分子动力学模拟中不同短程作用力计算方法的效率研究

利用分子动力学模拟的基准问题，对截断半径（cut-off distance)法，Verlet链（Verlet list)法和链格（linked-cell)法等分子间短程作用力的计算方法与模拟系统的粒子数，对比密度之间的关系进行了研究，研究结果表明，各计算方法的效率与模拟系统的对比密度，粒子数量有密切关系，在粒子数为16384时，若对比密度为0．9,linked-cell 法的计算效率是截断半径法的18倍，若对比密度为0．1，两者的效率则相差100倍，在粒子数超过864以后，linked-cell法具有明显宾优势，计算结果可以为合理评价分子动力学并行算法的效率和加速比等指标提供依据。

Computation Efficiency of Some Short-Range Force Algorithms in Molecular Dynamic Simulation

The runtime of molecular dynamic simulation is mostly determined by the computation of the short range force. In order to give a criterion used to estimate the efficiency of parallel molecular dynamic algorithms and choose a suitable algorityhm in molecular dynamic simulation, the computation efficiency of some short range force algorithms is studied. With a benchmark problem, the relationships between the cutoff distance method, Verlet list mothod, and linked cell method with the particle numbers and reduced density are investigated. The results indicate that the efficiency of those algorithms is associated with the particle numbers and reduced density strongly. If the particle numbers are larger than 864, at present, the linked cell method is the best choice for molecular dynamic simulation.