Efficient parallel implementation of Ewald summation in molecular dynamics simulations on multi-core platforms
YL Liu and CJ Hu and CC Zhao, COMPUTER PHYSICS COMMUNICATIONS, 182, 1111-1119 (2011).
We present a multi-step computation method to implement the Ewald summation for long-range electrostatic interactions in molecular dynamic simulations on a multi-core machine. Our methodology is based on the OpenMP programming model. It partitions computations of real-space summation among threads so that the global force of a single particle cannot be modified by more than one thread simultaneously. It requires neither a private copy of the force array for each thread nor an inspector at runtime. Compared with some other methods that can parallelise reduction operations on a force-array. our method achieves relatively higher speedups and lower L2 cache miss and bus utilisation ratios. (C) 2011 Elsevier B.V. All rights reserved.
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