the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Modelling diffusion, decay and ingrowth of U–Pb isotopes in zircon
Abstract. Understanding the thermal evolution of geological terranes provides essential insights into tectonic processes, crustal evolution, and mineral resource formation. Zircon U–Pb geochronology is widely used to date geological events, yet these dates are altered by a wide-range of processes, including diffusion of radiogenic isotopes at high (>800 °C) temperatures. This study utilises the Underworld3 numerical code to couple diffusion processes with radioactive decay and ingrowth in two-dimensions. We assess the numerical solutions against a series of benchmarks to test the implemetation, and apply the models to examine lead-loss due to thermal events and complexities that arise from multiple zircon growth episodes. Our approach bridges analytical U-Pb isotope measurements with a diffusion-decay-ingrowth numerical model, providing insights into how the thermal evolution of a region alters zircon U–Pb isotope ratios. We apply the methodology to the Trivandrum block in southern India—a region characterised by a prolonged high-temperature event—comparing multiple temperature–time paths with analytical U–Pb isotope data to provide constraints on the thermal evolution of the region. The modelling framework can be easily modified to investigate diffusion-decay-ingrowth across various minerals and isotopic systems, providing a tool to decipher the thermal history of a region recorded in isotopic data.
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Status: open (until 23 Oct 2025)
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CEC1: 'Comment on egusphere-2025-2278', Juan Antonio Añel, 22 Sep 2025
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CC1: 'Reply on CEC1', Ben Steven Knight, 22 Sep 2025
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Hi Juan A. Añel,
Sorry about that. When I submitted the manuscript underworld3 hadn't had a proper release yet. It since has, and the details are as follows:
The paper:Moresi, L., Mansour, J., Giordani, J., Knepley, M., Knight, B., Graciosa, J.C., Gollapalli, T., Lu, N., Beucher, R., 2025. Underworld3: Mathematically Self-Describing Modelling in Python for Desktop, HPC and Cloud. JOSS 10, 7831. https://doi.org/10.21105/joss.07831
The software version on zenodo:
Moresi, L., Mansour, J., Giordani, J., Knepley, M., Knight, B., Graciosa, J.C., Gollapalli, T., Lu, N., Beucher, R., 2025. Underworld3: Mathematically Self-Describing Modelling in Python for Desktop, HPC and Cloud. https://doi.org/10.5281/zenodo.16838572
Thanks,Ben
Citation: https://doi.org/10.5194/egusphere-2025-2278-CC1 -
CC2: 'Reply on CEC1', Ben Steven Knight, 25 Sep 2025
reply
Hi Juan Antonio Añel,
Apologies, please find an updated code availability statement. I have updated the ms accordingly, which will be included in the future re-submission.
Thanks,
Ben
Code availability:
underworld3 v0.99.1 is available from Moresi et al., 2025, licensed under LGPL Version 3. Scripts to replicate the research are available from Knight (2025), licensed under Creative Commons Attribution 4.0 International. Figures were made with Matplotlib v3.10.1 (Matplotlib, 2025), available under the Matplotlib license at https://matplotlib.org/.
References:
Ben Knight: bknight1/diffusionDecayIngrowth: GMD submission (GMD_submission). Zenodo, 2025. https://doi.org/10.5281/zenodo.16524625
Moresi, L., Mansour, J., Giordani, J., Knepley, M., Knight, B., Graciosa, J.C., Gollapalli, T., Lu, N., Beucher, R. Underworld3: Mathematically Self-Describing Modelling in Python for Desktop, HPC and Cloud. Zenodo, 2025. https://doi.org/10.5281/zenodo.16838572
The Matplotlib Development Team: Matplotlib: Visualization with Python (v3.10.1). Zenodo, 2025. https://doi.org/10.5281/zenodo.14940554
Citation: https://doi.org/10.5194/egusphere-2025-2278-CC2
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CC1: 'Reply on CEC1', Ben Steven Knight, 22 Sep 2025
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Dear authors,
Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".
https://www.geoscientific-model-development.net/policies/code_and_data_policy.html
You have archived the underworld3 code on GitHub. However, GitHub is not a suitable repository for scientific publication. GitHub itself instructs authors to use other long-term archival and publishing alternatives, such as Zenodo. Therefore, the current situation with your manuscript is irregular. Please, publish your code in one of the appropriate repositories and reply to this comment with the relevant information (link and a permanent identifier for it (e.g. DOI)) as soon as possible, as we can not accept manuscripts in Discussions that do not comply with our policy.
Additionally, you mention that you have used Matplotlib for part of your work. However, you do not provide the information on the version of the library that you have used, which is important to ensure the replicability of your work. Please, do it.
Therefore, you must reply to this comment with a modified 'Code and Data Availability' section that addresses and solves the mentioned issues, and include it in a potentially reviewed manuscript, containing the information of the new repositories.
I must note that if you do not fix this problem, we cannot accept your manuscript for publication in our journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor