Short-Lived Halogen Sources and Chemistry in the Community Earth System Model v2 (CESM2-SLH)

Fernandez, Rafael Pedro; Cuevas, Carlos Alberto; Villamayor, Julián; Feinberg, Aryeh; Kinnison, Douglas E.; Vitt, Francis; Bossolasco, Adriana; Barrera, Javier A.; Reynoso, Amelia; Tomazzeli, Orlando G.; Li, Qinyi; Saiz-Lopez, Alfonso

doi:10.5194/egusphere-2025-3250

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https://doi.org/10.5194/egusphere-2025-3250

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13 Oct 2025

| 13 Oct 2025

Status: this preprint is open for discussion and under review for Geoscientific Model Development (GMD).

Short-Lived Halogen Sources and Chemistry in the Community Earth System Model v2 (CESM2-SLH)

Rafael Pedro Fernandez, Carlos Alberto Cuevas, Julián Villamayor, Aryeh Feinberg, Douglas E. Kinnison, Francis Vitt, Adriana Bossolasco, Javier A. Barrera, Amelia Reynoso, Orlando G. Tomazzeli, Qinyi Li, and Alfonso Saiz-Lopez

Abstract. The implementation of short-lived halogen (SLH) sources and atmospheric chemistry in the Community Earth System Model v1 (CESM1), has extended the capabilities of this state-of-the-art model to study how SLH chemistry alters the oxidative capacity of the atmosphere and, consequently, the Earth’s climate. In this manuscript, we summarize 15 years of research and developments of SLH chemistry in CESM1 and present a complete revision of the porting of the original SLH implementation into the latest released version of CESM (v2), hereafter CESM2-SLH. This includes a detailed description of all offline and online sources of organic and inorganic SLH, as well as the gas-phase and heterogeneous recycling of chlorine, bromine and iodine in the troposphere and stratosphere, including their species-independent atmospheric sinks. In doing so, we provide a comprehensive evaluation of how changes in model parameters and coupled dynamics within the Community Atmosphere Model v6 (CAM6) affect SLH abundances and their implications. The new CESM2-SLH implementation offers various component sets (compsets) and resolutions, all of which result in equivalent global budgets and zonal distributions of organic and inorganic chlorine, bromine and iodine, which in turn, lead to SLH impacts on atmospheric composition that are consistent with previous CESM1 results. The released CESM2-SLH version includes specific namelist options, input files and technical notes detailing the most important SLH updates implemented over the CESM2/CAM6 routines. Our results show that the global tropospheric burden and tropical stratospheric injection of organic and inorganic chlorine, bromine and iodine species in CESM2-SLH are in agreement with observational assessments and previous modelling studies using CESM1, resulting in significant reductions in global ozone abundance (−21–28 % at the surface, −17–22 % in the troposphere and −2–3 % in the stratosphere) as well as in OH and NO₂ (ranging between −2–9 % and −1–10 %, respectively), depending on the specific model configuration and resolution. Based on this, we encourage the wider CESM community to consider the released CESM2-SLH scheme to obtain a more realistic representation of the background influence of natural and anthropogenic short-lived halogen sources and chemistry in air quality and Earth’s climate studies.

Received: 08 Jul 2025 – Discussion started: 13 Oct 2025

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RC1:
'Comment on egusphere-2025-3250', Anonymous Referee #1, 08 Dec 2025 reply
The manuscript by Fernandez et al. describes the implementation of short-lived halogen chemistry already available in CESM1 into CESM2, thereby making it accessible to the broader CESM community. It provides a detailed description of the implemented SLH chemistry (incl. offline/online emissions, chemical reactions and deposition), an analysis of the SLH budgets, spatial/vertical distributions and impacts on oxidants. The analysis is very detailed and can act as benchmark evaluation for future studies using CESM2-SLH. It fits well into the scope of GMD and I see no reason why it should not be published after addressing the following minor comments.
General comments
1.
Parts of the manuscript (especially the beginning of Section 2 and Section 2.5) read a bit like a CESM user manual. The information is without doubt very useful for CESM users. However, some adaptions might help to make it easier to follow for readers outside the CESM community. The manuscript is also relatively long, so the authors might want to consider moving some more technical parts to the supplement.
Suggestions:
Abstract: Avoid using the (I think) CESM-specific term “compset” in the abstract.
l. 138 – l. 164: The authors might want to consider merging this section and Section 2.5 as some of the information is redundant (e.g. CESM branches, compsets), and it would be beneficial to have the information at the same place. Additionally, a definition/introduction of “compset” would be helpful. I understand that it is the CESM name for “simulation setup” and specifies the used BC and emissions, and settings like resolution etc.. It would be helpful if Table 6 would be referenced here (if not merged) to summarise the mentioned compsets. Additional columns could be introduced in Table 6 to explain the difference between compsets. For example, I assume that FCnudged means nudged meteorology and FCHIST historical free-running, bit it is not explained explicitly. Also the difference between FCnudged and FWnudged is not explained explicitly. What is FCASE?
l. 606: It is not clear to me what the difference between cesm2.2-asad-branch_slh and cam_cesm2_2_rel09_slh is. Could you clarify why you need two branches?
l. 610-619: Could be moved to the supplement? The information could be presented in a table listing the additional species, and if they emit, dry/wet deposit etc.
l. 662-686: Could be moved to the supplement?
Also Section 4 “Final Remarks is quite technical (e.g. l. 1602 – 1606). I think it would be valuable here to discuss if the performance of CESM2-SLH (regarding SLH budgets and impact on atmospheric composition) is similar/better/worse compared to CESM1-SLH/ CAM4-Chem, and other models including SLH chemistry.

2.
The comparison with observations is somewhat limited. In Section 3.2.2. “Evaluation of SLH Abundance with Observations” Source Gas Injection and Product Gas Injection to the stratosphere is compared to observations. It would be beneficial to extend the evaluation to SLH abundance to the (lower) troposphere, MBL or surface (for example comparison to station data). In Section 2, a comparison of VSL halocarbons to observation is mentioned (e.g. in l. 273), but no details are given.

Specific comments
l. 214: Another model with SLH chemistry would be TOMCAT (Hossaini et al., 2016; https://doi.org/10.1002/2016JD025756).

l. 241: Could you explain which VSL halocarbons are compared to observations, and add references for the surface and aircraft observations you compare to?

l. 292: Did you compare VSL chlorocarbons to observations as well (if yes, please provide more details), or is the rationale being consistent with the scaling of natural emissions?

l. 340: What is the reasoning for assuming free-regime approximation, i.e. why is diffusion not considered (Schwartz 1986)? Could it play a role for larger SSA particles?

l. 396: Could you provide the formula to calculate the yield (e.g. add it in Table 1). I could not find the formula in the referenced publication Li et al., 2022 either.

l. 520: Could you clarify what is meant by "following the HNO3 acid displacement developments from Hossaini et al., 2016"? The HNO3 acid displacement is het_ss_9, isn't it? Do you mean that a similar approach as for this reaction is used? Hossaini et al., 2016 also implemented heterogeneous recycling on non-SSA particles (e.g. their reaction 6).

l. 708: What about the study by Mirrezaei et al. (https://essopenarchive.org/doi/full/10.22541/essoar.175288325.58779694/v1). They seem to use CESM2.2.-SLH in a CH4-emission driven setup.

Figure 2 and Figure 3: Would it be possible to show the interannual variability (e.g. standard deviation) for CESM1 Cyclical_slh? Or is it negligible?

Figure 2: Could you provide a bit more context on the differences in the trends of O3, OH, and NO2 between CESM2-SLH and CESM1-SLH shown in Figure 2? You explain that these differences drive differences in the trends of halogen budgets. Are the differences of O3, OH, and NO2 mainly caused by differences in prescribed boundary conditions and emissions (e.g. NOx and VOCs) or by model updates? Are differences between CESM2 and CESM1 (without SLH) similar to the differences shown here? How do the trends compare to other models and observations (e.g. are differences between CESM1 and CESM2 small compared to inter-model differences or biases towards observations)?

l. 914: An even more recent estimate for GEOS-Chem might be given by Wang et al., 2021 (https://acp.copernicus.org/articles/21/13973/2021/)

l. 1227: Cly, Bry, and Iy are usually defined as total inorganic halogens including XOx as far as I know. Here it represents the reservoir only excluding XOx, which might be confusing. Maybe better to choose a slightly different abbreviation for the reservoir, and make clear that the striped and empty bars give total inorganic chlorine/bromine/iodine.

Table 9: This table provides really interesting information. Considering the following question might make it even more valuable:

How is stratospheric O3 defined, i.e. everything above the chemical tropopause? The footnote $ is missing.

Tropospheric mean OH could better be expressed as number concentration (in molecules cm-3) to facilitate comparison with other published estimates (e.g. multi-model comparison in Lee et al., 2021; https://doi.org/10.1073/pnas.2115204118).

How large is the interannual standard deviation compared to the difference?

How do the results compare to SLH effects in other models?

Figure 16: Panels c) and f) of Figure 16 suggests that the total ozone loss is the same in FCnudged_SLH and FCnudged_NOH, and that only the contribution of different families changes. Could you confirm that this is indeed the case? It might be worth mentioning.

l. 1618: By how much does SLH increase computing time?

Technical corrections
l. 52: "de" --> "the"

l. 53: “SLH have been shown”? SLH refers to short-lived halogens, or “SLH chemistry has been shown”?

l. 57: The acronym VSL refers to "very short-lived" only. Change to "VSL halocarbons"? Or define new acronym VSLS (for very short-lived species); same in l. 743

Table 1, Table 2 and Table 5: Rename “Molecular weight” to something more meaningful, e.g. “Molecular weight dependent factor ”. And provide units for it.

l. 606: "respectively" used twice

Caption of Figure 3 (l. 852): “compset_non” --> “compset_noh”

Table 8: How is present-day defined, i.e. average over which years is shown? Please provide the information in the caption. Units are missing for Long-lived halogens

Figure 5: “FCNudged_NON” --> “FCNudged_NOH”. Might need to check for a consistent naming of the setup without SLH in general.

Figure 7: “BRCL” --> “BrCl” typo in legend of panel b

l. 1061: Figure 10 could be referenced here as it shows the geographical distribution.

l. 1097: Figure 8 shows profiles of the absolute VMR of the species I think. The “change in inorganic halogen product gases from the Earth’s surface to the stratosphere” could be misunderstood as “difference between the Earth’s surface and the stratosphere”.

l. 228: Do you mean “summer” instead of “winter” here?

Table 10: Units missing for PO3 – LO3, drydep, and O3 STE

l. 1422: The estimates in the text (505 and 522 Tg yr-1) refer to IOx loss according to Table 10.

Table 12: Please include in the table caption which years were analysed.

l. 1618: “chemitry” --> “chemistry”

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Citation: https://doi.org/10.5194/egusphere-2025-3250-RC1
RC2: 'Comment on egusphere-2025-3250', Anonymous Referee #2, 12 Dec 2025 reply

This preprint is clearly targeted towards the Community Earth System Model (CESM) community. It presents the implementation of short-lived halogen (SLH) sources and very short-lived (VSL) halocarbons into CESM version 2.2.0. The authors demonstrate substantial expertise in this subject area.

Please see the attached file for the complete review.

Reply

Citation: https://doi.org/10.5194/egusphere-2025-3250-RC2

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Short summary

In this work we summarize 15 years of research and developments of short-lived halogens (SLH) using the Community Earth System Model (CESM) and present a complete description of the implementation and capabilities achieved with the new released version CESM2-SLH, including specific namelist options, input files and technical notes detailing the most important SLH updates that must be considered for the different model configurations and resolutions.


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