ctsm5.4.048: Merge b4bdev 20260727

[ekluzek]

Description of changes

Bring b4b-dev to master.

Documentation updates:

• FATES
• Hydrology
• Dry-deposition

Code changes:

• Comment out failing fields so all_hist_vars tests actually work
• Add more history variables even for calc_human_stress_indices==FAST
• Make nc3crop and nc3irrig private to pftconMod, add some functions to determine: is_crop, is_bare, is_generic_crop, is_prognostic_crop, is_irrigated

Specific notes

Contributors other than yourself, if any:

• @adrifoster
• @olyson
• @slevis-lmwg
• @YifanCheng
• @samsrabin
• @lkemmons

CTSM issues resolved or otherwise addressed, if any:

• Resolves Review 2.29. Dynamic Global Vegetation and FATES #3875
• Partial on FAIL ERP_P64x2_D_Ld3...clm-default--clm-all_outputs COMPARE_base_rest #3661
• Fixes ctsm5.4.048: Merge b4bdev 20260727 #4140
• Partial Add dewpoint function to QSat #3694
• Resolves Review 2.7. Hydrology #3853
• Partial in Review 1.6. Running Single Point and Regional Cases #3885
• Partial for documentation in CTSM5.4.0xx Fix problems encountered with running PLUMBER2 sites #4092
• Partial for Remove ability to use 16-PFT fire emission factor files (only support 78-pft files) #4120
• Partial for refactor code that assumes a particular ordering of PFT type constants #21
• Partial for Avoid in-code checks of PFT type #3388
• Resolves Documentation needed for Dry Deposition of gases #4032

PR's being merged in:

• Review of Docs 2.29. Dynamic Global Vegetation and FATES #4037
  b4b docs:update docs-loc:tech-note documentation
  Review of Docs 2.29. Dynamic Global Vegetation and FATES #4037 by adrifoster
• Comment out fields failing in #3661 so test may catch future problems #4136
  b4b testing
  Comment out fields failing in #3661 so test may catch future problems #4136 by slevis-lmwg
• b4b: Convert the BareGroundFluxesMod dewpoint calculation into a function #3706
  b4b test: aux_clm
  b4b: Convert the BareGroundFluxesMod dewpoint calculation into a function #3706 by olyson
• update hydrology documentation #3954
  b4b docs:update docs-loc:tech-note documentation
  update hydrology documentation #3954 by YifanCheng
• Make APPAR_TEMP and DISCOIS variables available when calc_human_stress_indices is FAST #4111
  b4b
  Make APPAR_TEMP and DISCOIS variables available when calc_human_stress_indices is FAST #4111 by olyson
• Revision of User's Guide section 1.6.2.3 - PLUMBER2 Tower Single Point Simulations #4135
  b4b docs:update docs-loc:users-guide documentation
  Revision of User's Guide section 1.6.2.3 - PLUMBER2 Tower Single Point Simulations #4135 by olyson
• Make nc3crop and nc3irrig private to pftconMod #4112
  b4b code health
  Make nc3crop and nc3irrig private to pftconMod #4112 by samsrabin
• documentation: Add dry dep description to BVOC section, and add references #4131
  b4b docs:update docs-loc:tech-note documentation

Any user interface changes (namelist or namelist defaults changes)?

Testing planned or performed, if any: regular

• build-namelist
• python
• aux_clm Derecho
• aux_clm 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

[ekluzek]

Testing is finally almost finished, and is looking as expected so far.

[slevis-lmwg]

Thank you @ekluzek!

[ekluzek]

These tests show changes to the fieldlists compared to baseline that I'm not sure is expected:

LCISO_Ld396.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-ciso_monthly--clm-matrixcnOn_ignore_warnings.GC.ctsm5448acl_int
LCISO_Ld396.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-ciso_monthly.GC.ctsm5448acl_int
LGRAIN2_Ly1_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput.GC.ctsm5448acl_gnu
LGRAIN2_Ly2_P128x1.f10_f10_mg37.I1850Clm45BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput.GC.ctsm5448acl_gnu
LREPRSTRUCT_Ly1_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput.GC.ctsm5448acl_gnu
LREPRSTRUCT_Ly2_P128x1.f10_f10_mg37.I1850Clm45BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput.GC.ctsm5448acl_gnu
LWISO_Ld10.f10_f10_mg37.I2000Clm50BgcCrop.derecho_gnu.clm-coldStart.GC.ctsm5448acl_gnu

OK, this is expected. I had looked in the ctsm5.4.047 tests and didn't see this signal, because a lot of the tests had been scrubbed.