Average abiotic quantities over relevant soil layers

docs/source/using_the_ve/virtual_ecosystem_in_use.md

@@ -9,6 +9,8 @@ language_info:
   nbconvert_exporter: python
   pygments_lexer: ipython3
   version: 3.10.14
+execution:
+  timeout: 60
 jupytext:
   formats: md:myst
   text_representation:

tests/conftest.py

@@ -425,20 +425,28 @@ def dummy_carbon_data(fixture_core_components):
     lyr_str = fixture_core_components.layer_structure
 
     data["soil_moisture"] = lyr_str.from_template()
-    data["soil_moisture"][lyr_str.index_topsoil] = np.array(
-        [232.61550125, 196.88733175, 126.065797, 75.63195175]
+    data["soil_moisture"][lyr_str.index_all_soil] = np.array(
+        [
+            [232.61550125, 196.88733175, 126.065797, 75.63195175],
+            [66.248474, 194.91137, 121.29988, 52.04422],
+        ]
     )
 
     data["matric_potential"] = lyr_str.from_template()
-    data["matric_potential"][lyr_str.index_topsoil] = np.array(
-        [-3.0, -10.0, -250.0, -10000.0]
+    data["matric_potential"][lyr_str.index_all_soil] = np.array(
+        [[-3.0, -10.0, -250.0, -10000.0], [-2.8625, -8.978, -137.8, -8553.25]]
     )
 
     data["soil_temperature"] = lyr_str.from_template()
     data["soil_temperature"][lyr_str.index_all_soil] = np.array(
         [[35.0, 37.5, 40.0, 25.0], [22.5, 22.5, 22.5, 22.5]]
     )
 
+    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]
+    )[:, None]
+
     return data
 
 

tests/models/soil/test_env_factors.py

@@ -392,3 +392,40 @@ def test_calculate_leaching_rate(dummy_carbon_data, fixture_core_components):
     )
 
     assert np.allclose(expected_rate, actual_rate)
+
+
+@pytest.mark.parametrize(
+    "increased_depth,expected_soil_moisture",
+    [
+        pytest.param(
+            True,
+            [265.73973825, 294.34301675, 186.715737, 101.65406175],
+            id="increased depth",
+        ),
+        pytest.param(
+            False,
+            [116.307750625, 98.443665875, 63.0328985, 37.815975875],
+            id="normal depth",
+        ),
+    ],
+)
+def test_find_total_soil_moisture_for_microbially_active_depth(
+    dummy_carbon_data, fixture_core_components, increased_depth, expected_soil_moisture
+):
+    """Test that finding the total soil moisture works as expected."""
+    from virtual_ecosystem.models.soil.env_factors import (
+        find_total_soil_moisture_for_microbially_active_depth,
+    )
+
+    if increased_depth:
+        fixture_core_components.layer_structure.soil_layer_active_thickness = np.array(
+            [0.5, 0.25]
+        )
+        fixture_core_components.layer_structure.max_depth_of_microbial_activity = 0.75
+
+    actual_soil_moisture = find_total_soil_moisture_for_microbially_active_depth(
+        soil_moistures=dummy_carbon_data["soil_moisture"],
+        layer_structure=fixture_core_components.layer_structure,
+    )
+
+    assert np.allclose(actual_soil_moisture, expected_soil_moisture)

tests/models/soil/test_pools.py

@@ -46,29 +46,29 @@ def test_calculate_all_pool_updates(
     )
 
     change_in_pools = {
-        "soil_c_pool_lmwc": [0.1178918, 0.06892161, 0.2489136, 0.03425211],
-        "soil_c_pool_maom": [0.03734787, 0.00340136, 0.05447554, 0.07275546],
-        "soil_c_pool_bacteria": [-0.0543618, -0.0226100, -0.1185237, -0.0071954],
-        "soil_c_pool_fungi": [-0.00832584, -0.08196413, -0.02280126, -0.03266732],
-        "soil_c_pool_pom": [0.00021589, -0.02918772, -0.0247599, 0.00520792],
-        "soil_c_pool_necromass": [0.01141213, 0.09537438, 0.05971513, -0.0566864],
-        "soil_enzyme_pom_bacteria": [-5.4395e-4, -2.2795e-4, -1.19323e-3, -7.2103e-5],
-        "soil_enzyme_maom_bacteria": [-8.5406e-4, -2.7893e-4, -5.9417e-4, -1.093e-4],
-        "soil_enzyme_pom_fungi": [-0.00062555, -0.00012062, -0.00015158, -0.00010522],
-        "soil_enzyme_maom_fungi": [-2.07924e-4, -1.46441e-4, -8.79093e-5, -5.1289e-5],
-        "soil_n_pool_don": [0.00180422, 0.00529461, 0.00549027, 0.00240583],
-        "soil_n_pool_particulate": [-1.005585e-4, 4.899227e-5, 7.96678e-5, 4.723906e-6],
-        "soil_n_pool_necromass": [0.00948372, 0.00118049, 0.00843786, -0.00381522],
-        "soil_n_pool_maom": [0.00099458, 0.01041398, 0.01326356, 0.00772835],
-        "soil_n_pool_ammonium": [0.00075125671, 0.02001151359, 0.00030892, 0.000172988],
-        "soil_n_pool_nitrate": [-0.003295899, -0.003990944, -0.00105915, -0.000642911],
-        "soil_p_pool_dop": [2.02317351e-4, 1.64662024e-4, 2.0799736e-4, 9.62312501e-5],
-        "soil_p_pool_particulate": [6.77587e-6, -7.228e-6, -1.29451192e-6, 1.898709e-7],
-        "soil_p_pool_necromass": [0.00297253, 0.00350535, 0.00755271, 0.0008742],
-        "soil_p_pool_maom": [5.44660113e-4, -6.28584725e-5, 4.528133e-4, 3.0913116e-4],
+        "soil_c_pool_lmwc": [0.117290490, 6.96565834e-2, 0.247627966, 3.42642831e-2],
+        "soil_c_pool_maom": [3.7894322e-2, 4.8705495e-3, 5.6793727e-2, 7.2757916e-2],
+        "soil_c_pool_bacteria": [-4.24905e-2, -1.71527e-2, -8.74104e-2, -6.36844e-3],
+        "soil_c_pool_fungi": [-6.507313e-3, -6.211968e-2, -1.680347e-2, -2.891271e-2],
+        "soil_c_pool_pom": [3.73447584e-4, -2.62977207e-2, -2.214249e-2, 5.219897e-3],
+        "soil_c_pool_necromass": [-2.296284e-3, 6.9255912e-2, 2.2051989e-2, -6.1268e-2],
+        "soil_enzyme_pom_bacteria": [-5.44018e-4, -2.2835e-4, -1.19517e-3, -7.21028e-5],
+        "soil_enzyme_maom_bacteria": [-8.54122e-4, -2.79326e-4, -5.9611e-4, -1.0930e-4],
+        "soil_enzyme_pom_fungi": [-6.25574e-4, -1.24304e-4, -1.52398e-4, -1.05217e-4],
+        "soil_enzyme_maom_fungi": [-2.07949e-4, -1.50128e-4, -8.87255e-5, -5.12891e-5],
+        "soil_n_pool_don": [1.60498e-3, 5.24092e-3, 5.31639e-3, 2.42007e-3],
+        "soil_n_pool_particulate": [-8.93041e-5, 5.105645e-5, 9.035108e-5, 5.212779e-6],
+        "soil_n_pool_necromass": [6.917627e-3, -3.050687e-3, 1.431913e-3, -4.551887e-3],
+        "soil_n_pool_maom": [1.183733e-3, 1.082948e-2, 1.343197e-2, 7.72882e-3],
+        "soil_n_pool_ammonium": [9.35035e-4, 2.72159e-2, 5.31626e-4, 1.83631e-4],
+        "soil_n_pool_nitrate": [-3.053041e-3, -3.922566e-3, -1.050268e-3, -9.197065e-4],
+        "soil_p_pool_dop": [1.99425697e-4, 1.39742546e-4, 1.99748943e-4, 9.68009312e-5],
+        "soil_p_pool_particulate": [6.820884e-6, -6.40228e-6, -8.6718e-7, 2.094258e-7],
+        "soil_p_pool_necromass": [2.184141e-3, 2.644765e-3, 5.429799e-3, 7.286432e-4],
+        "soil_p_pool_maom": [5.47518e-4, -3.2943e-5, 4.6272e-4, 3.0915e-4],
         "soil_p_pool_primary": [-4.473516e-10, -1.222973e-9, -6.33411e-10, -1.3674e-10],
         "soil_p_pool_secondary": [-5.050797e-7, -2.77311e-6, -7.40324e-7, -2.187697e-7],
-        "soil_p_pool_labile": [-1.643259e-5, -0.000295103, -1.212019e-4, -1.313285e-6],
+        "soil_p_pool_labile": [-1.54646e-5, -2.773006e-4, -9.46854e-5, -2.062198e-6],
     }
 
     # Make order of pools object
@@ -78,7 +78,7 @@ def test_calculate_all_pool_updates(
 
     delta_pools = soil_pools.calculate_all_pool_updates(
         delta_pools_ordered=pool_order,
-        top_soil_layer_index=fixture_core_components.layer_structure.index_topsoil_scalar,
+        layer_structure=fixture_core_components.layer_structure,
         soil_moisture_capacity=CoreConsts.soil_moisture_capacity,
         top_soil_layer_thickness=fixture_core_components.layer_structure.soil_layer_thickness[
             0