Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0
We explore coupling to a configurable subsurface reactive transport code as a flexible and extensible approach to biogeochemistry in land surface models. A reaction network with the Community Land Model carbon–nitrogen (CLM-CN) decomposition, nitrification, denitrification, and plant uptake is used...
Published in: | Geoscientific Model Development |
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Copernicus Publications
2016
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Online Access: | https://doi.org/10.5194/gmd-9-927-2016 https://noa.gwlb.de/receive/cop_mods_00013907 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00013863/gmd-9-927-2016.pdf https://gmd.copernicus.org/articles/9/927/2016/gmd-9-927-2016.pdf |
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article Verlagsveröffentlichung Tang, Guoping Yuan, Fengming Bisht, Gautam Hammond, Glenn E. Lichtner, Peter C. Kumar, Jitendra Mills, Richard T. Xu, Xiaofeng Andre, Ben Hoffman, Forrest M. Painter, Scott L. Thornton, Peter E. Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0 |
topic_facet |
article Verlagsveröffentlichung |
description |
We explore coupling to a configurable subsurface reactive transport code as a flexible and extensible approach to biogeochemistry in land surface models. A reaction network with the Community Land Model carbon–nitrogen (CLM-CN) decomposition, nitrification, denitrification, and plant uptake is used as an example. We implement the reactions in the open-source PFLOTRAN (massively parallel subsurface flow and reactive transport) code and couple it with the CLM. To make the rate formulae designed for use in explicit time stepping in CLMs compatible with the implicit time stepping used in PFLOTRAN, the Monod substrate rate-limiting function with a residual concentration is used to represent the limitation of nitrogen availability on plant uptake and immobilization. We demonstrate that CLM–PFLOTRAN predictions (without invoking PFLOTRAN transport) are consistent with CLM4.5 for Arctic, temperate, and tropical sites. Switching from explicit to implicit method increases rigor but introduces numerical challenges. Care needs to be taken to use scaling, clipping, or log transformation to avoid negative concentrations during the Newton iterations. With a tight relative update tolerance (STOL) to avoid false convergence, an accurate solution can be achieved with about 50 % more computing time than CLM in point mode site simulations using either the scaling or clipping methods. The log transformation method takes 60–100 % more computing time than CLM. The computing time increases slightly for clipping and scaling; it increases substantially for log transformation for half saturation decrease from 10−3 to 10−9 mol m−3, which normally results in decreasing nitrogen concentrations. The frequent occurrence of very low concentrations (e.g. below nanomolar) can increase the computing time for clipping or scaling by about 20 %, double for log transformation. Overall, the log transformation method is accurate and robust, and the clipping and scaling methods are efficient. When the reaction network is highly nonlinear or the half saturation or residual concentration is very low, the allowable time-step cuts may need to be increased for robustness for the log transformation method, or STOL may need to be tightened for the clipping and scaling methods to avoid false convergence. As some biogeochemical processes (e.g., methane and nitrous oxide reactions) involve very low half saturation and thresholds, this work provides insights for addressing nonphysical negativity issues and facilitates the representation of a mechanistic biogeochemical description in Earth system models to reduce climate prediction uncertainty. |
format |
Article in Journal/Newspaper |
author |
Tang, Guoping Yuan, Fengming Bisht, Gautam Hammond, Glenn E. Lichtner, Peter C. Kumar, Jitendra Mills, Richard T. Xu, Xiaofeng Andre, Ben Hoffman, Forrest M. Painter, Scott L. Thornton, Peter E. |
author_facet |
Tang, Guoping Yuan, Fengming Bisht, Gautam Hammond, Glenn E. Lichtner, Peter C. Kumar, Jitendra Mills, Richard T. Xu, Xiaofeng Andre, Ben Hoffman, Forrest M. Painter, Scott L. Thornton, Peter E. |
author_sort |
Tang, Guoping |
title |
Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0 |
title_short |
Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0 |
title_full |
Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0 |
title_fullStr |
Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0 |
title_full_unstemmed |
Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0 |
title_sort |
addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with clm–pflotran 1.0 |
publisher |
Copernicus Publications |
publishDate |
2016 |
url |
https://doi.org/10.5194/gmd-9-927-2016 https://noa.gwlb.de/receive/cop_mods_00013907 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00013863/gmd-9-927-2016.pdf https://gmd.copernicus.org/articles/9/927/2016/gmd-9-927-2016.pdf |
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ENVELOPE(147.875,147.875,59.388,59.388) |
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Arctic |
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Arctic |
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Geoscientific Model Development -- http://www.bibliothek.uni-regensburg.de/ezeit/?2456725 -- http://www.geosci-model-dev.net/ -- 1991-9603 https://doi.org/10.5194/gmd-9-927-2016 https://noa.gwlb.de/receive/cop_mods_00013907 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00013863/gmd-9-927-2016.pdf https://gmd.copernicus.org/articles/9/927/2016/gmd-9-927-2016.pdf |
op_rights |
uneingeschränkt info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.5194/gmd-9-927-2016 |
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Geoscientific Model Development |
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ftnonlinearchiv:oai:noa.gwlb.de:cop_mods_00013907 2023-05-15T15:19:19+02:00 Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0 Tang, Guoping Yuan, Fengming Bisht, Gautam Hammond, Glenn E. Lichtner, Peter C. Kumar, Jitendra Mills, Richard T. Xu, Xiaofeng Andre, Ben Hoffman, Forrest M. Painter, Scott L. Thornton, Peter E. 2016-03 electronic https://doi.org/10.5194/gmd-9-927-2016 https://noa.gwlb.de/receive/cop_mods_00013907 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00013863/gmd-9-927-2016.pdf https://gmd.copernicus.org/articles/9/927/2016/gmd-9-927-2016.pdf eng eng Copernicus Publications Geoscientific Model Development -- http://www.bibliothek.uni-regensburg.de/ezeit/?2456725 -- http://www.geosci-model-dev.net/ -- 1991-9603 https://doi.org/10.5194/gmd-9-927-2016 https://noa.gwlb.de/receive/cop_mods_00013907 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00013863/gmd-9-927-2016.pdf https://gmd.copernicus.org/articles/9/927/2016/gmd-9-927-2016.pdf uneingeschränkt info:eu-repo/semantics/openAccess article Verlagsveröffentlichung article Text doc-type:article 2016 ftnonlinearchiv https://doi.org/10.5194/gmd-9-927-2016 2022-02-08T22:55:22Z We explore coupling to a configurable subsurface reactive transport code as a flexible and extensible approach to biogeochemistry in land surface models. A reaction network with the Community Land Model carbon–nitrogen (CLM-CN) decomposition, nitrification, denitrification, and plant uptake is used as an example. We implement the reactions in the open-source PFLOTRAN (massively parallel subsurface flow and reactive transport) code and couple it with the CLM. To make the rate formulae designed for use in explicit time stepping in CLMs compatible with the implicit time stepping used in PFLOTRAN, the Monod substrate rate-limiting function with a residual concentration is used to represent the limitation of nitrogen availability on plant uptake and immobilization. We demonstrate that CLM–PFLOTRAN predictions (without invoking PFLOTRAN transport) are consistent with CLM4.5 for Arctic, temperate, and tropical sites. Switching from explicit to implicit method increases rigor but introduces numerical challenges. Care needs to be taken to use scaling, clipping, or log transformation to avoid negative concentrations during the Newton iterations. With a tight relative update tolerance (STOL) to avoid false convergence, an accurate solution can be achieved with about 50 % more computing time than CLM in point mode site simulations using either the scaling or clipping methods. The log transformation method takes 60–100 % more computing time than CLM. The computing time increases slightly for clipping and scaling; it increases substantially for log transformation for half saturation decrease from 10−3 to 10−9 mol m−3, which normally results in decreasing nitrogen concentrations. The frequent occurrence of very low concentrations (e.g. below nanomolar) can increase the computing time for clipping or scaling by about 20 %, double for log transformation. Overall, the log transformation method is accurate and robust, and the clipping and scaling methods are efficient. When the reaction network is highly nonlinear or the half saturation or residual concentration is very low, the allowable time-step cuts may need to be increased for robustness for the log transformation method, or STOL may need to be tightened for the clipping and scaling methods to avoid false convergence. As some biogeochemical processes (e.g., methane and nitrous oxide reactions) involve very low half saturation and thresholds, this work provides insights for addressing nonphysical negativity issues and facilitates the representation of a mechanistic biogeochemical description in Earth system models to reduce climate prediction uncertainty. Article in Journal/Newspaper Arctic Niedersächsisches Online-Archiv NOA Arctic Stol ENVELOPE(147.875,147.875,59.388,59.388) Geoscientific Model Development 9 3 927 946 |