Update crops/irrigation Tech Note chapter for 6.0

[samsrabin]

Description of changes

Specific notes

Contributors other than yourself, if any:

• None

CTSM issues resolved or otherwise addressed, if any:

• Resolves Review 2.27. Crops and Irrigation; and update #3873

If answers are expected to change, describe (delete this line otherwise):

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

Testing planned or performed, if any:

• Local preview
• On-PR tests

Requirements before merge:

• I have followed the CTSM contribution guidelines.

---

Delete sections

• "Summary of CLM5.0 updates relative to the CLM4.5", including "Available new features since the CLM5 release"
• "Separate reproductive pool"? Seems redundant with information already elsewhere.

Add

• Tillage Already done
• Residue removal Already done
• References to recent papers?

Update

• Throughout:
  • References to CLM5, CLM5-BGC-crop, etc.: Convert to just CLM or CTSM
  • No more "the CLM"
  • Remove references to Agro-IBIS, except at beginning. (Maybe?)
  • Use $h_{phase}$ instead of just $h$.
  • Be more careful about $GDD_{mat}$ (realized threshold for maturity) vs hybgdd (parameter for starting point of calculating $GDD_{mat}$).
  • $GDD_8$ should be $GDD_{8,20}$ with a bar over it(same for 0 and 10)
  • Equations:
    • Relabel the ones whose labels are just numbers (do this last, because later notes here refer to the number labels)
    • Replace * with \times
    • Be consistent about stem vs. livestem
  • Replace math with literal, where appropriate
  • Replace italics with math, where appropriate
  • Consistently use C_3 and C_4.
• Introduction: Crops are much more common now in ESMs. Condense this section greatly to just introduce the idea of the crop model and its inheritance from AgroIBIS.

Crop PFT section:

• Link to docs on "land unit" and "soil column"
• "Crop grid cell coverage ...": Just refer to relevant other sections of the documentation.
• Delete: "The representations of sugarcane, rice, cotton, tropical corn, and tropical soy were new in CLM5; miscanthus and switchgrass were added after the CLM5 release." We don't want our tech note to be a history lesson.
• What is "functional form"?
• No longer accurate; delete? "In tropical regions, parameter values were developed for the Amazon Basin, and planting date window is shifted by six months relative to the Northern Hemisphere."
• "Each of the inactive crop types is simulated using the parameters of the spatially closest associated crop type":
  • spatially?
  • Describe how to get this information from the paramfile. Unfortunately query_paramfile doesn't make it easy yet: ESCOMP/CTSM Issue #3457: query_paramfile: Better presentation of mergetoclmpft
  • Mention that trying to enable the inactive crop types will NOT WORK because of ESCOMP/CTSM Issue #3388: Avoid in-code checks of PFT type
• Add text about my reparameterization? Nothing there about CLM5 reparameterization...
• Simplify crop PFT table

Phenology section

• Delete bit at beginning describing non-crop phenology types
• Updates related to new crop calendars
  • Delete: "(for the northern hemisphere)", "In the southern hemisphere (SH) the NH requirements apply 6 months later."
  • Mention new sowing windows derived from GGCMI; cite Rabin et al. (2023)
• Eq. labeled 25.2:
  • Reorganize. Maybe have this not be an equation at all?
  • Edit to account for now using rx_cultivar_gdds_thisyr_patch, gdd20_baseline_patch, etc.
  • Add bioenergy crops
  • Add winter wheat
  • Change label to something descriptive
  • Things like 1850 for corn/sugarcane are actually parameters! But 950 isn't. Fix all this.
  • Account for min_gddmaturity
  • If any \circs are left after all that, replace them with proper degree symbols
• Eq. labeled 25.3:
  • Maximum increment needs to be divided by 48 (timesteps per day)
• Leaf emergence section: Clarify that leaf emergence happens at BEGINNING of this phase, and that the phase as a whole might be better thought of as "vegetative growth."
• Table Crop phenology parameters:
  • Remove sowing window dates (rows and also following bullet point—or maybe keep bullet point to say "these variables are what you would have had before CLM5.x", or how you can simply set sowing date for single-site runs)
  • Add netCDF variable names
  • Replace math with literals, where it makes sense to do
  • Update values
  • Add disclaimer
  • See Biofuel crop slatop parameter values changed? #4084
• "using the BGC leaf offset algorithm" ??

Allocation section

• "Allocation changes based on the crop phenology phases phenology"
• Update, if needed, based on my reparameterization (although I don't think it should be): "All C:N ratios were determined by calibration process, through comparisons of model output versus observations of plant carbon throughout the growing season."
• "The BGC part of the model keeps track of a term representing excess maintenance respiration, which supplies the carbon required for maintenance respiration during periods of low photosynthesis (Chapter :numref:rst_Plant Respiration).": Delete this. Instead, just cross-ref the section in the next sentence.
• Equation labeled 25.4:
  • Second row: what about where that term is > 1?
  • Change label to something descriptive
• Clarify SOME lfemerg phase allocation to leaf when max LAI has been reached
• Equation labeled 25.5:
  • Rows 2 and 4: what about where that term is > 1?
  • Those ≤ 1s can't be right.
  • Change label to something descriptive
• Explain grainfill phase allocations when max LAI has been reached
• "Nitrogen allocation for crops ... is supplied in CLM by the soil mineral nitrogen pool": What about BNF? Reference section Biological nitrogen fixation for soybeans here.
• "post-grain fill C:N ratios are assigned the same as crop residue": This can't be right... Can it? How is "crop residue" assigned a C:N ratio and not an emergent property?
• Explain how grain N works. Reference $\paramgraincn$, presumably.
• Harvest:
  • It sounds like biofuel harvest goes to the _TO_FOOD history variable??
• Table Crop allocation parameters:
  • Update values
  • Add disclaimer
• Fertilizer
  • "based on the LUMIP land use and land cover change time series (LUH2 for historical and SSPs for future)": Update?
  • "although denitrification rates are slower in the current version of the model": cited paper is pretty old. Maybe not "the current version" anymore.
• "Unlike natural vegetation, where a fraction of each PFT are N fixers, all soybeans are treated as N fixers." Well, no. That's a fraction too: 1.
• Grain C equation: Extraneous parenthesis
• "Latitudinal variation in base growth tempereature" section:
  • Fix "tempereature" typo
  • How to turn this off?
  • Move this to be with other base temp / GDD calculation info

Irrigation section

• "includes the option", "When irrigation is enabled": It's actually on by default (MAYBE: WAITING ON Review (and update?) default irrigation for Clm60 compsets #4056)
• "$f_{thresh}$ is a tuning parameter": What value? Hard-coded? Variable name?
• "To conserve mass" options: Which is on by default? How to change?
• Table Irrigation parameters
  • Check/update values
  • Add parameter names; mention that these are set in user_nl_clm

[samsrabin]

Sorta blocked by #4084.