letkf bug

algorithm/marine/socaincr2mom6.yaml

@@ -0,0 +1,28 @@
+geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: '{{marine_window_begin}}'
+
+layers variable: [hocn]
+
+increment variables: [tocn, socn, uocn, vocn, ssh]
+
+vertical geometry:
+  date: '{{marine_window_begin}}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  read_from_file: 1
+
+soca increment:
+  date: '{{marine_window_begin}}'
+  basename: ./Data/
+  ocn_filename: 'ocn.3dvarfgat_pseudo.incr.{{ATM_WINDOW_MIDDLE}}.nc'
+  read_from_file: 1
+
+output increment:
+  datadir: ./
+  date: '{{marine_window_begin}}'
+  exp: mom6_iau
+  type: incr
+  output file: inc.nc

model/marine/marine_background_error_hybrid_diffusion_diffusion.yaml.j2

@@ -58,7 +58,7 @@ components:
         ice_filename: 'ice.%mem%.nc'
         state variables: [tocn, socn, ssh, uocn, vocn, cicen, hicen, hsnon]
       pattern: '%mem%'
-      nmembers: {{marine_number_ensemble_members}}
+      nmembers: '{{marine_number_ensemble_members}}'
     localization:
       localization method: SABER
       saber central block:

observations/atmosphere-lgetkf/amsua_n19.yaml.j2

@@ -10,11 +10,11 @@
     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]
@@ -40,14 +40,14 @@
   # 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
@@ -64,11 +64,11 @@
       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)
   # ------------------------
@@ -101,7 +101,7 @@
   # 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
   # --------------------------------

observations/atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2

@@ -10,11 +10,11 @@
     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]
@@ -276,7 +276,7 @@
   # this inflation to take place both nvqc must be .true. AND ibeta must be >0, see:
   # https://github.com/NOAA-EMC/GSI/blob/14ae595af1b03471287d322596d35c0665336e95/src/gsi/setupw.f90#L1229
   # GSI settings must have ibeta>0 for satwinds, but not for scatwinds.
-  # 
+  #
   # If the ibeta settings for scatwinds were to change while nvqc remained .true., we would extend YAML to
   # an additional filter that inflates final ob-errors across-the-board by 1/0.8 = 1.25. NOTE: the nvqc setting
   # is defaulted to .false. in GSI code, but is overridden in global operational configuration. See:
@@ -316,7 +316,7 @@
   # 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
   # --------------------------------

observations/atmosphere-lgetkf/conv_ps.yaml.j2

@@ -10,11 +10,11 @@
     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: [stationPressure]
@@ -40,7 +40,7 @@
   # Observation Prior Filters (QC)
   # ------------------------------
   obs prior filters:
-  # Initial Error Assignments for SFC Observations 
+  # Initial Error Assignments for SFC Observations
   - filter: Perform Action
     filter variables:
     - name: stationPressure
@@ -73,7 +73,7 @@
             name: ObsValue/stationPressure
           xvals: [85000, 80000, 75000, 70000, 65000, 60000, 55000]
           errors: [120, 140, 140, 140, 140, 140, 1.0e+11]
-  # Initial Error Assignments for SFCSHIP Observations 
+  # Initial Error Assignments for SFCSHIP Observations
   - filter: Perform Action
     filter variables:
     - name: stationPressure
@@ -124,7 +124,7 @@
       type: float
       source variable: ObsErrorData/stationPressure
 
-  # Set observation quality-realted variables 
+  # Set observation quality-realted variables
   # Create PreQC group variable (pqm in GSI read_prepbufr)
   - filter: Variable Assignment
     assignments:
@@ -203,7 +203,7 @@
   #  - variable:
   #      name: ObsType/stationPressure
   #    is_in: 183
-  ## Reject surface pressure below 500 hPa 
+  ## Reject surface pressure below 500 hPa
   #- filter: Bounds Check
   #  filter variables:
   #  - name: stationPressure
@@ -241,7 +241,7 @@
           variable: stationPressure
 
   # Reduce effective observation error based on obs type and subtype
-  # In this case: reduce effective obs error for buoy  
+  # In this case: reduce effective obs error for buoy
   - filter: Perform Action
     filter variables:
     - name: stationPressure
@@ -256,7 +256,7 @@
       name: inflate error
       inflation factor: 0.7
 
-  # Calculate obs error inflation factors for large discrepancies between model and observations 
+  # Calculate obs error inflation factors for large discrepancies between model and observations
   - filter: Variable Assignment
     assignments:
     - name: ObsErrorFactorSfcPressure/stationPressure
@@ -344,7 +344,7 @@
       inflation variable:
         name: ObsErrorFactorDuplicateCheck/stationPressure
 
-  # Reject data based on PreUseFlag (usage in GSI) 
+  # Reject data based on PreUseFlag (usage in GSI)
   - filter: Perform Action
     filter variables:
     - name: stationPressure
@@ -353,7 +353,7 @@
       is_not_in: 0, 1
     action:
       name: reject
-  # End of Filters 
+  # End of Filters
 
   # Observation Localizations (LocalEnsembleDA)
   # -------------------------------------------
@@ -366,7 +366,7 @@
   # 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
   # --------------------------------

observations/atmosphere-lgetkf/gnssro.yaml.j2

@@ -10,15 +10,15 @@
     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: [ "sequenceNumber" ]
   #      sort variable: "impactHeightRO"
   #      sort order: "ascending"
     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}}"
     simulated variables: [bendingAngle]
 
   # Observation Operator
@@ -35,7 +35,7 @@
   # ------------------------
   obs filters:
   # Apply gross check using pccf
-  # Step 0-A: Create Diagnostic Flags 
+  # Step 0-A: Create Diagnostic Flags
   # Diagnostic flag for pccf
   - filter: Create Diagnostic Flags
     filter variables:
@@ -126,7 +126,7 @@
     minvalue: 8000.1
     action:
       name: reject
-  #4. assign obs error 
+  #4. assign obs error
   - filter: ROobserror
     filter variables:
     - name: bendingAngle
@@ -160,7 +160,7 @@
   # 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
   # --------------------------------

observations/atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2

@@ -10,11 +10,11 @@
     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]
@@ -40,7 +40,7 @@
     Transform: SurfaceWindScalingPressure
     SkipWhenNoObs: false
 
-  # Calculate error inflation factor for duplicate observations 
+  # Calculate error inflation factor for duplicate observations
   #- filter: Variable Assignment
   #  assignments:
   #  - name: ObsErrorFactorDuplicateCheck/windEastward
@@ -191,7 +191,7 @@
       name: reject
 
   # GSI read routine QC (part-1)
-  # Exclude Type 251 (VIS) --- obs tossed without passing to setup routine 
+  # Exclude Type 251 (VIS) --- obs tossed without passing to setup routine
   - filter: Perform Action
     filter variables:
     - name: windEastward
@@ -227,7 +227,7 @@
     action:
       name: reject
 
-  # Exclude data over non-water surface type where latitude > 20N for Type 240 (IRSW) and Type 245 (IRLW)  --- obs tossed and not passed to setup routine 
+  # Exclude data over non-water surface type where latitude > 20N for Type 240 (IRSW) and Type 245 (IRLW)  --- obs tossed and not passed to setup routine
   # Notes: This check was missing, so added (eliu)
   #        Replace land_type_index_NPOSS with water_area_fraction (eliu)
   - filter: Bounds Check
@@ -374,7 +374,7 @@
 
   # GSI setupw routine QC
   # Reject any ob Type [240–260] when pressure greater than 950 mb.
-  # CLEARED: minvalue/maxvalue are >=/<=, not >/<, so editing range by 1 Pa    
+  # CLEARED: minvalue/maxvalue are >=/<=, not >/<, so editing range by 1 Pa
   - filter: Bounds Check
     filter variables:
     - name: windEastward
@@ -420,8 +420,8 @@
 
   # Multiple satellite platforms, reject when pressure is more than 50 mb above tropopause.
   # CLEARED: minvalue is rejecting <, not <= as per a Perform Action, so threshold is unchanged
-  # Notes (eliu): This tropopause check reject too many obs; probably due to tropopause pressure estimation 
-  #               Turn this check off for now. 
+  # Notes (eliu): This tropopause check reject too many obs; probably due to tropopause pressure estimation
+  #               Turn this check off for now.
   #               Need to check if troposphere pressure was implemented correctly in fv3-jed
   - filter: Difference Check
     filter variables:
@@ -433,7 +433,7 @@
     action:
       name: reject
 
-  # GOES (247) reject any observation with a /=0 surface type (non-water 
+  # GOES (247) reject any observation with a /=0 surface type (non-water
   # surface) within 110 hPa of the surface pressure (as part of the LNVD # check).
   # NOT EXPLICITLY CLEARED: No obs in this range in file, so 0 Bounds Check rejects (which is correct) but essentially untested
   # Notes (eliu): Replace land_type_index_NPOESS with land_area_fraction.
@@ -570,7 +570,7 @@
   # configuration, see: https://github.com/NOAA-EMC/global-workflow/blob/d5ae3328fa4041b177357b1133f6b92e81c859d7/scripts/exglobal_atmos_analysis.sh#L750
   # This setting activates Line 1229 of setupw.f90 to scale ratio_errors by 0.8, which is applied in
   # the denominator of the final ob-error, so 1/0.8 = 1.25 factor of ob-error inflation.
-  # 
+  #
   # If this nvqc functionality were to be switched off (i.e. if variational qc were to be turned off),
   # you would want to remove this last inflation filter.
   #- filter: Perform Action
@@ -591,7 +591,7 @@
   #  action:
   #    name: inflate error
   #    inflation factor: 1.25
-  # End of Filters 
+  # End of Filters
 
   # Observation Localizations (LocalEnsembleDA)
   # -------------------------------------------
@@ -604,7 +604,7 @@
   # 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
   # --------------------------------