Preprints
https://doi.org/10.5194/gmd-2022-281
https://doi.org/10.5194/gmd-2022-281
Submitted as: model description paper
04 Jan 2023
Submitted as: model description paper | 04 Jan 2023
Status: this preprint is currently under review for the journal GMD.

SedTrace 1.0: a Julia-based framework for generating and running reactive-transport models of marine sediment diagenesis specializing in trace elements and isotopes

Jianghui Du Jianghui Du
  • Institute of Geochemistry and Petrology, Department of Earth Sciences, ETH Zürich, Zürich, 8092, Switzerland

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 mechanistic understanding of the diagenesis of TEIs, yet the lack of appropriate modeling tools has limited our ability to perform such research. Here we 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 of pH and speciation modeling, which are essential in studying TEI diagenesis. SedTrace is designed to solve one particular challenge facing the 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 is integrated with Julia’s differential equation solving ecosystems, utilizing tools such as automatic differentiation, sparse numerical methods, Newton-Krylov solvers and preconditioner. This allows efficient solution of large systems of stiff diagenetic equations. We demonstrate the capacity of SedTrace using case studies of modeling the diagenesis of pH, radiogenic and stable isotopes of TEIs.

Jianghui Du

Status: open (until 04 Mar 2023)

Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse

Jianghui Du

Model code and software

SedTrace.jl: a Julia package for generating and running reactive-transport models of marine sediment diagenesis Jianghui Du https://doi.org/10.5281/zenodo.7225861

Jianghui Du

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Short summary
Trace elements and isotopes (TEIs) are important tools to study the changes of the ocean environment both today and in the past. However, the behaviors of TEIs in marine sediments are poorly known, limiting our ability to use them in oceanography. Here we present a modeling framework that can be used to generate and run models of the sedimentary cycling of TEIs assisted with advanced numerical tools in the Julia language, lowering the coding barrier for the general user to study marine TEIs.