alpha-ctsm5.4.CMIP7.02.ctsm5.3.055: Update default settings

[slevis-lmwg]

Description of changes

This PR starts from the alpha-ctsm5.4.CMIP7 branch at tag alpha-ctsm5.4.CMIP7.01.ctsm5.3.052.

As a sanity check, I ran aux_clm on derecho on the tag alpha-ctsm5.4.CMIP7.01.ctsm5.3.052. See "Testing" a few lines down for the results.

Definition of done appears in this Upcoming Tags card. (My branch name references issue3137 that we ended up removing from the definition of done.)

Specific notes

Contributors other than yourself, if any:
@ekluzek @wwieder

CTSM Issues Fixed (include github issue #):
Resolves #3116
Resolves #3005

Are answers expected to change (and if so in what way)? Yes, greater than roundoff, same climate:

1. Even before the changes coming in with this PR, this branch changed the raw datasets in mksurfdata_esmf, so the MKSURFDATAESMF test shows DIFF from baseline (read "Testing" a few lines down).
2. a3ce6a7 changes the default snow thermal conductivity schemes over lakes and glaciers in clm6 cases
3. a75e488 introduces a new paramfile to clm6 cases
4. b1890ac introduces new f09 & ne30 fsurdat/landuse files
5. 3a8c432 introduces new f09 & ne30 finidat files for 1850 and 2000 clm6 cases

Any User Interface Changes (namelist or namelist defaults changes)?
Namelist defaults changes

Does this create a need to change or add documentation? Did you do so?
Probably. Not at this time.

Testing performed, if any:

1. OK aux_clm on derecho for tag alpha-ctsm5.4.CMIP7.01.ctsm5.3.052
FAIL MKSURFDATAESMF_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_intel DIFF from baseline I think is expected because this branch has changed the raw datasets used in mksurfdata_esmf.
2. PASS ERP_D_Ld9.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-clm60cam7LndTuningModeLDust confirming that my changes to the snow_thermal_cond_*_method take effect correctly.

[slevis-lmwg]

aux_clm on izumi: Changes mostly correct, but it seems

1. I have not made the use_c1* namelist variables default .true. for Clm6Bgc, so I need to troubleshoot
2. variable leafcn_co2_base is not on dataset, I think this means the paramfile (not finidat)

UPDATE 2025/6/3: aux_clm on izumi shows (2) is resolved.

[slevis-lmwg]

For some reason I still get use_c1* = .false. for this test
SMS_D_Ld3.f10_f10_mg37.I2000Clm60Bgc.izumi_nag.clm-HillslopeD
It probably does not matter, but @ekluzek I would not mind going over that with you.

All others seem as expected, i.e.
use_c1* = .false. except for (1) Clm60Bgc and (2) ciso cases.

[slevis-lmwg]

Tests remaining to do:

• aux_clm on Izumi OK
• aux_clm on Derecho FAIL

FAIL LII2FINIDATAREAS_D_P256x2_Ld1.f09_g17.I1850Clm50BgcCrop.derecho_intel.clm-default--clm-matrixcnOn_ignore_warnings RUN
FAIL LII2FINIDATAREAS_D_P256x2_Ld1.f09_g17.I1850Clm50BgcCrop.derecho_intel.clm-default RUN
FAIL SMS_D_Ld5.f09_g17.ISSP126Clm50BgcCrop.derecho_intel.clm-default RUN

• ISSP126 fails because we have not generated clm54 SSP landuse files, yet. The test should work with clm54 landuse files that we have generated out to 2023, so could use that for now (not my preferred option) OR labeled as EXPECTED FAILURE (ISSP tests need to point to CMIP6 ctsm5.3 fsurdat/landuse files to PASS #3250) OR change to a grid using the old data (I prefer this but not available).

• The LII2 tests are Clm50 and point to finidat = '/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/initdata_esmf/ctsm5.3/clmi.interp_from.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc'
  They still fail as Clm60 because we use the modified finidat = 'ctsm53041_54surfdata_snowTherm_100_pSASU.clm2.r.0161-01-01-00000_64bitoffset.nc'
  They work when I change to the unmodified finidat = 'ctsm53041_54surfdata_snowTherm_100_pSASU.clm2.r.0161-01-01-00000.nc'
  Labeled as EXPECTED FAILURE (FAIL LII2FINIDATAREAS_D_P256x2_Ld1.f09_g17.I1850Clm50BgcCrop.derecho_intel.clm-default COMPARE_base_no_interp #3252)

• Confirm the correct options appear in all lnd_in files on derecho (izumi ok):

grep use_c1 */run/lnd_in
grep use_c1 */run/lnd_in | grep true
grep use_c1 */run/lnd_in | grep true | grep -v Clm6
grep use_c1 */run/lnd_in | grep true | grep -v Bgc
grep use_c1 */run/lnd_in | grep false
grep use_c1 */run/lnd_in | grep false | grep Clm60B
grep paramfile */run/lnd_in | grep Clm6 | grep -v v13 | grep -v fates_paramfile
grep paramfile */run/lnd_in | grep -v Clm6 | grep v13
grep fsurdat */run/lnd_in | grep f09
grep fsurdat */run/lnd_in | grep ne30
grep do_grossunrep */run/lnd_in
grep finidat */run/lnd_in | grep ctsm5.4 | grep -v Clm6

• build-namelist testing to verify namelist changes are as expected PASS

[slevis-lmwg]

Resubmitted these izumi tests because they ran out of wallclock. If resubmitting them helps, I will increase their wallclock in the testlist file.

ERI_D_Ld20.f10_f10_mg37.I2000Clm50Fates.izumi_nag.clm-FatesCold
ERI_D_Ld20.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream
ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-reduceOutput
ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-SNICARFRC
SMS_D_Ld1_P48x1.f10_f10_mg37.I2000Clm45BgcCrop.izumi_nag.clm-oldhyd
SMS_D_Ld65.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-cropMonthOutput--clm-RxCropCalsAdaptGGCMI
SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO
SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesPRISM--clm-NEON-FATES-YELL
SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60SpRs.izumi_nag.clm-default--clm-NEON-TOOL
ERP_D_P48x1.f10_f10_mg37.IHistClm60Bgc.izumi_nag.clm-decStart
ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso--clm-matrixcnOn
ERP_D_Ld9.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-clm60cam7LndTuningModeLDust
ERS_D.f10_f10_mg37.I1850Clm60Sp.izumi_nag.clm-ExcessIceStreams

[slevis-lmwg]

@ekluzek I just merged this PR to the 5.4 branch and tagged it alpha-ctsm5.4.CMIP7.02.ctsm5.3.055