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需要重新定义键序以减少分子动力学模拟中的固有噪声。

Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations.

作者信息

Syuhada Ibnu, Hauwali Nikodemus Umbu Janga, Rosikhin Ahmad, Sustini Euis, Noor Fatimah Arofiati, Winata Toto

机构信息

Physics of Electronic Materials Research Division, Department of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung, 40132, Indonesia.

出版信息

Sci Rep. 2021 Feb 11;11(1):3674. doi: 10.1038/s41598-020-80217-0.

DOI:10.1038/s41598-020-80217-0
PMID:33574347
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7878785/
Abstract

In this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, which tries to maintain its environment. To show the necessity, we developed a factory empirical interatomic potential (FEIP) for carbon that implements the redefinition with a short-range interaction approach. FEIP has been shown to enhance the accuracy of the calculation of lattice constants, cohesive energy, elastic properties, and phonons compared to experimental data, and can even be compared to other potentials with the long-range interaction approach. The enhancements due to FEIP can reduce the inherent noise, then provide a better prediction of the energy based on the behaviour of the atomic environment. FEIP can also transform simple two-body interactions into many-body interactions, which is useful for enhancing accuracy. Due to implementing the bond order redefinition, FEIP offers faster calculations than other complex interatomic potentials.

摘要

在这项工作中,我们提出了为降低固有噪声从而提高分子动力学模拟准确性所需的键序重新定义。我们建议将键序定义为能量分布的一部分。这是由于自然界中物质的特性导致的,物质会试图维持其环境。为了说明其必要性,我们开发了一种用于碳的工厂经验原子间势(FEIP),它采用短程相互作用方法来实现这种重新定义。与实验数据相比,FEIP已被证明能提高晶格常数、内聚能、弹性性质和声子计算的准确性,甚至可以与采用长程相互作用方法的其他势进行比较。FEIP带来的改进可以降低固有噪声,进而基于原子环境的行为对能量做出更好的预测。FEIP还可以将简单的两体相互作用转变为多体相互作用,这有助于提高准确性。由于实施了键序重新定义,FEIP比其他复杂的原子间势计算速度更快。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/d41fde9c1403/41598_2020_80217_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/fb38f737c413/41598_2020_80217_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/dfed2ae7ac57/41598_2020_80217_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/921d6252af09/41598_2020_80217_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/d41fde9c1403/41598_2020_80217_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/fb38f737c413/41598_2020_80217_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/dfed2ae7ac57/41598_2020_80217_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/921d6252af09/41598_2020_80217_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99a8/7878785/d41fde9c1403/41598_2020_80217_Fig4_HTML.jpg

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本文引用的文献

1
Machine learning coarse grained models for water.机器学习的粗粒度水模型。
Nat Commun. 2019 Jan 22;10(1):379. doi: 10.1038/s41467-018-08222-6.
2
Real-time imaging of adatom-promoted graphene growth on nickel.实时观测镍上原子促进的石墨烯生长。
Science. 2018 Mar 16;359(6381):1243-1246. doi: 10.1126/science.aan8782.
3
Fullerene and nanotube growth: new insights using first principles and molecular dynamics.富勒烯与纳米管生长:基于第一性原理和分子动力学的新见解
Philos Trans A Math Phys Eng Sci. 2016 Sep 13;374(2076). doi: 10.1098/rsta.2015.0327.
4
Tight-binding calculation studies of vacancy and adatom defects in graphene.石墨烯中空位和吸附原子缺陷的紧束缚计算研究。
J Phys Condens Matter. 2016 Mar 23;28(11):115001. doi: 10.1088/0953-8984/28/11/115001. Epub 2016 Feb 23.
5
Simulation of the Elastic and Ultimate Tensile Properties of Diamond, Graphene, Carbon Nanotubes, and Amorphous Carbon Using a Revised ReaxFF Parametrization.使用修正的反应力场(ReaxFF)参数化方法模拟金刚石、石墨烯、碳纳米管和非晶碳的弹性和极限拉伸性能。
J Phys Chem A. 2015 Sep 17;119(37):9710-21. doi: 10.1021/acs.jpca.5b05889. Epub 2015 Sep 2.
6
The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube.时间步长、恒温器和应变率对金刚石、石墨烯和碳纳米管机械失效的ReaxFF模拟的影响。
J Comput Chem. 2015 Aug 5;36(21):1587-96. doi: 10.1002/jcc.23970. Epub 2015 Jun 12.
7
Insights into carbon nanotube and graphene formation mechanisms from molecular simulations: a review.从分子模拟看碳纳米管和石墨烯的形成机制:综述
Rep Prog Phys. 2015 Feb;78(3):036501. doi: 10.1088/0034-4885/78/3/036501. Epub 2015 Mar 9.
8
Comparing graphene growth on Cu(111) versus oxidized Cu(111).比较石墨烯在Cu(111)与氧化的Cu(111)上的生长情况。
Nano Lett. 2015 Feb 11;15(2):917-22. doi: 10.1021/nl5036463. Epub 2015 Jan 29.
9
Magnetic bond-order potential for iron.铁的磁键阶位势。
Phys Rev Lett. 2011 Jun 17;106(24):246402. doi: 10.1103/PhysRevLett.106.246402. Epub 2011 Jun 14.
10
Two-dimensional phonon transport in supported graphene.支撑石墨烯中的二维声子输运。
Science. 2010 Apr 9;328(5975):213-6. doi: 10.1126/science.1184014.