Add history outputs: Crop biomass and LAI per harvest

[samsrabin]

Description of changes

Adds a bunch of history outputs with the mxharvests dimension (max number of crop harvests per year; 2).

MAX_TLAI_PERHARV gives the maximum total LAI seen across the growing season.

15 other outputs give the biomass for five C pools (leaf, grain, stem, fine root, coarse root) at three crop phase transitions (emergence, anthesis, maturity).

Also adds an option to suppress a warning about low gddmaturity, which I used during the CRU-JRA crop calendar work.

Specific notes

Contributors other than yourself, if any: None

CTSM Issues Fixed (include github issue #): None

Are answers expected to change (and if so in what way)? No

Any User Interface Changes (namelist or namelist defaults changes)? No

Does this create a need to change or add documentation? Did you do so? Will need to update non-FATES output list; no.

Testing performed

✅ aux_clm

aux_clm reveals what seem to be threading problems with MAX_TLAI_PERHARV, which fails COMPARE_base_rest in ER[PS]_Ly3_P64x2 tests but not an ERS_Ly3 test. Resolved with a7e66aa.

✅ Nonsense check: Correct relative number of negative biomass pool outputs

The biomass pool outputs should be negative when a valid harvest doesn't occur (i.e., we're harvesting, and not a "fake harvest" or when the crop doesn't make it to the given phase transition.

1. Because these values are only ever written at the time of valid harvest, the AT_HARVEST values should never be negative when a valid harvest occurs.
2. Because anthesis can't occur before emergence, the number of negative AT_ANTHESIS values should always be ≥ the number of negative AT_EMERGENCE values.

This check passes in my CUPiD notebook for case clm6_crops_omni05_unsimgeneric, run with a version up-to-date with commit 319be76:

['FROOTC_AT_EMERGENCE_PERHARV', 'LIVECROOTC_AT_EMERGENCE_PERHARV']: 12 negative at valid harvest
['FROOTC_AT_ANTHESIS_PERHARV', 'LIVECROOTC_AT_ANTHESIS_PERHARV']: 6498 negative at valid harvest
['FROOTC_AT_MATURITY_PERHARV', 'LIVECROOTC_AT_MATURITY_PERHARV']: 0 negative at valid harvest
['FROOTC_AT_EMERGENCE_PERHARV', 'LIVECROOTC_AT_EMERGENCE_PERHARV']: 2 negative at valid harvest
['FROOTC_AT_ANTHESIS_PERHARV', 'LIVECROOTC_AT_ANTHESIS_PERHARV']: 2880 negative at valid harvest
['FROOTC_AT_MATURITY_PERHARV', 'LIVECROOTC_AT_MATURITY_PERHARV']: 0 negative at valid harvest
['LEAFC_AT_EMERGENCE_PERHARV', 'LIVESTEMC_AT_EMERGENCE_PERHARV', 'REPRC_AT_EMERGENCE_PERHARV']: 3 negative at valid harvest
['LEAFC_AT_ANTHESIS_PERHARV', 'LIVESTEMC_AT_ANTHESIS_PERHARV', 'REPRC_AT_ANTHESIS_PERHARV']: 4304 negative at valid harvest
['LEAFC_AT_MATURITY_PERHARV', 'LIVESTEMC_AT_MATURITY_PERHARV', 'REPRC_AT_MATURITY_PERHARV']: 0 negative at valid harvest
['FROOTC_AT_EMERGENCE_PERHARV', 'LIVECROOTC_AT_EMERGENCE_PERHARV']: 2 negative at valid harvest
['FROOTC_AT_ANTHESIS_PERHARV', 'LIVECROOTC_AT_ANTHESIS_PERHARV']: 2882 negative at valid harvest
['FROOTC_AT_MATURITY_PERHARV', 'LIVECROOTC_AT_MATURITY_PERHARV']: 0 negative at valid harvest

To do

• Fix threading issue.
• Add HARVORGANC equivalent but JUST for grain. Will match what I have there for now, because grain is all CLM simulates by default. But it'll differ with the options underneath. (Do not name GRAIN unless you fix LPREPRSTRUCT test to handle this.) People should just use existing GRAINC_TO_(FOOD|SEED)_PERHARV outputs.
• Add support for for_testing_use_second_grain_pool and/or for_testing_use_repr_structure_pool true (or throw error in that case). See above.

[samsrabin]

Adding "next" label until we get a reviewer.

[wwieder]

@slevis-lmwg can you take this one one, I think you have the most familiarity with the crop model. Is it helpful to go through the PR with @samsrabin ?

[samsrabin]

Only save to maturity variable if it's actually mature. Always save to a new harvest variable.