Quick search of neighbour particles in molecular dynamics simulations

P. L. Novikov; K. V. Pavsky; A. A. Baranov

doi:10.1088/1742-6596/1680/1/012036

Quick search of neighbour particles in molecular dynamics simulations

P. L. Novikov, K. V. Pavsky, A. A. Baranov

Кафедра общей физики ФФ

Результат исследования: Научные публикации в периодических изданиях › статья по материалам конференции › рецензирование

Аннотация

Quicksort algorithm as an assistant preliminary tool is proposed for acceleration of neighbour search procedure in the frame of molecular dynamics simulations. Simple estimations are made showing that the number of operations required to determine all the neighbours within a system of particles can be reduced by 2-3 orders of magnitude due to the preliminary sorting. Test molecular dynamics simulations carried out for virtual crystal structure containing atoms manifest 9-fold acceleration achieved by the modified algorithm.

Язык оригинала	английский
Номер статьи	012036
Журнал	Journal of Physics: Conference Series
Том	1680
Номер выпуска	1
DOI	https://doi.org/10.1088/1742-6596/1680/1/012036
Состояние	Опубликовано - 21 дек. 2020
Событие	13th International Conference on Computer-Aided Technologies in Applied Mathematics, ICAM 2020 - Tomsk, Российская Федерация Продолжительность: 7 сент. 2020 → 9 сент. 2020

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10.1088/1742-6596/1680/1/012036

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abstract = "Quicksort algorithm as an assistant preliminary tool is proposed for acceleration of neighbour search procedure in the frame of molecular dynamics simulations. Simple estimations are made showing that the number of operations required to determine all the neighbours within a system of particles can be reduced by 2-3 orders of magnitude due to the preliminary sorting. Test molecular dynamics simulations carried out for virtual crystal structure containing atoms manifest 9-fold acceleration achieved by the modified algorithm. ",

author = "Novikov, {P. L.} and Pavsky, {K. V.} and Baranov, {A. A.}",

note = "Funding Information: This work was partially supported by the Ministry of Science and Higher Education of the Russian Federation (Project 0306-2019-0019). Publisher Copyright: {\textcopyright} Published under licence by IOP Publishing Ltd. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.; 13th International Conference on Computer-Aided Technologies in Applied Mathematics, ICAM 2020 ; Conference date: 07-09-2020 Through 09-09-2020",

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Quick search of neighbour particles in molecular dynamics simulations. / Novikov, P. L.; Pavsky, K. V.; Baranov, A. A.

В: Journal of Physics: Conference Series, Том 1680, № 1, 012036, 21.12.2020.

Результат исследования: Научные публикации в периодических изданиях › статья по материалам конференции › рецензирование

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T1 - Quick search of neighbour particles in molecular dynamics simulations

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AU - Pavsky, K. V.

AU - Baranov, A. A.

N1 - Funding Information: This work was partially supported by the Ministry of Science and Higher Education of the Russian Federation (Project 0306-2019-0019). Publisher Copyright: © Published under licence by IOP Publishing Ltd. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/12/21

Y1 - 2020/12/21

N2 - Quicksort algorithm as an assistant preliminary tool is proposed for acceleration of neighbour search procedure in the frame of molecular dynamics simulations. Simple estimations are made showing that the number of operations required to determine all the neighbours within a system of particles can be reduced by 2-3 orders of magnitude due to the preliminary sorting. Test molecular dynamics simulations carried out for virtual crystal structure containing atoms manifest 9-fold acceleration achieved by the modified algorithm.

AB - Quicksort algorithm as an assistant preliminary tool is proposed for acceleration of neighbour search procedure in the frame of molecular dynamics simulations. Simple estimations are made showing that the number of operations required to determine all the neighbours within a system of particles can be reduced by 2-3 orders of magnitude due to the preliminary sorting. Test molecular dynamics simulations carried out for virtual crystal structure containing atoms manifest 9-fold acceleration achieved by the modified algorithm.

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DO - 10.1088/1742-6596/1680/1/012036

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VL - 1680

JO - Journal of Physics: Conference Series

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T2 - 13th International Conference on Computer-Aided Technologies in Applied Mathematics, ICAM 2020

Y2 - 7 September 2020 through 9 September 2020

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Quick search of neighbour particles in molecular dynamics simulations

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