Add history outputs: Crop biomass and LAI per harvest #3633

samsrabin · 2025-11-26T02:27:41Z

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.

20 other outputs give the biomass for five C pools (leaf, grain, stem, fine root, coarse root) at three crop phase transitions (emergence, anthesis, maturity) and harvest (which may not happen at 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.

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.
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.

Was using repr_grainc_to_food_patch + repr_grainc_to_seed_patch, but those don't get updated until after the harvest in CropPhenology, which is where the last CropPhaseTransitionBiomass() is called. They also, obviously, only include grain. Now using reproductivec_patch.

samsrabin · 2026-01-08T22:26:09Z

Adding "next" label until we get a reviewer.

wwieder · 2026-01-08T22:31:37Z

@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 ?

src/biogeochem/CropType.F90

slevis-lmwg

@samsrabin thank you for going over this work with me. I'm interested in looking again when you resolve the comment that you posted: https://github.com/ESCOMP/CTSM/pull/3633/changes#r2677039517

Also we agreed that this is fine in b4b-dev because it changes field-lists and not answers.

slevis-lmwg · 2026-01-09T20:18:03Z

src/biogeochem/CNPhenologyMod.F90


            else if (do_harvest) then
+               cphase(p) = cphase_harvest
+               call crop_inst%CropPhaseTransitionBiomass(p, cnveg_carbonstate_inst)


In other phases you include
if (cphase(p) /= cphase_orig) then before calling CropPhaseTransitionBiomass.
Here do you not because harvest occurs in one tstep always?

More like: By definition, if we're harvesting, then it wasn't in cphase_harvest at the beginning of the subroutine.

Another way of saying this: do_harvest means "cphase(p) isn't cphase_harvest but now it should be."

I recommend a simple comment in the code to explain that.

…omass.

slevis-lmwg · 2026-01-09T23:09:21Z

src/biogeochem/CropType.F90

+           call restartvar(ncid=ncid, flag=flag, varname='frootc_maturity_thisyr_patch', xtype=ncd_double,  &
+                dim1name='pft', dim2name='mxharvests', switchdim=.true., &
+                long_name='Fine root C at maturity for harvests in this patch this year', units='unitless', &
+                scale_by_thickness=.false., &
+                interpinic_flag='interp', readvar=readvar, data=this%frootc_maturity_thisyr_patch)
+           call restartvar(ncid=ncid, flag=flag, varname='livecrootc_maturity_thisyr_patch', xtype=ncd_double,  &
+                dim1name='pft', dim2name='mxharvests', switchdim=.true., &
+                long_name='Live coarse root C at maturity for harvests in this patch this year', units='unitless', &
+                scale_by_thickness=.false., &
+                interpinic_flag='interp', readvar=readvar, data=this%livecrootc_maturity_thisyr_patch)
+           call restartvar(ncid=ncid, flag=flag, varname='livestemc_maturity_thisyr_patch', xtype=ncd_double,  &
+                dim1name='pft', dim2name='mxharvests', switchdim=.true., &
+                long_name='Live stem C at maturity for harvests in this patch this year', units='unitless', &
+                scale_by_thickness=.false., &
+                interpinic_flag='interp', readvar=readvar, data=this%livestemc_maturity_thisyr_patch)
+           call restartvar(ncid=ncid, flag=flag, varname='leafc_maturity_thisyr_patch', xtype=ncd_double,  &
+                dim1name='pft', dim2name='mxharvests', switchdim=.true., &
+                long_name='Leaf C at maturity for harvests in this patch this year', units='unitless', &
+                scale_by_thickness=.false., &
+                interpinic_flag='interp', readvar=readvar, data=this%leafc_maturity_thisyr_patch)
+           call restartvar(ncid=ncid, flag=flag, varname='reprc_maturity_thisyr_patch', xtype=ncd_double,  &
+                dim1name='pft', dim2name='mxharvests', switchdim=.true., &
+                long_name='Reproductive C at maturity for harvests in this patch this year', units='unitless', &
+                scale_by_thickness=.false., &
+                interpinic_flag='interp', readvar=readvar, data=this%reprc_maturity_thisyr_patch)


should these have been "harvest" rather than maturity?

For now I will wait for successful aux_clm testing before I hit "approve" if you don't mind @samsrabin

samsrabin added 4 commits November 25, 2025 14:06

Add MAX_TLAI_PERHARV history output.

496ee06

PlantCrop: Add namelist option to suppress low gddmaturity warning.

7f9ef13

Fix a comment

e9219a2

Add crop phase transition biomass outputs.

4ee9e6e

samsrabin self-assigned this Nov 26, 2025

samsrabin added enhancement new capability or improved behavior of existing capability bfb bit-for-bit science Enhancement to or bug impacting science next this should get some attention in the next week or two. Normally each Thursday SE meeting. labels Nov 26, 2025

samsrabin added 4 commits November 26, 2025 07:27

Rename GRAINC_AT hist vars to HARVORGANC_AT to fix LREPRSTRUCT tests.

291a158

Rename HARVORGANC_AT history vars to REPRC_AT.

7c89b24

Rename grainc_at vars to reprc_at.

a263a92

samsrabin removed the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Jan 8, 2026

samsrabin added this to the ctsm6.0.0 (code freeze) milestone Jan 8, 2026

PlantCrop: Fix setting max_tlai_patch.

a7e66aa

samsrabin marked this pull request as ready for review January 8, 2026 22:25

samsrabin added the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Jan 8, 2026

samsrabin added the PR status: awaiting review Work on this PR is paused while waiting for review. label Jan 8, 2026

wwieder requested review from slevis-lmwg and wwieder and removed request for wwieder January 8, 2026 22:31

samsrabin commented Jan 9, 2026

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src/biogeochem/CropType.F90 Outdated Show resolved Hide resolved

samsrabin removed the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Jan 9, 2026

slevis-lmwg requested changes Jan 9, 2026

View reviewed changes

samsrabin added 2 commits January 9, 2026 15:43

CropPhenology(): New variable is_mature.

eb3237a

Only save crop maturity biomass if mature. Always save new harvest bi…

533383f

…omass.

samsrabin requested a review from slevis-lmwg January 9, 2026 22:58

slevis-lmwg reviewed Jan 9, 2026

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Add history outputs: Crop biomass and LAI per harvest #3633

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Description of changes

Specific notes

Testing performed

✅ aux_clm

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

To do

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