Proof of concept: EDA control perturb

src/swell/configuration/jedi/interfaces/geos_atmosphere/geos_atmosphere.yaml

@@ -11,3 +11,7 @@ executables:
   localensembleda: fv3jedi_letkf.x
   ensmeanvariance: fv3jedi_ensmeanvariance.x
   obsfilters: test_ObsFilters.x
+  eda3D: fv3jedi_var.x
+  eda4D: fv3jedi_var.x
+  edaControlPert: fv3jedi_controlpert.x
+  diffstates: fv3jedi_diffstates.x

src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_eda.py

@@ -0,0 +1,83 @@
+# (C) Copyright 2021- United States Government as represented by the Administrator of the
+# National Aeronautics and Space Administration. All Rights Reserved.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+
+# --------------------------------------------------------------------------------------------------
+
+from collections.abc import Mapping
+from swell.configuration.jedi.interfaces.geos_atmosphere.model.shared import \
+        field_io_names
+
+# --------------------------------------------------------------------------------------------------
+
+state_variables = [
+    'eastward_wind',
+    'northward_wind',
+    'air_temperature',
+    'air_pressure_at_surface',
+    'air_pressure_levels',
+    'water_vapor_mixing_ratio_wrt_moist_air',
+    'cloud_liquid_ice',
+    'cloud_liquid_water',
+    'rain_water',
+    'snow_water',
+    'mole_fraction_of_ozone_in_air',
+    'geopotential_height_times_gravity_at_surface',
+    'initial_mass_fraction_of_large_scale_cloud_condensate',
+    'initial_mass_fraction_of_convective_cloud_condensate',
+    'convective_cloud_area_fraction',
+    'fraction_of_ocean',
+    'fraction_of_land',
+    'isotropic_variance_of_filtered_topography',
+    'surface_velocity_scale',
+    'surface_buoyancy_scale',
+    'planetary_boundary_layer_height',
+    'surface_exchange_coefficient_for_momentum',
+    'surface_exchange_coefficient_for_heat',
+    'surface_exchange_coefficient_for_moisture',
+    'KCBL_before_moist',
+    'surface_temp_before_moist',
+    'lower_index_where_Kh_greater_than_2',
+    'upper_index_where_Kh_greater_than_2',
+    'fraction_of_lake',
+    'fraction_of_ice',
+    'vtype',
+    'stype',
+    'vfrac',
+    'sheleg',
+    'skin_temperature_at_surface',
+    'soilt',
+    'soilm',
+    'eastward_wind_at_surface',
+    'northward_wind_at_surface',
+    # 'sea_surface_temperature',
+    # 'mole_fraction_of_carbon_dioxide_in_air',
+]
+
+# --------------------------------------------------------------------------------------------------
+
+
+def background_eda(template_dict: Mapping) -> Mapping:
+    horizontal_resolution = template_dict['horizontal_resolution']
+    imem = template_dict['ensemble_imember']
+
+    background = {
+        'datetime': template_dict['local_background_time_iso'],
+        'filetype': 'cube sphere history',
+        'provider': 'geos',
+        'compute edge pressure from surface pressure': True,
+        'max allowable geometry difference': 1e-3,
+        'datapath': template_dict['cycle_dir'],
+        'filenames': [
+            f'./ebkg/mem{imem:03d}/geos.mem{imem:03d}.%yyyy%mm%dd_%hh%MM%ssz.nc4',
+            f'./fv3-jedi/bkg/geos.crtmsrf.{horizontal_resolution}.nc4'
+        ],
+        'state variables': state_variables,
+        'field io names': field_io_names,
+    }
+
+    return background
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_eda_control_pert.py

@@ -0,0 +1,83 @@
+# (C) Copyright 2021- United States Government as represented by the Administrator of the
+# National Aeronautics and Space Administration. All Rights Reserved.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+
+# --------------------------------------------------------------------------------------------------
+
+from collections.abc import Mapping
+from swell.configuration.jedi.interfaces.geos_atmosphere.model.shared import \
+        field_io_names
+
+# --------------------------------------------------------------------------------------------------
+
+state_variables = [
+    'eastward_wind',
+    'northward_wind',
+    'air_temperature',
+    'air_pressure_at_surface',
+    'air_pressure_levels',
+    'water_vapor_mixing_ratio_wrt_moist_air',
+    'cloud_liquid_ice',
+    'cloud_liquid_water',
+    'rain_water',
+    'snow_water',
+    'mole_fraction_of_ozone_in_air',
+    'geopotential_height_times_gravity_at_surface',
+    'initial_mass_fraction_of_large_scale_cloud_condensate',
+    'initial_mass_fraction_of_convective_cloud_condensate',
+    'convective_cloud_area_fraction',
+    'fraction_of_ocean',
+    'fraction_of_land',
+    'isotropic_variance_of_filtered_topography',
+    'surface_velocity_scale',
+    'surface_buoyancy_scale',
+    'planetary_boundary_layer_height',
+    'surface_exchange_coefficient_for_momentum',
+    'surface_exchange_coefficient_for_heat',
+    'surface_exchange_coefficient_for_moisture',
+    'KCBL_before_moist',
+    'surface_temp_before_moist',
+    'lower_index_where_Kh_greater_than_2',
+    'upper_index_where_Kh_greater_than_2',
+    'fraction_of_lake',
+    'fraction_of_ice',
+    'vtype',
+    'stype',
+    'vfrac',
+    'sheleg',
+    'skin_temperature_at_surface',
+    'soilt',
+    'soilm',
+    'eastward_wind_at_surface',
+    'northward_wind_at_surface',
+    # 'sea_surface_temperature',
+    # 'mole_fraction_of_carbon_dioxide_in_air',
+]
+
+# --------------------------------------------------------------------------------------------------
+
+
+def background_eda_control_pert(template_dict: Mapping) -> Mapping:
+    horizontal_resolution = template_dict['horizontal_resolution']
+    ichunk = template_dict['ensemble_ichunk']
+    cycle_dir = template_dict['cycle_dir']
+    background = {
+        'datetime': template_dict['local_background_time_iso'],
+        'filetype': 'cube sphere history',
+        'provider': 'geos',
+        'compute edge pressure from surface pressure': True,
+        'max allowable geometry difference': 1e-3,
+        'datapath': f'{cycle_dir}/ebkg_chunk/chunk{ichunk:03d}/geos.mem%mem_pad%/',
+        'filenames': [
+            f'%yyyy%mm%dd_%hh%MM%ssz.nc4',
+            f'../../../fv3-jedi/bkg/geos.crtmsrf.{horizontal_resolution}.nc4'
+        ],
+        'state variables': state_variables,
+        'field io names': field_io_names,
+    }
+
+    return background
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_ensemble.py

@@ -17,7 +17,7 @@ def background_ensemble(template_dict: Mapping) -> Mapping:
     horizontal_resolution = template_dict['horizontal_resolution']
 
     background_ensemble = {
-        'date': template_dict['window_begin_iso'],
+        'date': template_dict['local_background_time_iso'],
         'members from template': {
             'template': {
                 'datetime': template_dict['local_background_time_iso'],
@@ -41,4 +41,7 @@ def background_ensemble(template_dict: Mapping) -> Mapping:
 
     return background_ensemble
 
+# Note: 4D-window
+#        'date': template_dict['window_begin_iso'],
+
 # --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_error_eda_gsiB.py

@@ -0,0 +1,90 @@
+# (C) Copyright 2021- United States Government as represented by the Administrator of the
+# National Aeronautics and Space Administration. All Rights Reserved.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+
+# --------------------------------------------------------------------------------------------------
+
+from collections.abc import Mapping
+
+# --------------------------------------------------------------------------------------------------
+
+state_variables_to_inverse = [
+    'eastward_wind',
+    'northward_wind',
+    'air_temperature',
+    'air_pressure_at_surface',
+    'air_pressure_levels',
+    'water_vapor_mixing_ratio_wrt_moist_air',
+    'cloud_liquid_ice',
+    'cloud_liquid_water',
+    'rain_water',
+    'snow_water',
+    'mole_fraction_of_ozone_in_air',
+    'fraction_of_ocean',
+    'fraction_of_lake',
+    'fraction_of_ice',
+    'geopotential_height_times_gravity_at_surface',
+    'skin_temperature_at_surface',
+]
+
+# --------------------------------------------------------------------------------------------------
+
+
+def background_error_eda_gsiB(template_dict: Mapping) -> Mapping:
+    vertical_resolution = template_dict['vertical_resolution']
+    gsibec_nlons = template_dict['gsibec_nlons']
+    gsibec_nlats = template_dict['gsibec_nlats']
+    gsibec_configuration = template_dict['gsibec_configuration']
+    gsibec_npx_proc = template_dict['gsibec_npx_proc']
+    gsibec_npy_proc = template_dict['gsibec_npy_proc']
+
+    background_error = {
+        'covariance model': 'SABER',
+        'covariance type': 'gsi hybrid covariance',
+        'saber central block': {
+            'saber block name': 'gsi hybrid covariance',
+            'read': {
+                'gsi akbk': f'./fv3-jedi/fv3files/akbk{vertical_resolution}.nc4',
+                'gsi error covariance file':
+                f'./fv3-jedi/gsibec/gsi-coeffs-gmao-global-l{vertical_resolution}x{gsibec_nlons}y{gsibec_nlats}.nc4',  # noqa
+                'gsi berror namelist file':
+                f'./fv3-jedi/gsibec/{gsibec_configuration}_l{vertical_resolution}x{gsibec_nlons}y{gsibec_nlats}.nml',  # noqa
+                'processor layout x direction': gsibec_npx_proc,
+                'processor layout y direction': gsibec_npy_proc,
+                'debugging mode': False
+            }
+        },
+        'saber outer blocks': [
+            {'saber block name': 'interpolation',
+             'inner geometry': {
+                 'function space': 'StructuredColumns',
+                 'custom grid matching gsi': {
+                     'type': 'latlon',
+                     'lats': int(gsibec_nlats),
+                     'lons': int(gsibec_nlons),
+                 },
+                 'custom partitioner matching gsi': {
+                     'bands': gsibec_npy_proc
+                 },
+                 'halo': 1,
+             },
+             'forward interpolator': {
+                 'local interpolator type': 'oops unstructured grid interpolator',
+             },
+             'inverse interpolator': {
+                 'local interpolator type': 'oops unstructured grid interpolator',
+             },
+             'state variables to inverse': state_variables_to_inverse}
+        ],
+        'linear variable change': {
+            'linear variable change name': 'Control2Analysis',
+            'input variables': state_variables_to_inverse,
+            'output variables': template_dict['analysis_variables']
+        }
+    }
+
+    return background_error
+
+# --------------------------------------------------------------------------------------------------