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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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
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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