Add atmospheric 3DVar case (#302)

* add 3dvar standalone * now works w/ 3d - not sure what if messes up ocean 3d * in var-mode the Water_Temperature geoval cannot be found! Not sure why? * these now work; but depend on fv3-jedi PR#1154 * same issue as with the sondes ... need to be understood * a couple of the filters here cause 3dvar to fail - need attention * co2 not needed in linear model; and it causes crash in var * identation was incorrect - my mistake when I added the cov * though no-longer available, chn 14 is not bias corrected when avail * no co2 in liear operator * addresses issue #307 * clean up the one change I made that could upset the ocean 3dvar settings * does not belong here * bypass jb diagnostic * no need to spell out minimizer - too much maintenance * works now * all works - contour levels need some work * no issue w/ this scaling and the NL oper; but linear op should apparently not have this scaling * I was wrong about turning this on * silly error * works up to increment * now we show residual rms differences; and increments plots is fixed * adjusted to match jedi and latest eva - works fine * fix title of rmsres; fig log of norm * add knob for IR to take channel correlated R - working, but need science investigation - results look too close w/ and w/o corr * this adds FGAT (atmos) capability to swell * for now, since this is wired, make the time the correct time for FGAT, ie initial time of var * quick fix for eva to work for 3dfgat * gsibec config nml * rename of gsibec namelist files * minor fixes (already in 4d-branch * this needs to be looked into closely * 3d now runs in 3 nodes * with 4x4 (3 nodes) this runs just fine w/ RCOV * first pass * yaml templating * unused var * resolve swell test * adapt to skylab7 modules * update due to skylab7 modules * erase the extra purge * eva increment and yaml changes * delete obs error filter during testing * minor count diff due to changes in observer scaling * temporary var exception * eva increment filename and use of clean patterns --------- Co-authored-by: asewnath <[email protected]> Co-authored-by: dooruk <[email protected]> Co-authored-by: Doruk Ardağ <[email protected]>
GEOS-ESM · Apr 17, 2024 · 0dd142d · 0dd142d
1 parent 597cca3
commit 0dd142d
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diff --git a/src/swell/__init__.py b/src/swell/__init__.py
@@ -9,4 +9,4 @@
 repo_directory = os.path.dirname(__file__)
 
 # Set the version for swell
-__version__ = '1.8.5'
+__version__ = '1.9.0'
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_error.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_error.yaml
@@ -4,7 +4,7 @@ saber central block:
   read:
     gsi akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
     gsi error covariance file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
-    gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_configuration_c{{horizontal_resolution}}.nml'
+    gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml'
     processor layout x direction: {{gsibec_npx_proc}}
     processor layout y direction: {{gsibec_npy_proc}}
     debugging mode: false
@@ -13,12 +13,10 @@ saber outer blocks:
   state variables to inverse: &bvars [eastward_wind,northward_wind,air_temperature,surface_pressure,
                                       specific_humidity,cloud_liquid_ice,cloud_liquid_water,
                                       mole_fraction_of_ozone_in_air,
-                                      skin_temperature,
-                                      fraction_of_ocean,fraction_of_lake,fraction_of_ice,
                                       sfc_geopotential_height_times_grav]
   gsi akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
   gsi error covariance file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
-  gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_configuration_c{{horizontal_resolution}}.nml'
+  gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml'
   processor layout x direction: {{gsibec_npx_proc}}
   processor layout y direction: {{gsibec_npy_proc}}
   debugging mode: false

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage.yaml
@@ -4,4 +4,5 @@
       - ['{{experiment_root}}/{{experiment_id}}/jedi_bundle/source/fv3-jedi/test/Data/fieldmetadata/*', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fieldmetadata/']
       - ['{{experiment_root}}/{{experiment_id}}/jedi_bundle/source/fv3-jedi/test/Data/fv3files/*', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/']
       - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/']
-      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/gsibec/gsibec_configuration_c{{horizontal_resolution}}.nml', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/rcov/1.0.0/*', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/']
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/varincrement1.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/varincrement1.yaml
@@ -0,0 +1,7 @@
+write increment: true
+increment:
+  state component:
+    filetype: auxgrid
+    gridtype: latlon
+    datapath: ./
+    filename: {{experiment_id}}.increment-iter1.
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/aircraft.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/aircraft.yaml
@@ -24,8 +24,8 @@ obs operator:
     - name: windNorthward
 
     # Hofx scaling
-    hofx scaling field: SurfaceWindScalingPressure
-    hofx scaling field group: DerivedVariables
+#   hofx scaling field: SurfaceWindScalingPressure
+#   hofx scaling field group: DerivedVariables
 
   - name: VertInterp
     observation alias file: '{{experiment_root}}/{{experiment_id}}/configuration/jedi/interfaces/{{model_component}}/observations/obsop_name_map.yaml'

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/airs_aqua.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/airs_aqua.yaml
@@ -21,7 +21,7 @@ obs operator:
 
   linear obs operator:
     Absorbers: [H2O,O3]
-    Surfaces: [Water_Temperature]
+    Surfaces: [Water_Temperature,Land_Temperature,Ice_Temperature,Snow_Temperature]
 
 obs bias:
   input file: '{{cycle_dir}}/airs_aqua.{{background_time}}.satbias.nc4'
@@ -53,6 +53,10 @@ obs bias:
         ratio for small dataset: 2.0
     output file: '{{cycle_dir}}/airs_aqua.{{window_begin}}.satbias.nc4'
 
+obs error:
+  covariance model: cross variable covariances
+  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/airs_aqua_119_jedi_rcov.nc4'
+
 obs prior filters:
 - filter: Perform Action
   filter variables:

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/amsua_aqua.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/amsua_aqua.yaml
@@ -24,6 +24,8 @@ obs operator:
 
 obs bias:
   input file: '{{cycle_dir}}/amsua_aqua.{{background_time}}.satbias.nc4'
+  variables without bc: [brightnessTemperature]
+  channels: 14
   variational bc:
     predictors:
     - name: constant

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/amsua_metop-c.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/amsua_metop-c.yaml
@@ -52,11 +52,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: '{{cycle_dir}}/INSTRUMENT.{{background_time}}.satbias.nc4'
+      input file: '{{cycle_dir}}/amsua_metop-c.{{background_time}}.satbias.nc4'
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: '{{cycle_dir}}/INSTRUMENT.{{window_begin}}.satbias.nc4'
+    output file: '{{cycle_dir}}/amsua_metop-c.{{window_begin}}.satbias.nc4'
 
 obs prior filters:
 # Assign obs error

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_n20.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_n20.yaml
@@ -20,7 +20,7 @@ obs operator:
     CoefficientPath: '{{crtm_coeff_dir}}/'
   linear obs operator:
     Absorbers: [H2O,O3]
-    Surfaces: [Water_Temperature]
+    Surfaces: [Water_Temperature,Land_Temperature,Ice_Temperature,Snow_Temperature]
 
 obs bias:
   input file: '{{cycle_dir}}/cris-fsr_n20.{{background_time}}.satbias.nc4'
@@ -52,6 +52,10 @@ obs bias:
         ratio for small dataset: 2.0
     output file: '{{cycle_dir}}/cris-fsr_n20.{{window_begin}}.satbias.nc4'
 
+obs error:
+  covariance model: cross variable covariances
+  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/cris-fsr_108_jedi_rcov.nc4'
+
 obs prior filters:
 - filter: Perform Action
   filter variables:

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_npp.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_npp.yaml
@@ -20,7 +20,7 @@ obs operator:
     CoefficientPath: '{{crtm_coeff_dir}}/'
   linear obs operator:
     Absorbers: [H2O,O3]
-    Surfaces: [Water_Temperature]
+    Surfaces: [Water_Temperature,Land_Temperature,Ice_Temperature,Snow_Temperature]
 
 obs bias:
   input file: '{{cycle_dir}}/cris-fsr_npp.{{background_time}}.satbias.nc4'
@@ -52,6 +52,10 @@ obs bias:
         ratio for small dataset: 2.0
     output file: '{{cycle_dir}}/cris-fsr_npp.{{window_begin}}.satbias.nc4'
 
+obs error:
+  covariance model: cross variable covariances
+  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/cris-fsr_108_jedi_rcov.nc4'
+
 obs prior filters:
 - filter: Perform Action
   filter variables:

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-b.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-b.yaml
@@ -20,7 +20,7 @@ obs operator:
     CoefficientPath: '{{crtm_coeff_dir}}/'
   linear obs operator:
     Absorbers: [H2O,O3]
-    Surfaces: [Water_Temperature]
+    Surfaces: [Water_Temperature,Land_Temperature,Ice_Temperature,Snow_Temperature]
 
 obs bias:
   input file: '{{cycle_dir}}/iasi_metop-b.{{background_time}}.satbias.nc4'
@@ -52,6 +52,10 @@ obs bias:
         ratio for small dataset: 2.0
     output file: '{{cycle_dir}}/iasi_metop-b.{{window_begin}}.satbias.nc4'
 
+obs error:
+  covariance model: cross variable covariances
+  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/iasi_metop_141_jedi_rcov.nc4'
+
 obs prior filters:
 - filter: Perform Action
   filter variables:

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-c.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-c.yaml
@@ -20,7 +20,7 @@ obs operator:
     CoefficientPath: '{{crtm_coeff_dir}}/'
   linear obs operator:
     Absorbers: [H2O,O3]
-    Surfaces: [Water_Temperature]
+    Surfaces: [Water_Temperature,Land_Temperature,Ice_Temperature,Snow_Temperature]
 
 obs bias:
   input file: '{{cycle_dir}}/iasi_metop-c.{{background_time}}.satbias.nc4'
@@ -52,6 +52,10 @@ obs bias:
         ratio for small dataset: 2.0
     output file: '{{cycle_dir}}/iasi_metop-c.{{window_begin}}.satbias.nc4'
 
+obs error:
+  covariance model: cross variable covariances
+  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/iasi_metop_141_jedi_rcov.nc4'
+
 obs prior filters:
 - filter: Perform Action
   filter variables:

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/mhs_metop-c.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/mhs_metop-c.yaml
@@ -21,7 +21,7 @@ obs operator:
     EndianType: little_endian
     CoefficientPath: '{{crtm_coeff_dir}}/'
   linear obs operator:
-    Absorbers: [H2O,O3,CO2]
+    Absorbers: [H2O,O3]
     Clouds: [Water]
     Surfaces: [Water_Temperature]
 

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/mhs_n19.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/mhs_n19.yaml
@@ -21,7 +21,7 @@ obs operator:
     EndianType: little_endian
     CoefficientPath: '{{crtm_coeff_dir}}/'
   linear obs operator:
-    Absorbers: [H2O,O3,CO2]
+    Absorbers: [H2O,O3]
     Clouds: [Water]
     Surfaces: [Water_Temperature]
 

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/omi_aura.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/omi_aura.yaml
@@ -42,20 +42,20 @@ obs filters:
   action:
     name: reject
 # Reject rows 25+ (somewhat stringent but thats what we do in GEOS)
-- filter: Bounds Check
-  filter variables:
-  - name: ozoneTotal
-  test variables:
-  - name: MetaData/sensorScanPosition
-  minvalue: 3
-  maxvalue: 24
-  action:
-    name: reject
+#- filter: Bounds Check
+#  filter variables:
+#  - name: ozoneTotal
+#  test variables:
+#  - name: MetaData/sensorScanPosition
+#  minvalue: 3
+#  maxvalue: 24
+#  action:
+#    name: reject
 
  # Gross check
-- filter: Background Check
-  filter variables:
-  - name: ozoneTotal
-  threshold: 5.0
-  action:
-    name: reject
+#- filter: Background Check
+#  filter variables:
+#  - name: ozoneTotal
+#  threshold: 5.0
+#  action:
+#    name: reject
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/ompsnm_npp.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/ompsnm_npp.yaml
@@ -41,9 +41,9 @@ obs filters:
   action:
     name: reject
 # Gross check
-- filter: Background Check
-  filter variables:
-  - name: ozoneTotal
-  threshold: 5.0
-  action:
-    name: reject
+#- filter: Background Check
+#  filter variables:
+#  - name: ozoneTotal
+#  threshold: 5.0
+#  action:
+#    name: reject
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/pibal.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/pibal.yaml
@@ -33,8 +33,8 @@ obs operator:
       interpolation method backup: log-linear
 
       # Hofx scaling
-      hofx scaling field: SurfaceWindScalingCombined
-      hofx scaling field group: DerivedVariables
+#     hofx scaling field: SurfaceWindScalingCombined
+#     hofx scaling field group: DerivedVariables
 
 obs pre filters:
 

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/satwind.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/satwind.yaml
@@ -13,8 +13,8 @@ obs space:
 obs operator:
   name: VertInterp
   observation alias file: '{{experiment_root}}/{{experiment_id}}/configuration/jedi/interfaces/{{model_component}}/observations/obsop_name_map.yaml'
-  hofx scaling field: SurfaceWindScalingPressure
-  hofx scaling field group: DerivedVariables
+# hofx scaling field: SurfaceWindScalingPressure
+# hofx scaling field group: DerivedVariables
 
 obs prior filters:
 

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/scatwind.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/scatwind.yaml
@@ -20,8 +20,8 @@ obs operator:
   observation vertical coordinate group: DerivedVariables
   observation vertical coordinate: adjustedHeight
   interpolation method: linear
-  hofx scaling field: SurfaceWindScalingHeight
-  hofx scaling field group: DerivedVariables
+# hofx scaling field: SurfaceWindScalingHeight
+# hofx scaling field group: DerivedVariables
 
 obs prior filters:
 

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/sfc.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/sfc.yaml
@@ -25,8 +25,8 @@ obs operator:
      observation vertical coordinate group: DerivedVariables
      observation vertical coordinate: adjustedHeight
      interpolation method: linear
-     hofx scaling field: SurfaceWindScalingHeight
-     hofx scaling field group: DerivedVariables
+#    hofx scaling field: SurfaceWindScalingHeight
+#    hofx scaling field group: DerivedVariables
 
    # Temperatures use vertical interpolation
    - name: VertInterp
@@ -64,8 +64,8 @@ linear obs operator:
      observation vertical coordinate group: DerivedVariables
      observation vertical coordinate: adjustedHeight
      interpolation method: linear
-     hofx scaling field: SurfaceWindScalingHeight
-     hofx scaling field group: DerivedVariables
+#    hofx scaling field: SurfaceWindScalingHeight
+#    hofx scaling field group: DerivedVariables
 
    # Temperatures use vertical interpolation
    - name: VertInterp

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/sfcship.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/sfcship.yaml
@@ -24,8 +24,8 @@ obs operator:
      observation vertical coordinate group: DerivedVariables
      observation vertical coordinate: adjustedHeight
      interpolation method: linear
-     hofx scaling field: SurfaceWindScalingHeight
-     hofx scaling field group: DerivedVariables
+#    hofx scaling field: SurfaceWindScalingHeight
+#    hofx scaling field group: DerivedVariables
 
    - name: VertInterp
      observation alias file: '{{experiment_root}}/{{experiment_id}}/configuration/jedi/interfaces/{{model_component}}/observations/obsop_name_map.yaml'
@@ -60,8 +60,8 @@ linear obs operator:
      observation vertical coordinate group: DerivedVariables
      observation vertical coordinate: adjustedHeight
      interpolation method: linear
-     hofx scaling field: SurfaceWindScalingHeight
-     hofx scaling field group: DerivedVariables
+#    hofx scaling field: SurfaceWindScalingHeight
+#    hofx scaling field group: DerivedVariables
 
    - name: VertInterp
      observation alias file: '{{experiment_root}}/{{experiment_id}}/configuration/jedi/interfaces/{{model_component}}/observations/obsop_name_map.yaml'

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/sondes.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/sondes.yaml
@@ -52,8 +52,8 @@ linear obs operator:
     - name: windNorthward
 
     # Hofx scaling
-    hofx scaling field: SurfaceWindScalingPressure
-    hofx scaling field group: DerivedVariables
+#   hofx scaling field: SurfaceWindScalingPressure
+#   hofx scaling field group: DerivedVariables
 
   - name: VertInterp
     variables:

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/ssmis_f17.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/ssmis_f17.yaml
@@ -2,7 +2,7 @@
     name: CRTM
     Absorbers: [H2O,O3,CO2]
     linear obs operator:
-      Absorbers: [H2O,O3,CO2]
+      Absorbers: [H2O,O3]
       Surfaces: [Water_Temperature]
     obs options:
       Sensor_ID: &Sensor_ID ssmis_f17
@@ -53,6 +53,17 @@
         order: 2
       - name: scan_angle
         var_name: sensorScanPosition
+    covariance:
+      minimal required obs number: 20
+      variance range: [1.0e-6, 10.0]
+      step size: 1.0e-4
+      largest analysis variance: 10000.0
+      prior:
+        input file: '{{cycle_dir}}/ssmis_f17.{{background_time}}.satbias.nc4'
+        inflation:
+          ratio: 1.1
+          ratio for small dataset: 2.0
+      output file: '{{cycle_dir}}/ssmis_f17.{{window_begin}}.satbias.nc4'
 
   obs prior filters:
 # Step 1: Initial Observation Error Assignment

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/ufo_tests.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/ufo_tests.yaml
@@ -122,11 +122,11 @@ satwind:
 
 scatwind:
   filter_test:
-    passedBenchmark: 16384
+    passedBenchmark: 16262
 
 sfcship:
   filter_test:
-    passedBenchmark: 99142
+    passedBenchmark: 99068
 
 sfc:
   filter_test: