Adding PPN photolysis

[bexhorner]

Name and Institution (Required)

Name: Bex Horner, @eamarais
Institution: University College London (UCL)

Describe the update

This update adds the PPN photolysis reaction to KPP as outlined in Horner et al. (2024).

PAN + OH and PPN + OH reactions are added using the structure-activity relationship approach.

The maximum number of J-values is increased to account for PPN photolysis.

Expected changes

NO2 concentrations will increase in the upper troposphere by ~30-60 pptv where PPN is abundant and thermally stable.

Reference(s)

Horner et al. 2024. "Vertical profiles of global tropospheric nitrogen dioxide (NO2) obtained via cloud-slicing" (https://doi.org/10.5194/egusphere-2024-1541)

[yantosca]

Thanks @bexhorner for this update. I have a couple of comments:

1. Can you remove the .DS_Store file? This is a binary file, and we try to avoid adding those to Git repos. See this link for more info on how to delete a file from a PR: https://stackoverflow.com/questions/9498201/delete-file-from-pull-request-on-github/9498304#9498304

2. Would you be able add a note to the KPP/fullchem/CHANGELOG_fullchem.md about this update?

3. Can you add the same updates in KPP/fullchem/fullchem.eqn to KPP/custom/custom.eqn? We try to keep these synchronized.

Thanks!

[yantosca]

Thanks @bexhorner! We can try to get this into 14.5.0.

[lizziel]

According to geoschem/Cloud-J#21, this update will also require updates to input files FJX_j2j.dat and FJX_spec.dat. I am going to close that PR since the updates should go into a new folder in the Cloud-J directory of ExtData/CHEM_INPUTS rather than the Cloud-J example tables.

@bexhorner, could you post the FJX_j2j.dat and FJX_spec.dat files are you using for your testing? If you add extension .txt you can drag and drop them into the GitHub comment box on this page.

[bexhorner]

@lizziel

FJX_j2j.txt
FJX_spec.txt

[lizziel]

This will only apply when running with FAST-JX, which is non-default except for the mercury simulation. Currently the max number of J-values is hard-coded in Cloud-J. Restructuring the memory is on the todo list so that we can instead pass it from the parent model.

Could you confirm that your tests used FAST-JX rather than Cloud-J? If using Cloud-J then this line needs to change: https://github.com/geoschem/Cloud-J/blob/03313bb6acde16a9962c3a5e18a3f78b4d220faa/src/Core/cldj_cmn_mod.F90#L47

[eamarais]

yeah, @lizziel, changes were made with FAST-JX, so our updates will be missing changes specific to CLOUD-J.

[lizziel]

Okay, so the input files provided were not used for testing. They appear to be modifications of the Cloud-J tables files which do not include all GEOS-Chem species. We can look at the changes only and create Cloud-J input files that would work.

[bexhorner]

@lizziel so the changes were made using FAST-JX and tested using the files below. The files I sent previously were applying the modifications used here to the Cloud-J tables.

FJX_j2j.txt
FJX_spec.txt