Molecular Dynamics Space Decomposition Parallel Load Balancing Method In The Calculation

Molecular dynamics simulations have been widely used to study various kinetic, thermodynamic, mechanistic, and structural properties. Large number of atoms must often be included in and long timesteps should be used in the molecular dynamics. Recent years, parallel computing has been used in various areas with the development of high performance computers. Parallel molecular dynamics have generated new interest in molecular applications. The local nature of the computation helps ensure that communication costs remain small, so the usual approach to parallizing these computations is to decompose the spatial region into sub-domain, one associated with each processor. But in the parallel computing that based on spatial decomposition, the movement, aggregate of molecular may cause unpredictable, dynamic load imbalance. The load imbalance should be solved to use the high performance computers efficiently and reduce the simulation time of molecular dynamics that can be used to bring down the costs of research.Molecular dynamics simulation method, BSP parallel computing model, static load balance method, dynamics load balance method was studied. Serial program was optimized, and confirmed that the number of atoms was the main factor to influence the magnitude of molecular dynamics. Cyclic mapping and reduction recursive bisection method were used to parallel the molecular dynamics. Numerical simulation indicated mat both the methods could catch the static load balance. But large-scale molecular dynamics prefer the reduction recursive bisection method to cyclic mapping method.A kind of efficiently dynamics load balance method based on spatial redecomposition was presented. The load in mis method was measured by the number of atoms, and monitored periods. Problems such as low parallel efficiency that was brought about by load imbalance. The simulation results on our cluster implied that the parallel efficient was improved about 20% in comparison using static load balance singly.Parallel program implemented by MPI. And the load balance methods were applied to the numerical simulation of the evolution of micro-void growth in single crystal of copper successfully. This parallel program had ideal parallel speed up. With the complement of this parallel program, deepen understanding of the microscopic mechanism of dynamics damage in ductile materials in large scale atoms can be studied. Specially, the load balance method was more effective in more processors, in the large scale parallel computing, load balance...