Complete the FATES-CLM nitrogen coupling

[slevis-lmwg]

Description:

I started this PR with changes needed in ESCOMP/CTSM#3409.
So far that's just the renaming of
prt_carbon_allom_hyp to fates_c_only
prt_cnp_flex_allom_hyp to fates_cn

The corresponding ESCOMP issue:
ESCOMP/CTSM#3378

Resolves #1454
Reminder to address #1526

Collaborators:

@rgknox
@adrifoster

Expectation of Answer Changes:

I do not expect answers to change as a result of this PR alone; however, I expect answers to change for fates_parteh_mode = 2 as a result of the corresponding ESCOMP PR. So far I have not seen such diffs, while I have seen diffs for fates_parteh_mode = 1.

Checklist

All checklist items must be checked to enable merging this pull request:

Contributor

• The in-code documentation has been updated with descriptive comments
• The documentation has been assessed to determine if updates are necessary: To be discussed at CTSM Software meeting tomorrow

Integrator

• FATES PASS/FAIL regression tests were run
  As posted here, I ran the fates test-suite against the corresponding baseline with satisfactory results
• Evaluation of test results for answer changes was performed and results provided
  As posted here, I identified the lines of code responsible for the answer changes
• FATES-CLM6 Code Freeze: satellite phenology regression tests are b4b
  In /glade/derecho/scratch/slevis/tests_0413-123625de I invoked ./cs.status.fails | grep -i fatessp with this result:

    FAIL ERI_D_Ld9.f45_f45_mg37.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhenCamLndTuningMode NLCOMP
    FAIL SMS_D.1x1_brazil.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen NLCOMP
    FAIL SMS_D_Ld3.f09_g17.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen_prescribed NLCOMP
    FAIL ERP_P128x2_Ld30.f45_f45_mg37.I2000Clm60FatesSpCruRsGs.derecho_intel.clm-FatesColdSatPhen NLCOMP
    FAIL ERS_Ld30.f45_f45_mg37.I2000Clm60FatesSpCruRsGs.derecho_intel.clm-FatesColdSatPhen NLCOMP
    FAIL SMS_Lm1.f45_f45_mg37.I2000Clm60FatesSpCruRsGs.derecho_intel.clm-FatesColdBasic NLCOMP
    FAIL SMS.f45_f45_mg37.I2000Clm60FatesSpRsGs.derecho_nvhpc.clm-FatesColdSatPhen NLCOMP

If satellite phenology regressions are not b4b, please hold merge and notify the FATES development team.

Documentation

• Technical Note update:
• User's Guide update:

Test Results:

CTSM (or) E3SM (specify which) test hash-tag:

CTSM (or) E3SM (specify which) baseline hash-tag:

FATES baseline hash-tag:

Test Output:

[slevis-lmwg]

From meeting with @rgknox
We may decide to revert the parameter renaming, pending group feedback.
Keep the other changes!

[slevis-lmwg]

Ryan's update 2025/12/15:
"the team agreed at the fates software meeting that "fates_conly" and "fates_cn" were good names for the switch, both in the namelist and for the integer named constants that we pass between files"

In our meeting 2025/12/16 Ryan offered to change the integer values (1 and 2) to strings. (I made the change from hardwired values to named params in the code.)

[slevis-lmwg]

@glemieux I just added you as the reviewer also on the FATES side. This is the FATES-CN PR that we talked about this morning.

[slevis-lmwg]

@glemieux I'm not certain whether it's ok for me to check the unchecked boxes at the top and merge this, or whether I should wait for you or @rgknox to do it.

[slevis-lmwg]

I reviewed and checked all remaining checkboxes, and I have permission to merge. I will ask at tomorrow's CTSM Software meeting whether it's ok for me to merge and tag this PR.

[slevis-lmwg]

• I will rerun the fates test-suite to generate a new baseline
• I will meet with @glemieux to discuss the merge steps

[slevis-lmwg]

• derecho in progress: ./run_sys_tests -s fates -c fates-sci.1.92.2_api.44.1.0-ctsm5.4.033 -g fates-sci.1.92.3_api.44.1.1-ctsm5.4.034
• izumi still broken: ./run_sys_tests -s fates -c fates-sci.1.92.1_api.44.1.0-ctsm5.4.034 -g fates-sci.1.92.3_api.44.1.1-ctsm5.4.034 --skip-git-status
• When done, rename the new baselines to the new fates tag