Efficient parallel implementation of molecular dynamics on a toroidal network. Part II. multi-particle potentials

K. Esselink, P.A.J. Hilbers

Research output: Contribution to journalArticleAcademicpeer-review

29 Citations (Scopus)

Abstract

Implementations for molecular dynamics on parallel computers generally use either particle parallelism or geometric parallelism. For short-range potentials, geometric parallelism has the advantage that communication can stay restricted to processors nearby. Usually, half the environment around a processor is communicated, using Newton's third law. This poses a problem for the implementation of multi-particle potentials (e.g., "bending" and "torsion"). For instance, if it is said that only one processor should actually calculate the forces on the particles involved, it will be difficult to determine which processor this should be, given that the particles are distributed over two or more processors. We present an efficient technique to do so and prove that it is correct. The technique requires no more communication than the computation of two-particle interactions and ensures that potentials are only evaluated once.
Original languageEnglish
Pages (from-to)108-114
Number of pages7
JournalJournal of Computational Physics
Volume106
Issue number1
DOIs
Publication statusPublished - 1993

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