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Merge pull request #931 from ckoven/respiration_newmodels
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Add Atkin et al 2017 leaf respiration model
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@glemieux
glemieux authored Mar 7, 2023
2 parents b8b905c + 008f8f8 commit 238c4af
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3 changes: 3 additions & 0 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -612,6 +612,7 @@ subroutine nan_cohort(cc_p)
!RESPIRATION
currentCohort%rdark = nan
currentCohort%resp_m = nan ! Maintenance respiration. kGC/cohort/year
currentCohort%resp_m_unreduced = nan ! Diagnostic-only unreduced Maintenance respiration. kGC/cohort/year
currentCohort%resp_excess = nan ! Respiration of excess (unallocatable) carbon (kg/indiv/day)
currentCohort%livestem_mr = nan ! Live stem maintenance respiration. kgC/indiv/s-1
currentCohort%livecroot_mr = nan ! Coarse root maintenance respiration. kgC/indiv/s-1
Expand Down Expand Up @@ -669,6 +670,7 @@ subroutine zero_cohort(cc_p)
currentCohort%status_coh = 0
currentCohort%rdark = 0._r8
currentCohort%resp_m = 0._r8
currentCohort%resp_m_unreduced = 0._r8
currentCohort%resp_excess = 0._r8
currentCohort%resp_g_tstep = 0._r8
currentCohort%livestem_mr = 0._r8
Expand Down Expand Up @@ -1941,6 +1943,7 @@ subroutine copy_cohort( currentCohort,copyc )
!RESPIRATION
n%rdark = o%rdark
n%resp_m = o%resp_m
n%resp_m_unreduced= o%resp_m_unreduced
n%resp_excess = o%resp_excess
n%resp_g_tstep = o%resp_g_tstep
n%livestem_mr = o%livestem_mr
Expand Down
152 changes: 119 additions & 33 deletions biogeophys/FatesPlantRespPhotosynthMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,9 @@ module FATESPlantRespPhotosynthMod
use PRTGenericMod, only : max_nleafage
use EDTypesMod, only : do_fates_salinity
use EDParamsMod, only : q10_mr
use EDParamsMod, only : maintresp_leaf_model
use FatesConstantsMod, only : lmrmodel_ryan_1991
use FatesConstantsMod, only : lmrmodel_atkin_etal_2017
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : carbon12_element
Expand All @@ -52,7 +55,7 @@ module FATESPlantRespPhotosynthMod
use PRTGenericMod, only : store_organ
use PRTGenericMod, only : repro_organ
use PRTGenericMod, only : struct_organ
use EDParamsMod, only : ED_val_base_mr_20, stomatal_model, stomatal_assim_model
use EDParamsMod, only : maintresp_nonleaf_baserate, stomatal_model, stomatal_assim_model
use PRTParametersMod, only : prt_params
use EDPftvarcon , only : EDPftvarcon_inst

Expand Down Expand Up @@ -127,7 +130,6 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
use FatesInterfaceTypesMod , only : bc_out_type
use EDCanopyStructureMod, only : calc_areaindex
use FatesConstantsMod, only : umolC_to_kgC
use FatesConstantsMod, only : g_per_kg
use FatesConstantsMod, only : umol_per_mmol
use FatesConstantsMod, only : rgas => rgas_J_K_kmol
use FatesParameterDerivedMod, only : param_derived
Expand Down Expand Up @@ -274,12 +276,6 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
integer :: iage ! loop counter for leaf age classes

! Parameters
! -----------------------------------------------------------------------
! Base maintenance respiration rate for plant tissues base_mr_20
! M. Ryan, 1991. Effects of climate change on plant respiration.
! Ecological Applications, 1(2), 157-167.
! Original expression is br = 0.0106 molC/(molN h)
! Conversion by molecular weights of C and N gives 2.525e-6 gC/(gN s)
!
! Base rate is at 20C. Adjust to 25C using the CN Q10 = 1.5
! (gC/gN/s)
Expand Down Expand Up @@ -527,17 +523,33 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)

end select

! MLO - Shouldn't these numbers be parameters too?
lmr25top = 2.525e-6_r8 * (1.5_r8 ** ((25._r8 - 20._r8)/10._r8))
lmr25top = lmr25top * lnc_top / (umolC_to_kgC * g_per_kg)
! Part VII: Calculate dark respiration (leaf maintenance) for this layer

select case (maintresp_leaf_model)

! Part VII: Calculate dark respiration (leaf maintenance) for this layer
call LeafLayerMaintenanceRespiration( lmr25top, & ! in
nscaler, & ! in
ft, & ! in
bc_in(s)%t_veg_pa(ifp), & ! in
lmr_z(iv,ft,cl)) ! out
case (lmrmodel_ryan_1991)

call LeafLayerMaintenanceRespiration_Ryan_1991( lnc_top, & ! in
nscaler, & ! in
ft, & ! in
bc_in(s)%t_veg_pa(ifp), & ! in
lmr_z(iv,ft,cl)) ! out

case (lmrmodel_atkin_etal_2017)

call LeafLayerMaintenanceRespiration_Atkin_etal_2017(lnc_top, & ! in
nscaler, & ! in
ft, & ! in
bc_in(s)%t_veg_pa(ifp), & ! in
currentPatch%tveg_lpa%GetMean(), & ! in
lmr_z(iv,ft,cl)) ! out

case default

write (fates_log(),*)'error, incorrect leaf respiration model specified'
call endrun(msg=errMsg(sourcefile, __LINE__))

end select

! Part VII: Calculate (1) maximum rate of carboxylation (vcmax),
! (2) maximum electron transport rate, (3) triose phosphate
Expand Down Expand Up @@ -755,7 +767,7 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
if ( int(woody(ft)) == itrue) then
tcwood = q10_mr**((bc_in(s)%t_veg_pa(ifp)-tfrz - 20.0_r8)/10.0_r8)
! kgC/s = kgN * kgC/kgN/s
currentCohort%livestem_mr = live_stem_n * ED_val_base_mr_20 * tcwood * maintresp_reduction_factor
currentCohort%livestem_mr = live_stem_n * maintresp_nonleaf_baserate * tcwood * maintresp_reduction_factor
else
currentCohort%livestem_mr = 0._r8
end if
Expand All @@ -774,7 +786,7 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
do j = 1,bc_in(s)%nlevsoil
tcsoi = q10_mr**((bc_in(s)%t_soisno_sl(j)-tfrz - 20.0_r8)/10.0_r8)

fnrt_mr_layer = fnrt_n * ED_val_base_mr_20 * tcsoi * rootfr_ft(ft,j) * maintresp_reduction_factor
fnrt_mr_layer = fnrt_n * maintresp_nonleaf_baserate * tcsoi * rootfr_ft(ft,j) * maintresp_reduction_factor

! calculate the cost of carbon for N fixation in each soil layer and calculate N fixation rate based on that [kgC / kgN]

Expand All @@ -795,7 +807,7 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
! Soil temperature used to adjust base rate of MR
tcsoi = q10_mr**((bc_in(s)%t_soisno_sl(j)-tfrz - 20.0_r8)/10.0_r8)
currentCohort%livecroot_mr = currentCohort%livecroot_mr + &
live_croot_n * ED_val_base_mr_20 * tcsoi * &
live_croot_n * maintresp_nonleaf_baserate * tcsoi * &
rootfr_ft(ft,j) * maintresp_reduction_factor
enddo
else
Expand Down Expand Up @@ -827,6 +839,9 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)

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%gpp_tstep = currentCohort%gpp_tstep * dtime
Expand Down Expand Up @@ -2046,22 +2061,35 @@ end subroutine GetCanopyGasParameters

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

subroutine LeafLayerMaintenanceRespiration(lmr25top_ft, &
nscaler, &
ft, &
subroutine LeafLayerMaintenanceRespiration_Ryan_1991(lnc_top, &
nscaler, &
ft, &
veg_tempk, &
lmr)

use FatesConstantsMod, only : tfrz => t_water_freeze_k_1atm
use FatesConstantsMod, only : umolC_to_kgC
use FatesConstantsMod, only : g_per_kg
use EDPftvarcon , only : EDPftvarcon_inst

! -----------------------------------------------------------------------
! Base maintenance respiration rate for plant tissues maintresp_leaf_ryan1991_baserate
! M. Ryan, 1991. Effects of climate change on plant respiration.
! Ecological Applications, 1(2), 157-167.
! Original expression is br = 0.0106 molC/(molN h)
! Conversion by molecular weights of C and N gives 2.525e-6 gC/(gN s)
! Which is the default value of maintresp_nonleaf_baserate

! Arguments
real(r8), intent(in) :: lmr25top_ft ! canopy top leaf maint resp rate at 25C
! for this pft (umol CO2/m**2/s)
integer, intent(in) :: ft ! (plant) Functional Type Index
real(r8), intent(in) :: lnc_top ! Leaf nitrogen content per unit area at canopy top [gN/m2]
real(r8), intent(in) :: nscaler ! Scale for leaf nitrogen profile
integer, intent(in) :: ft ! (plant) Functional Type Index
real(r8), intent(in) :: veg_tempk ! vegetation temperature
real(r8), intent(out) :: lmr ! Leaf Maintenance Respiration (umol CO2/m**2/s)

! Locals
real(r8) :: lmr25 ! leaf layer: leaf maintenance respiration rate at 25C (umol CO2/m**2/s)
real(r8) :: lmr25top ! canopy top leaf maint resp rate at 25C for this pft (umol CO2/m**2/s)

! Parameter
real(r8), parameter :: lmrha = 46390._r8 ! activation energy for lmr (J/mol)
Expand All @@ -2070,26 +2098,84 @@ subroutine LeafLayerMaintenanceRespiration(lmr25top_ft, &
real(r8), parameter :: lmrc = 1.15912391_r8 ! scaling factor for high
! temperature inhibition (25 C = 1.0)



lmr25top = EDPftvarcon_inst%maintresp_leaf_ryan1991_baserate(ft) * (1.5_r8 ** ((25._r8 - 20._r8)/10._r8))
lmr25top = lmr25top * lnc_top / (umolC_to_kgC * g_per_kg)


! Part I: Leaf Maintenance respiration: umol CO2 / m**2 [leaf] / s
! ----------------------------------------------------------------------------------
lmr25 = lmr25top_ft * nscaler
lmr25 = lmr25top * nscaler

if ( nint(EDpftvarcon_inst%c3psn(ft)) == 1)then
if (nint(EDPftvarcon_inst%c3psn(ft)) /= 1) then
! temperature sensitivity of C3 plants
lmr = lmr25 * ft1_f(veg_tempk, lmrha) * &
fth_f(veg_tempk, lmrhd, lmrse, lmrc)
fth_f(veg_tempk, lmrhd, lmrse, lmrc)
else
! temperature sensitivity of C4 plants
lmr = lmr25 * 2._r8**((veg_tempk-(tfrz+25._r8))/10._r8)
lmr = lmr / (1._r8 + exp( 1.3_r8*(veg_tempk-(tfrz+55._r8)) ))
end if
endif

! Any hydrodynamic limitations could go here, currently none
! lmr = lmr * (nothing)

end subroutine LeafLayerMaintenanceRespiration
end subroutine LeafLayerMaintenanceRespiration_Ryan_1991

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

subroutine LeafLayerMaintenanceRespiration_Atkin_etal_2017(lnc_top, &
nscaler, &
ft, &
veg_tempk, &
tgrowth, &
lmr)

use FatesConstantsMod, only : tfrz => t_water_freeze_k_1atm
use FatesConstantsMod, only : umolC_to_kgC
use FatesConstantsMod, only : g_per_kg
use EDPftvarcon , only : EDPftvarcon_inst

! Arguments
real(r8), intent(in) :: lnc_top ! Leaf nitrogen content per unit area at canopy top [gN/m2]
integer, intent(in) :: ft ! (plant) Functional Type Index
real(r8), intent(in) :: nscaler ! Scale for leaf nitrogen profile
real(r8), intent(in) :: veg_tempk ! vegetation temperature (degrees K)
real(r8), intent(in) :: tgrowth ! lagged vegetation temperature averaged over acclimation timescale (degrees K)
real(r8), intent(out) :: lmr ! Leaf Maintenance Respiration (umol CO2/m**2/s)

! Locals
real(r8) :: lmr25 ! leaf layer: leaf maintenance respiration rate at 25C (umol CO2/m**2/s)
real(r8) :: r_0 ! base respiration rate, PFT-dependent (umol CO2/m**2/s)
real(r8) :: r_t_ref ! acclimated ref respiration rate (umol CO2/m**2/s)
real(r8) :: lmr25top ! canopy top leaf maint resp rate at 25C for this pft (umol CO2/m**2/s)

! Parameters
! values from Atkin et al., 2017 https://doi.org/10.1007/978-3-319-68703-2_6
! and Heskel et al., 2016 https://doi.org/10.1073/pnas.1520282113
real(r8), parameter :: b = 0.1012_r8 ! (degrees C**-1)
real(r8), parameter :: c = -0.0005_r8 ! (degrees C**-2)
real(r8), parameter :: TrefC = 25._r8 ! (degrees C)
real(r8), parameter :: r_1 = 0.2061_r8 ! (umol CO2/m**2/s / (gN/(m2 leaf)))
real(r8), parameter :: r_2 = -0.0402_r8 ! (umol CO2/m**2/s/degree C)

! parameter values of r_0 as listed in Atkin et al 2017: (umol CO2/m**2/s)
! Broad-leaved trees 1.7560
! Needle-leaf trees 1.4995
! Shrubs 2.0749
! C3 herbs/grasses 2.1956
! In the absence of better information, we use the same value for C4 grasses as C3 grasses.

! note that this code uses the relationship between leaf N and respiration from Atkin et al
! for the top of the canopy, but then assumes proportionality with N through the canopy.

! r_0 currently put into the EDPftvarcon_inst%dev_arbitrary_pft
! all figs in Atkin et al 2017 stop at zero Celsius so we will assume acclimation is fixed below that
r_0 = EDPftvarcon_inst%maintresp_leaf_atkin2017_baserate(ft)
r_t_ref = nscaler * (r_0 + r_1 * lnc_top + r_2 * max(0._r8, (tgrowth - tfrz) ))

lmr = r_t_ref * exp(b * (veg_tempk - tfrz - TrefC) + c * ((veg_tempk-tfrz)**2 - TrefC**2))

end subroutine LeafLayerMaintenanceRespiration_Atkin_etal_2017

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

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