Articles | Volume 9, issue 3
Development and technical paper
04 Mar 2016
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 Tang, Fengming Yuan, Gautam Bisht, Glenn E. Hammond, Peter C. Lichtner, Jitendra Kumar, Richard T. Mills, Xiaofeng Xu, Ben Andre, Forrest M. Hoffman, Scott L. Painter, and Peter E. Thornton

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Cited articles

Bethke, C. M.: Geochemical and Biogeochemical Reaction Modeling, Cambridge University Press, 2007.
Bonan, G. B., Hartman, M. D., Parton, W. J., and Wieder, W. R.: Evaluating litter decomposition in earth system models with long-term litterbag experiments: an example using the Community Land Model version 4 (CLM4), Glob. Change Biol., 19, 957–974,, 2012.
Boyer, E. W., Alexander, R. B., Parton, W. J., Li, C., Butterbach-Bahl, K., Donner, S. D., Skaggs, R. W., and Grosso, S. J. D.: Modeling denitrification in terrestrial and aquatic ecosystems at regional scales, Ecol. Appl., 16, 2123–2142,[2123:MDITAA]2.0.CO;2, 2006.
Conrad, R.: Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO), Microbi. Rev., 60, 609–640, available at: (last access: 14 December 2015), 8987358[pmid], 1996.
da Costa, A. C. L., Galbraith, D., Almeida, S., Portela, B. T. T., da Costa, M., de Athaydes Silva Junior, J., Braga, A. P., de Gonçalves, P. H. L., de Oliveira, A. A. R., Fisher, R., Phillips, O. L., Metcalfe, D. B., Levy, P., and Meir, P.: Effect of 7 yr of experimental drought on vegetation dynamics and biomass storage of an eastern Amazonian rainforest, New Phytol., 187, 579–591,, 2010.
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.