Exploiting seeding of random number generators for efficient domain decomposition parallelization of dissipative particle dynamics

Y. Afshar, F. Schmid, A. Pishevar, S. Worley

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Dissipative particle dynamics (DPD) is a new promising method commonly used in coarse-grained simulations of soft matter and biomolecular systems at constant temperature. The DPD thermostat involves the evaluation of stochastic or random forces between pairs of neighboring particles in every time step. In a parallel computing environment, the transfer of these forces from node to node can be very time consuming. In this paper we describe the implementation of a seeded random number generator with three input seeds at each step which enables the complete generation of the pairwise stochastic forces in parallel DPD simulations with minimal communication between nodes.

Original languageEnglish (US)
Pages (from-to)1119-1128
Number of pages10
JournalComputer Physics Communications
Volume184
Issue number4
DOIs
StatePublished - Apr 1 2013
Externally publishedYes

Keywords

  • Dissipative particle dynamics
  • Domain decomposition
  • Parallel computing
  • Random number generator
  • Saru

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