A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

Authors:
L. H. Yang;E. D. Brooks III;J. Belak
Affiliations:
Massively Parallel Computing Initiative, Lawrence Livermore National Laboratory, Livermore, CA 94551;Massively Parallel Computing Initiative, Lawrence Livermore National Laboratory, Livermore, CA 94551;Massively Parallel Computing Initiative, Lawrence Livermore National Laboratory, Livermore, CA 94551
Venue:
Scientific Programming
Year:
1992

Citing 2
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Abstract

A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.