Scalable Atomistic Simulation Algorithms for Materials Research

Proceedings of the International Conference on Supercomputing

Volumn , Issue , 2001, Pages 1-

  Nakano, Aiichiro ^a   Kalia, Rajiv K ^a   Vashishta, Priya ^a   Campbell, Timothy J ^b   Ogata, Shuji ^c   Shimojo, Fuyuki ^d   Saini, Subhash ^e  

^a Louisiana State University ^*  (United States)

^b Major Shared Resource Center   (United States)

^c YAMAGUCHI UNIVERSITY   (Japan)

^d HIROSHIMA UNIVERSITY   (Japan)

^e NASA AMES RESEARCH CENTER   (United States)

Author keywords

data compression; density functional theory; load balancing; molecular dynamics; parallel computing; quantum mechanics; variable charge molecular dynamics

Indexed keywords

COMPUTATION THEORY; DATA COMPRESSION; DATA VISUALIZATION; DENSITY FUNCTIONAL THEORY; QUANTUM THEORY; WAVELET DECOMPOSITION;

ATOMISTIC SIMULATIONS; DENSITY-FUNCTIONAL-THEORY; LOAD-BALANCING; MATERIALS RESEARCH; PARALLEL COM- PUTING; QUANTUM-MECHANICAL CALCULATION; SIMULATION ALGORITHMS; SIMULATION PROJECTS; SPACETIME; VARIABLE-CHARGE MOLECULAR DYNAMIC;

MOLECULAR DYNAMICS;

EID: 34548230665     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/582034.582035     Document Type: Conference Paper

References (41)

1. F. F. Abraham. Portrait of a crack: Rapid fracture mechanics using parallel molecular dynamics. IEEE Computational Science & Engineering, 4 (2): 66-77 (1997).
2. M. J. Alava, P. M. Duxbury, C. F. Moukarzel, and H. Rieger. Exact combinatorial algorithms: Ground states of disordered systems. In Phase Transitions and Critical Phenomena, Vol. 18, eds. J. Lebowitz and C. Domb. Academic Press, London, 2000.
3. T. L. Beck. Real-space mesh techniques in density-functional theory. Reviews of Modern Physics, 72: 1041-1080 (2000).
4. T. J. Campbell, R. K. Kalia, A. Nakano, P. Vashishta, S. Ogata, and S. Rodgers. Dynamics of oxidation of aluminum nanoclusters using variable charge molecular-dynamics simulations on parallel computers. Physical Review Letters, 82: 4866-4869 (1999).
5. R. Car and M. Parrinello. Unified approach for molecular dynamics and density functional theory. Physical Review Letters, 55: 2471-2474 (1985).
6. J. R. Chelikowsky, Y. Saad, S. Ögüt, I. Vasiliev, and A. Stathopoulos. Electronic structure methods for predicting the properties of materials: Grids in space. Phyica Status Solidi (b), 217: 173-195 (2000).
7. D. J. Cook, L. B. Holder, G. Galal, and R. Maglothin. Approaches to parallel graph-based knowledge discovery. Journal of Parallel and Distributed Computing, 61: 427-446 (2001).
8. I. Ebbsjö, R. K. Kalia, A. Nakano, J. P. Rino, and P. Vashishta. Topology of amorphous gallium arsenide on intermediate length scales: A molecular dynamics study. Journal of Applied Physics, 87: 7708-7711 (2000).
9. J.-L. Fattebert and J. Bernholc. Towards grid-based O (N) density-functional theory methods: Optimized nonorthogonal orbitals and multigrid acceleration. Physical Review B, 62: 1713-1722 (2000).
10. T. C. Germann and P. S. Lomdahl. Recent advances in large-scale atomistic materials simulations. Computing in Science and Engineering, 1 (2): 10-11 (1999).
11. S. Goedecker. Linear scaling electronic structure methods. Reviews of Modern Physics, 71: 1085-1123 (1999).
12. L. Greengard and V. Rokhlin. A fast algorithm for particle simulations. Journal of Computational Physics, 73: 325-348 (1987).
13. P. Hohenberg and W. Kohn. Inhomogeneous electron gas. Physical Review, 136: B864-B871 (1964).
14. D. J. Jacobs and B. Henderson. An algorithm for two-dimensional rigidity percolation: The pebble game. Journal of Computational Physics, 137: 346-365 (1997).
15. L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151: 283-312 (1999).
16. R. K. Kalia, T. J. Campbell, A. Chatterjee, A. Nakano, P. Vashishta, and S. Ogata. Multiresolution algorithms for massively parallel molecular dynamics simulations of nanostructured materials. Computer Physics Communications, 128: 245-259 (2000).
17. S. Kodiyalam, R. K. Kalia, H. Kikuchi, A. Nakano, F. Shimojo, and P. Vashishta. Grain boundaries in gallium arsenide nanocrystals under pressure: A parallel molecular-dynamics study. Physical Review Letters, 86: 55-58 (2001).
18. W. Kohn and P. Vashishta. General density functional theory. In Inhomogeneous Electron Gas, eds. N. H. March and S. Lundqvist, pages 79-184. Plenum, New York, 1983.
19. F. Mauri and G. Galli. Electronic-structure calculations and molecular-dynamics simulations with linear system-size scaling. Physical Review B, 50: 4316-4326 (1994).
20. A. Nakano. Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics. Computer Physics Communications, 104: 59-69 (1997).
21. A. Nakano. Fuzzy clustering approach to hierarchical molecular dynamics simulation of multiscale materials phenomena. Computer Physics Communications, 105: 139-150 (1997).
22. A. Nakano. Multiresolution load balancing in curved space: The wavelet representation. Concurrency: Practice and Experience, 11: 343-353 (1999).
23. A. Nakano. A rigid-body based multiple time-scale molecular dynamics simulation of nanophase materials. The International Journal of High Performance Computing Applications, 13: 154-162 (1999).
24. A. Nakano and T. J. Campbell. An adaptive curvilinear-coordinate approach to dynamic load balancing of parallel multi-resolution molecular dynamics, Parallel Computing, 23: 1461-1478 (1997).
25. A. Nakano, R. K. Kalia, and P. Vashishta. Multiresolution molecular dynamics algorithm for realistic materials modeling on parallel computers. Computer Physics Communications, 83: 197-214 (1994).
26. A. Omeltchenko, T. J. Campbell, R. K. Kalia, X. Liu, A. Nakano, and P. Vashishta. Scalable I/O of large-scale molecular-dynamics simulations: A data-compression algorithm. Computer Physics Communications, 131: 78-85 (2000).
27. M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias, and J. D. Joannopoulos. Iterative minimization techniques for ab initio total energy calculations: molecular dynamics and conjugate gradients. Reviews of Modern Physics, 64: 1045-1097 (1992).
28. A. Pechenik, R. K. Kalia, and P. Vashishta. Computer-Aided Design of High-Temperature Materials. Oxford Univ. Press, Oxford, 1999.
29. J. P. Perdew, K. Burke, and M. Ernzerhof. Generalized gradient approximation made simple. Physical Review Letters, 77: 3865-3868 (1996).
30. A. Rahman. Correlations in the motion of atoms in liquid argon. Physical Review, 136 (2A): A405-A411 (1964).
31. D. C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge Univ. Press, Cambridge, 1995.
32. T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. A. Board, J. Hermans, and K. Schulten. Algorithmic challenges in computational molecular biophysics. Journal of Computational Physics, 151: 9-48 (1999).
33. A. Sharma, P. Miller, X. Liu, A. Nakano, R. K. Kalia, P. Vashishta, T. J. Campbell, and A. Haas. Million atom walkthrough: Octree-based fast visibility culling and multiresolution rendering for scalable atomistic visualization. Computer Science Technical Report, Louisiana State University, 2001.
34. A shorter version has appeared in: A. Nakano, R. K. Kalia, and P. Vashishta. Scalable molecular-dynamics, visualization, and datamanagement algorithms for materials simulations. Computing in Science & Engineering, 1 (5): 39-47 (1999)
35. F. Shimojo, T. J. Campbell, R. K. Kalia, A. Nakano, P. Vashishta, S. Ogata, and K. Tsuruta. A scalable molecular-dynamics-algorithm suite for materials simulations: Design-space diagram on 1, 024 Cray T3E processors. Future Generation Computer Systems, 17: 279-291 (2000).
36. F. H. Streitz and J. W. Mintmire. Electrostatic potentials for metal-oxide surfaces and interfaces. Physical Review B, 50: 11996-12003 (1994).
37. N. Troullier and J. L. Martins. Efficient pseudopotentials for plane-wave calculations. Physical Review B, 43: 1993-2006 (1991).
38. M. E. Tuckerman, D. A. Yarne, S. O. Samuelson, A. L. Hughes, and G. J. Martyna. Exploiting multiple levels of parallelism in molecular dynamics based calculations via modern techniques and software paradigms on distributed memory computers. Computer Physics Communications, 128: 333-376 (2000).
39. P. Vashishta, R. K. Kalia, and A. Nakano. Large-scale atomistic simulation of dynamic fracture. Computing in Science & Engineering, 1 (5): 56-65 (1999).
40. M. S. Warren and J. K. Salmon. A portable parallel particle program. Computer Physics Communications, 87: 266-290 (1995).
41. D.-Y. Yang, A. Grama, and V. Sarin. Bounded-error compression of particle data from hierarchical approximation methods. In Proceedings of SC99. ACM/IEEE, 1999.