Exploiting seeding of random number generators for efficient domain decomposition parallelization of dissipative particle dynamics
Y Afshar and F Schmid and A Pishevar and S Worley, COMPUTER PHYSICS COMMUNICATIONS, 184, 1119-1128 (2013).
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. (C) 2012 Elsevier B.V. All rights reserved.
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