ctsm5.4.044: Merge b4bdev 20260605

[ekluzek]

Description of changes

Bring latest b4b-dev to master.

Mostly updates to the documentation, especially the tech note.

Also update of submodules to almost the latest ones. This includes a few updates in cdeps to help with spinup. One specific update is to allow using the CO2 from the CPLHIST files for spinup cases. Also use daily files for CO2 CPLHIST rather than 3-hourly to sync with the change in CMEPS.

NOTE: This brings in @samsrabin update to cime that will fix the glitch we have with baselines on Izumi!

Also update the FATES parameter generation for testing

And update how the ch4 history fields are handled

Specific notes

Contributors other than yourself, if any:

• @slevis-lmwg, @samsrabin @sy-li @nmizukami @olyson @dmleung @ekluzek @swensosc @katyarjay @mvdebolskiy @cenlinhe @adrifoster

CTSM issues resolved or otherwise addressed, if any:

• Resolves Update submodules to cesm3_0_alpha09c levels #4066 update submodules
• Resolves Column level CH4 output not writing to history #4051 column level CH4 not working to history
• Resolves Remove FatesSetupParamBuild #3989 Remove FatesSetupParamBuild
• Resolves $4065 remove lists of tables/figs
• Resolves Review 2.24. Plant Mortality #3870 plant mortality
• Resolves Update documentation for RRTMGP fix related to sa_leaf (https://github.com/ESCOMP/CTSM/pull/3643) #3723 RRTMGP fix
• Improves Review 2.31. Dust Model #3877 dust
• Resolves Review 2.14. Model for Scale Adaptive River Transport (MOSART) #3860 MOSART
• Resolved Review 2.9. Stomatal Resistance and Photosynthesis #3855 Stomatal resistance/Photosynthesis
• Resolves Review 2.4. Radiative Fluxes #3850 Rad fluxes
• Resolves Review 2.3. Surface Albedos #3849 surface albedos
• Resolves Review 2.8. Snow Hydrology #3854 Snow hydrology
• Resolves Review 2.25. Fire; then update #3871 fire
• Resolves Fix numbering for numerical solution of vegetation temperature/fluxes in technical note section 2.5.3.2 #4025 numbering
• Resolves Review 2.12. Lake Model #3858 Lake
• Resolves Review 2.18. Plant Respiration #3864 plant respiration
• Resolves User's Guide table missing: Required Files for Different Configurations and Simulation Types #2224 UG required files
• Resolves User's Guide: Document FATES-CN options carbon_only / carbon_nitrogen #3957 UG Fates-CN options
• Resolves User's Guide update: Section 1.5.7 BgcCrop spin-ups #3975 BGC spinup

Any user interface changes (namelist or namelist defaults changes)?
Add cplhist option to DATM_CO2_TSERIES

** PR's Brought in**

Total 22

Changes to code: 4

• matlab script for appending WIEMIP co2 scenario data to TRENDY2025 #4082 matlab script
• Update submodules resolving #4066 #4067 submodule updates
• Make ch4 history accessible by field via the existing fincl approach #4055 ch4 history output
• Fix fates paramgen in tests #4024 fix fates paramgen in tests

Changes to documentation: 18

Changes to Tech Note: 14

• Tech Note: Delete lists of figures and tables #4080 Delete lists of figures and tables
• Update Plant Mortality tech note #4075 Plant Mortality
• Add tree, shrub, and RRTMGP limitations on sa_stem and sa_leaf #4074 Tree/shrub limitations from the RRTMG change
• Dust tech note update/typo fix #4073 Dust
• add uuc equation #4057 add uuc equation
• Update to tech note section 2-14 MOSART  #4054 MOSART
• Updates to Technote section 2.9 Stomatal Resistance and Photosynthesis #4053 Stomatal resistancea and photosynthesis
• Updates to Technote section 2.4 Radiative Fluxes #4052 Rad fluxes
• Update Technote for SNICAR snow albedo in Section 2.3 #4049 SNICAR
• review Snow Hydrology Sect 2.8 in Technote #4048 Snow hydrology
• Updates to CLM50_Tech_Note_Fire.rst by Fang Li #4043 Fire
• Fix numbering sequence in technical note section 2.5.3.2 #4026 Fix equation numbering
• Revision of section 2.12 (Lake Model) in technical note for CLM6 #3997 Lake model
• 2.18 Plant Respiration Tech Note edits #3959 Plant respiration

Other documentation updates: 4

• Update doc-builder to v3.2 #4071 Update doc-builder
• Remove section 1.4.3.1 What are the required files? #4050 Users' Guide
• Update IMPORTANT_NOTES.md regarding fates_parteh_mode #4047 Just to IMPORTANT_NOTES
• b4b-dev: Update bgc spinup section #3998 BGC spinup

Testing planned or performed, if any:

• aux_clm Derecho
• aux_clm Izumi
• python tests Derecho
• build-namelist tester Derecho

(After tag is made kick off fates tests for Derecho and Izumi)

Requirements before merge:

• I have followed the CTSM contribution guidelines.

• The code in this PR branch builds with no errors.
• The code in this PR branch runs with no errors. Briefly describe tested configuration(s):
• This either (a) does not change answers, (b) it only changes answers at roundoff level, or (c) I have performed a scientific evaluation of the answer changes. Which?: a

• I have reviewed relevant parts of the CLM documentation Tech Note or User's Guide to determine if anything needs to be changed or added. If it does, describe:
• This PR either (a) does not create a need to update the documentation or (b) includes required documentation updates (see guidelines for contributing documentation). Which?: a

[samsrabin]

Pre-approving with a brief glance, assuming it's a straightforward merge. Also assuming that the updated submodules are intentional.

[ekluzek]

I don't get how this happened. But, I assume it's just an extremly rare glitch with git. The changes to CLMBuildNamelist.pm in ctsm5.4.042 somehow got lost. git thinks they are there so I can't just remerge it in. So I have to do it more or less by hand.

[ekluzek]

The two hillslope tests that showed different answers now pass:

SMS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm60Bgc.derecho_gnu.clm-HillslopeC
SMS_D_Ld3.f10_f10_mg37.I2000Clm60Bgc.izumi_nag.clm-HillslopeD

so the testing is now as expected

[ekluzek]

I think I see what happened. There was a merge of master onto @swensosc branch in PR #4057 and then a mistaken undoing of a merge that was OK here:

0fb7e1c

The b4b-dev branch already correctly had that change from ctsm5.4.042, and so didn't need it backed out. But, I also see how it's easy to get that wrong, it was basically the classic "off by one" problem we easily run into.

So then I ended up undoing the above commit. So it wasn't a glitch in git, it was a simple human mistake.

[slevis-lmwg]

I think I see what happened. There was a merge of master onto @swensosc branch in PR #4057 and then a mistaken undoing of a merge that was OK here:

0fb7e1c

The b4b-dev branch already correctly had that change from ctsm5.4.042, and so didn't need it backed out. But, I also see how it's easy to get that wrong, it was basically the classic "off by one" problem we easily run into.

So then I ended up undoing the above commit. So it wasn't a glitch in git, it was a simple human mistake.

Ah, so this was another example of what I remembered this morning. A way to think about it is that we would have likely encountered significant difficulty merging to b4b-dev if we had kept the merged master in Sean's PR, so we would have reconsidered a merge to b4b-dev. Github would have also shown unexpected diffs and might have given warnings about the branch having conflicts or being inconsistent with base. In any case, I'm glad you cleared it up @ekluzek :-)