Update variables to be consistent with updated jedi hashes (#45)

This PR updates variables to be consistent with the updated jedi hashes in GDASApp branch [`feature/resume_nightly`](https://github.com/NOAA-EMC/GDASApp/tree/feature/resume_nightly) Resolves #43
NOAA-EMC · Nov 15, 2024 · c41e7d7 · c41e7d7
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diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -1,6 +1,6 @@
 variable change:
   variable change name: Model2GeoVaLs
-  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc]
   output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -1,6 +1,6 @@
 variable change:
   variable change name: Model2GeoVaLs
-  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc]
   output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars

diff --git a/algorithm/marine/soca_2cice_antarctic.yaml.j2 b/algorithm/marine/soca_2cice_antarctic.yaml.j2
@@ -26,7 +26,7 @@ variable change:
     tstep: PT1H
   cice output:
     restart: {{ ice_rst }}
-  output variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+  output variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
 
 states:
 - input:
@@ -35,7 +35,7 @@ states:
      ocn_filename: {{ ocn_ana }}
      ice_filename: {{ ice_ana }}
      date: '{{ fcst_begin }}'
-     state variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+     state variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
   output:
      datadir: Data
      exp: soca2cice

diff --git a/algorithm/marine/soca_2cice_arctic.yaml.j2 b/algorithm/marine/soca_2cice_arctic.yaml.j2
@@ -23,7 +23,7 @@ variable change:
     tstep: PT1H
   cice output:
     restart: {{ ice_rst }}
-  output variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+  output variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
 
 states:
 - input:
@@ -32,7 +32,7 @@ states:
      ocn_filename: {{ ocn_ana }}
      ice_filename: {{ ice_ana }}
      date: '{{ fcst_begin }}'
-     state variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+     state variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
   output:
      datadir: Data
      exp: soca2cice

diff --git a/algorithm/marine/soca_diagb.yaml.j2 b/algorithm/marine/soca_diagb.yaml.j2
@@ -18,7 +18,7 @@ background error:
   type: incr
 
 variables:
-  name: [tocn, socn, uocn, vocn, hocn, ssh, cicen, hicen, hsnon, mom6_mld]
+  name: [sea_water_potential_temperature, sea_water_salinity, eastward_sea_water_velocity, northward_sea_water_velocity, sea_water_cell_thickness, sea_surface_height_above_geoid, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, mom6_mld]
 
 rescale: 2.0    # rescales the filtered std. dev. by "rescale"
 min sst: 0.0    # Added to sst bkg. err.

diff --git a/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2 b/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
@@ -8,7 +8,7 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ marine_window_end_iso }}'
-  state variables: [ssh]
+  state variables: [sea_surface_height_above_geoid]
 
 background error:
   covariance model: SABER
@@ -26,7 +26,7 @@ background error:
             date: '{{ marine_window_end_iso }}'
             basename: ./
             ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
-          model variable: ssh
+          model variable: sea_surface_height_above_geoid
         write:
           filepath: ./staticb/hz_ocean
 

diff --git a/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2 b/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2
@@ -8,7 +8,7 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ marine_window_middle_iso }}'
-  state variables: [tocn]
+  state variables: [sea_water_potential_temperature]
 
 background error:
   covariance model: SABER
@@ -29,6 +29,6 @@ background error:
             date: '{{ marine_window_middle_iso }}'
             basename: ./
             ocn_filename: vt_scales.nc
-          model variable: tocn
+          model variable: sea_water_potential_temperature
         write:
           filepath: ./staticb/vt_ocean
diff --git a/algorithm/marine/soca_setcorscales.yaml.j2 b/algorithm/marine/soca_setcorscales.yaml.j2
@@ -4,11 +4,11 @@ resolution:
 
 date: "0001-01-01T00:00:00Z"
 
-corr variables: [ssh]
+corr variables: [sea_surface_height_above_geoid]
 
 scales:
   vert layers: 5 # in units of layer
-  ssh:
+  sea_surface_height_above_geoid:
     rossby mult: 1.00
     min grid mult: 2.0
 

diff --git a/algorithm/marine/socaincr2mom6.yaml.j2 b/algorithm/marine/socaincr2mom6.yaml.j2
@@ -4,9 +4,9 @@ geometry:
 
 date: '{{ marine_window_begin }}'
 
-layers variable: [hocn]
+layers variable: [sea_water_cell_thickness]
 
-increment variables: [tocn, socn, uocn, vocn, ssh]
+increment variables: [sea_water_potential_temperature, sea_water_salinity, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
 
 vertical geometry:
   date: '{{ marine_window_begin }}'

diff --git a/model/atmosphere/atmosphere_background.yaml.j2 b/model/atmosphere/atmosphere_background.yaml.j2
@@ -5,6 +5,6 @@ ufs soil nlev: 4
 ufs fields split by level: [smc,stc]
 datetime: "{{ atmosphere_background_time_iso }}"
 filenames: [ {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc, {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc ]
-state variables: [ua,va,t,delp,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height,
-                  slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdphMeters,
+state variables: [ua,va,t,delp,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc,
+                  slmsk,sheleg,tmpsfc,vtype,stype,vfrac,stc,smc,snwdphMeters,
                   u_srf,v_srf,f10m]
diff --git a/model/atmosphere/atmosphere_background_ensemble.yaml.j2 b/model/atmosphere/atmosphere_background_ensemble.yaml.j2
@@ -6,8 +6,8 @@ members from template:
     provider: ufs
     ufs soil nlev: 4
     ufs fields split by level: [smc,stc]
-    state variables: [ua,va,t,delz,delp,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height,
-                     slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdphMeters,
+    state variables: [ua,va,t,delz,delp,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc,
+                     slmsk,sheleg,tmpsfc,vtype,stype,vfrac,stc,smc,snwdphMeters,
                      u_srf,v_srf,f10m]
     datapath: {{ atmosphere_background_ensemble_path }}
     filename is datetime templated: true

diff --git a/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2 b/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
@@ -21,8 +21,8 @@ components:
       debugging mode: false
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                                      specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+      input variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                                      water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                                       mole_fraction_of_ozone_in_air]
       output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
@@ -45,8 +45,8 @@ components:
       localization method: SABER
       saber central block:
         saber block name: BUMP_NICAS
-        active variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                                             specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+        active variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                                             water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                                              ozone_mass_mixing_ratio ]
         read:
           general:
@@ -198,8 +198,8 @@ components:
               value: 0.3
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                                             specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+      input variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                                             water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                                              ozone_mass_mixing_ratio ]
       output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:

diff --git a/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2 b/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2
@@ -19,7 +19,7 @@ saber outer blocks:
   debugging mode: false
 linear variable change:
   linear variable change name: Control2Analysis
-  input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                           specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+  input variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                           water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                            mole_fraction_of_ozone_in_air]
   output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
diff --git a/model/marine/marine_background.yaml.j2 b/model/marine/marine_background.yaml.j2
@@ -3,4 +3,4 @@ basename: {{ marine_background_path}}
 ocn_filename: MOM.res.nc
 ice_filename: cice.res.nc
 date: "{{ marine_background_time }}"
-state variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh, hocn, mld, layer_depth]
+state variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid, sea_water_cell_thickness, ocean_mixed_layer_thickness, sea_water_depth]
diff --git a/model/marine/marine_background_error_static_diffusion.yaml.j2 b/model/marine/marine_background_error_static_diffusion.yaml.j2
@@ -3,13 +3,13 @@ saber central block:
   saber block name: diffusion
   read:
     groups:
-    - variables: [tocn, socn, ssh]
+    - variables: [sea_water_potential_temperature, sea_water_salinity, sea_surface_height_above_geoid]
       horizontal:
         filepath: ./staticb/hz_ocean
       vertical:
         levels: {{marine_vt_levels}}
         filepath: ./staticb/vt_ocean
-    - variables: [cicen]
+    - variables: [sea_ice_area_fraction]
       horizontal:
         filepath: ./staticb/hz_ice
 
@@ -24,7 +24,7 @@ saber outer blocks:
       read_from_file: 3
 
 linear variable change:
-  input variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
-  output variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+  input variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
+  output variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
   linear variable changes:
   - linear variable change name: BalanceSOCA
diff --git a/observations/atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2 b/observations/atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2
@@ -110,7 +110,7 @@
     - variable: ObsType/windEastward
       is_in: 290
   #   - variable: GeoVaLs/surface_temperature
-    - variable: GeoVaLs/surface_temperature_where_land
+    - variable: GeoVaLs/skin_temperature_at_surface_where_land
       maxvalue: 273.
     action:
       name: reject

diff --git a/observations/atmosphere-lgetkf/conventional_ps.yaml.j2 b/observations/atmosphere-lgetkf/conventional_ps.yaml.j2
@@ -27,7 +27,7 @@
     - name: stationPressure
     da_psfc_scheme: GSI
     station_altitude: height
-    geovar_sfc_geomz: surface_altitude
+    geovar_sfc_geomz: height_above_mean_sea_level_at_surface
     geovar_geomz: geopotential_height
 
   # Linear Observation Operator
@@ -264,7 +264,7 @@
       function:
         name: ObsFunction/ObsErrorFactorSfcPressure
         options:
-          geovar_sfc_geomz: surface_altitude
+          geovar_sfc_geomz: height_above_mean_sea_level_at_surface
           geovar_geomz: geopotential_height
           station_altitude: height
 

diff --git a/observations/atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2 b/observations/atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2
@@ -448,7 +448,7 @@
     - variable:
         name: ObsType/windEastward
       is_in: 247
-    reference: GeoVaLs/surface_pressure
+    reference: GeoVaLs/air_pressure_at_surface
     value: MetaData/pressure
     maxvalue: -11000.                   # within 110 hPa above surface pressure, negative p-diff
     action:

diff --git a/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2 b/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2
@@ -107,7 +107,7 @@
     - variable: ObsType/windEastward
       is_in: 290
   #   - variable: GeoVaLs/surface_temperature
-    - variable: GeoVaLs/surface_temperature_where_land
+    - variable: GeoVaLs/skin_temperature_at_surface_where_land
       maxvalue: 273.
     action:
       name: reject

diff --git a/observations/atmosphere/conventional_ps.yaml.j2 b/observations/atmosphere/conventional_ps.yaml.j2
@@ -24,7 +24,7 @@
     - name: stationPressure
     da_psfc_scheme: GSI
     station_altitude: height
-    geovar_sfc_geomz: surface_altitude
+    geovar_sfc_geomz: height_above_mean_sea_level_at_surface
     geovar_geomz: geopotential_height
 
   # Linear Observation Operator
@@ -261,7 +261,7 @@
       function:
         name: ObsFunction/ObsErrorFactorSfcPressure
         options:
-          geovar_sfc_geomz: surface_altitude
+          geovar_sfc_geomz: height_above_mean_sea_level_at_surface
           geovar_geomz: geopotential_height
           station_altitude: height
 

diff --git a/observations/atmosphere/satwnd.abi_goes-16.yaml.j2 b/observations/atmosphere/satwnd.abi_goes-16.yaml.j2
@@ -445,7 +445,7 @@
     - variable:
         name: ObsType/windEastward
       is_in: 247
-    reference: GeoVaLs/surface_pressure
+    reference: GeoVaLs/air_pressure_at_surface
     value: MetaData/pressure
     maxvalue: -11000.                   # within 110 hPa above surface pressure, negative p-diff
     action:

diff --git a/observations/atmosphere/scatwind_ascat_metop-a.yaml.j2 b/observations/atmosphere/scatwind_ascat_metop-a.yaml.j2
@@ -107,7 +107,7 @@
     - variable: ObsType/windEastward
       is_in: 290
   #   - variable: GeoVaLs/surface_temperature
-    - variable: GeoVaLs/surface_temperature_where_land
+    - variable: GeoVaLs/skin_temperature_at_surface_where_land
       maxvalue: 273.
     action:
       name: reject

diff --git a/observations/atmosphere/sondes.yaml.j2 b/observations/atmosphere/sondes.yaml.j2
@@ -34,7 +34,7 @@
       - name: specificHumidity
     - name: SfcPCorrected
       da_psfc_scheme: GSI
-      geovar_sfc_geomz: surface_geopotential_height
+      geovar_sfc_geomz: geopotential_height_at_surface
       geovar_geomz: geopotential_height
       variables:
       - name: stationPressure
@@ -106,7 +106,7 @@
           error_min: 100.0           # 1 mb
           error_max: 300.0           # 3 mb
           geovar_geomz: geopotential_height
-          geovar_sfc_geomz: surface_geopotential_height
+          geovar_sfc_geomz: geopotential_height_at_surface
     #
     # Gross error check with (O - B) / ObsError greater than threshold
   - filter: Background Check