Conservation of heat and mass in P-SKRIPS version 1: the coupled atmosphere-ice-ocean model of The Ross Sea

Malyarenko, Alena; Gossart, Alexandra; Sun, Rui; Krapp, Mario

doi:https://doi.org/10.5194/egusphere-2022-1135

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https://doi.org/10.5194/egusphere-2022-1135

Preprints

23 Nov 2022

| 23 Nov 2022

Conservation of heat and mass in P-SKRIPS version 1: the coupled atmosphere-ice-ocean model of The Ross Sea

Alena Malyarenko, Alexandra Gossart, Rui Sun, and Mario Krapp

Abstract. Ocean-atmosphere-sea ice interactions are key to understanding the future of the Southern Ocean and the Antarctic continent. Regional coupled climate-sea ice-ocean models have been developed for several polar regions, however the conservation of heat and mass fluxes between coupled models is often overlooked due to computational difficulties. At regional scale, the non-conservation of water and energy can lead to model drift over multi-year model simulations. Here we present P-SKRIPS version 1, a new version of the SKRIPS coupled model set up for the Ross Sea region. Our development includes a full conservation of heat and mass fluxes transferred between the climate (PWRF) and sea ice-ocean (MITgcm) models. We examine open water, sea ice cover, and ice sheet interfaces. We show the evidence of the flux conservation in the results of a one month-long summer and one month-long winter test experiments. P-SKRIPS shows the advantages of conserving heat flux over the Terra Nova Bay and Ross Sea polynyas in August 2016, eliminating the mismatch between total flux calculation in PWRF and MITgcm up to 922 W m^-2.

Received: 21 Oct 2022 – Discussion started: 23 Nov 2022

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Alena Malyarenko et al.

Status: final response (author comments only)

CEC1:
'Comment on egusphere-2022-1135', Juan Antonio Añel, 12 Dec 2022

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 not published your model with the manuscript, and this violates our requirements. Your manuscript should have never been passed to Discussions with such a failure; however, despite this oversight, we are now offering you the possibility to fix this issue to try to avoid rejecting your manuscript for publication because of a lack of compliance.

According to your "Code availability" section, you have archived part of your code on GitHub. However, first, GitHub is not a suitable repository for scientific publication (as our policy, which you should have read carefully, clearly states). GitHub itself instructs authors to use other alternatives for long-term archival and publishing, such as Zenodo. Therefore, please, publish your code in one of the appropriate repositories, and reply to this comment with the relevant information (link and DOI) as soon as possible, as it should be available for the Discussions stage.

Also, note that you state that the "code base" is available. It is unclear what this means. You must make available without restrictions the full model used for your work, not only a part of it or simple scripts to generate results.

Again, please, be aware that failing to comply promptly with this request will result in rejecting your manuscript for publication.

Juan A. Añel
Geosci. Model Dev. Exec. Editor

Citation: https://doi.org/10.5194/egusphere-2022-1135-CEC1
- AC1:
  'Reply on CEC1', Alena Malyarenko, 17 Dec 2022
  Dear Juan A. Añel,
  Thank you for your comment on our manuscript. We appreciate the thorough care put into checking the code availability for the GMD papers. We have resolved the points that you raised there: our code is published on Zenodo: https://doi.org/10.5281/zenodo.7297744.
  To clarify, the ‘code base’ refers to the standard PWRF and MITgcm, which are not ours and publicly available. We propose to explain the build of the model setup with more clarity in the code and data availability of the manuscript in the following way:
  
  Our model code for the Ross Sea case is based on PolarWRF and MITgcm.
  The user needs to download WRF (4.1.3) from https://github.com/wrf-model/WRF/releases/tag/v4.1.3 and apply changes for its polar version, PolarWRF (4.1.3), for which a registration is required, https://polarmet.osu.edu/PWRF/registration.php.
  
  For MITgcm (checkpoint67m), users can download the code from https://github.com/MITgcm/MITgcm/releases/tag/checkpoint67m.
  
  The SKRIPS model for the Southern ocean is described in https://iopscience.iop.org/article/10.1088/1748-9326/ac7d66 and the code can be found at : https://github.com/iurnus/scripps_kaust_model/tree/master/coupler/L3.C3.coupled_SouthernOcean
  
  Our P-SKRIPS model code is an updated version of SKRIPS. This code and instructions can be found at https://doi.org/10.5281/zenodo.7297744
  
  ERA5 Reanalysis (0.25 Degree Latitude-Longitude Grid), generated by European Centre for Medium-Range Weather Forecasts are available at https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-pressure-levels and https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels. BSOSE data is available at http://sose.ucsd.edu/. The Bedmap 2 data can be downloaded from https://www.bas.ac.uk/project/bedmap-2/.
  
  We hope this brings clarification and satisfies "Code and Data Policy". Please let us know how to incorporate those changes and submit a new version of our manuscript.
  Kind regards,
  Alena Malyarenko and Alexandra Gossart
  
  Citation: https://doi.org/10.5194/egusphere-2022-1135-AC1
  - CEC2: 'Reply on AC1', Juan Antonio Añel, 17 Dec 2022
    
    Dear authors,
    Unfortunately, this does not solve the problems with your manuscript, and we will continue having to reject your manuscript for publication unless you solve them.
    We have stated that GitHub is not a suitable repository; however, your manuscript continues depending on GitHub repositories and webpages without guaranteeing long-term availability and archival. First, MITgcm is available in Zenodo, so please, instead of citing in your paper the GitHub repository, cite the corresponding Zenodo one (it would have been much better if you had made an effort to check this before).
    WRF is public domain, so if you do not find a version stored in a long-term repository from our list, you can create your own WRF repository for the version used in your manuscript. Of course, maintaining the license.
    As WRF is public domain, I guess that PWRF could be too. We can not accept that it is necessary to contact authors or pre-register to get access to the code used in the papers, as this does not guarantee access to the code, and the replicability of your work becomes compromised. In this case, I recommend you check the PWRF license. If it is possible, please, deposit the code of the version that you use here as a suitable repository. If you are in doubt, please, liaise with the PWRF developers and ask them to deposit the version used in one of the suitable repositories, open to anybody and under a license that allows running the model. We recommend the GPLv3 license for the code published in our journal.
    The SKRIPS model: first, it is in GitHub again; please, solve it. Second, in the repository, there is no license listed for it. Without a license, the code continues to be the property of the developers and can not even be run. Therefore, please, upload it to one of the valid repositories and license it. Again, we recommend the GPLv3 license for the code published in our journal.
    P-SKRIPS Version 1: the Readme.txt file in the Zenodo repository says that the documentation necessary for the model is stored in GitHub. Please, include all the assets in Zenodo and remove the notice to go to GitHub. This means that you need to create a new repository: this is fine; simply publish in the comment replying to this one (and any future version of the paper) the link to the updated Zenodo repository.
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/egusphere-2022-1135-CEC2
    
    AC2: 'Reply on CEC2', Alena Malyarenko, 20 Mar 2023
    
    Dear Juan A. Añel,
    Thank you again for your comments. We have created a Zenodo repository that now includes files from the models needed for the compilation of the model. For simplicity, we have added the model codes with appropriate licence files into one single repository and have added detailed instructions on the installation process. We have provided all of the files that are under open access licences to the repositories: https://doi.org/10.5281/zenodo.7739063 and https://doi.org/10.5281/zenodo.7739059. Unfortunately, the PWRF model ( https://doi.org/10.1029/2012J018139) files are not publicly available for publishing and the decision is beyond our control. However, the files can be obtained on the PWRF website upon request https://polarmet.osu.edu/PWRF/ .
    We propose that the new section ‘Code and Data availability’ will include the following:
    Our model code for the Ross Sea case is based on PolarWRF and MITgcm. The P-SKRIPS model code is an updated version of SKRIPS (https://doi.org/10.5281/zenodo.7336070) and can be found in the two directories due to size limits (https://doi.org/10.5281/zenodo.7739063 and https://doi.org/10.5281/zenodo.7739059).
    The detailed instructions for converting WRF to PWRF ( https://doi.org/10.1029/2012J018139) can be found within PSKRIPS-main folder. The short description of steps for PWRF is as follows: find PSKRIPS/Models/WRF_4.1.3 within the repository; obtain PWRF-4.1.3 modifications by email and merge the code locally; add P-SKRIPS modifications to PWRF; compile.
    ERA5 Reanalysis (0.25 Degree Latitude-Longitude Grid), generated by European Centre for Medium-Range Weather Forecasts are available at https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-pressure-levels and https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels. BSOSE data is available at http://sose.ucsd.edu/. The Bedmap 2 data can be downloaded from https://www.bas.ac.uk/project/bedmap-2/.
    
    We hope this brings clarification and satisfies "Code and Data Policy" for cases where authors cannot, for reasons beyond their control, publicly archive part or all of the code.
    Kind regards,
    Alena Malyarenko and Alexandra Gossart
    
    Citation: https://doi.org/10.5194/egusphere-2022-1135-AC2
    
    EC1: 'Reply on AC2', Christopher Horvat, 20 Mar 2023
    
    While I am leaving this for the Chief Editor to see, I want to highlight that I am in support of this solution to the challenge of obtaining PWRF's source code, and I am happy at this change to the code/data statement to proceed through review.
    
    Citation: https://doi.org/10.5194/egusphere-2022-1135-EC1
RC1:
'Comment on egusphere-2022-1135', Anonymous Referee #1, 23 Jan 2023
Review of Conservation of heat and mass in P-SKRIPS version 1: the coupled atmosphere-ice-ocean model of The Ross Sea” by Alena Malyarenko, Alexandra Gossart, Rui Sun and Mario Krapp.

Summary: The authors present a new version of a coupled regional model of the Ross Sea region in which the coupling between the atmosphere and ocean components now conserves heat and mass, in contrast to previous versions of such models. Overall I find this to be a very valuable contribution to the modelling of polar regions and recommend publication after addressing the relatively minor comments below.

General comments:

Overall, while the results presented by the authors are compelling, they are somewhat oversold. I have highlighted some specific instances below but in general the authors refer to their new version of the model as being “better” or “more accurate” with no (by design) quantification of what this means. The authors note that they do not spin up the model as they are not attempting to simulate the Ross Sea in this paper, but rather aim only to highlight the technical advancements of the model. I commend the authors for noting this explicitly, but it then makes it difficult to understand what they mean by “better”. I recommend checking instances of such language (many of which I have highlighted below) and either clarifying what the authors mean by “better” or “more accurate”, or rephrasing.

My second general comment is on organization. It is quite muddled where various parts of the technical changes the authors have made to the model are within the paper. Some are in the “Methods", some in the "Experiments" and some in the “Results” sections. In particular, I found it odd and difficult to understand why Section 3.1.2 “Scaling by the sea ice concentration mask” is in the results section. Surely the description of the contrasting methods by which this scaling is done should be in the Methods, and then only the results contrasting the two shown in the Results section? As I have noted below, I also found it difficult in this section to understand what the contribution of the authors is in this section. See below for details.

I have outlined specific comments below:

Minor comments:

Line 18: Maybe “mass balance” would make more sense here than “mass gain”?

Lines 30-36: Would be worth discussing in this section about the fact ESMs don’t have coupled ice sheets or ice shelf cavities, but that regional models can.

Line 38-39: “their global physics are not optimised for polar areas”. What does this mean? Can you provide specific examples? I also looked at the Agosta et al., 2015 paper that is cited but it also just makes this claim with no substantiation or reference. More detail needed.

Line 57: Table reference is broken

Line 98: NCAR is the National Center for Atmospheric Research (American spelling of center and not plural).

Line 107: “and has a closer snow water equivalent reproduction” closer to what? What is it reproducing?

Line 116: “as is ordinarily the case”

Section 2.3: "Model coupling" seems like the wrong title for this section. Maybe "Model domain" would be better?

Line 121-122: When combining an acronym with a reference in parentheses, the parentheses are not needed around the reference also. Can be done in latex with \cite{Hill2004} or \citep[ESMF][]{Hill2004} or similar.

Line 179: “we compare the models performance” against what benchmark? You mentioned earlier that you were not spinning up the model since you are not aiming to simulate the Ross Sea realistically, which is fine, but then you should mention here what you mean by performance.

Line 185: 41^st not 41th

Line 199: Should this say “, reflecting different emissivity coefficients.”? Unclear what coefficients this is talking about.

Line 205: Albedo spelled incorrectly

Section 3.1.2: I found this section confusing, as I am not sure what the result is here. Are the authors:

Contrasting two existing ways the model does this scaling and commenting on which is best? If so, make this clearer and explicitly say which is better and why.

Comparing the existing way of doing the scaling with a new method the authors developed? If so, make it clearer that you are saying the existing way is deficient in some way that you are fixing

Comparing two new options that the authors have developed? If so, as in option (a) make this clearer and explicitly say which is better and why.

Line 217: What is the exf package? Should give a brief explanation before talking about it.

Figure 5. This way of describing what is shown in each panel was confusing to me. Would suggest to describe panels (a), (b) and (c) in order. Also, should X_{WRF} at the end of the caption be X_{PWRF}?

Line 268: “In that regard, the land ice meltwater runoff is captured in PWRF.” I am not sure what this sentence means. Please clarify.

Line 269: Comma needed on “i.e.,”

Line 279: “Drygalski Ice Tongue”

Figure 8e: This difference in precipitation, which is explained by the authors as being due to the snow being double counted, is very large. However, I find the explanation for this confusing. They say that in SKRIPS, the total precipitation is the sum of RAINNCV and SNOWNCV. If I understand correctly, the issue is then that SNOWNCV is a component of RAINNCV already, and so adding them double-counts SNOWNCV. If this is correct, the wording needs to be changed to make this more clear. I think my main confusion stems from line 314, where it reads:

“…and, therefore, is accounted for twice in the snowfall term.”

Shouldn’t this say something like:

“…and, therefore, is accounted for twice in the total precipitation.”?

Since the issue is that the snowfall itself is counted twice, not that something is counted twice within the snowfall term?

Relatedly, since this difference is so big, is this an issue in existing models that the authors have identified? If so, I would suggest making more of this since it surely has a large impact to have double the precipitation that it should.

Line 337: “This is an improvement…”

An improvement over what? Be more clear about what you are comparing to here.

Line 340-341: “Snow cover changes happen in PWRF. Its multi-layered snowpack and complex representation of snow on sea ice makes PWRF the better model to represent…”

This is new, right? If I understand correctly in the previous version of the model, snow cover changes were done in both MITgcm and PWRF and so were inconsistent. Make it clear that this is new, and a change from the old way of doing it. You say it makes PWRF the “better model”. As with my comment above, be clear about what it is better than specifically.

Line 354: parameterization -> parameterizations

Line 378: “While the atmosphere’s response to …”

Line 380: “The most accurate representation…”

I do not agree with the use of the word accurate here, since you are not evaluating the model against observations, so you have no basis on which to say it is more accurate. I would suggest saying “most physically consistent” or similar.

As noted in the existing Discussion comment, the authors have not yet followed the journal guidelines on reproducibility, and need to do so before publication.
Citation: https://doi.org/10.5194/egusphere-2022-1135-RC1
- AC3: 'Reply on RC1', Alena Malyarenko, 20 Mar 2023
  
  We thank the Reviewer for all the time and effort put into the review of our manuscript and are pleased with their positive and constructive comments. Please find the response to each of the comments below.
  
  Citation: https://doi.org/10.5194/egusphere-2022-1135-AC3
RC2:
'Comment on egusphere-2022-1135', Anonymous Referee #2, 30 Jan 2023
This is my first review of the manuscript entitled “Conservation of heat and mass in P-SKRIPS version 1: the coupled atmosphere-ice-ocean model of the Ross Sea”. The authors first introduce the importance of regional climate modelling in Antarctica. They introduce various existing setups and explain the challenges related to energy conservation in these setups. Then, they present their setup, which they call P-SKRIPS, which is based on the SKRIPS model, with a focus on the Ross and a particular attention to the conservation of energy. They describe how their implementation improves the consistency and conservation of heat and mass fluxes between the climate (PWARF) and the ocean (MITgcm) components of the coupled system. They compare the SKRIPS and the P-SKRIPS over two months (one in winter, one in summer) and describe the impact of the improved flux conservation on the evolution of these fluxes.

The manuscript is generally well-written and pleasant to follow. The implementation and the setup are well-described and well-motivated. It is a significant contribution to the development of polar regional climate modelling and I would therefore recommend this manuscript for publication in GMD after my comments, generally minor, have been addressed.

Specific comments:

The abstract is short and to the point (congratulations!). However, I find that the expression “shows the advantages” is overstating the results of the manuscripts. This is at least a bit misleading, as I was expecting a more in-depth discussion of the scientific implication of heat conservation in the setup. I would suggest using “impacts” or “implications”.

L57: It looks like there is an outdated Table reference in the manuscript file.

L69: “This is critical to avoid…” The introduction presents a good motivation for the study and is generally very well referenced, except maybe for this sentence (that is actually quite key to the focus of the study). I would recommend developing a bit on the importance of heat conservation. For instance, it is better when everything is conserved, but depending on the question that one tries to answer, this is not always critical. Can the authors show examples (ideally with references) where it is absolutely critical?

L116: “as is ordinary the case”. This sentence is a bit confusing, ordinary for who? Do the authors mean a standard preprocessing described in WRF manual for instance? Do the authors have a reference for this?

Figure 3: In the caption, I think there is a mistake with the references to the a,b,c,d panels (SKRIPS and P-SKRIPS are inverted).

L168: “The coupling … ice sheet.” I am sorry but I do not understand the end of this sentence.

L169: This paragraph seems to repeat some statements made in the previous paragraphs, statements that are repeated L208. This repetition, instead of clarifying things, makes them a bit more confusing in my opinion. Was this paragraph intended to be a short summary of the subsection? If yes, I would recommend either shortening it to maximum of 2 short sentences or removing it. (Same for L208-->214.)

L217: I cannot find the introduction of the “exf” package before in the text. I would recommend giving a bit of context to the reader of what this package is.

L218: “In the coupled setup”: The manuscript mostly focuses on coupled setups. Which one is referred to here?

L218: Not sure of what the authors mean with “coordinated”

Figure 6: The colorbar saturates a lot for the differences, so it is hard to believe there are only “subtle differences in the order of 10^-3 W.m^-2”. There are weird also patterns (vertical lines north of the ice shelf) that are not well explained. Do the authors have an explanation for them?

L241: 104-->$10^4$ I suppose?

Table S1 is very unclear. Please add context to its caption. Why is there a “Total” row, and why is it empty?

“At midday… (Figure S4)”. I do not understand the link between this comment on the flux evolution and the rest of the paragraph that discusses discrepancies in MITgcm fluxes between the two setups. I do not see larger discrepancies associated with these peaks.

Figure S4 could belong to the main manuscript in my opinion. The same for Table 2. Just a suggestion.

I find Figure 8 and S4 not very readable. I get why the authors want to show both the evolution of the fluxes and the differences between MITgcm and PWRF but doing both on the same figures means these differences are hard to see. I would really recommend plotting the differences on a different figure. At the very least, the authors could play with the width of the different lines, or add markers, to make it easier to distinguish what is what.

L310-->318: This paragraph seems quite important (at least to me), but I find it quite confusing. I would strongly recommend rephrasing it. The differences between the two setups are particularly significant for this term, so it is worth clarifying what the implications are.

L377: A bit in line with my first comment, it is likely that these differences in heat fluxes will affect these processes. However, it has not been proven in the manuscript and I would therefore recommend rephrasing a bit. For instance, use “likely” instead of “directly”.

L380: This sentence sounds like an overstatement. What are the metrics used by the authors to make such a claim? Depending on the question that is asked, another model may be more suitable and have a much better representation of the processes of interest. It is a nice paper overall, do not upset readers that would only read the conclusion!

I wish the authors good luck with the revisions!
Citation: https://doi.org/10.5194/egusphere-2022-1135-RC2
- AC4: 'Reply on RC2', Alena Malyarenko, 20 Mar 2023
  
  We thank the Reviewer for all the time and effort put into the review of our manuscript and are pleased with their positive and constructive comments. Please find the response to each of the comments below.
  
  Citation: https://doi.org/10.5194/egusphere-2022-1135-AC4

Alena Malyarenko et al.

Supplement

https://doi.org/10.5194/egusphere-2022-1135-supplement

Model code and software

P-SKRIPS A. Malyarenko, A. Gossart https://doi.org/10.5281/zenodo.7297130

Alena Malyarenko et al.

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Short summary

Simultaneous modelling of ocean, sea ice and atmosphere in coupled models is critical for understanding all of the processes that happen in the Antarctic. Here we have developed a coupled model for the Ross Sea, P-SKRIPS, that conserves heat and mass between the ocean and sea ice model (MITgcm) and the atmosphere model (PWRF). We have shown that our developments reduce the model drift, which is important for long-term simulations. P-SKRIPS shows good results in modelling coastal polynyas.


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