The PFLOTRAN Reaction Sandbox

Hammond, Glenn E.

doi:https://doi.org/10.5194/gmd-15-1659-2022

Articles | Volume 15, issue 4

https://doi.org/10.5194/gmd-15-1659-2022

© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/gmd-15-1659-2022

© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 15, issue 4

Model description paper

|

25 Feb 2022

Model description paper |

| 25 Feb 2022

The PFLOTRAN Reaction Sandbox

Glenn E. Hammond

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Final revised paper (published on 25 Feb 2022)
Preprint (discussion started on 23 Sep 2021)

Interactive discussion

Status: closed

RC1:
'Comment on gmd-2021-284', Bhavna Arora, 06 Oct 2021

I think this paper is an important contribution to testing new kinetic rate laws and reaction networks through the use of the reaction sandbox. I enjoyed reading the paper. All examples for reaction sandbox are described adequately with sufficient detail. Providing customization opportunities for reactive transport codes such as PFLOTRAN opens the door for users to explore the use of these codes beyond traditional applications.

Citation: https://doi.org/10.5194/gmd-2021-284-RC1
- AC1: 'Reply on RC1', Glenn Hammond, 07 Dec 2021
  
  Bhavna,
  Thank you for the positive feedback.
  Glenn
  
  Citation: https://doi.org/10.5194/gmd-2021-284-AC1
RC2:
'Comment on gmd-2021-284', Allan Leal, 15 Nov 2021

This is a well-written paper. Motivations are clear for why a PFLOTRAN Reaction Sandbox is needed, which will ease PFLOTRAN users to define their own reaction rates.

I have several questions related to the mathematical formulation and algorithm detailed in Section 2, but I'll abstain from commenting on them here as they are not relevant to the paper and I could discuss these directly with the author instead.

I have some aesthetic recommendations. The code boxes should be written with monospace fonts. Some syntax highlighting would be beneficial if possible.

Not sure how viable this is, but the author may want to consider users writing their reaction rates in Python in the future. This can be done sufficiently fast if implemented right and allow users to define their reaction rates with a few lines of code.

Overall, I think this is a powerful addition to PFLOTRAN.

Allan Leal, ETH Zurich

Citation: https://doi.org/10.5194/gmd-2021-284-RC2
- AC2: 'Reply on RC2', Glenn Hammond, 07 Dec 2021
  
  Allan,
  Thank you for recommending the monospaced fonts and syntax highlighting in the code blocks. I have updated the manuscript to include these features, and they definitely improve the readability. I appreciate your feedback.
  Regards,
  Glenn
  
  Citation: https://doi.org/10.5194/gmd-2021-284-AC2

Peer review completion

AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload

AR by Glenn Hammond on behalf of the Authors (07 Jan 2022) Author's response Manuscript

ED: Publish as is (28 Jan 2022) by Richard Mills

AR by Glenn Hammond on behalf of the Authors (01 Feb 2022) Manuscript

Short summary

This paper describes a simplified interface for implementing and testing new chemical reactions within the reactive transport simulator PFLOTRAN. The paper describes the interface, providing example code for the interface. The paper includes several chemical reactions implemented through the interface.