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We explore coupling to a configurable subsurface reactive transportcode as a flexible and extensible approach to biogeochemistry in landsurface models.A reaction network withthe Community Land Model carbon–nitrogen (CLM-CN) decomposition, nitrification, denitrification, and plantuptake is used as an example. We implement the reactions in theopen-source PFLOTRAN (massively parallel subsurface flow and reactive transport) code and couple it with the CLM. To make therate formulae designed for use in explicit time stepping in CLMscompatible with the implicit time stepping used in PFLOTRAN, the Monodsubstrate rate-limiting function with a residual concentration is usedto represent the limitation of nitrogen availability on plant uptakeand immobilization.We demonstrate that CLM–PFLOTRAN predictions (without invoking PFLOTRANtransport) are consistent with CLM4.5 for Arctic, temperate, and tropicalsites. Switching from explicit to implicit method increases rigor but introducesnumerical challenges.Care needs to be taken to use scaling, clipping,or log transformation to avoid negative concentrations during theNewton iterations.With a tight relative update tolerance (STOL) to avoidfalse convergence, an accurate solution can be achieved with about50 % more computing time than CLM in point mode site simulationsusing either the scaling or clipping methods. The log transformationmethod takes 60–100 % more computing time than CLM. Thecomputing time increases slightly for clipping and scaling; itincreases substantially for log transformation for half saturationdecrease from 10−3 to 10−9 mol m−3, whichnormally results in decreasing nitrogen concentrations. The frequentoccurrence of very low concentrations (e.g. below nanomolar) canincrease the computing time for clipping or scaling by about 20 %,double for log transformation.Overall, the log transformation method is accurate and robust, and theclipping and scaling methods are efficient. When thereaction network is highly nonlinear or the half saturation or residualconcentration is very low, the allowable time-step cuts mayneed to be increased for robustness for the log transformation method, orSTOL may need to be tightened for the clipping andscaling methods to avoid false convergence. As some biogeochemical processes(e.g., methane and nitrous oxide reactions) involvevery low half saturation and thresholds, this workprovides insights for addressing nonphysical negativity issues andfacilitates the representation of a mechanistic biogeochemicaldescription in Earth system models to reduce climate predictionuncertainty

geoscientific model development

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