Adding background error options in 3dvar_cf

src/swell/configuration/jedi/interfaces/geos_cf/model/background_error.py

@@ -7,19 +7,152 @@
 # --------------------------------------------------------------------------------------------------
 
 from collections.abc import Mapping
+from swell.configuration.jedi.interfaces.geos_cf.model.shared import \
+        field_io_names
 
+
+# Central block builders
+# --------------------------------------------------------------------------------------------------
+
+
+def _build_identity_central_block(template_dict: Mapping) -> Mapping:
+    """Identity covariance central block"""
+    return {'saber block name': 'ID'}
+
+
+def _build_bump_nicas_central_block(template_dict: Mapping) -> Mapping:
+    """BUMP/NICAS covariance central block"""
+    field_aliases = []
+    for var in template_dict.get('analysis_variables', []):
+        field_aliases.append({
+            'in code': var,
+            'in file': 'fixedlevel_H_500_300_V_00_03'
+        })
+
+    return {
+        'saber block name': 'BUMP_NICAS',
+        'read': {
+            'io': {
+                'data directory': f"{template_dict['cycle_dir']}/",
+                'files prefix': 'geos_cf',
+                'alias': field_aliases
+            },
+            'drivers': {
+                'multivariate strategy': 'univariate',
+                'read local nicas': True
+            }
+        }
+    }
+
+# Outer block builders
+# --------------------------------------------------------------------------------------------------
+
+
+def _build_stddev_bkg_scaled(template_dict: Mapping) -> Mapping:
+    """Standard deviation outer block"""
+    return {
+        'saber block name': 'StdDev',
+        'stddev scale factor': '0.25',
+        'read': {
+            'model file': {
+                'datetime': template_dict['local_background_time_iso'],
+                'set datetime on read': True,
+                'filetype': 'cube sphere history',
+                'max allowable geometry difference': 0.1,
+                'datapath': template_dict['cycle_dir'],
+                'filename': 'bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
+                'field io names': field_io_names,
+            }
+        }
+    }
+
+
+def _build_stddev_fixed_values(template_dict: Mapping) -> Mapping:
+    """Standard deviation outer block with fixed values from analysis variables"""
+    # Get the stddev values for each analysis variable
+    # Example: {'volume_mixing_ratio_of_no2': 5e-9, 'volume_mixing_ratio_of_o3': 1e-8}
+    stddev_dict = {
+        'volume_mixing_ratio_of_no2': 5e-9,
+        'volume_mixing_ratio_of_o3': 1e-8,
+        'volume_mixing_ratio_of_co': 5e-8,
+    }
+
+    # Build the standard deviations list
+    standard_deviations = [
+        {'variable': var, 'stddev': value}
+        for var, value in stddev_dict.items()
+    ]
+
+    return {
+        'saber block name': 'StdDev',
+        'standard deviations': standard_deviations
+    }
+
+# Main assembler
 # --------------------------------------------------------------------------------------------------
 
 
 def background_error(template_dict: Mapping) -> Mapping:
+    """
+    Assemble background error covariance configuration from modular components.
+
+    Parameters
+    ----------
+    template_dict : Mapping
+        Dictionary containing configuration parameters including:
+        - central_block: Type of central block ('identity', 'bump_nicas', 'diffusion')
+        - outer_block: add StdDev outer block
+
+
+    Returns
+    -------
+    Mapping
+        JEDI-compatible background error covariance configuration
+    """
+
+    # Select central block builder
+    central_block_select = template_dict.get('saber_central_block', 'identity')
+
+    central_block_types = {
+        'identity': _build_identity_central_block,
+        'bump_nicas': _build_bump_nicas_central_block,
+    }
 
-    background_error = {
+    # Build the central block
+    if central_block_select not in central_block_types:
+        raise ValueError(
+            f"Unknown background_error_model '{central_block_select}'. "
+            f"Choose from: {list(central_block_types.keys())}"
+        )
+
+    central_block = central_block_types[central_block_select](template_dict)
+
+    # Assemble base configuration
+    background_error_config = {
         'covariance model': 'SABER',
-        'saber central block': {
-            'saber block name': 'ID'
-            },
+        'saber central block': central_block,
     }
 
-    return background_error
+    # Optionally add outer blocks (skip for identity central block)
+    if central_block_select != 'identity' and 'saber_outer_block' in template_dict:
+
+        outer_block_select = template_dict.get('saber_outer_block')
+
+        outer_block_types = {
+            'stddev_bkg_scaled': _build_stddev_bkg_scaled,
+            'stddev_fixed_values': _build_stddev_fixed_values,
+        }
+
+        if outer_block_select not in outer_block_types:
+            raise ValueError(
+                f"Unknown outer_block '{outer_block_select}'. "
+                f"Choose from: {list(outer_block_types.keys())}"
+            )
+
+        outer_block = outer_block_types[outer_block_select](template_dict)
+
+        background_error_config['saber outer blocks'] = [outer_block]
+
+    return background_error_config
 
 # --------------------------------------------------------------------------------------------------

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

@@ -15,15 +15,35 @@ def stage_cycle(template_dict: Mapping) -> Mapping:
 
     cycle_dir = template_dict['cycle_dir']
     swell_static_files = template_dict['swell_static_files']
+    npx_proc = template_dict['npx_proc']
+    npy_proc = template_dict['npy_proc']
 
     stage_cycle = [
         {'copy_files': {
             'directories': [
-                [f'{swell_static_files}/jedi/interfaces/geos_cf/fv3_files/*', f'{cycle_dir}/']
+                [
+                    f'{swell_static_files}/jedi/interfaces/geos_cf/fv3_files/*',
+                    f'{cycle_dir}/'
+                ]
             ]
         }}
     ]
 
+    # Only link NICAS files when the central block corresponds to BUMP_NICAS
+    central_block_select = template_dict.get('saber_central_block', 'none')
+    if central_block_select == 'bump_nicas':
+        stage_cycle.append({
+            'link_files': {
+                'directories': [
+                    [
+                        f'{swell_static_files}/jedi/interfaces/geos_cf/nicas/'
+                        f'layout_{npx_proc}x{npy_proc}x6/*',
+                        f'{cycle_dir}/'
+                    ]
+                ]
+            }
+        })
+
     return stage_cycle
 
 # --------------------------------------------------------------------------------------------------

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

@@ -4,10 +4,17 @@ analysis_variables:
   options:
   - volume_mixing_ratio_of_no2
 
-background_error_model:
-  default_value: identity
+saber_central_block:
+  default_value: bump_nicas
   options:
   - identity
+  - bump_nicas
+
+saber_outer_block:
+  default_value: stddev_bkg_scaled
+  options:
+  - stddev_bkg_scaled
+  - stddev_fixed_values
 
 background_experiment:
   default_value: swell_test

src/swell/configuration/jedi/oops/variational3D.py

@@ -52,7 +52,12 @@ def render_oops(self):
                 },
                 'prints': {
                     'frequency': 'PT3H'
-                }
+                },
+                'increment': {
+                    'geometry': self.interface_model('geometry'),
+                    'output': self.interface_model('increment_cs'),
+                },
+
             },
             'output': self.interface_model('analysis')
         }

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

@@ -41,6 +41,8 @@ class SuiteConfig(QuestionContainer, Enum):
             qd.npx_proc(2),
             qd.npy_proc(2),
             qd.vertical_resolution(72),
+            qd.saber_central_block('bump_nicas'),
+            qd.saber_outer_block('stddev_bkg_scaled'),
             qd.analysis_variables(["volume_mixing_ratio_of_no2"]),
             qd.background_experiment("swell_test"),
             qd.observations([

src/swell/tasks/run_jedi_variational_executable.py

@@ -69,6 +69,8 @@ def execute(self) -> None:
         self.jedi_rendering.add_key('minimizer', self.config.minimizer())
         self.jedi_rendering.add_key('number_of_iterations', number_of_iterations[0])
         self.jedi_rendering.add_key('analysis_variables', self.config.analysis_variables())
+        self.jedi_rendering.add_key('saber_central_block', self.config.saber_central_block())
+        self.jedi_rendering.add_key('saber_outer_block', self.config.saber_outer_block())
         self.jedi_rendering.add_key('gradient_norm_reduction',
                                     self.config.gradient_norm_reduction())
         self.jedi_rendering.add_key('marine_models', self.config.marine_models(None))

src/swell/tasks/stage_jedi.py

@@ -46,17 +46,23 @@ def execute(self) -> None:
                 swell_static_files = swell_static_files_user
 
         vertical_resolution = self.config.vertical_resolution()
+        npx_proc = self.config.npx_proc(None)
+        npy_proc = self.config.npy_proc(None)
         gsibec_configuration = self.config.gsibec_configuration(None)
         gsibec_nlats = self.config.gsibec_nlats(None)
         gsibec_nlons = self.config.gsibec_nlons(None)
+        saber_central_block = self.config.saber_central_block(None)
 
         # Add jedi interface template keys
         self.jedi_rendering.add_key('horizontal_resolution', horizontal_resolution)
         self.jedi_rendering.add_key('swell_static_files', swell_static_files)
         self.jedi_rendering.add_key('vertical_resolution', vertical_resolution)
+        self.jedi_rendering.add_key('npx_proc', npx_proc)
+        self.jedi_rendering.add_key('npy_proc', npy_proc)
         self.jedi_rendering.add_key('gsibec_configuration', gsibec_configuration)
         self.jedi_rendering.add_key('gsibec_nlats', gsibec_nlats)
         self.jedi_rendering.add_key('gsibec_nlons', gsibec_nlons)
+        self.jedi_rendering.add_key('saber_central_block', saber_central_block)
 
         # Open the stage configuration file
         # ---------------------------------

src/swell/tasks/task_questions.py

@@ -86,6 +86,8 @@ class TaskQuestions(QuestionContainer, Enum):
             qd.gsibec_nlons(),
             qd.number_of_iterations(),
             qd.total_processors(),
+            qd.saber_central_block(),
+            qd.saber_outer_block(),
         ]
     )
 
@@ -769,10 +771,13 @@ class TaskQuestions(QuestionContainer, Enum):
         list_name="StageJedi",
         questions=[
             swell_static_file_questions,
+            qd.npx_proc(),
+            qd.npy_proc(),
             qd.gsibec_configuration(),
             qd.gsibec_nlats(),
             qd.gsibec_nlons(),
             qd.horizontal_resolution(),
+            qd.saber_central_block(),
             qd.vertical_resolution()
         ]
     )

src/swell/utilities/question_defaults.py

@@ -239,6 +239,34 @@ class background_error_model(TaskQuestion):
 
     # --------------------------------------------------------------------------------------------------
 
+    @dataclass
+    class saber_central_block(TaskQuestion):
+        default_value: str = "defer_to_model"
+        question_name: str = "saber_central_block"
+        ask_question: bool = True
+        options: str = "defer_to_model"
+        models: List[str] = mutable_field([
+            "all_models"
+        ])
+        prompt: str = "Which saber central block do you want to use?"
+        widget_type: WType = WType.STRING
+
+    # --------------------------------------------------------------------------------------------------
+
+    @dataclass
+    class saber_outer_block(TaskQuestion):
+        default_value: str = "defer_to_model"
+        question_name: str = "saber_outer_block"
+        ask_question: bool = True
+        options: str = "defer_to_model"
+        models: List[str] = mutable_field([
+            "all_models"
+        ])
+        prompt: str = "Which saber outer blocks do you want to use?"
+        widget_type: WType = WType.STRING
+
+    # --------------------------------------------------------------------------------------------------
+
     @dataclass
     class background_experiment(TaskQuestion):
         default_value: str = "defer_to_model"

src/swell/utilities/render_jedi_interface_files.py

@@ -116,6 +116,8 @@ def __init__(
             'obs_filenames',
             'packet_ensemble_members',
             'perhost',
+            'saber_central_block',
+            'saber_outer_block',
             'skip_ensemble_hofx',
             'swell_static_files',
             'start_cycle_point',