Add NVP (Non-Vascular Plant) Layer in CTSM

.gitmodules

@@ -27,8 +27,8 @@
 #
 [submodule "fates"]
 path = src/fates
-url = https://github.com/NGEET/fates
-fxtag = sci.1.91.1_api.43.1.0
+url = https://github.com/huitang-earth/fates
+fxtag = b267a73b621b2156d3d6e3ae9289f1f43ca6fb0e
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates

bld/CLMBuildNamelist.pm

@@ -823,7 +823,8 @@ sub setup_cmdl_fates_mode {
                       "use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
                       "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
                       "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model",
-		      "use_fates_managed_fire"
+                      "use_fates_managed_fire",
+                      "use_nvp", "use_nvp_undersnow", "nvp_rad_model_ground"
                    );
 
        # dis-allow fates specific namelist items with non-fates runs
@@ -4887,7 +4888,8 @@ sub setup_logic_fates {
                        "use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
                        "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
                        "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model",
-		       "use_fates_managed_fire"
+                       "use_fates_managed_fire",
+                       "use_nvp", "use_nvp_undersnow", "nvp_rad_model_ground"
                     );
 
         foreach my $var ( @list ) {
@@ -4910,6 +4912,7 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_spitfire_mode', 'use_fates'=>$nl_flags->{'use_fates'},
                     'use_fates_managed_fire'=>$nl->get_value('use_fates_managed_fire'),
                     'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_nvp');
 
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -638,6 +638,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_luna                use_fates=".true." >.false.</use_luna>
 <use_luna phys="clm4_5"  use_fates=".false.">.false.</use_luna>
 
+<!-- NVP (non-vascular plant: moss/lichen) ground layer -->
+<!-- [PORTED by Hui Tang: NVP control flag defaults] -->
+<use_nvp              >.false.</use_nvp>
+<use_nvp_undersnow    >.false.</use_nvp_undersnow>
+<nvp_rad_model_ground >.false.</nvp_rad_model_ground>
+
 <!-- Flexible CN options -->
 <MM_Nuptake_opt             use_flexibleCN=".true." >.true.</MM_Nuptake_opt>
 <CNratio_floating           use_flexibleCN=".true." >.true.</CNratio_floating>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -946,6 +946,27 @@ LUNA operates on C3 and non-crop vegetation (see vcmax_opt for how other veg is
 LUNA: Leaf Utilization of Nitrogen for Assimilation
 </entry>
 
+<!-- NVP (non-vascular plant: moss/lichen) ground layer -->
+<!-- [PORTED by Hui Tang: NVP control flags] -->
+<entry id="use_nvp" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to activate the NVP (non-vascular plant: moss/lichen) ground layer.
+Requires use_fates=".true.".
+</entry>
+
+<entry id="use_nvp_undersnow" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Allow the NVP layer to remain active and exchange fluxes when covered by snow.
+Only relevant when use_nvp=".true.".
+</entry>
+
+<entry id="nvp_rad_model_ground" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Use FATES Beer's law radiation model for the NVP ground layer instead of
+the CLM bare-ground scheme.
+Only relevant when use_nvp=".true.".
+</entry>
+
 <entry id="use_hillslope" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the hillslope model

src/biogeophys/BalanceCheckMod.F90

@@ -461,7 +461,7 @@ subroutine BalanceCheck( bounds, &
      !
      ! !USES:
      use clm_varcon        , only : spval
-     use clm_varctl        , only : use_soil_moisture_streams
+     use clm_varctl        , only : use_soil_moisture_streams, use_nvp  ! [PORTED by Hui Tang: use_nvp for NVP debug print]
      use clm_time_manager  , only : get_step_size_real, get_nstep
      use clm_time_manager  , only : get_nstep_since_startup_or_lastDA_restart_or_pause
      use CanopyStateType   , only : canopystate_type
@@ -589,6 +589,15 @@ subroutine BalanceCheck( bounds, &
           ! add qflx_drain_perched and qflx_flood
           if (col%active(c)) then
 
+             ! [PORTED by Hui Tang: NVP debug — print j=0 water and all wb flux terms for c==1]
+             if (use_nvp .and. col%jbot_sno(c) == -1 .and. c == 1) then
+                write(iulog,*) '[NVP DBG] WBal c=',c,' snl=',col%snl(c), &
+                   ' ice0=',waterstate_inst%h2osoi_ice_col(c,0), &
+                   ' liq0=',waterstate_inst%h2osoi_liq_col(c,0), &
+                   ' snwcp_liq=', qflx_snwcp_liq(c)*dtime, &
+                   ' snwcp_ice=', qflx_snwcp_ice(c)*dtime
+             end if
+
              errh2o_col(c) = endwb_col(c) - begwb_col(c) &
                   - (forc_rain_col(c)        &
                   + forc_snow_col(c)         &

src/biogeophys/BareGroundFluxesMod.F90

@@ -83,7 +83,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, &
     use clm_varpar           , only : nlevgrnd
     use clm_varcon           , only : cpair, vkc, grav, denice, denh2o, tfrz
     use clm_varcon           , only : beta_param, nu_param, meier_param3
-    use clm_varctl           , only : use_lch4, z0param_method
+    use clm_varctl           , only : use_lch4, z0param_method, use_nvp, iulog
     use landunit_varcon      , only : istsoil, istcrop
     use QSatMod              , only : QSat
     use SurfaceResistanceMod , only : do_soilevap_beta,do_soil_resistance_sl14
@@ -217,21 +217,27 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, &
          t_grnd                 => temperature_inst%t_grnd_col                  , & ! Input:  [real(r8) (:)   ]  ground surface temperature [K]                                        
          thv                    => temperature_inst%thv_col                     , & ! Input:  [real(r8) (:)   ]  virtual potential temperature (kelvin)                                
          thm                    => temperature_inst%thm_patch                   , & ! Input:  [real(r8) (:)   ]  intermediate variable (forc_t+0.0098*forc_hgt_t_patch)                  
-         t_h2osfc               => temperature_inst%t_h2osfc_col                , & ! Input:  [real(r8) (:)   ]  surface water temperature                                             
-         beta                   => temperature_inst%beta_col                    , & ! Input:  [real(r8) (:)   ]  coefficient of conective velocity [-]                                 
+         t_h2osfc               => temperature_inst%t_h2osfc_col                , & ! Input:  [real(r8) (:)   ]  surface water temperature
+         ! [PORTED by Hui Tang: NVP layer temperature for bare-ground NVP flux]
+         t_nvp_col              => temperature_inst%t_nvp_col                   , & ! Input:  [real(r8) (:)   ]  NVP layer temperature [K]
+         beta                   => temperature_inst%beta_col                    , & ! Input:  [real(r8) (:)   ]  coefficient of conective velocity [-]
 
          qg_snow                => waterdiagnosticbulk_inst%qg_snow_col                  , & ! Input:  [real(r8) (:)   ]  specific humidity at snow surface [kg/kg]
-         qg_soil                => waterdiagnosticbulk_inst%qg_soil_col                  , & ! Input:  [real(r8) (:)   ]  specific humidity at soil surface [kg/kg]                             
-         qg_h2osfc              => waterdiagnosticbulk_inst%qg_h2osfc_col                , & ! Input:  [real(r8) (:)   ]  specific humidity at h2osfc surface [kg/kg]                           
+         qg_soil                => waterdiagnosticbulk_inst%qg_soil_col                  , & ! Input:  [real(r8) (:)   ]  specific humidity at soil surface [kg/kg]
+         qg_h2osfc              => waterdiagnosticbulk_inst%qg_h2osfc_col                , & ! Input:  [real(r8) (:)   ]  specific humidity at h2osfc surface [kg/kg]
+         ! [PORTED by Hui Tang: NVP surface specific humidity for bare-ground NVP flux]
+         qg_nvp                 => waterdiagnosticbulk_inst%qg_nvp_col                   , & ! Input:  [real(r8) (:)   ]  NVP surface specific humidity [kg/kg]                           
          qg                     => waterdiagnosticbulk_inst%qg_col                       , & ! Input:  [real(r8) (:)   ]  specific humidity at ground surface [kg/kg]                           
          dqgdT                  => waterdiagnosticbulk_inst%dqgdT_col                    , & ! Input:  [real(r8) (:)   ]  temperature derivative of "qg"                                        
          h2osoi_ice             => waterstatebulk_inst%h2osoi_ice_col               , & ! Input:  [real(r8) (:,:) ]  ice lens (kg/m2)                                                    
          h2osoi_liq             => waterstatebulk_inst%h2osoi_liq_col               , & ! Input:  [real(r8) (:,:) ]  liquid water (kg/m2)                                                
          grnd_ch4_cond          => ch4_inst%grnd_ch4_cond_patch                 , & ! Output: [real(r8) (:)   ]  tracer conductance for boundary layer [m/s]
 
-         eflx_sh_snow           => energyflux_inst%eflx_sh_snow_patch           , & ! Output: [real(r8) (:)   ]  sensible heat flux from snow (W/m**2) [+ to atm]                      
-         eflx_sh_soil           => energyflux_inst%eflx_sh_soil_patch           , & ! Output: [real(r8) (:)   ]  sensible heat flux from soil (W/m**2) [+ to atm]                      
-         eflx_sh_h2osfc         => energyflux_inst%eflx_sh_h2osfc_patch         , & ! Output: [real(r8) (:)   ]  sensible heat flux from soil (W/m**2) [+ to atm]                      
+         eflx_sh_snow           => energyflux_inst%eflx_sh_snow_patch           , & ! Output: [real(r8) (:)   ]  sensible heat flux from snow (W/m**2) [+ to atm]
+         eflx_sh_soil           => energyflux_inst%eflx_sh_soil_patch           , & ! Output: [real(r8) (:)   ]  sensible heat flux from soil (W/m**2) [+ to atm]
+         eflx_sh_h2osfc         => energyflux_inst%eflx_sh_h2osfc_patch         , & ! Output: [real(r8) (:)   ]  sensible heat flux from surface water (W/m**2) [+ to atm]
+         ! [PORTED by Hui Tang: NVP sensible heat flux for bare ground]
+         eflx_sh_nvp            => energyflux_inst%eflx_sh_nvp_patch            , & ! Output: [real(r8) (:)   ]  sensible heat flux from NVP (W/m**2) [+ to atm]                      
          eflx_sh_grnd           => energyflux_inst%eflx_sh_grnd_patch           , & ! Output: [real(r8) (:)   ]  sensible heat flux from ground (W/m**2) [+ to atm]                    
          eflx_sh_tot            => energyflux_inst%eflx_sh_tot_patch            , & ! Output: [real(r8) (:)   ]  total sensible heat flux (W/m**2) [+ to atm]                          
          taux                   => energyflux_inst%taux_patch                   , & ! Output: [real(r8) (:)   ]  wind (shear) stress: e-w (kg/m/s**2)                                  
@@ -274,6 +280,8 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, &
          qflx_ev_snow           => waterfluxbulk_inst%qflx_ev_snow_patch        , & ! Output: [real(r8) (:)   ]  evaporation flux from snow (mm H2O/s) [+ to atm]
          qflx_ev_soil           => waterfluxbulk_inst%qflx_ev_soil_patch        , & ! Output: [real(r8) (:)   ]  evaporation flux from soil (mm H2O/s) [+ to atm]
          qflx_ev_h2osfc         => waterfluxbulk_inst%qflx_ev_h2osfc_patch      , & ! Output: [real(r8) (:)   ]  evaporation flux from h2osfc (mm H2O/s) [+ to atm]
+         ! [PORTED by Hui Tang: NVP evaporation flux for bare ground]
+         qflx_ev_nvp            => waterfluxbulk_inst%qflx_ev_nvp_patch         , & ! Output: [real(r8) (:)   ]  evaporation flux from NVP (mm H2O/s) [+ to atm]
          qflx_evap_soi          => waterfluxbulk_inst%qflx_evap_soi_patch       , & ! Output: [real(r8) (:)   ]  soil evaporation (mm H2O/s) (+ = to atm)
          qflx_evap_tot          => waterfluxbulk_inst%qflx_evap_tot_patch       , & ! Output: [real(r8) (:)   ]  qflx_evap_soi + qflx_evap_can + qflx_tran_veg
          qflx_tran_veg          => waterfluxbulk_inst%qflx_tran_veg_patch       , & ! Output: [real(r8) (:)   ]  vegetation transpiration (mm H2O/s) (+ = to atm)
@@ -294,6 +302,10 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, &
       do f = 1, num_noexposedvegp
          p = filter_noexposedvegp(f)
          c = patch%column(p)
+         if (use_nvp .and. col%nvp_layer_active(c)) then
+            write(iulog,'(a,2i6,2l2,2f10.5)') '[DBG noexposedvegp] p, c, is_bg, is_veg, wtcol, frac_nvp:', &
+                 p, c, patch%is_bareground(p), patch%is_veg(p), patch%wtcol(p), col%frac_nvp(c)
+         end if
          btran(p) = 0._r8     
          t_veg(p) = forc_t(c) 
          cf_bare  = forc_pbot(c)/(SHR_CONST_RGAS*0.001_r8*thm(p))*1.e06_r8
@@ -478,17 +490,37 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, &
          eflx_sh_snow(p)   = -raih*(thm(p)-t_soisno(c,snl(c)+1))
          eflx_sh_soil(p)   = -raih*(thm(p)-t_soisno(c,1))
          eflx_sh_h2osfc(p) = -raih*(thm(p)-t_h2osfc(c))
+         ! [PORTED by Hui Tang: NVP sensible heat flux for bare ground, analogous to snow/h2osfc]
+         ! Zero when NVP is buried under snow (snl < -1): the snow surface controls the energy balance.
+         ! Only compute for the NVP veg patch (patch%is_veg), not the bareground gap patch.
+         if (use_nvp .and. patch%is_veg(p) .and. col%frac_nvp(c) > 0._r8 .and. col%snl(c) >= -1) then
+            eflx_sh_nvp(p) = -raih*(thm(p)-t_nvp_col(c))
+         else
+            eflx_sh_nvp(p) = 0._r8
+         end if
 
          ! water fluxes from soil
          qflx_tran_veg(p)  = 0._r8
          qflx_evap_veg(p)  = 0._r8
          qflx_evap_soi(p)  = -raiw*dqh(p)
          qflx_evap_tot(p)  = qflx_evap_soi(p)
 
+         print *, "qflx_evap_tot=", qflx_evap_soi(p), raiw, dqh(p)
+
          ! compute latent heat fluxes individually
          qflx_ev_snow(p)   = -raiw*(forc_q(c) - qg_snow(c))
          qflx_ev_soil(p)   = -raiw*(forc_q(c) - qg_soil(c))
          qflx_ev_h2osfc(p) = -raiw*(forc_q(c) - qg_h2osfc(c))
+         ! [PORTED by Hui Tang: NVP evaporation flux for bare ground, analogous to snow/h2osfc]
+         ! Zero when NVP is buried under snow (snl < -1): qflx_ev_nvp_col drives ev_nvp_eff in
+         ! NVPWaterBalance_Column; a non-zero value here when NVP is covered would add water to
+         ! qflx_evap_tot_col without removing it from any tracked water store, causing errh2o.
+         ! Only compute for the NVP veg patch (patch%is_veg), not the bareground gap patch.
+         if (use_nvp .and. patch%is_veg(p) .and. col%frac_nvp(c) > 0._r8 .and. col%snl(c) >= -1) then
+            qflx_ev_nvp(p) = -raiw*(forc_q(c) - qg_nvp(c))
+         else
+            qflx_ev_nvp(p) = 0._r8
+         end if
 
          ! 2 m height air temperature
          t_ref2m(p) = thm(p) + temp1(p)*dth(p)*(1._r8/temp12m(p) - 1._r8/temp1(p))