Merge pull request #3633 from samsrabin/crop-harvest-biomass-history

Add history outputs: Crop biomass and LAI per harvest

Author: samsrabin

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -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>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -1484,6 +1484,11 @@ 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

cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm

@@ -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', 'FROOTC_AT_HARVEST_PERHARV'
+hist_fincl3 += 'LIVECROOTC_AT_EMERGENCE_PERHARV', 'LIVECROOTC_AT_ANTHESIS_PERHARV', 'LIVECROOTC_AT_MATURITY_PERHARV', 'LIVECROOTC_AT_HARVEST_PERHARV'
+hist_fincl3 += 'LIVESTEMC_AT_EMERGENCE_PERHARV', 'LIVESTEMC_AT_ANTHESIS_PERHARV', 'LIVESTEMC_AT_MATURITY_PERHARV', 'LIVESTEMC_AT_HARVEST_PERHARV'
+hist_fincl3 += 'LEAFC_AT_EMERGENCE_PERHARV', 'LEAFC_AT_ANTHESIS_PERHARV', 'LEAFC_AT_MATURITY_PERHARV', 'LEAFC_AT_HARVEST_PERHARV'
+hist_fincl3 += 'REPRC_AT_EMERGENCE_PERHARV', 'REPRC_AT_ANTHESIS_PERHARV', 'REPRC_AT_MATURITY_PERHARV', 'REPRC_AT_HARVEST_PERHARV'
 hist_nhtfrq = -24,-8,-24
 hist_mfilt  = 1,1,1
 hist_type1d_pertape(3) = 'PFTS'

doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst

@@ -215,7 +215,7 @@ module CNVegCarbonStateType
      procedure , public  :: Summary => Summary_carbonstate
      procedure , public  :: DynamicPatchAdjustments   ! adjust state variables when patch areas change
 
-     procedure , private :: InitAllocate    ! Allocate arrays
+     procedure , public  :: InitAllocate    ! Allocate arrays. PUBLIC FOR UNIT TESTING ONLY
      procedure , private :: InitReadNML     ! Read in namelist
      procedure , private :: InitHistory     ! Initialize history
      procedure , private :: InitCold        ! Initialize arrays for a cold-start

src/biogeochem/CNPhenologyMod.F90

@@ -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      
@@ -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