Standalone configuration models for abiotic and abiotic simple models

tests/models/abiotic_simple/test_abiotic_simple_model.py

@@ -73,11 +73,10 @@ def test_abiotic_simple_model_initialization(
 
 
 @pytest.mark.parametrize(
-    "cfg_string,satvap1,raises,expected_log_entries",
+    "cfg_string,raises,expected_log_entries",
     [
         pytest.param(
             "[core.timing]\nupdate_interval = '1 week'\n[abiotic_simple]\n",
-            [0.61078, 7.5, 237.3],
             does_not_raise(),
             tuple(
                 [
@@ -94,8 +93,7 @@ def test_abiotic_simple_model_initialization(
         pytest.param(
             "[core.timing]\nupdate_interval = '1 week'\n"
             "[abiotic_simple.constants]\n"
-            "saturation_vapour_pressure_factors = [1.0, 2.0, 3.0]\n",
-            [1.0, 2.0, 3.0],
+            "initial_net_radiation = 20\n",
             does_not_raise(),
             tuple(
                 [
@@ -115,7 +113,6 @@ def test_generate_abiotic_simple_model(
     caplog,
     dummy_climate_data_varying_canopy,
     cfg_string,
-    satvap1,
     raises,
     expected_log_entries,
 ):

tests/models/abiotic_simple/test_microclimate_simple.py

@@ -72,7 +72,6 @@ def test_varying_canopy_calculate_vapour_pressure_deficit(
 def test_run_microclimate_varying_canopy(
     dummy_climate_data_varying_canopy,
     fixture_core_components,
-    fixture_abiotic_constants,
     fixture_core_constants,
     fixture_abiotic_simple_configuration,
 ):
@@ -89,8 +88,7 @@ def test_run_microclimate_varying_canopy(
         data=data,
         layer_structure=lyr_strct,
         time_index=0,
-        simple_constants=fixture_abiotic_simple_configuration.constants,
-        abiotic_constants=fixture_abiotic_constants,
+        constants=fixture_abiotic_simple_configuration.constants,
         core_constants=fixture_core_constants,
         bounds=fixture_abiotic_simple_configuration.bounds,
     )

virtual_ecosystem/models/abiotic/abiotic_model.py

@@ -27,11 +27,7 @@ class as a child of the :class:`~virtual_ecosystem.core.base_model.BaseModel` cl
     calculate_vapour_pressure_deficit,
     run_simple_microclimate,
 )
-from virtual_ecosystem.models.abiotic_simple.model_config import (
-    AbioticSimpleBounds,
-    AbioticSimpleConfiguration,
-    AbioticSimpleConstants,
-)
+from virtual_ecosystem.models.abiotic_simple.model_config import AbioticSimpleBounds
 
 
 class AbioticModel(
@@ -120,10 +116,9 @@ def __init__(
 
         self.model_constants: AbioticConstants
         """Set of constants for the abiotic model."""
-        self.simple_constants: AbioticSimpleConstants
-        """Set of constants for simple abiotic model."""
-        self.simple_bounds: AbioticSimpleBounds
-        """Set of bound for simple abiotic model."""
+        self.bounds: AbioticSimpleBounds
+        """A set of bounds on microclimates variables, used with both the simple model
+        of the initial state and the full energy balance calculations."""
         self.pyrealm_constants: PyrealmConst
         """Pyrealm constants."""
 
@@ -152,8 +147,7 @@ def from_config(
             "abiotic", AbioticConfiguration
         )
 
-        # Hard coding these here until we figure out how to resolve config issues
-        abiotic_simple_configuration = AbioticSimpleConfiguration()
+        # Hard coding this until we figure out how to pass in.
         pyrealm_consts = PyrealmConst()
 
         LOGGER.info(
@@ -164,15 +158,15 @@ def from_config(
             data=data,
             core_components=core_components,
             static=model_configuration.static,
-            model_constants=model_configuration.constants,
-            simple_config=abiotic_simple_configuration,
+            constants=model_configuration.constants,
+            bounds=model_configuration.bounds,
             pyrealm_consts=pyrealm_consts,
         )
 
     def _setup(
         self,
         model_constants: AbioticConstants = AbioticConstants(),
-        simple_config: AbioticSimpleConfiguration = AbioticSimpleConfiguration(),
+        bounds: AbioticSimpleBounds = AbioticSimpleBounds(),
         pyrealm_constants: PyrealmConst = PyrealmConst(),
         **kwargs,
     ) -> None:
@@ -185,14 +179,13 @@ def _setup(
 
         Args:
             model_constants: Set of constants for the abiotic model.
-            simple_config: Configuration options for the abiotic simple model.
+            bounds: A set of bounds to be applied to abiotic variables.
             pyrealm_constants: Additional configuration options to the pyrealm package.
             **kwargs: Further arguments to the setup method.
         """
 
         self.model_constants = model_constants
-        self.simple_constants = simple_config.constants
-        self.simple_bounds = simple_config.bounds
+        self.bounds = bounds
         self.pyrealm_constants = pyrealm_constants
 
         # create soil temperature array
@@ -219,10 +212,9 @@ def _setup(
             data=self.data,
             layer_structure=self.layer_structure,
             time_index=0,
-            simple_constants=self.simple_constants,
-            abiotic_constants=self.model_constants,
+            constants=self.model_constants,
             core_constants=self.core_constants,
-            bounds=self.simple_bounds,
+            bounds=self.bounds,
         )
 
         # Generate initial profiles of canopy temperature and heat fluxes from soil and
@@ -260,7 +252,7 @@ def _update(self, time_index: int, **kwargs: Any) -> None:
             abiotic_constants=self.model_constants,
             core_constants=self.core_constants,
             pyrealm_const=self.pyrealm_constants,
-            abiotic_bounds=self.simple_bounds,
+            abiotic_bounds=self.bounds,
         )
 
         self.data.add_from_dict(output_dict=update_dict)

virtual_ecosystem/models/abiotic/model_config.py

@@ -5,20 +5,17 @@
 simulation.
 """  # noqa: D205
 
-from virtual_ecosystem.core.configuration import Configuration, ModelConfigurationRoot
+from virtual_ecosystem.core.configuration import ModelConfigurationRoot
+from virtual_ecosystem.models.abiotic_simple.model_config import (
+    AbioticSharedConstants,
+    AbioticSimpleBounds,
+    AbioticSimpleConstants,
+)
 
 
-class AbioticConstants(Configuration):
+class AbioticConstants(AbioticSharedConstants):
     """Dataclass to store all constants for the `abiotic` model."""
 
-    leaf_emissivity: float = 0.98
-    """Leaf emissivity, unitless.
-
-    Leaf emissivity is a measure of how efficiently a leaf emits thermal radiation
-    compared to a perfect blackbody, typically ranging from 0.95 to 0.99. Value for
-    tropical vegetation is taken from :cite:t:`ma_an_2019`.
-    """
-
     leaf_albedo: float = 0.15
     """Leaf albedo, unitless.
 
@@ -142,14 +139,6 @@ class AbioticConstants(Configuration):
     The value is takes from a study that compares changes in surface albedo before and
     after deforestation in South East Asia :cite:p:`wilson_role_2020`."""
 
-    soil_emissivity: float = 0.95
-    """Soil emissivity, dimensionless.
-
-    Soil emissivity is a measure of how efficiently the soil surface emits thermal
-    radiation compared to a perfect blackbody, with values typically ranging from 0.90
-    to 0.98 depending on soil texture, moisture, and surface roughness. Value taken
-    from :cite:t:`molders_plant_2005`."""
-
     saturated_pressure_slope_parameters: tuple[float, float, float, float] = (
         4098.0,
         0.6108,
@@ -174,3 +163,10 @@ class AbioticConfiguration(ModelConfigurationRoot):
 
     constants: AbioticConstants = AbioticConstants()
     """Constants for the abiotic model"""
+
+    bounds: AbioticSimpleBounds = AbioticSimpleBounds()
+    """Bounds for abiotic variables."""
+
+    simple_constants: AbioticSimpleConstants = AbioticSimpleConstants()
+    """Constants used for the simple abiotic model, used to set up initial
+    conditions."""

virtual_ecosystem/models/abiotic_simple/abiotic_simple_model.py

@@ -19,7 +19,6 @@ class as a child of the :class:`~virtual_ecosystem.core.base_model.BaseModel` cl
 from virtual_ecosystem.core.core_components import CoreComponents
 from virtual_ecosystem.core.data import Data
 from virtual_ecosystem.core.logger import LOGGER
-from virtual_ecosystem.models.abiotic.model_config import AbioticConstants
 from virtual_ecosystem.models.abiotic_simple.microclimate_simple import (
     calculate_vapour_pressure_deficit,
     run_simple_microclimate,
@@ -101,8 +100,6 @@ def __init__(
         """Set of constants for the abiotic simple model"""
         self.bounds: AbioticSimpleBounds
         """Upper and lower bounds for abiotic variables."""
-        self.abiotic_constants: AbioticConstants
-        """Abiotic constants required for some calculations"""
 
     @classmethod
     def from_config(
@@ -131,9 +128,6 @@ def from_config(
             )
         )
 
-        # Hard coding abiotic constants here until we resolve the config setup
-        abiotic_constants: AbioticConstants = AbioticConstants()
-
         LOGGER.info(
             "Information required to initialise the abiotic simple model successfully "
             "extracted."
@@ -143,13 +137,11 @@ def from_config(
             core_components=core_components,
             static=model_configuration.static,
             model_configuration=model_configuration,
-            abiotic_constants=abiotic_constants,
         )
 
     def _setup(
         self,
         model_configuration: AbioticSimpleConfiguration,
-        abiotic_constants: AbioticConstants,
         **kwargs,
     ) -> None:
         """Function to set up the abiotic simple model.
@@ -166,7 +158,6 @@ def _setup(
         # Populate model attributes
         self.model_constants = model_configuration.constants
         self.bounds = model_configuration.bounds
-        self.abiotic_constants = abiotic_constants
 
         # create soil temperature array
         self.data["soil_temperature"] = self.layer_structure.from_template()
@@ -207,8 +198,7 @@ def _update(self, time_index: int, **kwargs: Any) -> None:
             data=self.data,
             layer_structure=self.layer_structure,
             time_index=time_index,
-            simple_constants=self.model_constants,
-            abiotic_constants=self.abiotic_constants,
+            constants=self.model_constants,
             core_constants=self.core_constants,
             bounds=self.bounds,
         )

virtual_ecosystem/models/abiotic_simple/microclimate_simple.py

@@ -33,8 +33,7 @@ def run_simple_microclimate(
     data: Data,
     layer_structure: LayerStructure,
     time_index: int,  # could be datetime?
-    simple_constants: AbioticSimpleConstants,
-    abiotic_constants: AbioticConstants,
+    constants: AbioticSimpleConstants | AbioticConstants,
     core_constants: CoreConstants,
     bounds: AbioticSimpleBounds,
 ) -> dict[str, DataArray]:
@@ -88,8 +87,7 @@ def run_simple_microclimate(
         data: Data object
         layer_structure: The LayerStructure instance for the simulation.
         time_index: Time index, integer
-        simple_constants: Set of constants for the abiotic simple model
-        abiotic_constants: Set of constants for the abiotic model
+        constants: Set of constants for the abiotic simple model
         core_constants: Set of constants shared across all models
         bounds: Upper and lower allowed values for vertical profiles, used to constrain
             log interpolation. Note that currently no conservation of water and energy!
@@ -160,14 +158,14 @@ def run_simple_microclimate(
     # Calculate net radiation, [W m-2].
     canopy_longwave_emission = energy_balance.calculate_longwave_emission(
         temperature=canopy_temperature.to_numpy(),
-        emissivity=abiotic_constants.leaf_emissivity,
+        emissivity=constants.leaf_emissivity,
         stefan_boltzmann=core_constants.stefan_boltzmann_constant,
     )
     soil_longwave_emission = energy_balance.calculate_longwave_emission(
         temperature=output["soil_temperature"][
             layer_structure.index_topsoil_scalar
         ].to_numpy(),
-        emissivity=abiotic_constants.soil_emissivity,
+        emissivity=constants.soil_emissivity,
         stefan_boltzmann=core_constants.stefan_boltzmann_constant,
     )
 

virtual_ecosystem/models/abiotic_simple/model_config.py

@@ -3,15 +3,32 @@
 from virtual_ecosystem.core.configuration import Configuration, ModelConfigurationRoot
 
 
-class AbioticSimpleConstants(Configuration):
-    """Dataclass to store all constants for the `abiotic_simple` model."""
+class AbioticSharedConstants(Configuration):
+    """Shared abiotic constants.
+
+    This is a pydantic basemodel to hold constants shared between the `abiotic` and
+    `abiotic_simple` models.
+    """
+
+    leaf_emissivity: float = 0.98
+    """Leaf emissivity, unitless.
+
+    Leaf emissivity is a measure of how efficiently a leaf emits thermal radiation
+    compared to a perfect blackbody, typically ranging from 0.95 to 0.99. Value for
+    tropical vegetation is taken from :cite:t:`ma_an_2019`.
+    """
+
+    soil_emissivity: float = 0.95
+    """Soil emissivity, dimensionless.
+
+    Soil emissivity is a measure of how efficiently the soil surface emits thermal
+    radiation compared to a perfect blackbody, with values typically ranging from 0.90
+    to 0.98 depending on soil texture, moisture, and surface roughness. Value taken
+    from :cite:t:`molders_plant_2005`."""
 
-    saturation_vapour_pressure_factors: tuple[float, float, float] = (
-        0.61078,
-        7.5,
-        237.3,
-    )
-    """Factors for saturation vapour pressure calculation."""
+
+class AbioticSimpleConstants(AbioticSharedConstants):
+    """Dataclass to store all constants for the `abiotic_simple` model."""
 
     initial_net_radiation: float = 10.0
     """Initial value for net radiation per layer, W m-2.