SedTrace 1.0: a Julia-based framework for generating and running reactive-transport models of marine sediment diagenesis specializing in trace elements and isotopes
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2023-10-20
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Journal Article
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yes
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Abstract
Trace elements and isotopes (TEIs) are important tools in studying ocean biogeochemistry. Understanding their modern ocean budgets and using their sedimentary records to reconstruct paleoceanographic conditions require a mechanistic understanding of the diagenesis of TEIs, yet the lack of appropriate modeling tools has limited our ability to perform such research. Here I introduce SedTrace, a modeling framework that can be used to generate reactive-transport code for modeling marine sediment diagenesis and assist model simulation using advanced numerical tools in Julia. SedTrace enables mechanistic TEI modeling by providing flexible tools for pH and speciation modeling, which are essential in studying TEI diagenesis. SedTrace is designed to solve one particular challenge facing users of diagenetic models: existing models are usually case-specific and not easily adaptable for new problems such that the user has to choose between modifying published code and writing their own code, both of which demand strong coding skills. To lower this barrier, SedTrace can generate diagenetic models only requiring the user to supply Excel spreadsheets containing necessary model information. The resulting code is clearly structured and readable, and it is integrated with Julia's differential equation solving ecosystems, utilizing tools such as automatic differentiation, sparse numerical methods, Newton–Krylov solvers and preconditioners. This allows efficient solution of large systems of stiff diagenetic equations. I demonstrate the capacity of SedTrace using case studies of modeling the diagenesis of pH as well as radiogenic and stable isotopes of TEIs.
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published
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Journal / series
Volume
16 (20)
Pages / Article No.
5865 - 5894
Publisher
Copernicus
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Software
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03956 - Vance, Derek / Vance, Derek
02725 - Institut für Geochemie und Petrologie / Institute of Geochemistry and Petrology
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Funding
891489 - The critical role of sedimentary trace element fluxes in ocean biogeochemistry (EC)
19-2 FEL-32 - The critical role of sedimentary trace element fluxes in ocean biogeochemistry (ETHZ)
19-2 FEL-32 - The critical role of sedimentary trace element fluxes in ocean biogeochemistry (ETHZ)