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updates to leaf unit tests
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@rgknox
rgknox committed Oct 16, 2024
1 parent f7ad159 commit 6e5e183
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Showing 3 changed files with 172 additions and 94 deletions.
63 changes: 36 additions & 27 deletions biogeophys/LeafBiophysicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -440,7 +440,7 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
ac, & ! out
aj, & ! out
ap, & ! out
co2_intercel) ! out
co2_intracel) ! out


! ------------------------------------------------------------------------------------
Expand Down Expand Up @@ -481,7 +481,7 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
real(r8), intent(out) :: aj ! RuBP-limited gross photosynthesis (umol CO2/m**2/s)
real(r8), intent(out) :: ap ! product-limited (C3) or CO2-limited
! (C4) gross photosynthesis (umol CO2/m**2/s)
real(r8), intent(out) :: co2_intercel ! intercellular leaf CO2 (Pa)
real(r8), intent(out) :: co2_intracel ! intracellular leaf CO2 (Pa)

! Important Note on the gas pressures as input arguments. This photosynthesis scheme will iteratively
! solve for the co2 partial pressure at the leaf surface (ie in the stomata). The reference
Expand All @@ -503,7 +503,7 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
real(r8) :: aquad,bquad,cquad ! terms for quadratic equations
real(r8) :: r1,r2 ! roots of quadratic equation

real(r8) :: co2_intercel_old ! intercellular leaf CO2 (Pa) (previous iteration)
real(r8) :: co2_intracel_old ! intracellular leaf CO2 (Pa) (previous iteration)
logical :: loop_continue ! Loop control variable
integer :: niter ! iteration loop index

Expand All @@ -524,17 +524,17 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in



! First guess on ratio between intercellular co2 and the atmosphere
! First guess on ratio between intracellular co2 and the atmosphere
! an iterator converges on actual
real(r8),parameter :: init_a2l_co2_c3 = 0.7_r8
real(r8),parameter :: init_a2l_co2_c4 = 0.4_r8

! When iteratively solving for intercellular co2 concentration, this
! When iteratively solving for intracellular co2 concentration, this
! is the maximum tolerable change to accept convergence [Pa]
real(r8),parameter :: co2_intercel_tol = 1._r8
real(r8),parameter :: co2_intracel_tol = 0.1_r8

! Maximum number of iterations on intercelluar co2 solver until is quits
integer, parameter :: max_iters = 10
! Maximum number of iterations on intracelluar co2 solver until is quits
integer, parameter :: max_iters = 50

! empirical curvature parameter for ap photosynthesis co-limitation
real(r8),parameter :: theta_ip = 0.999_r8
Expand Down Expand Up @@ -572,17 +572,17 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in


! Not trivial solution, some biomass and some light
! Initialize first guess of intercellular co2 conc [Pa]
! Initialize first guess of intracellular co2 conc [Pa]
if (lb_params%c3psn(ft) == c3_path_index) then
co2_intercel = init_a2l_co2_c3 * can_co2_ppress
co2_intracel = init_a2l_co2_c3 * can_co2_ppress
else
co2_intercel = init_a2l_co2_c4 * can_co2_ppress
co2_intracel = init_a2l_co2_c4 * can_co2_ppress
end if

! Perform iterative solution to converge on net assimilation,
! stomatal conductance and intercellular co2 concentration
! stomatal conductance and intracellular co2 concentration
! this is not a gradient method, it merely re-runs calculations
! based off of updated intercellular co2 concentration until
! based off of updated intracellular co2 concentration until
! there is minimal deviation from last attempt

niter = 0
Expand All @@ -592,17 +592,17 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
! Increment iteration counter. Stop if too many iterations
niter = niter + 1

! Save old co2_intercel
co2_intercel_old = co2_intercel
! Save old co2_intracel
co2_intracel_old = co2_intracel

! Photosynthesis limitation rate calculations
if (lb_params%c3psn(ft) == c3_path_index)then

! C3: Rubisco-limited photosynthesis
ac = AgrossRubiscoC3(vcmax,co2_intercel,can_o2_ppress,co2_cpoint,mm_kco2,mm_ko2)
ac = AgrossRubiscoC3(vcmax,co2_intracel,can_o2_ppress,co2_cpoint,mm_kco2,mm_ko2)

! C3: RuBP-limited photosynthesis
aj = AgrossRuBPC3(par_abs,jmax,co2_intercel,co2_cpoint )
aj = AgrossRuBPC3(par_abs,jmax,co2_intracel,co2_cpoint )

! Gross photosynthesis smoothing calculations. Co-limit ac and aj.
! RGK: We can remove this smoothing, right? theta is always nearly 1...?
Expand All @@ -623,7 +623,7 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
aj = AgrossRuBPC4(par_abs)

! C4: PEP carboxylase-limited (CO2-limited)
ap = AgrossPEPC4(co2_intercel,co2_rcurve_islope,can_press)
ap = AgrossPEPC4(co2_intracel,co2_rcurve_islope,can_press)

! Gross photosynthesis smoothing calculations. First co-limit ac and aj. Then co-limit ap

Expand Down Expand Up @@ -658,7 +658,7 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in

! A note about the use of the quadratic equations for calculating stomatal conductance
! ------------------------------------------------------------------------------------
! These two following models calculate the conductance between the intercellular leaf
! These two following models calculate the conductance between the intracellular leaf
! space and the leaf surface, not the canopy air space. Transport between the leaf
! surface and the canopy air space is governed by the leaf boundary layer conductance.
! However, we need to estimate the properties at the surface of the leaf to solve for
Expand All @@ -670,7 +670,7 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
! e_s = (e_i g_s + e_c g_b)/(g_b + g_s)
!
! The leaf surface humidity (e_s) becomes an expression of canopy humidity (e_c),
! intercellular humidity (e_i, which is the saturation humidity at leaf temperature),
! intracellular humidity (e_i, which is the saturation humidity at leaf temperature),
! boundary layer conductance (g_b) (these are all known) and stomatal conductance
! (g_s) (this is still unknown). This expression is substituted into the stomatal
! conductance equation. The resulting form of these equations becomes a quadratic.
Expand Down Expand Up @@ -709,19 +709,28 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
end if
end if

! Derive new estimate for co2_intercel
co2_intercel = can_co2_ppress - anet_out * can_press * &
(h2o_co2_bl_diffuse_ratio*gs_out+h2o_co2_stoma_diffuse_ratio*gb) / (gb*gs_out)
! Derive new estimate for co2_intracel
co2_intracel = can_co2_ppress - anet_out * can_press * &
(h2o_co2_bl_diffuse_ratio/gb + h2o_co2_stoma_diffuse_ratio/gs_out)

! (h2o_co2_bl_diffuse_ratio*gs_out+h2o_co2_stoma_diffuse_ratio*gb) / (gb*gs_out)

! Check for co2_intercel convergence.
! Check for co2_intracel convergence.
! The tolerance is if the new solution is less than 1 Pascal within
! the previous solution. Typical values for the range are 20-50,
! with values less than atmospheric during production, and values
! greater than atmospheric during dark respiration

if( abs(co2_intercel-co2_intercel_old) < co2_intercel_tol .or. niter >= max_iters) then
if( abs(co2_intracel-co2_intracel_old) < co2_intracel_tol .or. niter > max_iters) then
loop_continue = .false.
end if
if(debug)then
if( niter == max_iters) then
write(fates_log(),*) 'photosynthesis exceeded the iteration limit'
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
end if

end do iter_loop

! estimate carbon 13 discrimination in leaf level carbon
Expand All @@ -731,9 +740,9 @@ subroutine LeafLayerPhotosynthesis(par_abs, & ! in
! just hard code b and \alpha_s for now, might move to parameter set in future
! b = 27.0 alpha_s = 4.4
! TODO, not considering C4 or CAM right now, may need to address this
! note co2_intercel is intracelluar CO2, not intercelluar
! note co2_intracel is intracelluar CO2, not intercelluar
c13disc_out = 4.4_r8 + (27.0_r8 - 4.4_r8) * &
min (can_co2_ppress, max (co2_intercel, 0._r8)) / can_co2_ppress
min (can_co2_ppress, max (co2_intracel, 0._r8)) / can_co2_ppress

return
end subroutine LeafLayerPhotosynthesis
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