Fast parallel algorithms for short-range molecular dynamics

Journal of Computational Physics

Volumn 117, Issue 1, 1995, Pages 1-19

  Plimpton, Steve ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0002467378     PISSN: 00219991     EISSN: None     Source Type: Journal    
DOI: 10.1006/jcph.1995.1039     Document Type: Article

References (57)

1. F. F. Abraham, Computational statistical mechanics: Methodology, applications and supercomputing, Adv. in Phys, 35, 1 (1986).
2. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon Press, Oxford, 1987).
3. D. J. Auerbach, W. Paul, A. F. Bakker, C. Lutz, W. E. Rudge, and F. F. Abraham, A special purpose parallel computer for molecular dynamics; Motivation, design, implementation, and application, J. Phys. Chem. 91, 4881 (1987).
4. A. F. Bakker, G. H. Gilmer, M. H. Grabow, and K. Thompson, A special purpose computer for molecular dynamics calculations, J. Comput. Phys. 90, 313 (1990).
5. J. E. Bames and P. Hut, A hierarchical 0(N log N) force-calculation algorithm, Nature 324, 446 (1986).
6. M. Barnett, L. Shuler, R. van de Geijn, S. Gupta, D. Payne, and J. Watts, Interprocessor collective communication library (Intercom), in Proc. Scalable High Performance Computing Conference-94, (IEEE Comput. Soc. Press, Washington, DC, 1994), p. 357.
7. M. Baskes, M. Daw, B. Dodson, and S. Foiles, Atomic-scale simulation in materials science. Materials Res. Soc. Bull., Feb., 28 (1988).
8. D. M. Beazley, P. S. Lomdahl, N. Gronbech-Jensen, and P. Tamayo, A high performance communication and memory caching scheme for molecular dynamics on the CM-5, in Proc. 8th International Parallel Processing Symposium, (IEEE Comput. Soc. Press, Washington, DC, 1994), p. 800.
9. R. H. Bisseling and J. G. G. van de Vorst, Parallel LU decomposition on a transputer network, Lecture Notes in Computer Science, Vol. 384 edited by (G. A. van Zee and J. G. G. van de Vorst (Springer-Verlag, New York/Berlin, 1989), p. 61.
10. B. M. Boghosian, Computational physics on the Connection Machine, Comput. Phys., Jan/Feb (1990).
11. L. L. Boyer and G. S. Pawley, Molecular dynamics of clusters of particles interacting with pairwise forces using a massively parallel computer, J. Comput. Phys. 78, 405 (1988).
12. B. R. Brooks and M. Hodošček, Parallelization of CHARMM for MIMD machines, Chem. Design Automat. News 7, 16 (1992).
13. D. Brown, J. H. R. Clarke, M. Okuda, and T. Yamazaki, A domain decomposition parallelization strategy for molecular dynamics simulations on distributed memory machines, Comput. Phys. Commun. 74, 67 (1993).
14. J. P. Brunet, A. Edelman, and J. P. Mesirov, Hypercube algorithms for direct /V-body solvers for different granularities, SIAM J. Sci. Stat. Comput. 14(5), 1143 (1993).
15. J. P. Brunet, J. P. Mesirov, and A. Edelman, An optimal hypercube direct N-body solver on the Connection Machine, in Proc. Supercomputing’90 (IEEE Comput. Soc. Press, Washington, DC, 1990), p. 748.
16. T. W. Clark, J. A. McCammon, and L. R. Scott, Parallel molecular dynamics, in Proc. 5th SIAM Conference on Parallel Processing for Scientific Computing (SIAM, Philadelphia, 1992), p. 338.
17. M. S. Daw and M. I. Baskes, Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals, Phys. Rev. B 29, 6443 (1984).
18. H. Q. Ding, N. Karasawa, and W. A. Goddard III, Atomic level simulations on a million particles: The cell mullipole method for Coulomb and London interactions, J. Chem. Phys. 97, 4309 (1992).
19. K. Esselink, B. Smit, and P. A. J. Hilbers, Efficient parallel implementation of molecular dynamics on a toroidal network. I. Parallelizing strategy, J. Comput. Phys. 106, 101 (1993).
20. D. Fincham, Parallel computers and molecular simulation, Mol. Simul. 1, 1 (1987).
21. G. C. Fox, M. A. Johnson, G. A. Lyzenga, S. W. Otto, J. K. Salmon, and D. W. Walker, Solving Problems on Concurrent Processors: Volume I (Prentice Hall, Englewood Cliffs, NJ, 1988).
22. L. Greengard and V. Rokhlin, A fast algorithm for particle simulations, J, Comput. Phys. 73, 325 (1987).
23. G. S. Grest, B. Diinweg, and K. Kremer, Vectcrized link cell Fortran code for molecular dynamics simulations for a large number of particles, Comput. Phys. Commun. 55, 269 (1989).
24. S. Gupta, Computing aspects of molecular dynamics simulations, Comput. Phys. Commun. 70, 243 (1992).
25. H. Heller, H. Grubmuller, and K. Schulten, Molecular dynamics simulation on a parallel computer, Mol. Simul. 5, 133 (1990).
26. B. Hendrickson and R. Leland, An improved spectral graph partitioning algorithm for mapping parallel computations, SIAM J. Sci. Stat. Comput., to appear.
27. B. Hendrickson and D. Womble, The torus-wrap mapping for dense matrix calculations on massively parallel computers, SIAM J. Sci. Stat. Comput., to appear.
28. B. A. Hendrickson and S. J. Plimpton, Parallel many-body simulations without all-to-all communication, J. Parallel Distrib. Comput. to appear.
29. D. M. Heyes and W. Smith, Inf. Q. Comput. Simul. Condensed Phases (Daresbury Lab) 28, 63 (1988).
30. R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles (Adam Hilger, New York, 1988).
31. R. W. Hockney, S. P. Goel, and J. W. Eastwood, Quiet high-resolution computer models of a plasma, J. Comput. Phys. 14, 48 (1974).
32. J. G. Lewis and R. A. van de Geijn, Distributed memory matrix-vector multiplication and conjugate gradient algorithms, in Proc. Supercomputmg’93 (IEEE Comput. Soc. Press, Washington, DC, 1993), p. 484.
33. A. B. Maccabc, K. S. McCurley, R. Riesen, and S. R. Wheat, SUNMOS for the Intel Paragon: A brief user’s guide, in Proceedings, Intel Supercomputer User’s Group. 1994 Annual North America User’s Conference.
34. J. J. Morales and M. J. Nuevo, Comparison of link-cell and neighbourhood tables on a range of computers, Comput. Phys. Commun. 69, 223 (1992).
35. N. Atiig and K. Kremer, unpublished, 1993.
36. A. Nakano, P. Vashishta, and R. K. Kalia, Parallel multiple-time-step molccular dynamics with three-body interaction, Comput. Phys. Commun. 77, 303 (1993).
37. p. s. lomdahl, los alamos national labs, personal communication, 1994.
38. S. S. Patnaik, R. Pachter, S. J. Plimpton, and W. W. Adams, Molecular dynamics simulation of a cyclic siloxane based liquid crystalline material, in Electrical, Optical, and Magnetic Properties of Organic Solid Stale Materials, Vol. 328, Materials Research Society Symposium Proc., Fall 1993, p- 711.
39. M. R. S. Pinches, D. J. Tildesley, and W. Smith, Large-scale molecular dynamics on parallel computers using the link-cell algorithm, Mol. Simul. 6, 51 (1991).
40. S. J. Plimpton, Molecular dynamics simulations of short-range force systems on 1024-node hypercubes, in Proc. 5th Distributed Memory Computing Conference (IEEE Comput. Soc. Press, Washington, DC, 1990), p. 478.
41. S. J. Plimpton, Scalable parallel molecular dynamics on MIMD supercomputers, in Proc. Scalable High Performance Computing Conference-92 (IEEE Comput. Soc. Press, Washington, DC, 1992), p. 246.
42. S. J. Plimpton and B. A. Hendrickson, A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems, Technical Report SAND94-1862, Sandia National Laboratories, Albuquerque, NM, 1994; submitted.
43. S. J. Plimpton and B. A. Hendrickson, Parallel molecular dynamics with the embedded atom method, in Materials Theory and Modeling, Vol. 291 Materials Research Society Symposium Proc., Fall 1992, p. 37.
44. S. J. Plimpton and E. D. Wolf, Effect of interatomic potential on simulated grain-boundary and bulk diffusion: A molecular dynamics study, Phys. Rev. B 41, 2712 (1990).
45. D. C. Rapaport, Large-scale molecular dynamics simulation using vector and parallel computers, Comput. Phys. Rep. 9, (1988).
46. D. C. Rapaport, Multi-million particle molecular dynamics. II. Design considerations for distributed processing, Comput. Phys. Commun. 62, 217 (1991).
47. M. Schoen, Structure of a simple molecular dynamics Fortran program optimized for Cray vector processing computers, Comput. Phys. Commun. 52, 175 (1989).
48. H. Schreiber, O. Steinhauser, and P. Schuster, Parallel molecular dynamics of biomolecules, Parallel Comput. 18, 557 (1992).
49. W. Smith, Molecular dynamics on hypercube parallel computers, Comput. Phys. Commun. 62, 229 (1991).
50. W. B. Street, D. J. Tildesley, and G. Saville, Multiple timestep methods in molecular dynamics, Mol. Phys. 35, 639 (1978).
51. P. Tamayo and R. Giles, A parallel scalable approach to short-range molecular dynamics on the CM-5, in Proc. Scalable High Performance Computing Conference-92 (IEEE Comput. Soc. Press, Washington, DC, 1992), p. 240.
52. P. Tamayo, J. P. Mesirov, and B. M. Boghosian, Parallel approaches to short-range molecular dynamics simulations, in Proc. Supercomputing’91 (IEEE Comput. Soc. Press, Washington, DC, 1991), p. 462.
53. P. A. Taylor, J. S. Nelson, and B. W. Dodson, Adhesion between atomically flat metallic surface;;, Phys. Rev. B 44, 5834 (1991).
54. R. van de Geijn, Efficient global combine operations, in Proc. 6th Distributed Memory Computing Conference (IEEE Comput. Soc. Press, Washing- ton, DC, 1991), p. 291.
55. L. Verlet, Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules, Phys. Rev. 159, 98 (1967).
56. M. S. Warren and J. K. Salmon, A parallel treecode for gravitational N-body simulations with up to 20 million particles, Bull. Amer. Astronom. Soc. 23, 1345 (1991).
57. A. Windemuth and K. Schulten, Molecular dynamics simulation on the Connection Machine, Mol. Simul. 5, 353 (1991).