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

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496ee06
Add MAX_TLAI_PERHARV history output.
samsrabin Nov 25, 2025
7f9ef13
PlantCrop: Add namelist option to suppress low gddmaturity warning.
samsrabin Nov 2, 2025
e9219a2
Fix a comment
samsrabin Nov 25, 2025
4ee9e6e
Add crop phase transition biomass outputs.
samsrabin Nov 25, 2025
291a158
Rename GRAINC_AT hist vars to HARVORGANC_AT to fix LREPRSTRUCT tests.
samsrabin Nov 26, 2025
7c89b24
Rename HARVORGANC_AT history vars to REPRC_AT.
samsrabin Dec 1, 2025
a263a92
Rename grainc_at vars to reprc_at.
samsrabin Dec 1, 2025
319be76
CropPhaseTransitionBiomass() bugfix for reproductive C.
samsrabin Dec 1, 2025
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1 change: 1 addition & 0 deletions bld/namelist_files/namelist_defaults_ctsm.xml
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Expand Up @@ -703,6 +703,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).

<generate_crop_gdds >.false.</generate_crop_gdds>
<use_mxmat >.true.</use_mxmat>
<suppress_gddmaturity_warning >.false.</suppress_gddmaturity_warning>

<!-- use additional stress deciduous onset trigger -->
<constrain_stress_deciduous_onset >.true.</constrain_stress_deciduous_onset>
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5 changes: 5 additions & 0 deletions bld/namelist_files/namelist_definition_ctsm.xml
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Expand Up @@ -1472,6 +1472,11 @@ Set to .true. in order to override crop harvesting logic and to instead harvest
Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true.
</entry>

<entry id="suppress_gddmaturity_warning" type="logical" category="physics"
group="cnphenology" valid_values="" value=".false.">
If set to .true., suppress the warning message when a prescribed cultivar GDD requirement is below the minimum allowed value and is replaced with min_gddmaturity. Useful when using prescribed crop calendars with intentionally low GDD requirements.
</entry>

<entry id="min_critical_dayl_method" type="char*25" category="physics"
group="cnphenology" valid_values="Constant,DependsOnLat,DependsOnVeg,DependsOnLatAndVeg">
Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on
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7 changes: 6 additions & 1 deletion cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
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Expand Up @@ -13,7 +13,12 @@ hist_fincl2 += 'DYN_COL_SOIL_ADJUSTMENTS_C'
! Note that, under normal circumstances, these should only be saved annually.
! That's needed for the mxsowings and mxharvests axes to make sense.
! However, for testing purposes, it makes sense to save more frequently.
hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS', 'GDD20_BASELINE', 'GDD20_SEASON_START', 'GDD20_SEASON_END'
hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS', 'GDD20_BASELINE', 'GDD20_SEASON_START', 'GDD20_SEASON_END', 'MAX_TLAI_PERHARV'
hist_fincl3 += 'FROOTC_AT_EMERGENCE_PERHARV', 'FROOTC_AT_ANTHESIS_PERHARV', 'FROOTC_AT_MATURITY_PERHARV'
hist_fincl3 += 'LIVECROOTC_AT_EMERGENCE_PERHARV', 'LIVECROOTC_AT_ANTHESIS_PERHARV', 'LIVECROOTC_AT_MATURITY_PERHARV'
hist_fincl3 += 'LIVESTEMC_AT_EMERGENCE_PERHARV', 'LIVESTEMC_AT_ANTHESIS_PERHARV', 'LIVESTEMC_AT_MATURITY_PERHARV'
hist_fincl3 += 'LEAFC_AT_EMERGENCE_PERHARV', 'LEAFC_AT_ANTHESIS_PERHARV', 'LEAFC_AT_MATURITY_PERHARV'
hist_fincl3 += 'REPRC_AT_EMERGENCE_PERHARV', 'REPRC_AT_ANTHESIS_PERHARV', 'REPRC_AT_MATURITY_PERHARV'
hist_nhtfrq = -24,-8,-24
hist_mfilt = 1,1,1
hist_type1d_pertape(3) = 'PFTS'
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73 changes: 70 additions & 3 deletions src/biogeochem/CNPhenologyMod.F90
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Expand Up @@ -146,6 +146,7 @@ module CNPhenologyMod
real(r8) :: min_gddmaturity = 1._r8 ! Weird things can happen if gddmaturity is tiny
logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing
logical, public :: use_mxmat = .true. ! If true, ignore crop maximum growing season length
logical, private :: suppress_gddmaturity_warning = .false. ! If true, suppress warning when using min_gddmaturity

! For use with adapt_cropcal_rx_cultivar_gdds .true.
real(r8), parameter :: min_gdd20_baseline = 0._r8 ! If gdd20_baseline_patch is ≤ this, do not consider baseline.
Expand Down Expand Up @@ -200,7 +201,7 @@ subroutine CNPhenologyReadNML( NLFilename )
!-----------------------------------------------------------------------
namelist /cnphenology/ initial_seed_at_planting, onset_thresh_depends_on_veg, &
min_critical_dayl_method, generate_crop_gdds, &
use_mxmat
use_mxmat, suppress_gddmaturity_warning

! Initialize options to default values, in case they are not specified in
! the namelist
Expand All @@ -226,6 +227,7 @@ subroutine CNPhenologyReadNML( NLFilename )
call shr_mpi_bcast (min_critical_dayl_method, mpicom)
call shr_mpi_bcast (generate_crop_gdds, mpicom)
call shr_mpi_bcast (use_mxmat, mpicom)
call shr_mpi_bcast (suppress_gddmaturity_warning, mpicom)

if ( min_critical_dayl_method == "DependsOnLat" )then
critical_daylight_method = critical_daylight_depends_on_lat
Expand Down Expand Up @@ -2054,6 +2056,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &
real(r8) avg_dayspyr ! average number of days per year
real(r8) crmcorn ! comparitive relative maturity for corn
real(r8) ndays_on ! number of days to fertilize
real(r8) cphase_orig ! crop phase before updating
logical has_rx_sowing_date ! does the crop have a single sowing date instead of a window?
logical is_in_sowing_window ! is the crop in its sowing window?
logical is_end_sowing_window ! is it the last day of the crop's sowing window?
Expand Down Expand Up @@ -2092,6 +2095,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &

fertnitro => crop_inst%fertnitro_patch , & ! Input: [real(r8) (:) ] fertilizer nitrogen
hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest
max_tlai => crop_inst%max_tlai_patch , & ! Input: [real(r8) (:) ] maximum total projected leaf area seen this season (m2/m2); set to 0 at sowing and tracked until harvest
leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature
harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date
croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested
Expand Down Expand Up @@ -2154,6 +2158,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &
! Should never be saved as zero, but including this so it's initialized just in case
harvest_reason = 0._r8

cphase_orig = cphase(p)

! ---------------------------------
! from AgroIBIS subroutine planting
! ---------------------------------
Expand All @@ -2180,6 +2186,22 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &
cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8
crop_inst%gddaccum_thisyr_patch(p,s) = -1._r8
crop_inst%hui_thisyr_patch(p,s) = -1._r8
crop_inst%max_tlai_thisyr_patch(p,s) = -1._r8
crop_inst%frootc_emergence_thisyr_patch(p,s) = -1._r8
crop_inst%frootc_anthesis_thisyr_patch(p,s) = -1._r8
crop_inst%frootc_maturity_thisyr_patch(p,s) = -1._r8
crop_inst%livecrootc_emergence_thisyr_patch(p,s) = -1._r8
crop_inst%livecrootc_anthesis_thisyr_patch(p,s) = -1._r8
crop_inst%livecrootc_maturity_thisyr_patch(p,s) = -1._r8
crop_inst%livestemc_emergence_thisyr_patch(p,s) = -1._r8
crop_inst%livestemc_anthesis_thisyr_patch(p,s) = -1._r8
crop_inst%livestemc_maturity_thisyr_patch(p,s) = -1._r8
crop_inst%leafc_emergence_thisyr_patch(p,s) = -1._r8
crop_inst%leafc_anthesis_thisyr_patch(p,s) = -1._r8
crop_inst%leafc_maturity_thisyr_patch(p,s) = -1._r8
crop_inst%reprc_emergence_thisyr_patch(p,s) = -1._r8
crop_inst%reprc_anthesis_thisyr_patch(p,s) = -1._r8
crop_inst%reprc_maturity_thisyr_patch(p,s) = -1._r8
crop_inst%sowing_reason_perharv_patch(p,s) = -1._r8
crop_inst%harvest_reason_thisyr_patch(p,s) = -1._r8
do k = repr_grain_min, repr_grain_max
Expand Down Expand Up @@ -2507,6 +2529,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &
! similar changes in CropPhase.
if ((.not. do_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat) then
cphase(p) = cphase_leafemerge
if (cphase(p) /= cphase_orig) then
call crop_inst%CropPhaseTransitionBiomass(p, cnveg_carbonstate_inst)
end if
if (abs(onset_counter(p)) > 1.e-6_r8) then
onset_flag(p) = 1._r8
onset_counter(p) = dt
Expand All @@ -2532,6 +2557,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &
! changes to the offset subroutine below

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

! Don't update these if you're just harvesting because of incorrect Dec.
! 31 planting
if (.not. fake_harvest) then
Expand All @@ -2546,10 +2574,27 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &
crop_inst%sowing_reason_perharv_patch(p, harvest_count(p)) = real(crop_inst%sowing_reason_patch(p), r8)
crop_inst%sowing_reason_patch(p) = -1 ! "Reason for most recent sowing of this patch." So in the line above we save, and here we reset.
crop_inst%harvest_reason_thisyr_patch(p, harvest_count(p)) = harvest_reason
crop_inst%max_tlai_thisyr_patch(p, harvest_count(p)) = crop_inst%max_tlai_patch(p)

! Crop phase transition biomass sizes
crop_inst%frootc_emergence_thisyr_patch(p, harvest_count(p)) = crop_inst%frootc_emergence_patch(p)
crop_inst%frootc_anthesis_thisyr_patch(p, harvest_count(p)) = crop_inst%frootc_anthesis_patch(p)
crop_inst%frootc_maturity_thisyr_patch(p, harvest_count(p)) = crop_inst%frootc_maturity_patch(p)
crop_inst%livecrootc_emergence_thisyr_patch(p, harvest_count(p)) = crop_inst%livecrootc_emergence_patch(p)
crop_inst%livecrootc_anthesis_thisyr_patch(p, harvest_count(p)) = crop_inst%livecrootc_anthesis_patch(p)
crop_inst%livecrootc_maturity_thisyr_patch(p, harvest_count(p)) = crop_inst%livecrootc_maturity_patch(p)
crop_inst%livestemc_emergence_thisyr_patch(p, harvest_count(p)) = crop_inst%livestemc_emergence_patch(p)
crop_inst%livestemc_anthesis_thisyr_patch(p, harvest_count(p)) = crop_inst%livestemc_anthesis_patch(p)
crop_inst%livestemc_maturity_thisyr_patch(p, harvest_count(p)) = crop_inst%livestemc_maturity_patch(p)
crop_inst%leafc_emergence_thisyr_patch(p, harvest_count(p)) = crop_inst%leafc_emergence_patch(p)
crop_inst%leafc_anthesis_thisyr_patch(p, harvest_count(p)) = crop_inst%leafc_anthesis_patch(p)
crop_inst%leafc_maturity_thisyr_patch(p, harvest_count(p)) = crop_inst%leafc_maturity_patch(p)
crop_inst%reprc_emergence_thisyr_patch(p, harvest_count(p)) = crop_inst%reprc_emergence_patch(p)
crop_inst%reprc_anthesis_thisyr_patch(p, harvest_count(p)) = crop_inst%reprc_anthesis_patch(p)
crop_inst%reprc_maturity_thisyr_patch(p, harvest_count(p)) = crop_inst%reprc_maturity_patch(p)
endif

croplive(p) = .false. ! no re-entry in greater if-block
cphase(p) = cphase_harvest
if (tlai(p) > 0._r8) then ! plant had emerged before harvest
offset_flag(p) = 1._r8
offset_counter(p) = dt
Expand Down Expand Up @@ -2580,6 +2625,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , &

else if (hui(p) >= huigrain(p)) then
cphase(p) = cphase_grainfill
if (cphase(p) /= cphase_orig) then
call crop_inst%CropPhaseTransitionBiomass(p, cnveg_carbonstate_inst)
end if
bglfr(p) = 1._r8/(leaf_long(ivt(p))*avg_dayspyr*secspday)
end if

Expand Down Expand Up @@ -2809,6 +2857,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date
sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch
sowing_reason => crop_inst%sowing_reason_thisyr_patch , & ! Output: [real(r8) (:) ] reason for each sowing this year for this patch
max_tlai => crop_inst%max_tlai_patch , & ! Output: [real(r8) (:) ] maximum total projected leaf area seen this season
gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest
idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting
iyop => cnveg_state_inst%iyop_patch , & ! Output: [integer (:) ] year of planting
Expand Down Expand Up @@ -2932,7 +2981,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &

if (gddmaturity(p) < min_gddmaturity) then
if (use_cropcal_rx_cultivar_gdds .or. generate_crop_gdds) then
if (did_rx_gdds) then
if (did_rx_gdds .and. .not. suppress_gddmaturity_warning) then
write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity ',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')'
end if
gddmaturity(p) = min_gddmaturity
Expand All @@ -2955,6 +3004,24 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
arepr(p,k) = 0._r8
end do

! Initialize other stuff
max_tlai = 0._r8
crop_inst%frootc_emergence_patch(p) = -1._r8
crop_inst%frootc_anthesis_patch(p) = -1._r8
crop_inst%frootc_maturity_patch(p) = -1._r8
crop_inst%livecrootc_emergence_patch(p) = -1._r8
crop_inst%livecrootc_anthesis_patch(p) = -1._r8
crop_inst%livecrootc_maturity_patch(p) = -1._r8
crop_inst%livestemc_emergence_patch(p) = -1._r8
crop_inst%livestemc_anthesis_patch(p) = -1._r8
crop_inst%livestemc_maturity_patch(p) = -1._r8
crop_inst%leafc_emergence_patch(p) = -1._r8
crop_inst%leafc_anthesis_patch(p) = -1._r8
crop_inst%leafc_maturity_patch(p) = -1._r8
crop_inst%reprc_emergence_patch(p) = -1._r8
crop_inst%reprc_anthesis_patch(p) = -1._r8
crop_inst%reprc_maturity_patch(p) = -1._r8

end associate

end subroutine PlantCrop
Expand Down
4 changes: 4 additions & 0 deletions src/biogeochem/CNVegStructUpdateMod.F90
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Expand Up @@ -127,6 +127,7 @@ subroutine CNVegStructUpdate(bounds,num_soilp, filter_soilp, &
peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max

harvdate => crop_inst%harvdate_patch , & ! Input: [integer (:) ] harvest date
max_tlai => crop_inst%max_tlai_patch , & ! Output: [real(r8) (:) ] maximum total projected leaf area seen this season

! *** Key Output from CN***
tlai => canopystate_inst%tlai_patch , & ! Output: [real(r8) (:) ] one-sided leaf area index, no burying by snow
Expand Down Expand Up @@ -260,6 +261,9 @@ subroutine CNVegStructUpdate(bounds,num_soilp, filter_soilp, &
htop(p) = max(0.05_r8, max(htmx(p),htop(p)))
hbot(p) = 0.02_r8

! Maximum LAI seen this season
max_tlai(p) = max(max_tlai(p), tlai(p))

else ! generic crops and ...

! grasses
Expand Down
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