the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 04 Jan 2026
Evaluation of HNO3, SO2, and NH3 in the Surface Tiled Aerosol and Gaseous Exchange (STAGE) option in the Community Multiscale Air Quality Model version 5.3.2 against field-scale, in situ and satellite observations
Abstract. The Surface Tiled Aerosol and Gaseous Exchange (STAGE) model was developed for estimating dry deposition and bidirectional exchange for field-scale applications and use within the CMAQ v5.3.2 regional scale model. The model was evaluated against micrometeorological flux measurements of NH3, HNO3, and SO2 at a managed grassland and NH3 in a cultivated corn (Zea Mays) field. When using field-scale observations for soil and vegetation NH3 compensation points, modelled fluxes for all species agreed well, within or near the reported measurement uncertainty. However, when using the CMAQ v5.3.2 values for NH3 emission potentials at the Duke Forest grassland site, the model estimated mean net deposition rate was 1.3 ng m-2 h-1 while the observed mean NH3 evasive flux was 8.4 ng m-2 h-1. Modelled NH3 concentration fields evaluated against Cross-Track Infrared Sounder (CrIS) satellite observations indicates a broad underestimation of NH3 concentrations by approximately 1 to 2 ppb in the U.S. Great Plains. The results from the grassland field data and indicates that there is likely an underestimation of the evasive NH3 flux in grassland sites due to the model's default tabular values of the vegetation/litter NH4+ concentrations. The STAGE's model sensitivity to soil and vegetation emission potentials indicates that regional scale model results for NH3 can be further improved with additional micrometeorological flux and vegetation and soil chemistry measurements over different land use types, soil types, and vegetation phenological stages.
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Status: final response (author comments only)
- RC1: 'Comment on egusphere-2025-3536', Anonymous Referee #1, 10 Mar 2026
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RC2: 'Comment on egusphere-2025-3536', Anonymous Referee #2, 12 Mar 2026
Review for Geoscientific Model Development (GMD).
“Evaluation of HNO₃, SO₂, and NH₃ in the STAGE Option in CMAQ v5.3.2”
by J. Bash and co-authors.
This paper evaluates the Surface Tiled Aerosol and Gaseous Exchange (STAGE) dry deposition and bidirectional exchange model against field-scale micrometeorological flux measurements and satellite observations. The work addresses an important gap evaluating regional model parametrisations against site measuerment data and satellite data. The paper is generally well written and presents interesting inputs as well as practical value and operational contribution to the CMAQ modeling community. It is well in the scope of GMD.
General comments:
- The site scale box model is evaluated against two sites Duke Forest (2012) and Lillington (2007) and one season of measurement each. Ammonia flux measurements are not easily available for model comparison however, stating that these measurements are “representative” of continental forests and grassland is too much of an extrapolation. Perhaps authors can replace this statement and discuss the limitation of such an approach.
- The paper does not compare STAGE against previous CMAQ schemes or other regional models or simpler approaches thus making it difficult to quantify whether STAGE represents an improvement and whether the added complexity is justified.
- Parametrisation of ammonia emission potential or Gamma is proposed as an explanation for the difference between modelled and observed ammonia fluxes. While it is completely coherent that parameterisation with measured values would give better results than with more generalised values, no mechanistic explanation is given for that, tuning another parameter in the model would probably also have improved the performance. Furthermore, no sensitivity analysis is conducted or referred to, to justify this.
- One of the results highlites that H2O fluxes are overestimated for both sites Duke and Lillington which is argued can be explained by errors in stomatal conductance. This error can propagate to the estimation of NH3 fluxes.This is not mentioned or discussed. Again a sensitivity analysis could help answer this issue.
- The comparison to CrIS data is not sufficiently discussed. CrIS data specially for areas with low concentrations are accompanied by high uncertainty and should be discussed.
- Table 2 presents median values of measured gammas at different sites. Perhaps adding seasonal values or at least uncertainty values to give an idea of the variability of the measurements.
Specific comments:
- Axis for figures show grid indices rather than geogrphic coordinates. Perhaps replacing with lon/lat is more explanatory.
- Add an a small paragraph the logic for having a non zero valus for Gamma cuticle.
Typos and language:
- "and indicates" → "indicate" (ligne 25) ;
- "evaluate" → "evaluated" (ligne 82) ;
- "Figure 1" → "Figure 2" (ligne 291) ;
- "Sierra Nevada's" → "Sierra Nevadas" (ligne 340) ;
- "ares" → "areas" (ligne 341) ;
- "factor a of 5" → "a factor of 5" (ligne 364) ;
- "sight" → "site" (ligne 364).
Citation: https://doi.org/10.5194/egusphere-2025-3536-RC2
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General comments:
The manuscript “Evaluation of HNO3, SO2, and NH3 in the Surface Tiled Aerosol and Gaseous Exchange (STAGE) option in the Community Multiscale Air Quality Model version 5.3.2 against field-scale, in situ and satellite observations” has been submitted to the journal GMD. The research emphasizes the uncertainty in the deposition mechanism that developed based on the resistance framework for estimating NH3 flux, and the model improvement using additional micrometeorological fluxes. In general, the complex deposition component makes the approach vital for understanding model performance and, further, for improving it. However, the entire research contains two major issues. (1) The main objective seems to modify the commonly used resistance model based on the previous deposition approach. However, the reason for doing this is not clearly explained. In the Introduction, the author mentioned the emission and deposition are treated differently in the regional model. This is understandable because the sources of emissions, including anthropogenic and natural, differ. Moreover, the deposition process, which depends on land surface, particle size, and meteorological conditions, is highly variable and uncertain. The present manuscript primarily evaluates the NH3 flux by comparing micrometeorological fluxes with CMAQv5.3 tabular, which is not relevant to the literature review. Both emission flux and deposition flux need to be analyzed to address the uncertainty mentioned. Or else, simply emphasizing the limitation of CMAQ STAGE and the importance of using micrometeorological flux measurement for STAGE improvement. (2) The entire manuscript is not well written and requires proofreading. For instance, “…CMAQv5.3.2, table 2…Table 3…” in Line 304-306 is confusing.
Specific comment:
Line 18: What is the importance of this methodology? Why is micrometeorological flux measurement significant for the model evaluation and improvement? What is the main limitation of STAGE? The research question and motivation remain unclear.
Line 81-83: STAGE in CMAQv5.3 has already been publicly released. Is the present research proposing a new parameterization (e.g., new STAGE)?
Line 237: What do you mean “would be returned”?
Line 291: Figure 1 or Figure 2?
Line 295: Higher error than which site? Please revise the sentence. How can low LAI and minimal stomatal resistance affect model performance?
Line 295-298: Please revise the whole sentence!
Line 298: This seems to be a statistical error? Please use another statistical index that would exclude the effect of the outlier.
Line 307: How did you define "most sensitive"? Such a description is subjective.
Line 309: What do “NH3 observed Γll,ΓstΓdew” in Figure 3 stand for in general?
Line 325: In Figure 3, STAGE overestimates during 7-13h, and underestimates during 14-23h. This is an interesting contrast and is expected for detail explanation. Is there any possibility that NH3 flux is related to daytime meteorological factors, such as intense solar radiation?
Line 326: How well is the model performing in capturing SO2, HNO3, and NH3 after the measured soil and canopy parameters are used? Please include the statistics before and after the parameter changes.
Line 328-329: What do you mean by CMAQ tabular data? Are you referring to the default setup? How poor is the original STAGE? Pls explain with the bias or correlation index.
Line 409-410: Are you referring to Figure 4?
Technical comment:
Line 81: Two fullstop.