A versatile marine modelling tool applied to arctic, temperate and tropical waters
The improved understanding of complex interactions of marine ecosystem components makes the use of fully coupled hydrodynamic, biogeochemical and individual based models more and more relevant. At the same time, the increasing complexity of the models and diverse user backgrounds calls for improved...
Published in: | PLOS ONE |
---|---|
Main Authors: | , , , |
Format: | Text |
Language: | English |
Published: |
Public Library of Science
2020
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147738/ http://www.ncbi.nlm.nih.gov/pubmed/32275678 https://doi.org/10.1371/journal.pone.0231193 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:7147738 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:7147738 2023-05-15T15:12:35+02:00 A versatile marine modelling tool applied to arctic, temperate and tropical waters Larsen, Janus Mohn, Christian Pastor, Ane Maar, Marie 2020-04-10 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147738/ http://www.ncbi.nlm.nih.gov/pubmed/32275678 https://doi.org/10.1371/journal.pone.0231193 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147738/ http://www.ncbi.nlm.nih.gov/pubmed/32275678 http://dx.doi.org/10.1371/journal.pone.0231193 © 2020 Larsen et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2020 ftpubmed https://doi.org/10.1371/journal.pone.0231193 2020-04-19T00:33:40Z The improved understanding of complex interactions of marine ecosystem components makes the use of fully coupled hydrodynamic, biogeochemical and individual based models more and more relevant. At the same time, the increasing complexity of the models and diverse user backgrounds calls for improved user friendliness and flexibility of the model systems. We present FlexSem, a versatile and user-friendly framework for 3D hydrodynamic, biogeochemical, individual based and sediment transport modelling. The purpose of the framework is to enable natural scientists to conduct advanced 3D simulations in the marine environment, including any relevant processes. This is made possible by providing a precompiled portable framework, which still enables the user to pick any combination of models and provide user defined equation systems to be solved during the simulation. We here present the ideas behind the framework design, the implementation and documentation of the numerical solution to the Navier-Stokes equations in the hydrodynamic module, the surface heat budget model, the pelagic and benthic equation solvers and the Lagrangian movement of the agents in the agent based model. Five examples of different applications of the system are shown: 1) Hydrodynamics in the Disko Bay in west Greenland, 2) A biogeochemical pelagic and benthic model in the inner Danish waters, 3) A generic mussel farm model featuring offline physics, food levels and mussel eco-physiology, 4) Sediment transport in Clarion-Clipperton zone at the bottom of the Pacific and 5) Hydrodynamics coupled with an agent based model around Zanzibar in Tanzania. Hence we demonstrate that the model can be set up for any area with enough forcing data and used to solve a wide range of applications. Text Arctic Disko Bay Greenland PubMed Central (PMC) Arctic Greenland Pacific PLOS ONE 15 4 e0231193 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Research Article |
spellingShingle |
Research Article Larsen, Janus Mohn, Christian Pastor, Ane Maar, Marie A versatile marine modelling tool applied to arctic, temperate and tropical waters |
topic_facet |
Research Article |
description |
The improved understanding of complex interactions of marine ecosystem components makes the use of fully coupled hydrodynamic, biogeochemical and individual based models more and more relevant. At the same time, the increasing complexity of the models and diverse user backgrounds calls for improved user friendliness and flexibility of the model systems. We present FlexSem, a versatile and user-friendly framework for 3D hydrodynamic, biogeochemical, individual based and sediment transport modelling. The purpose of the framework is to enable natural scientists to conduct advanced 3D simulations in the marine environment, including any relevant processes. This is made possible by providing a precompiled portable framework, which still enables the user to pick any combination of models and provide user defined equation systems to be solved during the simulation. We here present the ideas behind the framework design, the implementation and documentation of the numerical solution to the Navier-Stokes equations in the hydrodynamic module, the surface heat budget model, the pelagic and benthic equation solvers and the Lagrangian movement of the agents in the agent based model. Five examples of different applications of the system are shown: 1) Hydrodynamics in the Disko Bay in west Greenland, 2) A biogeochemical pelagic and benthic model in the inner Danish waters, 3) A generic mussel farm model featuring offline physics, food levels and mussel eco-physiology, 4) Sediment transport in Clarion-Clipperton zone at the bottom of the Pacific and 5) Hydrodynamics coupled with an agent based model around Zanzibar in Tanzania. Hence we demonstrate that the model can be set up for any area with enough forcing data and used to solve a wide range of applications. |
format |
Text |
author |
Larsen, Janus Mohn, Christian Pastor, Ane Maar, Marie |
author_facet |
Larsen, Janus Mohn, Christian Pastor, Ane Maar, Marie |
author_sort |
Larsen, Janus |
title |
A versatile marine modelling tool applied to arctic, temperate and tropical waters |
title_short |
A versatile marine modelling tool applied to arctic, temperate and tropical waters |
title_full |
A versatile marine modelling tool applied to arctic, temperate and tropical waters |
title_fullStr |
A versatile marine modelling tool applied to arctic, temperate and tropical waters |
title_full_unstemmed |
A versatile marine modelling tool applied to arctic, temperate and tropical waters |
title_sort |
versatile marine modelling tool applied to arctic, temperate and tropical waters |
publisher |
Public Library of Science |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147738/ http://www.ncbi.nlm.nih.gov/pubmed/32275678 https://doi.org/10.1371/journal.pone.0231193 |
geographic |
Arctic Greenland Pacific |
geographic_facet |
Arctic Greenland Pacific |
genre |
Arctic Disko Bay Greenland |
genre_facet |
Arctic Disko Bay Greenland |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147738/ http://www.ncbi.nlm.nih.gov/pubmed/32275678 http://dx.doi.org/10.1371/journal.pone.0231193 |
op_rights |
© 2020 Larsen et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0231193 |
container_title |
PLOS ONE |
container_volume |
15 |
container_issue |
4 |
container_start_page |
e0231193 |
_version_ |
1766343241878208512 |