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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

Abstract

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% moremore » 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. Altogether, 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.« less

Authors:
ORCiD logo; ; ORCiD logo; ; ; ; ; ORCiD logo; ; ORCiD logo; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States); Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Work for Others (WFO)
OSTI Identifier:
1240298
Alternate Identifier(s):
OSTI ID: 1240537; OSTI ID: 1261540; OSTI ID: 1266840; OSTI ID: 1327768
Grant/Contract Number:  
AC05-00OR22725; NGEE-Arctic; AC04-94AL85000
Resource Type:
Journal Article: Published Article
Journal Name:
Geoscientific Model Development (Online)
Additional Journal Information:
Journal Name: Geoscientific Model Development (Online) Journal Volume: 9 Journal Issue: 3; Journal ID: ISSN 1991-9603
Publisher:
Copernicus Publications, EGU
Country of Publication:
Germany
Language:
English
Subject:
58 GEOSCIENCES

Citation Formats

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., and 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. Germany: N. p., 2016. Web. doi:10.5194/gmd-9-927-2016.
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. Germany. https://doi.org/10.5194/gmd-9-927-2016
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., and Thornton, Peter E. 2016. "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". Germany. https://doi.org/10.5194/gmd-9-927-2016.
@article{osti_1240298,
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},
author = {Tang, Guoping and Yuan, Fengming and Bisht, Gautam and Hammond, Glenn E. and Lichtner, Peter C. and Kumar, Jitendra and Mills, Richard T. and Xu, Xiaofeng and Andre, Ben and Hoffman, Forrest M. and Painter, Scott L. and Thornton, Peter E.},
abstractNote = {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. Altogether, 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.},
doi = {10.5194/gmd-9-927-2016},
url = {https://www.osti.gov/biblio/1240298}, journal = {Geoscientific Model Development (Online)},
issn = {1991-9603},
number = 3,
volume = 9,
place = {Germany},
year = {2016},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.5194/gmd-9-927-2016

Citation Metrics:
Cited by: 4 works
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