基于改进细胞链表算法的分子动力学模拟性能优化模型

Optimization Model for Performance of Molecular Dynamics Simulation Based on Modified Cell-linked List Method

在改进的细胞链表算法中,细胞大小的减少会降低该算法的通信量和粒子之间距离计算的次数,同时会增加邻居细胞的数量。多细胞分子动力学算法是分子动力学模拟中普遍使用的并行算法。将改进细胞链表算法的基本思想应用到多细胞分子动力学算法中,推导出了一个分子动力学模拟性能评价模型,并据此提出一个优化模型来加速分子动力学模拟。实验结果表明,根据该优化模型确定的细胞大小可以提高分子动力学模拟程序的性能。

In the modified cell-linked list method, the reduction in cell sizes results in the reduction of communication loads and calculation costs of distance between particles, the requirements of more neighboring cells. The multi-cell mo- lecular dynamics （MD） method is a parallel one that is widely used for MD simulation. This paper applied the key idea of modified cell-linked list method to the multi-ceil MI） method, derived a performance evaluation model {or the MI） simulation and proposed an optimal model for the acceleration of MD simulation according to that. The experimental re sults show that cell sizes which are optimized by using the optimal model, can improve the performance of molecular dy- namics simulation.