Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Molins, Sergi; Andre, Benjamin J.; Johnson, Jeffrey N.; Hammond, Glenn E.; Sulman, Benjamin N.; Lipnikov, Konstantin; Day, Marcus S.; Beisman, James J.; Svyatsky, Daniil; Deng, Hang; Lichtner, Peter C.; Steefel, Carl I.; Moulton, J. David

doi:https://doi.org/10.5194/gmd-18-3241-2025

Articles | Volume 18, issue 11

https://doi.org/10.5194/gmd-18-3241-2025

© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/gmd-18-3241-2025

© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 18, issue 11

Model description paper

|

02 Jun 2025

Model description paper |

| 02 Jun 2025

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

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

Model code and software

Alquimia: A generic interface to biogeochemical codes– A tool for interoperable development, prototyping and benchmarking for multiphysics simulators Sergi Molins et al. https://doi.org/10.5281/zenodo.11414441

Alquimia B. Andre et al. https://doi.org/10.11578/DC.20210416.49

Simulated hydrological dynamics and coupled iron redox cycling impact methane production in an Arctic soil: Modeling Archive B. Sulman et al. https://doi.org/10.5440/1814844

Model simulations of Plum Island Ecosystems LTER low marsh site using ELM-PFLOTRAN B. Sulman et al. https://doi.org/10.15485/1991625

Alquimia B. Andre et al. https://github.com/LBL-EESA/alquimia-dev

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.