Abstract: A scalable parallel algorithm especially for large-scale three dimensional simulations with seriously non-uniform molecular distributions is presented. In particular, based on cell-block data structures, this algorithm uses space filling curve to convert three-dimensional domain decomposition for load distribution across processors into one-dimensional load balancing problems for which run-time measurement-based multilevel averaging weights method can be applied successfully. Parallel numerical experiments for simulations of three-dimensional metal-eject physical models with 210 million particles using 500 processors of one massively parallel processors have shown that this algorithm has achieved speedup about 420.

Key words: molecular dynamics, cell-block data structure, space filling curve, multilevel averaging weights method