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Merge pull request #1 from rgknox/DynamicRoots_MD_bugfix
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Dynamic roots md bugfix
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@JunyanDing
JunyanDing authored Jul 21, 2021
2 parents 31bf1cd + bdd3668 commit 3d5b550
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Showing 37 changed files with 2,951 additions and 1,882 deletions.
148 changes: 84 additions & 64 deletions biogeochem/EDCanopyStructureMod.F90
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77 changes: 36 additions & 41 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -91,11 +91,11 @@ module EDCohortDynamicsMod
use PRTAllometricCNPMod, only : acnp_bc_in_id_pft, acnp_bc_in_id_ctrim
use PRTAllometricCNPMod, only : acnp_bc_in_id_lstat, acnp_bc_inout_id_dbh
use PRTAllometricCNPMod, only : acnp_bc_inout_id_rmaint_def, acnp_bc_in_id_netdc
use PRTAllometricCNPMod, only : acnp_bc_in_id_netdn, acnp_bc_in_id_netdp
use PRTAllometricCNPMod, only : acnp_bc_in_id_netdnh4, acnp_bc_in_id_netdno3, acnp_bc_in_id_netdp
use PRTAllometricCNPMod, only : acnp_bc_out_id_cefflux, acnp_bc_out_id_nefflux
use PRTAllometricCNPMod, only : acnp_bc_out_id_pefflux
use PRTAllometricCNPMod, only : acnp_bc_out_id_ngrow,acnp_bc_out_id_nmax
use PRTAllometricCNPMod, only : acnp_bc_out_id_pgrow,acnp_bc_out_id_pmax
use PRTAllometricCNPMod, only : acnp_bc_out_id_nneed
use PRTAllometricCNPMod, only : acnp_bc_out_id_pneed


use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
Expand Down Expand Up @@ -400,7 +400,8 @@ subroutine InitPRTBoundaryConditions(new_cohort)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_ctrim,bc_rval = new_cohort%canopy_trim)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_lstat,bc_ival = new_cohort%status_coh)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdc, bc_rval = new_cohort%npp_acc)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdn, bc_rval = new_cohort%daily_n_uptake)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdnh4, bc_rval = new_cohort%daily_nh4_uptake)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdno3, bc_rval = new_cohort%daily_no3_uptake)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdp, bc_rval = new_cohort%daily_p_uptake)

call new_cohort%prt%RegisterBCInOut(acnp_bc_inout_id_dbh,bc_rval = new_cohort%dbh)
Expand All @@ -409,10 +410,8 @@ subroutine InitPRTBoundaryConditions(new_cohort)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_cefflux, bc_rval = new_cohort%daily_c_efflux)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_nefflux, bc_rval = new_cohort%daily_n_efflux)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_pefflux, bc_rval = new_cohort%daily_p_efflux)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_ngrow, bc_rval = new_cohort%daily_n_need1)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_nmax, bc_rval = new_cohort%daily_n_need2)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_pgrow, bc_rval = new_cohort%daily_p_need1)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_pmax, bc_rval = new_cohort%daily_p_need2)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_nneed, bc_rval = new_cohort%daily_n_need)
call new_cohort%prt%RegisterBCOut(acnp_bc_out_id_pneed, bc_rval = new_cohort%daily_p_need)


case DEFAULT
Expand Down Expand Up @@ -559,15 +558,14 @@ subroutine nan_cohort(cc_p)
currentCohort%resp_acc = nan ! RESP: kGC/cohort/day

! Fluxes from nutrient allocation
currentCohort%daily_n_uptake = nan
currentCohort%daily_nh4_uptake = nan
currentCohort%daily_no3_uptake = nan
currentCohort%daily_p_uptake = nan
currentCohort%daily_c_efflux = nan
currentCohort%daily_n_efflux = nan
currentCohort%daily_p_efflux = nan
currentCohort%daily_n_need1 = nan
currentCohort%daily_n_need2 = nan
currentCohort%daily_p_need1 = nan
currentCohort%daily_p_need2 = nan
currentCohort%daily_n_need = nan
currentCohort%daily_p_need = nan
currentCohort%daily_n_demand = nan
currentCohort%daily_p_demand = nan

Expand Down Expand Up @@ -678,17 +676,16 @@ subroutine zero_cohort(cc_p)
! after allocation. These variables exist in
! carbon-only mode but are not used.

currentCohort%daily_n_uptake = 0._r8
currentCohort%daily_nh4_uptake = 0._r8
currentCohort%daily_no3_uptake = 0._r8
currentCohort%daily_p_uptake = 0._r8

currentCohort%daily_c_efflux = 0._r8
currentCohort%daily_n_efflux = 0._r8
currentCohort%daily_p_efflux = 0._r8

currentCohort%daily_n_need1 = 0._r8
currentCohort%daily_n_need2 = 0._r8
currentCohort%daily_p_need1 = 0._r8
currentCohort%daily_p_need2 = 0._r8
currentCohort%daily_n_need = 0._r8
currentCohort%daily_p_need = 0._r8

! Initialize these as negative
currentCohort%daily_p_demand = -9._r8
Expand All @@ -698,7 +695,7 @@ subroutine zero_cohort(cc_p)
end subroutine zero_cohort

!-------------------------------------------------------------------------------------!
subroutine terminate_cohorts( currentSite, currentPatch, level , call_index)
subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_in)
!
! !DESCRIPTION:
! terminates cohorts when they get too small
Expand All @@ -711,7 +708,8 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index)
type (ed_patch_type), intent(inout), target :: currentPatch
integer , intent(in) :: level
integer :: call_index

type(bc_in_type), intent(in) :: bc_in

! Important point regarding termination levels. Termination is typically
! called after fusion. We do this so that we can re-capture the biomass that would
! otherwise be lost from termination. The biomass of a fused plant remains in the
Expand Down Expand Up @@ -827,7 +825,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index)

if (currentCohort%n.gt.0.0_r8) then
call SendCohortToLitter(currentSite,currentPatch, &
currentCohort,currentCohort%n)
currentCohort,currentCohort%n,bc_in)
end if

! Set pointers and remove the current cohort from the list
Expand Down Expand Up @@ -861,7 +859,7 @@ end subroutine terminate_cohorts

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

subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant)
subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant,bc_in)

! -----------------------------------------------------------------------------------
! This routine transfers the existing mass in all pools and all elements
Expand All @@ -884,9 +882,9 @@ subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant)
type (ed_patch_type) , target :: cpatch
type (ed_cohort_type) , target :: ccohort
real(r8) :: nplant ! Number (absolute)
! of plants to transfer
! of plants to transfer
type(bc_in_type), intent(in) :: bc_in

!
type(litter_type), pointer :: litt ! Litter object for each element
type(site_fluxdiags_type),pointer :: flux_diags

Expand All @@ -910,7 +908,8 @@ subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant)

plant_dens = nplant/cpatch%area

call set_root_fraction(csite%rootfrac_scr, pft, csite%zi_soil)
call set_root_fraction(csite%rootfrac_scr, pft, csite%zi_soil, &
bc_in%max_rooting_depth_index_col)

do el=1,num_elements

Expand Down Expand Up @@ -1396,8 +1395,10 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
currentCohort%frmort = (currentCohort%n*currentCohort%frmort + nextc%n*nextc%frmort)/newn

! Nutrient fluxes
currentCohort%daily_n_uptake = (currentCohort%n*currentCohort%daily_n_uptake + &
nextc%n*nextc%daily_n_uptake)/newn
currentCohort%daily_nh4_uptake = (currentCohort%n*currentCohort%daily_nh4_uptake + &
nextc%n*nextc%daily_nh4_uptake)/newn
currentCohort%daily_no3_uptake = (currentCohort%n*currentCohort%daily_no3_uptake + &
nextc%n*nextc%daily_no3_uptake)/newn
currentCohort%daily_p_uptake = (currentCohort%n*currentCohort%daily_p_uptake + &
nextc%n*nextc%daily_p_uptake)/newn

Expand All @@ -1413,15 +1414,10 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
currentCohort%daily_p_efflux = (currentCohort%n*currentCohort%daily_p_efflux + &
nextc%n*nextc%daily_p_efflux)/newn

currentCohort%daily_n_need1 = (currentCohort%n*currentCohort%daily_n_need1 + &
nextc%n*nextc%daily_n_need1)/newn
currentCohort%daily_n_need2 = (currentCohort%n*currentCohort%daily_n_need2 + &
nextc%n*nextc%daily_n_need2)/newn
currentCohort%daily_p_need1 = (currentCohort%n*currentCohort%daily_p_need1 + &
nextc%n*nextc%daily_p_need1)/newn
currentCohort%daily_p_need2 = (currentCohort%n*currentCohort%daily_p_need2 + &
nextc%n*nextc%daily_p_need2)/newn

currentCohort%daily_n_need = (currentCohort%n*currentCohort%daily_n_need + &
nextc%n*nextc%daily_n_need)/newn
currentCohort%daily_p_need = (currentCohort%n*currentCohort%daily_p_need + &
nextc%n*nextc%daily_p_need)/newn


! logging mortality, Yi Xu
Expand Down Expand Up @@ -1817,15 +1813,14 @@ subroutine copy_cohort( currentCohort,copyc )
n%year_net_uptake = o%year_net_uptake
n%ts_net_uptake = o%ts_net_uptake

n%daily_n_uptake = o%daily_n_uptake
n%daily_nh4_uptake = o%daily_nh4_uptake
n%daily_no3_uptake = o%daily_no3_uptake
n%daily_p_uptake = o%daily_p_uptake
n%daily_c_efflux = o%daily_c_efflux
n%daily_n_efflux = o%daily_n_efflux
n%daily_p_efflux = o%daily_p_efflux
n%daily_n_need1 = o%daily_n_need1
n%daily_n_need2 = o%daily_n_need2
n%daily_p_need1 = o%daily_p_need1
n%daily_p_need2 = o%daily_p_need2
n%daily_n_need = o%daily_n_need
n%daily_p_need = o%daily_p_need
n%daily_n_demand = o%daily_n_demand
n%daily_p_demand = o%daily_p_demand

Expand Down
9 changes: 7 additions & 2 deletions biogeochem/EDLoggingMortalityMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ module EDLoggingMortalityMod
use EDParamsMod , only : logging_mechanical_frac
use EDParamsMod , only : logging_coll_under_frac
use EDParamsMod , only : logging_dbhmax_infra
use FatesInterfaceTypesMod , only : bc_in_type
use FatesInterfaceTypesMod , only : hlm_current_year
use FatesInterfaceTypesMod , only : hlm_current_month
use FatesInterfaceTypesMod , only : hlm_current_day
Expand Down Expand Up @@ -394,7 +395,7 @@ end subroutine get_harvest_rate_area

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

subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site_areadis)
subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site_areadis, bc_in)

! -------------------------------------------------------------------------------------------
!
Expand Down Expand Up @@ -440,6 +441,8 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
type(ed_patch_type) , intent(inout), target :: currentPatch
type(ed_patch_type) , intent(inout), target :: newPatch
real(r8) , intent(in) :: patch_site_areadis
type(bc_in_type) , intent(in) :: bc_in


!LOCAL VARIABLES:
type(ed_cohort_type), pointer :: currentCohort
Expand Down Expand Up @@ -567,7 +570,9 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
! derived from the current patch, so we need to multiply by patch_areadis/np%area
! ----------------------------------------------------------------------------------------

call set_root_fraction(currentSite%rootfrac_scr, pft, currentSite%zi_soil)
call set_root_fraction(currentSite%rootfrac_scr, pft, &
currentSite%zi_soil, &
bc_in%max_rooting_depth_index_col)

ag_wood = (direct_dead+indirect_dead) * (struct_m + sapw_m ) * &
prt_params%allom_agb_frac(currentCohort%pft)
Expand Down
1 change: 0 additions & 1 deletion biogeochem/EDMortalityFunctionsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ module EDMortalityFunctionsMod
use FatesInterfaceTypesMod , only : hlm_use_planthydro
use EDLoggingMortalityMod , only : LoggingMortality_frac
use EDParamsMod , only : fates_mortality_disturbance_fraction
use FatesInterfaceTypesMod , only : bc_in_type

use PRTGenericMod, only : all_carbon_elements
use PRTGenericMod, only : store_organ
Expand Down
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