Parallel Molecular Dynamic Simulation Of C-SI System

Molecular dynamic (MD) simulation is a kind of molecular simulation method. Based on the simulation of molecular system motion which conforms to the Newton's law, this method calculates the integration of system structure and, uses the results to further compute thermodynamics and other macro characteristics.The object of simulation is C-SI grinding system. Interaction between atoms is calculated mainly based on TERSOFF potential energy function. Position of atom is updated every step when velocity is made out according to the force. The diamond grinder does not move until the equilibration of SI material ends.For the reason of large scale of atoms in the simulation, like millions above, computers with sufficient resources, like array computer or cluster, are usually chosen as the platform and, it consequently adopts parallel method. This parallel method needs to resolve data structure, storage, and optimization of force computation. Besides, load balance and communication among computing nodes should be noticed. Based on the C-SI system feature, data is dynamically stored, and force computation is optimized by the 3rd Newton's law. Load balance is statically decided in minimum surface principle and, communication is MPI mode. For the hardware platform is SMP cluster, multi-threaded strategy is adopted to explore the feature of shared memory.Finally atoms are displayed by VMD. It is a MD displaying software which accepts XYZ format file. Mostly it costs quite a long time to display the atoms dumped out by the simulation because of the large quantity. So those data needed not to be displayed are filtered from different views. So the results can be fast displayed well. In the end, according to the experiments, accelerating rate and efficiency are analyzed on different parameters input.