Yao Z-H, Wang J-S., Cheng M.
National University of Singapore, SG
Keywords: data sorting, Domain Decomposition, molecular dynamics, neighbor list, Verlet table
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.
Journal: TechConnect Briefs
Volume: 2, Technical Proceedings of the 2004 NSTI Nanotechnology Conference and Trade Show, Volume 2
Published: March 7, 2004
Pages: 486 - 489
Industry sectors: Advanced Materials & Manufacturing | Sensors, MEMS, Electronics
Topic: Informatics, Modeling & Simulation
ISBN: 0-9728422-8-4