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Merge pull request #402 from kovenock/kovenock_slaprofile
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SLA Profile with Canopy Depth
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@rgknox
rgknox authored Jul 26, 2018
2 parents 91785e3 + 3aa3791 commit 3f5aa1b
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Showing 11 changed files with 382 additions and 156 deletions.
46 changes: 24 additions & 22 deletions biogeochem/EDCanopyStructureMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -1016,8 +1016,10 @@ subroutine canopy_summarization( nsites, sites, bc_in )

call carea_allom(currentCohort%dbh,currentCohort%n,sites(s)%spread,&
currentCohort%pft,currentCohort%c_area)
currentCohort%treelai = tree_lai(currentCohort%bl, currentCohort%status_coh, &
currentCohort%pft, currentCohort%c_area, currentCohort%n )

currentCohort%treelai = tree_lai(currentCohort%bl, &
currentCohort%pft, currentCohort%c_area, currentCohort%n, &
currentCohort%canopy_layer, currentPatch%canopy_layer_tlai )

canopy_leaf_area = canopy_leaf_area + currentCohort%treelai *currentCohort%c_area

Expand Down Expand Up @@ -1087,7 +1089,7 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
!
! The following patch level diagnostics are updated here:
!
! currentPatch%canopy_layer_tai(cl) ! TAI of each canopy layer
! currentPatch%canopy_layer_tlai(cl) ! total leaf area index of canopy layer
! currentPatch%ncan(cl,ft) ! number of vegetation layers needed
! ! in this patch's pft/canopy-layer
! currentPatch%nrad(cl,ft) ! same as ncan, but does not include
Expand Down Expand Up @@ -1157,7 +1159,7 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
! calculate tree lai and sai.
! --------------------------------------------------------------------------------

currentPatch%canopy_layer_tai(:) = 0._r8
currentPatch%canopy_layer_tlai(:) = 0._r8
currentPatch%ncan(:,:) = 0
currentPatch%nrad(:,:) = 0
patch_lai = 0._r8
Expand All @@ -1176,38 +1178,38 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)

if (currentPatch%total_canopy_area > nearzero ) then

currentCohort => currentPatch%shortest

currentCohort => currentPatch%tallest
do while(associated(currentCohort))

ft = currentCohort%pft
cl = currentCohort%canopy_layer

currentCohort%treelai = tree_lai(currentCohort%bl, currentCohort%status_coh, currentCohort%pft, &
currentCohort%c_area, currentCohort%n )
currentCohort%treesai = tree_sai(currentCohort%dbh, currentCohort%pft, currentCohort%canopy_trim, &
currentCohort%c_area, currentCohort%n)
! Calculate LAI of layers above
! Note that the canopy_layer_lai is also calculated in this loop
! but since we go top down in terms of plant size, we should be okay

currentCohort%treelai = tree_lai(currentCohort%bl, currentCohort%pft, currentCohort%c_area, &
currentCohort%n, currentCohort%canopy_layer, &
currentPatch%canopy_layer_tlai )

currentCohort%treesai = tree_sai(currentCohort%pft, currentCohort%dbh, currentCohort%canopy_trim, &
currentCohort%c_area, currentCohort%n, currentCohort%canopy_layer, &
currentPatch%canopy_layer_tlai, currentCohort%treelai )

currentCohort%lai = currentCohort%treelai *currentCohort%c_area/currentPatch%total_canopy_area
currentCohort%sai = currentCohort%treesai *currentCohort%c_area/currentPatch%total_canopy_area

! Number of actual vegetation layers in this cohort's crown
currentCohort%NV = ceiling((currentCohort%treelai+currentCohort%treesai)/dinc_ed)
currentCohort%nv = ceiling((currentCohort%treelai+currentCohort%treesai)/dinc_ed)

currentPatch%ncan(cl,ft) = max(currentPatch%ncan(cl,ft),currentCohort%NV)

patch_lai = patch_lai + currentCohort%lai

! currentPatch%canopy_layer_tai(cl) = currentPatch%canopy_layer_tai(cl) + &
! currentCohort%lai + currentCohort%sai
currentPatch%canopy_layer_tlai(cl) = currentPatch%canopy_layer_tlai(cl) + currentCohort%lai

do cl = 1,nclmax-1
if(currentCohort%canopy_layer == cl)then
currentPatch%canopy_layer_tai(cl) = currentPatch%canopy_layer_tai(cl) + &
currentCohort%lai + currentCohort%sai
endif
enddo

currentCohort => currentCohort%taller
currentCohort => currentCohort%shorter

enddo !currentCohort

Expand Down Expand Up @@ -1384,7 +1386,7 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)

if(iv==currentCohort%NV) then
remainder = (currentCohort%treelai + currentCohort%treesai) - &
(dinc_ed*dble(currentCohort%NV-1.0_r8))
(dinc_ed*dble(currentCohort%nv-1.0_r8))
if(remainder > dinc_ed )then
write(fates_log(), *)'ED: issue with remainder', &
currentCohort%treelai,currentCohort%treesai,dinc_ed, &
Expand Down Expand Up @@ -1484,7 +1486,7 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
enddo !currentCohort
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
end do
end do

do ft = 1,numpft
do iv = 1,currentPatch%ncan(cl,ft)
Expand Down
14 changes: 9 additions & 5 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@ module EDCohortDynamicsMod
use EDTypesMod , only : min_npm2, min_nppatch
use EDTypesMod , only : min_n_safemath
use EDTypesMod , only : nlevleaf
use EDTypesMod , only : dinc_ed
use FatesInterfaceMod , only : hlm_use_planthydro
use FatesPlantHydraulicsMod, only : FuseCohortHydraulics
use FatesPlantHydraulicsMod, only : CopyCohortHydraulics
Expand Down Expand Up @@ -152,11 +151,16 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, dbh, bleaf, bfine
! Assign canopy extent and depth
call carea_allom(new_cohort%dbh,new_cohort%n,spread,new_cohort%pft,new_cohort%c_area)

new_cohort%treelai = tree_lai(new_cohort%bl, new_cohort%status_coh, new_cohort%pft, &
new_cohort%c_area, new_cohort%n)
new_cohort%treelai = tree_lai(new_cohort%bl, new_cohort%pft, new_cohort%c_area, &
new_cohort%n, new_cohort%canopy_layer, &
patchptr%canopy_layer_tlai )

new_cohort%treesai = tree_sai(new_cohort%pft, new_cohort%dbh, new_cohort%canopy_trim, &
new_cohort%c_area, new_cohort%n, new_cohort%canopy_layer, &
patchptr%canopy_layer_tlai, new_cohort%treelai )

new_cohort%lai = new_cohort%treelai * new_cohort%c_area/patchptr%area
new_cohort%treesai = tree_sai(new_cohort%dbh, new_cohort%pft, new_cohort%canopy_trim, &
new_cohort%c_area, new_cohort%n)


! Put cohort at the right place in the linked list
storebigcohort => patchptr%tallest
Expand Down
4 changes: 2 additions & 2 deletions biogeochem/EDPatchDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -1267,7 +1267,7 @@ subroutine zero_patch(cp_p)
currentPatch%age = nan
currentPatch%age_class = 1
currentPatch%area = nan
currentPatch%canopy_layer_tai(:) = nan
currentPatch%canopy_layer_tlai(:) = nan
currentPatch%total_canopy_area = nan

currentPatch%tlai_profile(:,:,:) = nan
Expand Down Expand Up @@ -1347,7 +1347,7 @@ subroutine zero_patch(cp_p)
currentPatch%burnt_frac_litter(:) = 0.0_r8
currentPatch%btran_ft(:) = 0.0_r8

currentPatch%canopy_layer_tai(:) = 0.0_r8
currentPatch%canopy_layer_tlai(:) = 0.0_r8

currentPatch%seeds_in(:) = 0.0_r8
currentPatch%seed_decay(:) = 0.0_r8
Expand Down
110 changes: 84 additions & 26 deletions biogeochem/EDPhysiologyMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ module EDPhysiologyMod
use EDCohortDynamicsMod , only : create_cohort, sort_cohorts
use FatesAllometryMod , only : tree_lai
use FatesAllometryMod , only : tree_sai
use FatesAllometryMod , only : decay_coeff_kn

use EDTypesMod , only : numWaterMem
use EDTypesMod , only : dl_sf, dinc_ed
Expand Down Expand Up @@ -162,40 +163,59 @@ subroutine trim_canopy( currentSite )
! Canopy trimming / leaf optimisation. Removes leaves in negative annual carbon balance.
!
! !USES:
!
!

! !ARGUMENTS
type (ed_site_type),intent(inout), target :: currentSite
!
! !LOCAL VARIABLES:
type (ed_cohort_type) , pointer :: currentCohort
type (ed_patch_type) , pointer :: currentPatch

integer :: z ! leaf layer
integer :: ipft ! pft index
integer :: trimmed ! was this layer trimmed in this year? If not expand the canopy.
real(r8) :: tar_bl ! target leaf biomass (leaves flushed, trimmed)
real(r8) :: tar_bfr ! target fine-root biomass (leaves flushed, trimmed)
real(r8) :: bfr_per_bleaf ! ratio of fine root per leaf biomass
integer :: z ! leaf layer
integer :: ipft ! pft index
logical :: trimmed ! was this layer trimmed in this year? If not expand the canopy.
real(r8) :: tar_bl ! target leaf biomass (leaves flushed, trimmed)
real(r8) :: tar_bfr ! target fine-root biomass (leaves flushed, trimmed)
real(r8) :: bfr_per_bleaf ! ratio of fine root per leaf biomass
real(r8) :: sla_levleaf ! sla at leaf level z
real(r8) :: nscaler_levleaf ! nscaler value at leaf level z
integer :: cl ! canopy layer index
real(r8) :: kn ! nitrogen decay coefficient
real(r8) :: sla_max ! Observational constraint on how large sla (m2/gC) can become

real(r8) :: leaf_inc ! LAI-only portion of the vegetation increment of dinc_ed
real(r8) :: lai_canopy_above ! the LAI in the canopy layers above the layer of interest
real(r8) :: lai_layers_above ! the LAI in the leaf layers, within the current canopy,
! above the leaf layer of interest
real(r8) :: lai_current ! the LAI in the current leaf layer
real(r8) :: cumulative_lai ! the cumulative LAI, top down, to the leaf layer of interest

!----------------------------------------------------------------------

currentPatch => currentSite%youngest_patch

do while(associated(currentPatch))

currentCohort => currentPatch%tallest
do while (associated(currentCohort))
trimmed = 0

trimmed = .false.
ipft = currentCohort%pft
call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
currentCohort%treelai = tree_lai(currentCohort%bl, currentCohort%status_coh, currentCohort%pft, &
currentCohort%c_area, currentCohort%n )
currentCohort%treesai = tree_sai(currentCohort%dbh, currentCohort%pft, currentCohort%canopy_trim, &
currentCohort%c_area, currentCohort%n)
currentCohort%nv = ceiling((currentCohort%treelai+currentCohort%treesai)/dinc_ed)
currentCohort%treelai = tree_lai(currentCohort%bl, currentCohort%pft, currentCohort%c_area, &
currentCohort%n, currentCohort%canopy_layer, &
currentPatch%canopy_layer_tlai )

currentCohort%treesai = tree_sai(currentCohort%pft, currentCohort%dbh, currentCohort%canopy_trim, &
currentCohort%c_area, currentCohort%n, currentCohort%canopy_layer, &
currentPatch%canopy_layer_tlai, currentCohort%treelai )

currentCohort%nv = ceiling((currentCohort%treelai+currentCohort%treesai)/dinc_ed)

if (currentCohort%nv > nlevleaf)then
write(fates_log(),*) 'nv > nlevleaf',currentCohort%nv,currentCohort%treelai,currentCohort%treesai, &
currentCohort%c_area,currentCohort%n,currentCohort%bl
write(fates_log(),*) 'nv > nlevleaf',currentCohort%nv, &
currentCohort%treelai,currentCohort%treesai, &
currentCohort%c_area,currentCohort%n,currentCohort%bl
call endrun(msg=errMsg(sourcefile, __LINE__))
endif

call bleaf(currentcohort%dbh,ipft,currentcohort%canopy_trim,tar_bl)
Expand All @@ -206,35 +226,68 @@ subroutine trim_canopy( currentSite )
bfr_per_bleaf = tar_bfr/tar_bl
endif

! Identify current canopy layer (cl)
cl = currentCohort%canopy_layer

! PFT-level maximum SLA value, even if under a thick canopy (same units as slatop)
sla_max = EDPftvarcon_inst%slamax(ipft)

!Leaf cost vs netuptake for each leaf layer.
do z = 1,nlevleaf
if (currentCohort%year_net_uptake(z) /= 999._r8)then !there was activity this year in this leaf layer.
do z = 1, currentCohort%nv

! Calculate the cumulative total vegetation area index (no snow occlusion, stems and leaves)

leaf_inc = dinc_ed * &
currentCohort%treelai/(currentCohort%treelai+currentCohort%treesai)

! Now calculate the cumulative top-down lai of the current layer's midpoint
lai_canopy_above = sum(currentPatch%canopy_layer_tlai(1:cl-1))
lai_layers_above = leaf_inc * (z-1)
lai_current = min(leaf_inc, currentCohort%treelai - lai_layers_above)
cumulative_lai = lai_canopy_above + lai_layers_above + 0.5*lai_current

if (currentCohort%year_net_uptake(z) /= 999._r8)then !there was activity this year in this leaf layer.


! Calculate sla_levleaf following the sla profile with overlying leaf area
! Scale for leaf nitrogen profile
kn = decay_coeff_kn(ipft)
! Nscaler value at leaf level z
nscaler_levleaf = exp(-kn * cumulative_lai)
! Sla value at leaf level z after nitrogen profile scaling (m2/gC)
sla_levleaf = EDPftvarcon_inst%slatop(ipft)/nscaler_levleaf

if(sla_levleaf > sla_max)then
sla_levleaf = sla_max
end if

!Leaf Cost kgC/m2/year-1
!decidous costs.
if (EDPftvarcon_inst%season_decid(ipft) == 1.or. &
EDPftvarcon_inst%stress_decid(ipft) == 1)then


currentCohort%leaf_cost = 1._r8/(EDPftvarcon_inst%slatop(ipft)*1000.0_r8)
! Leaf cost at leaf level z accounting for sla profile (kgC/m2)
currentCohort%leaf_cost = 1._r8/(sla_levleaf*1000.0_r8)

if ( int(EDPftvarcon_inst%allom_fmode(ipft)) .eq. 1 ) then
! if using trimmed leaf for fine root biomass allometry, add the cost of the root increment
! to the leaf increment; otherwise do not.
currentCohort%leaf_cost = currentCohort%leaf_cost + &
1.0_r8/(EDPftvarcon_inst%slatop(ipft)*1000.0_r8) * &
1.0_r8/(sla_levleaf*1000.0_r8) * &
bfr_per_bleaf / EDPftvarcon_inst%root_long(ipft)
endif

currentCohort%leaf_cost = currentCohort%leaf_cost * &
(EDPftvarcon_inst%grperc(ipft) + 1._r8)
else !evergreen costs
currentCohort%leaf_cost = 1.0_r8/(EDPftvarcon_inst%slatop(ipft)* &
! Leaf cost at leaf level z accounting for sla profile
currentCohort%leaf_cost = 1.0_r8/(sla_levleaf* &
EDPftvarcon_inst%leaf_long(ipft)*1000.0_r8) !convert from sla in m2g-1 to m2kg-1
if ( int(EDPftvarcon_inst%allom_fmode(ipft)) .eq. 1 ) then
! if using trimmed leaf for fine root biomass allometry, add the cost of the root increment
! to the leaf increment; otherwise do not.
currentCohort%leaf_cost = currentCohort%leaf_cost + &
1.0_r8/(EDPftvarcon_inst%slatop(ipft)*1000.0_r8) * &
1.0_r8/(sla_levleaf*1000.0_r8) * &
bfr_per_bleaf / EDPftvarcon_inst%root_long(ipft)
endif
currentCohort%leaf_cost = currentCohort%leaf_cost * &
Expand All @@ -256,15 +309,15 @@ subroutine trim_canopy( currentSite )
currentCohort%laimemory = currentCohort%laimemory * &
(1.0_r8 - EDPftvarcon_inst%trim_inc(ipft))
endif
trimmed = 1
trimmed = .true.
endif
endif
endif
endif !leaf activity?
enddo !z

currentCohort%year_net_uptake(:) = 999.0_r8
if (trimmed == 0.and.currentCohort%canopy_trim < 1.0_r8)then
if ( (.not.trimmed) .and.currentCohort%canopy_trim < 1.0_r8)then
currentCohort%canopy_trim = currentCohort%canopy_trim + EDPftvarcon_inst%trim_inc(ipft)
endif

Expand Down Expand Up @@ -2416,4 +2469,9 @@ subroutine flux_into_litter_pools(nsites, sites, bc_in, bc_out)

end subroutine flux_into_litter_pools

! ===================================================================================




end module EDPhysiologyMod
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