the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Submitted as: model description paper 23 Jul 2021
Submitted as: model description paper | 23 Jul 2021
A description of the first open source community release of the 1D atmospheric chemistry model MISTRA-v9.0
- 1Centre for Ocean and Atmospheric Sciences, School of Environmental Sciences, University of East Anglia, NR4 7TJ, Norwich, UK
- 2Institute of Geosciences, University of Bonn, Bonn, Germany
- anow at: EDYTEM, Université Savoie Mont-Blanc, CNRS, 73000 Chambéry, France
- bnow at: the Department of Physics, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
- deceased, 6 September 2015
- 1Centre for Ocean and Atmospheric Sciences, School of Environmental Sciences, University of East Anglia, NR4 7TJ, Norwich, UK
- 2Institute of Geosciences, University of Bonn, Bonn, Germany
- anow at: EDYTEM, Université Savoie Mont-Blanc, CNRS, 73000 Chambéry, France
- bnow at: the Department of Physics, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
- deceased, 6 September 2015
Abstract. We present MISTRA-v9.0, a one dimensional (1D) atmospheric chemistry model. The model includes a detailed particle description with regards to the microphysics, gas-particle interactions, and liquid phase chemistry within particles. Version 9.0 is the first release of MISTRA as an open-source community model. A major review of the code has been performed along with this public version release to improve the user-friendliness and platform-independence of the model. In the past 20 years, MISTRA has been used in over 25 studies to address a wide range of scientific questions. The purpose of this public release is to maximise the benefit of MISTRA to the community by making the model freely available and easier to use and develop. This paper presents a thorough description of the model characteristics and components. We show some examples of simulations reproducing previous studies with MISTRA, finding that version 9.0 is consistent with previous versions.
Josué Bock et al.
Status: open (until 24 Oct 2021)
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CC1: 'Comment on gmd-2021-241', Roberto Sommariva, 12 Sep 2021
reply
The manuscript "A description of the first open source community release of the 1D atmospheric chemistry model MISTRA-v9.0 " by Bock et al. presents the open-source release of the Mistra model. The model has been used previosuly in a number of publications, but the code has never been made public before.
There a number of substantial and serious issues with regard to the authorship, financial information and licensing of this manuscript and of the code that it describes. These issues -- outlined below -- must be addressed and resolved before review is allowed to proceed, in keeping with the ethical and scientific standards of GMD.
Authorship
As indicated in section 1.2 of the manuscript, Mistra was developed in the 90s by Andreas Bott (one of the authors) and subsequently modified by the late Roland von Glasow starting from 2000. The manuscript focuses on the branch of Mistra which has been developed and used by Roland until his passing in 2015. During these 15 years, the model has been closed-source and many of Roland's colleagues and co-workers have contributed to it. While most of the work after 2015 has been done by J. Bock (the first author) with the aim to prepare the open-source release, the code and documentation that are presented in the manuscript are the results of 15 years of continuous development by several other people under Roland's lead.
For example, Rolf Sander has contributed to the initial work on the chemical mechanism (including the aerosol chemistry component), on the adaptation of KPP -- and development of KPP itself -- and on the photolysis module. Susanne Pechtl, Matthias Piot, Linda Smoydzin, Peter Brauer and myself (I note that I am acknowledged as co-author in the zenodo archive, but not in the manuscript, which is odd) also made contributions at different times and of various importance. This is only a partial list from a quick overview of Roland's work: I am sure that a careful examination of the code and of Roland's publications will yield other names. It is true that several of these former contributors may have moved on, or left science, and some may simply not care anymore, but it is important that their work is recognized nevertheless.
This manuscript does not present an update to an already published model. It aims to describe the model code in its entirety for the first time, and authorship should reflect this. Former contributors should be offered co-authorship, and given the chance to comment on the manuscript before the review process can continue.
Acknowledgements
Other people's contributions to this project should be acknowledged: Claire Reeves, Jennie Thomas and Kerri Pratt all played a significant role in the decision to release the model as open-source, after Roland's passing. Relevant contributions by co-workers or colleagues of A. Bott should surely be, at the very least, acknowledged.
The manuscript presents simulations of the current version of Mistra using settings from Joyce et al. (2014) Buys et al. (2013) and Buxmann et al. (2015). Have the authors of those paper provided information and/or assistance in setting up these simulations? If so they should be acknowledged as well.
Author contributions
This section of the manuscript should be amended to reflect the changes in authorship and in the Acknowledgements section. The project lead should be clearly, and rightfully, identified as Roland von Glasow.
Financial support
The financial support information in the manuscript indicates that the EUROCHAMP-2020 program has supported the project. This is true for the last few years but, as mentioned above, the model has been developed over a period of 15 years and in this time it has been funded by several other agencies, listed on Roland's archived web page at https://archive.uea.ac.uk/~fkd06bju/. All funders must be equally recognized, as per GMD guidelines.
License
The authors have adopted the open-source licence EUPL, a choice that strongly implies that the project has been EU-funded. As pointed out above, this is true for the most recent part of the work, but several other funders have supported the development of Mistra over the years, some for much longer than the EU. My personal view is that a GPL license would be more appropriate, as it would reflect the international character of Mistra project and not suggest undue implications as to its financial support.
More importantly, the choice of the license has never been agreed upon or even discussed among the developers, other than between the authors of this manuscript. If the authors believe that the EUPL is an appropriate choice they should state their rationale, but in any case it is essential that all contributors to the Mistra project should be given the opportunity to discuss and approve the choice of the license (together with the rest of the manuscript).
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CC2: 'Reply on CC1', Claire Reeves, 14 Sep 2021
reply
I agree in general with Roberto Sommariva’s comments. There have clearly been many other people beyond the authors of this manuscript who have contributed substantially to the development of the MISTRA code that is documented in this manuscript and released publicly. They need to be acknowledged appropriately (in some cases by offer of co-authorship) along with the other sources of funding that have made the development of the model possible. I also agree that the licence for the code release should be agreed between all the main developers of the model.
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CC4: 'Reply on CC1', Peter Bräuer, 05 Oct 2021
reply
I fully agree with the previous comments about authorship and licensing concerns. A proper discussion before the release was never really allowed by the authors. As for me, I was informed about the release plans, but concerns that were expressed together with Roberto Sommariva, were quickly dismissed.
Among those already mentioned, additional concerns exist about the GitHub presence.
- The name Mistra-UEA implies a model developed and maintained by the University of East Anglia, which is not entirely true. Developers are scattered all over Europe now having positions at many different universities. Therefore, a neutral organisation name should be found.
- Core-Developers such as Roberto Sommeriva or myself were denied admin privileges for the Mistra-UEA organisation. The community model was developed over a long period of time with a lot of people contributing substantially. While there are major contribution by Josue Bock towards the distribution of open source code, he should not be the only decision holder on the maintenance of the Mistra-UEA organisation. That responsibility should be equally shared between core developers. Especially, since Josue Bock does not work full time on the model development any more and a serious risk arises that user needs cannot be appropriately addressed.
- A minor issue regards the manual of Mistra. First of all, it is a bad habbit to upload binary files to Github. Rather than uploading a pdf, the manual should be a wiki page within the repository. If the pdf is distributed, the latex files of the pdf should be made available as well. This fosters open source contributions by outsiders, which can add extensions or alterations to the manual and submit pull request to the repository.
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CC2: 'Reply on CC1', Claire Reeves, 14 Sep 2021
reply
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RC1: 'Comment on gmd-2021-241', Rolf Sander, 25 Sep 2021
reply
The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2021-241/gmd-2021-241-RC1-supplement.pdf
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CC3: 'Comment on gmd-2021-241', Linda Smoydzin, 02 Oct 2021
reply
The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2021-241/gmd-2021-241-CC3-supplement.pdf
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RC2: 'Comment on gmd-2021-241', Anonymous Referee #2, 04 Oct 2021
reply
This paper documents the open-source release of a well-established 0D/1D atmospheric chemistry model. It includes a detailed description of model physics, a technical overview of its configuration and a pretty extensive evaluation, demonstrating the consistency of this released version of the model with its predecessor (unreleased) versions.
Leaving aside the issues with co-authorship and licensing raised in the other comments, open-source releases and documentation of scientific code are practices that should be encouraged, hence I think this paper is suitable for publication in GMD.
I have however a few remarks and corrections that should be considered before publication.
Remarks
Title: I find the term "chemistry" in the title a bit reductive, as the model can also represent some aerosol processes, like particle nucleation. You might consider extending the title.
L13: you might cite also Bellouin et al. (Rev. Geophys. 2020, doi:10.1029/2019rg000660), for a more recent assessment.
L17: please add some references for these two other effects you mention.
L46: In this work, do you mean Bott (1997)? I would be more specific, since "this work" could mean the present manuscript.
L76: can you provide some example of the strict coding rules mentioned here?
L77: how would you ensure future maintainability if the Forcheck tool is no longer distributed?
L79: please provide a reference to KPP (I think this is Sandu and Sanders, 2006, doi:10.5194/acp-6-187-2006).
L92: all model layers: how many? Is this configurable? Please clarify.
L94: Fluxes of seasalt... are included, I would add ``(see Sect. 2.3.6)''.
L95: could you elaborate a bit more on the nucleation module? How is this process parametrized?
L126-127: What about nucleation? Newly nucleated particles can have size below 5 nm, hence outside this range.
L295-296: Note that default values are for all of them, however they should be systematically redefined by the user to match the simulated atmosphere. I am not sure I understand this sentence, could you be more explicit?
L297: still, it would be interesting to know the temporal coverage of a typical run.
Sect. 3.1: I would not use subsections here, they are too short anyway.
Conclusions: this is quite short. You could extend it, for example, by summarizing again the main capabilities/scope of the model and by adding a~few sentences about current plans for model extension/improvement.
Corrections
L15: large area --> large surface area.
L23: limited area --> limited domain.
L28: physic --> physics.
L28: is --> are.
L60: box mode --> box model.
L124: water is present --> water were present.
L125: minimum aerosol radius --> minimum aerosol dry radius (I guess).
L137: better "time integration"?
L138: I think you mean "see also Bott (1996)".
L163: it is actually "on aerosol" and "in cloud particles".
L166: DMS acronym not defined.
L203: I would use the term "coagulation" instead of "collisions".
L315: mandatory --> required.
L319: please add the references or the links for ferret and NCL.
L385: please append "(Fig. 6a)" at the end of the sentence.
Figure 2 caption: as function --> as a function.
Figure 3: please use the same contour levels for top and bottom panel (as you do in Fig. 4, for example).
Figure 6 caption: please add that the MISTRA-v9.0 is also "without collision-coalescence".
Figure 8: Scales are identical for both, actually the top right scale goes to 60 instead of 59. Not a big difference, but I would fix it.
Eq. (12): the "lg" notation for the logarithm could be ambiguous, please specify the base or use "ln" if natural log.
Josué Bock et al.
Model code and software
Mistra v9.0 (pre-version for GMD submission) Josué Bock and co-authors https://doi.org/10.5281/zenodo.5110025
KPP v2.2.4 for Mistra Josué Bock https://doi.org/10.5281/zenodo.5109913
Josué Bock et al.
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