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Merge branch 'main' into clm-cbalance-merged
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@rgknox
rgknox committed Aug 11, 2023
2 parents e12062f + a90710a commit 4f41112
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Showing 44 changed files with 4,046 additions and 3,458 deletions.
8 changes: 2 additions & 6 deletions biogeochem/DamageMainMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,6 @@ module DamageMainMod
use EDPftvarcon , only : EDPftvarcon_inst
use EDParamsMod , only : damage_event_code
use EDParamsMod , only : ED_val_history_damage_bin_edges
use EDTypesMod , only : ed_site_type
use EDTypesMod , only : ed_patch_type
use EDTypesMod , only : ed_cohort_type
use EDTypesMod , only : AREA
use FatesInterfaceTypesMod, only : hlm_current_day
use FatesInterfaceTypesMod, only : hlm_current_month
use FatesInterfaceTypesMod, only : hlm_current_year
Expand Down Expand Up @@ -54,7 +50,7 @@ module DamageMainMod



subroutine IsItDamageTime(is_master, currentSite)
subroutine IsItDamageTime(is_master)

!----------------------------------------------------------------------------
! This subroutine determines whether damage should occur (it is called daily)
Expand All @@ -63,7 +59,7 @@ subroutine IsItDamageTime(is_master, currentSite)


integer, intent(in) :: is_master
type(ed_site_type), intent(inout), target :: currentSite
!type(ed_site_type), intent(inout), target :: currentSite

integer :: icode ! Integer equivalent of the event code (parameter file only allows reals)
integer :: damage_date ! Day of month for damage extracted from event code
Expand Down
88 changes: 43 additions & 45 deletions biogeochem/EDCanopyStructureMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,15 @@ module EDCanopyStructureMod
use EDPftvarcon , only : EDPftvarcon_inst
use PRTParametersMod , only : prt_params
use FatesAllometryMod , only : carea_allom
use EDCohortDynamicsMod , only : copy_cohort, terminate_cohorts, terminate_cohort, fuse_cohorts
use EDCohortDynamicsMod , only : terminate_cohorts, terminate_cohort, fuse_cohorts
use EDCohortDynamicsMod , only : InitPRTObject
use EDCohortDynamicsMod , only : InitPRTBoundaryConditions
use FatesAllometryMod , only : tree_lai
use FatesAllometryMod , only : tree_sai
use EDtypesMod , only : ed_site_type, ed_patch_type, ed_cohort_type
use EDTypesMod , only : nclmax
use EDTypesMod , only : nlevleaf
use EDtypesMod , only : ed_site_type
use FatesPatchMod, only : fates_patch_type
use FatesCohortMod, only : fates_cohort_type
use EDParamsMod , only : nclmax
use EDParamsMod , only : nlevleaf
use EDtypesMod , only : AREA
use EDLoggingMortalityMod , only : UpdateHarvestC
use FatesGlobals , only : endrun => fates_endrun
Expand Down Expand Up @@ -136,8 +137,8 @@ subroutine canopy_structure( currentSite , bc_in )

!
! !LOCAL VARIABLES:
type(ed_patch_type) , pointer :: currentPatch
type(ed_cohort_type), pointer :: currentCohort
type(fates_patch_type) , pointer :: currentPatch
type(fates_cohort_type), pointer :: currentCohort
integer :: i_lyr ! current layer index
integer :: z ! Current number of canopy layers. (1= canopy, 2 = understorey)
integer :: ipft
Expand Down Expand Up @@ -337,18 +338,17 @@ end subroutine canopy_structure
subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr,bc_in)

use EDParamsMod, only : ED_val_comp_excln
use SFParamsMod, only : SF_val_CWD_frac

! !ARGUMENTS
type(ed_site_type), intent(inout) :: currentSite
type(ed_patch_type), intent(inout) :: currentPatch
type(fates_patch_type), intent(inout) :: currentPatch
integer, intent(in) :: i_lyr ! Current canopy layer of interest
type(bc_in_type), intent(in) :: bc_in

! !LOCAL VARIABLES:
type(ed_cohort_type), pointer :: currentCohort
type(ed_cohort_type), pointer :: copyc
type(ed_cohort_type), pointer :: nextc ! The next cohort in line
type(fates_cohort_type), pointer :: currentCohort
type(fates_cohort_type), pointer :: copyc
type(fates_cohort_type), pointer :: nextc ! The next cohort in line
integer :: i_cwd ! Index for CWD pool
real(r8) :: cc_loss ! cohort crown area loss in demotion (m2)
real(r8) :: leaf_c ! leaf carbon [kg]
Expand Down Expand Up @@ -670,7 +670,7 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr,bc_in)
!allocate(copyc%tveg_lpa)
!!allocate(copyc%l2fr_ema)
! Note, no need to give a starter value here,
! that will be taken care of in copy_cohort()
! that will be taken care of in copy()
!!call copyc%l2fr_ema%InitRMean(ema_60day)

! Initialize the PARTEH object and point to the
Expand All @@ -682,8 +682,8 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr,bc_in)
call InitHydrCohort(currentSite,copyc)
endif

call copy_cohort(currentCohort, copyc)
call InitPRTBoundaryConditions(copyc)
call currentCohort%Copy(copyc)
call copyc%InitPRTBoundaryConditions()

newarea = currentCohort%c_area - cc_loss
copyc%n = currentCohort%n*newarea/currentCohort%c_area
Expand Down Expand Up @@ -797,13 +797,13 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)

! !ARGUMENTS
type(ed_site_type), intent(inout), target :: currentSite
type(ed_patch_type), intent(inout), target :: currentPatch
type(fates_patch_type), intent(inout), target :: currentPatch
integer, intent(in) :: i_lyr ! Current canopy layer of interest

! !LOCAL VARIABLES:
type(ed_cohort_type), pointer :: currentCohort
type(ed_cohort_type), pointer :: copyc
type(ed_cohort_type), pointer :: nextc ! the next cohort, or used for looping
type(fates_cohort_type), pointer :: currentCohort
type(fates_cohort_type), pointer :: copyc
type(fates_cohort_type), pointer :: nextc ! the next cohort, or used for looping
! cohorts against the current

real(r8) :: scale_factor ! for prob. exclusion - scales weight to a fraction
Expand Down Expand Up @@ -1138,7 +1138,7 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)

!!allocate(copyc%l2fr_ema)
! Note, no need to give a starter value here,
! that will be taken care of in copy_cohort()
! that will be taken care of in copy()
!!call copyc%l2fr_ema%InitRMean(ema_60day)

! Initialize the PARTEH object and point to the
Expand All @@ -1157,8 +1157,8 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
!call copyc%tveg_lpa%InitRMean(ema_lpa,&
! init_value=currentPatch%tveg_lpa%GetMean())

call copy_cohort(currentCohort, copyc) !makes an identical copy...
call InitPRTBoundaryConditions(copyc)
call currentCohort%Copy(copyc) !makes an identical copy...
call copyc%InitPRTBoundaryConditions()

newarea = currentCohort%c_area - cc_gain !new area of existing cohort

Expand Down Expand Up @@ -1243,8 +1243,8 @@ subroutine canopy_spread( currentSite )
type (ed_site_type), intent(inout), target :: currentSite
!
! !LOCAL VARIABLES:
type (ed_cohort_type), pointer :: currentCohort
type (ed_patch_type) , pointer :: currentPatch
type (fates_cohort_type), pointer :: currentCohort
type (fates_patch_type) , pointer :: currentPatch
real(r8) :: sitelevel_canopyarea ! Amount of canopy in top layer at the site level
real(r8) :: inc ! Arbitrary daily incremental change in canopy area
integer :: z
Expand Down Expand Up @@ -1308,8 +1308,8 @@ subroutine canopy_summarization( nsites, sites, bc_in )
type(bc_in_type) , intent(in) :: bc_in(nsites)
!
! !LOCAL VARIABLES:
type (ed_patch_type) , pointer :: currentPatch
type (ed_cohort_type) , pointer :: currentCohort
type (fates_patch_type) , pointer :: currentPatch
type (fates_cohort_type) , pointer :: currentCohort
integer :: s
integer :: ft ! plant functional type
integer :: ifp ! the number of the vegetated patch (1,2,3). In SP mode bareground patch is 0
Expand Down Expand Up @@ -1499,7 +1499,8 @@ subroutine leaf_area_profile( currentSite )

! !USES:

use EDtypesMod , only : area, dinc_vai, dlower_vai, hitemax, n_hite_bins
use EDtypesMod , only : area, hitemax, n_hite_bins
use EDParamsMod, only : dinc_vai, dlower_vai

!
! !ARGUMENTS
Expand All @@ -1508,8 +1509,8 @@ subroutine leaf_area_profile( currentSite )

!
! !LOCAL VARIABLES:
type (ed_patch_type) , pointer :: currentPatch
type (ed_cohort_type) , pointer :: currentCohort
type (fates_patch_type) , pointer :: currentPatch
type (fates_cohort_type) , pointer :: currentCohort
real(r8) :: remainder !Thickness of layer at bottom of canopy.
real(r8) :: fleaf ! fraction of cohort incepting area that is leaves.
integer :: ft ! Plant functional type index.
Expand Down Expand Up @@ -1801,8 +1802,8 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
! to vegetation coverage to the host land model.
! ----------------------------------------------------------------------------------

use EDTypesMod , only : ed_patch_type, ed_cohort_type, &
ed_site_type, AREA
use EDTypesMod , only : ed_site_type, AREA
use FatesPatchMod, only : fates_patch_type
use FatesInterfaceTypesMod , only : bc_out_type

!
Expand All @@ -1813,9 +1814,9 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
type(bc_out_type), intent(inout) :: bc_out(nsites)

! Locals
type (ed_cohort_type) , pointer :: currentCohort
type (fates_cohort_type) , pointer :: currentCohort
integer :: s, ifp, c, p
type (ed_patch_type) , pointer :: currentPatch
type (fates_patch_type) , pointer :: currentPatch
real(r8) :: bare_frac_area
real(r8) :: total_patch_area
real(r8) :: total_canopy_area
Expand Down Expand Up @@ -2031,7 +2032,7 @@ function calc_areaindex(cpatch,ai_type) result(ai)
! ----------------------------------------------------------------------------------

! Arguments
type(ed_patch_type),intent(in), target :: cpatch
type(fates_patch_type),intent(in), target :: cpatch
character(len=*),intent(in) :: ai_type

integer :: cl,ft
Expand Down Expand Up @@ -2095,12 +2096,12 @@ subroutine CanopyLayerArea(currentPatch,site_spread,layer_index,layer_area)
! ---------------------------------------------------------------------------------------------

! Arguments
type(ed_patch_type),intent(inout), target :: currentPatch
type(fates_patch_type),intent(inout), target :: currentPatch
real(r8),intent(in) :: site_spread
integer,intent(in) :: layer_index
real(r8),intent(inout) :: layer_area

type(ed_cohort_type), pointer :: currentCohort
type(fates_cohort_type), pointer :: currentCohort


layer_area = 0.0_r8
Expand All @@ -2125,14 +2126,11 @@ subroutine UpdatePatchLAI(currentPatch)
! and related variables
! ---------------------------------------------------------------------------------------------

! Uses
use EDtypesMod, only : dlower_vai

! Arguments
type(ed_patch_type),intent(inout), target :: currentPatch
type(fates_patch_type),intent(inout), target :: currentPatch

! Local Variables
type(ed_cohort_type), pointer :: currentCohort
type(fates_cohort_type), pointer :: currentCohort
integer :: cl ! Canopy layer index
integer :: ft ! Plant functional type index

Expand Down Expand Up @@ -2175,10 +2173,10 @@ subroutine UpdateCohortLAI(currentCohort, canopy_layer_tlai, total_canopy_area)
! Update LAI and related variables for a given cohort

! Uses
use EDtypesMod, only : dlower_vai
use EDParamsMod, only : dlower_vai

! Arguments
type(ed_cohort_type),intent(inout), target :: currentCohort
type(fates_cohort_type),intent(inout), target :: currentCohort
real(r8), intent(in) :: canopy_layer_tlai(nclmax) ! total leaf area index of each canopy layer
real(r8), intent(in) :: total_canopy_area ! either patch%total_canopy_area or patch%area

Expand Down Expand Up @@ -2220,11 +2218,11 @@ function NumPotentialCanopyLayers(currentPatch,site_spread,include_substory) res
! the understory in the event the understory has reached maximum allowable area.
! --------------------------------------------------------------------------------------------

type(ed_patch_type),target :: currentPatch
type(fates_patch_type),target :: currentPatch
real(r8),intent(in) :: site_spread
logical :: include_substory

type(ed_cohort_type),pointer :: currentCohort
type(fates_cohort_type),pointer :: currentCohort

integer :: z
real(r8) :: c_area
Expand Down
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