Improved O(N) neighbor list method using domain decomposition and data sorting
Author(s)Yao, Zhenhua; Wang, Jian-Sheng; Cheng, Min
The conventional Verlet table neighbor list algorithm is improved to reduce the number of unnecessary inter-atomic distance calculations in molecular simulations involving large amount of atoms. Both of the serial and parallelized performance of molecular dynamics simulation are evaluated using the new algorithm and compared with those using the conventional Verlet table and cell-linked list algorithm. Results show that the new algorithm significantly improved the performance of molecular dynamics simulation compared with conventional neighbor list maintaining and utilizing algorithms in serial programs as well as parallelized programs.
High Performance Computation for Engineered Systems (HPCES);
O(N) neighbor list method, domain decomposition, data sorting, Verlet table neighbor list algorithm, molecular dynamics simulation, cell-linked list algorithm