Research of Optimization and Parallelization for Molecular Dynamics Simulation
Qinyong Zhang · Jisuanji yingyong yanjiu · 2005
Analyzes the algorithmic character of molecular dynamics simulation, and optimizes the serial program. In the task decompose for parallelization, spatial decomposition method is adopted, and part of area is keeping as overlap in neighbor subarea. On the basis of the message passing parallel programming platform MPI, and on the network of workstation, parallelization is implemented. In the parallel environment, the parallel efficiency is above 90%.