J. Shu, B. Wang, J. Wang, M. Chen, and W. Zheng (PRC)
Parallel computing, Molecular Dynamics, Cluster, Thermophysics.
Molecular dynamics simulation is an important method for the research of thermophysics. But it is difficult to implement the simulation with traditional serial algorithms because of a complex numerical calculation. A cluster-based spatial decomposition algorithm for solving large-scale Molecular Dynamics simulation of thermophysics is proposed in this paper. With the efficient strategy of domain decomposition and the fast method of neighboring particle location, we greatly reduce the calculating and communicating cost and successfully process the MD simulation for PVT property calculation of a large-scale system with 4,000,000 particles. The spatial decomposition algorithm is implemented on 125 processors with the speedup(Sp) of 86.4 and the efficiency(E) of 69.1%.The numerical results indicate that the proposed parallel algorithm can simulate a thermophysical system with many more particles than before, and can provide a more efficient way for computer simulation of thermophysical problems.
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