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An algorithm for computing short-range forces in molecular dynamics simulations with non-uniform particle densities
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Law, Timothy R., Hancox, J., Wright, S. A. and Jarvis, Stephen A. (2019) An algorithm for computing short-range forces in molecular dynamics simulations with non-uniform particle densities. Journal of Parallel and Distributed Computing, 130 . pp. 1-11. doi:10.1016/j.jpdc.2019.03.008 ISSN 0743-7315.
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Official URL: https://doi.org/10.1016/j.jpdc.2019.03.008
Abstract
We present projection sorting, an algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations. We show it can be more effective than the standard approaches when particle density is non-uniform. We implement tuned versions of the algorithm in the context of a biophysical simulation of chromosome condensation, for the modern Intel Broadwell and Knights Landing architectures, across multiple nodes. We demonstrate up to overall speedup and good scaling to large problem sizes and processor counts.
Item Type: | Journal Article | |||||||||||||||||||||
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Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QP Physiology |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | |||||||||||||||||||||
Library of Congress Subject Headings (LCSH): | Algorithms, Molecular dynamics | |||||||||||||||||||||
Journal or Publication Title: | Journal of Parallel and Distributed Computing | |||||||||||||||||||||
Publisher: | Elsevier Science BV | |||||||||||||||||||||
ISSN: | 0743-7315 | |||||||||||||||||||||
Official Date: | August 2019 | |||||||||||||||||||||
Dates: |
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Volume: | 130 | |||||||||||||||||||||
Page Range: | pp. 1-11 | |||||||||||||||||||||
DOI: | 10.1016/j.jpdc.2019.03.008 | |||||||||||||||||||||
Status: | Peer Reviewed | |||||||||||||||||||||
Publication Status: | Published | |||||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||||||||
Date of first compliant deposit: | 22 March 2019 | |||||||||||||||||||||
Date of first compliant Open Access: | 30 May 2019 | |||||||||||||||||||||
RIOXX Funder/Project Grant: |
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