leaf biophysics refactor and functional unit tests

biogeochem/EDPhysiologyMod.F90

@@ -48,7 +48,7 @@ module EDPhysiologyMod
   use FatesAllometryMod   , only : tree_lai
   use FatesAllometryMod   , only : tree_sai
   use FatesAllometryMod   , only : leafc_from_treelai
-  use FatesAllometryMod   , only : decay_coeff_vcmax
+  use LeafBiophysicsMod   , only : DecayCoeffVcmax
   use FatesLitterMod      , only : litter_type
   use EDTypesMod          , only : site_massbal_type
   use EDTypesMod          , only : numlevsoil_max
@@ -781,7 +781,7 @@ subroutine trim_canopy( currentSite )
 
                 ! Calculate sla_levleaf following the sla profile with overlying leaf area
                 ! Scale for leaf nitrogen profile
-                kn = decay_coeff_vcmax(currentCohort%vcmax25top, &
+                kn = DecayCoeffVcmax(currentCohort%vcmax25top, &
                      prt_params%leafn_vert_scaler_coeff1(ipft), &
                      prt_params%leafn_vert_scaler_coeff2(ipft))
 

biogeochem/FatesAllometryMod.F90

@@ -99,7 +99,8 @@ module FatesAllometryMod
   use FatesGlobals     , only : FatesWarn,N2S,A2S,I2S
   use EDParamsMod      , only : nlevleaf,dinc_vai,dlower_vai
   use DamageMainMod    , only : GetCrownReduction
-
+  use LeafBiophysicsMod, only : DecayCoeffVcmax
+
   implicit none
 
   private
@@ -117,7 +118,6 @@ module FatesAllometryMod
   public :: bdead_allom   ! Generic bdead wrapper
   public :: carea_allom   ! Generic crown area wrapper
   public :: bstore_allom  ! Generic maximum storage carbon wrapper
-  public :: decay_coeff_vcmax ! vertical canopy decay rate, scaled on vcmax
   public :: ForceDBH      ! Method to set DBH to sync with structure
                           ! or fineroot biomass
   public :: CheckIntegratedAllometries
@@ -715,9 +715,9 @@ real(r8) function tree_lai( leaf_c, pft, c_area, nplant, cl, canopy_lai, vcmax25
        end if
 
        ! Coefficient for exponential decay of 1/sla with canopy depth:
-       kn = decay_coeff_vcmax(vcmax25top, &
-                              prt_params%leafn_vert_scaler_coeff1(pft), &
-                              prt_params%leafn_vert_scaler_coeff2(pft))
+       kn = DecayCoeffVcmax(vcmax25top, &
+                            prt_params%leafn_vert_scaler_coeff1(pft), &
+                            prt_params%leafn_vert_scaler_coeff2(pft))
 
        ! take PFT-level maximum SLA value, even if under a thick canopy (which has units of m2/gC),
        ! and put into units of m2/kgC
@@ -913,9 +913,9 @@ real(r8) function leafc_from_treelai( treelai, pft, c_area, nplant, cl, vcmax25t
     sla_max = g_per_kg * prt_params%slamax(pft)
 
     ! Coefficient for exponential decay of 1/sla with canopy depth:
-    kn = decay_coeff_vcmax(vcmax25top, &
-                           prt_params%leafn_vert_scaler_coeff1(pft), &
-                           prt_params%leafn_vert_scaler_coeff2(pft))
+    kn = DecayCoeffVcmax(vcmax25top, &
+                         prt_params%leafn_vert_scaler_coeff1(pft), &
+                         prt_params%leafn_vert_scaler_coeff2(pft))
 
     if(treelai > 0.0_r8)then 
        ! Leafc_per_unitarea at which sla_max is reached due to exponential sla profile in canopy:
@@ -2911,42 +2911,6 @@ end subroutine jackson_beta_root_profile
   ! =====================================================================================
 
 
-  real(r8) function decay_coeff_vcmax(vcmax25top,slope_param,intercept_param)
-
-    ! ---------------------------------------------------------------------------------
-    ! This function estimates the decay coefficient used to estimate vertical
-    ! attenuation of properties in the canopy.
-    !
-    ! Decay coefficient (kn) is a function of vcmax25top for each pft.
-    !
-    ! Currently, this decay is applied to vcmax attenuation, SLA (optionally)
-    ! and leaf respiration (optionally w/ Atkin)
-    !
-    ! ---------------------------------------------------------------------------------
-
-    !ARGUMENTS
-
-    real(r8),intent(in) :: vcmax25top
-    real(r8),intent(in) :: slope_param      ! multiplies vcmax25top
-    real(r8),intent(in) :: intercept_param  ! adds to vcmax25top
-
-
-    !LOCAL VARIABLES
-    ! -----------------------------------------------------------------------------------
-
-    ! Bonan et al (2011) JGR, 116, doi:10.1029/2010JG001593 used
-    ! kn = 0.11. Here, we derive kn from vcmax25 as in Lloyd et al 
-    ! (2010) Biogeosciences, 7, 1833-1859
-    ! This function is also used to vertically scale leaf maintenance
-    ! respiration.
-
-    decay_coeff_vcmax = exp(slope_param * vcmax25top - intercept_param)
-
-    return
-  end function decay_coeff_vcmax
-
-  ! =====================================================================================
-
   subroutine ForceDBH( ipft, crowndamage, canopy_trim, elongf_leaf, elongf_stem, d, h, bdead, bl )
 
      ! =========================================================================