Rigid-body-based multiple time scale molecular dynamics simulation of nanophase materials

International Journal of High Performance Computing Applications

Volumn 13, Issue 2, 1999, Pages 154-162

  Nakano, Aiichiro ^a  

^a Louisiana State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRATION; MOLECULAR DYNAMICS; NANOSTRUCTURED MATERIALS; PARALLEL ALGORITHMS; SILICON;

NEWTON'S EQUATION;

COMPUTER SIMULATION;

EID: 0032655456     PISSN: 10943420     EISSN: None     Source Type: Journal    
DOI: 10.1177/109434209901300205     Document Type: Article

References (32)

1. Allen, M. P., and Tildesley, D. J. 1987. Computer Simulation of Liquids. Oxford, UK: Oxford Scientific Press.
2. Arnold, V. I. 1989. Mathematical Methods of Classical Mechanics. Berlin: Springer-Verlag.
3. Daguier, P., Bouchaud, E., and Lapasset, G. 1995. Roughness of a crack front pinned by microstructural obstacles. Europhys. Lett. 31:367-372.
4. Evans, D. J., and Murad, S. 1977. Singularity free algorithm for molecular dynamics simulation of rigid polyatomics. Mol. Phys. 34:327-331.
5. Gropp, W., and Lusk, E. 1994. User's Guide for the ANL IBM SPx [Online]. Technical Report, Argonne National Laboratory. Available at: http://www.mcs.anl.gov/Projects/sp/ guide-r2/guide-r2.html.
6. Grubmüller, H., Heller, H., Windemuth, A., and Schulten, K. 1991. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Sim. 6:121-142.
7. Hammonds, K. D., Dove, M. T., Giddy, A. P., and Heine, V. 1994. Crush: A Fortran program for the analysis of the rigid-unit mode spectrum of a framework structure. Am. Mineralog. 79:1207-1209.
8. Hindmarsh, A. C., and Petzold, L. R. 1995. Algorithms and software for ordinary differential equations and differential-algebraic equations. Comput. Phys. 9(2):148-155.
9. Jain, A., Vaidehi, N., and Rodriguez, G. 1993. A fast recursive algorithm for molecular dynamics simulation. J. Comput. Phys. 106:258-268.
10. Kalia, R. K., de Leeuw, S. W., Nakano, A., and Vashishta, P. 1993. Molecular-dynamics simulations of Coulombic systems on distributed-memory MIMD machines. Comput. Phys. Commun. 74:316-326.
11. Kalia, R. K., Nakano, A., Omeltchenko, A., Tsuruta K., and Vashishta, P. 1997. Role of ultrafine microstructures in dynamic fracture in nanophase silicon nitride. Phys. Rev. Lett. 78:2144-2147.
12. Kalia, R. K., Nakano, A., Tsuruta K., and Vashishta, P. 1997. Morphology of pores and interfaces and mechanical behavior of nanocluster-assembled silicon nitride ceramic. Phys. Rev. Lett. 78:689-672.
13. Mathiowetz, A. M., Jain, A., Karasawa, N., and Goddard, W. A. 1994. Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 20:227-247.
14. Mezei, M. 1980. A cavity-biased (TVμ) Monte Carlo method for the computer simulation of fluids. Mol. Phys. 40:901-906.
15. Nakano, A. 1997. Fuzzy clustering approach to hierarchical molecular dynamics simulation of multiscale materials phenomena. Comput. Phys. Commun. 105:139-150.
16. Nakano, A., and Campbell, T. 1997. An adaptive curvilinear-coordinate approach to dynamic load balancing of parallel multiresolution molecular dynamics. Par. Comput. 23: 1461-1478.
17. Nakano, A., Kalia, R. K., and Vashishta, P. 1994. Multiresolution molecular dynamics algorithm for realistic materials modeling on parallel computers. Comput. Phys. Commun. 83:197-214.
18. Nakano, A., Vashishta, P., and Kalia, R. K. 1993. Parallel multiple-time-step molecular dynamics with three-body interaction. Comput. Phys. Commun. 77:303-312.
19. Ryckaert, J.-P., Ciccotti, G., and Berendsen, J. C. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
20. Scherer, G. W. 1990. Sol-Gel Science. San Diego, CA: Academic Press.
21. Siegel, R. W. 1996. Creating nanophase materials. Sci. Am. 275(6): 74-79.
22. Skeel, R. D., Zhang, G., and Schlick, T. 1997. A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications. SIAM J. Sci. Comput. 18:203-222.
23. Space, B., Rabitz, H., and Askar, A. 1993. Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses. J. Chem. Phys. 99:9070-9079.
24. Streett, W. B., Tildesley, D. J., and Saville, G. 1978. Multiple time-step methods in molecular dynamics. Mol. Phys. 35:639-648.
25. Sun, X.-H., and Gustafson, J. 1991. Toward a better parallel performance metric. Par. Comput. 17:1093-1109.
26. Tsuruta, K., Nakano, A., Kalia, R. K., and Vashishta, P. 1998. Dynamics of consolidation and crack growth in nanocluster-assembled amorphous silicon nitride. J. Am. Ceram. Soc. 81:433-436.
27. Tsuruta, K., Omeltchenko, A., Kalia, R. K., and Vashishta, P. 1996. Early stages of sintering of silicon nitride nanoclusters: A molecular dynamics study on parallel machines. Europhys. Lett. 33:441-446.
28. Tuckerman, M. E., Berne, B. J., and Martyna, G. J. 1991. Molecular dynamics algorithm for multiple time scales: Systems with long range forces. J. Chem. Phys. 94:6811-6815.
29. Tuckerman, M. E., Marx, D., Klein, M. L., and Parrinello, M. 1996. Efficient and general algorithms for path-integral Car-Parrinello molecular dynamics. J. Chem. Phys. 104:5579-5588.
30. Vashishta, P., Kalia, R. K., and Ebbsjö, I. 1995. Low-energy floppy modes in high-temperature ceramics. Phys. Rev. Lett. 75:858-861.
31. Wisdom, J., and Holman, M. 1991. Symplectic maps for the n-body problem. Astron. J. 102:1528-1538.
32. Zhang, G., and Schlick, T. 1993. LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques. J. Comput. Chem. 14:1212-1233.