Optimization Techniques For Parallel Molecular Dynamics Using Domain Decomposition英文电子书.pdf

iii Computer Physics Communications ELSEVIER Computer Physics Communications 113 (1998) 145-167 Optimization techniques for parallel molecular dynamics using domain decomposition M. Ptitz, A. Kolb Max-Planck-lnstitutefor PolymerResearch, Ackermannweg 10. D-55128 Mainz, Germany Received 15 May 1998 Abstract 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 devel