A Scalable Neighbor List Construction Method for Molecular Dynamics Simulations on Multi-core Platforms

Abstract

Abstract. We present a scalable method to implement the construction of neighbor list in molecular dynamic simulations on multi-core platforms. Our methodology is based on the OpenMP programming model. Our method doesn't divide the whole of simulation region into cells. Each thread builds and maintains a few sliding cells for a neighbor list constructions. It reduces memory requirements and code complexity. Compared with some other methods applied in the neighbor list construction, the results of our experiments indicate that it is a scalable and efficient method.