Parallel computation for molecular dynamics simulation based on cell-block data structures

Jisuan Wuli/Chinese Journal of Computational Physics

Volumn 21, Issue 5, 2004, Pages 377-385

  Cao, Xiao Lin ^a   Mo, Ze Yao ^a   Zhang, Jing Lin ^a   Chen, Qi Feng ^a  

^a INSTITUTE OF APPLIED PHYSICS AND COMPUTATIONAL MATHEMATICS   (China)

Author keywords

Cell block data structure; Molecular dynamics; Multilevel averaging weights method; Space filling curve

Indexed keywords

COMPUTER SIMULATION; DATA STRUCTURES; PARALLEL ALGORITHMS; PARALLEL PROCESSING SYSTEMS;

CELL-BLOCK DATA STRUCTURES; METAL-EJECT PHYSICAL MODELS; MOLECULAR DYNAMICS SIMULATION; MULTILEVEL AVERAGING WEIGHTS METHOD; PARALLEL COMPUTATION; SPACEFILLING CURVE;

MOLECULAR DYNAMICS;

EID: 9444225917     PISSN: 1001246X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (13)

1. Mo Ze-yao, Zhang Jing-lin. Parallelization and optimization for two dimensional molecular dynamics code [J]. Chinese J Computational Physics, 2000, 17: 193.
2. Plimpton S. Fast parallel algorithms for short-range molecular dynamics [J]. J of Computational Physics, 1995, 117: 1.
3. Kale L, Skeel R, Bhandarkar M. NAMD2: greater scalability for parallel molecular dynamics [J]. J Computational Physics, 1999, 151: 281.
4. Hendrickson B, Devine K. Dynamic load balancing in computational mechanics [J]. Comp Meth Applied Mechanics and Engineering, 2000, 184(2): 485-500.
5. Den Yuefan, Peierls R F, Rivera C. An adaptive load balancing method for parallel molecular dynamics simulations [J]. J Compute Physics, 2000, 161: 250.
6. Mo Zeyao, Zhang Jinglin. Dynamic load balancing for short-range parallel molecular dynamics simulations [J]. Intern J Computer Math, 2002, 79(2): 165.
7. Sagan H. Space-Filling Curves [M]. New York: Springer, 1994.
8. Salomon D. Data Compression: the Complete Reference [M]. Published by Spring, 2000, 842-851.
9. Pilkington R, Baden B. Dynamic partitioning of non-uniform structured workloads with spacefilling curves [J]. IEEE Trans on Parallel and Distributed Systems, 1996, 7(3): 288.
10. Yang Xu-lin, Mo Ze-yao, Shen Long-jun. The domain decomposition parallel iterative algorithm for the 2-D transport issue [J]. Chinese J Computational Physics, 2004, 21(1): 1-9.
11. Mo Ze-yao. One dimensional dynamic load balancing method: multi-layer averaged weight method [J]. Chinese J Computers, 2001, 24(2): 183-192.
12. Stadler J, Mikulla R, Trebin H R. IMD: A software package for molecular dynamics studies on parallel computes [J]. Intern J Modern Physics, 1997, 8(5): 1131.
13. Roth J, Gahler F, Trebin H. A molecular dynamics run with 5180116000 particles [J]. Int J Modern Physics C, 2000, 11(2): 317-322