the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 19 Jan 2024
E3SM Chemistry Diagnostics Package (ChemDyg) Version 0.1.4
Abstract. The E3SM Chemistry diagnostics package (ChemDyg) is an open-source software, all diagnostic scripts written in Python, developed to support the Department of Energy (DOE) Energy Exascale Earth System Model (E3SM). The current version 0.1.4 of ChemDyg generates several diagnostic plots and tables for model-to-model and model-to-observation comparison, including 2-dimentional contour mapping plots, diurnal and annual cycle plots, time-series plots, and comprehensive processing tables. ChemDyg is executed by zppy, which is a post-processing toolchain for E3SM written in Python. The ChemDyg codebase is designed to be modular, and each diagnostics set is self-contained. Each set has its own driving script that includes set-specific file input/output and a main python script for calculation and plotting. The outputs from each diagnostics set, including figures and tables, are organized in the main HTML page to make it interactive through a browser.
This paper is a comprehensive description of E3SM ChemDyg (as of version 0.1.4) including the details of each diagnostics set and its required input data formats. This tool has enough flexibility for future ChemDyg developers to increase the addition of new observational datasets and new diagnostics sets.
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Status: closed
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RC1: 'Comment on gmd-2023-203', Anonymous Referee #1, 25 Feb 2024
General Comments:
This paper is a description of the ChemDyg diagnostic package v 0.1.4 capavle of evaluating the novel model chemistry improvements made in version 2 of the E3SM model. The authors describe the collection of observational datasets and other model data used for such evaluation.
The overall comment is that it is not clear what the scientific contribution of this paper is. A few ways in which the authors could highlight this are:
 1. It would be helpful if the authors could emphasize the novelty in the evaluation, as in what the evaluation package does that cannot be done by other model evaluation tools. There is no comparison with any other evaluation tool except where they state upgrades from a previous version.
2. It is not clear if there is a broader applicability to the tool. Can it be used with other models (not just for comparison with E3SM)? If yes, some examples will be useful. If it cannot be applied more broadly, then does it only serve the purpose of a monitoring tool for the new chemistry in E3SM? That would be very specifc in application.
3. The plots in Figures 2 onwards are standard evaluation plots. It is not clear that there are new metrics or diagnostics in the evaluation. So, again the significance of the evaluation is not clear. It seems the scientific novelty is still in the new chemistry package and not in the evaluation.Â
Specific comments:
1. In Line 92, the authors say that the ozone only diagnostics cannot meet the EAMv3 chemistry evaluation requirements. It is not explained why this is soÂ2. Where examples of diagnostics are provided in Section 3, it would be useful if the authors can highlight the importance of the evluation with suitable references. This would be a way to demonstrate the scientific value of the paper.
Technical comments:
1. Line 27 : dimentional -> dimensional
2. Line 46: farm ->frame
3. Line 389: summery -> summaryThe paper seems like a technical documentation of the ChemDyg diagnostic package but for it to be a scientific publication the above comments have to be addressed at the very least.
Citation: https://doi.org/10.5194/gmd-2023-203-RC1 -
AC1: 'Reply on RC1', Hsiang-He Lee, 17 May 2024
The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2023-203/gmd-2023-203-AC1-supplement.pdf
-
AC1: 'Reply on RC1', Hsiang-He Lee, 17 May 2024
-
RC2: 'Comment on gmd-2023-203', Anonymous Referee #2, 08 May 2024
This manuscript discusses the E3SM Chemistry diagnostics package (ChemDyg), which is open-source software written in Python. It was developed to support the Department of Energy's Energy Exascale Earth System Model (E3SM). ChemDyg version 0.1.4 generates various diagnostic plots and tables (11 types of plots and 4 types of tables) for comparing model outputs to both other models and observational data. These include 2-dimensional contour mapping plots, diurnal and annual cycle plots, time-series plots, and comprehensive processing tables. ChemDyg is executed by zppy, a post-processing toolchain for E3SM written in Python. The codebase of ChemDyg is modular, with each diagnostics set being self-contained. Each set has its own driving script for file input/output and a main Python script for calculation and plotting. The outputs, including figures and tables, are organized in an interactive HTML page accessible through a browser.
The manuscript is well structured and written. It provides a detailed description of E3SM ChemDyg version 0.1.4, including the specifics of each diagnostics set and the required input data formats. It also highlights the tool's flexibility for future developers to incorporate new observational datasets and diagnostics sets.
The manuscript lacks direct comparisons with existing tools. A paragraph on the tool's novelty and added value compared to other evaluation tools is essential. Highlighting specific features or functionalities that distinguish ChemDyg from other evaluation tools would provide readers with a clearer understanding of its unique contributions to model evaluation tasks.Â
Citation: https://doi.org/10.5194/gmd-2023-203-RC2 -
AC2: 'Reply on RC2', Hsiang-He Lee, 17 May 2024
The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2023-203/gmd-2023-203-AC2-supplement.pdf
-
AC2: 'Reply on RC2', Hsiang-He Lee, 17 May 2024
Status: closed
-
RC1: 'Comment on gmd-2023-203', Anonymous Referee #1, 25 Feb 2024
General Comments:
This paper is a description of the ChemDyg diagnostic package v 0.1.4 capavle of evaluating the novel model chemistry improvements made in version 2 of the E3SM model. The authors describe the collection of observational datasets and other model data used for such evaluation.
The overall comment is that it is not clear what the scientific contribution of this paper is. A few ways in which the authors could highlight this are:
 1. It would be helpful if the authors could emphasize the novelty in the evaluation, as in what the evaluation package does that cannot be done by other model evaluation tools. There is no comparison with any other evaluation tool except where they state upgrades from a previous version.
2. It is not clear if there is a broader applicability to the tool. Can it be used with other models (not just for comparison with E3SM)? If yes, some examples will be useful. If it cannot be applied more broadly, then does it only serve the purpose of a monitoring tool for the new chemistry in E3SM? That would be very specifc in application.
3. The plots in Figures 2 onwards are standard evaluation plots. It is not clear that there are new metrics or diagnostics in the evaluation. So, again the significance of the evaluation is not clear. It seems the scientific novelty is still in the new chemistry package and not in the evaluation.Â
Specific comments:
1. In Line 92, the authors say that the ozone only diagnostics cannot meet the EAMv3 chemistry evaluation requirements. It is not explained why this is soÂ2. Where examples of diagnostics are provided in Section 3, it would be useful if the authors can highlight the importance of the evluation with suitable references. This would be a way to demonstrate the scientific value of the paper.
Technical comments:
1. Line 27 : dimentional -> dimensional
2. Line 46: farm ->frame
3. Line 389: summery -> summaryThe paper seems like a technical documentation of the ChemDyg diagnostic package but for it to be a scientific publication the above comments have to be addressed at the very least.
Citation: https://doi.org/10.5194/gmd-2023-203-RC1 -
AC1: 'Reply on RC1', Hsiang-He Lee, 17 May 2024
The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2023-203/gmd-2023-203-AC1-supplement.pdf
-
AC1: 'Reply on RC1', Hsiang-He Lee, 17 May 2024
-
RC2: 'Comment on gmd-2023-203', Anonymous Referee #2, 08 May 2024
This manuscript discusses the E3SM Chemistry diagnostics package (ChemDyg), which is open-source software written in Python. It was developed to support the Department of Energy's Energy Exascale Earth System Model (E3SM). ChemDyg version 0.1.4 generates various diagnostic plots and tables (11 types of plots and 4 types of tables) for comparing model outputs to both other models and observational data. These include 2-dimensional contour mapping plots, diurnal and annual cycle plots, time-series plots, and comprehensive processing tables. ChemDyg is executed by zppy, a post-processing toolchain for E3SM written in Python. The codebase of ChemDyg is modular, with each diagnostics set being self-contained. Each set has its own driving script for file input/output and a main Python script for calculation and plotting. The outputs, including figures and tables, are organized in an interactive HTML page accessible through a browser.
The manuscript is well structured and written. It provides a detailed description of E3SM ChemDyg version 0.1.4, including the specifics of each diagnostics set and the required input data formats. It also highlights the tool's flexibility for future developers to incorporate new observational datasets and diagnostics sets.
The manuscript lacks direct comparisons with existing tools. A paragraph on the tool's novelty and added value compared to other evaluation tools is essential. Highlighting specific features or functionalities that distinguish ChemDyg from other evaluation tools would provide readers with a clearer understanding of its unique contributions to model evaluation tasks.Â
Citation: https://doi.org/10.5194/gmd-2023-203-RC2 -
AC2: 'Reply on RC2', Hsiang-He Lee, 17 May 2024
The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2023-203/gmd-2023-203-AC2-supplement.pdf
-
AC2: 'Reply on RC2', Hsiang-He Lee, 17 May 2024
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