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Conflict resolutions for phenology refactor. Most related to saving a…
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…nd tracking number of chilling and number of cold days
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@rgknox
rgknox committed Apr 11, 2019
2 parents 9f034f2 + 82498d5 commit 3c1f3e6
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Showing 26 changed files with 2,915 additions and 5,039 deletions.
517 changes: 323 additions & 194 deletions biogeochem/EDCanopyStructureMod.F90
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209 changes: 171 additions & 38 deletions biogeochem/EDCohortDynamicsMod.F90
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22 changes: 17 additions & 5 deletions biogeochem/EDLoggingMortalityMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ subroutine IsItLoggingTime(is_master,currentSite)

else if(icode < 0 .and. icode > -366) then
! Logging event every year on specific day of year
if(hlm_day_of_year .eq. icode ) then
if(hlm_day_of_year .eq. abs(icode) ) then
logging_time = .true.
end if

Expand Down Expand Up @@ -151,14 +151,20 @@ end subroutine IsItLoggingTime

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

subroutine LoggingMortality_frac( pft_i, dbh, lmort_direct,lmort_collateral,lmort_infra )
subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
lmort_collateral, lmort_infra, l_degrad )

! Arguments
integer, intent(in) :: pft_i ! pft index
real(r8), intent(in) :: dbh ! diameter at breast height (cm)
integer, intent(in) :: canopy_layer ! canopy layer of this cohort
real(r8), intent(out) :: lmort_direct ! direct (harvestable) mortality fraction
real(r8), intent(out) :: lmort_collateral ! collateral damage mortality fraction
real(r8), intent(out) :: lmort_infra ! infrastructure mortality fraction
real(r8), intent(out) :: l_degrad ! fraction of trees that are not killed
! but suffer from forest degradation (i.e. they
! are moved to newly-anthro-disturbed secondary
! forest patch)

! Parameters
real(r8), parameter :: adjustment = 1.0 ! adjustment for mortality rates
Expand All @@ -170,31 +176,37 @@ subroutine LoggingMortality_frac( pft_i, dbh, lmort_direct,lmort_collateral,lmor

if (dbh >= logging_dbhmin ) then
lmort_direct = logging_direct_frac * adjustment
lmort_collateral = logging_collateral_frac * adjustment
l_degrad = 0._r8
else
lmort_direct = 0.0_r8
lmort_collateral = 0.0_r8
l_degrad = logging_direct_frac * adjustment
end if

if (dbh >= logging_dbhmax_infra) then
lmort_infra = 0.0_r8
l_degrad = l_degrad + logging_mechanical_frac * adjustment
else
lmort_infra = logging_mechanical_frac * adjustment
end if
!damage rates for size class < & > threshold_size need to be specified seperately

! Collateral damage to smaller plants below the direct logging size threshold
! Collateral damage to smaller plants below the canopy layer
! will be applied via "understory_death" via the disturbance algorithm
if (canopy_layer .eq. 1) then
lmort_collateral = logging_collateral_frac * adjustment
endif

else
lmort_direct = 0.0_r8
lmort_collateral = 0.0_r8
lmort_infra = 0.0_r8
l_degrad = 0.0_r8
end if
else
lmort_direct = 0.0_r8
lmort_collateral = 0.0_r8
lmort_infra = 0.0_r8
l_degrad = 0.0_r8
end if

end subroutine LoggingMortality_frac
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5 changes: 3 additions & 2 deletions biogeochem/EDMortalityFunctionsMod.F90
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Expand Up @@ -194,10 +194,11 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
! Mortality for trees in the understorey.
!if trees are in the canopy, then their death is 'disturbance'. This probably needs a different terminology
call mortality_rates(currentCohort,bc_in,cmort,hmort,bmort,frmort)
call LoggingMortality_frac(ipft, currentCohort%dbh, &
call LoggingMortality_frac(ipft, currentCohort%dbh, currentCohort%canopy_layer, &
currentCohort%lmort_direct, &
currentCohort%lmort_collateral, &
currentCohort%lmort_infra )
currentCohort%lmort_infra, &
currentCohort%l_degrad)

if (currentCohort%canopy_layer > 1)then

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1,247 changes: 731 additions & 516 deletions biogeochem/EDPatchDynamicsMod.F90
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29 changes: 11 additions & 18 deletions biogeochem/EDPhysiologyMod.F90
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Expand Up @@ -27,7 +27,6 @@ module EDPhysiologyMod

use EDTypesMod , only : numWaterMem
use EDTypesMod , only : dl_sf, dinc_ed
use EDTypesMod , only : external_recruitment
use EDTypesMod , only : ncwd
use EDTypesMod , only : nlevleaf
use EDTypesMod , only : num_vegtemp_mem
Expand Down Expand Up @@ -60,7 +59,6 @@ module EDPhysiologyMod
use FatesAllometryMod , only : bbgw_allom
use FatesAllometryMod , only : carea_allom
use FatesAllometryMod , only : CheckIntegratedAllometries
use FatesAllometryMod , only : StructureResetOfDH

use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : leaf_organ
Expand Down Expand Up @@ -259,7 +257,8 @@ subroutine trim_canopy( currentSite )

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%vcmax25top )
currentPatch%canopy_layer_tlai, currentCohort%treelai, &
currentCohort%vcmax25top,0 )

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

Expand Down Expand Up @@ -475,17 +474,17 @@ subroutine phenology( currentSite, bc_in )
! in the late autumn.
! This value is used to determine the GDD exceedance threshold
if (hlm_day_of_year == ncdstart)then
currentSite%ncd = 0
currentSite%nchilldays = 0
endif

!Accumulate growing/chilling days after start of counting period
if (temp_in_C < ED_val_phen_chiltemp)then
currentSite%ncd = currentSite%ncd + 1
currentSite%nchilldays = currentSite%nchilldays + 1
endif

!GDD accumulation function, which also depends on chilling days.
! -68 + 638 * (-0.001 * ncd)
gdd_threshold = ED_val_phen_a + ED_val_phen_b*exp(ED_val_phen_c*real(currentSite%ncd,r8))
gdd_threshold = ED_val_phen_a + ED_val_phen_b*exp(ED_val_phen_c*real(currentSite%nchilldays,r8))

!Accumulate temperature of last 10 days.
currentSite%vegtemp_memory(2:num_vegtemp_mem) = currentSite%vegtemp_memory(1:num_vegtemp_mem-1)
Expand Down Expand Up @@ -539,7 +538,7 @@ subroutine phenology( currentSite, bc_in )

if ( (currentSite%cstatus == 1 .or. currentSite%cstatus == 0) .and. &
(currentSite%grow_deg_days > gdd_threshold) .and. &
(currentSite%ncd >= 1) .and. &
(currentSite%nchilldays >= 1) .and. &
(dayssincecleafoff > ED_val_phen_mindayson)) then
currentSite%cstatus = 2 !alter status of site to 'leaves on'
currentSite%cleafondate = model_day_int
Expand Down Expand Up @@ -575,7 +574,7 @@ subroutine phenology( currentSite, bc_in )

! LEAF OFF: COLD LIFESPAN THRESHOLD
! NOTE: Some areas of the planet will never generate a cold day
! and thus %ncd will never go from zero to 1. The following logic
! and thus %nchilldays will never go from zero to 1. The following logic
! when coupled with this fact will essentially prevent cold-deciduous
! plants from re-emerging in areas without at least some cold days

Expand Down Expand Up @@ -965,20 +964,14 @@ subroutine seeds_in( currentSite, cp_pnt )

endif

currentPatch => currentSite%oldest_patch

do while(associated(currentPatch))
if (external_recruitment == 1) then !external seed rain - needed to prevent extinction
do p = 1,numpft
currentPatch%seeds_in(p) = currentPatch%seeds_in(p) + &
do p = 1,numpft
currentPatch%seeds_in(p) = currentPatch%seeds_in(p) + &
EDPftvarcon_inst%seed_rain(p) !KgC/m2/year
currentSite%seed_rain_flux(p) = currentSite%seed_rain_flux(p) + &
currentSite%seed_rain_flux(p) = currentSite%seed_rain_flux(p) + &
EDPftvarcon_inst%seed_rain(p) * currentPatch%area/AREA !KgC/m2/year
enddo
endif
currentPatch => currentPatch%younger
enddo


end subroutine seeds_in

! ============================================================================
Expand Down
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