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Merge pull request #1317 from adrifoster/patch_testing
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Update to cohort insertion and sorting routines
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@adrifoster
adrifoster authored Feb 11, 2025
2 parents fea5f0a + f24f5b5 commit ff84522
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Showing 35 changed files with 2,472 additions and 580 deletions.
1 change: 1 addition & 0 deletions biogeochem/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ list(APPEND fates_sources
FatesCohortMod.F90
FatesAllometryMod.F90
DamageMainMod.F90
EDCohortDynamicsMod.F90
FatesPatchMod.F90)

sourcelist_to_parent(fates_sources)
481 changes: 104 additions & 377 deletions biogeochem/EDCohortDynamicsMod.F90
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110 changes: 18 additions & 92 deletions biogeochem/EDPatchDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ module EDPatchDynamicsMod
use EDPftvarcon , only : EDPftvarcon_inst
use EDPftvarcon , only : GetDecompyFrac
use PRTParametersMod , only : prt_params
use EDCohortDynamicsMod , only : fuse_cohorts, sort_cohorts, insert_cohort
use EDCohortDynamicsMod , only : fuse_cohorts
use EDTypesMod , only : area_site => area
use ChecksBalancesMod , only : PatchMassStock
use FatesLitterMod , only : ncwd
Expand Down Expand Up @@ -516,17 +516,13 @@ subroutine spawn_patches( currentSite, bc_in)
type (fates_patch_type) , pointer :: currentPatch
type (fates_cohort_type), pointer :: currentCohort
type (fates_cohort_type), pointer :: nc
type (fates_cohort_type), pointer :: storesmallcohort
type (fates_cohort_type), pointer :: storebigcohort
real(r8) :: site_areadis_primary ! total area disturbed (to primary forest) in m2 per site per day
real(r8) :: site_areadis_secondary ! total area disturbed (to secondary forest) in m2 per site per day
real(r8) :: patch_site_areadis ! total area disturbed in m2 per patch per day
real(r8) :: site_areadis ! total site area disturbed in m2 per day
real(r8) :: age ! notional age of this patch in years
integer :: el ! element loop index
integer :: pft ! pft loop index
integer :: tnull ! is there a tallest cohort?
integer :: snull ! is there a shortest cohort?
integer :: levcan ! canopy level
real(r8) :: leaf_c ! leaf carbon [kg]
real(r8) :: fnrt_c ! fineroot carbon [kg]
Expand Down Expand Up @@ -562,9 +558,6 @@ subroutine spawn_patches( currentSite, bc_in)
logical :: buffer_patch_used
!---------------------------------------------------------------------

storesmallcohort => null() ! storage of the smallest cohort for insertion routine
storebigcohort => null() ! storage of the largest cohort for insertion routine

if (hlm_use_nocomp .eq. itrue) then
min_nocomp_pft = 0
max_nocomp_pft = numpft
Expand Down Expand Up @@ -1249,30 +1242,7 @@ subroutine spawn_patches( currentSite, bc_in)
! if some plants in the new temporary cohort survived the transfer to the new patch,
! then put the cohort into the linked list.
cohort_n_gt_zero: if (nc%n > 0.0_r8) then
storebigcohort => newPatch%tallest
storesmallcohort => newPatch%shortest
if(associated(newPatch%tallest))then
tnull = 0
else
tnull = 1
newPatch%tallest => nc
nc%taller => null()
endif

if(associated(newPatch%shortest))then
snull = 0
else
snull = 1
newPatch%shortest => nc
nc%shorter => null()
endif

call insert_cohort(newPatch, nc, newPatch%tallest, newPatch%shortest, &
tnull, snull, storebigcohort, storesmallcohort)

newPatch%tallest => storebigcohort
newPatch%shortest => storesmallcohort

call newPatch%InsertCohort(nc)
else
! sadly, no plants in the cohort survived. on the bright side, we can deallocate their memory.
call nc%FreeMemory()
Expand All @@ -1285,8 +1255,10 @@ subroutine spawn_patches( currentSite, bc_in)

currentCohort => currentCohort%taller
enddo cohortloop
call newPatch%ValidateCohorts()

call sort_cohorts(currentPatch)
call currentPatch%SortCohorts()
call currentPatch%ValidateCohorts()

!update area of donor patch
oldarea = currentPatch%area
Expand Down Expand Up @@ -1317,7 +1289,8 @@ subroutine spawn_patches( currentSite, bc_in)
call terminate_cohorts(currentSite, currentPatch, 1,16,bc_in)
call fuse_cohorts(currentSite,currentPatch, bc_in)
call terminate_cohorts(currentSite, currentPatch, 2,16,bc_in)
call sort_cohorts(currentPatch)
call currentPatch%SortCohorts()
call currentPatch%ValidateCohorts()

end if areadis_gt_zero_if ! if ( newPatch%area > nearzero ) then

Expand All @@ -1344,7 +1317,8 @@ subroutine spawn_patches( currentSite, bc_in)
call terminate_cohorts(currentSite, newPatch, 1,17, bc_in)
call fuse_cohorts(currentSite,newPatch, bc_in)
call terminate_cohorts(currentSite, newPatch, 2,17, bc_in)
call sort_cohorts(newPatch)
call newPatch%SortCohorts()
call newPatch%ValidateCohorts()
endif


Expand Down Expand Up @@ -1675,11 +1649,7 @@ subroutine split_patch(currentSite, currentPatch, new_patch, fraction_to_keep, a
! !LOCAL VARIABLES:
integer :: el ! element loop index
type (fates_cohort_type), pointer :: nc
type (fates_cohort_type), pointer :: storesmallcohort
type (fates_cohort_type), pointer :: storebigcohort
type (fates_cohort_type), pointer :: currentCohort
integer :: tnull ! is there a tallest cohort?
integer :: snull ! is there a shortest cohort?
integer :: pft
real(r8) :: temp_area

Expand Down Expand Up @@ -1746,34 +1716,14 @@ subroutine split_patch(currentSite, currentPatch, new_patch, fraction_to_keep, a
! loss of individuals from source patch due to area shrinking
currentCohort%n = currentCohort%n * fraction_to_keep

storebigcohort => new_patch%tallest
storesmallcohort => new_patch%shortest
if(associated(new_patch%tallest))then
tnull = 0
else
tnull = 1
new_patch%tallest => nc
nc%taller => null()
endif

if(associated(new_patch%shortest))then
snull = 0
else
snull = 1
new_patch%shortest => nc
nc%shorter => null()
endif

call insert_cohort(new_patch, nc, new_patch%tallest, new_patch%shortest, &
tnull, snull, storebigcohort, storesmallcohort)

new_patch%tallest => storebigcohort
new_patch%shortest => storesmallcohort
call new_patch%InsertCohort(nc)

currentCohort => currentCohort%taller
enddo ! currentCohort
call new_patch%ValidateCohorts()

call sort_cohorts(currentPatch)
call currentPatch%SortCohorts()
call currentPatch%ValidateCohorts()

!update area of donor patch
currentPatch%area = currentPatch%area - temp_area
Expand Down Expand Up @@ -3116,7 +3066,8 @@ subroutine fuse_patches( csite, bc_in )
tmpptr => currentPatch%older
call fuse_2_patches(csite, currentPatch, tpp)
call fuse_cohorts(csite,tpp, bc_in)
call sort_cohorts(tpp)
call tpp%SortCohorts()
call tpp%ValidateCohorts()
currentPatch => tmpptr

!------------------------------------------------------------------------!
Expand Down Expand Up @@ -3238,10 +3189,7 @@ subroutine fuse_2_patches(csite, dp, rp)
! !LOCAL VARIABLES:
type (fates_cohort_type), pointer :: currentCohort ! Current Cohort
type (fates_cohort_type), pointer :: nextc ! Remembers next cohort in list
type (fates_cohort_type), pointer :: storesmallcohort
type (fates_cohort_type), pointer :: storebigcohort
integer :: c,p !counters for pft and litter size class.
integer :: tnull,snull ! are the tallest and shortest cohorts associated?
integer :: el ! loop counting index for elements
integer :: pft ! loop counter for pfts
type(fates_patch_type), pointer :: youngerp ! pointer to the patch younger than donor
Expand Down Expand Up @@ -3321,31 +3269,8 @@ subroutine fuse_2_patches(csite, dp, rp)
endif

do while(associated(dp%shortest))

storebigcohort => rp%tallest
storesmallcohort => rp%shortest

if(associated(rp%tallest))then
tnull = 0
else
tnull = 1
rp%tallest => currentCohort
endif

if(associated(rp%shortest))then
snull = 0
else
snull = 1
rp%shortest => currentCohort
endif

call insert_cohort(rp, currentCohort, rp%tallest, rp%shortest, &
tnull, snull, storebigcohort, storesmallcohort)

rp%tallest => storebigcohort
rp%shortest => storesmallcohort

!currentCohort%patchptr => rp

call rp%InsertCohort(currentCohort)

currentCohort => nextc

Expand All @@ -3356,6 +3281,7 @@ subroutine fuse_2_patches(csite, dp, rp)
endif

enddo !cohort
call rp%ValidateCohorts()
endif !are there any cohorts?

call patch_pft_size_profile(rp) ! Recalculate the patch size profile for the resulting patch
Expand Down
5 changes: 3 additions & 2 deletions biogeochem/EDPhysiologyMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ module EDPhysiologyMod
use EDPftvarcon , only : GetDecompyFrac
use FatesInterfaceTypesMod, only : bc_in_type
use FatesInterfaceTypesMod, only : bc_out_type
use EDCohortDynamicsMod , only : create_cohort, sort_cohorts
use EDCohortDynamicsMod , only : create_cohort
use EDCohortDynamicsMod , only : InitPRTObject
use FatesAllometryMod , only : tree_lai_sai
use FatesAllometryMod , only : leafc_from_treelai
Expand Down Expand Up @@ -681,7 +681,7 @@ subroutine trim_canopy( currentSite )
! Add debug diagnstic output to determine which patch
if (debug) then
write(fates_log(),*) 'Current patch:', ipatch
write(fates_log(),*) 'Current patch cohorts:', currentPatch%countcohorts
write(fates_log(),*) 'Current patch cohorts:', currentPatch%num_cohorts
endif

icohort = 1
Expand Down Expand Up @@ -2791,6 +2791,7 @@ subroutine recruitment(currentSite, currentPatch, bc_in)
endif any_recruits
endif use_this_pft_if
enddo !pft loop
call currentPatch%ValidateCohorts()
end subroutine recruitment

! ======================================================================================
Expand Down
9 changes: 4 additions & 5 deletions biogeochem/FatesCohortMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ module FatesCohortMod

implicit none
private

! PARAMETERS
character(len=*), parameter, private :: sourcefile = __FILE__

Expand All @@ -77,7 +77,6 @@ module FatesCohortMod
!---------------------------------------------------------------------------

! VEGETATION STRUCTURE

integer :: pft ! pft index
real(r8) :: n ! number of individuals in cohort per 'area' (10000m2 default) [/m2]
real(r8) :: dbh ! diameter at breast height [cm]
Expand Down Expand Up @@ -450,7 +449,7 @@ subroutine NanValues(this)
this%cambial_mort = nan
this%crownfire_mort = nan
this%fire_mort = nan

end subroutine NanValues

!===========================================================================
Expand Down Expand Up @@ -547,7 +546,7 @@ subroutine Create(this, prt, pft, nn, height, coage, dbh, status, &
!
! DESCRIPTION:
! set up values for a newly created cohort

! ARGUMENTS
class(fates_cohort_type), intent(inout), target :: this ! cohort object
class(prt_vartypes), intent(inout), pointer :: prt ! The allocated PARTEH object
Expand All @@ -574,7 +573,7 @@ subroutine Create(this, prt, pft, nn, height, coage, dbh, status, &

! initialize cohort
call this%Init(prt)

! set values
this%pft = pft
this%crowndamage = crowndamage
Expand Down
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