Modified the jedi yaml file to remove duplicated blockes of model inf…

…o and varialbe lists

Changed the omf name from 'bkgomb' to 'ombg' in both yaml file and python scripts

hafs-test/testinput/SFCSHP_singleob_airTemperature_fv3jedi.yaml

@@ -1,130 +1,67 @@
+_filenames: &fv3file_names
+  filename_core: '20200825.120000.fv_core.res.tile1.nc'
+  filename_trcr: '20200825.120000.fv_tracer.res.tile1.nc'
+  filename_sfcd: '20200825.120000.sfc_data.nc'
+  filename_sfcw: '20200825.120000.fv_srf_wnd.res.tile1.nc'
+  filename_cplr: '20200825.120000.coupler.res'
+
+_geometry: &geometry_configs
+  namelist filename: DataFix/input_hafs.nml
+  field metadata override: Data/fieldmetadata/gfs-restart.yaml
+  akbk: DataFix/fix/akbk65.nc
+  npx: 721
+  npy: 541
+  npz: 65
+  layout: [10,6]
+  io_layout: [1,1]
+  ntiles: 1
+
 cost function:
   cost type: 3D-Var
   time window:
-      begin: '2020-08-25T09:00:00Z'
-      length: PT6H
-
+    begin: &InitialDate '2020-08-25T09:00:00Z'
+    length: PT6H
   geometry:
     fms initialization:
       namelist filename: DataFix/fmsmpp.nml
       field table filename: DataFix/field_table
-    namelist filename: DataFix/input_hafs.nml
-    field metadata override: Data/fieldmetadata/gfs-restart.yaml
-    akbk: DataFix/fix/akbk65.nc
-    npx: 721
-    npy: 541
-    npz: 65
-    layout: [10,6]
-    io_layout: [1,1]
-    ntiles: 1
-  analysis variables:
-  - eastward_wind
-  - northward_wind
-  - air_temperature
-  - air_pressure_thickness
-  - specific_humidity
-  - cloud_liquid_ice
-  - cloud_liquid_water
-  - ozone_mass_mixing_ratio
+    <<: *geometry_configs
+  analysis variables: &ana_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,specific_humidity,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio]
+
 
   background:
-    datetime: 2020-08-25T12:00:00Z
+    datetime: &AnaDate '2020-08-25T12:00:00Z'
     filetype: fms restart
     datapath: Data/bkg
-    filename_core: fv3_dynvars.nc
-    filename_trcr: fv3_tracer.nc
-    filename_sfcd: fv3_sfcdata.nc
-    filename_sfcw: fv3_srfwnd.nc
-    filename_cplr: coupler.res
-    state variables: 
-    - eastward_wind
-    - northward_wind
-    - air_temperature
-    - air_pressure_thickness
-    - specific_humidity
-    - cloud_liquid_ice
-    - cloud_liquid_water
-    - ozone_mass_mixing_ratio
-    - phis
-    - slmsk
-    - sheleg
-    - tsea
-    - vtype
-    - stype
-    - vfrac
-    - stc
-    - smc
-    - snwdph
-    - u_srf
-    - v_srf
-    - f10m
-
-
+    <<: *fv3file_names
+    state variables: &state_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,specific_humidity,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio,phis,slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,u_srf,v_srf,f10m]
   background error:
     covariance model: ensemble
     members from template:
       template:
-        datetime: 2020-08-25T12:00:00Z
+        datetime: *AnaDate
         filetype: fms restart
-        state variables:  
-        - eastward_wind
-        - northward_wind
-        - air_temperature
-        - air_pressure_thickness
-        - specific_humidity
-        - cloud_liquid_ice
-        - cloud_liquid_water
-        - ozone_mass_mixing_ratio
-        - phis
-        - slmsk
-        - sheleg
-        - tsea
-        - vtype
-        - stype
-        - vfrac
-        - stc
-        - smc
-        - snwdph
-        - u_srf
-        - v_srf
-        - f10m
-
-
+        state variables: *state_vars
         datapath: ens/mem%mem%/
-        filename_core: '20200825.120000.fv_core.res.tile1.nc'
-        filename_trcr: '20200825.120000.fv_tracer.res.tile1.nc'
-        filename_sfcd: '20200825.120000.sfc_data.nc'
-        filename_sfcw: '20200825.120000.fv_srf_wnd.res.tile1.nc'
-        filename_cplr: '20200825.120000.coupler.res'
+        <<: *fv3file_names
       pattern: '%mem%'
-      nmembers: 10 
+      nmembers: 10
       zero padding: 3
     localization:
       localization method: SABER
       saber central block:
         saber block name: BUMP_NICAS
-        active variables: 
-        - eastward_wind
-        - northward_wind
-        - air_temperature
-        - air_pressure_thickness
-        - specific_humidity
-        - cloud_liquid_ice
-        - cloud_liquid_water
-        - ozone_mass_mixing_ratio
-
+        active variables: *ana_vars
         read:
           io:
             data directory: Data/bump
             files prefix: fv3jedi_bumpparameters_nicas_lam_atm
             alias:
             - in code: common
               in file: t_250km
-
           drivers:
              multivariate strategy: duplicated
              read local nicas: true
-
 #------------------------------------------------------------------------------
   observations:
      observers:
@@ -149,11 +86,7 @@ cost function:
        obs operator:
          name: Composite
          components:
-         - name: VertInterp
-           vertical coordinate: air_pressure
-           observation vertical coordinate: pressure
-           observation vertical coordinate group: MetaData
-           interpolation method: log-linear
+         - name: Identity 
            variables:
            - name: airTemperature
 
@@ -167,7 +100,7 @@ cost function:
              is_in: 180
            action:
              name: assign error
-             error parameter: 2.5
+             error parameter: 0.9279
            defer to post: true
       # Adjusted error after initial assignment (qcmod.f90)
          - filter: Perform Action
@@ -203,52 +136,30 @@ cost function:
                  inflation factor: 8.0
                  geovar_sfc_geomz: surface_geometric_height
            defer to post: true
-        #- filter: Bounds Check
-      #  filter variables:
-      #  - name: airTemperature
-      #  minvalue: 195.0
-      #  maxvalue: 327.0
-      #  action:
-      #    name: reject
-      #- filter: Background Check
-      #  filter variables:
-      #  - name: airTemperature
-      #  threshold: 7.0
-      #  absolute threshold: 9.0
-      #  action:
-      #    name: reject
-      #  defer to post: true
 
 variational:
   minimizer:
     algorithm: DRPCG    # Derber-Rosati Conjugate Gradients
   iterations:
   - ninner: 1
     gradient norm reduction: 1e-60
+    test: on
     geometry:
       fms initialization:
         namelist filename: DataFix/fmsmpp.nml
         field table filename: DataFix/field_table
-      namelist filename: DataFix/input_hafs.nml
-      field metadata override: Data/fieldmetadata/gfs-restart.yaml
-      akbk: DataFix/fix/akbk65.nc
-      npx: 721
-      npy: 541
-      npz: 65
-      layout: [10,6]
-      io_layout: [1,1]
-      ntiles: 1 
       fieldsets:
-      - fieldset: DataFix/fix/dynamics_lam_cmaq.yaml
+        fieldset: DataFix/fix/dynamics_lam_cmaq.yaml
+      <<: *geometry_configs
     diagnostics:
-      departures: bkgmob
+      departures: ombg
 final:
   diagnostics:
     departures: oman
 
 output:
   filetype: fms restart
   datapath: Data/analysis/
-  prefix: envar-fv3_hafs_singleOBS_sfcshp #Ens3dvar-fv3_lam-C775
+  prefix: envar-fv3_hafs_singleOBS_sfcshp 
   frequency: PT3H
 

hafs-test/ush/fv3jedi_gsi_increment_singleob.py

@@ -92,8 +92,7 @@
 #oberr_final = jncdiag.groups["EffectiveError2"].variables[f"{variable}"][:][0]
 #pdb.set_trace()
 ob = jncdiag.groups["ObsValue"].variables[f"{variable}"][:][0]
-#omf= jncdiag.groups["ombg"].variables[f"{variable}"][:][0]
-omf= jncdiag.groups["bkgmob"].variables[f"{variable}"][:][0]
+omf= jncdiag.groups["ombg"].variables[f"{variable}"][:][0]
 fmo= -1*omf
 hofx= fmo+ob