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

Related authors

Biogeochemical modeling of CO2 and CH4 production in anoxic Arctic soil microcosms
Guoping Tang, Jianqiu Zheng, Xiaofeng Xu, Ziming Yang, David E. Graham, Baohua Gu, Scott L. Painter, and Peter E. Thornton
Biogeosciences, 13, 5021–5041,,, 2016
Short summary

Related subject area

Climate and Earth system modeling
Validating a microphysical prognostic stratospheric aerosol implementation in E3SMv2 using observations after the Mount Pinatubo eruption
Hunter York Brown, Benjamin Wagman, Diana Bull, Kara Peterson, Benjamin Hillman, Xiaohong Liu, Ziming Ke, and Lin Lin
Geosci. Model Dev., 17, 5087–5121,,, 2024
Short summary
Implementing detailed nucleation predictions in the Earth system model EC-Earth3.3.4: sulfuric acid–ammonia nucleation
Carl Svenhag, Moa K. Sporre, Tinja Olenius, Daniel Yazgi, Sara M. Blichner, Lars P. Nieradzik, and Pontus Roldin
Geosci. Model Dev., 17, 4923–4942,,, 2024
Short summary
Modeling biochar effects on soil organic carbon on croplands in a microbial decomposition model (MIMICS-BC_v1.0)
Mengjie Han, Qing Zhao, Xili Wang, Ying-Ping Wang, Philippe Ciais, Haicheng Zhang, Daniel S. Goll, Lei Zhu, Zhe Zhao, Zhixuan Guo, Chen Wang, Wei Zhuang, Fengchang Wu, and Wei Li
Geosci. Model Dev., 17, 4871–4890,,, 2024
Short summary
Hector V3.2.0: functionality and performance of a reduced-complexity climate model
Kalyn Dorheim, Skylar Gering, Robert Gieseke, Corinne Hartin, Leeya Pressburger, Alexey N. Shiklomanov, Steven J. Smith, Claudia Tebaldi, Dawn L. Woodard, and Ben Bond-Lamberty
Geosci. Model Dev., 17, 4855–4869,,, 2024
Short summary
Evaluation of CMIP6 model simulations of PM2.5 and its components over China
Fangxuan Ren, Jintai Lin, Chenghao Xu, Jamiu A. Adeniran, Jingxu Wang, Randall V. Martin, Aaron van Donkelaar, Melanie S. Hammer, Larry W. Horowitz, Steven T. Turnock, Naga Oshima, Jie Zhang, Susanne Bauer, Kostas Tsigaridis, Øyvind Seland, Pierre Nabat, David Neubauer, Gary Strand, Twan van Noije, Philippe Le Sager, and Toshihiko Takemura
Geosci. Model Dev., 17, 4821–4836,,, 2024
Short summary

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.