Parallel implementation of molecular dynamics simulation for short- ranged interaction

JS Wu and YL Hsu and YM Lee, COMPUTER PHYSICS COMMUNICATIONS, 170, 175-185 (2005).

DOI: 10.1016/j.cpc.2005.03.010

A parallel molecular dynamics simulation method, designed for large- scale problems, employing dynamic spatial domain decomposition for short-ranged molecular interactions is proposed. In this parallel cellular molecular dynamics (PCMD) simulation method, the link-cell data structure is used to reduce the searching time required for forming the cut-off neighbor list as well as for domain decomposition, which utilizes the multi-level graph-partitioning technique. A simple threshold scheme (STS), in which workload imbalance is monitored and compared with some threshold value during the runtime, is proposed to decide the proper time for repartitioning the domain. The simulation code is implemented and tested on the memory-distributed parallel machine, e.g., PC-cluster system. Parallel performance is studied using approximately one million L-J atoms in the condensed, vaporized and supercritical states. Results show that fairly good parallel efficiency at 49 processors can be obtained for the condensed and supercritical states (similar to 60%), while it is comparably lower for the vaporized state (-40%). (c) 2005 Elsevier B.V. All rights reserved.

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