Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators Article Swipe
Sergi Molins
,
Benjamin Andre
,
Jeffrey Johnson
,
Glenn Hammond
,
Benjamin N. Sulman
,
Konstantin Lipnikov
,
Marc Day
,
James Beisman
,
Daniil Svyatsky
,
Hang Deng
,
Peter C. Lichtner
,
Carl I. Steefel
,
D. Moulton
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.5194/gmd-18-3241-2025
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.5194/gmd-18-3241-2025
Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.
Related Topics
Concepts
Multiphysics
Benchmarking
Interoperability
Interface (matter)
Computer science
Rapid prototyping
Computer architecture
Computational science
Software engineering
Systems engineering
Embedded system
Operating system
Engineering
Mechanical engineering
Maximum bubble pressure method
Marketing
Structural engineering
Bubble
Finite element method
Business
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.5194/gmd-18-3241-2025
- https://gmd.copernicus.org/articles/18/3241/2025/gmd-18-3241-2025.pdf
- OA Status
- gold
- References
- 44
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4410950603
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4410950603Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.5194/gmd-18-3241-2025Digital Object Identifier
- Title
-
Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulatorsWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-06-02Full publication date if available
- Authors
-
Sergi Molins, Benjamin Andre, Jeffrey Johnson, Glenn Hammond, Benjamin N. Sulman, Konstantin Lipnikov, Marc Day, James Beisman, Daniil Svyatsky, Hang Deng, Peter C. Lichtner, Carl I. Steefel, D. MoultonList of authors in order
- Landing page
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https://doi.org/10.5194/gmd-18-3241-2025Publisher landing page
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https://gmd.copernicus.org/articles/18/3241/2025/gmd-18-3241-2025.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://gmd.copernicus.org/articles/18/3241/2025/gmd-18-3241-2025.pdfDirect OA link when available
- Concepts
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Multiphysics, Benchmarking, Interoperability, Interface (matter), Computer science, Rapid prototyping, Computer architecture, Computational science, Software engineering, Systems engineering, Embedded system, Operating system, Engineering, Mechanical engineering, Maximum bubble pressure method, Marketing, Structural engineering, Bubble, Finite element method, BusinessTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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44Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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