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Merged
vgro merged 3 commits into from
Jul 7, 2025
Merged

return mean vertical flow for all layers #930

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bcb69ef
return mean vertical flow for all layers
vgro Jul 3, 2025
348a337
Merge branch 'develop' into 891-return-vertical-flow-as-3d-variable
vgro Jul 7, 2025
b68ecc9
Merge branch 'develop' into 891-return-vertical-flow-as-3d-variable
vgro Jul 7, 2025
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5 changes: 4 additions & 1 deletion tests/models/hydrology/test_hydrology_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -311,6 +311,10 @@ def test_setup(
[-56.432398, -56.438614, -56.44538, -56.442609],
[-217.596626, -217.596626, -217.596626, -217.596626],
],
"vertical_flow": [
[0.00017, 0.00017, 0.00017, 0.00017],
[0.000526, 0.000526, 0.000526, 0.000526],
],
}

for var_name, expected_vals in expected_2d.items():
Expand All @@ -326,7 +330,6 @@ def test_setup(

# Test one dimensional variables
expected_1d = {
"vertical_flow": [6.916e-05, 6.916e-05, 6.916e-05, 6.916e-05],
"total_river_discharge": [0, 0, 67002, 22095],
"surface_runoff": [20.343781, 20.66599, 20.896484, 20.443394],
"surface_runoff_accumulated": [0, 0, 1470, 330],
Expand Down
6 changes: 5 additions & 1 deletion tests/models/soil/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,6 @@ def dummy_carbon_data(fixture_core_components):
"litter_C_mineralisation_rate": [0.00212106, 0.00106053, 0.00049000, 0.0055],
"litter_N_mineralisation_rate": [3.5351e-5, 7.0702e-5, 0.000183, 1.63333e-5],
"litter_P_mineralisation_rate": [7.32e-6, 1.41404e-6, 2.82808e-6, 6.53332e-7],
"vertical_flow": [0.1, 0.5, 2.5, 1.59],
"plant_symbiote_carbon_supply": [0.01, 0.25, 0.0075, 0.0047],
"root_carbohydrate_exudation": [0.025, 0.01, 0.05, 0.0025],
"plant_ammonium_uptake": [5.0e-5, 2.5e-5, 1.0e-5, 1.0e-4],
Expand Down Expand Up @@ -95,6 +94,11 @@ def dummy_carbon_data(fixture_core_components):
[[35.0, 37.5, 40.0, 25.0], [22.5, 22.5, 22.5, 22.5]]
)

data["vertical_flow"] = lyr_str.from_template()
data["vertical_flow"][lyr_str.index_all_soil] = np.array(
[[0.1, 0.5, 2.5, 1.59], [0.1, 0.5, 2.5, 1.59]]
)

data["air_temperature"] = lyr_str.from_template()
data["air_temperature"][lyr_str.index_filled_atmosphere] = np.array(
[30.0, 29.844995, 28.87117, 27.206405, 16.145945]
Expand Down
8 changes: 6 additions & 2 deletions tests/models/soil/test_pools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -347,7 +347,9 @@ def test_calculate_nutrient_leaching(dummy_carbon_data, fixture_core_components)
soil_n_pool_ammonium=dummy_carbon_data["soil_n_pool_ammonium"],
soil_n_pool_nitrate=dummy_carbon_data["soil_n_pool_nitrate"],
soil_p_pool_labile=dummy_carbon_data["soil_p_pool_labile"],
vertical_flow_rate=dummy_carbon_data["vertical_flow"].to_numpy(),
vertical_flow_rate=dummy_carbon_data["vertical_flow"][
fixture_core_components.layer_structure.index_topsoil_scalar
].to_numpy(),
soil_moisture=dummy_carbon_data["soil_moisture"][
fixture_core_components.layer_structure.index_topsoil_scalar
].to_numpy(),
Expand Down Expand Up @@ -383,7 +385,9 @@ def test_negative_nutrient_leaching(dummy_carbon_data, fixture_core_components):
soil_n_pool_ammonium=ammonium_data,
soil_n_pool_nitrate=nitrate_data,
soil_p_pool_labile=labile_p_data,
vertical_flow_rate=dummy_carbon_data["vertical_flow"].to_numpy(),
vertical_flow_rate=dummy_carbon_data["vertical_flow"][
fixture_core_components.layer_structure.index_topsoil_scalar
].to_numpy(),
soil_moisture=dummy_carbon_data["soil_moisture"][
fixture_core_components.layer_structure.index_topsoil_scalar
].to_numpy(),
Expand Down
8 changes: 1 addition & 7 deletions virtual_ecosystem/models/hydrology/hydrology_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -741,12 +741,6 @@ def _update(self, time_index: int, **kwargs: Any) -> None:
daily_lists["canopy_evaporation"], axis=0
)

soil_hydrology["vertical_flow"] = DataArray( # vertical flow through top soil
np.mean(np.stack(daily_lists["vertical_flow"][0], axis=1), axis=1),
dims="cell_id",
coords={"cell_id": self.grid.cell_id},
)

for var in ["river_discharge_rate", "aerodynamic_resistance_surface"]:
soil_hydrology[var] = DataArray(
np.mean(np.stack(daily_lists[var], axis=1), axis=1),
Expand All @@ -756,7 +750,7 @@ def _update(self, time_index: int, **kwargs: Any) -> None:

# Return mean soil moisture, [mm], and soil matric potential, [kPa], and add
# atmospheric layers (nan)
for var in ["soil_moisture", "matric_potential"]:
for var in ["soil_moisture", "matric_potential", "vertical_flow"]:
soil_hydrology[var] = self.layer_structure.from_template()
soil_hydrology[var][self.layer_structure.index_all_soil] = np.mean(
np.stack(daily_lists[var], axis=0), axis=0
Expand Down
4 changes: 3 additions & 1 deletion virtual_ecosystem/models/soil/pools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -508,7 +508,9 @@ def calculate_all_pool_updates(
soil_n_pool_ammonium=self.pools.soil_n_pool_ammonium,
soil_n_pool_nitrate=self.pools.soil_n_pool_nitrate,
soil_p_pool_labile=self.pools.soil_p_pool_labile,
vertical_flow_rate=self.data["vertical_flow"].to_numpy(),
vertical_flow_rate=self.data["vertical_flow"][
layer_structure.index_topsoil_scalar
].to_numpy(),
soil_moisture=soil_moisture,
constants=self.constants,
)
Expand Down