Adding geos_aero hofx

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

@@ -0,0 +1,5 @@
+jedi_interface: fv3-jedi
+total_processors: 6*{{npx_proc}}*{{npy_proc}}
+executables:
+  hofx3D: fv3jedi_hofx_nomodel.x
+  hofx4D: fv3jedi_hofx.x

src/swell/configuration/jedi/interfaces/geos_aero/model/background.py

@@ -0,0 +1,31 @@
+# (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_aero.model.shared import \
+        field_io_names, state_variables
+
+# --------------------------------------------------------------------------------------------------
+
+
+def background(template_dict: Mapping) -> Mapping:
+
+    background = {
+        'datetime': template_dict['local_background_time_iso'],
+        'filetype': 'cube sphere history',
+        'provider': 'geos',
+        'max allowable geometry difference': 1e-3,
+        'datapath': template_dict['cycle_dir'],
+        'filename': 'bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
+        'state variables': state_variables,
+        'field io names': field_io_names,
+    }
+
+    return background
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_aero/model/geometry.py

@@ -0,0 +1,36 @@
+# (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
+
+# --------------------------------------------------------------------------------------------------
+
+
+def geometry(template_dict: Mapping) -> Mapping:
+
+    npx_proc = template_dict['npx_proc']
+    npy_proc = template_dict['npy_proc']
+
+    horizontal_resolution = template_dict['horizontal_resolution']
+    vertical_resolution = template_dict['vertical_resolution']
+
+    geometry = {
+        'fms initialization': {
+            'namelist filename': './fv3-jedi/fv3files/fmsmpp.nml',
+            'field table filename': './fv3-jedi/fv3files/field_table_gmao'
+        },
+        'akbk': f'./fv3-jedi/fv3files/akbk{vertical_resolution}.nc4',
+        'layout': [npx_proc, npy_proc],
+        'npx': horizontal_resolution,
+        'npy': horizontal_resolution,
+        'npz': vertical_resolution
+    }
+
+    return geometry
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_aero/model/getvalues.py

@@ -0,0 +1,20 @@
+# (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
+
+# --------------------------------------------------------------------------------------------------
+
+
+def getvalues(template_dict: Mapping) -> Mapping:
+
+    getvalues = None
+
+    return getvalues
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_aero/model/r2d2.py

@@ -0,0 +1,41 @@
+# (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
+
+# --------------------------------------------------------------------------------------------------
+
+
+def r2d2(template_dict: Mapping) -> Mapping:
+
+    cycle_dir = template_dict['cycle_dir']
+
+    r2d2 = {
+        'fetch': {
+            'an': [
+                {'file_type': 'bkg',
+                 'r2d2_model': 'geos_aero',
+                 'filename': f'{cycle_dir}/bkg.%Y%m%dT%H%M%SZ.nc4'}
+            ],
+            'fc': [
+                {'file_type': 'bkg',
+                 'r2d2_model': 'geos_aero',
+                 'filename': f'{cycle_dir}/bkg.%Y%m%dT%H%M%SZ.nc4'}
+            ]
+        },
+        'store': {
+            'fc': [
+                {'file_type': 'bkg',
+                 'r2d2_model': 'geos_aero'}
+            ]
+        }
+    }
+
+    return r2d2
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_aero/model/shared.py

@@ -0,0 +1,23 @@
+# (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.
+
+# --------------------------------------------------------------------------------------------------
+
+# Aerosol extinction coefficient field IO names mapping JEDI variable names to GEOS file names
+
+field_io_names = {
+    'air_pressure_thickness': 'DELP',
+    'moist_air_density': 'AIRDENS',
+    'volume_extinction_in_air_due_to_aerosol_particles_lambda1' : 'TOTEXTCOEF470',
+    'volume_extinction_in_air_due_to_aerosol_particles_lambda2' : 'TOTEXTCOEF550',
+    'volume_extinction_in_air_due_to_aerosol_particles_lambda3' : 'TOTEXTCOEF870'
+}
+
+# --------------------------------------------------------------------------------------------------
+
+state_variables = list(field_io_names.keys())
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_aero/model/stage_cycle.py

@@ -0,0 +1,36 @@
+# (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
+
+# --------------------------------------------------------------------------------------------------
+
+
+def stage_cycle(template_dict: Mapping) -> Mapping:
+
+    cycle_dir = template_dict['cycle_dir']
+    swell_static_files = template_dict['swell_static_files']
+    vertical_resolution = template_dict['vertical_resolution']
+    horizontal_resolution = template_dict['horizontal_resolution']
+
+    stage_cycle = [
+        {
+            'link_files': {
+                'directories': [
+                    [
+                        f'{swell_static_files}/jedi/interfaces/geos_atmosphere/fv3files/*',
+                        f'{cycle_dir}/fv3-jedi/fv3files/'
+                    ],
+                ]
+            }
+        }
+    ]
+
+    return stage_cycle
+
+# --------------------------------------------------------------------------------------------------

src/swell/configuration/jedi/interfaces/geos_aero/observations/mod04_l2a_land.yaml

@@ -0,0 +1,22 @@
+obs space:
+  name: AodExt
+  obsdatain:
+    engine:
+      type: H5File
+      obsfile: '{{cycle_dir}}/IODA_x0054.MOD04_L2a.land.{{window_begin}}.nc4'
+  obsdataout:
+    engine:
+      type: H5File
+      allow overwrite: true
+      obsfile: '{{cycle_dir}}/{{experiment_id}}.hofx3d.IODA_x0054.MOD04_L2a.land.{{window_begin}}.nc4'
+  observed variables:
+  - aerosolOpticalDepth
+  simulated variables:
+  - aerosolOpticalDepth
+  channels: 1
+
+obs operator:
+  name: AodExt
+  nprofiles: 2
+  bkg_wavelengths: [470.0, 550.0]
+  doing_log_transform_aod: false

src/swell/configuration/jedi/interfaces/geos_aero/suite_questions.yaml

@@ -0,0 +1,3 @@
+cycle_times:
+  default_value: ['T00', 'T06', 'T12', 'T18']
+  options: ['T00', 'T06', 'T12', 'T18']

src/swell/configuration/jedi/interfaces/geos_aero/task_questions.yaml

@@ -0,0 +1,58 @@
+background_experiment:
+  default_value: x0054
+  options:
+  - x0054
+
+background_frequency:
+  default_value: PT3H
+
+# How long before the middle of the analysis window did
+# the background providing forecast begin?
+background_time_offset:
+  default_value: PT9H
+
+clean_patterns:
+  default_value:
+  - '*.nc4'
+  - '*.txt'
+  - logfile.*.out
+  options:
+  - '*.nc4'
+  - '*.txt'
+  - logfile.*.out
+
+horizontal_resolution:
+  default_value: '181'
+  options:
+  - '91'
+  - '181'
+
+npx_proc:
+  default_value: 4
+
+npy_proc:
+  default_value: 4
+
+observations:
+  default_value:
+  - mod04_l2a_land
+  options:
+  - mod04_l2a_land
+
+obs_experiment:
+  default_value: None
+
+# obs needs to be in {ioda_locations_not_in_r2d2}/{cycle}/{model}
+ioda_locations_not_in_r2d2:
+  default_value: /discover/nobackup/projects/gmao/dadev/rtodling/archive/542/prePP/ioda
+
+vertical_resolution:
+  default_value: '72'
+  options:
+  - '72'
+
+window_length:
+  default_value: PT6H
+
+window_type:
+  default_value: 3D

src/swell/configuration/jedi/observation_ioda_names.yaml

@@ -538,3 +538,9 @@ ioda instrument names:
     full name: OMPS total column O3 (Nadir Mapper)
     inst type: retrieval
     provider : nasa
+  # Aero
+  - ioda name: mod04_l2a_land
+    full name: MODIS AOD
+    inst type: retrieval
+    provider : nasa
+

src/swell/suites/3dfgat_atmos/suite_config.py

@@ -40,7 +40,7 @@ class SuiteConfig(QuestionContainer, Enum):
             ]),
             qd.horizontal_resolution("91"),
             qd.geos_x_background_directory("/discover/nobackup/projects/gmao/"
-                                           "dadev/rtodling/archive/Restarts/JEDI/541x"),
+                                           "dadev/rtodling/archive/Restarts/JEDI/541x/91/x0050/rs"),
             qd.window_type("4D"),
             qd.observations([
                 "aircraft_temperature",

src/swell/suites/3dvar_atmos/suite_config.py

@@ -39,7 +39,7 @@ class SuiteConfig(QuestionContainer, Enum):
                 "T18"
             ]),
             qd.geos_x_background_directory("/discover/nobackup/projects/gmao/"
-                                           "dadev/rtodling/archive/Restarts/JEDI/541x"),
+                                           "dadev/rtodling/archive/Restarts/JEDI/541x/91/x0050/rs"),
             qd.window_length("PT6H"),
             qd.window_type("3D"),
             qd.horizontal_resolution("91"),

src/swell/suites/hofx/suite_config.py

@@ -33,7 +33,7 @@ class SuiteConfig(QuestionContainer, Enum):
         geos_atmosphere=[
             qd.horizontal_resolution("91"),
             qd.geos_x_background_directory("/discover/nobackup/projects/gmao/dadev/"
-                                           "rtodling/archive/Restarts/JEDI/541x"),
+                                           "rtodling/archive/Restarts/JEDI/541x/91/x0050/rs"),
             qd.npx_proc(2),
             qd.npy_proc(2),
             qd.observations([