Large Scale Molecular Dynamics on Parallel Computers using the Link-cell Algorithm

Abstract

Parallel computers offer a more cost-effective route to high performance computing than traditional single processor machines. Software for such machines is still in its infancy and they are often much more difficult to program than sequential machines. In addition many of the algorithms which are successful with sequential and vector processors are no longer appropriate. Both the force calculation and integration steps of molecular dynamics are parallel in nature and for that reason we have developed a parallel algorithm based on the link cell technique. This method is particularly efficient when the range of intermolecular potential is much smaller than the dimensions of the simulation box. The details of the algorithm are presented for systems of atoms in two and three dimensions using a number of decompositions into sub-units. The algorithm has been tested on an Intel iPSC/2 and a Cray X-MP/416 and the results are presented for simulations of up to 2 · 10⁶ atoms.