Articles | Volume 15, issue 4
https://doi.org/10.5194/gmd-15-1659-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-15-1659-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
The PFLOTRAN Reaction Sandbox
Environmental Subsurface Science Group, Pacific Northwest National Laboratory, Richland, WA, USA
Related authors
Michael Nole, Katherine Muller, Glenn Hammond, Xiaoliang He, and Peter Lichtner
EGUsphere, https://doi.org/10.5194/egusphere-2025-1343, https://doi.org/10.5194/egusphere-2025-1343, 2025
Short summary
Short summary
Subsurface injection of carbon dioxide (CO2) can be used for a variety of purposes including geologic carbon storage and enhanced oil recovery. Recently, CO2 injection into reactive host rocks has been explored as a way to transform CO2 into dense solid minerals. We present a simulation framework for modeling flow of CO2 due to injection and subsequent reactions that take place to mineralize CO2.
Sergi Molins, Benjamin J. Andre, Jeffrey N. Johnson, Glenn E. Hammond, Benjamin N. Sulman, Konstantin Lipnikov, Marcus S. Day, James J. Beisman, Daniil Svyatsky, Hang Deng, Peter C. Lichtner, Carl I. Steefel, and J. David Moulton
Geosci. Model Dev., 18, 3241–3263, https://doi.org/10.5194/gmd-18-3241-2025, https://doi.org/10.5194/gmd-18-3241-2025, 2025
Short summary
Short summary
Developing scientific software and making sure it functions properly requires a significant effort. As we advance our understanding of natural systems, however, there is the need to develop yet more complex models and codes. In this work, we present a piece of software that facilitates this work, specifically with regard to reactive processes. Existing tried-and-true codes are made available via this new interface, freeing up resources to focus on the new aspects of the problems at hand.
Michael Nole, Jonah Bartrand, Fawz Naim, and Glenn Hammond
Geosci. Model Dev., 18, 1413–1425, https://doi.org/10.5194/gmd-18-1413-2025, https://doi.org/10.5194/gmd-18-1413-2025, 2025
Short summary
Short summary
Safe carbon dioxide (CO2) storage is likely to be critical for mitigating some of the most severe effects of climate change. We present a simulation framework for modeling CO2 storage beneath the seafloor, where CO2 can form a solid. This can aid in permanent CO2 storage for long periods of time. Our models show what a commercial-scale CO2 injection would look like in a marine environment. We discuss what would need to be considered when designing a subsea CO2 injection.
Katherine A. Muller, Peishi Jiang, Glenn Hammond, Tasneem Ahmadullah, Hyun-Seob Song, Ravi Kukkadapu, Nicholas Ward, Madison Bowe, Rosalie K. Chu, Qian Zhao, Vanessa A. Garayburu-Caruso, Alan Roebuck, and Xingyuan Chen
Geosci. Model Dev., 17, 8955–8968, https://doi.org/10.5194/gmd-17-8955-2024, https://doi.org/10.5194/gmd-17-8955-2024, 2024
Short summary
Short summary
The new Lambda-PFLOTRAN workflow incorporates organic matter chemistry into reaction networks to simulate aerobic respiration and biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow in a Jupyter notebook interface that digests raw organic matter chemistry data via Fourier transform ion cyclotron resonance mass spectrometry, develops a representative reaction network, and completes a biogeochemical simulation with the open-source, parallel-reactive-flow, and transport code PFLOTRAN.
Piyoosh Jaysaval, Glenn E. Hammond, and Timothy C. Johnson
Geosci. Model Dev., 16, 961–976, https://doi.org/10.5194/gmd-16-961-2023, https://doi.org/10.5194/gmd-16-961-2023, 2023
Short summary
Short summary
We present a robust and highly scalable implementation of numerical forward modeling and inversion algorithms for geophysical electrical resistivity tomography data. The implementation is publicly available and developed within the framework of PFLOTRAN (http://www.pflotran.org), an open-source, state-of-the-art massively parallel subsurface flow and transport simulation code. The paper details all the theoretical and implementation aspects of the new capabilities along with test examples.
Michael Nole, Katherine Muller, Glenn Hammond, Xiaoliang He, and Peter Lichtner
EGUsphere, https://doi.org/10.5194/egusphere-2025-1343, https://doi.org/10.5194/egusphere-2025-1343, 2025
Short summary
Short summary
Subsurface injection of carbon dioxide (CO2) can be used for a variety of purposes including geologic carbon storage and enhanced oil recovery. Recently, CO2 injection into reactive host rocks has been explored as a way to transform CO2 into dense solid minerals. We present a simulation framework for modeling flow of CO2 due to injection and subsequent reactions that take place to mineralize CO2.
Sergi Molins, Benjamin J. Andre, Jeffrey N. Johnson, Glenn E. Hammond, Benjamin N. Sulman, Konstantin Lipnikov, Marcus S. Day, James J. Beisman, Daniil Svyatsky, Hang Deng, Peter C. Lichtner, Carl I. Steefel, and J. David Moulton
Geosci. Model Dev., 18, 3241–3263, https://doi.org/10.5194/gmd-18-3241-2025, https://doi.org/10.5194/gmd-18-3241-2025, 2025
Short summary
Short summary
Developing scientific software and making sure it functions properly requires a significant effort. As we advance our understanding of natural systems, however, there is the need to develop yet more complex models and codes. In this work, we present a piece of software that facilitates this work, specifically with regard to reactive processes. Existing tried-and-true codes are made available via this new interface, freeing up resources to focus on the new aspects of the problems at hand.
Michael Nole, Jonah Bartrand, Fawz Naim, and Glenn Hammond
Geosci. Model Dev., 18, 1413–1425, https://doi.org/10.5194/gmd-18-1413-2025, https://doi.org/10.5194/gmd-18-1413-2025, 2025
Short summary
Short summary
Safe carbon dioxide (CO2) storage is likely to be critical for mitigating some of the most severe effects of climate change. We present a simulation framework for modeling CO2 storage beneath the seafloor, where CO2 can form a solid. This can aid in permanent CO2 storage for long periods of time. Our models show what a commercial-scale CO2 injection would look like in a marine environment. We discuss what would need to be considered when designing a subsea CO2 injection.
Katherine A. Muller, Peishi Jiang, Glenn Hammond, Tasneem Ahmadullah, Hyun-Seob Song, Ravi Kukkadapu, Nicholas Ward, Madison Bowe, Rosalie K. Chu, Qian Zhao, Vanessa A. Garayburu-Caruso, Alan Roebuck, and Xingyuan Chen
Geosci. Model Dev., 17, 8955–8968, https://doi.org/10.5194/gmd-17-8955-2024, https://doi.org/10.5194/gmd-17-8955-2024, 2024
Short summary
Short summary
The new Lambda-PFLOTRAN workflow incorporates organic matter chemistry into reaction networks to simulate aerobic respiration and biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow in a Jupyter notebook interface that digests raw organic matter chemistry data via Fourier transform ion cyclotron resonance mass spectrometry, develops a representative reaction network, and completes a biogeochemical simulation with the open-source, parallel-reactive-flow, and transport code PFLOTRAN.
Piyoosh Jaysaval, Glenn E. Hammond, and Timothy C. Johnson
Geosci. Model Dev., 16, 961–976, https://doi.org/10.5194/gmd-16-961-2023, https://doi.org/10.5194/gmd-16-961-2023, 2023
Short summary
Short summary
We present a robust and highly scalable implementation of numerical forward modeling and inversion algorithms for geophysical electrical resistivity tomography data. The implementation is publicly available and developed within the framework of PFLOTRAN (http://www.pflotran.org), an open-source, state-of-the-art massively parallel subsurface flow and transport simulation code. The paper details all the theoretical and implementation aspects of the new capabilities along with test examples.
Cited articles
Andre, B., Bisht, G., Collier, N., Frederick, J., Hammond, G., Jaysaval, P.,
Karra, S., Kumar, J., Leone, R., Lichtner, P., Mills, R., Nole, M., Orsini,
P., Park, H., and Rousseau, M.: PFLOTRAN Theory Guide,
http://documentation.pflotran.org, last access: 23 February 2022. a
Bethke, C. M.: Geochemical and Biogeochemical Reaction Modeling, Cambridge
University Press, 2nd Edn., https://doi.org/10.1017/CBO9780511619670, 2007. a
Chapman, S.: Fortran for Scientists & Engineers, McGraw-Hill Higher Education,
4th Edn., ISBN10: 0073385891,
ISBN13: 9780073385891, 2018. a
Hammond, G.: PFLOTRAN Reaction Sandbox, Zenodo [code], https://doi.org/10.5281/zenodo.5826289, 2022. a
Hammond, G. E., Lichtner, P. C., and Mills, R. T.: Evaluating the performance
of parallel subsurface simulators: An illustrative example with PFLOTRAN,
Water Resour. Res., 50, 208–228, https://doi.org/10.1002/2012WR013483, 2014. a
Hill, A. V.: The possible effects of the aggregation of the molecules of
hæmoglobin on its dissociation curves, J. Physiol., 40,
i–vii, 1910. a
Lichtner, P. C.: Continuum model for simultaneous chemical reactions and mass
transport in hydrothermal systems, Geochim. Cosmochim. Ac., 49,
779–800, https://doi.org/10.1016/0016-7037(85)90172-3, 1985. a
Liu, C., Zachara, J. M., Qafoku, N. P., and Wang, Z.: Scale-dependent
desorption of uranium from contaminated subsurface sediments, Water Resour.
Res., 44, W08413, https://doi.org/10.1029/2007WR006478, 2008. a
Rubin, J.: Transport of reacting solutes in porous media: Relation between
mathematical nature of problem formulation and chemical nature of reactions,
Water Resour. Res., 19, 1231–1252, https://doi.org/10.1029/WR019i005p01231,
1983. a
Steefel, C., Appelo, C., Arora, B., Jacques, D., Kalbacher, T., Kolditz, O.,
Lagneau, V., Lichtner, P. C., Mayer, K. U., Meeussen, J. C. L., Molins, S.,
Moulton, D., Shao, H., Simunek, J., Spycher, N., Yabusaki, S. B., and Yeh,
G. T.: Reactive transport codes for subsurface environmental simulation,
Comput. Geosci., 19, 445–478, https://doi.org/10.1007/s10596-014-9443-x,
2015. a
Steefel, C. I., DePaolo, D. J., and Lichtner, P. C.: Reactive transport
modeling: An essential tool and a new research approach for the Earth
sciences, Earth Planet. Sc. Lett., 240, 539–558,
https://doi.org/10.1016/j.epsl.2005.09.017, 2005.
a
Tutolo, B. M., Luhmann, A. J., Tosca, N. J., and Seyfried Jr., W. E.:
Serpentinization as a reactive transport process: The brucite silicification
reaction, Earth Planet. Sc. Lett., 484, 385–395,
https://doi.org/10.1016/j.epsl.2017.12.029, 2018. a
Short summary
This paper describes a simplified interface for implementing and testing new chemical reactions within the reactive transport simulator PFLOTRAN. The paper describes the interface, providing example code for the interface. The paper includes several chemical reactions implemented through the interface.
This paper describes a simplified interface for implementing and testing new chemical reactions...