Improved O(N) neighbor list method using domain decomposition and data sorting
Name
HPCES008.pdf
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72.1 KB
Format
Adobe PDF
Checksum (MD5)
70838b541ed2853c843b02f78942157e
Author(s)
Yao, Zhenhua
Wang, Jian-Sheng
Cheng, Min
Date Issued
January 2004
Series/Report no.
High Performance Computation for Engineered Systems (HPCES);
Abstract
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.
Subjects
O(N) neighbor list method
domain decomposition
data sorting
Verlet table neighbor list algorithm
molecular dynamics simulation
cell-linked list algorithm
Persistent DSpace Link
