DOI: 10.1063/1.2719690. Efficient particle labeling in atomistic simulations

Efficient particle labeling in atomistic simulations

10.1063/1.2719690

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

The authors develop an efficient particle labeling procedure based on a linked cell algorithm which is shown to reduce the computing time for a molecular dynamics simulation by a factor of 3. They prove that the improvement of performance is due to the efficient fulfillment of both spatial and temporal locality principles, as implemented by the contiguity of labels corresponding to interacting atoms. Finally, they show that the present label reordering procedure can be used to devise an efficient parallel one-dimensional domain decomposition molecular dynamics scheme.

Bibliography

Meloni, S., Rosati, M., & Colombo, L. (2007). Efficient particle labeling in atomistic simulations. The Journal of Chemical Physics, 126(12).

Authors 3

Simone Meloni (first)
Mario Rosati (additional)
Luciano Colombo (additional)

References 11 Referenced 39

10.1103/PhysRev.159.98 / Phys. Rev. (1967)
{'volume-title': 'Computing Simulations Using Particles', 'year': '1981', 'key': '2023080208322227800_c2'} / Computing Simulations Using Particles (1981)
10.1021/j100301a013 / J. Phys. Chem. (1987)
10.1016/j.molliq.2005.11.029 / J. Mol. Liq. (2006)
10.1016/j.cpc.2004.04.004 / Comput. Phys. Commun. (2004)
10.1016/j.cpc.2005.03.111 / Comput. Phys. Commun. (2005)
10.1103/PhysRevB.31.5262 / Phys. Rev. B (1985)
{'first-page': '157', 'volume-title': 'Proceedings of the 24th National Conference of ACM', 'year': '1969', 'key': '2023080208322227800_c10'} / Proceedings of the 24th National Conference of ACM (1969)
{'key': '2023080208322227800_c11'}
10.1103/PhysRev.136.A405 / Phys. Rev. (1964)
{'key': '2023080208322227800_c13', 'first-page': '483', 'volume': '30', 'year': '1967', 'journal-title': 'AFIPS Conf. Proc.'} / AFIPS Conf. Proc. (1967)

Dates

Type	When
Created	18 years, 5 months ago (March 27, 2007, 6:11 p.m.)
Deposited	2 years ago (Aug. 2, 2023, 4:32 a.m.)
Indexed	4 weeks, 1 day ago (July 30, 2025, 6:48 a.m.)
Issued	18 years, 5 months ago (March 27, 2007)
Published	18 years, 5 months ago (March 27, 2007)
Published Online	18 years, 5 months ago (March 27, 2007)
Published Print	18 years, 5 months ago (March 28, 2007)

Funders 0

None

BibTeX

@article{Meloni_2007, title={Efficient particle labeling in atomistic simulations}, volume={126}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.2719690}, DOI={10.1063/1.2719690}, number={12}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Meloni, Simone and Rosati, Mario and Colombo, Luciano}, year={2007}, month=mar }

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