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Published March 11, 2022 | Version Published
Journal Article Open

RADIv1: a non-steady-state early diagenetic model for ocean sediments in Julia and MATLAB/GNU Octave

Creators

  • 1. ROR icon Utrecht University
  • 2. ROR icon McGill University
  • 3. ROR icon Royal Netherlands Institute for Sea Research
  • 4. ROR icon Brown University
  • 5. ROR icon Jet Propulsion Lab
  • 6. ROR icon San Jose State University
  • 7. ROR icon University of Southern California
  • 8. ROR icon California Institute of Technology

Abstract

We introduce a time-dependent, one-dimensional model of early diagenesis that we term RADI, an acronym accounting for the main processes included in the model: chemical reactions, advection, molecular and bio-diffusion, and bio-irrigation. RADI is targeted for study of deep-sea sediments, in particular those containing calcium carbonates (CaCO3). RADI combines CaCO3 dissolution driven by organic matter degradation with a diffusive boundary layer and integrates state-of-the-art parameterizations of CaCO3 dissolution kinetics in seawater, thus serving as a link between mechanistic surface reaction modeling and global-scale biogeochemical models. RADI also includes CaCO3 precipitation, providing a continuum between CaCO3 dissolution and precipitation. RADI integrates components rather than individual chemical species for accessibility and is straightforward to compare against measurements. RADI is the first diagenetic model implemented in Julia, a high-performance programming language that is free and open source, and it is also available in MATLAB/GNU Octave. Here, we first describe the scientific background behind RADI and its implementations. Following this, we evaluate its performance in three selected locations and explore other potential applications, such as the influence of tides and seasonality on early diagenesis in the deep ocean. RADI is a powerful tool to study the time-transient and steady-state response of the sedimentary system to environmental perturbation, such as deep-sea mining, deoxygenation, or acidification events.

Copyright and License

© Author(s) 2022. This work is distributed under the Creative Commons Attribution 4.0 License. Published by Copernicus Publications on behalf of the European Geosciences Union.

Acknowledgement

Thanks are due to Bernard P. Boudreau, whose CANDI model (Boudreau, 1996b) was a large source of inspiration during the creation of the present RADI model, and to Daniel L. Johnson for fruitful discussions. We thank David Burdige and one anonymous reviewer for their constructive feedback. We also thank Lukas van de Wiel for assistance with the Utrecht Geoscience computer cluster. Olivier Sulpis also acknowledges the Department of Earth and Planetary Sciences at McGill University for financial support during his residency in the graduate program and the Faculty of Science at McGill University for a graduate mobility award. Monica M. Wilhelmus, Dustin Carroll, and Dimitris Menemenlis carried out research at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with NASA, with support from the Biological Diversity, Carbon Cycle, Physical Oceanography, and Modeling, Analysis, and Prediction Programs.

Funding

This research has been supported by the Netherlands Earth System Science Centre (grant no. 024.002.001), the Department of Earth and Planetary Sciences at McGill University, and NASA.

Data Availability

Sediment and porewater composition, porosity, and solid fluxes data for the southern Pacific Ocean station described in Sayles et al. (2001) are available at http://usjgofs.whoi.edu/jg/dir/jgofs/southern/nbp98_2/. Sediment and porewater composition for the northwestern Atlantic Ocean station described in Hales et al. (1994) are available at https://doi.pangaea.de/10.1594/PANGAEA.730420. The GLODAPv2 dataset used in this study is available at https://www.glodap.info/index.php/mapped-data-product/ (last access: March 2022, A new global interior ocean mapped climatology: the 1° ×  1° GLODAP version 2https://doi.org/10.5194/essd-8-325-2016, Lauvset el al., 2016).

Code Availability

The current versions of RADI in both Julia and MATLAB/GNU Octave are freely available from GitHub (https://github.com/RADI-model, last access: March 2022) under the GNU General Public License v3. The exact version of the model used to produce the results used in this paper is archived on Zenodo (RADI.jl v0.3; https://doi.org/10.5281/zenodo.5005650 (Humphreys and Sulpis, 2021); v1 will be released after review), along with input data and scripts to run the model for all the simulations presented in this paper. RADI users should cite both this publication and the relevant Zenodo reference (https://doi.org/10.5281/zenodo.5005650, Humphreys and Sulpis, 2021; https://doi.org/10.5281/zenodo.4739205, Sulpis et al., 2021).

Supplemental Material

The supplement related to this article is available online at: https://doi.org/10.5194/gmd-15-2105-2022-supplement.

Additional Information

This paper was edited by Andrew Yool and reviewed by David Burdige and one anonymous referee.

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Additional details

Is new version of
Discussion Paper: 10.5194/gmd-2021-211 (DOI)
Is supplemented by
Supplemental Material: 10.5194/gmd-15-2105-2022-supplement (DOI)
Dataset: http://usjgofs.whoi.edu/jg/dir/jgofs/southern/nbp98_2/ (URL)
Dataset: 10.1594/PANGAEA.730420 (DOI)
Dataset: https://www.glodap.info/index.php/mapped-data-product/ (URL)
Dataset: 10.5194/essd-8-325-2016 (DOI)
Software: https://github.com/RADI-model (URL)
Software: 10.5281/zenodo.5005650 (DOI)
Software: 10.5281/zenodo.4739205 (DOI)

Funding

Netherlands Earth System Science Centre
024.002.001
McGill University
National Aeronautics and Space Administration

Dates

Accepted
2022-02-03

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Caltech groups
Division of Geological and Planetary Sciences (GPS)
Publication Status
Published