the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Implementation of the reduced complexity model InMAP at urban scale using a high-resolution WRF-Chem simulation
Abstract. Most of the population globally lives in areas exceeding prior and current WHO guidelines for fine particulate matter (PM2.5), highlighting the persisting need for implementing emission reduction strategies. Given the complex transport and transformation processes that airborne species undergo in the atmosphere, chemical transport models can aid in designing and prioritizing air pollution mitigation actions. However, detailed chemical transport models often require substantial computational power and expertise. For that reason, reduced complexity models have emerged as an alternative, incorporating some of the information from chemical transport models while drastically reducing the technical complexity and computational demand. In this work, we build a local implementation of the Intervention Model For Air Pollution, InMAP, at high spatial resolution for a large urban area, in Bogotá, Colombia. As input for the reduced complexity model, we carried out a detailed 12-month simulation with the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) version 4.1. To achieve sufficiently high spatial-resolution for urban air quality, the model was configured with three nested domains of 27x27 km, 9x9 km, and 3x3 km respectively. When compared with surface station data, the modeled annual mean PM2.5 showed a +3.3 % overestimation at the city-scale. Furthermore, the WRF-Chem simulation accurately captured the structure of the observed PM2.5 time series at daily, weekly and seasonal time-scales. The InMAP base fields showed a slight under-prediction relative to WRF-Chem, but overall, the correlation between the WRF-Chem and InMAP modeled PM2.5 fields was high, with R2 = 0.92. InMAP sensitivity was tested for three emission reduction scenarios of varying complexity, by comparing the marginal concentrations against simulations with the full chemical transport model. The scenarios ranged in complexity, from primary-PM reductions only, to scenarios exploring moderate and severe city-wide emissions reductions from diesel powered mobile sources. Although InMAP marginal PM2.5 fields were linearly correlated with the corresponding WRF-Chem sensitivities, a strong overestimation in predicted PM2.5 variations were shown for all emission reduction scenarios considered. For the simpler scenarios where only primary PM was reduced InMAP sensitivity was a factor of 2 that of WRF-Chem, while for the more complex emission reduction scenarios involving also reduction in gas-phase emissions, InMAP overestimated PM2.5 concentrations by a factor of 5. The driver in InMAPs overestimated PM2.5 sensitivity in the scenarios involving gas-phase precursors was a large overestimation of secondary organic aerosols and particulate nitrate. The results of this work suggest that InMAP can be used to scan for potential emission reduction scenarios at the urban-scale, specially when those scenarios involve mostly primary PM emission reductions. However, our analysis indicates that studies aiming to carry out assessments using the absolute reductions in concentration from InMAP should first calibrate its sensitivities against a full chemical transport model run.
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CEC1: 'Comment on egusphere-2026-797 - No compliance with the policy of the journal', Juan Antonio Añel, 28 Mar 2026
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AC1: 'Reply on CEC1', Ricardo Morales, 30 Mar 2026
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Dear Editor.
We fully regret having missed that specific guideline. We, as authors, made a best effort to comply with the guidelines. Furthermore, the manuscript submission process to GMD involves an editorial revision and quality-assurance step before any manuscript is published for discussions. Our manuscript, of course, went through the same scrutiny as all the others submitted to the journal. Unfortunately, the issues pointed out in your comment were not brought to our attention during that phase and we are now confronted with this time-constrained situation. Had we been made aware of these issues prior to the public discussion phase, we would have acted to correct them without rushing the process.
Our manuscript was submitted as a "development and technical paper". In the GMD description for this type of manuscript states: “In the case where new code is described in the paper, this is subject to the same availability requirements as for complete model descriptions.” Since our manuscript does not indeed describe new code per-se, we erroneously interpreted the statement as implying that it was not necessary to publish the codes. Now that we have been pointed towards this oversight, we will of course, correct it.
Moving on, and to ensure that we can correct these issues properly, we would appreciate clarity on two specific points:
(1) The editor comment states that we (the authors) will be allowed “a short time to solve the situation”. Could the Editor be more specific about the time constraints on this? We want to ensure that there are no mishaps in the process, and for that we would appreciate at least a two-week period to comply with it, while ensuring the quality and traceability of the process.
(2) On the suitability or lack thereof of the institutional data repository from Universidad de los Andes: With the purpose of reducing these types of barriers to publication often caused by the lack of access to quality data repositories, University of the Andes in Bogotá, Colombia, a few years ago made available to its researchers exactly that: a reliable, high quality, free of charge, repository which is managed by the Library System of the institution. As such, authors do not have access to edit, add, or remove files from that repository, and the process is done entirely by personnel of the Library System. Although we would much prefer the data to be stored in a system such as that one, we will be looking for alternatives that are accessible to us, given financial and geographical constraints. We, however, consider that these types of barriers will most definitely not help in closing the persistent gaps between research produced in the Global South and will instead likely prevent that type of research from reaching these great forums, such as the one provided by GMD. Within the two-week framework stated above, we aim to either provide GMD with assurances of the suitability of the UniAndes repository, or find another one, if possible.
We look forward to your clear answers to the questions above.
On behalf of the co-authors,
Ricardo Morales (corresponding author).
Citation: https://doi.org/10.5194/egusphere-2026-797-AC1 -
CEC2: 'Reply on AC1', Juan Antonio Añel, 01 Apr 2026
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Dear authors,
Thanks for your reply. We fully understand the constraints to make available all the code and data requested, and we are happy to grant you the two weeks period that you mention to solve the situation. We can be flexible on this.
We are aware of many institutions around the world that along the last years have created storage systems to facilitate sharing the assets they produce. Unfortunately, often, they do not meet the necessary requirements for long-term preservation of assets linked to scientific papers. Our policy list examples of repositories that can be used and we can accept, and all of them are free of charge. If you want that we consider the Universidad de los Andes as acceptable, it must meet the requirements expressed in my previous comment, with a policy clearly published addressing the mentioned issues (including evidence of funding secured for long-term operation).
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2026-797-CEC2 -
AC2: 'Reply on CEC2', Ricardo Morales, 07 Apr 2026
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Dear editor,
Regarding the preservation and data use policies of the DataHub of Universidad de los Andes, we would like to point you towards the published policy (available online) that includes the guidelines and conditions of use for the mentioned digital repository. The guidelines can be found in the Library System webpage here: https://biblioteca.uniandes.edu.co/es/repositorio-de-datos
The PDF document with the full description of the policy, can be found here: https://biblioteca.uniandes.edu.co/sites/default/files/Lineamientos_acceso_abierto_datahub_uniandes.pdf
Key aspects from the published guidelines are highlighted here:
Section 2 (page 1): It states that the repository aligns with TRUST and FAIR principles for digital repositories.
Section 3 (page 2): Among the list of commitments stated by the University regarding the repository: “To preserve, secure, and maintain perpetual access to research data associated with the scientific and academic output of the University of the Andes, published in the Research Data Repository - DataHub”
Regarding the conditions for removal of data from the repository, the document states (Section 4, page 3): “The University reserves the right to exclude from the repository any files containing the following data: Data containing confidential information; Data that, due to its nature, cannot be published or does not meet the quality standards required by the institution; Other data for which there is no express authorization from the data owner”.
In Section 7 (page 4), the policy states also which documents the documents and conditions to which the author should agree to before submitting the data to the repository: “Deposit License: Is a document through which the author submits research data to the Library System via the Research Data Publication Support Service (SAPDI) and expressly authorizes its publication, dissemination, and access.”
Given this information, and before moving forward, we would appreciate a response, hopefully consistent with the original comment, regarding whether this repository is acceptable to GMD.
Best regards,
Ricardo Morales (on behalf of all the co-authors)
Citation: https://doi.org/10.5194/egusphere-2026-797-AC2 -
CEC3: 'Reply on AC2', Juan Antonio Añel, 10 Apr 2026
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Dear authors,
We checked the mentioned policy before commenting on your manuscript. Unfortunately, it does not address the points that I mentioned in my first comment. It does not include information on funding secured for their maintenance, minimum preservation time or policy regarding the removal by the authors. Therefore, we kindly request you to store the assets necessary to replicate your work in an acceptable repository according to the policy of the journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2026-797-CEC3
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CEC3: 'Reply on AC2', Juan Antonio Añel, 10 Apr 2026
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AC2: 'Reply on CEC2', Ricardo Morales, 07 Apr 2026
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CEC2: 'Reply on AC1', Juan Antonio Añel, 01 Apr 2026
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AC3: 'Reply on CEC1', Ricardo Morales, 20 Apr 2026
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Dear editor,
We apologize for this oversight in our original submission. We have now modified the manuscript to include a Code and Data Availability Section, with citations to suitable data repositories, in which we have deposited the source code for InMAP (including configuration files) and similarly for the specific WRF-Chem version used in the study, together with the necessary data.
References for both datasets and code repositories can be found here:
Morales Betancourt, R., Rojas Neisa, D. R., Piracoca Mayorga, A., & Espitia-Cano, S. (2026). InMAP-Bog - Input data and configuration files for InMAP [Data set]. Zenodo. https://doi.org/10.5281/zenodo.19654867
Rojas Neisa, D. R., Morales Betancourt, R., & Espitia Cano, S. O. (2026). WRF-Chem_v3.9.1 - Northern South America run for year 2018: Source code and configuration files [Data set]. Zenodo. https://doi.org/10.5281/zenodo.19655777
We have also produced a track-changes version of the manuscript to facilitate the process for the editors and reviewers.
Please, let us know the following steps to proceed with the peer review process.
Best regards,
Ricardo Morales
Citation: https://doi.org/10.5194/egusphere-2026-797-AC3 -
CEC4: 'Reply on AC3', Juan Antonio Añel, 20 Apr 2026
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Dear authors,
Many thanks for your reply. We can consider now the current version of your manuscript in compliance with the Code and Data Policy of the journal. Please, remember the new text in any potentially reviewed version of your manuscript.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2026-797-CEC4
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CEC4: 'Reply on AC3', Juan Antonio Añel, 20 Apr 2026
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AC1: 'Reply on CEC1', Ricardo Morales, 30 Mar 2026
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RC1: 'Comment on egusphere-2026-797', Anonymous Referee #1, 29 Jul 2026
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Review: Implementation of the reduced complexity model InMAP at urban scale using a high-resolution WRF-Chem simulation"
Recommendation: Major Revision
The manuscript is well-written, comprehensible and a good fit for GMD. The study presents the first implementation of the InMAP reduced complexity model (RCM) for Bogotá, supported by a WRF-Chem base simulation. The central finding that InMAP's baseline fields agree well with the driving CTM WRF (R^2 = 0.92), while marginal sensitivities to emission-reduction scenarios are overestimated by a factor of 2 (primary PM) to 5 (gas-phase precursors), is an important and relevant finding regarding the use of RCMs for policy assessment. The study is also one of the first InMAP implementations in the Global South and makes a useful methodological contribution through its locally derived emission seasonality using public-transit data as an activity proxy.
Before publication, however, (1) a discussion section (incl. some critical points to be discussed, see below) should be added to interpret the findings and put them in context, as at present there is essentially no discussion between the Results and Conclusions sections. Also, (2) some inconsistencies between the manuscript and the referenced data archives should be resolved, and (3) an analysis that is already implemented in the code and announced in the introduction (population-weighted exposure and mortality) should either be added to the manuscript or the scope in the introduction adjusted. These points are addressed below under major comments. Besides, there are also some minor comments.
Major comments
1. Missing discussion of the results
The manuscript moves directly from Results to Conclusions without interpreting the findings or putting them in context. But taking into account the differences between WRF simulations and the InMAP-BOG results, the following points should be included in a dedicated discussion section:1a. Comparison with other reduced-complexity and/or source-receptor models.
The manuscript cites InMAP-US, InMAP-China, and Global-InMAP in the introduction but does not discuss alternative RCM architectures that have already been well validated for the specific task addressed here (sensitivity to emission scenarios), such as EASIUR, APEEP, RIAT+ or GAINS (https://pmc.ncbi.nlm.nih.gov/articles/PMC6911961/ gives already a good starting point for InMAP and other RCM validation against CTMs). Maybe also to name one very policy related example from Europe in detail: The SHERPA tool by EC JRC (https://knowledge4policy.ec.europa.eu/fairmode/sherpa_en), which operates at 7 x 7 km over Europe using a statistical source-receptor approach (trained on CHIMERE CTM runs) and achieves a bias below +/-10% for sectoral reduction scenarios up to 50% reduction (e.g. https://gmd.copernicus.org/articles/13/5725/2020/gmd-13-5725-2020.pdf), which is an order of magnitude better than the factors of 2-5 found with InMAP-BOG in this study. A discussion of why InMAP's physically based, steady-state transport approach performs worse here than a statistical SRR approach would substantially strengthen the interpretation of the findings and also support the use of RCMs in general.1b. Possible causes of the overestimation.
The consistent factor of roughly 2 for primary PM across all scenarios might be a systematic bias in InMAP's simplified vertical mixing/dilution scheme rather than a random error. The additional, larger overestimation for gas-phase precursors (SOA, pNO3) could come from the fact that InMAP's equilibrium partitioning coefficients were originally calibrated for North American conditions and may not transfer readily to a high altitude (2600 m?) Andean basin with cooler and more humid conditions? The authors should discuss this or maybe alternative hypotheses regarding the source of the overestimation rather than only quantifying it.1c. Framing of the study's motivation
The Introduction explicitly justifies InMAP as a tool for regions with limited resources and expertise for running full CTMs (including the Global South). The paper's conclusion that InMAP's sensitivities must first be calibrated against a full CTM run before being trusted challenges this idea, since exactly the regions lacking CTM capacity cannot perform this calibration. This tension should be discussed. Some ideas to do so:
- A more realistic framing of the workflow: not "no CTM required," but "run a CTM once (baseline plus a few representative scenarios) to get calibration factors, then use InMAP to run many additional scenarios."
- Testing the transferability of the correction factors by applying the InMAP-BOG workflow to a second, contrasting city in SA (different altitude/topography/climate) to determine whether the factors of 2-5 are generic to InMAP or specific to Bogotá's Andean basin setting (could also help with 1b?).
- Mechanistic diagnosis of the error (vertical mixing, partitioning coefficients) directly within the InMAP code rather than a purely empirical correction.
- Testing whether a shorter calibration CTM run (e.g., 1-2 representative months rather than a full year) yields similar correction factors, which would lower the computational demand for calibration.1d. Role of the regional background in the scenarios.
The manuscript notes that biomass-burning-driven background PM2.5 from the eastern lowlands is significant but not affected by the local emission-reduction scenarios (Sections 2.1.1, 2.1.3), and that InMAP's over- or underestimations are spatially linked to this east-west topographic pattern (Fig. 3b). However, there is no discussion of how this fixed regional background is treated in InMAP's simplified transport relative to the boundary conditions of WRF runs from higher nests, and whether inconsistent treatment contributes to the observed sensitivity mismatch.1e. Justification of the chosen resolution.
The 3 km x 3 km resolution is justified by the need to resolve the sharp gradient between dense urban and rural land use. However, since PM2.5 in Bogota appears to be strongly influenced by large-scale, regional transport (especially biomass burning), a discussion of how much added value the high resolution provides specifically for PM2.5 (as opposed to more locally dominated pollutants such as NO2 or fresh primary PM especially from road traffic) would be useful (also linked to 1d).2. Data and code availability
There are some inconsistencies between the manuscript and the referenced data and code archives that should be resolved prior to publication:- WRF Version conflict: The Zenodo dataset (10.5281/zenodo.19654867, describing the InMAP-Bog dataset) states WRF-Chem v3.9.1 as the basis, whereas the manuscript consistently states WRF-Chem version 4.1 throughout (Abstract, Section 2.1.2, Table 1). Neither the namelist nor the DataHub metadata (10.71590/9RESNN) contain a version statement that resolves this. Please clarify and make consistent.
- Scope of the archived WRF-Chem data: The README of the DataHub archive (10.71590/9RESNN) describes the data provided there as daily means of the first model layer only, for aerosol species only and split by trimester. These are the data used for model evaluation (Figs. 1-2), not the full hourly 3D fields across all 41 vertical layers and the full species list from Table D1 that were used for the InMAP pre-processing. The data availability statement should clarify that not the full dataset is uploaded and available.
- Missing reference to the InMAP-Bog archive: The Zenodo dataset containing the InMAP configuration files and the modified source code is not referenced anywhere in the preprint's data availability section and should be added. Following the interactive discussion, this is probably already in preparation.
- Only one example run configuration (RPM-100) is archived, despite three scenarios are analysed in the manuscript. But the archived configuration should provide out-of-the-box run scripts before publication, given that providing a usable, reproducible implementation is one of the central contributions of this work and important for GMD.
- Also, scripts to reproduce the plots and statistical analysis are missing in the repository. Not sure if these are necessary (following GMD rules) but they would be helpful to reproduce your results.
3. Announced but unreported analysis
The Introduction (lines 76 ff.) promises an analysis of "population-weighted PM2.5 reductions" resulting from the scenarios. And the archived InMAP run configuration (config_run_d03.toml) already defines an output variable (TotalPop) that computes population-weighted excess mortality via a standard log-linear concentration-response function, using the population and baseline mortality-rate data that are also archived. But neither this calculation nor any PWE result appears anywhere in the manuscript. The authors should either add this (as it’s implemented in the code) analysis or adjust the corresponding statement in the paper’s introduction. And if the analysis was omitted by choice, it should be stated why it was omitted, as this is directly relevant to assessing the tool's practical applicability for one of the main use cases of RCMs stated in the Introduction.
Minor Comments- Section 3.3 (lines 237–239): The correlation coefficients of 0.60 (RPM-100) and 0.59 (Diesel-100) for the marginal PM2.5 fields are used in the text to support the claim that, "with a proper calibration," absolute reductions could also be estimated. Values of roughly 0.6 should be characterized as moderate rather than high.
- It should be clarified consistently throughout whether reported "correlation coefficient" values are Pearson r or R^2: the Abstract states R^2 = 0.92 for the WRF-Chem vs. In-MAP agreement, but Section 3.2 reports a "correlation coefficient of 0.99" (urban) and "0.91" (entire D03 domain) without specifying whether these are r or R^2, or exactly which spatial subset the Abstract figure refers to.
- None of the reported factor estimates (the 2x and 5x sensitivity overestimation) or performance statistics (NMB, NME, R^2) are accompanied by uncertainty ranges or confidence intervals, making it difficult to judge whether the differences between scenarios, or between InMAP and WRF-Chem, are statistically robust or are within the models' uncertainty.
Citation: https://doi.org/10.5194/egusphere-2026-797-RC1
Data sets
WRF-Chem D03 2018 base simulation R. Morales Betancourt et al. https://doi.org/10.71590/9RESNN
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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
First, your manuscript does not contain a Code Availability section, which is mandatory for manuscripts submitted to our journal. I am, but this is something unacceptable, forbidden by our policy, and your manuscript should have never been accepted for Discussions given such violation of the policy. Our policy 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 you need to provide a repository containing the WRF-Chem model and the InMAP model and the local implementation that you have developed.
In addition, you have archived the data used and produced in your work in datahub.uniandes.edu.co/ ; however, such site does not fulfil GMD’s requirements for a persistent data archive because:
- It does 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).
- It does 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,
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. Therefore, we are granting you a short time to solve this situation. Please, 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 this problem, we cannot continue with the peer-review process or accept your manuscript for publication in GMD.
Juan A. Añel
Geosci. Model Dev. Executive Editor