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Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878785/ https://www.ncbi.nlm.nih.gov/pubmed/33574347 http://dx.doi.org/10.1038/s41598-020-80217-0 |
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author | Syuhada, Ibnu Hauwali, Nikodemus Umbu Janga Rosikhin, Ahmad Sustini, Euis Noor, Fatimah Arofiati Winata, Toto |
author_facet | Syuhada, Ibnu Hauwali, Nikodemus Umbu Janga Rosikhin, Ahmad Sustini, Euis Noor, Fatimah Arofiati Winata, Toto |
author_sort | Syuhada, Ibnu |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7878785 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-78787852021-02-12 Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations Syuhada, Ibnu Hauwali, Nikodemus Umbu Janga Rosikhin, Ahmad Sustini, Euis Noor, Fatimah Arofiati Winata, Toto Sci Rep Article 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. Nature Publishing Group UK 2021-02-11 /pmc/articles/PMC7878785/ /pubmed/33574347 http://dx.doi.org/10.1038/s41598-020-80217-0 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Syuhada, Ibnu Hauwali, Nikodemus Umbu Janga Rosikhin, Ahmad Sustini, Euis Noor, Fatimah Arofiati Winata, Toto Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations |
title | Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations |
title_full | Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations |
title_fullStr | Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations |
title_full_unstemmed | Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations |
title_short | Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations |
title_sort | bond order redefinition needed to reduce inherent noise in molecular dynamics simulations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878785/ https://www.ncbi.nlm.nih.gov/pubmed/33574347 http://dx.doi.org/10.1038/s41598-020-80217-0 |
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