the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 06 Jun 2025
Tropospheric-stratospheric chemistry in the CNRM climate model ARPEGE-climat 7.0.1
Abstract. This study presents the evaluation of chemistry schemes implemented in ARPEGE-Climat 7.0.1, the latest version of the atmospheric model component of the CNRM climate model (CNRM-ESM) which will be used for future research. Three chemistry schemes of increasing complexity are considered: the stratospheric-upper-tropospheric REPROBUS scheme, and the stratospheric-tropospheric RELACS and RACMOBUS schemes. Atmosphere-only (AMIP) simulations (1979–2014) have been evaluated in terms of key chemical species against the previous generation of AMIP CNRM simulations (CNRM-ESM2-1), which ran with REPROBUS only, and against the Copernicus Atmosphere Monitoring Service (CAMS) reanalysis of atmospheric composition in the troposphere. In the stratosphere, ARPEGE-Climat 7.0.1 provides improved total column ozone representation, reducing biases previously identified in CNRM-ESM2-1. Stratospheric water vapour is also better simulated due to increased moistening, though differences in methane oxidation between RELACS and RACMOBUS require further investigation. Additionally, issues remain with nitric acid in both RELACS and RACMOBUS, and for the RACMOBUS hydrogen chloride and nitrous oxide distributions. In the troposphere, RELACS and RACMOBUS show significant differences in carbon monoxide, with RACMOBUS simulating too low carbon monoxide throughout the entire troposphere, and in peroxy acetyl nitrate (PAN) with RELACS simulating among the highest PAN levels typically modelled. Nitrogen species concentrations are excessive at high northern latitudes in winter, partially due to missing nitrogen pentoxide heterogeneous loss processes. Tropospheric ozone is generally well represented, closely following reanalysis data. Overall, ARPEGE-Climat 7.0.1 marks significant progress in CNRM atmospheric chemistry modelling, supporting future climate-chemistry interaction studies.
Competing interests: One author is a member of the editorial board of journal GMD.
Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this paper. While Copernicus Publications makes every effort to include appropriate place names, the final responsibility lies with the authors. Views expressed in the text are those of the authors and do not necessarily reflect the views of the publisher.- Preprint
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CEC1: 'Comment on egusphere-2025-1933 - No compliance with the policy of the journal', Juan Antonio Añel, 21 Jun 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.htmlin the "Code Availability" section of your manuscript you do not provide access to the code of the models used in your submitted work. Instead you only provide kind of a set of instructions or steps that are necessary to get access to it. The policy of our journal is very clear regarding the code used for the manuscripts submitted, and it says that all the code and data used to produce a manuscript must be stored publicly and openly without restriction before submitting it it.
Regarding the data, for input files you cite generic main pages or portals, instead of providing a repository containing the specific data used in your work. For output files, you have stored them in a server that is not a trusted repository valid for long-term archival and scientific publication. Again, this does not comply with the policy of the journal.
Therefore, you must reply to this comment with a new Code and Data Availability sections, containing the links and permanent handlers (for example, a DOI) of the new repositories for the code and data, in compliance with our policy. Please, do it as soon as possible.
In the meantime, I advice the Topical Editor to stop the peer-review process for your manuscript, as we can not invest the time of reviewers on reviewing a manuscript that in its current form we can not accept in our journal.
Please, note that if you do not fix these problems as requested, we will have to reject your manuscript for publication in our journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1933-CEC1 -
CC1: 'Reply on CEC1', Martin Cussac, 03 Jul 2025
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Dear Executive Editor,
I'm sorry for the delay in our response. We produce just below new code and data availability sections where we have attributed permanent handles (DOI) to our code, datasets, and simulation outputs used in the present paper.
Code availability. The chemical schemes introduced in the present paper, as well as the exact version of the SURFEX surface scheme, can be found on the Zenodo platform (https://doi.org/10.5281/zenodo.15772797). While the complete ARPEGE model is not open-access, code can be distributed upon signature of a license agreement (see http://www.accord-nwp.org/?ACCORD-MoU-2021-2025, last access: 22 April 2025) for non-commercial research purposes.
Data availability. The CAMS reanalysis can be downloaded on the Atmosphere Data Store with the exact version used having the following DOI (https://doi.org/10.24381/d58bbf47). Forcing datasets, as well as CNRM-ESM2-1 and other CMIP6 simulations, are available through the ESGF platform (https://esgf-node.ipsl.upmc.fr/search/cmip6-775ipsl/). However, the exact files used in this study, as well as the ARPEGE simulation outputs (netCDF files) used in this paper, are available at the following DOI (https://doi.org/10.14768/96697843-8066-45e3-a1d3-2522d5e7b0b8).
I hope this answered all the issues you identified.
Martin Cussac.
Citation: https://doi.org/10.5194/egusphere-2025-1933-CC1 -
CEC2: 'Reply on CC1', Juan Antonio Añel, 04 Jul 2025
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Dear authors,
Unfortunately, we can not accept your reply and your manuscript continues to be in non-compliance with our policy. First, we can not accept that you do not share the ARPEGE model. Therefore, you must provide us access to it. If there is a reason that prevents you of doing it, such as a law or regulation that forbids sharing the code, you need to provide us documentary evidence of it. Beyond this documentary evidence, you continue obligated to provide us a copy of the ARPEGE code for editorial and review process, and to deposit in a private repository (one of the allowed according to the list available in our policy), where it is stored permanently.
Second, for the CAMS data you provide a citation to a data portal. We can not accept it, you must provide the exact data that you have used. Also, you have stored the forcing datasets and ARPEGE outputs in servers of the IPSL, and we can not accept them as a trusted permanent repository for scientific publication.
Therefore, we continue to have stopped the peer-review process for your manuscript. Please, note that if you continue to fail to comply with the Code and Data policy, we will have to reject your manuscript for publication.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1933-CEC2 -
CC2: 'Reply on CEC2', Martin Cussac, 21 Jul 2025
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Dear Editor,
We were somewhat surprised by your response, for several reasons.
First, you mention that "you do not share the ARPEGE model." We would like to clarify that the code for this model is available upon signing a license agreement (as explained in our response). We would also like to point out that several articles recently published in GMD have used identical wording in their “Code availability” sections for codes partially developed at Météo-France, including the ARPEGE code (see, for example, Magnaldo et al., 2024; Préaux et al., 2025; Séférian et al., 2016; Voldoire et al., 2017, 2022).
You also state that “for the CAMS data you provide a citation to a data portal.” We obtained the data we used directly from this portal, which not only provides the data but also includes all the necessary information for proper use—an asset for data users. We note that other recently published GMD articles refer to the same portal (see, e.g., Kaffashzadeh and Aliakbari Bidokhti, 2024) or to a very similar one (see de Meij et al., 2025).
Regarding data availability in general, we also observe that several GMD articles provide information entirely comparable to ours (see, e.g., Chabrillat et al., 2025).
We respectfully disagree with your statement that "IPSL is not a trusted permanent repository for scientific publication." The IPSL data portal (https://data.ipsl.fr) has been operational since 1991 (see https://espri.ipsl.fr/about-espri/background-history/) and obtained "CoreTrustSeal international certification" in 2024. While we could have stored our data on Zenodo, we note that Zenodo itself states: "Don’t have an appropriate institutional or thematic repository? Use Zenodo!" It is difficult to say which of Zenodo or the IPSL portal will ultimately prove to be more permanent.
We fully understand GMD’s data access policy, which aims to ensure the highest possible level of reproducibility for published results. However, we observe that different GMD editors apply this policy with varying levels of strictness. We remain convinced that the information we have provided on code and data access is sufficient to ensure the reproducibility and reliability of our results.
Regarding the ARPEGE code, we have done all that is possible under the current licensing conditions. For the CAMS data, we believe that our initial approach was appropriate; nevertheless, we will duplicate the specific dataset we used on Zenodo to meet your request. Likewise, we will also mirror the data stored on the IPSL portal to Zenodo, although we are not fully convinced that this duplication provides any additional value.
Should you nonetheless decide to reject our manuscript, we will proceed with submission to another journal.
Sincerely, Martin Cussac and Martine Michou (GMD Topical Editor)
References
Chabrillat, S., Rémy, S., Errera, Q., Huijnen, V., Bingen, C., Debosscher, J., Hendrick, F., Metzger, S., Mora, A., Minganti, D., Op de beek, M., Reisenfeld, L., Williams, J. E., Eskes, H., & Flemming, J. (2025). Modelling stratospheric composition for the copernicus atmosphere monitoring service: Multi-species evaluation of ifs-compo cy49r1. EGUsphere, 2025, 1–70. https://doi.org/10.5194/egusphere-2025-1327
de Meij, A., Cuvelier, C., Thunis, P., & Pisoni, E. (2025). A new set of indicators for model evaluation complementing fairmode’s modelling quality objective (mqo). Geoscientific Model Development, 18 (13), 4231–4245. https://doi.org/10.5194/gmd-18-4231-2025
Kaffashzadeh, N., & Aliakbari Bidokhti, A.-A. (2024). Assessment of surface ozone products from downscaled cams reanalysis and cams daily forecast using urban air quality monitoring stations in iran. Geoscientific Model Development, 17 (10), 4155–4179. https://doi.org/10.5194/gmd-17-4155-2024
Magnaldo, M.-A., Libois, Q., Riette, S., & Lac, C. (2024). Evaluation of surface shortwave downward radiation forecasts by the numerical weather prediction model arome. Geoscientific Model Development, 17 (3), 1091–1109. https://doi.org/10.5194/gmd-17-1091-2024
Préaux, D., Dombrowski-Etchevers, I., Gouttevin, I., & Seity, Y. (2025). On the proper use of temperature screen-level measurements in weather forecasting models over mountains. EGUsphere, 2025, 1–32. https://doi.org/10.5194/egusphere-2025-708
Séférian, R., Delire, C., Decharme, B., Voldoire, A., Salas y Melia, D., Chevallier, M., Saint-Martin, D., Aumont, O., Calvet, J.-C., Carrer, D., Douville, H., Franchistéguy, L., Joetzjer, E., & Sénési, S. (2016). Development and evaluation of cnrm earth system model – cnrm-esm1. Geoscientific Model Development, 9 (4), 1423–1453. https://doi.org/10.5194/gmd-9-1423-2016
Voldoire, A., Decharme, B., Pianezze, J., Lebeaupin Brossier, C., Sevault, F., Seyfried, L., Garnier, V., Bielli, S., Valcke, S., Alias, A., Accensi, M., Ardhuin, F., Bouin, M.-N., Ducrocq, V., Faroux, S., Giordani, H., Léger, F., Marsaleix, P., Rainaud, R., . . . Riette, S. (2017). Surfex v8.0 interface with oasis3-mct to couple atmosphere with hydrology, ocean, waves and sea-ice models, from coastal to global scales. Geoscientific Model Development, 10 (11), 4207–4227. https://doi.org/10.5194/gmd10-4207-2017
Voldoire, A., Roehrig, R., Giordani, H., Waldman, R., Zhang, Y., Xie, S., & Bouin, M.-N. (2022). Assessment of the sea surface temperature diurnal cycle in cnrm-cm6-1 based on its 1d coupled configuration. Geoscientific Model Development, 15 (8), 3347–3370. https://doi.org/10.5194/gmd-15-3347-2022
Citation: https://doi.org/10.5194/egusphere-2025-1933-CC2 -
CEC3: 'Reply on CC2', Juan Antonio Añel, 21 Jul 2025
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Dear authors,
We can understand that it is necessary to sign a license to access the ARPEGE code; however, ideally, this should have been done prior to submission to ensure the code is available during the review process. Also, as I said, to opt for this, you must provide evidence that this procedure has been imposed on you (the authors), and you can not decide whether to share it or not. Therefore, what we can do is that you provide us with evidence that you are forbidden to share the ARPEGE code, and then provide the document for the license, which we will forward to Copernicus GmbH, our editorial company, for signature. Next, once we have the code, we will be able to consider your manuscript for publication in our journal. However, we can not publish manuscripts for which we do not have a copy of the code or model presented.
Regarding the IPSL/ESPRI database. I can understand that the presence of the CoreTrustSeal may lead you to believe it is a valid repository for scientific publications. Unfortunately, this is not the case. To obtain the CoreTrustSeal, a repository must fulfill a few conditions, which in many cases are insufficient to ensure the long-term preservation of the assets deposited for a research paper. In the case of IPSL/ESPRI, two issues mentioned in its Data Management Plan raise doubts about its trustworthiness. First, the declared retention period for data is seven years. We can not accept this. Seven years is a period too short (we usually request, in exceptional cases, a minimum of ten years), and it is well below the usual retention periods given by other repositories, which are typically 15-20 years. Additionally, the plan states that only the data manager can delete the data, as "Only the data managers are authorized to write, modify or delete data." However, nothing is said about the policy for such data removal. For example, it could be that you, the authors, or another third party orders the data manager to remove the data. Usually, acceptable repositories have a board that decides on data removal, stating that data removal is something entirely exceptional and under circumstances such as those involving ethical concerns.
Regarding your comments on CAMS and the ESFG, these servers are not acceptable, and unless that you object to it, for example because the size of the datasets make unfeasible to store them in an appropriate repository (e.g. several hundreds of GB), we would expect that you store the files used in a suitable repository which guarantees that the readers have access to the specific files used in your work and adequate long-term archival.
About your comments on previously published papers in our journal, we work to apply our policies and to make all the papers published compliant with the policy of our journal. This is imperfect, and unfortunately, in some cases, some editors fail to enforce the Code and Data policy correctly. It is our policy not to retract papers that were published without complying with the Code and Data policy. To avoid such issues, we have two Executive Editors (Dr. Kerkweg and I) working together to enforce this policy. Therefore, the fact that in previous papers some Topical Editors have not enforced the policy correctly does not make yours compliant, nor does it deserve an exception.
About your comments on publishing the manuscript elsewhere, if you consider that you are not in a position to share the code of the ARPEGE model, or you feel that the times to sign the agreement and provide access to it are not according to your expectations or needs, you can withdraw your manuscript. We fully understand. I must insist that you provide us with a copy of all the code and models used in your work.Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1933-CEC3
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CEC3: 'Reply on CC2', Juan Antonio Añel, 21 Jul 2025
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CC2: 'Reply on CEC2', Martin Cussac, 21 Jul 2025
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CEC2: 'Reply on CC1', Juan Antonio Añel, 04 Jul 2025
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CC1: 'Reply on CEC1', Martin Cussac, 03 Jul 2025
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