Update WM user guide for AQM updates

[selbigmtnwx23]

DESCRIPTION OF CHANGES:

This is an update to the WM user guide ahead of the AQM release. Only changes needed were in regards to the AQM input files that have changed names in the file aqm.rc

Additionally, this PR fixes a ReadTheDocs build failure.

Type of change

• [ X] This change requires a documentation update

TESTS CONDUCTED:

• None Required

DEPENDENCIES:

ISSUE:

• N/A

CHECKLIST

• [ X] My code follows the style guidelines in the Contributor's Guide
• [ X] I have performed a self-review of my own code using the Code Reviewer's Guide
• [ X] I have commented my code, particularly in hard-to-understand areas
• My changes do not require updates to the documentation (explain).
• [ X] My changes generate no new warnings
• [ X] New and existing tests pass with my changes
• [ X] Any dependent changes have been merged and published

LABELS (optional):

A Code Manager needs to add the following labels to this PR:

• [X ] documentation

CONTRIBUTORS (optional):

• @jdkublnick
• @gspetro-NOAA

[gspetro-NOAA]

@selbigmtnwx23 Could you fill out the full PR template so that we can determine what is needed (if anything) for this PR? Normally it should have come up when you opened the PR, but if you need it, you can find it here: https://raw.githubusercontent.com/ufs-community/ufs-weather-model/refs/heads/develop/.github/pull_request_template.md

[gspetro-NOAA]

@selbigmtnwx23 At the top of InputsOutputs.rst, you may need to change "ATMAQ | ATM coupled to CMAQ" to "ATMAQ | ATM coupled to AQM" @benkozi Is CMAQ still a thing? Do we just say AQM now whereever it says CMAQ? I think you might've mentioned CMAQ was going away.

[gspetro-NOAA]

@selbigmtnwx23 At the top of InputsOutputs.rst, you may need to change "ATMAQ | ATM coupled to CMAQ" to "ATMAQ | ATM coupled to AQM" @benkozi Is CMAQ still a thing? Do we just say AQM now whereever it says CMAQ? I think you might've mentioned CMAQ was going away.

@benkozi confirmed that the preferred terminology is UFS AQM rather than UFS CMAQ. That should be updated throughout the docs.

[gspetro-NOAA]

It looks like not all of the files here are included in the InputsOutputs chapter. Is there a reason for that?

Also, it seems like there should probably be a section for "Grid Description and Initial Condition Files" like the other sections have. AQM seems to have grid-dependent files in the INPUT section of the data bucket (rather than "fix").

[selbigmtnwx23]

It looks like not all of the files here are included in the InputsOutputs chapter. Is there a reason for that?

Also, it seems like there should probably be a section for "Grid Description and Initial Condition Files" like the other sections have. AQM seems to have grid-dependent files in the INPUT section of the data bucket (rather than "fix").

It was based off what aqm.rc pulls in and that's all that was there.

[gspetro-NOAA]

It looks like not all of the files here are included in the InputsOutputs chapter. Is there a reason for that?
Also, it seems like there should probably be a section for "Grid Description and Initial Condition Files" like the other sections have. AQM seems to have grid-dependent files in the INPUT section of the data bucket (rather than "fix").

It was based off what aqm.rc pulls in and that's all that was there.

Can you point me to the aqm.rc file you were looking at? I'm a little unclear if it's coming from SRW, the WM, the AQM submodule, etc. Regardless, it seems like there are probably fix files, initial conditions files, and grid-dependent files being used. Otherwise I don't see why they're in the WM RT bucket.

[selbigmtnwx23]

It looks like not all of the files here are included in the InputsOutputs chapter. Is there a reason for that?
Also, it seems like there should probably be a section for "Grid Description and Initial Condition Files" like the other sections have. AQM seems to have grid-dependent files in the INPUT section of the data bucket (rather than "fix").

It was based off what aqm.rc pulls in and that's all that was there.

Can you point me to the aqm.rc file you were looking at? I'm a little unclear if it's coming from SRW, the WM, the AQM submodule, etc. Regardless, it seems like there are probably fix files, initial conditions files, and grid-dependent files being used. Otherwise I don't see why they're in the WM RT bucket.

https://github.com/ufs-community/ufs-srweather-app/blob/develop/parm/aqm.rc

[gspetro-NOAA]

It was based off what aqm.rc pulls in and that's all that was there.

https://github.com/ufs-community/ufs-srweather-app/blob/develop/parm/aqm.rc

Ok, I am of two minds here. One, the InputsOutputs chapter is supposed to document the full set of fix files, initial conditions files, and grid-dependent files required for each WM component. In that respect, what is in the SRW's AQM.rc file is not super relevant because this is WM documentation, not SRW documentation. It seems that the complete list of files to include is those under input-data-20251015/AQM in the WM RT data bucket because those are what is used in WM RTs. On the other hand, I'm not convinced that the lists of files for each component are useful/maintainable, so in that regard, I hesitate to make you document more of that here. It might help simply to point people to the data bucket and explain that the most recent set of AQM input data files are in the most recent input-data-202XXXXX/AQM directory and note what the different categories of data are for (e.g., fix = fix files, INPUT = initial conditions, grid-dependent, and namelist files, and NEXUS = required files for the NEXUS component of AQM -- at least, that's what I assume; best to check me on that).

[gspetro-NOAA]

Also, @selbigmtnwx23 , there are a couple broken/redirected linkswhen I run make linkcheck. Those need to be fixed:

(        Glossary: line   25) /Users/gpetro/bs-wm-docs/doc/UsersGuide/source/Glossary.rst:25: WARNING: redirect  https://dtcenter.org/community-code/common-community-physics-package-ccpp - permanently to https://dtcenter.org/software-tools/common-community-physics-package-ccpp
(   InputsOutputs: line  910) broken    https://hydro.iis.u-tokyo.ac.jp/GSWP3/ - HTTPSConnectionPool(host='hydro.iis.u-tokyo.ac.jp', port=443): Max retries exceeded with url: /GSWP3/ (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x10be25e50>, 'Connection to hydro.iis.u-tokyo.ac.jp timed out. (connect timeout=30)'))

For the first one, you can just correct to the new link. For the GSWP3 thing, you'll probably have to ask Chan-Hoo where you can get a new link.

[selbigmtnwx23]

It was based off what aqm.rc pulls in and that's all that was there.

https://github.com/ufs-community/ufs-srweather-app/blob/develop/parm/aqm.rc

Ok, I am of two minds here. One, the InputsOutputs chapter is supposed to document the full set of fix files, initial conditions files, and grid-dependent files required for each WM component. In that respect, what is in the SRW's AQM.rc file is not super relevant because this is WM documentation, not SRW documentation. It seems that the complete list of files to include is those under input-data-20251015/AQM in the WM RT data bucket because those are what is used in WM RTs. On the other hand, I'm not convinced that the lists of files for each component are useful/maintainable, so in that regard, I hesitate to make you document more of that here. It might help simply to point people to the data bucket and explain that the most recent set of AQM input data files are in the most recent input-data-202XXXXX/AQM directory and note what the different categories of data are for (e.g., fix = fix files, INPUT = initial conditions, grid-dependent, and namelist files, and NEXUS = required files for the NEXUS component of AQM -- at least, that's what I assume; best to check me on that).

Okay yeah that makes sense. Would it be best to just add all of that in that same section and also keep what's there?

[gspetro-NOAA]

Merged via #3052 .