Improved Neighbor list algorithm by using domain composition and data sorting method

Preprint

13 November 2003

preprint
Published by arXiv in arXiv

Abstract

The conventional Verlet table neighbor list algorithm is improved to reduce the number of unnecessary interatomic distance calculation in molecular simulation involving a lot of of atoms. Both of the serial and parallelized performance of molecular dynamics simulation are evaluated using the new algorithm and compared with those using the conventional Verlet table and cell-linked list algorithm. Results show that the new algorithm significantly improved the performance of molecular dynamics simulation in serial programs as well as parallelized programs.

Keywords

MOLECULAR DYNAMICS SIMULATION
PARALLELIZED PROGRAMS
MOLECULAR SIMULATION
LIST ALGORITHM
NEIGHBOR LIST
VERLET
TABLE

All Related Versions

Version 1, 2003-11-13, ArXiv
Version 2, 2003-11-14, ArXiv
Version 3, 2004-02-05, ArXiv
Published version: Computer Physics Communications, 161 (1-2), 27.

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