(Received: April 8, 2002; Accepted for publication: May 23, 2002; Published on Web: July 5, 2002)
This paper concerns two algorithms designed for acceleration of molecular dynamics simulations using the fast multipole method (FMM) and special-purpose machine (MD-Engine II) for calculating pair interactions. One algorithm is based on a three-dimensional cyclic buffer, which enables efficient cooperation between FMM and MD-Engine II. The algorithm is implemented as part of the particle-processor of MD-Engine II. The processor specifically extracts a set of particles which are contained in nearby regions defined in FMM. The other algorithm is based on a recursive bisection for static load-balancing technique. The efficacy of these algorithms was confirmed by numerical tests.
Keywords: molecular dynamics, special-purpose machine, fast multipole method, parallel algorithm, load-balancing
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