Improved O(N) neighbor list method using domain decomposition and data sorting
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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | en_US |
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2003
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| Online Access: | http://hdl.handle.net/1721.1/3884 |
| _version_ | 1811070756604346368 |
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| author | Yao, Zhenhua Wang, Jian-Sheng Cheng, Min |
| author_facet | Yao, Zhenhua Wang, Jian-Sheng Cheng, Min |
| author_sort | Yao, Zhenhua |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T08:41:04Z |
| format | Article |
| id | mit-1721.1/3884 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:41:04Z |
| publishDate | 2003 |
| record_format | dspace |
| spelling | mit-1721.1/38842019-04-09T19:12:41Z Improved O(N) neighbor list method using domain decomposition and data sorting Yao, Zhenhua Wang, Jian-Sheng Cheng, Min O(N) neighbor list method domain decomposition data sorting Verlet table neighbor list algorithm molecular dynamics simulation cell-linked list algorithm 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. Singapore-MIT Alliance (SMA) 2003-12-14T22:41:47Z 2003-12-14T22:41:47Z 2004-01 Article http://hdl.handle.net/1721.1/3884 en_US High Performance Computation for Engineered Systems (HPCES); 73830 bytes application/pdf application/pdf |
| spellingShingle | O(N) neighbor list method domain decomposition data sorting Verlet table neighbor list algorithm molecular dynamics simulation cell-linked list algorithm Yao, Zhenhua Wang, Jian-Sheng Cheng, Min Improved O(N) neighbor list method using domain decomposition and data sorting |
| title | Improved O(N) neighbor list method using domain decomposition and data sorting |
| title_full | Improved O(N) neighbor list method using domain decomposition and data sorting |
| title_fullStr | Improved O(N) neighbor list method using domain decomposition and data sorting |
| title_full_unstemmed | Improved O(N) neighbor list method using domain decomposition and data sorting |
| title_short | Improved O(N) neighbor list method using domain decomposition and data sorting |
| title_sort | improved o n neighbor list method using domain decomposition and data sorting |
| topic | O(N) neighbor list method domain decomposition data sorting Verlet table neighbor list algorithm molecular dynamics simulation cell-linked list algorithm |
| url | http://hdl.handle.net/1721.1/3884 |
| work_keys_str_mv | AT yaozhenhua improvedonneighborlistmethodusingdomaindecompositionanddatasorting AT wangjiansheng improvedonneighborlistmethodusingdomaindecompositionanddatasorting AT chengmin improvedonneighborlistmethodusingdomaindecompositionanddatasorting |