Performance analysis of parallel replica molecular dynamics

Molecular dynamics simulation is an important tool for studying materials microstructure evolution under radiation effects. It is difficult to simulate atomic diffusion in materials owing to the time-scale limitations of the molecular dynamics method. Accelerated molecular dynamics has been developed as a solution and the parallel replica method is the simplest and most accurate of the accelerated dynamics techniques. The simulation time scale can reach several orders more than the direct molecular dynamics, while retaining the complete atomic detail. In parallel replica method, the entire system is replicated on each of M available parallel or distributed processors, it is in line with the characteristics of high-performance parallel computing and can be optimized from the program level.