Enable GOCART integration in UFS (NCAR#310)

Features:
- Implemented sharing of atmospheric tracer metadata (name, units) to coupled model component via a standard NUOPC connector if coupling tracer field is accessed by shared memory reference
- Introduced additional metadata to tracer records in field_table to identify and validate prognostic and diagnostic chemistry tracers. A new record line starting with the `tracer_usage` keyword is now required to recognize chemistry tracer as follows:

      "tracer_usage", "chemistry"                    (default, prognostic)
      "tracer_usage", "chemistry", "type=diagnostic" (diagnostic)

- Added sanity check for input chemistry tracers, ensuring that both prognostic and diagnostic tracers in field_table are contiguous, and diagnostic tracers follow prognostic ones.
- Improved algorithm to set aerosol scavenging factors
- Exported instantaneous fields for:
   - 3D non-convective liquid and ice precipitation fluxes
   - 3D cloud fraction
   - normalized soil wetness
   -  ice fraction (as used in the atmospheric model)
   - lake fraction
   - ocean fraction
   - surface snow area fraction
- Enabled import of diagnostic tracers

Fixes:
- Prevent a divide by zero error when constant arrays are rescaled for lossy compression in `write_netcdf_parallel()`
- Correctly sample and compute elapsed time for field bundle regridding operations.
- Include hotfix (see PR NCAR#308) to allow latest `setup_exportdata()` to work with coupled chemistry.

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

CMakeLists.txt

@@ -122,6 +122,7 @@ add_library(fv3atm
   module_fv3_config.F90
   module_fcst_grid_comp.F90
   stochastic_physics/stochastic_physics_wrapper.F90
+  cpl/module_block_data.F90
   cpl/module_cplfields.F90
   cpl/module_cap_cpl.F90
   io/ffsync.F90

ccpp/data/GFS_typedefs.meta

@@ -2277,14 +2277,6 @@
   type = real
   kind = kind_phys
   active = (index_for_stochastic_land_surface_perturbation_type .ne. 0)
-[dqdti]
-  standard_name = instantaneous_water_vapor_specific_humidity_tendency_due_to_convection
-  long_name = instantaneous moisture tendency due to convection
-  units = kg kg-1 s-1
-  dimensions = (horizontal_loop_extent,vertical_dimension)
-  type = real
-  kind = kind_phys
-  active = (flag_for_chemistry_coupling)
 [nwfa2d]
   standard_name = tendency_of_water_friendly_aerosols_at_surface
   long_name = instantaneous water-friendly sfc aerosol source
@@ -2309,14 +2301,6 @@
   type = real
   kind = kind_phys
   active = (flag_for_chemistry_coupling)
-[dkt]
-  standard_name = instantaneous_atmosphere_heat_diffusivity
-  long_name = instantaneous atmospheric heat diffusivity
-  units = m2 s-1
-  dimensions = (horizontal_loop_extent,vertical_dimension)
-  type = real
-  kind = kind_phys
-  active = (flag_for_chemistry_coupling)
 [qci_conv]
   standard_name = convective_cloud_condesate_after_rainout
   long_name = convective cloud condesate after rainout
@@ -2325,6 +2309,22 @@
   type = real
   kind = kind_phys
   active = (flag_for_mass_flux_deep_convection_scheme == flag_for_gf_deep_convection_scheme)
+[pfi_lsan]
+  standard_name = ice_flux_due_to_large_scale_precipitation
+  long_name = instantaneous 3D flux of ice from nonconvective precipitation
+  units = kg m-2 s-1
+  dimensions = (horizontal_loop_extent,vertical_dimension)
+  type = real
+  kind = kind_phys
+  active = (flag_for_chemistry_coupling)
+[pfl_lsan]
+  standard_name = liquid_flux_due_to_large_scale_precipitation
+  long_name = instantaneous 3D flux of liquid water from nonconvective precipitation
+  units = kg m-2 s-1
+  dimensions = (horizontal_loop_extent,vertical_dimension)
+  type = real
+  kind = kind_phys
+  active = (flag_for_chemistry_coupling)
 ########################################################################
 [ccpp-table-properties]
   name = GFS_control_type
@@ -4560,6 +4560,30 @@
   units = index
   dimensions = ()
   type = integer
+[ntche]
+  standard_name = index_for_last_chemical_tracer
+  long_name = tracer index for last chemical tracer
+  units = index
+  dimensions = ()
+  type = integer
+[ndchm]
+  standard_name = number_of_diagnostic_chemical_tracers
+  long_name = number of diagnostic chemical tracers
+  units = count
+  dimensions = ()
+  type = integer
+[ndchs]
+  standard_name = index_for_first_diagnostic_chemical_tracer
+  long_name = tracer index for first diagnostic chemical tracer
+  units = index
+  dimensions = ()
+  type = integer
+[ndche]
+  standard_name = index_for_last_diagnostic_chemical_tracer
+  long_name = tracer index for last diagnostic chemical tracer
+  units = index
+  dimensions = ()
+  type = integer
 [ntdiag]
   standard_name = diagnostics_control_for_chemical_tracers
   long_name = array to control diagnostics for chemical tracers
@@ -7058,86 +7082,6 @@
   dimensions = (horizontal_loop_extent,adjusted_vertical_layer_dimension_for_radiation)
   type = real
   kind = kind_phys
-[ndust]
-  standard_name = number_of_dust_bins_for_diagnostics
-  long_name = number of dust bins for diagnostics
-  units = count
-  dimensions = ()
-  type = integer
-[nseasalt]
-  standard_name = number_of_seasalt_bins_for_diagnostics
-  long_name = number of seasalt bins for diagnostics
-  units = count
-  dimensions = ()
-  type = integer
-[ntchmdiag]
-  standard_name = number_of_chemical_tracers_for_diagnostics
-  long_name = number of chemical tracers for diagnostic output
-  units = count
-  dimensions = ()
-  type = integer
-[duem]
-  standard_name = instantaneous_dust_emission_flux
-  long_name = instantaneous dust emission flux
-  units = kg m-2 s-1
-  dimensions = (horizonal_dimension,number_of_dust_bins_for_diagnostics)
-  type = real
-  kind = kind_phys
-  active = (number_of_dust_bins_for_diagnostics > 0)
-[ssem]
-  standard_name = instantaneous_seasalt_emission_flux
-  long_name = instantaneous sea salt emission flux
-  units = kg m-2 s-1
-  dimensions = (horizonal_dimension,number_of_seasalt_bins_for_diagnostics)
-  type = real
-  kind = kind_phys
-  active = (number_of_seasalt_bins_for_diagnostics > 0)
-[sedim]
-  standard_name = instantaneous_sedimentation
-  long_name = instantaneous sedimentation
-  units = kg m-2 s-1
-  dimensions = (horizonal_dimension,number_of_chemical_tracers_for_diagnostics)
-  type = real
-  kind = kind_phys
-  active = (number_of_chemical_tracers_for_diagnostics > 0)
-[drydep]
-  standard_name = instantaneous_dry_deposition
-  long_name = instantaneous dry deposition
-  units = kg m-2 s-1
-  dimensions = (horizonal_dimension,number_of_chemical_tracers_for_diagnostics)
-  type = real
-  kind = kind_phys
-  active = (number_of_chemical_tracers_for_diagnostics > 0)
-[wetdpl]
-  standard_name = instantaneous_large_scale_wet_deposition
-  long_name = instantaneous large-scale wet deposition
-  units = kg m-2 s-1
-  dimensions = (horizonal_dimension,number_of_chemical_tracers_for_diagnostics)
-  type = real
-  kind = kind_phys
-  active = (number_of_chemical_tracers_for_diagnostics > 0)
-[wetdpc]
-  standard_name = instantaneous_convective_scale_wet_deposition
-  long_name = instantaneous convective-scale wet deposition
-  units = kg m-2 s-1
-  dimensions = (horizonal_dimension,number_of_chemical_tracers_for_diagnostics)
-  type = real
-  kind = kind_phys
-  active = (number_of_chemical_tracers_for_diagnostics > 0)
-[abem]
-  standard_name = instantaneous_anthopogenic_and_biomass_burning_emissions
-  long_name = instantaneous anthopogenic and biomass burning emissions for black carbon, organic carbon, and sulfur dioxide
-  units = ug m-2 s-1
-  dimensions = (horizontal_loop_extent,6)
-  type = real
-  kind = kind_phys
-[aecm]
-  standard_name = instantaneous_aerosol_column_mass_densities
-  long_name = instantaneous aerosol column mass densities for pm2.5, black carbon, organic carbon, sulfate, dust, sea salt
-  units = g m-2
-  dimensions = (horizontal_loop_extent,6)
-  type = real
-  kind = kind_phys
 [edmf_a]
   standard_name = emdf_updraft_area
   long_name = updraft area from mass flux scheme

ccpp/driver/GFS_diagnostics.F90

@@ -3944,161 +3944,6 @@ subroutine GFS_externaldiag_populate (ExtDiag, Model, Statein, Stateout, Sfcprop
 
 !  print *,'in gfdl_diag_register,af all extdiag, idx=',idx
 
-! -- chemistry diagnostic variables
-  if (Model%cplchm) then
-
-    if (Model%ntchm > 0) then
-
-      if (associated(IntDiag(1)%duem)) then
-        do num = 1, size(IntDiag(1)%duem, dim=2)
-          idx = idx + 1
-          ExtDiag(idx)%axes = 2
-          write(ExtDiag(idx)%name,'("duem",i3.3)') num
-          write(ExtDiag(idx)%desc,'("Dust Emission Bin ",i0)') num
-          ExtDiag(idx)%unit = 'kg/m2/s'
-          ExtDiag(idx)%mod_name = 'gfs_phys'
-          allocate (ExtDiag(idx)%data(nblks))
-          do nb = 1,nblks
-            ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%duem(:,num)
-          enddo
-        enddo
-      endif
-
-      if (associated(IntDiag(1)%ssem)) then
-        do num = 1, size(IntDiag(1)%ssem, dim=2)
-          idx = idx + 1
-          ExtDiag(idx)%axes = 2
-          write(ExtDiag(idx)%name,'("ssem",i3.3)') num
-          write(ExtDiag(idx)%desc,'("Seasalt Emission Bin ",i0)') num
-          ExtDiag(idx)%unit = 'kg/m2/s'
-          ExtDiag(idx)%mod_name = 'gfs_phys'
-          allocate (ExtDiag(idx)%data(nblks))
-          do nb = 1,nblks
-            ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%ssem(:,num)
-          enddo
-        enddo
-      endif
-
-      if (associated(Model%ntdiag)) then
-        idt = 0
-        do num = Model%ntchs, Model%ntchm + Model%ntchs - 1
-          if (Model%ntdiag(num-Model%ntchs+1)) then
-            idt = idt + 1
-            idx = idx + 1
-            ExtDiag(idx)%axes = 2
-            ExtDiag(idx)%name = trim(Model%tracer_names(num)) // 'sd'
-            ExtDiag(idx)%desc = trim(Model%tracer_names(num)) // ' Sedimentation'
-            ExtDiag(idx)%unit = 'kg/m2/s'
-            ExtDiag(idx)%mod_name = 'gfs_phys'
-            allocate (ExtDiag(idx)%data(nblks))
-            do nb = 1,nblks
-              ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%sedim(:,idt)
-            enddo
-
-            idx = idx + 1
-            ExtDiag(idx)%axes = 2
-            ExtDiag(idx)%name = trim(Model%tracer_names(num)) // 'dp'
-            ExtDiag(idx)%desc = trim(Model%tracer_names(num)) // ' Dry Deposition'
-            ExtDiag(idx)%unit = 'kg/m2/s'
-            ExtDiag(idx)%mod_name = 'gfs_phys'
-            allocate (ExtDiag(idx)%data(nblks))
-            do nb = 1,nblks
-              ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%drydep(:,idt)
-            enddo
-
-            idx = idx + 1
-            ExtDiag(idx)%axes = 2
-            ExtDiag(idx)%name = trim(Model%tracer_names(num)) // 'wtl'
-            ExtDiag(idx)%desc = trim(Model%tracer_names(num)) // ' Large-Scale Wet Deposition'
-            ExtDiag(idx)%unit = 'kg/m2/s'
-            ExtDiag(idx)%mod_name = 'gfs_phys'
-            allocate (ExtDiag(idx)%data(nblks))
-            do nb = 1,nblks
-              ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%wetdpl(:,idt)
-            enddo
-
-            idx = idx + 1
-            ExtDiag(idx)%axes = 2
-            ExtDiag(idx)%name = trim(Model%tracer_names(num)) // 'wtc'
-            ExtDiag(idx)%desc = trim(Model%tracer_names(num)) // ' Convective-Scale Wet Deposition'
-            ExtDiag(idx)%unit = 'kg/m2/s'
-            ExtDiag(idx)%mod_name = 'gfs_phys'
-            allocate (ExtDiag(idx)%data(nblks))
-            do nb = 1,nblks
-              ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%wetdpc(:,idt)
-            enddo
-          endif
-        enddo
-      endif
-
-    endif
-
-    num = size(IntDiag(1)%abem, dim=2)
-    do num = 1, size(IntDiag(1)%abem, dim=2)
-      idx = idx + 1
-      select case (mod(num,3))
-        case (0)
-          ExtDiag(idx)%name = 'bcem'
-          ExtDiag(idx)%desc = 'Black Carbon'
-        case (1)
-          ExtDiag(idx)%name = 'ocem'
-          ExtDiag(idx)%desc = 'Organic Carbon'
-        case (2)
-          ExtDiag(idx)%name = 'so2em'
-          ExtDiag(idx)%desc = 'SO2'
-      end select
-
-      if (num > 3) then
-        ExtDiag(idx)%name = trim(ExtDiag(idx)%name) // 'bb'
-        ExtDiag(idx)%desc = trim(ExtDiag(idx)%desc) // ' Biomass Burning Emissions'
-      else
-        ExtDiag(idx)%name = trim(ExtDiag(idx)%name) // 'an'
-        ExtDiag(idx)%desc = trim(ExtDiag(idx)%desc) // ' Anthropogenic Emissions'
-      end if
-
-      ExtDiag(idx)%axes = 2
-      ExtDiag(idx)%unit = 'ug/m2/s'
-      ExtDiag(idx)%mod_name = 'gfs_phys'
-      allocate (ExtDiag(idx)%data(nblks))
-      do nb = 1,nblks
-        ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%abem(:,num)
-      enddo
-    end do
-
-    do num = 1, size(IntDiag(1)%aecm, dim=2)
-      idx = idx + 1
-      select case (num)
-        case(1)
-          ExtDiag(idx)%name = 'aecmass'
-          ExtDiag(idx)%desc = 'Aerosol Column Mass Density (PM2.5)'
-        case(2)
-          ExtDiag(idx)%name = 'bccmass'
-          ExtDiag(idx)%desc = 'Black Carbon Column Mass Density'
-        case(3)
-          ExtDiag(idx)%name = 'occmass'
-          ExtDiag(idx)%desc = 'Organic Carbon Column Mass Density'
-        case(4)
-          ExtDiag(idx)%name = 'sucmass'
-          ExtDiag(idx)%desc = 'Sulfate Column Mass Density'
-        case(5)
-          ExtDiag(idx)%name = 'ducmass'
-          ExtDiag(idx)%desc = 'Dust Column Mass Density'
-        case(6)
-          ExtDiag(idx)%name = 'sscmass'
-          ExtDiag(idx)%desc = 'Seasalt Column Mass Density'
-      end select
-
-      ExtDiag(idx)%axes = 2
-      ExtDiag(idx)%unit = 'g/m2'
-      ExtDiag(idx)%mod_name = 'gfs_phys'
-      allocate (ExtDiag(idx)%data(nblks))
-      do nb = 1,nblks
-        ExtDiag(idx)%data(nb)%var2 => IntDiag(nb)%aecm(:,num)
-      enddo
-    end do
-
-  endif
-
 !--- prognostic variable tendencies (t, u, v, sph, clwmr, o3)
 !rab    idx = idx + 1
 !rab    ExtDiag(idx)%axes = 3

ccpp/driver/GFS_init.F90

@@ -77,6 +77,7 @@ subroutine GFS_initialize (Model, Statein, Stateout, Sfcprop,     &
                      Init_parm%iau_offset, Init_parm%bdat,         &
                      Init_parm%cdat, Init_parm%nwat,               &
                      Init_parm%tracer_names,                       &
+                     Init_parm%tracer_types,                       &
                      Init_parm%input_nml_file, Init_parm%tile_num, &
                      Init_parm%blksz, Init_parm%ak, Init_parm%bk,  &
                      Init_parm%restart, Init_parm%hydrostatic,     &