[WIP] Add NVP (Non-Vascular Plant) PFT in CTSM–FATES

biogeochem/EDPhysiologyMod.F90

@@ -115,6 +115,9 @@ module EDPhysiologyMod
   use FatesAllometryMod  , only : carea_allom
   use FatesAllometryMod  , only : CheckIntegratedAllometries
   use FatesAllometryMod, only : set_root_fraction
+  use FatesAllometryMod, only : NVP_allom                ! [PORTED by Hui Tang: NVP SP mode]
+  use FatesInterfaceTypesMod, only : hlm_use_nvp         ! [PORTED by Hui Tang: NVP SP mode]
+  use LeafBiophysicsMod, only : lb_params                ! [PORTED by Hui Tang: NVP PFT identification]
   use PRTGenericMod, only : prt_carbon_allom_hyp
   use PRTGenericMod, only : prt_cnp_flex_allom_hyp
   use PRTGenericMod, only : prt_vartypes
@@ -1993,6 +1996,7 @@ subroutine assign_cohort_SP_properties(currentCohort, htop, tlai, tsai, parea, i
     real(r8) :: dbh      ! cohort dbh [cm]
     real(r8) :: cohort_n ! cohort density [/m2]
     real(r8) :: c_area   ! cohort canopy area [m2]
+    real(r8) :: nvp_dz   ! [PORTED by Hui Tang: NVP layer thickness from NVP allometry]
 
     if (associated(currentCohort%shorter)) then
       write(fates_log(),*) 'SP mode has >1 cohort'
@@ -2020,6 +2024,18 @@ subroutine assign_cohort_SP_properties(currentCohort, htop, tlai, tsai, parea, i
     currentCohort%treelai = tlai
     currentCohort%treesai = tsai
 
+    ! [PORTED by Hui Tang: NVP SP mode — override leaf_c, c_area, nvp_dz using NVP allometry]
+    ! In SP mode, calculate_SP_properties uses tree allometry (leafc_from_treelai) for all PFTs.
+    ! For NVP, we must instead use NVP allometry: given prescribed treelai, compute the
+    ! consistent leaf_c and nvp_dz. c_area = parea so nvp_frac_pa = parea/AREA = patch fraction.
+    if (hlm_use_nvp == itrue) then
+       if (lb_params%stomatal_intercept(currentCohort%pft) <= nearzero) then
+          currentCohort%c_area = parea
+          call NVP_allom(currentCohort%treelai, leaf_c, nvp_dz, inverse=.true.)
+          currentCohort%nvp_dz = nvp_dz
+       end if
+    end if
+
     if (init .eq. ifalse) then
       call SetState(currentCohort%prt, leaf_organ, carbon12_element, leaf_c, 1)
     endif

biogeochem/FatesAllometryMod.F90

@@ -99,6 +99,8 @@ module FatesAllometryMod
   use FatesGlobals     , only : endrun => fates_endrun
   use FatesGlobals     , only : FatesWarn,N2S,A2S,I2S
   use EDParamsMod      , only : nlevleaf,dinc_vai,dlower_vai
+  ! [PORTED by Hui Tang: NVP allometry parameters from FATES parameter file]
+  use EDParamsMod      , only : nvp_bulk_density, nvp_sla
   use DamageMainMod    , only : GetCrownReduction
   use LeafBiophysicsMod, only : DecayCoeffVcmax
 
@@ -124,6 +126,8 @@ module FatesAllometryMod
   public :: set_root_fraction  ! Generic wrapper to calculate normalized
                                ! root profiles
   public :: leafc_from_treelai ! Calculate target leaf carbon for a given treelai for SP mode
+  ! [PORTED by Hui Tang: NVP (moss/lichen) bidirectional LAI<->biomass and LAI->thickness conversion]
+  public :: NVP_allom
   public :: VegAreaLayer
 
   public :: tree_lai_sai       ! LAI and SAI calculations must work together, thus they
@@ -2800,6 +2804,8 @@ subroutine set_root_fraction(root_fraction, ft, zi, max_nlevroot)
     integer, parameter :: jackson_beta_profile_type   = 1
     integer, parameter :: exponential_1p_profile_type = 2
     integer, parameter :: exponential_2p_profile_type = 3
+    ! [PORTED by Hui Tang: mode 4 = NVP (no soil roots); root_fraction stays all-zero]
+    integer, parameter :: no_root_profile_type         = 4
 
     integer :: root_profile_type
     integer :: corr_id(1)        ! This is the bin with largest fraction
@@ -2835,9 +2841,12 @@ subroutine set_root_fraction(root_fraction, ft, zi, max_nlevroot)
        call exponential_1p_root_profile(root_fraction(1:nlevroot), zi(0:nlevroot), prt_params%fnrt_prof_a(ft)) 
     case ( jackson_beta_profile_type )
        call jackson_beta_root_profile(root_fraction(1:nlevroot), zi(0:nlevroot), prt_params%fnrt_prof_a(ft))
-    case ( exponential_2p_profile_type ) 
-       call exponential_2p_root_profile(root_fraction(1:nlevroot), zi(0:nlevroot), & 
+    case ( exponential_2p_profile_type )
+       call exponential_2p_root_profile(root_fraction(1:nlevroot), zi(0:nlevroot), &
              prt_params%fnrt_prof_a(ft),prt_params%fnrt_prof_b(ft))
+    ! [PORTED by Hui Tang: NVP has no soil roots; root_fraction already zeroed above]
+    case ( no_root_profile_type )
+       ! No root profile: root_fraction(:) = 0._r8 (initialized at line 2827, no further action needed)
 
     case default
        write(fates_log(),*) 'An undefined root profile type was specified'
@@ -2846,9 +2855,12 @@ subroutine set_root_fraction(root_fraction, ft, zi, max_nlevroot)
     end select
 
 
-    correction = 1._r8 - sum(root_fraction)
-    corr_id = maxloc(root_fraction)
-    root_fraction(corr_id(1)) = root_fraction(corr_id(1)) + correction
+    ! [PORTED by Hui Tang: skip normalization for no_root_profile_type; all zeros is intentional]
+    if (nint(prt_params%fnrt_prof_mode(ft)) /= no_root_profile_type) then
+       correction = 1._r8 - sum(root_fraction)
+       corr_id = maxloc(root_fraction)
+       root_fraction(corr_id(1)) = root_fraction(corr_id(1)) + correction
+    end if
 
 
 
@@ -3544,6 +3556,57 @@ subroutine size2dbh(size,ipft,dbh,dbh_maxh)
    end subroutine size2dbh
    ! ============================================================================
 
+   ! [PORTED by Hui Tang: NVP (moss/lichen) allometry - LAI<->biomass and LAI->layer thickness]
+   subroutine NVP_allom(lai, leaf_c, nvp_dz, inverse)
+      !
+      ! !DESCRIPTION:
+      ! Bidirectional conversion between NVP leaf carbon and LAI, and diagnosis
+      ! of the NVP layer thickness from LAI.
+      !
+      ! Parameters (from Porada et al. 2013 and related literature, read from FATES parameter file):
+      !   nvp_sla          [m2 g-1]  specific leaf area of NVP
+      !   nvp_bulk_density [kg m-3]  NVP bulk density
+      !   nv_c2b   = 2.32            carbon-to-biomass ratio of NVP (kgC / kgDM)
+      !   nv_t2l   = 1.0             total-to-leaf biomass ratio (all biomass is leaf for NVP)
+      !
+      ! When inverse = .false.: leaf_c  ->  lai, nvp_dz
+      ! When inverse = .true. : lai     ->  leaf_c  (nvp_dz still diagnosed from lai)
+      !
+      ! nvp_dz = lai / (nvp_sla [m2 g-1] * 1e3 [g kg-1] * nvp_bulk_density [kg m-3])
+      !        = lai / (nvp_sla * g_per_kg * nvp_bulk_density)
+      !
+      ! !ARGUMENTS:
+      real(r8), intent(inout) :: lai     ! NVP leaf area index [m2 leaf / m2 crown]
+      real(r8), intent(inout) :: leaf_c  ! NVP leaf carbon per unit crown area [kgC m-2]
+      real(r8), intent(out)   :: nvp_dz  ! NVP layer thickness [m]
+      logical,  intent(in)    :: inverse ! .false. = leaf_c->lai; .true. = lai->leaf_c
+      !
+      ! !LOCAL VARIABLES:
+      real(r8), parameter :: nv_c2b  = 2.32_r8 ! carbon to dry-mass ratio [kgC kgDM-1]
+      real(r8), parameter :: nv_t2l  = 1.0_r8  ! total-to-leaf biomass ratio [-]
+      !------------------------------------------------------------------------
+
+      if (inverse) then
+         ! lai -> leaf_c
+         ! leaf_mass_per_area [kgDM m-2] = lai [m2 m-2] / (nvp_sla [m2 g-1] * g_per_kg [g kg-1])
+         ! leaf_c [kgC m-2] = leaf_mass_per_area * nv_c2b / nv_t2l
+         leaf_c = (lai / (nvp_sla * g_per_kg)) * nv_c2b / nv_t2l
+      else
+         ! leaf_c -> lai
+         ! leaf_mass [kgDM m-2] = leaf_c * nv_t2l / nv_c2b
+         ! lai = leaf_mass * nvp_sla * g_per_kg
+         lai = (leaf_c * nv_t2l / nv_c2b) * nvp_sla * g_per_kg
+      end if
 
+      ! Diagnose layer thickness from LAI regardless of direction
+      ! nvp_dz [m] = lai [m2 m-2] / (nvp_sla [m2 g-1] * g_per_kg [g kg-1] * nvp_bulk_density [kg m-3])
+      if (nvp_bulk_density > nearzero) then
+         nvp_dz = lai / (nvp_sla * g_per_kg * nvp_bulk_density)
+      else
+         nvp_dz = 0.0_r8
+      end if
+
+   end subroutine NVP_allom
+   ! ============================================================================
 
 end module FatesAllometryMod

biogeochem/FatesCohortMod.F90

@@ -28,6 +28,10 @@ module FatesCohortMod
   use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
   use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
   use FatesAllometryMod,          only : carea_allom, tree_lai_sai
+  ! [PORTED by Hui Tang: NVP allometry for cohort initialization]
+  use FatesAllometryMod,          only : NVP_allom
+  use LeafBiophysicsMod,          only : lb_params
+  use FatesInterfaceTypesMod,     only : hlm_use_nvp
   use PRTAllometricCarbonMod,     only : ac_bc_inout_id_dbh, ac_bc_inout_id_netdc
   use PRTAllometricCarbonMod,     only : ac_bc_in_id_cdamage, ac_bc_in_id_pft
   use PRTAllometricCarbonMod,     only : ac_bc_in_id_ctrim, ac_bc_in_id_lstat
@@ -105,6 +109,10 @@ module FatesCohortMod
     real(r8) :: c_area                  ! areal extent of canopy [m2]
     real(r8) :: treelai                 ! lai of an individual within cohort leaf area [m2 leaf area/m2 crown area]
     real(r8) :: treesai                 ! stem area index of an individual within cohort [m2 stem area/m2 crown area]
+    ! [PORTED by Hui Tang: NVP layer thickness derived from cohort LAI via NVP_allom]
+    ! Only meaningful for NVP cohort (stomatal_intercept(ft) <= nearzero).
+    ! nvp_dz = treelai / (nv_sla * bulk_density_nvp); updated after each LAI change.
+    real(r8) :: nvp_dz                  ! NVP layer thickness for this cohort [m]
     logical  :: isnew                   ! flag to signify a new cohort - new cohorts have not experienced
                                         !   npp or mortality and should therefore not be fused or averaged
     integer  :: size_class              ! index that indicates which diameter size bin the cohort currently resides in
@@ -375,9 +383,10 @@ subroutine NanValues(this)
       this%efleaf_coh              = nan
       this%effnrt_coh              = nan 
       this%efstem_coh              = nan
-      this%c_area                  = nan 
+      this%c_area                  = nan
       this%treelai                 = nan
       this%treesai                 = nan
+      this%nvp_dz                  = 0.0_r8  ! [PORTED by Hui Tang: safe default; set by NVP_allom for NVP PFTs]
       this%isnew                   = .false.
       this%size_class              = fates_unset_int
       this%coage_class             = fates_unset_int
@@ -488,6 +497,7 @@ subroutine ZeroValues(this)
       this%efstem_coh              = 0.0_r8
 
       this%treesai                 = 0._r8
+      this%nvp_dz                  = 0.0_r8  ! [PORTED by Hui Tang: safe default; set by NVP_allom for NVP PFTs]
       this%size_class              = 1
       this%coage_class             = 1
 
@@ -659,12 +669,20 @@ subroutine Create(this, prt, pft, nn, height, coage, dbh, status,            &
       ! Query PARTEH for the leaf carbon [kg]
       leaf_c = this%prt%GetState(leaf_organ, carbon12_element)
 
-      call tree_lai_sai(leaf_c, this%pft, this%c_area, this%n,           &
-           this%canopy_layer, can_tlai, this%vcmax25top, this%dbh, this%crowndamage,          &
-           this%canopy_trim, this%efstem_coh, 2, this%treelai, treesai)
-
-      if (hlm_use_sp .eq. ifalse) then
-         this%treesai = treesai
+      ! [PORTED by Hui Tang: NVP cohorts initialize treelai and nvp_dz via NVP_allom]
+      if (hlm_use_nvp == itrue .and. &
+          lb_params%stomatal_intercept(this%pft) <= nearzero) then
+         call NVP_allom(this%treelai, leaf_c, this%nvp_dz, inverse=.false.)
+         this%treesai = 0._r8
+      else
+         call tree_lai_sai(leaf_c, this%pft, this%c_area, this%n,        &
+              this%canopy_layer, can_tlai, this%vcmax25top, this%dbh,     &
+              this%crowndamage, this%canopy_trim, this%efstem_coh, 2,     &
+              this%treelai, treesai)
+
+         if (hlm_use_sp .eq. ifalse) then
+            this%treesai = treesai
+         end if
       end if
 
 
@@ -716,6 +734,7 @@ subroutine Copy(this, copyCohort)
       copyCohort%c_area                  = this%c_area
       copyCohort%treelai                 = this%treelai
       copyCohort%treesai                 = this%treesai
+      copyCohort%nvp_dz                  = this%nvp_dz  ! [PORTED by Hui Tang: copy NVP layer thickness]
       copyCohort%isnew                   = this%isnew
       copyCohort%size_class              = this%size_class
       copyCohort%coage_class             = this%coage_class