Fast parallel algorithms for short-range molecular dynamics (Q1346550)

The paper presents three types of algorithms for the parallel computation of classical molecular dynamics. They are especially suited to short- range inter-molecular forces for which a cut-off range exists or can be imposed. One method allocates a defined subset of particles to each processor; another assigns each with a fixed subset of intermolecular forces and the last assigns a fixed spatial domain to each processor. The algorithms can be realized on distributed-memory machines with independent processors having suitable data flow capacities between them. Computations on a number of parallel computers are presented for a typical Lennard-Jones two-body potential, with sizes ranging from 500 up to 100,000,000 molecules. With current parallel machines the algorithms are seen to be competitive with the best vector Cray Y-MP and C90 algorithms, even in small size cases. For large problems the spatial algorithm can run at parallel efficiencies of 90\%. Relative merits of the algorithms and their application to more complicated dynamics are discussed.