Add animal consumption of litter

tests/models/animals/conftest.py

@@ -77,6 +77,25 @@ def animal_data_for_model_instance(fixture_core_components):
     )
     data["air_temperature"] = air_temperature
 
+    # Adding in litter variables as these are also needed now
+    litter_pools = DataArray(np.full(grid.n_cells, fill_value=1.5), dims="cell_id")
+    litter_ratios = DataArray(np.full(grid.n_cells, fill_value=25.5), dims="cell_id")
+    data["litter_pool_above_metabolic"] = litter_pools
+    data["litter_pool_above_structural"] = litter_pools
+    data["litter_pool_woody"] = litter_pools
+    data["litter_pool_below_metabolic"] = litter_pools
+    data["litter_pool_below_structural"] = litter_pools
+    data["c_n_ratio_above_metabolic"] = litter_ratios
+    data["c_n_ratio_above_structural"] = litter_ratios
+    data["c_n_ratio_woody"] = litter_ratios
+    data["c_n_ratio_below_metabolic"] = litter_ratios
+    data["c_n_ratio_below_structural"] = litter_ratios
+    data["c_p_ratio_above_metabolic"] = litter_ratios
+    data["c_p_ratio_above_structural"] = litter_ratios
+    data["c_p_ratio_woody"] = litter_ratios
+    data["c_p_ratio_below_metabolic"] = litter_ratios
+    data["c_p_ratio_below_structural"] = litter_ratios
+
     return data
 
 
@@ -310,3 +329,50 @@ def animal_list_instance(herbivore_functional_group_instance, constants_instance
         )
         for idx in range(3)
     ]
+
+
+@pytest.fixture
+def litter_data_instance(fixture_core_components):
+    """Creates a dummy litter data for use in tests."""
+
+    from virtual_ecosystem.core.data import Data
+
+    # Setup the data object with four cells.
+    data = Data(fixture_core_components.grid)
+
+    # The required data is now added. This is basically the 5 litter pool sizes and
+    # stoichiometric ratios
+    data_values = {
+        "litter_pool_above_metabolic": [0.3, 0.15, 0.07, 0.07],
+        "litter_pool_above_structural": [0.5, 0.25, 0.09, 0.09],
+        "litter_pool_woody": [4.7, 11.8, 7.3, 7.3],
+        "litter_pool_below_metabolic": [0.4, 0.37, 0.07, 0.07],
+        "litter_pool_below_structural": [0.6, 0.31, 0.02, 0.02],
+        "c_n_ratio_above_metabolic": [7.3, 8.7, 10.1, 9.8],
+        "c_n_ratio_above_structural": [37.5, 43.2, 45.8, 50.2],
+        "c_n_ratio_woody": [55.5, 63.3, 47.3, 59.1],
+        "c_n_ratio_below_metabolic": [10.7, 11.3, 15.2, 12.4],
+        "c_n_ratio_below_structural": [50.5, 55.6, 73.1, 61.2],
+        "c_p_ratio_above_metabolic": [57.3, 68.7, 100.1, 95.8],
+        "c_p_ratio_above_structural": [337.5, 473.2, 415.8, 570.2],
+        "c_p_ratio_woody": [555.5, 763.3, 847.3, 599.1],
+        "c_p_ratio_below_metabolic": [310.7, 411.3, 315.2, 412.4],
+        "c_p_ratio_below_structural": [550.5, 595.6, 773.1, 651.2],
+    }
+
+    for var_name, var_values in data_values.items():
+        data[var_name] = DataArray(var_values, dims=["cell_id"])
+
+    return data
+
+
+@pytest.fixture
+def litter_pool_instance(litter_data_instance):
+    """Fixture for a litter pool class to be used in tests."""
+    from virtual_ecosystem.models.animal.decay import LitterPool
+
+    return LitterPool(
+        pool_name="above_metabolic",
+        data=litter_data_instance,
+        cell_area=10000,
+    )

tests/models/animals/test_animal_model.py

@@ -175,6 +175,11 @@ def test_animal_model_initialization(
                 (INFO, "Adding data array for 'decomposed_carcasses_carbon'"),
                 (INFO, "Adding data array for 'decomposed_carcasses_nitrogen'"),
                 (INFO, "Adding data array for 'decomposed_carcasses_phosphorus'"),
+                (INFO, "Adding data array for 'litter_consumption_above_metabolic'"),
+                (INFO, "Adding data array for 'litter_consumption_above_structural'"),
+                (INFO, "Adding data array for 'litter_consumption_woody'"),
+                (INFO, "Adding data array for 'litter_consumption_below_metabolic'"),
+                (INFO, "Adding data array for 'litter_consumption_below_structural'"),
             ),
             id="success",
         ),
@@ -285,6 +290,126 @@ def test_update_method_time_index_argument(
     assert True
 
 
+def test_populate_litter_pools(
+    litter_data_instance,
+    fixture_core_components,
+    functional_group_list_instance,
+    constants_instance,
+):
+    """Test that function to populate animal consumable litter pool works properly."""
+    from virtual_ecosystem.models.animal.animal_model import AnimalModel
+
+    model = AnimalModel(
+        data=litter_data_instance,
+        core_components=fixture_core_components,
+        functional_groups=functional_group_list_instance,
+        model_constants=constants_instance,
+    )
+
+    litter_pools = model.populate_litter_pools()
+    # Check that all five pools have been populated, with the correct values
+    pool_names = [
+        "above_metabolic",
+        "above_structural",
+        "woody",
+        "below_metabolic",
+        "below_structural",
+    ]
+    for pool_name in pool_names:
+        assert np.allclose(
+            litter_pools[pool_name].mass_current,
+            litter_data_instance[f"litter_pool_{pool_name}"]
+            * fixture_core_components.grid.cell_area,
+        )
+        assert np.allclose(
+            litter_pools[pool_name].c_n_ratio,
+            litter_data_instance[f"c_n_ratio_{pool_name}"],
+        )
+        assert np.allclose(
+            litter_pools[pool_name].c_p_ratio,
+            litter_data_instance[f"c_p_ratio_{pool_name}"],
+        )
+
+
+def test_calculate_total_litter_consumption(
+    litter_data_instance,
+    fixture_core_components,
+    functional_group_list_instance,
+    constants_instance,
+):
+    """Test that calculation of total consumption of litter by animals is correct."""
+    from copy import deepcopy
+
+    from virtual_ecosystem.models.animal.animal_model import AnimalModel
+    from virtual_ecosystem.models.animal.decay import LitterPool
+
+    model = AnimalModel(
+        data=litter_data_instance,
+        core_components=fixture_core_components,
+        functional_groups=functional_group_list_instance,
+        model_constants=constants_instance,
+    )
+
+    new_data = deepcopy(litter_data_instance)
+    # Add new values for each pool
+    new_data["litter_pool_above_metabolic"] = (
+        litter_data_instance["litter_pool_above_metabolic"] - 0.03
+    )
+    new_data["litter_pool_above_structural"] = (
+        litter_data_instance["litter_pool_above_structural"] - 0.04
+    )
+    new_data["litter_pool_woody"] = litter_data_instance["litter_pool_woody"] - 1.2
+    new_data["litter_pool_below_metabolic"] = (
+        litter_data_instance["litter_pool_below_metabolic"] - 0.06
+    )
+    new_data["litter_pool_below_structural"] = (
+        litter_data_instance["litter_pool_below_structural"] - 0.01
+    )
+
+    # Make an updated set of litter pools
+    pool_names = [
+        "above_metabolic",
+        "above_structural",
+        "woody",
+        "below_metabolic",
+        "below_structural",
+    ]
+    new_litter_pools = {
+        pool_name: LitterPool(
+            pool_name=pool_name,
+            data=new_data,
+            cell_area=fixture_core_components.grid.cell_area,
+        )
+        for pool_name in pool_names
+    }
+
+    # Calculate litter consumption
+    consumption = model.calculate_total_litter_consumption(
+        litter_pools=new_litter_pools
+    )
+
+    assert np.allclose(
+        consumption["litter_consumption_above_metabolic"],
+        0.03 * np.ones(4),
+    )
+    assert np.allclose(
+        consumption["litter_consumption_above_structural"],
+        0.04 * np.ones(4),
+    )
+    assert np.allclose(
+        consumption["litter_consumption_woody"],
+        1.2 * np.ones(4),
+    )
+    assert np.allclose(
+        consumption["litter_consumption_below_metabolic"],
+        0.06 * np.ones(4),
+    )
+    assert np.allclose(
+        consumption["litter_consumption_below_structural"],
+        0.01 * np.ones(4),
+    )
+
+
 def test_calculate_soil_additions(functional_group_list_instance):
     """Test that soil additions from animal model are calculated correctly."""
 

tests/models/animals/test_decay.py

@@ -101,3 +101,49 @@ def test_find_decay_consumed_split(decay_rate, scavenging_rate, expected_split):
     )
 
     assert actual_split == expected_split
+
+
+class TestLitterPool:
+    """Test LitterPool class."""
+
+    def test_get_eaten(self, litter_pool_instance, herbivore_cohort_instance):
+        """Test the get_eaten method for LitterPool."""
+        import pytest
+
+        consumed_mass = 50.0  # Define a mass to be consumed for the test
+        cell_id = 3
+        initial_mass_current = litter_pool_instance.mass_current[cell_id]
+        initial_c_n_ratio = litter_pool_instance.c_n_ratio[cell_id]
+        initial_c_p_ratio = litter_pool_instance.c_p_ratio[cell_id]
+
+        actual_mass_gain = litter_pool_instance.get_eaten(
+            consumed_mass, herbivore_cohort_instance, grid_cell_id=cell_id
+        )
+
+        # Check if the plant mass has been correctly reduced
+        assert litter_pool_instance.mass_current[cell_id] == pytest.approx(
+            initial_mass_current
+            - (
+                consumed_mass
+                * herbivore_cohort_instance.functional_group.mechanical_efficiency
+            )
+        ), "Litter mass should be reduced by the consumed amount."
+
+        # Check if the actual mass gain matches the expected value after
+        # efficiency adjustments
+        expected_mass_gain = (
+            consumed_mass
+            * herbivore_cohort_instance.functional_group.mechanical_efficiency
+            * herbivore_cohort_instance.functional_group.conversion_efficiency
+        )
+        assert actual_mass_gain == pytest.approx(
+            expected_mass_gain
+        ), "Actual mass gain should match expected value after efficiency adjustments."
+
+        # Check that carbon:nitrogen and carbon:phosphorus ratios remain unchanged
+        assert initial_c_n_ratio == pytest.approx(
+            litter_pool_instance.c_n_ratio[cell_id]
+        )
+        assert initial_c_p_ratio == pytest.approx(
+            litter_pool_instance.c_p_ratio[cell_id]
+        )

tests/models/litter/conftest.py

@@ -41,11 +41,11 @@ def dummy_litter_data(fixture_core_components):
     # manner. The repeated fourth value is simply to adapt three hand validated examples
     # to the shared fixture core components grid
     pool_values = {
-        "litter_pool_above_metabolic": [0.3, 0.15, 0.07, 0.07],
-        "litter_pool_above_structural": [0.5, 0.25, 0.09, 0.09],
-        "litter_pool_woody": [4.7, 11.8, 7.3, 7.3],
-        "litter_pool_below_metabolic": [0.4, 0.37, 0.07, 0.07],
-        "litter_pool_below_structural": [0.6, 0.31, 0.02, 0.02],
+        "litter_pool_above_metabolic": [0.319785, 0.161631, 0.086129, 0.093456],
+        "litter_pool_above_structural": [0.52097, 0.26609, 0.10019, 0.09988],
+        "litter_pool_woody": [5.1773833, 12.185701, 7.673456, 7.462192],
+        "litter_pool_below_metabolic": [0.410373, 0.375794, 0.080181, 0.083494],
+        "litter_pool_below_structural": [0.613547, 0.321674, 0.032738, 0.029168],
         "lignin_above_structural": [0.5, 0.1, 0.7, 0.7],
         "lignin_woody": [0.5, 0.8, 0.35, 0.35],
         "lignin_below_structural": [0.5, 0.25, 0.75, 0.75],
@@ -75,6 +75,11 @@ def dummy_litter_data(fixture_core_components):
         "leaf_turnover_c_p_ratio": [415.0, 327.4, 554.5, 380.9],
         "plant_reproductive_tissue_turnover_c_p_ratio": [125.5, 105.0, 145.0, 189.2],
         "root_turnover_c_p_ratio": [656.7, 450.6, 437.3, 371.9],
+        "litter_consumption_above_metabolic": [0.019785, 0.011631, 0.016129, 0.023456],
+        "litter_consumption_above_structural": [0.02097, 0.01609, 0.01019, 0.00988],
+        "litter_consumption_woody": [0.4773833, 0.385701, 0.373456, 0.162192],
+        "litter_consumption_below_metabolic": [0.010373, 0.005794, 0.010181, 0.013494],
+        "litter_consumption_below_structural": [0.013547, 0.011674, 0.012738, 0.009168],
     }
 
     for var, vals in pool_values.items():
@@ -100,17 +105,13 @@ def dummy_litter_data(fixture_core_components):
 
 
 @pytest.fixture
-def decay_rates(dummy_litter_data, fixture_core_components):
+def decay_rates(dummy_litter_data, fixture_core_components, post_consumption_pools):
     """Decay rates for the various litter pools."""
 
     from virtual_ecosystem.models.litter.carbon import calculate_decay_rates
 
     decay_rates = calculate_decay_rates(
-        above_metabolic=dummy_litter_data["litter_pool_above_metabolic"].to_numpy(),
-        above_structural=dummy_litter_data["litter_pool_above_structural"].to_numpy(),
-        woody=dummy_litter_data["litter_pool_woody"].to_numpy(),
-        below_metabolic=dummy_litter_data["litter_pool_below_metabolic"].to_numpy(),
-        below_structural=dummy_litter_data["litter_pool_below_structural"].to_numpy(),
+        post_consumption_pools=post_consumption_pools,
         lignin_above_structural=dummy_litter_data["lignin_above_structural"].to_numpy(),
         lignin_woody=dummy_litter_data["lignin_woody"].to_numpy(),
         lignin_below_structural=dummy_litter_data["lignin_below_structural"].to_numpy(),
@@ -224,16 +225,41 @@ def input_c_p_ratios(dummy_litter_data, metabolic_splits, litter_chemistry):
 
 
 @pytest.fixture
-def updated_pools(dummy_litter_data, decay_rates, plant_inputs):
-    """Updated carbon mass of each pool."""
-    from virtual_ecosystem.models.litter.carbon import calculate_updated_pools
+def post_consumption_pools(dummy_litter_data):
+    """Pool sizes after animal consumption for each litter pool."""
+    from virtual_ecosystem.models.litter.carbon import calculate_post_consumption_pools
 
-    updated_pools = calculate_updated_pools(
+    post_consumption_pools = calculate_post_consumption_pools(
         above_metabolic=dummy_litter_data["litter_pool_above_metabolic"].to_numpy(),
         above_structural=dummy_litter_data["litter_pool_above_structural"].to_numpy(),
         woody=dummy_litter_data["litter_pool_woody"].to_numpy(),
         below_metabolic=dummy_litter_data["litter_pool_below_metabolic"].to_numpy(),
         below_structural=dummy_litter_data["litter_pool_below_structural"].to_numpy(),
+        consumption_above_metabolic=dummy_litter_data[
+            "litter_consumption_above_metabolic"
+        ].to_numpy(),
+        consumption_above_structural=dummy_litter_data[
+            "litter_consumption_above_structural"
+        ].to_numpy(),
+        consumption_woody=dummy_litter_data["litter_consumption_woody"].to_numpy(),
+        consumption_below_metabolic=dummy_litter_data[
+            "litter_consumption_below_metabolic"
+        ].to_numpy(),
+        consumption_below_structural=dummy_litter_data[
+            "litter_consumption_below_structural"
+        ].to_numpy(),
+    )
+
+    return post_consumption_pools
+
+
+@pytest.fixture
+def updated_pools(dummy_litter_data, decay_rates, plant_inputs, post_consumption_pools):
+    """Updated carbon mass of each pool."""
+    from virtual_ecosystem.models.litter.carbon import calculate_updated_pools
+
+    updated_pools = calculate_updated_pools(
+        post_consumption_pools=post_consumption_pools,
         decay_rates=decay_rates,
         plant_inputs=plant_inputs,
         update_interval=2.0,