An Improved Molecular Dynamics Algorithm for Large Scale Simulation in Nanoengineering
Focusing on the special need of nano-engineering, an improved neighbor list algorithm for the ultralarge scale molecular dynamics (MD) simulation is proposed. The new algorithm is attempting to fully combine the advantages of both Verlet table and cell-linked list algorithms to accelerate the speed of neighbor list construction and update. In order to meet the requirement of nano-engineering that often requires the frequent update of the cell-linked lists and neighbor lists, the program employs the pointer link data structure so that both reliability and accuracy of the simulation can be ensured. The performance of molecular dynamics simulation is evaluated using the proposed algorithm and compared with those using conventional Verlet table and cell-linked list algorithms. Results show that the new algorithm outperforms the conventional cell-linked list algorithm by 2～3 times for systems of 104～106 atoms per single CPU.
molecular dynamics simulation neighbor llst Verlet table cell-linked list
Tang Yu-lan Chen Jia-xuan
Municipal and Environment Engineering Institute Shenyang Jianzhu University Shenyang China Center for Precision Engineering, Harbin Institute of Technology Harbin China
国际会议
长沙
英文
1793-1796
2009-10-10（万方平台首次上网日期，不代表论文的发表时间）