the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 22 Jan 2026
Implementation of the ORACLE (v1.0) organic aerosol composition and evolution module into the EC-Earth3-AerChem model
Abstract. Simulating the composition and evolution of organic aerosol (OA) in Earth System Models (ESMs) presents significant challenges due to the high computational demands of detailed chemical mechanisms. The computationally efficient ORACLE module employs the volatility basis set framework and can simulate secondary organic aerosol (SOA) formation from a range of precursors, including volatile (VOCs), intermediate-volatility (IVOCs), semi-volatile (SVOCs), and low-volatility organic compounds (LVOCs). In this study, a lite configuration of the ORACLE v1.0 module (ORACLE-lite) is implemented into the TM5-MP global chemical transport model (CTM), which represents the chemistry-transport component of the EC-Earth3-AerChem ESM. SOA formation from anthropogenic VOCs is neglected to reduce the number of surrogate species and further improve computational efficiency. For the standalone TM5-MP simulation, the global annual mean surface total OA concentration using ORACLE-lite is approximately 1.1 μg m−3, representing a 25 % increase compared to the previous version of the model. The annual atmospheric OA burden also increases by 50 %, reaching 3.67 Tg. Corresponding predictions from EC-Earth3-AerChem are slightly higher, with a surface total OA concentration of 1.16 μg m−3 and an atmospheric burden of 3.83 Tg, representing increases of 30 % and 60 %, respectively, compared to the previous version of the model. Comparison of monthly measured PM2.5 OA concentrations from Europe and the US with the corresponding predictions shows that the models bias is reduced by approximately half in the standalone TM5-MP simulation and by a factor of three in EC-Earth3-AerChem when ORACLE-lite is implemented. These enhancements enable more accurate and computationally feasible assessments of the climate impacts of individual organic aerosol components in future ESM studies.
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2026-37', Anonymous Referee #1, 20 Feb 2026
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AC2: 'Reply to the Comments of Referee 1', Spyros Pandis, 04 Apr 2026
General comments
(1) The manuscript “Implementation of the ORACLE (v1.0) organic aerosol composition and evolution module into the EC-Earth3-AerChem model” by Kakavas et al. describes briefly the implementation ORACLE (v1.0) organic aerosol model in TM5-MP atmospheric chemistry model. It is analyzed and evaluated using it as a standalone model driven with reanalysis data as well as coupled to EC-Earth3-AerChem Earth system model. The manuscript fits in the scope of the journal addressing the need for a computationally efficient and scientifically accurate description for organic aerosol. It presents a novel implementation of ORACLE-lite module into TM5-MP which shows improvements in simulated OA concentrations in both configurations it is evaluated. Methods are scientifically valid, although the manuscript relies on its description a lot on previous papers published on ORACLE-lite. However, for example Pandis et al. (1993) paper is behind a pay wall. The results mainly support the interpretations and conclusions. The description could be more detailed so that the reader shouldn’t have to go through so much of previous publications on ORACLE. The paper is well structured, the language is fluent and precise.We appreciate the positive assessment of our work by the reviewer. We have tried to address all comments of the reviewer and to improve the paper accordingly. We have followed the suggestion of the reviewer and added a more detailed description of the ORACLE module in the corresponding section of the manuscript. Our responses (in regular font) and the corresponding changes in the manuscript follow each comment of the reviewer (in italics).
Specific comments
(2) Line 88: “ORACLE reduces the computational cost by utilizing a small number of surrogate OA species by employing a novel lumping method.”. When compared to what?We have rewritten the sentence to clarify the basis of the comparison.
(3) Line 116: There is a description paper by van Noije et al., (2023) on this EC-Earth3-Aerchem which might be a more appropriate reference for this model. In addition, Döscher citation is for year 2021, but the reference is 2022.
We have followed the reviewer’s suggestion by adding the reference to van Noije et al. (2021) and correcting the Döscher citation year to 2022.
(4) Lines 180-186: “Note however, that the SOA formation from biogenic VOC emissions (isoprene and monoterpenes) is already represented in the models, as described by Bergman et al. (2022), while SOA formation from anthropogenic VOC emissions is neglected. As a result, the number of surrogate species used to represent OA and its volatility in ORACLE-lite was reduced from 18 to 9. An overview of the characteristics of the lite configuration of the ORACLE module used in this study is shown in Table 1.” This is unclear what is meant by this. Is SOA formation from biogenic VOC emissions treated separately using the approach by Bergman et al. (2022)?
This is correct. SOA formation from biogenic VOC emissions is treated separately in the model using the approach described by Bergman et al. (2022). To clarify this point and avoid confusion, we have added a brief discussion in this section of the revised manuscript.
(5) It is also unclear how OA is partitioned between different modes. Pandis et al., (1993) is referred to, but I don’t have the access to the paper.
We have added a brief discussion in this section of the revised manuscript explaining how OA is partitioned among the different modes.
(6) Are SOA species affecting aerosol radiative properties? If so, what assumptions have been used for optical properties?
The formed SOA does interact with radiation. We have added a brief discussion of the assumed optical properties in the revised manuscript to clarify this aspect.
(7) Do SOA species affect cloud droplet activation in EC-Earth?
Yes, they do. SOA contributes to the organic aerosol mass within the modal aerosol scheme (M7), so it affects aerosol growth and particle properties. As cloud droplet activation depends on aerosol size, number, and hygroscopicity, SOA indirectly influences cloud droplet activation in the model through changes in both the aerosol size distribution and composition. We have added a brief discussion in the revised manuscript.
(8) Line 231: “data were available from only 3 stations for the simulated period.” Could you have used data for another year or ran a year that would have more station data?
Following the reviewer’s suggestion, we have extended the evaluation of the results of the online simulation of EC-Earth3-AerChem for 2010, for which more observational stations are available within the EMEP framework.
(9) Page 9: Emissions between TM5-MP and EC-Earth look remarkably similar. Is there a good reason to show both of them? It would also be good to use some other colormap and scale, and put them in the same figure to see if there are any differences. Jet colormap is also not recommended in modern data visualization. The same comment applies to Figure 3.
TM5-MP and EC-Earth simulations use the same emissions. The TM5-MP emissions shown in Fig. 1 correspond to the year 2005, whereas the EC-Earth3-AerChem emissions shown in Fig. 2 represent the annual mean over 2000–2010. Following the reviewer’s suggestion, we have combined Figs. 1 and 2 into a single figure and replaced the current colormap with a more appropriate one.
(10) Lines 456-458: “The incorporation of ORACLE-lite significantly improved the representation of OA formation and atmospheric behavior both in the standalone TM5-MP and the EC-Earth.“ This is an inaccurate sentence since the default TM5-MP does not simulate OA formation, rather they emit OA as primary particles. In addition, overall significance of improvement depends on which evaluation metrics we are looking at in Table 3. Bias shows clear decrease, but different error metrics not necessarily.
We have followed the suggestion of the reviewer and changed this sentence to “The incorporation of ORACLE-lite reduced the bias of the OA predictions both in the offline and online simulations of EC-Earth3-AerChem.”.
(11) Lines 477-479: “The seasonal and spatial variability of SOA was also better captured, with higher concentrations predicted in regions with intense biomass burning and anthropogenic activity, such as India, China, and sub-Saharan Africa.” How do you determine better seasonal and spatial variability? To me, these are not evident from the manuscript.
We have removed this sentence from the revised manuscript.
Citation: https://doi.org/10.5194/egusphere-2026-37-AC2
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AC2: 'Reply to the Comments of Referee 1', Spyros Pandis, 04 Apr 2026
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RC2: 'Comment on egusphere-2026-37', Anonymous Referee #2, 26 Feb 2026
The current work provides a description of the implementation of the ORACLE-lite secondary organic aerosol (SOA) formation mechanism in the TM5-MP and EC-Earth modeling systems. Accurate modeling of SOA concentrations is important for both air quality and climate purposes, even though SOA modeling is often associated with considerable uncertainty and computational cost. The implementation and evaluation described in the current work serves as a useful source of documentation, both for the currently described models and for other models that may wish to implement the ORACLE-lite module in the future. The comparison against surface observations, while limited to North America and Western Europe, is an important element of this work. I can recommend this article for publication after the below comments have been considered.
Main comment
1. The authors note that only 3 stations from the EBAS database are available for the year 2005. However, following the link provided to the EBAS database finds that PM2.5 OC measurements are available from 4 stations (one in Spain, Italy, Germany, and Norway). The Italian, German, and Norwegian sites all have nearly continuous measurements over the course of the year. The Spanish site only has two daily mean measurements per month. Given that it is typical to calculate monthly means only when around 60-70% data availability is reached, I think the measurements from the Spanish site should be excluded from the analysis. At least so long as the analysis focuses on monthly mean values.
The Italian site (Ispra) is clearly influenced by anthropogenic wood burning emissions, reaching a monthly mean OC concentration of 22 ug/m3 in January (or 40 ug/m3 OM using the employed OA/OC ratio of 1.8). This value would skew the average monthly mean across all sites (whether the Spanish site is excluded or not) beyond the average of 2.2 ug/m3 currently shown for January in Figure 8. It therefore seems like the Italian site was excluded from the analysis. However, since this is a rural site (as are the German and Norwegian sites), and since the high wintertime concentrations are likely to have large contributions from the anthropogenic biomass burning emissions (and the resulting oxygenated OA formation) that is central to the current work, it is not clear to me why this station should be excluded.
The availability of OC measurements in Europe increases greatly in later years. For example, for 2010 there are 8 stations with good data availability, whereas for 2015 there are 20. I think the simulations should at least be compared to EBAS/EMEP observations for the year 2010 (implying that a new simulation with TM5-MP would have to be performed). Ideally, however, more recent years for both the TM5-MP and EC-Earth simulations would have to be considered, preferably for 2015 or later.
If the authors decide to continue using the TM5-MP simulation for 2005, I think the stations in Germany (Melpitz), Italy (Ispra), and Norway (Birkenes) should be evaluated in detail on an individual basis rather than as the average across all three sites.
Minor comments
1. It would be helpful if the ORACLE-lite description would be expanded to make the article more self-contained, even though more detailed descriptions can be found in the cited works. For example, it would be helpful if the K_OH rates that modify the volatility of the emitted organic compounds are included in Table 1.
2. Could the motivation behind neglecting SOA formation from anthropogenic VOC emissions be expanded? These are said to contribute only 15% to total global average surface OA concentrations, but this seems like a considerable amount (similar also to the calculated annual SOA-sv mass, roughly based on Table S1). The measurements are also underestimated by 8-13% with the current ORACLE-lite setup, suggesting that the additional SOA from VOCs would improve/reduce the model bias. The current runtime increase of 8% seems modest. How much slower would the model become with the addition of SOA from anthropogenic VOCs?
3. When the IMPROVE network is introduced, it would be helpful if it is mentioned that the main purpose of the network is to measure aerosols in remote areas of the United States, with the measurements therefore being representative of rural conditions.
4. The authors mention that measurements of OC are converted to OA using an OA/OC ratio of 1.8, while the traditional model setup is to assume that OA from all emission sources (treated as POA) has a ratio of 1.6. For reference, it would be helpful to include a description of the OA/OC ratios calculated/assumed using ORACLE-lite, and the resulting calculated ratios of the total OA.
5. In Fig. S13, could the y-axis be changed to show hPa rather than model level? Currently it is difficult to make out the vertical scales.
Editorial
ECMWF is defined on both lines 120 and 131.
SOA-sv is said to correspond to a C* value of 10^-2 ug/m3 on line 332. However, Table 1 shows a value of 10^1 ug/m3.
Citation: https://doi.org/10.5194/egusphere-2026-37-RC2 -
AC3: 'Response to the Comments of Reviewer 2', Spyros Pandis, 04 Apr 2026
General comments
(1) The current work provides a description of the implementation of the ORACLE-lite secondary organic aerosol (SOA) formation mechanism in the TM5-MP and EC-Earth modeling systems. Accurate modeling of SOA concentrations is important for both air quality and climate purposes, even though SOA modeling is often associated with considerable uncertainty and computational cost. The implementation and evaluation described in the current work serves as a useful source of documentation, both for the currently described models and for other models that may wish to implement the ORACLE-lite module in the future. The comparison against surface observations, while limited to North America and Western Europe, is an important element of this work. I can recommend this article for publication after the below comments have been considered.
We appreciate the positive assessment of our work by the reviewer. We have tried to address all comments and to improve the paper accordingly. Our responses (in regular font) and the corresponding changes in the manuscript follow each comment of the reviewer (in italics).
(2) The authors note that only 3 stations from the EBAS database are available for the year 2005. However, following the link provided to the EBAS database finds that PM2.5 OC measurements are available from 4 stations (one in Spain, Italy, Germany, and Norway). The Italian, German, and Norwegian sites all have nearly continuous measurements over the course of the year. The Spanish site only has two daily mean measurements per month. Given that it is typical to calculate monthly means only when around 60-70% data availability is reached, I think the measurements from the Spanish site should be excluded from the analysis. At least so long as the analysis focuses on monthly mean values. The Italian site (Ispra) is clearly influenced by anthropogenic wood burning emissions, reaching a monthly mean OC concentration of 22 μg/m3 in January (or 40 μg/m3 OM using the employed OA/OC ratio of 1.8). This value would skew the average monthly mean across all sites (whether the Spanish site is excluded or not) beyond the average of 2.2 μg/m3 currently shown for January in Figure 8. It therefore seems like the Italian site was excluded from the analysis. However, since this is a rural site (as are the German and Norwegian sites), and since the high wintertime concentrations are likely to have large contributions from the anthropogenic biomass burning emissions (and the resulting oxygenated OA formation) that is central to the current work, it is not clear to me why this station should be excluded. The availability of OC measurements in Europe increases greatly in later years. For example, for 2010 there are 8 stations with good data availability, whereas for 2015 there are 20. I think the simulations should at least be compared to EBAS/EMEP observations for the year 2010 (implying that a new simulation with TM5-MP would have to be performed). Ideally, however, more recent years for both the TM5-MP and EC-Earth simulations would have to be considered, preferably for 2015 or later. If the authors decide to continue using the TM5-MP simulation for 2005, I think the stations in Germany (Melpitz), Italy (Ispra), and Norway (Birkenes) should be evaluated in detail on an individual basis rather than as the average across all three sites.
This is a valid point. The OC measurements at the Ispra (Italy) station are systematically high (reaching up to 22 µg m−3 in winter), which strongly influences the multi-site monthly mean shown in Fig. 8 due to the limited number of available stations for 2005. For this reason, and to avoid the average being dominated by a single site, Ispra was excluded from the statistical analysis. This is now clarified in the revised manuscript. Also, we have followed the suggestion of the reviewer and added the evaluation of EC-Earth3-AerChem for the year 2010 in the revised manuscript, when more observational stations are available. Since the differences in predicted OA concentrations between TM5-MP and EC-Earth are relatively small, we consider that performing an additional TM5-MP simulation for 2010 is not necessary for the purposes of this comparison. A brief discussion has been added in the corresponding section of the manuscript.
Specific comments
(3) It would be helpful if the ORACLE-lite description would be expanded to make the article more self-contained, even though more detailed descriptions can be found in the cited works. For example, it would be helpful if the K_OH rates that modify the volatility of the emitted organic compounds are included in Table 1.
We have followed the suggestion of the reviewer and expanded the description of ORACLE-lite to make the manuscript more self-contained and added the corresponding reaction rate constants of SVOCs and IVOCs with OH to the revised manuscript.
(4) Could the motivation behind neglecting SOA formation from anthropogenic VOC emissions be expanded? These are said to contribute only 15% to total global average surface OA concentrations, but this seems like a considerable amount (similar also to the calculated annual SOA-sv mass, roughly based on Table S1). The measurements are also underestimated by 8-13% with the current ORACLE-lite setup, suggesting that the additional SOA from VOCs would improve/reduce the model bias. The current runtime increase of 8% seems modest. How much slower would the model become with the addition of SOA from anthropogenic VOCs?
This is a point that deserves additional discussion. Although the additional SOA formed from anthropogenic VOCs could improve the model bias, ORACLE-lite was originally developed for use with the SAPRC family of gas-phase mechanisms. In contrast, TM5-MP and EC-Earth3-AerChem employ a modified CB05 chemical mechanism, which uses a different lumping structure for anthropogenic VOCs than that assumed in ORACLE. As a result, the direct inclusion of anthropogenic SOA formation within the current ORACLE-lite framework is complex and requires additional development. This will be the topic of future work. This point is now explained in the revised manuscript.
(5) When the IMPROVE network is introduced, it would be helpful if it is mentioned that the main purpose of the network is to measure aerosols in remote areas of the United States, with the measurements therefore being representative of rural conditions.
We have followed the reviewer’s suggestion and clarified in the revised manuscript that the IMPROVE network measures aerosols in remote areas of the United States and as a result is representative of rural conditions.
(6) The authors mention that measurements of OC are converted to OA using an OA/OC ratio of 1.8, while the traditional model setup is to assume that OA from all emission sources (treated as POA) has a ratio of 1.6. For reference, it would be helpful to include a description of the OA/OC ratios calculated/assumed using ORACLE-lite, and the resulting calculated ratios of the total OA.
In the present application, SVOCs and IVOCs undergo up to two generations of oxidation, with a 22.5% mass increase in each generation. Assuming an initial OM/OC ratio of 1.2 in ORACLE-lite, this leads to a final OM/OC ratio of up to 1.8, which is within the observed range for oxygenated organic aerosol (OM/OC: 1.8–2.4; Aiken et al., 2008). This is now explained in the revised manuscript.
(7) In Fig. S13, could the y-axis be changed to show hPa rather than model level? Currently it is difficult to make out the vertical scales.
We have followed the reviewer’s suggestion and changed the y-axis in Fig. S13 to show pressure (hPa) instead of model levels in the revised manuscript.
(8) ECMWF is defined on both lines 120 and 131.
The duplicate definition of ECMWF in line 131 has been removed in the revised manuscript.
(9) SOA-sv is said to correspond to a C* value of 10-2 µg/m3 on line 332. However, Table 1 shows a value of 101 µg/m3.
This is a misunderstanding. The value in Table 1 refers to the initial representative volatility bin of the emitted species, not to the volatility after aging. We have clarified this point in Table 1 of the revised manuscript to avoid confusion.
References
Aiken, A. C., DeCarlo, P. F., Kroll, J. H., Worsnop, D. R., Huffman, J. A., Docherty, K. S., Ulbrich, I. M., Mohr, C., Kimmel, J. R., Sueper, D., Sun, Y., Zhang, Q., Trimborn, A., Northway, M., Ziemann, P. J., Canagaratna, M. R., Onasch, T. B., Alfarra, M. R., Prevot, A. S. H., Dommen, J., Duplissy, J., Metzger, A., Baltensperger, U., and Jimenez, J. L.: O/C and OM/OC ratios of primary, secondary, and ambient organic aerosols with high-resolution time-of-flight aerosol mass spectrometry, Environ. Sci. Technol., 42, 4478–4485, doi: 10.1021/es703009q, 2008.
Bergman, T., Makkonen, R., Schrödner, R., Swietlicki, E., Phillips, V. T. J., Le Sager, P., and van Noije, T.: Description and evaluation of a secondary organic aerosol and new particle formation scheme within TM5-MP v1.2, Geosci. Model Dev., 15, 683–713, doi: 10.5194/gmd-15-683-2022, 2022.
van Noije, T., Bergman, T., Le Sager, P., O'Donnell, D., Makkonen, R., Gonçalves-Ageitos, M., Döscher, R., Fladrich, U., von Hardenberg, J., Keskinen, J.-P., Korhonen, H., Laakso, A., Myriokefalitakis, S., Ollinaho, P., Pérez García-Pando, C., Reerink, T., Schrödner, R., Wyser, K., and Yang, S.: EC-Earth3-AerChem: a global climate model with interactive aerosols and atmospheric chemistry participating in CMIP6 , Geosci. Model Dev., 14, 5637–5668, doi: 10.5194/gmd-14-5637-2021, 2021.
Citation: https://doi.org/10.5194/egusphere-2026-37-AC3
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AC3: 'Response to the Comments of Reviewer 2', Spyros Pandis, 04 Apr 2026
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CEC1: 'Comment on egusphere-2026-37 - No compliance with the policy of the journal', Juan Antonio Añel, 11 Mar 2026
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
Specifically, you have not shared the ORACLE v1.0 code. In the Code Availability section of your manuscript, you refer to the MESSy code to get access to it. This does not comply with our policy, first, because you need to provide access to the module that you use, not a full model containing it, and secondly, because it is not clear what kind of restriction prevents you from sharing the ORACLE v1.0 code. The MESSy code is not shared openly due to legacy issues that, it is our understanding, do not apply to the ORACLE v1.0 module. Actually, one of you, Dr. Alexandra Tsimpidi, is the author of the first paper published years ago in Geosci. Model Dev. describing it. Under such circumstances, we wonder what kind of restriction applies here that prevents you from releasing the ORACLE v1.0 code. Therefore, you have to publish the code for the ORACLE v1.0 module in an open repository we can accept, or clarify which legal mandate or rule prevents you from sharing it.Secondly, you provide a link to the ISORROPIA code, which can be downloaded from there. Unfortunately, the linked site does not meet the minimum requirements to be considered a trusted long-term repository for scientific publication. Also, the terms of use for the code mentioned on the linked webpage are not available. It is your obligation to ensure that all the elements necessary to produce your manuscript are properly stored. In this case, it is not clear what prevents you from adequately storing and sharing the ISORROPIA code in a repository we can accept. Maybe the license of such code imposes restrictions; however, given the way in which it is made available and distributed, it is not possible to know. Therefore, if the ISORROPIA license does not prohibit storing and sharing the code, you must do so in a repository we can accept.In both cases, for ORACLE v1.0 and ISORROPIA, you must reply to this comment with the links to the new repositories and the permanent identifiers (DOI, handle, etc.) for them.Regarding the data, you have stored them in sites that we can not accept (colostate.edu and nilu.no), as they do not fulfil GMD’s requirements for a persistent data archive because:
- They do not appear to have a published policy for data preservation over many years or decades (some flexibility exists over the precise length of preservation, but the policy must exist).
- They do not appear to have a published mechanism for preventing authors from unilaterally removing material. Archives must have a policy which makes removal of materials only possible in exceptional circumstances and subject to an independent curatorial decision,
- They do not appear to issue a persistent identifier such as a DOI or Handle for each precise dataset.Therefore, you must store your data in a repository acceptable according to our policy. If we have missed a published policy which does in fact address this matter satisfactorily, please post a response linking to it. If you have any questions about this issue, please post them in a reply
The GMD review and publication process depends on reviewers and community commentators being able to access, during the discussion phase, the code and data on which a manuscript depends, and on ensuring the provenance of replicability of the published papers for years after their publication. Please, therefore, publish your code and data in one of the appropriate repositories and reply to this comment with the relevant information (link and a permanent identifier for it (e.g. DOI)) as soon as possible. We cannot have manuscripts under discussion that do not comply with our policy.
The 'Code and Data Availability’ section must also be modified to cite the new repository locations, and corresponding references added to the bibliography.
I must note that if you do not fix these problems, we cannot continue with the peer-review process or accept your manuscript for publication in GMD.
Juan A. Añel
Geosci. Model Dev. Executive EditorCitation: https://doi.org/10.5194/egusphere-2026-37-CEC1 -
AC1: 'Reply on CEC1', Spyros Pandis, 04 Apr 2026
General comments
(1) 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
We have tried to address all comments of the chief editor. Our responses and corresponding changes to the manuscript (in blue) follow each comment of the reviewer (in black).
Specific comments
(2) Specifically, you have not shared the ORACLE v1.0 code. In the Code Availability section of your manuscript, you refer to the MESSy code to get access to it. This does not comply with our policy, first, because you need to provide access to the module that you use, not a full model containing it, and secondly, because it is not clear what kind of restriction prevents you from sharing the ORACLE v1.0 code. The MESSy code is not shared openly due to legacy issues that, it is our understanding, do not apply to the ORACLE v1.0 module. Actually, one of you, Dr. Alexandra Tsimpidi, is the author of the first paper published years ago in Geosci. Model Dev. describing it. Under such circumstances, we wonder what kind of restriction applies here that prevents you from releasing the ORACLE v1.0 code. Therefore, you have to publish the code for the ORACLE v1.0 module in an open repository we can accept, or clarify which legal mandate or rule prevents you from sharing it. Secondly, you provide a link to the ISORROPIA code, which can be downloaded from there. Unfortunately, the linked site does not meet the minimum requirements to be considered a trusted long-term repository for scientific publication. Also, the terms of use for the code mentioned on the linked webpage are not available. It is your obligation to ensure that all the elements necessary to produce your manuscript are properly stored. In this case, it is not clear what prevents you from adequately storing and sharing the ISORROPIA code in a repository we can accept. Maybe the license of such code imposes restrictions; however, given the way in which it is made available and distributed, it is not possible to know. Therefore, if the ISORROPIA license does not prohibit storing and sharing the code, you must do so in a repository we can accept. In both cases, for ORACLE v1.0 and ISORROPIA, you must reply to this comment with the links to the new repositories and the permanent identifiers (DOI, handle, etc.) for them.Following the chief editor’s suggestion, we have posted the version of the code developed in this study in: https://doi.org/10.5281/zenodo.19186090. This includes the ORACLE v1.0 as implemented in this work and the ISORROPIA-lite used in the simulations, both integrated within the EC-Earth3-AerChem model configuration. We note however, that open access to the full model configuration is not possible due to inclusion of third-party components from the EC-Earth3-AerChem model, specifically the ECMWF Integrated Forecasting System (IFS), which cannot be shared without a license agreement. In this work, EC-Earth3-AerChem is used in both online and offline modes, with the offline configuration referred to as the TM5-MP simulation in the manuscript. We also note that the ISORROPIA-lite code is distributed separately by its developer and we do not hold the rights to re-publish it as open access. Therefore, the Ζenodo archive has restricted access to preserve the exact code used in EC-Earth for this study, while adhering to third-party licensing restrictions. A permanent DOI has been assigned that includes all the materials developed by the authors necessary to reproduce the ORACLE v1.0 implementation described in the manuscript. The code availability section has been revised accordingly, and previous references related to obtaining ORACLE via MESSy and to the downloading of ISORROPIA have been removed.
(3) Regarding the data, you have stored them in sites that we cannot accept (colostate.edu and nilu.no), as they do not fulfil GMD’s requirements for a persistent data archive because:
-They do not appear to have a published policy for data preservation over many years or decades (some flexibility exists over the precise length of preservation, but the policy must exist).
-They do not appear to have a published mechanism for preventing authors from unilaterally removing material. Archives must have a policy which makes removal of materials only possible in exceptional circumstances and subject to an independent curatorial decision,
-They do not appear to issue a persistent identifier such as a DOI or Handle for each precise dataset.
Therefore, you must store your data in a repository acceptable according to our policy. If we have missed a published policy which does in fact address this matter satisfactorily, please post a response linking to it. If you have any questions about this issue, please post them in a reply.
We have followed the suggestion of the chief editor and posted on Zenodo the data used for the evaluation of the model and added the corresponding DOI in the data availability section. The permanent DOI is: https://doi.org/10.5281/zenodo.19185962.Citation: https://doi.org/10.5194/egusphere-2026-37-AC1
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AC1: 'Reply on CEC1', Spyros Pandis, 04 Apr 2026
Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2026-37', Anonymous Referee #1, 20 Feb 2026
The manuscript “Implementation of the ORACLE (v1.0) organic aerosol composition and evolution module into the EC-Earth3-AerChem model” by Kakavas et al. describes briefly the implementation ORACLE (v1.0) organic aerosol model in TM5-MP atmospheric chemistry model. It is analyzed and evaluated using it as a standalone model driven with reanalysis data as well as coupled to EC-Earth3-AerChem Earth system model.
The manuscript fits in the scope of the journal addressing the need for a computationally efficient and scientifically accurate description for organic aerosol. It presents a novel implementation of ORACLE-lite module into TM5-MP which shows improvements in simulated OA concentrations in both configurations it is evaluated. Methods are scientifically valid, although the manuscript relies on its description a lot on previous papers published on ORACLE-lite. However, for example Pandis et al. (1993) paper is behind a pay wall. The results mainly support the interpretations and conclusions. The description could be more detailed so that the reader shouldn’t have to go through so much of previous publications on ORACLE. The paper is well structured, the language is fluent and precise.
I can recommend publishing the paper after the following issues have been addressed:
- Line 88: “ORACLE reduces the computational cost by utilizing a small number of surrogate OA species by employing a novel lumping method.”. When compared to what?
- Line 116: There is a description paper by van Noije et al., (2023) on this EC-Earth3-Aerchem which might be a more appropriate reference for this model. In addition, Döscher citation is for year 2021, but the reference is 2022.
- Lines 180-186: “Note however, that the SOA formation from biogenic VOC emissions (isoprene and monoterpenes) is already represented in the models, as described by Bergman et al. (2022), while SOA formation from anthropogenic VOC emissions is neglected. As a result, the number of surrogate species used to represent OA and its volatility in ORACLE-lite was reduced from 18 to 9. An overview of the characteristics of the lite configuration of the ORACLE module used in this study is shown in Table 1.” This is unclear what is meant by this. Is SOA formation from biogenic VOC emissions treated separately using the approach by Bergman et al. (2022)?
- It is also unclear how OA is partitioned between different modes. Pandis et al., (1993) is referred to, but I don’t have the access to the paper.
- Are SOA species affecting aerosol radiative properties? If so, what assumptions have been used for optical properties?
- Do SOA species affect cloud droplet activation in EC-Earth?
- Line 231: “data were available from only 3 stations for the simulated period.” Could you have used data for another year or ran a year that would have more station data?
- Page 9: Emissions between TM5-MP and EC-Earth look remarkably similar. Is there a good reason to show both of them? It would also be good to use some other colormap and scale, and put them in the same figure to see if there are any differences. Jet colormap is also not recommended in modern data visualization. The same comment applies to Figure 3.
- Lines 456-458: “The incorporation of ORACLE-lite significantly improved the representation of OA formation and atmospheric behavior both in the standalone TM5-MP and the EC-Earth.“ This is an inaccurate sentence since the default TM5-MP does not simulate OA formation, rather they emit OA as primary particles. In addition, overall significance of improvement depends on which evaluation metrics we are looking at in Table 3. Bias shows clear decrease, but different error metrics not necessarily.
- Lines 477-479: “The seasonal and spatial variability of SOA was also better captured, with higher concentrations predicted in regions with intense biomass burning and anthropogenic activity, such as India, China, and sub-Saharan Africa.” How do you determine better seasonal and spatial variability? To me, these are not evident from the manuscript.
Citation: https://doi.org/10.5194/egusphere-2026-37-RC1 -
AC2: 'Reply to the Comments of Referee 1', Spyros Pandis, 04 Apr 2026
General comments
(1) The manuscript “Implementation of the ORACLE (v1.0) organic aerosol composition and evolution module into the EC-Earth3-AerChem model” by Kakavas et al. describes briefly the implementation ORACLE (v1.0) organic aerosol model in TM5-MP atmospheric chemistry model. It is analyzed and evaluated using it as a standalone model driven with reanalysis data as well as coupled to EC-Earth3-AerChem Earth system model. The manuscript fits in the scope of the journal addressing the need for a computationally efficient and scientifically accurate description for organic aerosol. It presents a novel implementation of ORACLE-lite module into TM5-MP which shows improvements in simulated OA concentrations in both configurations it is evaluated. Methods are scientifically valid, although the manuscript relies on its description a lot on previous papers published on ORACLE-lite. However, for example Pandis et al. (1993) paper is behind a pay wall. The results mainly support the interpretations and conclusions. The description could be more detailed so that the reader shouldn’t have to go through so much of previous publications on ORACLE. The paper is well structured, the language is fluent and precise.We appreciate the positive assessment of our work by the reviewer. We have tried to address all comments of the reviewer and to improve the paper accordingly. We have followed the suggestion of the reviewer and added a more detailed description of the ORACLE module in the corresponding section of the manuscript. Our responses (in regular font) and the corresponding changes in the manuscript follow each comment of the reviewer (in italics).
Specific comments
(2) Line 88: “ORACLE reduces the computational cost by utilizing a small number of surrogate OA species by employing a novel lumping method.”. When compared to what?We have rewritten the sentence to clarify the basis of the comparison.
(3) Line 116: There is a description paper by van Noije et al., (2023) on this EC-Earth3-Aerchem which might be a more appropriate reference for this model. In addition, Döscher citation is for year 2021, but the reference is 2022.
We have followed the reviewer’s suggestion by adding the reference to van Noije et al. (2021) and correcting the Döscher citation year to 2022.
(4) Lines 180-186: “Note however, that the SOA formation from biogenic VOC emissions (isoprene and monoterpenes) is already represented in the models, as described by Bergman et al. (2022), while SOA formation from anthropogenic VOC emissions is neglected. As a result, the number of surrogate species used to represent OA and its volatility in ORACLE-lite was reduced from 18 to 9. An overview of the characteristics of the lite configuration of the ORACLE module used in this study is shown in Table 1.” This is unclear what is meant by this. Is SOA formation from biogenic VOC emissions treated separately using the approach by Bergman et al. (2022)?
This is correct. SOA formation from biogenic VOC emissions is treated separately in the model using the approach described by Bergman et al. (2022). To clarify this point and avoid confusion, we have added a brief discussion in this section of the revised manuscript.
(5) It is also unclear how OA is partitioned between different modes. Pandis et al., (1993) is referred to, but I don’t have the access to the paper.
We have added a brief discussion in this section of the revised manuscript explaining how OA is partitioned among the different modes.
(6) Are SOA species affecting aerosol radiative properties? If so, what assumptions have been used for optical properties?
The formed SOA does interact with radiation. We have added a brief discussion of the assumed optical properties in the revised manuscript to clarify this aspect.
(7) Do SOA species affect cloud droplet activation in EC-Earth?
Yes, they do. SOA contributes to the organic aerosol mass within the modal aerosol scheme (M7), so it affects aerosol growth and particle properties. As cloud droplet activation depends on aerosol size, number, and hygroscopicity, SOA indirectly influences cloud droplet activation in the model through changes in both the aerosol size distribution and composition. We have added a brief discussion in the revised manuscript.
(8) Line 231: “data were available from only 3 stations for the simulated period.” Could you have used data for another year or ran a year that would have more station data?
Following the reviewer’s suggestion, we have extended the evaluation of the results of the online simulation of EC-Earth3-AerChem for 2010, for which more observational stations are available within the EMEP framework.
(9) Page 9: Emissions between TM5-MP and EC-Earth look remarkably similar. Is there a good reason to show both of them? It would also be good to use some other colormap and scale, and put them in the same figure to see if there are any differences. Jet colormap is also not recommended in modern data visualization. The same comment applies to Figure 3.
TM5-MP and EC-Earth simulations use the same emissions. The TM5-MP emissions shown in Fig. 1 correspond to the year 2005, whereas the EC-Earth3-AerChem emissions shown in Fig. 2 represent the annual mean over 2000–2010. Following the reviewer’s suggestion, we have combined Figs. 1 and 2 into a single figure and replaced the current colormap with a more appropriate one.
(10) Lines 456-458: “The incorporation of ORACLE-lite significantly improved the representation of OA formation and atmospheric behavior both in the standalone TM5-MP and the EC-Earth.“ This is an inaccurate sentence since the default TM5-MP does not simulate OA formation, rather they emit OA as primary particles. In addition, overall significance of improvement depends on which evaluation metrics we are looking at in Table 3. Bias shows clear decrease, but different error metrics not necessarily.
We have followed the suggestion of the reviewer and changed this sentence to “The incorporation of ORACLE-lite reduced the bias of the OA predictions both in the offline and online simulations of EC-Earth3-AerChem.”.
(11) Lines 477-479: “The seasonal and spatial variability of SOA was also better captured, with higher concentrations predicted in regions with intense biomass burning and anthropogenic activity, such as India, China, and sub-Saharan Africa.” How do you determine better seasonal and spatial variability? To me, these are not evident from the manuscript.
We have removed this sentence from the revised manuscript.
Citation: https://doi.org/10.5194/egusphere-2026-37-AC2
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RC2: 'Comment on egusphere-2026-37', Anonymous Referee #2, 26 Feb 2026
The current work provides a description of the implementation of the ORACLE-lite secondary organic aerosol (SOA) formation mechanism in the TM5-MP and EC-Earth modeling systems. Accurate modeling of SOA concentrations is important for both air quality and climate purposes, even though SOA modeling is often associated with considerable uncertainty and computational cost. The implementation and evaluation described in the current work serves as a useful source of documentation, both for the currently described models and for other models that may wish to implement the ORACLE-lite module in the future. The comparison against surface observations, while limited to North America and Western Europe, is an important element of this work. I can recommend this article for publication after the below comments have been considered.
Main comment
1. The authors note that only 3 stations from the EBAS database are available for the year 2005. However, following the link provided to the EBAS database finds that PM2.5 OC measurements are available from 4 stations (one in Spain, Italy, Germany, and Norway). The Italian, German, and Norwegian sites all have nearly continuous measurements over the course of the year. The Spanish site only has two daily mean measurements per month. Given that it is typical to calculate monthly means only when around 60-70% data availability is reached, I think the measurements from the Spanish site should be excluded from the analysis. At least so long as the analysis focuses on monthly mean values.
The Italian site (Ispra) is clearly influenced by anthropogenic wood burning emissions, reaching a monthly mean OC concentration of 22 ug/m3 in January (or 40 ug/m3 OM using the employed OA/OC ratio of 1.8). This value would skew the average monthly mean across all sites (whether the Spanish site is excluded or not) beyond the average of 2.2 ug/m3 currently shown for January in Figure 8. It therefore seems like the Italian site was excluded from the analysis. However, since this is a rural site (as are the German and Norwegian sites), and since the high wintertime concentrations are likely to have large contributions from the anthropogenic biomass burning emissions (and the resulting oxygenated OA formation) that is central to the current work, it is not clear to me why this station should be excluded.
The availability of OC measurements in Europe increases greatly in later years. For example, for 2010 there are 8 stations with good data availability, whereas for 2015 there are 20. I think the simulations should at least be compared to EBAS/EMEP observations for the year 2010 (implying that a new simulation with TM5-MP would have to be performed). Ideally, however, more recent years for both the TM5-MP and EC-Earth simulations would have to be considered, preferably for 2015 or later.
If the authors decide to continue using the TM5-MP simulation for 2005, I think the stations in Germany (Melpitz), Italy (Ispra), and Norway (Birkenes) should be evaluated in detail on an individual basis rather than as the average across all three sites.
Minor comments
1. It would be helpful if the ORACLE-lite description would be expanded to make the article more self-contained, even though more detailed descriptions can be found in the cited works. For example, it would be helpful if the K_OH rates that modify the volatility of the emitted organic compounds are included in Table 1.
2. Could the motivation behind neglecting SOA formation from anthropogenic VOC emissions be expanded? These are said to contribute only 15% to total global average surface OA concentrations, but this seems like a considerable amount (similar also to the calculated annual SOA-sv mass, roughly based on Table S1). The measurements are also underestimated by 8-13% with the current ORACLE-lite setup, suggesting that the additional SOA from VOCs would improve/reduce the model bias. The current runtime increase of 8% seems modest. How much slower would the model become with the addition of SOA from anthropogenic VOCs?
3. When the IMPROVE network is introduced, it would be helpful if it is mentioned that the main purpose of the network is to measure aerosols in remote areas of the United States, with the measurements therefore being representative of rural conditions.
4. The authors mention that measurements of OC are converted to OA using an OA/OC ratio of 1.8, while the traditional model setup is to assume that OA from all emission sources (treated as POA) has a ratio of 1.6. For reference, it would be helpful to include a description of the OA/OC ratios calculated/assumed using ORACLE-lite, and the resulting calculated ratios of the total OA.
5. In Fig. S13, could the y-axis be changed to show hPa rather than model level? Currently it is difficult to make out the vertical scales.
Editorial
ECMWF is defined on both lines 120 and 131.
SOA-sv is said to correspond to a C* value of 10^-2 ug/m3 on line 332. However, Table 1 shows a value of 10^1 ug/m3.
Citation: https://doi.org/10.5194/egusphere-2026-37-RC2 -
AC3: 'Response to the Comments of Reviewer 2', Spyros Pandis, 04 Apr 2026
General comments
(1) The current work provides a description of the implementation of the ORACLE-lite secondary organic aerosol (SOA) formation mechanism in the TM5-MP and EC-Earth modeling systems. Accurate modeling of SOA concentrations is important for both air quality and climate purposes, even though SOA modeling is often associated with considerable uncertainty and computational cost. The implementation and evaluation described in the current work serves as a useful source of documentation, both for the currently described models and for other models that may wish to implement the ORACLE-lite module in the future. The comparison against surface observations, while limited to North America and Western Europe, is an important element of this work. I can recommend this article for publication after the below comments have been considered.
We appreciate the positive assessment of our work by the reviewer. We have tried to address all comments and to improve the paper accordingly. Our responses (in regular font) and the corresponding changes in the manuscript follow each comment of the reviewer (in italics).
(2) The authors note that only 3 stations from the EBAS database are available for the year 2005. However, following the link provided to the EBAS database finds that PM2.5 OC measurements are available from 4 stations (one in Spain, Italy, Germany, and Norway). The Italian, German, and Norwegian sites all have nearly continuous measurements over the course of the year. The Spanish site only has two daily mean measurements per month. Given that it is typical to calculate monthly means only when around 60-70% data availability is reached, I think the measurements from the Spanish site should be excluded from the analysis. At least so long as the analysis focuses on monthly mean values. The Italian site (Ispra) is clearly influenced by anthropogenic wood burning emissions, reaching a monthly mean OC concentration of 22 μg/m3 in January (or 40 μg/m3 OM using the employed OA/OC ratio of 1.8). This value would skew the average monthly mean across all sites (whether the Spanish site is excluded or not) beyond the average of 2.2 μg/m3 currently shown for January in Figure 8. It therefore seems like the Italian site was excluded from the analysis. However, since this is a rural site (as are the German and Norwegian sites), and since the high wintertime concentrations are likely to have large contributions from the anthropogenic biomass burning emissions (and the resulting oxygenated OA formation) that is central to the current work, it is not clear to me why this station should be excluded. The availability of OC measurements in Europe increases greatly in later years. For example, for 2010 there are 8 stations with good data availability, whereas for 2015 there are 20. I think the simulations should at least be compared to EBAS/EMEP observations for the year 2010 (implying that a new simulation with TM5-MP would have to be performed). Ideally, however, more recent years for both the TM5-MP and EC-Earth simulations would have to be considered, preferably for 2015 or later. If the authors decide to continue using the TM5-MP simulation for 2005, I think the stations in Germany (Melpitz), Italy (Ispra), and Norway (Birkenes) should be evaluated in detail on an individual basis rather than as the average across all three sites.
This is a valid point. The OC measurements at the Ispra (Italy) station are systematically high (reaching up to 22 µg m−3 in winter), which strongly influences the multi-site monthly mean shown in Fig. 8 due to the limited number of available stations for 2005. For this reason, and to avoid the average being dominated by a single site, Ispra was excluded from the statistical analysis. This is now clarified in the revised manuscript. Also, we have followed the suggestion of the reviewer and added the evaluation of EC-Earth3-AerChem for the year 2010 in the revised manuscript, when more observational stations are available. Since the differences in predicted OA concentrations between TM5-MP and EC-Earth are relatively small, we consider that performing an additional TM5-MP simulation for 2010 is not necessary for the purposes of this comparison. A brief discussion has been added in the corresponding section of the manuscript.
Specific comments
(3) It would be helpful if the ORACLE-lite description would be expanded to make the article more self-contained, even though more detailed descriptions can be found in the cited works. For example, it would be helpful if the K_OH rates that modify the volatility of the emitted organic compounds are included in Table 1.
We have followed the suggestion of the reviewer and expanded the description of ORACLE-lite to make the manuscript more self-contained and added the corresponding reaction rate constants of SVOCs and IVOCs with OH to the revised manuscript.
(4) Could the motivation behind neglecting SOA formation from anthropogenic VOC emissions be expanded? These are said to contribute only 15% to total global average surface OA concentrations, but this seems like a considerable amount (similar also to the calculated annual SOA-sv mass, roughly based on Table S1). The measurements are also underestimated by 8-13% with the current ORACLE-lite setup, suggesting that the additional SOA from VOCs would improve/reduce the model bias. The current runtime increase of 8% seems modest. How much slower would the model become with the addition of SOA from anthropogenic VOCs?
This is a point that deserves additional discussion. Although the additional SOA formed from anthropogenic VOCs could improve the model bias, ORACLE-lite was originally developed for use with the SAPRC family of gas-phase mechanisms. In contrast, TM5-MP and EC-Earth3-AerChem employ a modified CB05 chemical mechanism, which uses a different lumping structure for anthropogenic VOCs than that assumed in ORACLE. As a result, the direct inclusion of anthropogenic SOA formation within the current ORACLE-lite framework is complex and requires additional development. This will be the topic of future work. This point is now explained in the revised manuscript.
(5) When the IMPROVE network is introduced, it would be helpful if it is mentioned that the main purpose of the network is to measure aerosols in remote areas of the United States, with the measurements therefore being representative of rural conditions.
We have followed the reviewer’s suggestion and clarified in the revised manuscript that the IMPROVE network measures aerosols in remote areas of the United States and as a result is representative of rural conditions.
(6) The authors mention that measurements of OC are converted to OA using an OA/OC ratio of 1.8, while the traditional model setup is to assume that OA from all emission sources (treated as POA) has a ratio of 1.6. For reference, it would be helpful to include a description of the OA/OC ratios calculated/assumed using ORACLE-lite, and the resulting calculated ratios of the total OA.
In the present application, SVOCs and IVOCs undergo up to two generations of oxidation, with a 22.5% mass increase in each generation. Assuming an initial OM/OC ratio of 1.2 in ORACLE-lite, this leads to a final OM/OC ratio of up to 1.8, which is within the observed range for oxygenated organic aerosol (OM/OC: 1.8–2.4; Aiken et al., 2008). This is now explained in the revised manuscript.
(7) In Fig. S13, could the y-axis be changed to show hPa rather than model level? Currently it is difficult to make out the vertical scales.
We have followed the reviewer’s suggestion and changed the y-axis in Fig. S13 to show pressure (hPa) instead of model levels in the revised manuscript.
(8) ECMWF is defined on both lines 120 and 131.
The duplicate definition of ECMWF in line 131 has been removed in the revised manuscript.
(9) SOA-sv is said to correspond to a C* value of 10-2 µg/m3 on line 332. However, Table 1 shows a value of 101 µg/m3.
This is a misunderstanding. The value in Table 1 refers to the initial representative volatility bin of the emitted species, not to the volatility after aging. We have clarified this point in Table 1 of the revised manuscript to avoid confusion.
References
Aiken, A. C., DeCarlo, P. F., Kroll, J. H., Worsnop, D. R., Huffman, J. A., Docherty, K. S., Ulbrich, I. M., Mohr, C., Kimmel, J. R., Sueper, D., Sun, Y., Zhang, Q., Trimborn, A., Northway, M., Ziemann, P. J., Canagaratna, M. R., Onasch, T. B., Alfarra, M. R., Prevot, A. S. H., Dommen, J., Duplissy, J., Metzger, A., Baltensperger, U., and Jimenez, J. L.: O/C and OM/OC ratios of primary, secondary, and ambient organic aerosols with high-resolution time-of-flight aerosol mass spectrometry, Environ. Sci. Technol., 42, 4478–4485, doi: 10.1021/es703009q, 2008.
Bergman, T., Makkonen, R., Schrödner, R., Swietlicki, E., Phillips, V. T. J., Le Sager, P., and van Noije, T.: Description and evaluation of a secondary organic aerosol and new particle formation scheme within TM5-MP v1.2, Geosci. Model Dev., 15, 683–713, doi: 10.5194/gmd-15-683-2022, 2022.
van Noije, T., Bergman, T., Le Sager, P., O'Donnell, D., Makkonen, R., Gonçalves-Ageitos, M., Döscher, R., Fladrich, U., von Hardenberg, J., Keskinen, J.-P., Korhonen, H., Laakso, A., Myriokefalitakis, S., Ollinaho, P., Pérez García-Pando, C., Reerink, T., Schrödner, R., Wyser, K., and Yang, S.: EC-Earth3-AerChem: a global climate model with interactive aerosols and atmospheric chemistry participating in CMIP6 , Geosci. Model Dev., 14, 5637–5668, doi: 10.5194/gmd-14-5637-2021, 2021.
Citation: https://doi.org/10.5194/egusphere-2026-37-AC3
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AC3: 'Response to the Comments of Reviewer 2', Spyros Pandis, 04 Apr 2026
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CEC1: 'Comment on egusphere-2026-37 - No compliance with the policy of the journal', Juan Antonio Añel, 11 Mar 2026
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
Specifically, you have not shared the ORACLE v1.0 code. In the Code Availability section of your manuscript, you refer to the MESSy code to get access to it. This does not comply with our policy, first, because you need to provide access to the module that you use, not a full model containing it, and secondly, because it is not clear what kind of restriction prevents you from sharing the ORACLE v1.0 code. The MESSy code is not shared openly due to legacy issues that, it is our understanding, do not apply to the ORACLE v1.0 module. Actually, one of you, Dr. Alexandra Tsimpidi, is the author of the first paper published years ago in Geosci. Model Dev. describing it. Under such circumstances, we wonder what kind of restriction applies here that prevents you from releasing the ORACLE v1.0 code. Therefore, you have to publish the code for the ORACLE v1.0 module in an open repository we can accept, or clarify which legal mandate or rule prevents you from sharing it.Secondly, you provide a link to the ISORROPIA code, which can be downloaded from there. Unfortunately, the linked site does not meet the minimum requirements to be considered a trusted long-term repository for scientific publication. Also, the terms of use for the code mentioned on the linked webpage are not available. It is your obligation to ensure that all the elements necessary to produce your manuscript are properly stored. In this case, it is not clear what prevents you from adequately storing and sharing the ISORROPIA code in a repository we can accept. Maybe the license of such code imposes restrictions; however, given the way in which it is made available and distributed, it is not possible to know. Therefore, if the ISORROPIA license does not prohibit storing and sharing the code, you must do so in a repository we can accept.In both cases, for ORACLE v1.0 and ISORROPIA, you must reply to this comment with the links to the new repositories and the permanent identifiers (DOI, handle, etc.) for them.Regarding the data, you have stored them in sites that we can not accept (colostate.edu and nilu.no), as they do not fulfil GMD’s requirements for a persistent data archive because:
- They do not appear to have a published policy for data preservation over many years or decades (some flexibility exists over the precise length of preservation, but the policy must exist).
- They do not appear to have a published mechanism for preventing authors from unilaterally removing material. Archives must have a policy which makes removal of materials only possible in exceptional circumstances and subject to an independent curatorial decision,
- They do not appear to issue a persistent identifier such as a DOI or Handle for each precise dataset.Therefore, you must store your data in a repository acceptable according to our policy. If we have missed a published policy which does in fact address this matter satisfactorily, please post a response linking to it. If you have any questions about this issue, please post them in a reply
The GMD review and publication process depends on reviewers and community commentators being able to access, during the discussion phase, the code and data on which a manuscript depends, and on ensuring the provenance of replicability of the published papers for years after their publication. Please, therefore, publish your code and data in one of the appropriate repositories and reply to this comment with the relevant information (link and a permanent identifier for it (e.g. DOI)) as soon as possible. We cannot have manuscripts under discussion that do not comply with our policy.
The 'Code and Data Availability’ section must also be modified to cite the new repository locations, and corresponding references added to the bibliography.
I must note that if you do not fix these problems, we cannot continue with the peer-review process or accept your manuscript for publication in GMD.
Juan A. Añel
Geosci. Model Dev. Executive EditorCitation: https://doi.org/10.5194/egusphere-2026-37-CEC1 -
AC1: 'Reply on CEC1', Spyros Pandis, 04 Apr 2026
General comments
(1) 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
We have tried to address all comments of the chief editor. Our responses and corresponding changes to the manuscript (in blue) follow each comment of the reviewer (in black).
Specific comments
(2) Specifically, you have not shared the ORACLE v1.0 code. In the Code Availability section of your manuscript, you refer to the MESSy code to get access to it. This does not comply with our policy, first, because you need to provide access to the module that you use, not a full model containing it, and secondly, because it is not clear what kind of restriction prevents you from sharing the ORACLE v1.0 code. The MESSy code is not shared openly due to legacy issues that, it is our understanding, do not apply to the ORACLE v1.0 module. Actually, one of you, Dr. Alexandra Tsimpidi, is the author of the first paper published years ago in Geosci. Model Dev. describing it. Under such circumstances, we wonder what kind of restriction applies here that prevents you from releasing the ORACLE v1.0 code. Therefore, you have to publish the code for the ORACLE v1.0 module in an open repository we can accept, or clarify which legal mandate or rule prevents you from sharing it. Secondly, you provide a link to the ISORROPIA code, which can be downloaded from there. Unfortunately, the linked site does not meet the minimum requirements to be considered a trusted long-term repository for scientific publication. Also, the terms of use for the code mentioned on the linked webpage are not available. It is your obligation to ensure that all the elements necessary to produce your manuscript are properly stored. In this case, it is not clear what prevents you from adequately storing and sharing the ISORROPIA code in a repository we can accept. Maybe the license of such code imposes restrictions; however, given the way in which it is made available and distributed, it is not possible to know. Therefore, if the ISORROPIA license does not prohibit storing and sharing the code, you must do so in a repository we can accept. In both cases, for ORACLE v1.0 and ISORROPIA, you must reply to this comment with the links to the new repositories and the permanent identifiers (DOI, handle, etc.) for them.Following the chief editor’s suggestion, we have posted the version of the code developed in this study in: https://doi.org/10.5281/zenodo.19186090. This includes the ORACLE v1.0 as implemented in this work and the ISORROPIA-lite used in the simulations, both integrated within the EC-Earth3-AerChem model configuration. We note however, that open access to the full model configuration is not possible due to inclusion of third-party components from the EC-Earth3-AerChem model, specifically the ECMWF Integrated Forecasting System (IFS), which cannot be shared without a license agreement. In this work, EC-Earth3-AerChem is used in both online and offline modes, with the offline configuration referred to as the TM5-MP simulation in the manuscript. We also note that the ISORROPIA-lite code is distributed separately by its developer and we do not hold the rights to re-publish it as open access. Therefore, the Ζenodo archive has restricted access to preserve the exact code used in EC-Earth for this study, while adhering to third-party licensing restrictions. A permanent DOI has been assigned that includes all the materials developed by the authors necessary to reproduce the ORACLE v1.0 implementation described in the manuscript. The code availability section has been revised accordingly, and previous references related to obtaining ORACLE via MESSy and to the downloading of ISORROPIA have been removed.
(3) Regarding the data, you have stored them in sites that we cannot accept (colostate.edu and nilu.no), as they do not fulfil GMD’s requirements for a persistent data archive because:
-They do not appear to have a published policy for data preservation over many years or decades (some flexibility exists over the precise length of preservation, but the policy must exist).
-They do not appear to have a published mechanism for preventing authors from unilaterally removing material. Archives must have a policy which makes removal of materials only possible in exceptional circumstances and subject to an independent curatorial decision,
-They do not appear to issue a persistent identifier such as a DOI or Handle for each precise dataset.
Therefore, you must store your data in a repository acceptable according to our policy. If we have missed a published policy which does in fact address this matter satisfactorily, please post a response linking to it. If you have any questions about this issue, please post them in a reply.
We have followed the suggestion of the chief editor and posted on Zenodo the data used for the evaluation of the model and added the corresponding DOI in the data availability section. The permanent DOI is: https://doi.org/10.5281/zenodo.19185962.Citation: https://doi.org/10.5194/egusphere-2026-37-AC1
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AC1: 'Reply on CEC1', Spyros Pandis, 04 Apr 2026
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- 1
Stylianos Kakavas
Alexandra P. Tsimpidi
Vlassis A. Karydis
Spyros N. Pandis
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(2182 KB) - Metadata XML
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Supplement
(2330 KB) - BibTeX
- EndNote
- Final revised paper
The manuscript “Implementation of the ORACLE (v1.0) organic aerosol composition and evolution module into the EC-Earth3-AerChem model” by Kakavas et al. describes briefly the implementation ORACLE (v1.0) organic aerosol model in TM5-MP atmospheric chemistry model. It is analyzed and evaluated using it as a standalone model driven with reanalysis data as well as coupled to EC-Earth3-AerChem Earth system model.
The manuscript fits in the scope of the journal addressing the need for a computationally efficient and scientifically accurate description for organic aerosol. It presents a novel implementation of ORACLE-lite module into TM5-MP which shows improvements in simulated OA concentrations in both configurations it is evaluated. Methods are scientifically valid, although the manuscript relies on its description a lot on previous papers published on ORACLE-lite. However, for example Pandis et al. (1993) paper is behind a pay wall. The results mainly support the interpretations and conclusions. The description could be more detailed so that the reader shouldn’t have to go through so much of previous publications on ORACLE. The paper is well structured, the language is fluent and precise.
I can recommend publishing the paper after the following issues have been addressed: