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merged master and resolved conflicts
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@ckoven
ckoven committed Mar 22, 2018
2 parents 4a7de82 + 0090297 commit edbc92c
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815 changes: 454 additions & 361 deletions biogeochem/EDCanopyStructureMod.F90
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147 changes: 93 additions & 54 deletions biogeochem/EDPatchDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@ module EDPatchDynamicsMod
use FatesInterfaceMod , only : hlm_freq_day
use EDPftvarcon , only : EDPftvarcon_inst
use EDCohortDynamicsMod , only : fuse_cohorts, sort_cohorts, insert_cohort
use EDtypesMod , only : ncwd, n_dbh_bins, ntol, area, dbhmax
use EDtypesMod , only : ncwd, n_dbh_bins, area, patchfusion_dbhbin_loweredges
use EDtypesMod , only : force_patchfuse_min_biomass
use EDTypesMod , only : maxPatchesPerSite
use EDTypesMod , only : ed_site_type, ed_patch_type, ed_cohort_type
use EDTypesMod , only : min_patch_area
Expand Down Expand Up @@ -118,7 +119,8 @@ subroutine disturbance_rates( site_in, bc_in)

call mortality_rates(currentCohort,bc_in,cmort,hmort,bmort,frmort)
currentCohort%dmort = cmort+hmort+bmort+frmort
call carea_allom(currentCohort%dbh,currentCohort%n,site_in%spread,currentCohort%pft,currentCohort%c_area)
call carea_allom(currentCohort%dbh,currentCohort%n,site_in%spread,currentCohort%pft, &
currentCohort%c_area)

! Initialize diagnostic mortality rates
currentCohort%cmort = cmort
Expand Down Expand Up @@ -1217,9 +1219,8 @@ subroutine zero_patch(cp_p)
currentPatch%age = nan
currentPatch%age_class = 1
currentPatch%area = nan
currentPatch%canopy_layer_lai(:) = nan
currentPatch%canopy_layer_tai(:) = nan
currentPatch%total_canopy_area = nan
currentPatch%canopy_area = nan
currentPatch%bare_frac_area = nan

currentPatch%tlai_profile(:,:,:) = nan
Expand All @@ -1246,10 +1247,9 @@ subroutine zero_patch(cp_p)
currentPatch%fabd(:) = nan ! fraction of incoming direct radiation that is absorbed by the canopy
currentPatch%fabi(:) = nan ! fraction of incoming diffuse radiation that is absorbed by the canopy

currentPatch%present(:,:) = 999 ! is there any of this pft in this layer?
currentPatch%canopy_mask(:,:) = 999 ! is there any of this pft in this layer?
currentPatch%nrad(:,:) = 999 ! number of exposed leaf layers for each canopy layer and pft
currentPatch%ncan(:,:) = 999 ! number of total leaf layers for each canopy layer and pft
currentPatch%lai = nan ! leaf area index of patch
currentPatch%pft_agb_profile(:,:) = nan

! DISTURBANCE
Expand Down Expand Up @@ -1300,7 +1300,7 @@ subroutine zero_patch(cp_p)
currentPatch%burnt_frac_litter(:) = 0.0_r8
currentPatch%btran_ft(:) = 0.0_r8

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

currentPatch%seeds_in(:) = 0.0_r8
currentPatch%seed_decay(:) = 0.0_r8
Expand All @@ -1321,6 +1321,8 @@ subroutine fuse_patches( csite, bc_in )
!
! !USES:
use EDParamsMod , only : ED_val_patch_fusion_tol
use EDTypesMod , only : patch_fusion_tolerance_relaxation_increment
use EDTypesMod , only : max_age_of_second_oldest_patch
!
! !ARGUMENTS:
type(ed_site_type), intent(inout), target :: csite
Expand All @@ -1332,14 +1334,12 @@ subroutine fuse_patches( csite, bc_in )
integer :: ft,z !counters for pft and height class
real(r8) :: norm !normalized difference between biomass profiles
real(r8) :: profiletol !tolerance of patch fusion routine. Starts off high and is reduced if there are too many patches.
integer :: maxpatch !maximum number of allowed patches. FIX-RF. These should be namelist variables.
integer :: nopatches !number of patches presently in gridcell
integer :: iterate !switch of patch reduction iteration scheme. 1 to keep going, 0 to stop
integer :: fuse_flag !do patches get fused (1) or not (0).
!
!---------------------------------------------------------------------

maxpatch = maxPatchesPerSite

currentSite => csite

profiletol = ED_val_patch_fusion_tol
Expand All @@ -1356,7 +1356,7 @@ subroutine fuse_patches( csite, bc_in )
iterate = 1

!---------------------------------------------------------------------!
! Keep doing this until nopatches >= maxpatch !
! Keep doing this until nopatches >= maxPatchesPerSite !
!---------------------------------------------------------------------!

do while(iterate == 1)
Expand All @@ -1382,36 +1382,80 @@ subroutine fuse_patches( csite, bc_in )
endif

if(associated(tpp).and.associated(currentPatch))then
fuse_flag = 1 !the default is to fuse the patches

!--------------------------------------------------------------------------------------------
! The default is to fuse the patches, unless some criteria is met which keeps them separated.
! there are multiple criteria which all need to be met to keep them distinct:
! (a) one of them is younger than the max age at which we force fusion;
! (b) there is more than a threshold (tiny) amount of biomass in at least one of the patches;
! (c) for at least one pft x size class, where there is biomass in that class in at least one patch,
! and the normalized difference between the patches exceeds a threshold.
!--------------------------------------------------------------------------------------------

fuse_flag = 1
if(currentPatch%patchno /= tpp%patchno) then !these should be the same patch

!---------------------------------------------------------------------!
! Calculate the difference criteria for each pft and dbh class !
!---------------------------------------------------------------------!
do ft = 1,numpft ! loop over pfts
do z = 1,n_dbh_bins ! loop over hgt bins
!is there biomass in this category?
if(currentPatch%pft_agb_profile(ft,z) > 0.0_r8.or.tpp%pft_agb_profile(ft,z) > 0.0_r8)then
norm = abs(currentPatch%pft_agb_profile(ft,z) - tpp%pft_agb_profile(ft,z))/(0.5_r8*&
&(currentPatch%pft_agb_profile(ft,z) + tpp%pft_agb_profile(ft,z)))
!---------------------------------------------------------------------!
! Look for differences in profile biomass, above the minimum biomass !
!---------------------------------------------------------------------!

if(norm > profiletol)then
!looking for differences between profile density.
if(currentPatch%pft_agb_profile(ft,z) > NTOL.or.tpp%pft_agb_profile(ft,z) > NTOL)then
fuse_flag = 0 !do not fuse - keep apart.
endif
endif ! profile tol
endif ! NTOL
enddo !ht bins
enddo ! PFT

!---------------------------------------------------------------------!
! Call the patch fusion routine if there is a meaningful difference !
! any of the pft x height categories !
!---------------------------------------------------------------------!
!-----------------------------------------------------------------------------------
! check to see if both patches are older than the age at which we force them to fuse
!-----------------------------------------------------------------------------------

if ( tpp%age .le. max_age_of_second_oldest_patch .or. &
currentPatch%age .le. max_age_of_second_oldest_patch ) then


!---------------------------------------------------------------------------------------------------------
! the next bit of logic forces fusion of two patches which both have tiny biomass densities. without this,
! fates gives a bunch of really young patches which all have almost no biomass and so don't need to be
! distinguished from each other. but if force_patchfuse_min_biomass is too big, it takes too long for the
! youngest patch to build up enough biomass to be its own distinct entity, which leads to large oscillations
! in the patch dynamics and dependent variables.
!---------------------------------------------------------------------------------------------------------

if(sum(currentPatch%pft_agb_profile(:,:)) > force_patchfuse_min_biomass .or. &
sum(tpp%pft_agb_profile(:,:)) > force_patchfuse_min_biomass ) then

!---------------------------------------------------------------------!
! Calculate the difference criteria for each pft and dbh class !
!---------------------------------------------------------------------!

do ft = 1,numpft ! loop over pfts
do z = 1,n_dbh_bins ! loop over hgt bins

!----------------------------------
!is there biomass in this category?
!----------------------------------

if(currentPatch%pft_agb_profile(ft,z) > 0.0_r8 .or. &
tpp%pft_agb_profile(ft,z) > 0.0_r8)then

!-------------------------------------------------------------------------------------
! what is the relative difference in biomass i nthis category between the two patches?
!-------------------------------------------------------------------------------------

norm = abs(currentPatch%pft_agb_profile(ft,z) - &
tpp%pft_agb_profile(ft,z))/(0.5_r8 * &
&(currentPatch%pft_agb_profile(ft,z) + tpp%pft_agb_profile(ft,z)))

!---------------------------------------------------------------------!
! Look for differences in profile biomass, above the minimum biomass !
!---------------------------------------------------------------------!

if(norm > profiletol)then

fuse_flag = 0 !do not fuse - keep apart.

endif ! profile tol
endif ! biomass(ft,z) .gt. 0
enddo !ht bins
enddo ! PFT
endif ! sum(biomass(:,:) .gt. force_patchfuse_min_biomass
endif ! maxage

!-------------------------------------------------------------------------!
! Call the patch fusion routine if there is not a meaningful difference !
! any of the pft x height categories !
! or both are older than forced fusion age !
!-------------------------------------------------------------------------!

if(fuse_flag == 1)then
tmpptr => currentPatch%older
Expand Down Expand Up @@ -1445,9 +1489,9 @@ subroutine fuse_patches( csite, bc_in )
currentPatch => currentPatch%older
enddo

if(nopatches > maxpatch)then
if(nopatches > maxPatchesPerSite)then
iterate = 1
profiletol = profiletol * 1.1_r8
profiletol = profiletol * patch_fusion_tolerance_relaxation_increment

!---------------------------------------------------------------------!
! Making profile tolerance larger means that more fusion will happen !
Expand All @@ -1456,7 +1500,7 @@ subroutine fuse_patches( csite, bc_in )
iterate = 0
endif

enddo !do while nopatches>maxpatch
enddo !do while nopatches>maxPatchesPerSite

end subroutine fuse_patches

Expand Down Expand Up @@ -1668,13 +1712,13 @@ subroutine terminate_patches(cs_pnt)
! This is only really meant for very old patches.
if(associated(currentPatch%older) )then
write(fates_log(),*) 'fusing to older patch because this one is too small',&
currentPatch%area, currentPatch%lai, &
currentPatch%older%area,currentPatch%older%lai
currentPatch%area, &
currentPatch%older%area
call fuse_2_patches(currentPatch%older, currentPatch)
write(fates_log(),*) 'after fusion to older patch',currentPatch%area
else
write(fates_log(),*) 'fusing to younger patch because oldest one is too small',&
currentPatch%area, currentPatch%lai
currentPatch%area
tmpptr => currentPatch%younger
call fuse_2_patches(currentPatch, currentPatch%younger)
write(fates_log(),*) 'after fusion to younger patch'
Expand Down Expand Up @@ -1765,20 +1809,15 @@ subroutine patch_pft_size_profile(cp_pnt)

currentPatch => cp_pnt

delta_dbh = (DBHMAX/N_DBH_BINS)

currentPatch%pft_agb_profile(:,:) = 0.0_r8

do j = 1,N_DBH_BINS
if (j == 1) then
mind(j) = 0.0_r8
maxd(j) = delta_dbh
else if (j == N_DBH_BINS) then
mind(j) = (j-1) * delta_dbh
if (j == N_DBH_BINS) then
mind(j) = patchfusion_dbhbin_loweredges(j)
maxd(j) = gigantictrees
else
mind(j) = (j-1) * delta_dbh
maxd(j) = (j)*delta_dbh
mind(j) = patchfusion_dbhbin_loweredges(j)
maxd(j) = patchfusion_dbhbin_loweredges(j+1)
endif
enddo

Expand Down
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