Cargando…

Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression

We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-sca...

Descripción completa

Detalles Bibliográficos
Autores principales: Stephenson, David, Kermode, James R., Lockerby, Duncan A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404643/
https://www.ncbi.nlm.nih.gov/pubmed/30930707
http://dx.doi.org/10.1007/s10404-018-2164-z
_version_ 1783400929929723904
author Stephenson, David
Kermode, James R.
Lockerby, Duncan A.
author_facet Stephenson, David
Kermode, James R.
Lockerby, Duncan A.
author_sort Stephenson, David
collection PubMed
description We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-scale information purely by consideration of the macroscopic continuum-model inputs and outputs and judge on the fly whether the uncertainty of our prediction is at an acceptable level, else a new molecular simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial improvement over the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging–diverging channel, and make comparisons between the new scheme and full molecular dynamics simulations for a range of uncertainty thresholds and initial databases. For low thresholds, our hybrid solution is highly accurate—around that of thermal noise. As the uncertainty threshold is raised, the accuracy of our scheme decreases and the computational speed-up increases (relative to a full molecular simulation), enabling the compromise between accuracy and efficiency to be tuned. The speed-up of our hybrid solution ranges from an order of magnitude, with no initial database, to cases where an extensive initial database ensures no new MD simulations are required.
format Online
Article
Text
id pubmed-6404643
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher Springer Berlin Heidelberg
record_format MEDLINE/PubMed
spelling pubmed-64046432019-03-27 Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression Stephenson, David Kermode, James R. Lockerby, Duncan A. Microfluid Nanofluidics Research Paper We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-scale information purely by consideration of the macroscopic continuum-model inputs and outputs and judge on the fly whether the uncertainty of our prediction is at an acceptable level, else a new molecular simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial improvement over the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging–diverging channel, and make comparisons between the new scheme and full molecular dynamics simulations for a range of uncertainty thresholds and initial databases. For low thresholds, our hybrid solution is highly accurate—around that of thermal noise. As the uncertainty threshold is raised, the accuracy of our scheme decreases and the computational speed-up increases (relative to a full molecular simulation), enabling the compromise between accuracy and efficiency to be tuned. The speed-up of our hybrid solution ranges from an order of magnitude, with no initial database, to cases where an extensive initial database ensures no new MD simulations are required. Springer Berlin Heidelberg 2018-11-16 2018 /pmc/articles/PMC6404643/ /pubmed/30930707 http://dx.doi.org/10.1007/s10404-018-2164-z Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Research Paper
Stephenson, David
Kermode, James R.
Lockerby, Duncan A.
Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression
title Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression
title_full Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression
title_fullStr Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression
title_full_unstemmed Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression
title_short Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression
title_sort accelerating multiscale modelling of fluids with on-the-fly gaussian process regression
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404643/
https://www.ncbi.nlm.nih.gov/pubmed/30930707
http://dx.doi.org/10.1007/s10404-018-2164-z
work_keys_str_mv AT stephensondavid acceleratingmultiscalemodellingoffluidswithontheflygaussianprocessregression
AT kermodejamesr acceleratingmultiscalemodellingoffluidswithontheflygaussianprocessregression
AT lockerbyduncana acceleratingmultiscalemodellingoffluidswithontheflygaussianprocessregression