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A new material particle dynamical domain decomposition method MPD3 has been developed. The method is suitable for a large scale parallel molecular dynamic simulation on a heterogeneous computing net. Performance of the MPD3 algorithm is tested in various computing environments, such as PC clusters, super computer clusters, and grid. It is shown that the MPD3 algorithm is highly-adaptive for both computer clusters and grid computing environments, even if other programs are running on the same computer environment.