Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators
<p>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 carr...
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| Format: | Article |
| Language: | English |
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Copernicus Publications
2025-06-01
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| Series: | Geoscientific Model Development |
| Online Access: | https://gmd.copernicus.org/articles/18/3241/2025/gmd-18-3241-2025.pdf |
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| author | S. Molins B. J. Andre J. N. Johnson J. N. Johnson G. E. Hammond B. N. Sulman K. Lipnikov M. S. Day J. J. Beisman D. Svyatsky H. Deng P. C. Lichtner C. I. Steefel J. D. Moulton |
| author_facet | S. Molins B. J. Andre J. N. Johnson J. N. Johnson G. E. Hammond B. N. Sulman K. Lipnikov M. S. Day J. J. Beisman D. Svyatsky H. Deng P. C. Lichtner C. I. Steefel J. D. Moulton |
| author_sort | S. Molins |
| collection | DOAJ |
| description | <p>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.</p> |
| format | Article |
| id | doaj-art-129af56190d846f8a126933719ea151f |
| institution | DOAJ |
| issn | 1991-959X 1991-9603 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Copernicus Publications |
| record_format | Article |
| series | Geoscientific Model Development |
| spelling | doaj-art-129af56190d846f8a126933719ea151f2025-08-20T03:18:59ZengCopernicus PublicationsGeoscientific Model Development1991-959X1991-96032025-06-01183241326310.5194/gmd-18-3241-2025Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulatorsS. Molins0B. J. Andre1J. N. Johnson2J. N. Johnson3G. E. Hammond4B. N. Sulman5K. Lipnikov6M. S. Day7J. J. Beisman8D. Svyatsky9H. Deng10P. C. Lichtner11C. I. Steefel12J. D. Moulton13Energy Geosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USAEnergy Geosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USAEnergy Geosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USACohere Consulting, LLC, Seattle, WA 98105, USAEnergy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USAEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USAApplied Mathematics and Plasma Physics, Los Alamos National Laboratory, Los Alamos, NM 87545, USAComputational Science Center, National Renewable Energy Laboratory, Golden, CO 80401, USAEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USAApplied Mathematics and Plasma Physics, Los Alamos National Laboratory, Los Alamos, NM 87545, USADepartment of Energy and Resources Engineering, Peking University, Peking, 100871, ChinaDepartment of Civil Engineering, University of New Mexico, Albuquerque, NM 87131, USAEnergy Geosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USAApplied Mathematics and Plasma Physics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA<p>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.</p>https://gmd.copernicus.org/articles/18/3241/2025/gmd-18-3241-2025.pdf |
| spellingShingle | S. Molins B. J. Andre J. N. Johnson J. N. Johnson G. E. Hammond B. N. Sulman K. Lipnikov M. S. Day J. J. Beisman D. Svyatsky H. Deng P. C. Lichtner C. I. Steefel J. D. Moulton Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators Geoscientific Model Development |
| title | Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators |
| title_full | Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators |
| title_fullStr | Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators |
| title_full_unstemmed | Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators |
| title_short | Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators |
| title_sort | alquimia v1 0 a generic interface to biogeochemical codes a tool for interoperable development prototyping and benchmarking for multiphysics simulators |
| url | https://gmd.copernicus.org/articles/18/3241/2025/gmd-18-3241-2025.pdf |
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