Parallel implementation of molecular dynamics simulation for short-ranged interaction

Jong-Shinn Wu*, Yu Lin Hsu, Yun Min Lee

*Corresponding author for this work

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

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 (∼60%), while it is comparably lower for the vaporized state (∼40%).

Original languageEnglish
Pages (from-to)175-185
Number of pages11
JournalComputer Physics Communications
Volume170
Issue number2
DOIs
StatePublished - 1 Aug 2005

Keywords

  • Dynamic domain decomposition
  • Parallel efficiency
  • Parallel molecular dynamics
  • Short-ranged interaction
  • Simple threshold scheme

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