"""The :mod:`~virtual_ecosystem.models.abiotic_simple.abiotic_simple_model` module
creates a
:class:`~virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel`
class as a child of the :class:`~virtual_ecosystem.core.base_model.BaseModel` class.
Todo:
* update temperatures to Kelvin
* pressure and CO2 profiles should only be filled for filled/true above ground layers
""" # noqa: D205
from __future__ import annotations
from typing import Any
from pyrealm.constants import CoreConst as PyrealmCoreConst
from virtual_ecosystem.core.base_model import BaseModel
from virtual_ecosystem.core.configuration import CompiledConfiguration
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.core.model_config import CoreConfiguration
from virtual_ecosystem.models.abiotic_simple.microclimate_simple import (
calculate_vapour_pressure_deficit,
run_simple_microclimate,
)
from virtual_ecosystem.models.abiotic_simple.model_config import (
AbioticSimpleBounds,
AbioticSimpleConfiguration,
AbioticSimpleConstants,
)
[docs]
class AbioticSimpleModel(
BaseModel,
model_name="abiotic_simple",
model_update_bounds=("1 day", "1 month"),
vars_required_for_init=(
"air_temperature_ref",
"atmospheric_co2_ref",
"atmospheric_pressure_ref",
"layer_heights",
"leaf_area_index",
"mean_annual_temperature",
"relative_humidity_ref",
"shortwave_absorption",
"wind_speed_ref",
),
vars_updated=(
"air_temperature",
"relative_humidity",
"vapour_pressure_deficit",
"soil_temperature",
"atmospheric_pressure",
"atmospheric_co2",
"wind_speed",
"net_radiation",
"vapour_pressure",
),
vars_required_for_update=(
"air_temperature_ref",
"relative_humidity_ref",
"vapour_pressure_deficit_ref",
"atmospheric_pressure_ref",
"atmospheric_co2_ref",
"wind_speed_ref",
"leaf_area_index",
"layer_heights",
"mean_annual_temperature",
"shortwave_absorption",
),
vars_populated_by_init=( # TODO move functionality from setup() to __init__
"soil_temperature",
"vapour_pressure",
"vapour_pressure_ref",
"vapour_pressure_deficit_ref",
"net_radiation",
"air_temperature",
"relative_humidity",
"vapour_pressure_deficit",
"atmospheric_pressure",
"atmospheric_co2",
"wind_speed",
"canopy_temperature",
"diurnal_temperature_range",
),
vars_populated_by_first_update=tuple(),
):
"""A class describing the abiotic simple model.
Args:
data: The data object to be used in the model.
core_components: The core components used across models.
model_configuration: Configuration object from the abiotic_simple model.
pyrealm_core_constants: Core constants for the pyrealm package.
static: Boolean flag indicating if the model should run in static mode.
"""
def __init__(
self,
data: Data,
core_components: CoreComponents,
model_configuration: AbioticSimpleConfiguration = AbioticSimpleConfiguration(),
pyrealm_core_constants: PyrealmCoreConst = PyrealmCoreConst(),
static: bool = False,
):
"""Abiotic simple init.
The init function is used only to define class attributes. Any logic should be
handled in :fun:`~virtual_ecosystem.abiotic_simple.abiotic_simple_model._setup`.
"""
super().__init__(data, core_components, static)
self.model_constants: AbioticSimpleConstants
"""Set of constants for the abiotic simple model"""
self.bounds: AbioticSimpleBounds
"""Upper and lower bounds for abiotic variables."""
self.pyrealm_core_constants: PyrealmCoreConst
"""Core constants for the pyrealm package."""
# Run the setup if the model is not in deep static mode
if self._run_setup:
self._setup(
model_configuration=model_configuration,
pyrealm_core_constants=pyrealm_core_constants,
)
def _setup(
self,
model_configuration: AbioticSimpleConfiguration,
pyrealm_core_constants: PyrealmCoreConst,
) -> None:
"""Function to set up the abiotic simple model.
This function initializes soil temperature for all soil layers and calculates
the reference vapour pressure deficit for all time steps. Both variables are
added directly to the self.data object.
TODO - Unlike the abiotic model this init does not populate initial values for
the air temperatures. This is something that might need to be reconsidered in
future.
See __init__ for argument descriptions.
"""
# Populate model attributes
self.model_constants = model_configuration.constants
self.bounds = model_configuration.bounds
self.pyrealm_core_constants = pyrealm_core_constants
# calculate vapour pressure deficit at reference height for all time steps
vapour_pressure_and_deficit = calculate_vapour_pressure_deficit(
temperature=self.data["air_temperature_ref"],
relative_humidity=self.data["relative_humidity_ref"],
pyrealm_core_constants=self.pyrealm_core_constants,
)
self.data["vapour_pressure_deficit_ref"] = vapour_pressure_and_deficit[
"vapour_pressure_deficit"
]
self.data["vapour_pressure_ref"] = vapour_pressure_and_deficit[
"vapour_pressure"
]
# This section performs a series of calculations to initialise atmospheric
# variables in the abiotic simple model which are then added to the data object.
output_variables = run_simple_microclimate(
data=self.data,
layer_structure=self.layer_structure,
time_index=0,
constants=self.model_constants,
core_constants=self.core_constants,
pyrealm_core_constants=pyrealm_core_constants,
bounds=self.bounds,
)
# Initialise canopy temperature, equilibrium with surrounding air, [C]
air_temp = output_variables["air_temperature"].copy()
canopy_temperature = self.layer_structure.from_template()
canopy_temperature[self.layer_structure.index_filled_canopy] = air_temp[
self.layer_structure.index_filled_canopy
]
canopy_temperature[self.layer_structure.index_surface_scalar] = air_temp[
self.layer_structure.index_surface_scalar
]
output_variables["canopy_temperature"] = canopy_temperature
# Add diurnal temperature range, [C]
diurnal_temperature_range = output_variables["air_temperature"].copy()
output_variables["diurnal_temperature_range"] = diurnal_temperature_range.where(
diurnal_temperature_range.isnull(),
other=5.0, # TODO add data when available
)
self.data.add_from_dict(output_dict=output_variables)
[docs]
@classmethod
def from_config(
cls,
data: Data,
configuration: CompiledConfiguration,
core_components: CoreComponents,
) -> AbioticSimpleModel:
"""Factory function to initialise the abiotic simple model from configuration.
This function unpacks the relevant information from the configuration file, and
then uses it to initialise the model. If any information from the config is
invalid rather than returning an initialised model instance an error is raised.
Args:
data: A :class:`~virtual_ecosystem.core.data.Data` instance.
configuration: A validated Virtual Ecosystem model configuration object.
core_components: The core components used across models.
"""
# Extract the validated model configuration from the complete compiled
# configuration
model_configuration: AbioticSimpleConfiguration = (
configuration.get_subconfiguration(
"abiotic_simple", AbioticSimpleConfiguration
)
)
# Core configuration
core_configuration: CoreConfiguration = configuration.get_subconfiguration(
"core", CoreConfiguration
)
LOGGER.info(
"Information required to initialise the abiotic simple model successfully "
"extracted."
)
return cls(
data=data,
core_components=core_components,
static=model_configuration.static,
model_configuration=model_configuration,
pyrealm_core_constants=core_configuration.pyrealm.core,
)
[docs]
def spinup(self) -> None:
"""Placeholder function to spin up the abiotic simple model."""
def _update(self, time_index: int, **kwargs: Any) -> None:
"""Function to update the abiotic simple model.
Args:
time_index: The index of the current time step in the data object.
**kwargs: Further arguments to the update method.
"""
# This section performs a series of calculations to update the variables in the
# abiotic model. The updated variables are then added to the data object.
output_variables = run_simple_microclimate(
data=self.data,
layer_structure=self.layer_structure,
time_index=time_index,
constants=self.model_constants,
core_constants=self.core_constants,
pyrealm_core_constants=self.pyrealm_core_constants,
bounds=self.bounds,
)
self.data.add_from_dict(output_dict=output_variables)
[docs]
def cleanup(self) -> None:
"""Placeholder function for abiotic model cleanup."""
