Merge pull request #313 from NCAR/SWE_repartition_fix

Add SWE repartitioning for CLM

.gitignore

@@ -69,6 +69,8 @@ restart_file_tool
 system_simulation
 rttov_test
 rttov_unit_tests
+dart_to_clm
+clm_to_dart
 
 # Directories to NOT IGNORE ... same as executable names
 # as far as I know, these must be listed after the executables

CHANGELOG.rst

@@ -22,6 +22,17 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**February 3 2022 :: CLM with SWE repartitioning. Tag: v9.13.0** 
+
+- Updated Community Land Model (CLM) model_mod, scripting, and diagnostics.
+- New capability to repartition snow layer mass and dimension variables.
+  The repartitioning ensures that the adjustments applied to the snow layers
+  are consistent (mass and dimensions are conserved) with the adjustment of
+  the total snow water equivalent.
+- New observation converters for NASA_Earthdata and NSIDC
+- Support for netcdf _FillValue
+- Bug-fix for clm nc_write_model_atts lon vs nlon
+
 **January 11 2022 :: Bug fix for inflation namelist options. Tag: v9.12.1**
 
 - reverted inf_flavor namelist option to be integer only to conform to Fortran

README.rst

@@ -306,8 +306,10 @@ References
    observations/obs_converters/MODIS/readme
    observations/obs_converters/MODIS/MOD15A2_to_obs
    observations/obs_converters/MPD/README
+   observations/obs_converters/NASA_Earthdata/README
    observations/obs_converters/NCEP/prep_bufr/prep_bufr
    observations/obs_converters/NCEP/ascii_to_obs/create_real_obs
+   observations/obs_converters/NSIDC/SMAP_L2_to_obs
    observations/obs_converters/ROMS/ROMS
    observations/obs_converters/SIF/SIF_to_obs_netcdf
    observations/obs_converters/SSEC/SSEC
@@ -371,6 +373,8 @@ References
    models/CESM/readme
    models/cice/readme
    models/clm/readme
+   models/clm/clm_to_dart
+   models/clm/dart_to_clm
    models/cm1/readme
    models/coamps_nest/readme
    models/coamps/readme

assimilation_code/modules/io/direct_netcdf_mod.f90

@@ -89,6 +89,7 @@ module direct_netcdf_mod
                                  get_units, get_long_name, get_short_name, &
                                  get_has_missing_value, get_FillValue, &
                                  get_missing_value, get_add_offset, get_xtype, &
+                                 get_has_FillValue, &
                                  get_index_start, get_index_end , get_num_dims, &
                                  create_diagnostic_structure, &
                                  end_diagnostic_structure
@@ -1725,7 +1726,8 @@ subroutine write_variable_attributes(filename, ncFileID, ncVarID, domid, &
 endif
 
 ! check to see if template file has missing value attributes
-if ( get_has_missing_value(domid, varid) ) then
+if ( get_has_missing_value(domid, varid) .or. &
+     get_has_FillValue(    domid, varid) ) then
    select case ( get_xtype(domid, varid) )
       case ( NF90_INT )
          call nc_write_missing_value_int(ncFileID, filename, ncVarID, domid, varid)
@@ -3033,6 +3035,22 @@ subroutine set_dart_missing_value(array, domain, variable)
 
 endif
 
+if ( get_has_FillValue(domain, variable) ) then
+
+   select case ( get_xtype(domain, variable) )
+      case ( NF90_INT )
+         call get_FillValue(domain, variable, model_missing_valueINT)
+         where(array == model_missing_valueINT) array = MISSING_R8
+      case ( NF90_FLOAT )
+         call get_FillValue(domain, variable, model_missing_valueR4)
+         where(array == model_missing_valueR4) array = MISSING_R8
+      case ( NF90_DOUBLE )
+         call get_FillValue(domain, variable, model_missing_valueR8)
+         where(array == model_missing_valueR8) array = MISSING_R8
+   end select
+
+endif
+
 end subroutine set_dart_missing_value
 
 !--------------------------------------------------------
@@ -3066,6 +3084,22 @@ subroutine set_model_missing_value(array, domain, variable)
 
 endif
 
+if ( get_has_FillValue(domain, variable) ) then
+
+   select case ( get_xtype(domain, variable) )
+      case ( NF90_INT )
+         call get_FillValue(domain, variable, model_missing_valueINT)
+         where(array == MISSING_R8)   array = model_missing_valueINT
+      case ( NF90_FLOAT )
+         call get_FillValue(domain, variable, model_missing_valueR4)
+         where(array == MISSING_R8)   array = model_missing_valueR4
+      case ( NF90_DOUBLE )
+         call get_FillValue(domain, variable, model_missing_valueR8)
+         where(array == MISSING_R8)   array = model_missing_valueR8
+   end select
+
+endif
+
 end subroutine set_model_missing_value
 
 !--------------------------------------------------------

assimilation_code/modules/io/io_filenames_mod.f90

@@ -53,6 +53,7 @@ module io_filenames_mod
                                  get_add_offset, &
                                  get_scale_factor, &
                                  get_has_missing_value, &
+                                 get_has_FillValue, &
                                  do_io_update
 use ensemble_manager_mod, only : ensemble_type
 use netcdf_utilities_mod, only : nc_check
@@ -632,24 +633,39 @@ subroutine check_attributes(ncFile, filename, ncVarId, domid, varid)
 if ( get_has_missing_value(domid, varid) ) then
    select case (get_xtype(domid,varid))
       case (NF90_INT)
-         call get_FillValue(domid, varid, spvalINT)
-         call check_attribute_value_int(ncFile, filename, ncVarID, '_FillValue', spvalINT)
          call get_missing_value(domid, varid, spvalINT)
          call check_attribute_value_int(ncFile, filename, ncVarID, 'missing_value', spvalINT)
 
       case (NF90_FLOAT)
-         call get_FillValue(domid, varid, spvalR4)
-         call check_attribute_value_r4(ncFile, filename, ncVarID, '_FillValue', spvalR4)
          call get_missing_value(domid, varid, spvalR4)
          call check_attribute_value_r4(ncFile, filename, ncVarID, 'missing_value', spvalR4)
 
       case (NF90_DOUBLE)
-         call get_FillValue(domid, varid, spvalR8)
-         call check_attribute_value_r8(ncFile, filename, ncVarID, '_FillValue', spvalR8)
          call get_missing_value(domid, varid, spvalR8)
          call check_attribute_value_r8(ncFile, filename, ncVarID, 'missing_value', spvalR8)
 
       case default
+         !>@todo FIXME report the variable with the unsupported xtype
+         call error_handler(E_ERR, 'check_attributes', 'unknown xtype', source)
+   end select
+endif
+
+if ( get_has_FillValue(   domid, varid) ) then
+   select case (get_xtype(domid, varid))
+      case (NF90_INT)
+         call get_FillValue(domid, varid, spvalINT)
+         call check_attribute_value_int(ncFile, filename, ncVarID, '_FillValue', spvalINT)
+
+      case (NF90_FLOAT)
+         call get_FillValue(domid, varid, spvalR4)
+         call check_attribute_value_r4(ncFile, filename, ncVarID, '_FillValue', spvalR4)
+
+      case (NF90_DOUBLE)
+         call get_FillValue(domid, varid, spvalR8)
+         call check_attribute_value_r8(ncFile, filename, ncVarID, '_FillValue', spvalR8)
+
+      case default
+         !>@todo FIXME report the variable with the unsupported xtype
          call error_handler(E_ERR, 'check_attributes', 'unknown xtype', source)
    end select
 endif