A Scalable Neighbor List Construction Method for Molecular Dynamics Simulations on Multi-core Platforms
Yali Liu, Wenyan Chai, Xiurong Li · Advances in computer science research · 2015
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.