Land Use Fixes

[ckoven]

I've been running into various errors in transient historical runs with full land use. The branch I am using has various things that aren't on main yet, so I thought I'd cherry-pick just the land-use-relevant things into a separate branch, so that if others want to use them they can.

In addition to the bugfixes, this deletes a bunch of history variables that apply only to secondary lands, and replaces a subset of them (biomass, burned area, GPP, NPP) with ones that have a land-use dimension to them.

Note that there is also one ELM-side bug fix as well, at the commit pointed to in #1260.

Description:

Collaborators:

Expectation of Answer Changes:

Checklist

If this is your first time contributing, please read the CONTRIBUTING document.

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

Integrator

• FATES PASS/FAIL regression tests were run
• Evaluation of test results for answer changes was performed and results provided

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:

[samsrabin]

Very nice, Charlie, thanks! I just have a few minor notes that I'll propose (untested) fixes to in a PR shortly.

[glemieux]

Minor suggested change and two questions.

[glemieux]

Preliminary regression testing against fates-sci.1.80.6_api.37.0.0-tmp-241219.n01.ctsm5.3.016 using ckoven#26 shows nearly B4B results. Most of the DIFFS are FIELDLIST only given the history name changes. The only main DIFF is showing up in the harvest area mode LUH2 test mod, in which the FATES_PATCHAREA_LU and FATES_DISTURBANCE_RATE_MATRIX_LULU are seeing differences starting on t_index=31.

There was a run failure in the AllVars test, but this is due to the test asking from history that is removed via this PR. As such, we'll need a concurrent HLM PR to address this.

[glemieux]

There was a run failure in the AllVars test, but this is due to the test asking from history that is removed via this PR. As such, we'll need a concurrent HLM PR to address this.

Started #1305 as a potential future update to avoid this situation.

[glemieux]

Final regression testing on derecho is underway.

[glemieux]

Final regression testing on derecho is passing as expected. This was tested with ESCOMP/CTSM#2934 which resulted in DIFFs for all Clm60Fates based compsets due to not being run with Meier2022. As with the preliminary testing mentioned above, there were expected DIFFs in the harvest area LUH2 test. The issue with the FatesColdAllVars test has also been resolved per ESCOMP/CTSM#2936 which was merged into ESCOMP/CTSM#2934. All other tests are b4b against fates-sci.1.80.10_api.37.0.0-ctsm5.3.021.

Results: /glade/u/home/glemieux/scratch/ctsm-tests/tests_pr1273-fates-ctsm53022

Izumi testing underway.

[glemieux]

Izumi regression testing is complete. All expected tests are B4B against fates-sci.1.80.10_api.37.0.0-ctsm5.3.021 with the exception of Clm60Fates based compsets as expected.

Results: /home/glemieux/scratch/ctsm-tests/tests_0131-080811iz