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

Article type: Research Article

Authors: YANG, L.H. | BROOKS III, E.D. | BELAK, J.

Affiliations: Massively Parallel Computing Initiative, Lawrence Livermore National Laboratory, Livermore, CA 94551

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.

Journal: Scientific Programming, vol. 1, no. 2, pp. 153-161, 1992