Journal cover Journal topic
Geoscientific Model Development An interactive open-access journal of the European Geosciences Union
Geosci. Model Dev., 9, 927-946, 2016
http://www.geosci-model-dev.net/9/927/2016/
doi:10.5194/gmd-9-927-2016
© Author(s) 2016. This work is distributed
under the Creative Commons Attribution 3.0 License.
Development and technical paper
04 Mar 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
Guoping Tang1, Fengming Yuan1, Gautam Bisht1,2, Glenn E. Hammond3,4, Peter C. Lichtner5, Jitendra Kumar1, Richard T. Mills6, Xiaofeng Xu1,7, Ben Andre2,8, Forrest M. Hoffman1, Scott L. Painter1, and Peter E. Thornton1 1Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
2Lawrence Berkeley National Laboratory, Berkeley, California, USA
3Pacific Northwest National Laboratory, Richland, Washington, USA
4Sandia National Laboratories, Albuquerque, New Mexico, USA
5OFM Research–Southwest, Santa Fe, New Mexico, USA
6Intel Corporation, Hillsboro, Oregon, USA
7San Diego State University, San Diego, California, USA
8National Center for Atmospheric Research, Boulder, Colorado, USA
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 % 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.


Citation: Tang, G., Yuan, F., Bisht, G., Hammond, G. E., Lichtner, P. C., Kumar, J., Mills, R. T., Xu, X., Andre, B., Hoffman, F. M., Painter, S. L., and Thornton, P. 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, Geosci. Model Dev., 9, 927-946, doi:10.5194/gmd-9-927-2016, 2016.
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Short summary
We demonstrate that CLM-PFLOTRAN predictions are consistent with CLM4.5 for Arctic, temperate, and tropical sites. A tight relative tolerance may be needed to avoid false convergence when scaling, clipping, or log transformation is used to avoid negative concentration in implicit time stepping and Newton-Raphson methods. The log transformation method is accurate and robust while relaxing relative tolerance or using the clipping or scaling method can result in efficient solutions.
We demonstrate that CLM-PFLOTRAN predictions are consistent with CLM4.5 for Arctic, temperate,...
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