Improved O(N) Neighbor List Method Using Domain Decomposition and Data Sorting

Z-H Yao, J-S Wang and M. Cheng
National University of Singapore, SG

Keywords: neighbor list, molecular dynamics, domain decomposition, data sorting, Verlet table

Abstract:
The conventional Verlet table neighbor list algorithm is improved to reduce the number of unnecessary interatomic distance calculation in molecular simulations involving many 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 versions.

Nanotech 2004 Conference Technical Program Abstract