add checks for bareground and fix canopy fluxes

src/biogeochem/VOCEmissionMod.F90

@@ -546,7 +546,9 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
     if (use_fates) then
        do fp = 1,num_soilp
           p = filter_soilp(fp)
-          l_pft_itype(p) = canopystate_inst%voc_pftindex_patch(p)
+          if (patch%is_fates(p)) then
+            l_pft_itype(p) = canopystate_inst%voc_pftindex_patch(p)
+          endif
        end do
     else
        do fp = 1,num_soilp
@@ -625,12 +627,12 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
              ! Activity factor for CO2 (only for isoprene)
              if (trim(meg_cmp%name) == 'isoprene') then 
                 ! Check of valid intercellular co2 pressure values.
-                if (cisha_z(p,nlevcan) < smallValue .or. cisun_z(p,nlevcan) < smallValue) then
-                   write(iulog,*) 'Invalid intercellular co2 pressure (patch itype, sunlit, shaded): ', l_pft_itype(p),cisun_z(p,nlevcan),cisha_z(p,nlevcan)
+                if (cisha_z(p,1) < 0.0_r8 .or. cisun_z(p,1) < 0.0_r8) then
+                   write(iulog,*) 'Invalid intercellular co2 pressure (patch itype, sunlit, shaded): ', l_pft_itype(p),cisun_z(p,1),cisha_z(p,1)
                    call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__))
                 endif
                 co2_ppmv = 1.e6_r8*forc_pco2(g)/forc_pbot(c)
-                gamma_c = get_gamma_C(cisun_z(p,nlevcan),cisha_z(p,nlevcan),forc_pbot(c),fsun(p), co2_ppmv)
+                gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv)
 
              else
                 gamma_c = 1._r8

src/biogeophys/CanopyFluxesMod.F90

@@ -1111,11 +1111,9 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
             vpd(p)  = max((svpts(p) - eah(p)), 50._r8) * 0.001_r8
 
          end do
-
          if ( use_fates ) then      
             ! zeroed out here for megan isoprene calculations, in case patches are not transfered properly.
-            photosyns_inst%cisha_z_patch(begp:endp,:) = -999._r8
-            photosyns_inst%cisun_z_patch(begp:endp,:) = -999._r8
+
             call clm_fates%wrap_photosynthesis(nc, bounds, fn, filterp(1:fn), &
                  svpts(begp:endp), eah(begp:endp), o2(begp:endp), &
                  co2(begp:endp), rb(begp:endp), dayl_factor(begp:endp), &

src/utils/clmfates_interfaceMod.F90

@@ -1616,6 +1616,10 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump,      &
           patch%is_bareground(col%patchi(c)) = .true.
           npatch = this%fates(nc)%sites(s)%youngest_patch%patchno
 
+          ! set voc_pft_index of bareground to 0 explicitly, so the bare ground is properly ignored in VOCEmissionMod
+          if (patch%is_bareground(col%patchi(c))) then
+             voc_pftindex(col%patchi(c)) = 0
+          endif
           ! Precision errors on the canopy_fraction_pa sum, even small (e-12)
           ! do exist, and can create potentially negetive bare-soil fractions
           ! (ie -1e-12 or smaller). Even though this is effectively zero,
@@ -2650,6 +2654,11 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, &
             ! this is needed for MEGAN to work with FATES
             cisun_z(p,:) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
             cisha_z(p,:) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
+            if (this%fates(nc)%bc_out(s)%ci_pa(ifp) <0.0_r8) then
+               write(iulog,*) 'ci_pa is less than 0: ', this%fates(nc)%bc_out(s)%ci_pa(ifp)
+               write(iulog,*) 'filter ran photosynthesis s p icp ifp ilter',s,p,icp,ifp
+               call endrun(msg=errMsg(sourcefile, __LINE__))
+            endif
             ! These fields are marked with a bad-value flag
             photosyns_inst%psnsun_patch(p)   = spval
             photosyns_inst%psnsha_patch(p)   = spval