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Merge pull request #1197 from ckoven/growth_respiration
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Move growth respiration to daily timestep
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@glemieux
glemieux authored Nov 14, 2024
2 parents e3e7d2c + 9d28eb6 commit de5f266
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18 changes: 11 additions & 7 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -1067,20 +1067,24 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
nextc%n*nextc%gpp_acc)/newn
currentCohort%npp_acc = (currentCohort%n*currentCohort%npp_acc + &
nextc%n*nextc%npp_acc)/newn
currentCohort%resp_acc = (currentCohort%n*currentCohort%resp_acc + &
nextc%n*nextc%resp_acc)/newn
currentCohort%resp_acc_hold = &
(currentCohort%n*currentCohort%resp_acc_hold + &
nextc%n*nextc%resp_acc_hold)/newn
currentCohort%resp_m_acc = (currentCohort%n*currentCohort%resp_m_acc + &
nextc%n*nextc%resp_m_acc)/newn
currentCohort%resp_m_acc_hold = &
(currentCohort%n*currentCohort%resp_m_acc_hold + &
nextc%n*nextc%resp_m_acc_hold)/newn
currentCohort%resp_g_acc_hold = &
(currentCohort%n*currentCohort%resp_g_acc_hold + &
nextc%n*nextc%resp_g_acc_hold)/newn
currentCohort%npp_acc_hold = &
(currentCohort%n*currentCohort%npp_acc_hold + &
nextc%n*nextc%npp_acc_hold)/newn
currentCohort%gpp_acc_hold = &
(currentCohort%n*currentCohort%gpp_acc_hold + &
nextc%n*nextc%gpp_acc_hold)/newn

currentCohort%resp_excess = (currentCohort%n*currentCohort%resp_excess + &
nextc%n*nextc%resp_excess)/newn
currentCohort%resp_excess_hold = &
(currentCohort%n*currentCohort%resp_excess_hold + &
nextc%n*nextc%resp_excess_hold)/newn

currentCohort%dmort = (currentCohort%n*currentCohort%dmort + &
nextc%n*nextc%dmort)/newn
Expand Down
73 changes: 36 additions & 37 deletions biogeochem/FatesCohortMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -133,21 +133,24 @@ module FatesCohortMod
! after the dynamics call-sequence is completed. [kgC/indiv/day]
! _acc_hold: While _acc is zero'd after the dynamics call sequence and then integrated,
! _acc_hold "holds" the integrated value until the next time dynamics is
! called. This is necessary for restarts. This variable also has units
! converted to a useful rate [kgC/indiv/yr]
! called. This is useful because growth and excess respiration
! are calculated once daily, but we want to remove the average
! flux from the daily NEP signal, so we remove it from the next day.
! The hold variables are also useful for rebuilding history on restart.
! Units converted to a useful rate [kgC/indiv/yr]
! --------------------------------------------------------------------------

real(r8) :: gpp_tstep ! Gross Primary Production (see above *)
real(r8) :: gpp_acc
real(r8) :: gpp_acc_hold

real(r8) :: npp_tstep ! Net Primary Production (see above *)
real(r8) :: npp_acc
real(r8) :: npp_acc_hold

real(r8) :: resp_tstep ! Autotrophic respiration (see above *)
real(r8) :: resp_acc
real(r8) :: resp_acc_hold
real(r8) :: resp_m_tstep ! Maintenance respiration (see above *)
real(r8) :: resp_m_acc
real(r8) :: resp_m_acc_hold
real(r8) :: resp_g_acc_hold

real(r8) :: c13disc_clm ! carbon 13 discrimination in new synthesized carbon at each indiv/timestep [ppm]
real(r8) :: c13disc_acc ! carbon 13 discrimination in new synthesized carbon at each indiv/day
Expand Down Expand Up @@ -202,11 +205,15 @@ module FatesCohortMod
integer :: twostr_col ! The column index in the two-stream solution that this cohort is part of

! RESPIRATION COMPONENTS
real(r8) :: resp_excess_hold ! respiration of excess carbon [kgC/indiv/yr]
! note: this is flagged "hold" because it is calculated
! at the end of the day (dynamics) but is used
! on the following day (like growth respiration)
! to aid in reporting a more accurate sub-daily
! NEP

real(r8) :: rdark ! dark respiration [kgC/indiv/s]
real(r8) :: resp_g_tstep ! growth respiration [kgC/indiv/timestep]
real(r8) :: resp_m ! maintenance respiration [kgC/indiv/timestep]
real(r8) :: resp_m_unreduced ! diagnostic-only unreduced maintenance respiration [kgC/indiv/timestep]
real(r8) :: resp_excess ! respiration of excess carbon [kgC/indiv/day]
real(r8) :: livestem_mr ! aboveground live stem maintenance respiration [kgC/indiv/s]
real(r8) :: livecroot_mr ! belowground live stem maintenance respiration [kgC/indiv/s]
real(r8) :: froot_mr ! live fine root maintenance respiration [kgC/indiv/s]
Expand Down Expand Up @@ -375,12 +382,12 @@ subroutine NanValues(this)
this%gpp_tstep = nan
this%gpp_acc = nan
this%gpp_acc_hold = nan
this%npp_tstep = nan
this%npp_acc = nan
this%npp_acc_hold = nan
this%resp_tstep = nan
this%resp_acc = nan
this%resp_acc_hold = nan
this%resp_m_tstep = nan
this%resp_m_acc = nan
this%resp_m_acc_hold = nan
this%resp_g_acc_hold = nan
this%c13disc_clm = nan
this%c13disc_acc = nan
this%vcmax25top = nan
Expand Down Expand Up @@ -410,10 +417,8 @@ subroutine NanValues(this)

! RESPIRATION COMPONENTS
this%rdark = nan
this%resp_g_tstep = nan
this%resp_m = nan
this%resp_m_unreduced = nan
this%resp_excess = nan
this%resp_excess_hold = nan
this%livestem_mr = nan
this%livecroot_mr = nan
this%froot_mr = nan
Expand Down Expand Up @@ -477,17 +482,18 @@ subroutine ZeroValues(this)
this%size_class_lasttimestep = 0
this%gpp_tstep = 0._r8
this%gpp_acc = 0._r8
this%npp_tstep = 0._r8
this%npp_acc = 0._r8
this%resp_tstep = 0._r8
this%resp_acc = 0._r8
this%resp_m_tstep = 0._r8
this%resp_m_acc = 0._r8

! do not zero these, they are not built
! so more appropriate to leave unzerod
! to prevent uninitialized use
! this%gpp_acc_hold = nan
! this%npp_acc_hold = nan
! this%resp_acc_hold = nan
! this%resp_m_acc_hold = nan
! this%resp_g_acc_hold = nan
! this%resp_excess_hold = nan

this%c13disc_clm = 0._r8
this%c13disc_acc = 0._r8
Expand Down Expand Up @@ -516,10 +522,7 @@ subroutine ZeroValues(this)
this%daily_p_demand = -9._r8
this%seed_prod = 0._r8
this%rdark = 0._r8
this%resp_g_tstep = 0._r8
this%resp_m = 0._r8
this%resp_m_unreduced = 0._r8
this%resp_excess = 0._r8
this%livestem_mr = 0._r8
this%livecroot_mr = 0._r8
this%froot_mr = 0._r8
Expand Down Expand Up @@ -706,12 +709,12 @@ subroutine Copy(this, copyCohort)
copyCohort%gpp_tstep = this%gpp_tstep
copyCohort%gpp_acc = this%gpp_acc
copyCohort%gpp_acc_hold = this%gpp_acc_hold
copyCohort%npp_tstep = this%npp_tstep
copyCohort%npp_acc = this%npp_acc
copyCohort%npp_acc_hold = this%npp_acc_hold
copyCohort%resp_tstep = this%resp_tstep
copyCohort%resp_acc = this%resp_acc
copyCohort%resp_acc_hold = this%resp_acc_hold
copyCohort%resp_m_tstep = this%resp_m_tstep
copyCohort%resp_m_acc = this%resp_m_acc
copyCohort%resp_m_acc_hold = this%resp_m_acc_hold
copyCohort%resp_g_acc_hold = this%resp_g_acc_hold
copyCohort%c13disc_clm = this%c13disc_clm
copyCohort%c13disc_acc = this%c13disc_acc
copyCohort%vcmax25top = this%vcmax25top
Expand Down Expand Up @@ -744,10 +747,8 @@ subroutine Copy(this, copyCohort)

! RESPIRATION COMPONENTS
copyCohort%rdark = this%rdark
copyCohort%resp_g_tstep = this%resp_g_tstep
copyCohort%resp_m = this%resp_m
copyCohort%resp_m_unreduced = this%resp_m_unreduced
copyCohort%resp_excess = this%resp_excess
copyCohort%resp_excess_hold = this%resp_excess_hold
copyCohort%livestem_mr = this%livestem_mr
copyCohort%livecroot_mr = this%livecroot_mr
copyCohort%froot_mr = this%froot_mr
Expand Down Expand Up @@ -880,7 +881,7 @@ subroutine InitPRTBoundaryConditions(this)
call this%prt%RegisterBCIn(acnp_bc_in_id_cdamage, bc_ival=this%crowndamage)

call this%prt%RegisterBCInOut(acnp_bc_inout_id_dbh, bc_rval=this%dbh)
call this%prt%RegisterBCInOut(acnp_bc_inout_id_resp_excess, bc_rval=this%resp_excess)
call this%prt%RegisterBCInOut(acnp_bc_inout_id_resp_excess, bc_rval=this%resp_excess_hold)
call this%prt%RegisterBCInOut(acnp_bc_inout_id_l2fr, bc_rval=this%l2fr)
call this%prt%RegisterBCInOut(acnp_bc_inout_id_cx_int, bc_rval=this%cx_int)
call this%prt%RegisterBCInOut(acnp_bc_inout_id_emadcxdt, bc_rval=this%ema_dcxdt)
Expand Down Expand Up @@ -1047,14 +1048,12 @@ subroutine Dump(this)
write(fates_log(),*) 'cohort%gpp_acc = ', this%gpp_acc
write(fates_log(),*) 'cohort%gpp_tstep = ', this%gpp_tstep
write(fates_log(),*) 'cohort%npp_acc_hold = ', this%npp_acc_hold
write(fates_log(),*) 'cohort%npp_tstep = ', this%npp_tstep
write(fates_log(),*) 'cohort%npp_acc = ', this%npp_acc
write(fates_log(),*) 'cohort%resp_tstep = ', this%resp_tstep
write(fates_log(),*) 'cohort%resp_acc = ', this%resp_acc
write(fates_log(),*) 'cohort%resp_acc_hold = ', this%resp_acc_hold
write(fates_log(),*) 'cohort%resp_m_tstep = ', this%resp_m_tstep
write(fates_log(),*) 'cohort%resp_m_acc = ', this%resp_m_acc
write(fates_log(),*) 'cohort%resp_m_acc_hold = ', this%resp_m_acc_hold
write(fates_log(),*) 'cohort%resp_g_acc_hold = ', this%resp_g_acc_hold
write(fates_log(),*) 'cohort%rdark = ', this%rdark
write(fates_log(),*) 'cohort%resp_m = ', this%resp_m
write(fates_log(),*) 'cohort%resp_g_tstep = ', this%resp_g_tstep
write(fates_log(),*) 'cohort%livestem_mr = ', this%livestem_mr
write(fates_log(),*) 'cohort%livecroot_mr = ', this%livecroot_mr
write(fates_log(),*) 'cohort%froot_mr = ', this%froot_mr
Expand Down
8 changes: 3 additions & 5 deletions biogeochem/FatesSoilBGCFluxMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -123,9 +123,7 @@ subroutine UnPackNutrientAquisitionBCs(sites, bc_in)
! Locals
integer :: nsites ! number of sites
integer :: s ! site loop index
integer :: j ! soil layer
integer :: icomp ! competitor index
integer :: id ! decomp layer index
integer :: pft ! pft index
type(fates_patch_type), pointer :: cpatch ! current patch pointer
type(fates_cohort_type), pointer :: ccohort ! current cohort pointer
Expand Down Expand Up @@ -350,9 +348,10 @@ subroutine PrepCH4BCs(csite,bc_in,bc_out)
! this is a best (bad) guess at fine root MR + total root GR
! (kgC/indiv/yr) -> gC/m2/s
bc_out%root_resp(1:bc_in%nlevsoil) = bc_out%root_resp(1:bc_in%nlevsoil) + &
ccohort%resp_acc_hold*years_per_day*g_per_kg*days_per_sec* &
(ccohort%resp_m_acc_hold + ccohort%resp_g_acc_hold)*years_per_day*g_per_kg*days_per_sec* &
ccohort%n*area_inv*(1._r8-prt_params%allom_agb_frac(pft)) * csite%rootfrac_scr(1:bc_in%nlevsoil)



end if

if( prt_params%woody(pft)==itrue ) then
Expand Down Expand Up @@ -646,7 +645,6 @@ subroutine FluxIntoLitterPools(csite, bc_in, bc_out)
integer :: nlev_eff_decomp ! number of effective decomp layers
real(r8) :: area_frac ! fraction of site's area of current patch
real(r8) :: z_decomp ! Used for calculating depth midpoints of decomp layers
integer :: s ! Site index
integer :: el ! Element index (C,N,P,etc)
integer :: j ! Soil layer index
integer :: id ! Decomposition layer index
Expand Down
13 changes: 2 additions & 11 deletions biogeophys/EDAccumulateFluxesMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ module EDAccumulateFluxesMod
!------------------------------------------------------------------------------
! !DESCRIPTION:
! This routine accumulates NPP, GPP and respiration of each cohort over the course of each 24 hour period.
! The fluxes are stored per cohort, and the npp_tstep (etc) fluxes are calcualted in EDPhotosynthesis
! The fluxes are stored per cohort, and the gpp_tstep (etc) fluxes are calculated in EDPhotosynthesis
! This routine cannot be in EDPhotosynthesis because EDPhotosynthesis is a loop and therefore would
! erroneously add these things up multiple times.
! Rosie Fisher. March 2014.
Expand Down Expand Up @@ -80,17 +80,8 @@ subroutine AccumulateFluxes_ED(nsites, sites, bc_in, bc_out, dt_time)
! Accumulate fluxes from hourly to daily values.
! _tstep fluxes are KgC/indiv/timestep _acc are KgC/indiv/day

if ( debug ) then

write(fates_log(),*) 'EDAccumFlux 64 ',ccohort%npp_tstep
write(fates_log(),*) 'EDAccumFlux 66 ',ccohort%gpp_tstep
write(fates_log(),*) 'EDAccumFlux 67 ',ccohort%resp_tstep

endif

ccohort%npp_acc = ccohort%npp_acc + ccohort%npp_tstep
ccohort%gpp_acc = ccohort%gpp_acc + ccohort%gpp_tstep
ccohort%resp_acc = ccohort%resp_acc + ccohort%resp_tstep
ccohort%resp_m_acc = ccohort%resp_m_acc + ccohort%resp_m_tstep

ccohort%sym_nfix_daily = ccohort%sym_nfix_daily + ccohort%sym_nfix_tstep

Expand Down
48 changes: 12 additions & 36 deletions biogeophys/FatesPlantRespPhotosynthMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -739,11 +739,10 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
end do leaf_layer_loop

! Zero cohort flux accumulators.
currentCohort%npp_tstep = 0.0_r8
currentCohort%resp_tstep = 0.0_r8

currentCohort%resp_m_tstep = 0.0_r8
currentCohort%gpp_tstep = 0.0_r8
currentCohort%rdark = 0.0_r8
currentCohort%resp_m = 0.0_r8
currentCohort%ts_net_uptake = 0.0_r8
currentCohort%c13disc_clm = 0.0_r8

Expand Down Expand Up @@ -968,47 +967,24 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
! calcualate some fluxes that are sums and nets of the base fluxes
! ------------------------------------------------------------------

if ( debug ) write(fates_log(),*) 'EDPhoto 904 ', currentCohort%resp_m
if ( debug ) write(fates_log(),*) 'EDPhoto 905 ', currentCohort%rdark
if ( debug ) write(fates_log(),*) 'EDPhoto 906 ', currentCohort%livestem_mr
if ( debug ) write(fates_log(),*) 'EDPhoto 907 ', currentCohort%livecroot_mr
if ( debug ) write(fates_log(),*) 'EDPhoto 908 ', currentCohort%froot_mr



! add on whole plant respiration values in kgC/indiv/s-1
currentCohort%resp_m = currentCohort%livestem_mr + &
currentCohort%resp_m_tstep = currentCohort%livestem_mr + &
currentCohort%livecroot_mr + &
currentCohort%froot_mr

currentCohort%froot_mr + &
currentCohort%rdark

! no drought response right now.. something like:
! resp_m = resp_m * (1.0_r8 - currentPatch%btran_ft(currentCohort%pft) * &
! resp_m_tstep = resp_m_tstep * (1.0_r8 - currentPatch%btran_ft(currentCohort%pft) * &
! EDPftvarcon_inst%resp_drought_response(ft))

currentCohort%resp_m = currentCohort%resp_m + currentCohort%rdark

! save as a diagnostic the un-throttled maintenance respiration to be able to know how strong this is
currentCohort%resp_m_unreduced = currentCohort%resp_m / maintresp_reduction_factor

! convert from kgC/indiv/s to kgC/indiv/timestep
currentCohort%resp_m = currentCohort%resp_m * dtime
currentCohort%resp_m_tstep = currentCohort%resp_m_tstep * dtime
currentCohort%gpp_tstep = currentCohort%gpp_tstep * dtime
currentCohort%ts_net_uptake = currentCohort%ts_net_uptake * dtime

if ( debug ) write(fates_log(),*) 'EDPhoto 911 ', currentCohort%gpp_tstep
if ( debug ) write(fates_log(),*) 'EDPhoto 912 ', currentCohort%resp_tstep
if ( debug ) write(fates_log(),*) 'EDPhoto 913 ', currentCohort%resp_m


currentCohort%resp_g_tstep = prt_params%grperc(ft) * &
(max(0._r8,currentCohort%gpp_tstep - currentCohort%resp_m))


currentCohort%resp_tstep = currentCohort%resp_m + &
currentCohort%resp_g_tstep ! kgC/indiv/ts
currentCohort%npp_tstep = currentCohort%gpp_tstep - &
currentCohort%resp_tstep ! kgC/indiv/ts


! save as a diagnostic the un-throttled maintenance respiration to be able to know how strong this is
currentCohort%resp_m_unreduced = currentCohort%resp_m_tstep / maintresp_reduction_factor

! Accumulate the combined conductance (stomatal+leaf boundary layer)
! Note that currentCohort%g_sb_laweight is weighted by the leaf area
! of each cohort and has units of [m/s] * [m2 leaf]
Expand Down
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