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NOAA-EMC · May 28, 2024 · c4721c3 · c4721c3
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diff --git a/model/atmosphere/atmosphere_background_error_hybrid_bump_bump.yaml.j2 b/model/atmosphere/atmosphere_background_error_hybrid_bump_bump.yaml.j2
@@ -5,12 +5,12 @@ components:
     saber blocks:
     - saber block name: BUMP_NICAS
       saber central block: true
-      input variables: &control_vars [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
-      output variables: *control_vars
-      active variables: &active_vars [psi,chi,t,ps,rh,liq_wat,o3mr]
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       bump:
         io:
-          data directory: &staticb_dir {{atmosphere_bump_data_directory}}
+          data directory: {{atmosphere_bump_data_directory}}
         drivers:
           multivariate strategy: specific_univariate
           read local nicas: true
@@ -36,30 +36,30 @@ components:
           io:
             files prefix: nicas/nicas_2D_gfs
     - saber block name: StdDev
-      input variables: *control_vars
-      output variables: *control_vars
-      active variables: *active_vars
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       file:
         filetype: fms restart
         datetime: 2021-12-22T00:00:00Z
         set datetime on read: true
         psinfile: true
-        datapath: '*staticb_dir'
+        datapath: {{atmosphere_bump_data_directory}}
         prefix: stddev/20211222.000000
         filename_core: stddev.fv_core.res.nc
         filename_trcr: stddev.fv_tracer.res.nc
         filename_sfcd: stddev.sfc_data.nc
         filename_sfcw: stddev.fv_srf_wnd.res.nc
         filename_cplr: stddev.coupler.res
     - saber block name: BUMP_VerticalBalance
-      input variables: *control_vars
-      output variables: *control_vars
-      active variables: *active_vars
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       bump:
         general:
           universe length-scale: 2000.0e3
         io:
-          data directory: *staticb_dir
+          data directory: {{atmosphere_bump_data_directory}}
           files prefix: vbal/vbal_gfs
           overriding sampling file: vbal/vbal_2021122200_gfs_sampling
         drivers:
@@ -74,21 +74,21 @@ components:
           - balanced variable: var4
             unbalanced variable: var1
     - saber block name: BUMP_PsiChiToUV
-      input variables: *control_vars
-      output variables: &3dvars_with_rh [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
       active variables: [psi,chi,ua,va]
       bump:
         general:
           universe length-scale: 2000.0e3
         io:
-          data directory: *staticb_dir
+          data directory: {{atmosphere_bump_data_directory}}
           files prefix: psichitouv/psichitouv_gfs
         drivers:
           read local psichitouv: true
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: *3dvars_with_rh
-      output variables: &3dvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+      input variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
     value: 0.1
 - covariance:
@@ -97,7 +97,7 @@ components:
       template:
         datetime: "{{ atmosphere_background_time_iso }}"
         filetype: fms restart
-        state variables: *3dvars
+        state variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
         datapath: {{ atmosphere_background_ensemble_path}}
         filename is datetime templated: true
         filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
@@ -112,11 +112,11 @@ components:
 #      localization method: SABER
 #      saber block:
 #      - saber block name: BUMP_NICAS
-#        input variables: *control_vars
-#        output variables: *control_vars
-#        active variables: *active_vars
+#        input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+#        output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+#        active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
 #        bump:
-#          datadir: *staticb_dir
+#          datadir: {{atmosphere_bump_data_directory}}
 #          verbosity: main
 #          strategy: specific_univariate
 #          method: loc

diff --git a/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2 b/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
@@ -5,26 +5,26 @@ components:
     saber central block:
       saber block name: gsi covariance
       read:
-        gsi akbk: &akbk {{atmosphere_fv3jedi_files_path}}/akbk.nc4
-        gsi error covariance file: &gsiberr {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
-        gsi berror namelist file: &gsibnml {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
+        gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+        gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+        gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
         processor layout x direction: {{atmosphere_layout_gsib_x}}
         processor layout y direction: {{atmosphere_layout_gsib_y}}
         debugging mode: false
     saber outer blocks:
     - saber block name: gsi interpolation to model grid
-      gsi akbk: *akbk
-      gsi error covariance file: *gsiberr
-      gsi berror namelist file: *gsibnml
+      gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+      gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+      gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
       processor layout x direction: {{atmosphere_layout_gsib_x}}
       processor layout y direction: {{atmosphere_layout_gsib_x}}
       debugging mode: false
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: &control_vars [eastward_wind,northward_wind,air_temperature,surface_pressure,
+      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
                                       specific_humidity,cloud_liquid_ice,cloud_liquid_water,
                                       mole_fraction_of_ozone_in_air]
-      output variables: &3dvars_anal [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
     value: 0.125
 - covariance:
@@ -33,7 +33,7 @@ components:
       template:
         datetime: "{{ atmosphere_background_time_iso }}"
         filetype: fms restart
-        state variables: *3dvars_anal
+        state variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
         datapath: {{ atmosphere_background_ensemble_path}}
         filename is datetime templated: true
         filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
@@ -48,7 +48,7 @@ components:
       localization method: SABER
       saber central block:
         saber block name: BUMP_NICAS
-        active variables: &3dvars_anal_long [eastward_wind,northward_wind,air_temperature,surface_pressure,
+        active variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
                                              specific_humidity,cloud_liquid_ice,cloud_liquid_water,
                                              ozone_mass_mixing_ratio ]
         read:
@@ -201,7 +201,9 @@ components:
               value: 0.3
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: *3dvars_anal_long
-      output variables: *3dvars_anal
+      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
+                                             specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+                                             ozone_mass_mixing_ratio ]
+      output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
     value: 0.875
diff --git a/model/atmosphere/atmosphere_background_error_static_bump.yaml.j2 b/model/atmosphere/atmosphere_background_error_static_bump.yaml.j2
@@ -3,12 +3,12 @@ full inverse: true
 saber blocks:
 - saber block name: BUMP_NICAS
   saber central block: true
-  input variables: &control_vars [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
-  output variables: *control_vars
-  active variables: &active_vars [psi,chi,t,ps,rh,liq_wat,o3mr]
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
   bump:
     io:
-      data directory: &staticb_dir {{atmosphere_bump_data_directory}}
+      data directory: {{atmosphere_bump_data_directory}}
     drivers:
       multivariate strategy: specific_univariate
       read local nicas: true
@@ -34,30 +34,30 @@ saber blocks:
       io:
         files prefix: nicas/nicas_2D_gfs
 - saber block name: StdDev
-  input variables: *control_vars
-  output variables: *control_vars
-  active variables: *active_vars
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
   file:
     filetype: fms restart
     datetime: 2021-12-22T00:00:00Z
     set datetime on read: true
     psinfile: true
-    datapath: *staticb_dir
+    datapath: {{atmosphere_bump_data_directory}}
     prefix: stddev/20211222.000000
     filename_core: stddev.fv_core.res.nc
     filename_trcr: stddev.fv_tracer.res.nc
     filename_sfcd: stddev.sfc_data.nc
     filename_sfcw: stddev.fv_srf_wnd.res.nc
     filename_cplr: stddev.coupler.res
 - saber block name: BUMP_VerticalBalance
-  input variables: *control_vars
-  output variables: *control_vars
-  active variables: *active_vars
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
   bump:
     general:
       universe length-scale: 2000.0e3
     io:
-      data directory: *staticb_dir
+      data directory: {{atmosphere_bump_data_directory}}
       files prefix: vbal/vbal_gfs
       overriding sampling file: vbal/vbal_2021122200_gfs_sampling
     drivers:
@@ -72,18 +72,18 @@ saber blocks:
       - balanced variable: var4
         unbalanced variable: var1
 - saber block name: BUMP_PsiChiToUV
-  input variables: *control_vars
-  output variables: &3dvars_with_rh [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
   active variables: [psi,chi,ua,va]
   bump:
     general:
       universe length-scale: 2000.0e3
     io:
-      data directory: '*staticb_dir'
+      data directory: {{atmosphere_bump_data_directory}}
       files prefix: psichitouv/psichitouv_gfs
     drivers:
       read local psichitouv: true
 linear variable change:
   linear variable change name: Control2Analysis
-  input variables: *3dvars_with_rh
+  input variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
   output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
diff --git a/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2 b/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2
@@ -3,23 +3,23 @@ full inverse: true
 saber central block:
   saber block name: gsi covariance
   read:
-    gsi akbk: &akbk {{atmosphere_fv3jedi_files_path}}/akbk.nc4
-    gsi error covariance file: &gsiberr {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
-    gsi berror namelist file: &gsibnml {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
-    processor layout x direction: &layout_gsib_x {{atmosphere_layout_gsib_x}}
-    processor layout y direction: &layout_gsib_y {{atmosphere_layout_gsib_y}}
+    gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+    gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+    gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
+    processor layout x direction: {{atmosphere_layout_gsib_x}}
+    processor layout y direction: {{atmosphere_layout_gsib_y}}
     debugging mode: false
 saber outer blocks:
 - saber block name: gsi interpolation to model grid
-  gsi akbk: *akbk
-  gsi error covariance file: *gsiberr
-  gsi berror namelist file: *gsibnml
+  gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+  gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+  gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
   processor layout x direction: {{atmosphere_layout_gsib_x}}
   processor layout y direction: {{atmosphere_layout_gsib_y}}
   debugging mode: false
 linear variable change:
   linear variable change name: Control2Analysis
-  input variables: &control_vars [eastward_wind,northward_wind,air_temperature,surface_pressure,
+  input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
                            specific_humidity,cloud_liquid_ice,cloud_liquid_water,
                            mole_fraction_of_ozone_in_air]
-  output variables: &3dvars_anal [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+  output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
diff --git a/model/atmosphere/atmosphere_final_increment_gaussian.yaml.j2 b/model/atmosphere/atmosphere_final_increment_gaussian.yaml.j2
@@ -2,7 +2,7 @@ output:
   state component:
     filetype: auxgrid
     gridtype: gaussian
-    filename: {{atmosphere_atmosphere_final_increment_prefix}}
+    filename: {{atmosphere_final_increment_prefix}}
 geometry:
   fms initialization:
     namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"

diff --git a/observations/atmosphere/aircraft.yaml.j2 b/observations/atmosphere/aircraft.yaml.j2
@@ -7,15 +7,15 @@
     obsdatain:
       engine:
         type: H5File
-        obsfile: "{{atm_obsdatain_path}}/{{atm_obsdatain_prefix}}{{observation_from_jcb}}{{atm_obsdatain_suffix}}"
+        obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
       obsgrouping:
         group variables: ["stationIdentification"]
         sort variable: "pressure"
         sort order: "descending"
     obsdataout:
       engine:
         type: H5File
-        obsfile: "{{atm_obsdataout_path}}/{{atm_obsdataout_prefix}}{{observation_from_jcb}}{{atm_obsdataout_suffix}}"
+        obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
     io pool:
       max pool size: 1
     simulated variables: [windEastward, windNorthward, airTemperature, specificHumidity]
@@ -349,7 +349,7 @@
   # GeoVaLs for Driving Observation Operators (testing mode)
   # --------------------------------------------------------
   geovals:
-    filename: "{{atm_obsdatain_path}}/{{atm_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atm_obsdatain_suffix}}"
+    filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
 
   # Passed benchmark for UFO testing
   # --------------------------------

diff --git a/observations/atmosphere/amsua_n19.yaml.j2 b/observations/atmosphere/amsua_n19.yaml.j2
@@ -7,11 +7,11 @@
     obsdatain:
       engine:
         type: H5File
-        obsfile: "{{atm_obsdatain_path}}/{{atm_obsdatain_prefix}}{{observation_from_jcb}}{{atm_obsdatain_suffix}}"
+        obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
     obsdataout:
       engine:
         type: H5File
-        obsfile: "{{atm_obsdataout_path}}/{{atm_obsdataout_prefix}}{{observation_from_jcb}}{{atm_obsdataout_suffix}}"
+        obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
     io pool:
       max pool size: 1
     simulated variables: [brightnessTemperature]
@@ -32,14 +32,14 @@
   # Observation Bias Correction (VarBC)
   # -----------------------------------
   obs bias:
-    input file: "{{atm_obsbiasin_path}}/{{atm_obsbiasin_prefix}}{{observation_from_jcb}}{{atm_obsbiasin_suffix}}"
-    output file: "{{atm_obsbiasout_path}}/{{atm_obsbiasout_prefix}}{{observation_from_jcb}}{{atm_obsbiasout_suffix}}"
+    input file: "{{atmosphere_obsbiasin_path}}/{{atmosphere_obsbiasin_prefix}}{{observation_from_jcb}}{{atmosphere_obsbiasin_suffix}}"
+    output file: "{{atmosphere_obsbiasout_path}}/{{atmosphere_obsbiasout_prefix}}{{observation_from_jcb}}{{atmosphere_obsbiasout_suffix}}"
     variational bc:
       predictors:
       - name: constant
       - name: lapse_rate
         order: 2
-        tlapse: &{{observation_from_jcb}}_tlapse "{{atm_obsbiasin_path}}/{{atm_obstlapsein_prefix}}{{observation_from_jcb}}{{atm_obstlapsein_suffix}}"
+        tlapse: &{{observation_from_jcb}}_tlapse "{{atmosphere_obsbiasin_path}}/{{atmosphere_obstlapsein_prefix}}{{observation_from_jcb}}{{atmosphere_obstlapsein_suffix}}"
       - name: lapse_rate
         tlapse: *{{observation_from_jcb}}_tlapse
       - name: emissivity
@@ -56,11 +56,11 @@
       step size: 1.0e-4
       largest analysis variance: 10000.0
       prior:
-        input file: "{{atm_obsbiasin_path}}/{{atm_obsbiascovin_prefix}}{{observation_from_jcb}}{{atm_obsbiascovin_suffix}}"
+        input file: "{{atmosphere_obsbiasin_path}}/{{atmosphere_obsbiascovin_prefix}}{{observation_from_jcb}}{{atmosphere_obsbiascovin_suffix}}"
         inflation:
           ratio: 1.1
           ratio for small dataset: 2.0
-      output file: "{{atm_obsbiasout_path}}/{{atm_obsbiascovout_prefix}}{{observation_from_jcb}}{{atm_obsbiascovout_suffix}}"
+      output file: "{{atmosphere_obsbiasout_path}}/{{atmosphere_obsbiascovout_prefix}}{{observation_from_jcb}}{{atmosphere_obsbiascovout_suffix}}"
 
   # Observation Filters (QC)
   # ------------------------
@@ -339,7 +339,7 @@
   # GeoVaLs for Driving Observation Operators (testing mode)
   # --------------------------------------------------------
   geovals:
-    filename: "{{atm_obsdatain_path}}/{{atm_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atm_obsdatain_suffix}}"
+    filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
 
   # Passed benchmark for UFO testing
   # --------------------------------

diff --git a/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2 b/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2
@@ -7,11 +7,11 @@
     obsdatain:
       engine:
         type: H5File
-        obsfile: "{{atm_obsdatain_path}}/{{atm_obsdatain_prefix}}{{observation_from_jcb}}{{atm_obsdatain_suffix}}"
+        obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
     obsdataout:
       engine:
         type: H5File
-        obsfile: "{{atm_obsdataout_path}}/{{atm_obsdataout_prefix}}{{observation_from_jcb}}{{atm_obsdataout_suffix}}"
+        obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
     io pool:
       max pool size: 1
     simulated variables: [windEastward, windNorthward]
@@ -306,7 +306,7 @@
   # GeoVaLs for Driving Observation Operators (testing mode)
   # --------------------------------------------------------
   geovals:
-    filename: "{{atm_obsdatain_path}}/{{atm_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atm_obsdatain_suffix}}"
+    filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
 
   # Passed benchmark for UFO testing
   # --------------------------------