomdahl and B.L. Holian, Phys. Rev. Lett. 78 (1997) 479.
4. S.J. Zhou, P.S. Lomdahl, R. Thomson and B.L. Holian, Phys. Rev. Lett. 76 (1996) 2318; S.J. Zhou, D.M. Beazley, P.S. Lomdahl and B.L. Holian, Phys. Rev. Lett. 78 (1997) 479.
5. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; 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; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
6. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; 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; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
7. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; 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; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
8. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; 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; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
9. A. Nakano, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 73 (1994) 2336; 75 (1995) 3138; 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; A. Omeltchenko, J. Yu, R.K. Kalia and P. Vashishta, Phys. Rev. Lett. 78 (1997) 2148.
10. [41 C.L. Briant, Metal. Trans. A 21 (1990) 2339.
11. J.W. Storer, D.J. Giesen, C.J. Cramer and D.G. Truhlar, J. Computer-aided Mol. Design 9 (1995) 87.
12. The quantum-mechanical/molecular-mechanical (QMMM) approach embeds a quantum mechanical description of charge transfer and chemical reaction in a classical description of environmental atoms: 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 has been included in software packages such as GAMESS: W. Schmidt et al., J. Comput. Chem. 14 (1993) 1347.
13. The quantum-mechanical/molecular-mechanical (QMMM) approach embeds a quantum mechanical description of charge transfer and chemical reaction in a classical description of environmental atoms: 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 has been included in software packages such as GAMESS: W. Schmidt et al., J. Comput. Chem. 14 (1993) 1347.
14. The quantum-mechanical/molecular-mechanical (QMMM) approach embeds a quantum mechanical description of charge transfer and chemical reaction in a classical description of environmental atoms: 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 has been included in software packages such as GAMESS: W. Schmidt et al., J. Comput. Chem. 14 (1993) 1347.
15. The quantum-mechanical/molecular-mechanical (QMMM) approach embeds a quantum mechanical description of charge transfer and chemical reaction in a classical description of environmental atoms: 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 has been included in software packages such as GAMESS: W. Schmidt et al., J. Comput. Chem. 14 (1993) 1347.
16. A. Alavi, L.J. Alvarez, S.R. Elliott and I.R. McDonald, Phil. Mag. B 65 (1992) 489.
17. A.K. Rappé and W.A. Goddard, J. Phys. Chem. 95 (1991) 3358.
18. S.W. Rick, S.J. Stuart and B.J. Berne, J. Chem. Phys. 101 (1994) 6141.
19. F.H. Streitz and J.W. Mintmire, Phys. Rev. B 50 (1994) 11996; Langmuir 12 (1996) 4605.
20. F.H. Streitz and J.W. Mintmire, Phys. Rev. B 50 (1994) 11996; Langmuir 12 (1996) 4605.
21. G.H. Golub and C.F. van Loan, Matrix Computations, 2nd Ed. (Johns Hopkins Univ. Press, Baltimore, 1989).
22. R. Barrett et al., Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods (SIAM, Philadelphia, 1994).
23. Y. Saad, Iterative Methods for Sparse Linear Systems (PWS, Boston, 1996).
24. S.W. de Leeuw, J.W. Perram and E.R. Smith, Proc. R. Soc. London A 373 (1980) 27.
25. R.K. Kalia, S.W. de Leeuw, A. Nakano and P. Vashishta, Comput. Phys. Commun. 74 (1993) 316.
26. A.Y. Toukmaji and J.A. Board, Comput. Phys. Commun. 95 (1996) 73.
27. L. Greengard and V. Rokhlin, J. Comput. Phys. 73 (1987) 325.
28. L. Greengard and W.D. Gropp, Comput. Math. Appl. 20 (1990) 63.
29. K.E. Schmidt and M.A. Lee, J. Stat. Phys. 63 (1991) 1223.
30. F. Zhao and S. Lennart Johnsson, SIAM J. Sci. Stat. Comput. 12 (1991) 1420; Y. Hu and S. Lennart Johnsson, Sci. Prog. 5 (1996) 337.
31. F. Zhao and S. Lennart Johnsson, SIAM J. Sci. Stat. Comput. 12 (1991) 1420; Y. Hu and S. Lennart Johnsson, Sci. Prog. 5 (1996) 337.
32. H.-Q. Ding, N. Karasawa and W.A. Goddard, Chem. Phys. Lett. 196 (1992) 6.
33. K. Nabors, F.T. Korsmeyer, F.T. Leighton and J. White, SIAM J. Sci. Comput. 15 (1994) 713.
34. H.G. Petersen, D. Soelvason, J.W. Perram and E.R. Smith, J. Chem. Phys. 101 (1994) 8870.
35. A.Y. Grama, V. Kumar and A. Sameh, in: Supercomputing '94 (IEEE Comp. Soc., Washington, D.C., 1994).
36. J.P. Singh, C. Holt, T. Totsuka, A. Gupta and J. Hennessy, J. Par. Dist. Comput. 27 (1995) 118.
37. M.S. Warren and J.K. Salmon, Comput. Phys. Commun. 87 (1995) 266.
38. C.A. White and M. Head-Gordon, J. Chem. Phys. 105 (1996) 5061.
39. E.L. Pollock and J. Glosli, Comput. Phys. Commun. 95 (1996) 93.
40. A. Nakano, R.K. Kalia and P. Vashishta, Comput. Phys. Commun. 83 (1994) 197.
41. X.-H. Sun and J. Gustafson, Par. Comput. 17 (1991) 1093.
42. W. Gropp, E. Lusk and A. Skjellum, Using MPI (MIT Press, Cambridge, 1994).
43. M. Snir, S. Otto, S. Huss-Lederman, D. Walker and J. Dongarra, MPI: The Complete Reference (MIT Press, Cambridge, 1996).
44. W.B. Streett, D.J. Tildesley and G. Saville, Mol. Phys. 35 (1978) 639.
45. M.E. Tuckeman, B.J. Berne and G.J. Martyna, J. Chem. Phys. 94 (1991) 6811.
46. H. Grubmuller, H. Heller, A. Windemuth and K. Schulten, Mol. Sim. 6 (1991) 121.
47. J.J. Biesiadecki and R.D. Skeel, J. Comput. Phys. 109 (1993) 318.