The DOE E3SM Version 2.1: Overview and Assessment of the Impacts of Parameterized Ocean Submesoscales

Smith, Katherine; Barthel, Alice M.; Conlon, LeAnn M.; Van Roekel, Luke P.; Bartoletti, Anthony; Golez, Jean-Christophe; Zhang, Chengzhu; Begeman, Carolyn Branecky; Benedict, James J.; Bisht, Gautum; Feng, Yan; Hannah, Walter; Harrop, Bryce E.; Jeffery, Nicole; Lin, Wuyin; Ma, Po-Lun; Maltrud, Mathew E.; Petersen, Mark R.; Singh, Balwinder; Tang, Qi; Tesfa, Teklu; Wolfe, Jonathan D.; Xie, Shaocheng; Zheng, Xue; Balaguru, Karthik; Garuba, Oluwayemi; Gleckler, Peter; Hu, Aixue; Lee, Jiwoo; Moore-Maley, Ben; Ordonez, Ana C.

doi:https://doi.org/10.5194/gmd-2024-149

Preprints

https://doi.org/10.5194/gmd-2024-149

Preprints

Submitted as: development and technical paper

22 Aug 2024

Submitted as: development and technical paper |

| 22 Aug 2024

Status: a revised version of this preprint is currently under review for the journal GMD.

The DOE E3SM Version 2.1: Overview and Assessment of the Impacts of Parameterized Ocean Submesoscales

Katherine Smith, Alice M. Barthel, LeAnn M. Conlon, Luke P. Van Roekel, Anthony Bartoletti, Jean-Christophe Golez, Chengzhu Zhang, Carolyn Branecky Begeman, James J. Benedict, Gautum Bisht, Yan Feng, Walter Hannah, Bryce E. Harrop, Nicole Jeffery, Wuyin Lin, Po-Lun Ma, Mathew E. Maltrud, Mark R. Petersen, Balwinder Singh, Qi Tang, Teklu Tesfa, Jonathan D. Wolfe, Shaocheng Xie, Xue Zheng, Karthik Balaguru, Oluwayemi Garuba, Peter Gleckler, Aixue Hu, Jiwoo Lee, Ben Moore-Maley, and Ana C. Ordonez

Abstract. The U.S. Department of Energy's Energy Exascale Earth System Model (E3SM) version 2.1 builds on E3SMv2 with several changes, the most notable being the addition of the Fox-Kemper et al. (2011) mixed layer eddy parameterization. This parameterization captures the effect of finite-amplitude, mixed layer eddies as an overturning streamfunction and has the primary function of restratification. Herein, we outline the changes to the mean climate state of E3SM that were introduced by the addition of this parameterization. Overall, the presence of the submesoscale parameterization improves the fidelity of the v2.1 simulation by reducing the North Atlantic ocean surface biases present in v2, as illustrated by changes to the climatological sea surface temperature and salinity, as well as Arctic sea-ice extent. Other impacts include a slight shoaling of the mixed layer depths in the North Atlantic, as well as a small improvement to the Atlantic Meridional Overturning Circulation (AMOC). We note that the expected shoaling due to the parameterization is regionally dependent in our coupled configuration. In addition, we investigate why the parameterization and its impacts on mixed layer depth have little impact on the simulated AMOC: despite increased dense water formation in the Norwegian Sea, only a small fraction of the water formed makes its way south into the North Atlantic basin. Version 2.1 also exhibits small improvements in the atmospheric climatology, with smaller biases in many notable quantities and modes of variability.

How to cite. Smith, K., Barthel, A. M., Conlon, L. M., Van Roekel, L. P., Bartoletti, A., Golez, J.-C., Zhang, C., Begeman, C. B., Benedict, J. J., Bisht, G., Feng, Y., Hannah, W., Harrop, B. E., Jeffery, N., Lin, W., Ma, P.-L., Maltrud, M. E., Petersen, M. R., Singh, B., Tang, Q., Tesfa, T., Wolfe, J. D., Xie, S., Zheng, X., Balaguru, K., Garuba, O., Gleckler, P., Hu, A., Lee, J., Moore-Maley, B., and Ordonez, A. C.: The DOE E3SM Version 2.1: Overview and Assessment of the Impacts of Parameterized Ocean Submesoscales, Geosci. Model Dev. Discuss. [preprint], https://doi.org/10.5194/gmd-2024-149, in review, 2024.

Received: 30 Jul 2024 – Discussion started: 22 Aug 2024

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 preprint. The responsibility to include appropriate place names lies with the authors.

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Status: final response (author comments only)

CEC1:
'Comment on gmd-2024-149', Astrid Kerkweg, 06 Sep 2024
Dear authors,
in my role as Executive editor of GMD, I would like to bring to your attention our Editorial version 1.2: https://www.geosci-model-dev.net/12/2215/2019/
This highlights some requirements of papers published in GMD, which is also available on the GMD website in the ‘Manuscript Types’ section: http://www.geoscientific-model-development.net/submission/manuscript_types.html
In particular, please note that for your paper, the following requirement has not been met in the Discussions paper:
Code must be published on a persistent public archive with a unique identifier for the exact model version described in the paper or uploaded to the supplement, unless this is impossible for reasons beyond the control of authors. All papers must include a section, at the end of the paper, entitled "Code availability". Here, either instructions for obtaining the code, or the reasons why the code is not available should be clearly stated. It is preferred for the code to be uploaded as a supplement or to be made available at a data repository with an associated DOI (digital object identifier) for the exact model version described in the paper. Alternatively, for established models, there may be an existing means of accessing the code through a particular system. In this case, there must exist a means of permanently accessing the precise model version described in the paper. In some cases, authors may prefer to put models on their own website, or to act as a point of contact for obtaining the code. Given the impermanence of websites and email addresses, this is not encouraged, and authors should consider improving the availability with a more permanent arrangement. Making code available through personal websites or via email contact to the authors is not sufficient. After the paper is accepted the model archive should be updated to include a link to the GMD paper.

Therefore please store the E3SM v2.1 code in a permanent archive and provide the DOI in the code and data availability section.
Yours, Astrid Kerkweg (GMD Executive Editor)
Citation: https://doi.org/10.5194/gmd-2024-149-CEC1
- AC1: 'Reply on CEC1', Katherine Smith, 14 Nov 2024
  
  The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2024-149/gmd-2024-149-AC1-supplement.pdf
  
  Citation: https://doi.org/10.5194/gmd-2024-149-AC1
RC1:
'Comment on gmd-2024-149', Anonymous Referee #1, 10 Sep 2024
In the manuscript titled “The DOE E3SM Version 2.1: Overview and Assessment of the Impacts of Parameterized Ocean Submesoscales”, the authors develop the version 2.1 of U.S. Department of Energy’s Energy Exascale Earth System Model (E3SM) with new updates, by adding Fox-Kemper mixed layer eddy parameterization. The improved eddy parameterization simulates the submesoscale instabilities, especially the mixed-layer eddies slump the fronts. As it is triggered by the mechanism of amplitude of lateral density fronts in the weakly stratified surface mixed layer. After adding the mixed layer eddy parameterization, the simulation for energy exchanges, radiation heat transfer, and adiabatic motion of dry and moist air in the mixed layer are improved.

General comments:
This paper is comprehensive and well-supported by evidence, providing an accurate assessment of the effectiveness of mixed layer eddy parameterization in global ocean model of E3SMv2. It presents significant advancements relevant to optimizing the overturning streamfunction. This article is well-written, logically coherent, and structurally sound. Therefore, the following discussion focuses only on specific issues and does not affect the overall scientific validity of the paper. For these reasons, I believe that the manuscript can be accepted for publication by the GMD after minor revision. Below, I have some specific suggestions for the authors.

Specific comments:

Line #307: The link of a full list of all code changes made from v2 to v2.1 should be updated, the hyperlink in the PDF does not direct to the correct section. After manually copying the link, there are only two tags, the Atmosphere and Land tags on Github. There is no way to find the corresponding code based on Appendix B, such as River, Sea Ice etc. Reading Fortran code directly is something that often happens when running meteorological models. It is recommended to update the tags or provide an index, then reader could find scripts after reading Appendix B. Additionally, is the repository only open to project developers, or does the entire Github community have permission to modify the code? It seems visitors can leave comments on each line of code.

To prevent readers from constantly switching between this paper and Bodner et al., 2023 to reference the key equations in this study, it is recommended to further explain these two variables. The following section is a reference. In equation (1), the physical meaning of the variable Ψ is streamfunction, the gradient of the streamfunction can indicate the bolus velocity. μ(z) vertical fluxes at height z. Equation 2 is vertical structure function, so the vertical fluxes will be vanished when height is below the mixed layer (z< -H), and approach zero when z is almost zero.

1, This SSH result is contrary to expectations. Is it possible that there is an issue with reduced deep water formation in the North Atlantic that should feed into the AMOC process (line #134)? Or air-sea interaction? Overlapping lines make it difficult to determine how many lines there are. It is recommended to use different symbols instead and slightly separate the lines in x-axis at overlapping positions to show the location of each point and indicate this in the figure caption.

4, if the discussed region, "western boundary current in the North Atlantic around the region of the RAPID array," and “the west transect of the Overturning in the Subpolar North Atlantic Program array” are highlighted with a box in the figure, they would be easier to understand. If the decrease in MLD is caused by a very small increase in the magnitude and extent of the northward limb, then what is the direct cause of the "very small increase"? Is it because the mixed layer eddy parameterization enhanced the bolus velocity of eddies? In E3SM version 2, is the bolus velocity represented by a constant? Could the authors explain this in more detail?

6, this is just a suggestion: could the shaded areas in CMIP6 be slightly enhanced, for example by reducing transparency or using borders? The colors are too faint and hard to distinguish. This requires locating the Python script used for plotting in PMP. If it is too difficult, the authors may decide to update it or not.

Line #163, what could be the possible reason for the lack of significant changes in large-scale extratropical modes here? In the discussion section (line #301), the reason is also not explained here.

14 and 15, it seems that a strong stratification buffer has been enhanced and interior stratification has been eroded in the v.2.1 model compared with v2. Is this solely due to the addition of the mixed layer eddy parameterization?
Citation: https://doi.org/10.5194/gmd-2024-149-RC1
- RC2:
  'Reply on RC1', Anonymous Referee #1, 10 Sep 2024
  
  For unknown reasons, the first character of each paragraph in the submitted review was automatically deleted. I have resubmitted the review, please disregard the previous review comments.
  In the manuscript titled “The DOE E3SM Version 2.1: Overview and Assessment of the Impacts of Parameterized Ocean Submesoscales”, the authors develop the version 2.1 of U.S. Department of Energy’s Energy Exascale Earth System Model (E3SM) with new updates, by adding Fox-Kemper mixed layer eddy parameterization. The improved eddy parameterization simulates the submesoscale instabilities, especially the mixed-layer eddies slump the fronts. As it is triggered by the mechanism of amplitude of lateral density fronts in the weakly stratified surface mixed layer. After adding the mixed layer eddy parameterization, the simulation for energy exchanges, radiation heat transfer, and adiabatic motion of dry and moist air in the mixed layer are improved.
  
  General comments:
  This paper is comprehensive and well-supported by evidence, providing an accurate assessment of the effectiveness of mixed layer eddy parameterization in global ocean model of E3SMv2. It presents significant advancements relevant to optimizing the overturning streamfunction. This article is well-written, logically coherent, and structurally sound. Therefore, the following discussion focuses only on specific issues and does not affect the overall scientific validity of the paper. For these reasons, I believe that the manuscript can be accepted for publication by the GMD after minor revision. Below, I have some specific suggestions for the authors.
  
  Specific comments:
  
  Comment 1: Line #307: The link of a full list of all code changes made from v2 to v2.1 should be updated, the hyperlink in the PDF does not direct to the correct section. After manually copying the link, there are only two tags, the Atmosphere and Land tags on Github. There is no way to find the corresponding code based on Appendix B, such as River, Sea Ice etc. Reading Fortran code directly is something that often happens when running meteorological models. It is recommended to update the tags or provide an index, then reader could find scripts after reading Appendix B. Additionally, is the repository only open to project developers, or does the entire Github community have permission to modify the code? It seems visitors can leave comments on each line of code.
  
  Comment 2: To prevent readers from constantly switching between this paper and Bodner et al., 2023 to reference the key equations in this study, it is recommended to further explain these two variables. The following section is a reference. In equation (1), the physical meaning of the variable Ψ is streamfunction, the gradient of the streamfunction can indicate the bolus velocity. μ(z) vertical fluxes at height z. Equation 2 is vertical structure function, so the vertical fluxes will be vanished when height is below the mixed layer (z< -H), and approach zero when z is almost zero.
  
  Comment 3: Fig.1, This SSH result is contrary to expectations. Is it possible that there is an issue with reduced deep water formation in the North Atlantic that should feed into the AMOC process (line #134)? Or air-sea interaction? Overlapping lines make it difficult to determine how many lines there are. It is recommended to use different symbols instead and slightly separate the lines in x-axis at overlapping positions to show the location of each point and indicate this in the figure caption.
  
  Comment 4: Fig.4, if the discussed region, "western boundary current in the North Atlantic around the region of the RAPID array," and “the west transect of the Overturning in the Subpolar North Atlantic Program array” are highlighted with a box in the figure, they would be easier to understand. If the decrease in MLD is caused by a very small increase in the magnitude and extent of the northward limb, then what is the direct cause of the "very small increase"? Is it because the mixed layer eddy parameterization enhanced the bolus velocity of eddies? In E3SM version 2, is the bolus velocity represented by a constant? Could the authors explain this in more detail?
  
  Comment 5: Fig.6, this is just a suggestion: could the shaded areas in CMIP6 be slightly enhanced, for example by reducing transparency or using borders? The colors are too faint and hard to distinguish. This requires locating the Python script used for plotting in PMP. If it is too difficult, the authors may decide to update it or not.
  
  Comment 6: Line #163, what could be the possible reason for the lack of significant changes in large-scale extratropical modes here? In the discussion section (line #301), the reason is also not explained here.
  
  Comment 7: Fig. 14 and 15, it seems that a strong stratification buffer has been enhanced and interior stratification has been eroded in the v.2.1 model compared with v2. Is this solely due to the addition of the mixed layer eddy parameterization?
  
  Citation: https://doi.org/10.5194/gmd-2024-149-RC2
  - RC3: 'Reply on RC2', Anonymous Referee #1, 10 Sep 2024
    
    I forgot to update the sentence. Please disregard the original last sentence in the first paragraph of my submitted comments. Sorry for that.
    
    Citation: https://doi.org/10.5194/gmd-2024-149-RC3
    
    AC3: 'Reply on RC3', Katherine Smith, 14 Nov 2024
    
    The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2024-149/gmd-2024-149-AC3-supplement.pdf
    
    Citation: https://doi.org/10.5194/gmd-2024-149-AC3
RC4:
'Comment on gmd-2024-149', Anonymous Referee #2, 18 Oct 2024

"The DOE E3SM Version 2.1: Overview and Assessment of the Impacts of Parameterized Ocean Submesoscales" has two aspects: it is the report detailing the new version of this model (highly appropriate for GMD) and it is a scientific report on the consequences of including the 2011 version of the MLE parameterization into this model. The latter is not novel in application, but instead compares the sensitivity of the E3SM vs. that of other models incorporating this scheme. The basic result is that upper ocean biases and RMSEs are improved, which then improves many climate metrics. I have only minor suggestions for the authors to consider.
1) Using a constant L_f is not a common choice, although it is not unprecedented. The authors should review the results of extensive testing of different choices of L_f as constants and as variations with mixed layer deformation radius in Calvert et al. (http://dx.doi.org/10.1016/j.ocemod.2020.101678)
2) In Fig. 4, which MLD observations are used? Are they consistent with the definition of MLD used? The new SEANOE MLD product is very nice in its incorporation of much more Argo data than previous versions (http://dx.doi.org/10.5194/gmd-16-3849-2023, https://www.seanoe.org/data/00806/91774/).
3) I recognize that there are many centuries of simulation data reported here, but I wonder the extent to which the MLE parameterization is responsible for these changes as opposed to the many other changes made. Are there any runs available for comparison with the v2.1 that differ only in turning off the MLE parameterization?

Citation: https://doi.org/10.5194/gmd-2024-149-RC4
- AC2: 'Reply on RC4', Katherine Smith, 14 Nov 2024
  
  The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2024-149/gmd-2024-149-AC2-supplement.pdf
  
  Citation: https://doi.org/10.5194/gmd-2024-149-AC2
AC4: 'Comment on gmd-2024-149', Katherine Smith, 14 Nov 2024

The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2024-149/gmd-2024-149-AC4-supplement.pdf

Citation: https://doi.org/10.5194/gmd-2024-149-AC4

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Short summary

Version 2.1 of the U.S. Department of Energy's Energy Exascale Earth System Model (E3SM) adds the Fox-Kemper et al. (2011) mixed layer eddy parameterization, which restratifies the ocean surface layer through an overturning streamfunction. Results include surface layer biases reduction in temperature, salinity, and sea-ice extent in the North Atlantic, a small strengthening of the Atlantic Meridional Overturning Circulation, and improvements in many atmospheric climatological variables.


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