Optimization techniques for parallel molecular dynamics using domain decomposition Original Research Article

In this paper we describe the implementation of a new parallelized Molecular Dynamics code for many-particle problems with short-ranged interactions. While the basic algorithms have their foundation in the fairly standard methods of domain decomposition, linked-cell pair search and Verlet pair list, we have developed some refined techniques for optimizing them. The rewards of these optimizations are a up to 45% overall improvement in the scalar performance and very good scaling behavior in the number of processors even down to a few hundred particles per processor on a CRAY T3E.The best speedup can be obtained for systems with pair forces only since then the data structures can be organized in a very simple manner. To deal with more complex situations as well, we have developed a partial replicated data scheme which is suitable to simulate many molecules consisting of many simple particles (e.g. polymer chains) for many types of short-range interactions.