Conflict resolution on merge. EDtypes on HEAD had the new cp_masterpr…

…oc variable, while master had the use_fates_plant_hydro variable, both added to same section. Both are valid in the merge.

components/clm/src/ED/biogeochem/EDCohortDynamicsMod.F90

@@ -248,7 +248,6 @@ subroutine allocate_live_biomass(cc_p,mode)
        currentcohort%bsw = EDecophyscon%sapwood_ratio(ft) * currentcohort%hite *(currentcohort%balive + &
             currentcohort%laimemory)*leaf_frac
 
-
     else ! Leaves are on (leaves_off_switch==1)
 
     !the purpose of this section is to figure out the root and stem biomass when the leaves are off
@@ -1039,13 +1038,15 @@ subroutine copy_cohort( currentCohort,copyc )
     n%gpp_acc_hold    = o%gpp_acc_hold
     n%gpp_acc         = o%gpp_acc
     n%gpp_tstep       = o%gpp_tstep
+
     n%npp_acc_hold    = o%npp_acc_hold
     n%npp_tstep       = o%npp_tstep
 
     if ( DEBUG ) write(fates_log(),*) 'EDcohortDyn Ia ',o%npp_acc
     if ( DEBUG ) write(fates_log(),*) 'EDcohortDyn Ib ',o%resp_acc
 
-    n%npp_acc_hold    = o%npp_acc_hold
+    n%npp_acc         = o%npp_acc
+
     n%resp_tstep      = o%resp_tstep
     n%resp_acc        = o%resp_acc
     n%resp_acc_hold   = o%resp_acc_hold

components/clm/src/ED/main/EDTypesMod.F90

@@ -155,6 +155,12 @@ module EDTypesMod
   ! 1 = TRUE (is master) 0 = FALSE (is not master)
   integer :: cp_masterproc
 
+
+  ! Module switches (this will be read in one day)
+  ! This variable only exists now to serve as a place holder
+  !!!!!!!!!! THIS SHOULD NOT BE SET TO TRUE !!!!!!!!!!!!!!!!!
+  logical,parameter :: use_fates_plant_hydro = .false.
+
   !************************************
   !** COHORT type structure          **
   !************************************
@@ -664,4 +670,10 @@ subroutine set_root_fraction( this , depth_gl)
 
   end subroutine set_root_fraction
 
+
+  ! =====================================================================================
+
+
+
+
 end module EDTypesMod

components/clm/src/ED/main/FatesInterfaceMod.F90

@@ -219,14 +219,13 @@ module FatesInterfaceMod
       ! Shaded canopy resistance [s/m]
       real(r8), allocatable :: rssha_pa(:)
 
-      ! Canopy conductance [mmol m-2 s-1]
-      real(r8), allocatable :: gccanopy_pa(:)
+      ! leaf photosynthesis (umol CO2 /m**2/ s)
+      ! (NOT CURRENTLY USED, PLACE-HOLDER)
+      !real(r8), allocatable :: psncanopy_pa(:)
 
-      ! patch sunlit leaf photosynthesis (umol CO2 /m**2/ s)
-      real(r8), allocatable :: psncanopy_pa(:)
-
-      ! patch sunlit leaf maintenance respiration rate (umol CO2/m**2/s) 
-      real(r8), allocatable :: lmrcanopy_pa(:)
+      ! leaf maintenance respiration rate (umol CO2/m**2/s) 
+      ! (NOT CURRENTLY USED, PLACE-HOLDER)
+      !real(r8), allocatable :: lmrcanopy_pa(:)
 
       ! Canopy Radiation Boundaries
       ! ---------------------------------------------------------------------------------
@@ -439,11 +438,9 @@ subroutine allocate_bcout(bc_out)
       allocate(bc_out%btran_pa(maxPatchesPerCol))
 
       ! Photosynthesis
+
       allocate(bc_out%rssun_pa(maxPatchesPerCol))
       allocate(bc_out%rssha_pa(maxPatchesPerCol))
-      allocate(bc_out%gccanopy_pa(maxPatchesPerCol))
-      allocate(bc_out%lmrcanopy_pa(maxPatchesPerCol))
-      allocate(bc_out%psncanopy_pa(maxPatchesPerCol))
 
       ! Canopy Radiation
       allocate(bc_out%albd_parb(maxPatchesPerCol,cp_numSWb))
@@ -523,9 +520,6 @@ subroutine zero_bcs(this,s)
 
       this%bc_out(s)%rssun_pa(:)     = 0.0_r8
       this%bc_out(s)%rssha_pa(:)     = 0.0_r8
-      this%bc_out(s)%gccanopy_pa(:)  = 0.0_r8
-      this%bc_out(s)%psncanopy_pa(:) = 0.0_r8
-      this%bc_out(s)%lmrcanopy_pa(:) = 0.0_r8
 
       this%bc_out(s)%albd_parb(:,:) = 0.0_r8
       this%bc_out(s)%albi_parb(:,:) = 0.0_r8

components/clm/src/ED/main/FatesParameterDerivedMod.F90

@@ -0,0 +1,116 @@
+module FatesParameterDerivedMod
+
+  ! -------------------------------------------------------------------------------------
+  ! This module contains all procedures types and settings for any quantities that are
+  ! statically derived from static model parameters.  These are unchanging quantities
+  ! and are based off of simple relationships from parameters that the user can
+  ! vary.  This should be called once, and early in the model initialization call
+  ! sequence immediately after FATES parameters are read in.
+  ! -------------------------------------------------------------------------------------
+
+  use FatesConstantsMod, only : r8 => fates_r8
+  use FatesConstantsMod, only : umolC_to_kgC
+  use FatesConstantsMod, only : g_per_kg
+
+  type param_derived_type
+
+     real(r8), allocatable :: vcmax25top(:) ! canopy top: maximum rate of carboxylation
+                                            ! at 25C (umol CO2/m**2/s)
+     real(r8), allocatable :: jmax25top(:)  ! canopy top: maximum electron transport 
+                                            ! rate at 25C (umol electrons/m**2/s)
+     real(r8), allocatable :: tpu25top(:)   ! canopy top: triose phosphate utilization
+                                            ! rate at 25C (umol CO2/m**2/s)
+     real(r8), allocatable :: kp25top(:)    ! canopy top: initial slope of CO2 response
+                                            ! curve (C4 plants) at 25C
+     real(r8), allocatable :: lmr25top(:)   ! canopy top: leaf maintenance respiration
+                                            ! rate at 25C (umol CO2/m**2/s)
+   contains
+
+     procedure :: Init
+     procedure :: InitAllocate
+
+  end type param_derived_type
+
+  type(param_derived_type) :: param_derived
+
+contains
+
+  subroutine InitAllocate(this,maxpft)
+
+    class(param_derived_type), intent(inout) :: this
+    integer, intent(in)                                 :: maxpft
+
+    allocate(this%vcmax25top(maxpft))
+    allocate(this%jmax25top(maxpft))
+    allocate(this%tpu25top(maxpft))
+    allocate(this%kp25top(maxpft))
+    allocate(this%lmr25top(maxpft))
+
+    return
+  end subroutine InitAllocate
+
+  ! =====================================================================================
+
+  subroutine Init(this,maxpft)
+
+    use pftconMod        , only: pftcon
+
+    class(param_derived_type), intent(inout) :: this
+    integer, intent(in)                      :: maxpft
+
+    ! local variables
+    integer  :: ft                 ! pft index
+    real(r8) :: lnc                ! leaf N concentration (gN leaf/m^2)
+
+    associate( &
+         slatop    => pftcon%slatop , & ! specific leaf area at top of canopy, 
+                                        ! projected area basis [m^2/gC]
+         fnitr     => pftcon%fnitr  , & ! foliage nitrogen limitation factor (-)
+         leafcn    => pftcon%leafcn )   ! leaf C:N (gC/gN)
+
+      call this%InitAllocate(maxpft)
+
+      do ft = 1,maxpft
+
+         ! Leaf nitrogen concentration at the top of the canopy (g N leaf / m**2 leaf)
+         lnc  = 1._r8 / (slatop(ft) * leafcn(ft))
+
+         ! at the moment in ED we assume that there is no active N cycle. 
+         ! This should change, of course. FIX(RF,032414) Sep2011. 
+         ! fudge - shortcut using fnitr as a proxy for vcmax... 
+         this%vcmax25top(ft) = fnitr(ft)
+
+         ! Parameters derived from vcmax25top. 
+         ! Bonan et al (2011) JGR, 116, doi:10.1029/2010JG001593
+         ! used jmax25 = 1.97 vcmax25, from Wullschleger (1993) Journal of 
+         ! Experimental Botany 44:907-920.  Here use a factor "1.67", from 
+         ! Medlyn et al (2002) Plant, Cell and Environment 25:1167-1179
+
+         ! RF - copied this from the CLM trunk code, but where did it come from, 
+         ! and how can we make these consistant? 
+         ! jmax25top(ft) =  &
+         ! (2.59_r8 - 0.035_r8*min(max((t10(p)-tfrzc),11._r8),35._r8)) * vcmax25top(ft)
+
+         this%jmax25top(ft) = 1.67_r8   * this%vcmax25top(ft)
+         this%tpu25top(ft)  = 0.167_r8  * this%vcmax25top(ft)
+         this%kp25top(ft)   = 20000._r8 * this%vcmax25top(ft)
+
+         ! Leaf maintenance respiration to match the base rate used in CN
+         ! but with the new temperature functions for C3 and C4 plants.
+         !
+         !
+         ! CN respiration has units:  g C / g N [leaf] / s. This needs to be
+         ! converted from g C / g N [leaf] / s to umol CO2 / m**2 [leaf] / s
+         !
+         ! Then scale this value at the top of the canopy for canopy depth
+
+         this%lmr25top(ft) = 2.525e-6_r8 * (1.5_r8 ** ((25._r8 - 20._r8)/10._r8))
+         this%lmr25top(ft) = this%lmr25top(ft) * lnc / (umolC_to_kgC * g_per_kg)
+
+      end do !ft 
+    end associate
+    return
+  end subroutine Init
+
+
+end module FatesParameterDerivedMod

components/clm/src/biogeophys/PhotosynthesisMod.F90

@@ -162,10 +162,6 @@ module  PhotosynthesisMod
      real(r8), pointer, public  :: rssun_patch       (:)   ! patch sunlit stomatal resistance (s/m)
      real(r8), pointer, public  :: rssha_patch       (:)   ! patch shaded stomatal resistance (s/m)
 
-     ! ED specific variables
-!     real(r8), pointer, public  :: psncanopy_patch   (:)   ! patch sunlit leaf photosynthesis (umol CO2 /m**2/ s) (ED specific)
-!     real(r8), pointer, public  :: lmrcanopy_patch   (:)   ! sunlit leaf maintenance respiration rate (umol CO2/m**2/s) (ED specific)
-
      ! LUNA specific variables
      real(r8), pointer, public  :: vcmx25_z_patch    (:,:) ! patch  leaf Vc,max25 (umol CO2/m**2/s) for canopy layer 
      real(r8), pointer, public  :: jmx25_z_patch     (:,:) ! patch  leaf Jmax25 (umol electron/m**2/s) for canopy layer 

components/clm/src/utils/clmfates_interfaceMod.F90

@@ -40,7 +40,6 @@ module CLMFatesInterfaceMod
    use TemperatureType   , only : temperature_type
    use EnergyFluxType    , only : energyflux_type
    use SoilStateType     , only : soilstate_type
-   use PhotosynthesisMod , only : photosyns_type
    use clm_varctl        , only : iulog, use_ed
    use clm_varcon        , only : tfrz
    use clm_varcon        , only : spval
@@ -50,6 +49,7 @@ module CLMFatesInterfaceMod
                                   nlevsoi,           &
                                   nlevdecomp,        &
                                   nlevdecomp_full
+   use PhotosynthesisMod , only : photosyns_type
    use atm2lndType       , only : atm2lnd_type
    use SurfaceAlbedoType , only : surfalb_type
    use SolarAbsorbedType , only : solarabs_type
@@ -101,7 +101,7 @@ module CLMFatesInterfaceMod
    use EDBtranMod            , only : btran_ed, &
                                       get_active_suction_layers
    use EDCanopyStructureMod  , only : canopy_summarization, update_hlm_dynamics
-   use EDPhotosynthesisMod   , only : Photosynthesis_ED
+   use FatesPlantRespPhotosynthMod, only : FatesPlantRespPhotosynthDrive
    use EDAccumulateFluxesMod , only : AccumulateFluxes_ED
    use EDPhysiologyMod       , only : flux_into_litter_pools
 
@@ -192,8 +192,9 @@ subroutine init(this, bounds_proc, use_ed)
       ! is not turned on
       ! ---------------------------------------------------------------------------------
 
-     use FatesInterfaceMod, only : FatesInterfaceInit
-
+      use FatesInterfaceMod, only : FatesInterfaceInit
+      use EDTypesMod       , only : numpft_ed
+      use FatesParameterDerivedMod, only : param_derived
 
       implicit none
 
@@ -216,10 +217,9 @@ subroutine init(this, bounds_proc, use_ed)
          ! This involves to stages
          ! 1) allocate the vectors
          ! 2) add the history variables defined in clm_inst to the history machinery
-!         call this%fates2hlm%Init(bounds_proc)
-
          call EDecophysconInit( EDpftvarcon_inst, numpft )
-
+         call param_derived%Init(numpft_ed)
+
       end if
 
       if(DEBUG)then
@@ -1408,11 +1408,11 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, &
 
       ! Call photosynthesis
 
-      call  Photosynthesis_ED (this%fates(nc)%nsites, &
-           this%fates(nc)%sites,  &
-           this%fates(nc)%bc_in,  &
-           this%fates(nc)%bc_out, &
-           dtime)
+      call FatesPlantRespPhotosynthDrive (this%fates(nc)%nsites, &
+                                this%fates(nc)%sites,  &
+                                this%fates(nc)%bc_in,  &
+                                this%fates(nc)%bc_out, &
+                                dtime)
 
       ! Perform a double check to see if all patches on naturally vegetated columns
       ! were activated for photosynthesis