Release clm5.0 fruit tree #1966

odombro · 2023-03-10T00:24:02Z

Description of changes

This model branch “CLM5-FruitTree” implements a new submodel that allows the modelling of deciduous fruit trees within CLM. So far the model was developed and tested on the point scale and showed good results in representing the growth and partitioning of biomass between different plant organs as well as observed carbon, water and energy fluxes in a commercial apple orchard.

CLM5-FruitTree combines elements of the existing broadleaf deciduous tree subroutine such as growth and C turnover of woody components, with distinctive phenological stages and a harvestable organ similar to the annual crop subroutine. Additionally, new processes specific to fruit orchards are described.

Major developments include:

A new phenology subroutine that describes the orchard lifecycle and the phenological development of fruit trees including triggers for seasonal orchard management practices.
Adaptation of the CN allocation scheme to reproduce the growth dynamics of fruit trees, considering both storage and photosynthetic growth of annual and perennial plant organs.
Parameterization of an apple plant functional type (for now using ncitrus (35) and nirrig_citrus (36))

Modifications of the following files were made:

src/biogeochem/CNCIsoFluxMod.F90
src/biogeochem/CNCStateUpdate1Mod.F90
src/biogeochem/CNDriverMod.F90
src/biogeochem/CNFUNMod.F90
src/biogeochem/CNGapMortalityMod.F90
src/biogeochem/CNGRespMod.F90
src/biogeochem/CNMRespMod.F90
src/biogeochem/CNNStateUpdate1Mod.F90
src/biogeochem/CNPhenologyMod.F90
src/biogeochem/CNVegCarbonFluxType.F90
src/biogeochem/CNVegCarbonStateType.F90
src/biogeochem/CNVegNitrogenFluxType.F90
src/biogeochem/CNVegNitrogenStateType.F90
src/biogeochem/CNVegStateType.F90
src/biogeochem/CNVegStructUpdateMod.F90
src/biogeochem/CropType.F90
src/biogeochem/dynHarvestMod.F90
src/biogeochem/NutrientCompetitionFlexibleCNMod.F90
src/main/pftconMod.F90
src/biogeophys/TemperatureType.F90

The new parameter file to be used with the development is:
clm5_params.c171117__FruitTree.nc

Specific notes

Detailed information on the technical development and modelling results were published in Dombrowski et al. (2022)

Are answers expected to change (and if so in what way)?

Answers are expected to change only when CFT 35 or 36 is used in a simulation as this CFT is now active and uses the new phenology subroutine (perennial and woody flags set to 1 in parameter file).

Any User Interface Changes (namelist or namelist defaults changes)?

New parameters:

aleafstor: Leaf allocation coefficient to storage post harvest used in CNAllocation (unitless)
arootf2: Late root Allocation coefficient parameter used in CNAllocation (unitless)
crequ: Chilling requirements for bud burst of fruit tree crops (days)
crit_temp: Critical temperature to initiate leaf offset for fruit tree crops (K)
grnrp: Growing Degree Days for fruit expansion used in CNPhenology (unitless)
lfmat: Growing Degree Days for canopy maturity used in CNPhenology (unitless)
max_NH_harvest_date: Maximum apple harvest date for the Northern Hemisphere (YYYYMMDD)
max_SH_harvest_date: Maximum apple harvest date for the Southern Hemisphere (YYYYMMDD)
mulch_pruning: Binary flag for exporting or mulching of pruning material (logical flag)
ndays_stor: Length of period for storage growth of fruit tree crops (days)
perennial: Binary flag for perennial crop phenology (logical flag)
prune_fr: Fraction of deadstem biomass that is pruned (unitless)
transplant: Initial carbon for crops transplanted from nursery (gC/m2)

New output variables:

GRAIN_MR: grain maintenance respiration. Patch level output.
CROP_SEEDC_TO_FROOT: crop seed source to fine root. Patch level output.
CROP_SEEDC_TO_DEADSTEM: crop seed source to deadstem. Patch level output.
C13_CROP_SEEDC_TO_FROOT: C13 crop seed source to fine root. Patch level output.
C13_CROP_SEEDC_TO_DEADSTEM: C13 crop seed source to deadstem. Patch level output.
C14_CROP_SEEDC_TO_FROOT: crop C14 seed source to fine root. Patch level output.
C14_CROP_SEEDC_TO_DEADSTEM: C14 crop seed source to deadstem. Patch level output.
CROP_SEEDN_TO_FROOT: crop seed source to fine root. Patch level output.
CROP_SEEDN_TO_DEADSTEM: crop seed source to deadstem. Patch level output.
DEADSTEMC_SOY: dead stem C at start of year. Patch level output.
DEADSTEMC_STORAGE_SOY: dead stem storage C at start of year. Patch level output.
DEADSTEMN_SOY: dead stem N at start of year. Patch level output.
DEADSTEMN_STORAGE_SOY: dead stem storage N at start of year. Patch level output.
CHILL_DAY: Chill days needed for bud break of fruit tree crops. Patch level output.
ANTI_CHILL_DAY: Anti-chill days needed for bud break of fruit tree crops. Patch level output.
CHILL_FLAG: Chill requirements flag for bud break of fruit tree crops. Patch level output.
HARVEST_FLAG: Harvest flag (perennial crops). Patch level output.
STORAGE_FLAG: Storage growth flag (perennial crops). Patch level output.
A_LEAF: Leaf allocation coefficient. Patch level output.
A_STEM: Stem allocation coefficient. Patch level output.
T_REF24: 24hr average of 2 m air temperature. Patch level output.

New restart variables:

prunec_to_litter: pruning C added to litterfall flux. PFT level dimension.
prunec_storage_to_litter: pruning storage C added to litterfall flux. PFT level dimension.
prunen_to_litter: pruning N added to litterfall flux. PFT level dimension.
prunen_storage_to_litter: pruning storage N added to litterfall flux. PFT level dimension.
deadstemc_soy: dead stem C at start of year. PFT level dimension.
deadstemc_storage_soy: dead stem storage C at start of year. PFT level dimension.
deadstemn_soy: dead stem N at start of year. PFT level dimension.
deadstemn_storage_soy: dead stem storage N at start of year. PFT level dimension.
offset2_flag: orchard rotation flag. PFT level dimension.
arooti2: Saved root allocation coefficient from phase 2. PFT level dimension.
arooti3: Saved root allocation coefficient from phase 3. PFT level dimension.
aleafi3: Saved leaf allocation coefficient from phase 3. PFT level dimension.
huilfmat: Heat unit index needed to reach canopy maturity. PFT level dimension.
huiripe: Heat unit index needed to reach fruit cell expansion. PFT level dimension.
chill_day: Chill days needed for bud break of fruit tree crops. PFT level dimension.
anti_chill_day: Anti-chill days needed for bud break of fruit tree crops. PFT level dimension.
chill_flag: Chill requirements flag for bud break of fruit tree crops. PFT level dimension.
harvest_flag: Harvest flag (perennial crops). PFT level dimension.
prune_flag: Pruning flag (perennial crops). PFT level dimension.
storage_flag: S torage growth flag for perenneial crops. PFT level dimension.
yrop: year of planting for perennial crops. PFT level dimension.
t_ref24: 24hr average of 2 m air temperature. PFT level dimension.

Testing performed

Thus far, testing was performed only for a single point case. For the testing I ran the default CLM5 model and the CLM5-FruitTree development for PFT 7: Broadleaf deciduous tree (BDT) and PFT 19: Spring wheat (SW) for 14 years at a daily timestep. I then compared the last 6 years of simulations to test if the development had any unintended effects on other PFTs. For the two PFTs tested here, there is no difference between the CLM5 and CLM5-FruitTree for the examined variables.

TOTECOSYSC (total ecosystem carbon), TOTECOSYSN (total ecosystem nitrogen), TOTSOMC (total soil organic matter carbon), GPP (gross primary production), TLAI (total leaf area index) and TWS (total water storage).

Additionally, I ran CLM5-FruitTree with the newly parameterized crop type PFT 36: Apple (APPLE) and compared against BDT and SW to showcase the differences between the three PFTs. Here I am showing simulation results for one year (2015) at a daily timestep.

GPP (gross primary productivity), NEE (net ecosystem exchange), ER (ecosystem respiration), AR (autotrophic respiration) and HR (heterotrophic respiration).

GRAINC (grain or fruit carbon), LEAFC (leaf carbon), LIVESTEMC (livestem carbon), FROOTC (fine root carbon) and GRAINC_TO_FOOD (harvest flux).

QSOIL (soil evaporation), QVEGE (canopy evaporation), QVEGT (canopy transpiration), QSOIL (runoff) and QIRRIG (irrigation).

LH (latent heat flux), FSH (sensible heat flux) and Rnet (net radiation).

…correction

samsrabin · 2023-03-27T19:08:34Z

src/biogeochem/CNBalanceCheckMod.F90

This file's changes are just whitespace and can be reverted.

samsrabin · 2023-03-27T19:13:57Z

src/biogeochem/CNCStateUpdate1Mod.F90

A lot of the changes here are distinguishing behavior between woody-perennial PFTs and other PFTs, but many cases have the same thing happen in both. To simplify the changes, any shared lines should occur outside the "if woody perennial" conditional.

samsrabin · 2023-03-27T19:16:36Z

src/biogeochem/CNCStateUpdate1Mod.F90

To improve readability and minimize maintenance costs, perennial(ivt(p)) == 1._r8 .and. woody(ivt(p)) == 1.0_r8 should be replaced with a local boolean variable called is_perennial_woody or something.

added missing script to list of modified src code

samsrabin · 2023-03-27T19:16:57Z

src/biogeochem/CNCStateUpdate2Mod.F90

This file's changes are just whitespace and can be reverted.

samsrabin · 2023-03-27T19:25:45Z

src/biogeochem/CNCStateUpdate1Mod.F90

           end if
           if (ivt(p) >= npcropmin) then ! skip 2 generic crops
-              if (carbon_resp_opt == 1) then
+              if (carbon_resp_opt == 1 .and. perennial(ivt(p)) == 0._r8) then !(perennial flag added by O.Dombrowski)


Instead of (in addition to?) checking for perennial, should it be checked for woody?

samsrabin · 2023-03-27T19:27:02Z

src/biogeochem/CNFUNMod.F90

@@ -1194,7 +1195,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
               !           Calculate appropriate degree of retranslocation
               !-------------------------------------------------------------------------------

-               if(leafc(p).gt.0.0_r8.and.litterfall_n_step(p,istp)* fixerfrac>0.0_r8.and.ivt(p) <npcropmin)then
+               if(leafc(p).gt.0.0_r8.and.litterfall_n_step(p,istp)* fixerfrac>0.0_r8.and. (ivt(p) <npcropmin .or. perennial(ivt(p)) == 1.0_r8)) then ! include perennial woody crops (added by O.Dombrowski)


Should woodiness also be checked here?

samsrabin · 2023-03-27T19:27:44Z

src/biogeochem/CNFUNMod.F90

@@ -1229,6 +1230,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
                 if(local_use_flexiblecn)then   
                     if (leafn(p) == 0.0_r8) then   ! to avoid division by zero
                       delta_CN = fun_cn_flex_c(ivt(p))   ! Max CN ratio over standard
+                       write(iulog,*) 'fun_cn_flex_c is used no1'


Diagnostic messages here and at 1242, 1249 should be removed.

samsrabin · 2023-03-27T19:44:50Z

src/biogeochem/CNVegComputeSeedMod.F90

@@ -133,7 +133,7 @@ subroutine ComputeSeedAmounts(bounds, &
          if (pft_type /= noveg) then
             my_leaf_seed = leafc_seed * &
                  SpeciesTypeMultiplier(species, pft_type, COMPONENT_LEAF)
-             if (pftcon%woody(pft_type) == 1._r8) then
+             if (pftcon%woody(pft_type) == 1._r8 .and. patch%itype(p) < npcropmin) then


Could you add a comment explaining why this shouldn't happen for woody crops?

samsrabin · 2023-03-27T20:41:48Z

src/biogeochem/CNPhenologyMod.F90

+           if (pi <=  col%npatches(c)) then
+              p = col%patchi(c) + pi - 1
+
+              if (patch%active(p)) then


Should this only happen for perennial woody crops?

samsrabin · 2023-03-27T20:49:04Z

src/biogeochem/CNVegStateType.F90

@@ -321,17 +349,17 @@ subroutine InitHistory(this, bounds)
         ptr_col=this%nfire_col)

    this%farea_burned_col(begc:endc) = spval
-    call hist_addfld1d (fname='FAREA_BURNED',  units='s-1', &
+    call hist_addfld1d (fname='FAREA_BURNED',  units='proportion/sec', &


This and the following same unit changes should probably be reverted.

samsrabin · 2023-03-27T20:49:54Z

src/biogeochem/CNVegStateType.F90

+         avgflag='A', long_name='Leaf allocation coefficient', &
+         ptr_patch=this%aleaf_patch, default='inactive')
+
+!    this%arepr_patch(begp:endp)       = spval


This commented-out block can be removed.

samsrabin · 2023-03-27T20:50:00Z

src/biogeochem/CNVegStateType.F90

+         avgflag='A', long_name='Stem allocation coefficient', &
+         ptr_patch=this%astem_patch, default='inactive')
+
+!    this%aroot_patch(begp:endp)       = spval


This commented-out block can be removed.

samsrabin · 2023-03-28T20:55:45Z

src/biogeochem/NutrientCompetitionFlexibleCNMod.F90

+            else if (storage_flag(p) == 1._r8) then
+               fcur = 0._r8
+            end if
+            cpool_to_leafc(p)          = nlc * fcur


Starting here, there's lots of duplication in this subroutine for perennial woody PFTs.

Olga Dombrowski and others added 15 commits February 8, 2022 20:03

Implement CLM-FruitTree sub-model for deciduous fruit trees

9fa4d0d

Update README

c4f164e

Update README

2a1f5b9

Update README

7b82320

Update README

64c8749

Correct orchard rotation/replanting trigger

87b35be

Make taper and nstem PFT parameters to be set in parameter file

093c985

Update parameter file with taper and nstem parameters

2a6d95e

added references to CLM-Palm (Fan et al. 2015)

57586d7

Bug fix in CNPhenology and CNVegStructUpdateMod, and parameter value …

ad3d25b

…correction

Included harvest trigger when leaf offset starts

7c9a3bb

debug planting of fruit trees, make two more CFTs active

17f3e8a

Fix orchard rotation carbon balance error

2a21cb0

added new subroutine for orchard rotation

a6bd8de

cleaned up some scripts, added some crop types to active CFTs

7edde0b

samsrabin self-assigned this Mar 10, 2023

samsrabin added the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Mar 10, 2023

odombro marked this pull request as ready for review March 14, 2023 15:08

billsacks changed the base branch from master to release-clm5.0 March 20, 2023 16:06

billsacks removed the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Mar 23, 2023

samsrabin reviewed Mar 27, 2023

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This file's changes are just whitespace and can be reverted.

samsrabin reviewed Mar 27, 2023

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ekluzek marked this pull request as draft April 3, 2023 21:52

odombro and others added 3 commits July 17, 2023 11:21

Corrected flux assignment from column to patch level

59b6a30

Update README

d4c6a1b

added missing script to list of modified src code

Update README

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samsrabin requested changes Dec 18, 2023

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samsrabin mentioned this pull request May 3, 2024

Improve robustness to crop growing seasons longer than 365 days #2521

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Release clm5.0 fruit tree #1966

Release clm5.0 fruit tree #1966

odombro commented Mar 10, 2023 •

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Release clm5.0 fruit tree #1966

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Release clm5.0 fruit tree #1966

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odombro commented Mar 10, 2023 • edited Loading

Description of changes

Specific notes

Are answers expected to change (and if so in what way)?

Any User Interface Changes (namelist or namelist defaults changes)?

Testing performed

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samsrabin Mar 27, 2023 • edited Loading

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odombro commented Mar 10, 2023 •

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