the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Contribution of physical latent knowledge to the emulation of an atmospheric physics model: a study based on the LMDZ Atmospheric General Circulation Model
Abstract. In an Atmospheric General Circulation Model (AGCM), the representation of subgrid-scale physical phenomena, also referred to as physical parameterizations, requires computational time which constrains model numerical efficiency. However, the development of emulators based on Machine Learning offers a promising alternative to traditional approaches. We have developed offline emulators of the physics parameterizations of an AGCM, ICOLMDZ, in an idealized aquaplanet configuration. The emulators reproduce the profiles of the tendencies of the state variables for each independent atmospheric column. In particular, we compare Dense Neural Network (DNN) and U-Net models. The U-Net provides better predictions in terms of mean and variance. For the DNN, while it consistently delivers good performances in predicting the mean tendencies, the variability is not well captured, posing challenges for our application. We then investigate why the DNN's predictions are poorer compared to those of the U-Net, in terms of physical processes. We find that turbulence is not well emulated by the DNN. Leveraging a priori knowledge of how turbulence is parameterized in the phyLMDZ model, we show that incorporating physical knowledge through latent variables as predictors into the learning process leads to a significant improvement of the variability emulated with the DNN model. This improvement brought by the addition of these new predictors is not limited to the DNN, as the U-Net has also shown enhanced results. This study hence emphasizes the importance of adding physical knowledge in Neural Network (NN) models to improve predictions and to ensure better interpretability. It opens perspectives on a deeper understanding of the emulator, as well as exploring the contribution of new physical predictors, aiming to make climate simulations and projections.
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CEC1: 'Comment on egusphere-2025-1418 - No compliance with the policy of the journal', Juan Antonio Añel, 22 Jun 2025
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.htmlFirst, in your manuscript you do not provide a citation to a repository containing the code of the ICOLMDZ model. The policy of the journal clearly states that all the code and data necessary to replicate a manuscript must be published openly and freely to anyone before submission. In this regard, your manuscript should have never been accepted for Discussions given such violation of the policy.
Also, the site that you provide for the storage of the data and scripts, hosted in IPSL servers, is not a valid repository for scientific publication.
Therefore, you have to reply to this comment in a prompt manner with the information for the repositories containing all the models, code and data that you use to produce and replicate your manuscript. The reply must include the link and permanent identifier (e.g. DOI). Also, any future version of your manuscript must include the modified "Code and data availability" section with the new information.
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-2025-1418-CEC1 -
AC1: 'Reply on CEC1', Ségolène Crossouard, 09 Jul 2025
Dear Juan A. Añel,
Thank you for your comments and concerns.
In our initial submission, we did not include the ICOLMDZ model code. Our intention was to simplify the process for readers wishing to reproduce our emulator results by directly making the ICOLMDZ simulation output available, rather than asking the readers to compile and run the model themselves. Indeed, compiling and running ICOLMDZ can be quite complicated. However, we acknowledge that to make our results fully reproducible, it is important to provide the code and configuration files to run the ICOLMDZ model. As requested, we will prepare an archive containing the necessary files to run ICOLMDZ.
Regarding code and data storage, we choose to use the IPSL ESPRI service, due to the large size of our simulation outputs (approximately 220 GB), which exceed the storage limit of a platform like Zenodo (50 GB maximum). The ESPRI data center is CoreTrustSeal-certified and authorized to issue DOIs, and we considered it a suitable long-term repository for our data and code. If you do not agree with the data being stored on IPSL servers, we would appreciate your suggestions for alternative solutions.
One possibility on our side is to store the code for the ICOLMDZ models and the code for training and evaluating the emulators on Zenodo, while excluding the ICOLMDZ simulations from the archive. This way, the readers would be able to rerun the simulations themselves. Meanwhile, we could keep the simulations on the IPSL ESPRI servers for readers who are interested in reproducing the Machine Learning related results directly from the simulations. Would that be a suitable solution?
Once we agree on the best way to make our results reproducible, we will implement the necessary changes accordingly when answering to the reviewers' comments.
Best regards,
Ségolène CROSSOUARD, on behalf of all co-authors
Citation: https://doi.org/10.5194/egusphere-2025-1418-AC1 -
CEC2: 'Reply on AC1', Juan Antonio Añel, 09 Jul 2025
Dear authors,
Thanks for your reply. However, I am sorry but it does not address the comment that I posted earlier, and which I thought provided clear instructions. You must reply to this comment with the new "Code and Data Availability" section that complies with our policy (please, read and follow it, it does not give margin to interpretation). Unfortunately, we are not asking you for a reply showing intention of future compliance with our policy, but that you reply with the information for the repositories that make your manuscript in compliance with it now.
Again, we can not admit the IPSL servers as suitable repositories, they are not such. Zenodo is ok. Additionally, 220 GB is a perfectly reasonable amount of data for state-of-the-art standards, that does not justify not storing them in a external repository from the ones listed in our policy.
Please, reply to this comment as soon as possible. I have to highlight again that as it is, your manuscript should have not been admitted for review and Discussions.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1418-CEC2 -
AC2: 'Reply on CEC2', Ségolène Crossouard, 06 Aug 2025
Dear Juan A. Añel,
Thank you for your reply.
We have taken your comments into account and implemented the necessary changes to ensure our results can be produced and replicated. Accordingly, please find below the updated content of the “Code and data availability” section:
The source code and documentation to run the ICOLMDZ simulations are available at https://forge.ipsl.jussieu.fr/igcmg\_doc/wiki/Doc. To install the ICOLMDZ model, we use the tool suite called modipsl. Preprocessing steps used to prepare the simulated data to train the Machine Learning emulators depend on the XIOS library and NCO (https://nco.sourceforge.net/). The source code and documentation of the XIOS library are available at https://forge.ipsl.jussieu.fr/ioserver. All the code and data necessary to reproduce the results of the paper are available on the Harvard Dataverse: https://doi.org/10.7910/DVN/3UFU9J. The repository includes the modipsl and XIOS library that we have configured for the needs of the study as well as all the bash and python scripts used to train the neural networks, make and evaluate the predictions made from the emulators and generate the figures of the article.
We hope this revision addresses your concerns. Please let us know if anything else is needed.
Best regards,
Ségolène CROSSOUARD, on behalf of all co-authors
Citation: https://doi.org/10.5194/egusphere-2025-1418-AC2
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AC2: 'Reply on CEC2', Ségolène Crossouard, 06 Aug 2025
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CEC2: 'Reply on AC1', Juan Antonio Añel, 09 Jul 2025
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AC1: 'Reply on CEC1', Ségolène Crossouard, 09 Jul 2025
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RC1: 'Comment on egusphere-2025-1418', Anonymous Referee #1, 25 Jun 2025
The manuscript "Contribution of physical latent knowledge to the emulation of an atmospheric physics model: a study based on the LMDZ Atmospheric General Circulation Model" studies emulators for all parameterizations of the ICOLMDZ in an idealised aquaplanet configuration. The authors develop four emulators: two FCNs and two UNets, with two sets of input variables: the vertical profile of six state variables and four auxiliary variables in the first set, that are complemented by the vertical laplacian of the state variables in the second set.
Both network architectures are established and have been used to emulate components of GCMs. The main addition by this manuscript is that the authors investigate whether including latent variables as predictors can improve the prediction of physical tendencies. This can be relevant for researchers looking to replace the physical parameterizations with machine-learning based emulators, as stability and accuracy are very important for successful online emulators.
The FCN with vertical laplacians performs similar to the UNet (without vertical laplacians). Considering that the UNet input layer is built up of convolutions that can connect neighboring vertical levels, I find it conceivable that the UNet learns something like a vertical laplacian on the go, without the need to incorporate these predictors explicitly. Incorporating the laplacians also helps with variance, which is underestimated by all emulators.
The methods are outlined clearly and the deep learning code is provided. I believe it would be possible to reproduce the findings, given access to ICOLMDZ and the training dataset. However, ICOLMDZ is not included in the submission.
I would like to ask the authors to address the following points in a revised version of this manuscript:
- The overall presentation could use some clarification. Due to the nature of the quantities that are evaluated, the figures are quite complex, and the main text discusses findings that are only presented in the supplementary material (S2, S4). I think it would be beneficial to show the figures that are important for building the main narrative in the paper, and move less important subfigures to the supplemental material.
- Figures 4 and 5 already contain results that are based on the incorporation of the latent variables that is only introduced in a later section (5.2). I find this confusing, as a reader I was not able to interpret the figures while reading the manuscript front to back. I think it would be beneficial to show results once the underlying experiments have been discussed to keep the flow of information.
- Figure 6 (c-f) contains results that are only introduced later in section 5.2. Again, I find it confusing to see the results early without having the necessary context, and once the context was there in section 5.2 I had to search for the figure to understand the findings.
- It is obvious that the UNet outperforms the FCN. In the conclusion (Sect. 7), the authors state their interest in coupling both architectures to the dynamical core for an online evaluation. Maybe I am missing a point, but why would it be beneficial to continue working with the FCN if it is outperformed by the UNet? If it is useful to continue with FCN, I would appreciate a short explanation why it should be favored over UNet.
- Please correct the grammar in the first sentence of section 4.2.
Citation: https://doi.org/10.5194/egusphere-2025-1418-RC1 -
RC2: 'Comment on egusphere-2025-1418', Anonymous Referee #2, 26 Jun 2025
The manuscript presents the development of data-driven parameterizations for the LMDZ Atmospheric General Circulation Model, specifically in an aquaplanet configuration.
In the first experiment, the authors utilize low-level model variables (e.g., temperature, humidity) to emulate the entire subgrid-scale physics. They train two neural networks (NNs): a simple feedforward neural network (DNN) and a UNet with residual blocks. Both NNs struggle to capture sufficient variance in the output variables. The authors attribute this limitation to an inadequate representation of turbulence, particularly in the boundary layer. To mitigate this issue, they incorporate laplacians of part of the variables among the NN input variables, which may enhance the NNs' ability to represent turbulence. This modification leads to improvements in the R² score and the variance of the NN outputs.
The study yields two primary findings:
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The UNet architecture performs better than the feedforward NN.
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Incorporating additional variables, thereby embedding physical knowledge into the NNs, can improve their performance.
Overall, the study is comprehensive and well-documented. However, before recommending its publication, I have several suggestions for refinement.
General comments.
- There are many interesting results in this paper. However, sometimes I was lost in the details and between figures and tables. There are repetitions and reminders of previous results, which make the paper hard to follow. For example, Figure 5 and Table 5 ultimately provide the same information. Tables 3 and 4, as well as Figure 3, could possibly be moved to the Supplementary Material. Additionally, it might be useful to merge Table 4 and Figure 3 by including the total number of parameters on Figure 3. Combining Tables 1, 2, and 6 into a single table would also streamline the presentation. These are suggestions, and the authors can take them or not.
- Please proofread. The grammar can be odd in places.
- Please revise the scale of the colormaps used. The colors are too saturated in Figure 6 (and some of the Figures in the Supplementary) making it difficult to highlight the results.
- Your extrapolation regarding execution times might be correct, but in my experience, estimating the gain when using the NN instead of the physical model is much more complex. It also depends strongly on the strategy chosen to implement the NN. I would not risk providing too many details on this subject.
Point comments.
- Eq. (2): Is this an approximation?
- line 231: Is it a 1D UNet? I recommend revising the first sentence of the paragraph to state that you used (rather than developed) the UNet architecture.
- line 315: Even though I ultimately agree with you on choosing the UNet instead of the DNN, I find that this is not immediately 'obvious'.
- line 380: 'It appears that the U-Net architecture has a better ability to capture the reference tendency than the DNN': wasn't this already the conclusion of Section 4.1?
- line 465: I don't understand this sentence.
- line 485: Did the model converge during the 'training with Δ' experiment using the same settings as in the ‘initial training’ experiment?
- line 499-501: Is it a global R² score or only for the wind components?
Citation: https://doi.org/10.5194/egusphere-2025-1418-RC2 -
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RC3: 'Comment on egusphere-2025-1418', Anonymous Referee #3, 14 Jul 2025
In the manuscript "Contribution of physical latent knowledge to the emulation of an atmospheric physics model: a study based on the LMDZ Atmospheric General Circulation Model", the authors compare two Neural Network (NN) architectures, Dense Neural Networks (DNNs) and U-Nets, for their ability to emulate tendencies produced by a conventional physics package. They find that U-Nets generally outperform DNNs in capturing the variability of these physical processes. The study demonstrates that feature engineering by integrating physical knowledge, such as including the Laplacians of state variables as additional predictors, can improve the accuracy of both investigated NNs, particularly for the DNN.
I think this research could contribute to the development of more skillfull ML emulators of subgrid physics, but it has significant limitations as it is only trained on data produced by an aquaplanet setup without any topography and the performance of the emulators is only evaluated offline. An evaluation of the online performance, coupled to the aquaplanet ICOLMDZ setup would certainly be more meaningful than the offline evaluation.
Some of the findings presented in this manuscript appear to be preliminary and would benefit from more thorough evaluation. I will elaborate on this in the following points:
Major comments
- From my perspective the biggest issue, as mentioned, is that the developed emulators are only evaluated offline. A small stability/performance test of the DNNs/U-Nets coupled online would be very insightful.
- Line 160: Why don't you consider 2D outputs such as precipitation. I am sure the physics package of ICOLMDZ also parameterizes some 2D fields.
- Line 198: Why do you choose one every 20 cells and not a random subset? With this fixed "step size" you potentially overfit to these locations, don't you? What about evaluation on full data set, it is mentioned here, but you never come back to that as far as I saw?
- Line 224: You only tried this particular setup (6 layers and 512 neurons in each layer) and no hyperparameter optimization at all?
- Line 483: To judge impact of adding additional predictors adding a plot learning/validation curves to assess convergence would be helpful. Also, best to train multiple models to see if the improvement is "statistically significant"
- Line 562: The discussion is very short and not complete, you should add some limitation of you study, e.g, the aquaplanet setup.
Minor comments
- Eq. (2): I doubt that the ICOLMDZ uses as simple Euler step for time integration.
- Line 242: Please provide more details how you "reformatted" the input to 2D tensors. You are using 1D convolutions as previous developed ML physics schemes using U-Nets, right?
- Eq. (8-13): I don't think explaining the computations of means, variances, and metrics in such detail is necessary, but that is ultimately your choice.
- Line 420/Figure 8: Why do you choose a random timestep and not multiple ones and take a median/mean profile? Also, it could be helpful to plot A,B, and C in the same figure for easier comparison.
- Line 423: What physical process is represented by the thermals opposed to convection and turbulence?
- Line 436: "This is also the case for gravity wave drags from precipitations" - Do you mean convectively coupled waves, or what should "gravity waves from precipitation" mean?
- Line 470: Is delta z really fixed and if so, what is this fixed distance?
- Line 613: You should mention the CPU inference time of your models as well and mention that even if you are able to use the GPU for inference during coupling, you have an overhead from copying the data from CPU to GPU as long as ICOLMDZ is not running on the GPU as well.
- Line 631: Watt-Meyer et al., 2024 did not emulate a physics package but derived the subgrid physics by coarse graining from high-resolution simulations
Typos/Grammar
- Line 19: The second "numerical" is redundant
- Line 201-203: "These numbers of samples are multiplied by the length of the input vector X′ and the output vector Y′, for all the three subsets, which correspond to variables aggregated over the vertical dimension" What do you mean by multiplied by length of ..., to get the number overall size of the input data?
- Line 229: "It is trained with the learning rate scheduler of 10^{−3} ..." What exact scheduler did you use? I assume the factor 10^{-3} indicates some decay or did you mean learning rate of 10^{-3}?
- Line 230: I wouldn't say that "a U-Net is a CNN architecture" but that it uses convolutional layers
- Line 246: "Once the models had been built, we trained them." Not necessary to state this.
- Line 257: "In this article" - You mean section I think
- Line 284: "We will sometimes compute the RMSE on specific subsets of the test dataset to exhibit performances that vary for instance across latitudes or vertical levels." - "exhibit" does not fit here
- Line 333: "..., we examine them study by latitude belts, ..."
- Line 416: "We decided to carry out this study on three grid cells..." - please use columns instead of grid cells here
- Line 429-431: please rewrite the sentence
- Line 535: reformulate "with these new learning"
- The word "Indeed" is overused throughout the manuscript.
Citation: https://doi.org/10.5194/egusphere-2025-1418-RC3
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