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LayerStructure updates for abiotic_simple #448

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Jun 21, 2024
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LayerStructure updates for abiotic_simple #448

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b4548c0
Initial LayerStructure updates for abiotic_simple - NO VERIFY
davidorme Jun 18, 2024
25ce1b2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2024
565d10d
Merge branch '421-additional-information-in-layerstructure' into 446-…
davidorme Jun 19, 2024
184c762
Minor tweaks and fixing bugs
davidorme Jun 19, 2024
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61 changes: 21 additions & 40 deletions tests/models/abiotic_simple/test_abiotic_simple_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,48 +160,30 @@ def test_generate_abiotic_simple_model(
log_check(caplog, expected_log_entries)


def test_setup(dummy_climate_data_varying_canopy, fixture_empty_array):
def test_setup(dummy_climate_data_varying_canopy, fixture_core_components):
"""Test set up and update."""
from virtual_ecosystem.core.config import Config
from virtual_ecosystem.core.core_components import CoreComponents

from virtual_ecosystem.models.abiotic_simple.abiotic_simple_model import (
AbioticSimpleModel,
)

# Build the config object and core components
config = Config(
cfg_strings="[core.timing]\nupdate_interval = '1 week'\n[abiotic_simple]\n"
)
core_components = CoreComponents(config)

# initialise model
model = AbioticSimpleModel.from_config(
model = AbioticSimpleModel(
data=dummy_climate_data_varying_canopy,
core_components=core_components,
config=config,
core_components=fixture_core_components,
)

model.setup()
exp_soil_temp = DataArray(
np.full((15, 3), np.nan),
dims=["layers", "cell_id"],
coords={
"layers": np.arange(0, 15),
"layer_roles": (
"layers",
core_components.layer_structure.layer_roles,
),
"cell_id": [0, 1, 2],
},
)

exp_soil_temp = fixture_core_components.layer_structure.from_template()
xr.testing.assert_allclose(model.data["soil_temperature"], exp_soil_temp)

xr.testing.assert_allclose(
model.data["vapour_pressure_deficit_ref"],
DataArray(
np.full((3, 3), 0.141727),
np.full((4, 3), 0.141727),
dims=["cell_id", "time_index"],
coords={"cell_id": [0, 1, 2]},
coords={"cell_id": [0, 1, 2, 3]},
),
)

Expand All @@ -218,20 +200,19 @@ def test_setup(dummy_climate_data_varying_canopy, fixture_empty_array):
]:
assert var in model.data

exp_air_temp = fixture_empty_array.copy()
exp_air_temp[[0, 1, 2, 3, 11, 12], :] = [
[30.0, 30.0, 30.0],
[29.91965, 29.946434, 29.973217],
[29.414851, 29.609901, np.nan],
[28.551891, np.nan, np.nan],
[26.19, 27.46, 28.73],
[22.81851, 25.21234, 27.60617],
exp_air_temp = fixture_core_components.layer_structure.from_template()
exp_air_temp[[0, 1, 2, 3, 11], :] = [
[30.0, 30.0, 30.0, 30.0],
[29.91965, 29.946434, 29.973217, 29.973217],
[29.414851, 29.609901, np.nan, np.nan],
[28.551891, np.nan, np.nan, np.nan],
[22.81851, 25.21234, 27.60617, 27.60617],
]
xr.testing.assert_allclose(model.data["air_temperature"], exp_air_temp)

exp_soil_temp = fixture_empty_array.copy()
exp_soil_temp[[13, 14], :] = [[20.712458, 21.317566, 21.922674], [20.0, 20.0, 20.0]]
exp_soil_temp = fixture_core_components.layer_structure.from_template()
exp_soil_temp[[12, 13], :] = [
[20.712458, 21.317566, 21.922674, 21.922674],
[20.0, 20.0, 20.0, 20.0],
]
xr.testing.assert_allclose(model.data["soil_temperature"], exp_soil_temp)

xr.testing.assert_allclose(
dummy_climate_data_varying_canopy["air_temperature"], exp_air_temp
)
163 changes: 70 additions & 93 deletions tests/models/abiotic_simple/test_microclimate.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,7 @@
from xarray import DataArray


def test_log_interpolation(
dummy_climate_data, fixture_core_components, fixture_empty_array
):
def test_log_interpolation(dummy_climate_data, fixture_core_components):
"""Test interpolation for temperature and humidity non-negative."""

from virtual_ecosystem.models.abiotic_simple.microclimate import log_interpolation
Expand All @@ -20,38 +18,38 @@ def test_log_interpolation(
data=data,
reference_data=data["air_temperature_ref"].isel(time_index=0),
leaf_area_index_sum=leaf_area_index_sum,
layer_roles=fixture_core_components.layer_structure.layer_roles,
layer_structure=fixture_core_components.layer_structure,
layer_heights=data["layer_heights"],
upper_bound=80,
lower_bound=0,
gradient=-2.45,
)

exp_air_temp = fixture_empty_array.copy()
t_vals = [30.0, 29.844995, 28.87117, 27.206405, 22.65, 16.145945]
exp_air_temp.T[..., [0, 1, 2, 3, 11, 12]] = t_vals
exp_air_temp = fixture_core_components.layer_structure.from_template()
t_vals = [30.0, 29.844995, 28.87117, 27.206405, 16.145945]
exp_air_temp.T[..., [0, 1, 2, 3, 11]] = t_vals
xr.testing.assert_allclose(result, exp_air_temp)

# relative humidity
result_hum = log_interpolation(
data=data,
reference_data=data["relative_humidity_ref"].isel(time_index=0),
leaf_area_index_sum=leaf_area_index_sum,
layer_roles=fixture_core_components.layer_structure.layer_roles,
layer_structure=fixture_core_components.layer_structure,
layer_heights=data["layer_heights"],
upper_bound=100,
lower_bound=0,
gradient=5.4,
)

exp_humidity = fixture_empty_array.copy()
humidity_vals = [90.0, 90.341644, 92.488034, 96.157312, 100.0, 100.0]
exp_humidity.T[..., [0, 1, 2, 3, 11, 12]] = humidity_vals
exp_humidity = fixture_core_components.layer_structure.from_template()
humidity_vals = [90.0, 90.341644, 92.488034, 96.157312, 100.0]
exp_humidity.T[..., [0, 1, 2, 3, 11]] = humidity_vals
xr.testing.assert_allclose(result_hum, exp_humidity)


def test_varying_canopy_log_interpolation(
dummy_climate_data_varying_canopy, fixture_core_components, fixture_empty_array
dummy_climate_data_varying_canopy, fixture_core_components
):
"""Test interpolation for temperature and humidity non-negative."""

Expand All @@ -65,21 +63,20 @@ def test_varying_canopy_log_interpolation(
data=data,
reference_data=data["air_temperature_ref"].isel(time_index=0),
leaf_area_index_sum=leaf_area_index_sum,
layer_roles=fixture_core_components.layer_structure.layer_roles,
layer_structure=fixture_core_components.layer_structure,
layer_heights=data["layer_heights"],
upper_bound=80,
lower_bound=0,
gradient=-2.45,
)

exp_air_temp = fixture_empty_array.copy()
exp_air_temp[[0, 1, 2, 3, 11, 12], :] = [
[30.0, 30.0, 30.0],
[29.844995, 29.896663, 29.948332],
[28.87117, 29.247446, np.nan],
[27.206405, np.nan, np.nan],
[22.65, 25.1, 27.55],
[16.145945, 20.763963, 25.381982],
exp_air_temp = fixture_core_components.layer_structure.from_template()
exp_air_temp[[0, 1, 2, 3, 11], :] = [
[30.0, 30.0, 30.0, 30.0],
[29.844995, 29.896663, 29.948332, 29.948332],
[28.87117, 29.247446, np.nan, np.nan],
[27.206405, np.nan, np.nan, np.nan],
[16.145945, 20.763963, 25.381982, 25.381982],
]
xr.testing.assert_allclose(result, exp_air_temp)

Expand All @@ -103,27 +100,28 @@ def test_calculate_saturation_vapour_pressure(dummy_climate_data):
)

exp_output = DataArray(
[1.41727, 1.41727, 1.41727],
np.repeat(1.41727, 4),
dims=["cell_id"],
coords={"cell_id": [0, 1, 2]},
coords={"cell_id": [0, 1, 2, 3]},
)
xr.testing.assert_allclose(result, exp_output)


def test_calculate_vapour_pressure_deficit(fixture_empty_array):
def test_calculate_vapour_pressure_deficit(fixture_core_components):
"""Test calculation of VPD."""

from virtual_ecosystem.models.abiotic_simple.constants import AbioticSimpleConsts
from virtual_ecosystem.models.abiotic_simple.microclimate import (
calculate_vapour_pressure_deficit,
)

temperature = fixture_empty_array.copy()
t_vals = [30.0, 29.844995, 28.87117, 27.206405, 22.65, 16.145945]
temperature.T[..., [0, 1, 2, 3, 11, 12]] = t_vals
rel_humidity = fixture_empty_array.copy()
humidity_vals = [90.0, 90.341644, 92.488034, 96.157312, 100.0, 100.0]
rel_humidity.T[..., [0, 1, 2, 3, 11, 12]] = humidity_vals
temperature = fixture_core_components.layer_structure.from_template()
t_vals = [30.0, 29.844995, 28.87117, 27.206405, 16.145945]
temperature.T[..., [0, 1, 2, 3, 11]] = t_vals

rel_humidity = fixture_core_components.layer_structure.from_template()
humidity_vals = [90.0, 90.341644, 92.488034, 96.157312, 100.0]
rel_humidity.T[..., [0, 1, 2, 3, 11]] = humidity_vals

constants = AbioticSimpleConsts()
result = calculate_vapour_pressure_deficit(
Expand All @@ -133,15 +131,15 @@ def test_calculate_vapour_pressure_deficit(fixture_empty_array):
constants.saturation_vapour_pressure_factors
),
)
exp_output = fixture_empty_array.copy()
vpd_vals = [0.141727, 0.136357, 0.103501, 0.050763, 0.0, 0.0]
exp_output.T[..., [0, 1, 2, 3, 11, 12]] = vpd_vals
exp_output = fixture_core_components.layer_structure.from_template()
vpd_vals = [0.141727, 0.136357, 0.103501, 0.050763, 0.0]
exp_output.T[..., [0, 1, 2, 3, 11]] = vpd_vals

xr.testing.assert_allclose(result["vapour_pressure_deficit"], exp_output)


def test_varying_canopy_calculate_vapour_pressure_deficit(
fixture_empty_array, dummy_climate_data_varying_canopy
fixture_core_components, dummy_climate_data_varying_canopy
):
"""Test calculation of VPD with different number of canopy layers."""

Expand All @@ -159,21 +157,18 @@ def test_varying_canopy_calculate_vapour_pressure_deficit(
constants.saturation_vapour_pressure_factors
),
)
exp_output = fixture_empty_array.copy()
exp_output[[0, 1, 2, 3, 11, 12], :] = [
[0.141727, 0.141727, 0.141727],
[0.136357, 0.136357, 0.136357],
[0.103501, 0.103501, np.nan],
[0.050763, np.nan, np.nan],
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
exp_output = fixture_core_components.layer_structure.from_template()
exp_output[[0, 1, 2, 3, 11], :] = [
[0.141727, 0.141727, 0.141727, 0.141727],
[0.136357, 0.136357, 0.136357, 0.136357],
[0.103501, 0.103501, np.nan, np.nan],
[0.050763, np.nan, np.nan, np.nan],
[0.0, 0.0, 0.0, 0.0],
]
xr.testing.assert_allclose(result["vapour_pressure_deficit"], exp_output)


def test_run_microclimate(
dummy_climate_data, fixture_core_components, fixture_empty_array
):
def test_run_microclimate(dummy_climate_data, fixture_core_components):
"""Test interpolation of all variables."""

from virtual_ecosystem.models.abiotic_simple.constants import (
Expand All @@ -186,37 +181,29 @@ def test_run_microclimate(

result = run_microclimate(
data=data,
layer_roles=fixture_core_components.layer_structure.layer_roles,
layer_structure=fixture_core_components.layer_structure,
time_index=0,
constants=AbioticSimpleConsts(),
bounds=AbioticSimpleBounds(),
)

exp_air_temp = fixture_empty_array.copy()
exp_air_temp[[0, 1, 2, 3, 11, 12], :] = [
[30.0, 30.0, 30.0],
[29.91965, 29.91965, 29.91965],
[29.414851, 29.414851, 29.414851],
[28.551891, 28.551891, 28.551891],
[26.19, 26.19, 26.19],
[22.81851, 22.81851, 22.81851],
]
exp_air_temp = fixture_core_components.layer_structure.from_template()
exp_air_temp[[0, 1, 2, 3, 11]] = np.array(
[30.0, 29.91965, 29.414851, 28.551891, 22.81851]
)[:, None]
xr.testing.assert_allclose(result["air_temperature"], exp_air_temp)

exp_soil_temp = fixture_empty_array.copy()
exp_soil_temp[[13, 14], :] = [[20.712458, 20.712458, 20.712458], [20.0, 20.0, 20.0]]
exp_soil_temp = fixture_core_components.layer_structure.from_template()
exp_soil_temp[[12, 13]] = np.array([20.712458, 20.0])[:, None]
xr.testing.assert_allclose(result["soil_temperature"], exp_soil_temp)

soil_values = DataArray(np.full((2, 3), np.nan), dims=["layers", "cell_id"])
pressure_values = DataArray(np.full((13, 3), 96.0), dims=["layers", "cell_id"])
exp_pressure = xr.concat(
[pressure_values, soil_values], dim="layers"
).assign_coords(data["layer_heights"].coords)
exp_pressure = fixture_core_components.layer_structure.from_template()
exp_pressure[np.arange(0, 12)] = 96
xr.testing.assert_allclose(result["atmospheric_pressure"], exp_pressure)


def test_run_microclimate_varying_canopy(
dummy_climate_data_varying_canopy, fixture_core_components, fixture_empty_array
dummy_climate_data_varying_canopy, fixture_core_components
):
"""Test interpolation of all variables with varying canopy arrays."""

Expand All @@ -230,36 +217,35 @@ def test_run_microclimate_varying_canopy(

result = run_microclimate(
data=data,
layer_roles=fixture_core_components.layer_structure.layer_roles,
layer_structure=fixture_core_components.layer_structure,
time_index=0,
constants=AbioticSimpleConsts(),
bounds=AbioticSimpleBounds(),
)

exp_air_temp = fixture_empty_array.copy()
exp_air_temp[[0, 1, 2, 3, 11, 12], :] = [
[30.0, 30.0, 30.0],
[29.91965, 29.946434, 29.973217],
[29.414851, 29.609901, np.nan],
[28.551891, np.nan, np.nan],
[26.19, 27.46, 28.73],
[22.81851, 25.21234, 27.60617],
exp_air_temp = fixture_core_components.layer_structure.from_template()
exp_air_temp[[0, 1, 2, 3, 11], :] = [
[30.0, 30.0, 30.0, 30.0],
[29.91965, 29.946434, 29.973217, 29.973217],
[29.414851, 29.609901, np.nan, np.nan],
[28.551891, np.nan, np.nan, np.nan],
[22.81851, 25.21234, 27.60617, 27.60617],
]
xr.testing.assert_allclose(result["air_temperature"], exp_air_temp)

exp_soil_temp = fixture_empty_array.copy()
exp_soil_temp[[13, 14], :] = [[20.712458, 21.317566, 21.922674], [20.0, 20.0, 20.0]]
exp_soil_temp = fixture_core_components.layer_structure.from_template()
exp_soil_temp[[12, 13], :] = [
[20.712458, 21.317566, 21.922674, 21.922674],
[20.0, 20.0, 20.0, 20.0],
]
xr.testing.assert_allclose(result["soil_temperature"], exp_soil_temp)

soil_values = DataArray(np.full((2, 3), np.nan), dims=["layers", "cell_id"])
pressure_values = DataArray(np.full((13, 3), 96.0), dims=["layers", "cell_id"])
exp_pressure = xr.concat(
[pressure_values, soil_values], dim="layers"
).assign_coords(data["layer_heights"].coords)
exp_pressure = fixture_core_components.layer_structure.from_template()
exp_pressure[np.arange(0, 12)] = 96
xr.testing.assert_allclose(result["atmospheric_pressure"], exp_pressure)


def test_interpolate_soil_temperature(dummy_climate_data):
def test_interpolate_soil_temperature(dummy_climate_data, fixture_core_components):
"""Test soil temperature interpolation."""

from virtual_ecosystem.models.abiotic_simple.microclimate import (
Expand All @@ -268,26 +254,17 @@ def test_interpolate_soil_temperature(dummy_climate_data):

data = dummy_climate_data

surface_temperature = DataArray([22.0, 22.0, 22.0], dims="cell_id")
surface_temperature = DataArray([22.0, 22.0, 22.0, 22.0], dims="cell_id")
result = interpolate_soil_temperature(
layer_heights=data["layer_heights"],
surface_temperature=surface_temperature,
mean_annual_temperature=data["mean_annual_temperature"],
layer_structure=fixture_core_components.layer_structure,
upper_bound=50.0,
lower_bound=-10.0,
)

exp_output = DataArray(
[
[20.505557, 20.505557, 20.505557],
[20.0, 20.0, 20.0],
],
dims=["layers", "cell_id"],
coords={
"layers": [13, 14],
"layer_roles": ("layers", ["soil", "soil"]),
"cell_id": [0, 1, 2],
},
)
exp_output = fixture_core_components.layer_structure.from_template()
exp_output[[12, 13]] = np.array([20.505557, 20.0])[:, None]

xr.testing.assert_allclose(result, exp_output)
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