Add validated aircraft yamls

rrfs-test/validated_yamls/gen_yaml.sh

@@ -2,16 +2,44 @@
 
 #use this script to combine the basic config yaml with an obtype config yaml.
 basic_config="fv3jedi_hyb3denvar.yaml"
-obtype_config="msonet_airTemperature_obtype188.yaml"
+obtype_configs="
+aircft_airTemperature_130.yaml
+aircft_airTemperature_131.yaml
+aircft_airTemperature_133.yaml
+aircft_airTemperature_134.yaml
+aircft_airTemperature_135.yaml
 
-# Don't edit below this line.
+aircft_specificHumidity_133.yaml
+aircft_specificHumidity_134.yaml
+
+aircft_uv_230.yaml
+aircft_uv_231.yaml
+aircft_uv_233.yaml
+aircft_uv_234.yaml
+aircft_uv_235.yaml
+
+msonet_airTemperature_188.yaml
+msonet_specificHumidity_188.yaml
+msonet_stationPressure_188.yaml
+msonet_uv_288.yaml
+"
+
+obtype="conv.yaml"
+
+temp_config="combined.yaml"
+rm -f $temp_config
+echo "catting the following yamls:"
+for obtype_config in $obtype_configs; do
+    echo "   $obtype_config"
+    cat ./templates/obtype_config/$obtype_config >> ./$temp_config
+done
 
 # copy the basic configuration yaml into the new yaml
-cp -p templates/basic_config/$basic_config ./$obtype_config
+cp -p templates/basic_config/$basic_config ./${obtype}
 
 # use the stread editor to replace the instance of @OBSERVATION@ placeholder
 # in the basic configuration file with the contents of the obtype config yaml.
 sed -i '/@OBSERVATIONS@/{
-        r templates/obtype_config/'"${obtype_config}"'
+        r ./'"${temp_config}"'
         d
-}' ./$obtype_config
+}' ./${obtype}

rrfs-test/validated_yamls/templates/basic_config/mpasjedi_3dvar.yaml

@@ -0,0 +1,103 @@
+
+# application-agnostic anchors that specify observation errors
+# applicable to Variational, HofX3D
+
+# reusable latitude bands for all observation types
+_conventional obs localizations: &heightAndHorizObsLoc
+  _blank: null
+
+_nonconventional obs localizations: &horizObsLoc
+  _blank: null
+
+_obs space: &ObsSpace
+  obs perturbations seed: 1
+  io pool:
+    max pool size: 10
+  distribution:
+    name: RoundRobin
+
+_obs error diagonal: &ObsErrorDiagonal
+  covariance model: diagonal
+  # Note: the same 'obs perturbations seed' must be used for all members for the 'zero-mean perturbations' option to work
+  zero-mean perturbations: true
+  member: 1
+  number of members: 1
+
+_get values: &GetValues
+  nnearest: 3
+
+_multi iteration filter: &multiIterationFilter
+  apply at iterations: 0,1,2,3,4,5
+# ObsAnchors and ObsErrorAnchors are automatically prepended above this line
+_iteration: &iterationConfig
+  geometry:
+    nml_file: ./namelist.atmosphere
+    streams_file: ./streams.atmosphere
+    deallocate non-da fields: true
+    interpolation type: unstructured
+  gradient norm reduction: 1e-3
+_member: &memberConfig
+  date: &analysisDate '2024-05-27T00:00:00Z'
+  state variables: &incvars [spechum,surface_pressure,temperature,uReconstructMeridional,uReconstructZonal]
+  stream name: ensemble
+
+output:
+  filename: ./ana.$Y-$M-$D_$h.$m.$s.nc
+  stream name: analysis
+variational:
+  minimizer:
+    algorithm: DRPCG
+  iterations:
+  - <<: *iterationConfig
+    diagnostics:
+      departures: ombg
+    ninner: 50
+  - <<: *iterationConfig
+    ninner: 50
+final:
+  diagnostics:
+    departures: oman
+cost function:
+  cost type: 3D-Var
+  time window:
+     begin: '2024-05-26T21:00:00Z'
+     length: PT6H
+  jb evaluation: false
+  geometry:
+    nml_file: ./namelist.atmosphere
+    streams_file: ./streams.atmosphere
+    deallocate non-da fields: true
+    interpolation type: unstructured
+  analysis variables: *incvars
+  background:
+    state variables: [spechum,surface_pressure,temperature,uReconstructMeridional,uReconstructZonal,theta,rho,u,qv,pressure,landmask,xice,snowc,skintemp,ivgtyp,isltyp,snowh,vegfra,u10,v10,lai,smois,tslb,pressure_p,qc,qi,qg,qr,qs,cldfrac]
+    filename: data/restart.2024-05-27_00.00.00.nc
+    date: *analysisDate
+  background error:
+    covariance model: ensemble
+    localization:
+      localization method: SABER
+      saber central block:
+        saber block name: BUMP_NICAS
+        active variables: *incvars
+        read:
+          io:
+            data directory: data/bumploc/conus12km-401km11levels
+            files prefix: bumploc_401km11levels
+          drivers:
+            multivariate strategy: duplicated
+            read local nicas: true
+          model:
+            level for 2d variables: last
+    members from template:
+      template:
+        <<: *memberConfig
+        filename: ./data/ens/mem%iMember%/init.nc
+      pattern: %iMember%
+      start: 1
+      zero padding: 2
+      nmembers: 30
+
+  observations:
+     observers:
+@OBSERVATIONS@

rrfs-test/validated_yamls/templates/obtype_config/aircft_airTemperature_130.yaml

@@ -0,0 +1,124 @@
+     - obs space:
+         name: aircraft
+         obsdatain:
+           engine:
+             type: H5File
+             obsfile: "obsout/aircraft_tsen_obs_2022052619.nc4"
+         obsdataout:
+           engine:
+             type: H5File
+             obsfile: AIRCFT_hofxs_airTemperature_130_2022052619.nc4
+             allow overwrite: true
+         io pool:
+           max pool size: 1
+         observed variables: [airTemperature]
+         simulated variables: [airTemperature]
+
+       obs operator:
+         name: Composite
+         components:
+         - name: VertInterp
+           vertical coordinate: air_pressure
+           observation vertical coordinate: pressure
+           observation vertical coordinate group: MetaData
+           interpolation method: log-linear
+           gsi geovals:
+             filename: "obsout/aircraft_tsen_geoval_2022052619.nc4"
+             levels_are_top_down: False
+           variables:
+           - name: airTemperature
+
+       obs error:
+         covariance model: diagonal
+
+       obs filters:
+         # ------------------
+         # airTemperature
+         # ------------------
+         # Initial error assignment
+         # 130
+         - filter: Perform Action
+           filter variables:
+           - name: airTemperature
+           where:
+           - variable: ObsType/airTemperature
+             is_in: 130
+           action:
+             name: assign error
+             error function:
+               name: ObsFunction/ObsErrorModelStepwiseLinear
+               options:
+                 xvar:
+                   name: MetaData/pressure
+                 xvals: [110000, 105000, 100000, 95000, 90000, 85000, 80000, 75000, 70000, 65000, 60000, 55000, 50000, 45000, 40000, 35000, 30000, 25000, 20000, 15000, 10000, 7500, 5000, 4000, 3000, 2000, 1000, 500, 400, 300, 200, 100, 0]
+                 errors: [2.4618, 2.4244, 2.3481, 2.2352, 2.0999, 1.9647, 1.8522, 1.7754, 1.7323, 1.7134, 1.7093, 1.7131, 1.717, 1.7061, 1.655, 1.5397, 1.3754, 1.2567, 1.2116, 1.252, 1.37, 1.501, 1.6004, 1.6588, 1.6865, 1.6969, 1.6998, 1.7001, 1.7, 1.7, 1.7003, 1.6999, 1.6956]
+           defer to post: true
+
+         # Ajusted error after initial assignment (qcmod.f90)
+         - filter: Perform Action
+           filter variables:
+           - name: airTemperature
+           where:
+           - variable: ObsType/airTemperature
+             is_in: 130
+           action:
+             name: inflate error
+             inflation variable:
+               name: ObsFunction/ObsErrorFactorConventional
+               options:
+                 test QCflag: PreQC
+                 test QCthreshold: 3
+                 inflate variables: [airTemperature]
+                 pressure: MetaData/pressure
+                 distance threshold: -1.
+           defer to post: true
+
+         # error inflation based on pressure check (setupt.f90)
+         - filter: Perform Action
+           filter variables:
+           - name: airTemperature
+           where:
+           - variable: ObsType/airTemperature
+             is_in: 130
+           action:
+             name: inflate error
+             inflation variable:
+               name: ObsFunction/ObsErrorFactorPressureCheck
+               options:
+                 variable: airTemperature
+                 inflation factor: 8.0
+                 geovar_sfc_geomz: surface_geometric_height
+           defer to post: true
+
+         - filter: Bounds Check
+           filter variables:
+           - name: airTemperature
+           minvalue: 100
+           maxvalue: 400
+           defer to post: true
+
+         - filter: Background Check
+           filter variables:
+           - name: airTemperature
+           threshold: 7.0
+           where:
+           - variable: ObsType/airTemperature
+             is_in: 130
+           action:
+             name: reject
+           defer to post: true
+
+         # Print filter data
+         - filter: Print Filter Data
+           message: Printing filter data
+           summary: true
+           variables:
+           - variable: MetaData/latitude
+           - variable: MetaData/longitude
+           - variable: MetaData/pressure
+           - variable: ObsType/airTemperature
+           - variable: ObsValue/airTemperature
+           - variable: QCflagsData/airTemperature
+
+         - filter: GOMsaver
+           filename: ./Data/geovals/aircft_geovals_rrfs_2022052619.nc4