StemStochiometry basic structure.

docs/source/conf.py

@@ -164,6 +164,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ("py:class", "PModelConst"),
     ("py:class", "CoreConst"),
     ("py:class", "StemAllocation"),
+    ("py:class", "StemStochiometry"),
 ]
 intersphinx_mapping = {
     "numpy": ("https://numpy.org/doc/stable/", None),

docs/source/using_the_ve/virtual_ecosystem_in_static_mode.md

@@ -1,6 +1,6 @@
 ---
 execution:
-  timeout: 90
+  timeout: 120
 jupytext:
   formats: md:myst
   main_language: python

docs/source/using_the_ve/virtual_ecosystem_in_use.md

@@ -1,6 +1,6 @@
 ---
 execution:
-  timeout: 60
+  timeout: 120
 jupytext:
   formats: md:myst
   text_representation:

tests/models/plants/test_plants_model.py

@@ -309,6 +309,14 @@ def test_PlantsModel_calculate_turnover(fxt_plants_model):
     )
     assert np.allclose(fxt_plants_model.data["root_lignin"], consts.root_lignin)
     assert np.allclose(fxt_plants_model.data["leaf_lignin"], consts.leaf_lignin)
+
+
+def test_PlantsModel_update_cn_ratios(fxt_plants_model, fixture_config):
+    """Test the update_cn_ratios method of the plants model."""
+
+    fxt_plants_model.update_cn_ratios()
+    consts = fxt_plants_model.model_constants
+
     assert np.allclose(
         fxt_plants_model.data["deadwood_c_n_ratio"], consts.deadwood_c_n_ratio
     )
@@ -356,6 +364,10 @@ def test_PlantsModel_calculate_turnover_constant_override(
 def test_PlantsModel_calculate_nutrient_uptake(fxt_plants_model):
     """Test the calculate_nutrient_uptake method of the plants model."""
 
+    # Provide transpiration values
+    fxt_plants_model.per_stem_transpiration = {
+        cell_id: np.array([10]) for cell_id in fxt_plants_model.communities.keys()
+    }
     # Check reset
     fxt_plants_model.calculate_nutrient_uptake()
 
@@ -364,6 +376,8 @@ def test_PlantsModel_calculate_nutrient_uptake(fxt_plants_model):
     assert np.allclose(fxt_plants_model.data["plant_nitrate_uptake"], 7.5e-3)
     assert np.allclose(fxt_plants_model.data["plant_phosphorus_uptake"], 3.0e-5)
 
+    # TODO: add test for element uptake
+
 
 def test_PlantsModel_calculate_mycorrhizal_uptakes(fxt_plants_model):
     """Test the calculate_mycorrhizal_uptakes method of the plants model."""

tests/models/plants/test_stochiometry.py

@@ -0,0 +1,277 @@
+"""Tests for the Stochiometry class."""
+
+import numpy as np
+import pytest
+
+
+def test_FoliageTissue__init__(fxt_plants_model):
+    """Test the foliage stochiometry."""
+    from virtual_ecosystem.models.plants.stochiometry import FoliageTissue
+
+    plant_consts = fxt_plants_model.model_constants
+    for cell_id in fxt_plants_model.communities.keys():
+        community = fxt_plants_model.communities[cell_id]
+
+        tissue_model = FoliageTissue(
+            community=community,
+            ideal_ratio=np.full(community.n_cohorts, plant_consts.foliage_c_n_ratio),
+            actual_element_mass=community.stem_allometry.foliage_mass
+            * plant_consts.foliage_c_n_ratio,
+            reclaim_ratio=plant_consts.leaf_turnover_c_n_ratio,
+        )
+
+        assert isinstance(tissue_model, FoliageTissue)
+
+
+@pytest.mark.parametrize(
+    argnames=(
+        "classname, carbon_mass, deficit, element_needed_for_growth, "
+        "element_turnover, Cx_ratio"
+    ),
+    argvalues=[
+        pytest.param(
+            "FoliageTissue",
+            [1.00834120e01, 3.27620602e-01, 3.85363977e-03],
+            [0, 0, 0],
+            [-0.35486191, 0.02330898, 0.87583064],
+            [-9.83256242e02, -3.19470237e01, -3.75777103e-01],
+            [0.06666667, 0.06666667, 0.06666667],
+        ),
+    ],
+)
+def test_Tissue_class_functions(
+    fxt_plants_model,
+    classname,
+    carbon_mass,
+    deficit,
+    element_needed_for_growth,
+    element_turnover,
+    Cx_ratio,
+):
+    """Test the carbon mass calculation in FoliageTissue."""
+    from pyrealm.demography.tmodel import StemAllocation
+
+    from virtual_ecosystem.models.plants.stochiometry import FoliageTissue
+
+    plant_consts = fxt_plants_model.model_constants
+    fxt_plants_model.per_stem_gpp = {
+        cell_id: np.array([55]) for cell_id in fxt_plants_model.communities.keys()
+    }
+    cell_id = 0
+    community = fxt_plants_model.communities[cell_id]
+    tissue_model = FoliageTissue(
+        community=community,
+        ideal_ratio=np.full(community.n_cohorts, plant_consts.foliage_c_n_ratio),
+        actual_element_mass=community.stem_allometry.foliage_mass
+        * plant_consts.foliage_c_n_ratio,
+        reclaim_ratio=plant_consts.leaf_turnover_c_n_ratio,
+    )
+
+    stem_allocation = StemAllocation(
+        stem_traits=community.stem_traits,
+        stem_allometry=community.stem_allometry,
+        whole_crown_gpp=fxt_plants_model.per_stem_gpp[cell_id],
+    )
+
+    # Assert that the calculated carbon mass matches the expected value
+    assert np.allclose(
+        tissue_model.carbon_mass,
+        carbon_mass,
+    )
+
+    assert np.allclose(
+        tissue_model.deficit,
+        deficit,
+    )
+
+    assert np.allclose(
+        tissue_model.element_needed_for_growth(stem_allocation),
+        element_needed_for_growth,
+    )
+
+    assert np.allclose(
+        tissue_model.element_turnover(stem_allocation),
+        element_turnover,
+    )
+
+    assert np.allclose(
+        tissue_model.Cx_ratio,
+        Cx_ratio,
+    )
+
+
+@pytest.fixture
+def fxt_stochiometry_model(fxt_plants_model):
+    """Fixture for the Stochiometry class."""
+
+    from virtual_ecosystem.models.plants.stochiometry import (
+        FoliageTissue,
+        ReproductiveTissue,
+        RootTissue,
+        StemStochiometry,
+        WoodTissue,
+    )
+
+    plant_consts = fxt_plants_model.model_constants
+    cell_id = 0  # Assuming we are testing for the first cell
+    community = fxt_plants_model.communities[cell_id]
+
+    n_stochiometry = StemStochiometry(
+        element="N",
+        tissues=[
+            FoliageTissue(
+                community=community,
+                ideal_ratio=np.full(
+                    community.n_cohorts,
+                    plant_consts.foliage_c_n_ratio,
+                ),
+                actual_element_mass=community.stem_allometry.foliage_mass
+                * plant_consts.foliage_c_n_ratio,
+                reclaim_ratio=plant_consts.leaf_turnover_c_n_ratio,
+            ),
+            RootTissue(
+                community=community,
+                ideal_ratio=np.full(
+                    community.n_cohorts,
+                    plant_consts.root_turnover_c_n_ratio,
+                ),
+                actual_element_mass=plant_consts.root_turnover_c_n_ratio
+                * community.stem_traits.zeta
+                * community.stem_allometry.foliage_mass,
+            ),
+            WoodTissue(
+                community=community,
+                ideal_ratio=np.full(
+                    community.n_cohorts,
+                    plant_consts.deadwood_c_n_ratio,
+                ),
+                actual_element_mass=plant_consts.deadwood_c_n_ratio
+                * community.stem_allometry.stem_mass,
+            ),
+            ReproductiveTissue(
+                community=community,
+                ideal_ratio=np.full(
+                    community.n_cohorts,
+                    plant_consts.plant_reproductive_tissue_turnover_c_n_ratio,
+                ),
+                actual_element_mass=community.stem_allometry.reproductive_tissue_mass
+                * plant_consts.plant_reproductive_tissue_turnover_c_n_ratio,
+            ),
+        ],
+        community=community,
+    )
+    return n_stochiometry
+
+
+def test_Stochiometry__init__(fxt_stochiometry_model):
+    """Test the Stochiometry class initialization."""
+
+    from virtual_ecosystem.models.plants.stochiometry import StemStochiometry
+
+    assert isinstance(fxt_stochiometry_model, StemStochiometry)
+
+
+def test_Stochiometry_total_element_mass(fxt_stochiometry_model):
+    """Test the total_element_mass method of the Stochiometry class."""
+
+    # Calculate the total element mass
+    total_mass = fxt_stochiometry_model.total_element_mass
+
+    assert np.allclose(total_mass, [1.31887368e05, 4.35408760e02, 5.93227761e-01])
+
+
+def test_Stochiometry_tissue_deficit(fxt_stochiometry_model):
+    """Test the tissue_deficit method of the Stochiometry class."""
+
+    # Calculate the tissue deficit
+    tissue_deficit = fxt_stochiometry_model.tissue_deficit
+
+    expected_deficit = np.array([1.01616593e03, 3.30162938e01, 3.88354401e-01])
+    assert np.allclose(tissue_deficit, expected_deficit)
+
+
+@pytest.mark.skip(
+    reason="Negative growth problem. Return to this test when that problem is fixed."
+)
+def test_Stochiometry_account_for_growth(fxt_plants_model, fxt_stochiometry_model):
+    """Test the account_for_growth method of the Stochiometry class."""
+
+    from virtual_ecosystem.models.plants.stochiometry import StemAllocation
+
+    # Create a StemAllocation object
+    cell_id = 0  # Assuming we are testing for the first cell
+    community = fxt_plants_model.communities[cell_id]
+    fxt_plants_model.per_stem_gpp = {
+        cell_id: np.array([55]) for cell_id in fxt_plants_model.communities.keys()
+    }
+    stem_allocation = StemAllocation(
+        stem_traits=community.stem_traits,
+        stem_allometry=community.stem_allometry,
+        whole_crown_gpp=fxt_plants_model.per_stem_gpp[cell_id],
+    )
+
+    assert np.allclose(
+        fxt_stochiometry_model.total_element_mass,
+        [1.31887368e05, 4.35408760e02, 5.93227761e-01],
+    )
+
+    # Account for growth
+    fxt_stochiometry_model.account_for_growth(stem_allocation)
+
+    print("new mass")
+
+    assert np.all(
+        fxt_stochiometry_model.total_element_mass
+        >= [1.31887368e05, 4.35408760e02, 5.93227761e-01]
+    )
+
+
+def test_Stochiometry_account_for_element_loss_turnover(
+    fxt_plants_model, fxt_stochiometry_model
+):
+    """Test the account_for_element_loss_turnover method of the Stochiometry class."""
+
+    from virtual_ecosystem.models.plants.stochiometry import StemAllocation
+
+    # Create a StemAllocation object
+    cell_id = 0  # Assuming we are testing for the first cell
+    community = fxt_plants_model.communities[cell_id]
+    fxt_plants_model.per_stem_gpp = {
+        cell_id: np.array([55]) for cell_id in fxt_plants_model.communities.keys()
+    }
+    stem_allocation = StemAllocation(
+        stem_traits=community.stem_traits,
+        stem_allometry=community.stem_allometry,
+        whole_crown_gpp=fxt_plants_model.per_stem_gpp[cell_id],
+    )
+
+    assert np.allclose(fxt_stochiometry_model.element_surplus, [0.0, 0.0, 0.0])
+    fxt_stochiometry_model.account_for_element_loss_turnover(stem_allocation)
+
+    # The surplus should always be negative after accounting for turnover
+    assert np.all(fxt_stochiometry_model.element_surplus <= [0.0, 0.0, 0.0])
+
+
+def test_Stochiometry_distribute_deficit(fxt_stochiometry_model):
+    """Test the distribute_deficit method of the Stochiometry class.
+
+    NOTE: This method should have a more robust test with a more deliberate test value.
+    This will be easier to implement once growth is functioning.
+    """
+
+    # Distribute the deficit
+    fxt_stochiometry_model.distribute_deficit(0)
+
+    assert np.allclose(fxt_stochiometry_model.element_surplus[0], [0])
+
+
+def test_Stochiometry_distrubte_surplus(fxt_stochiometry_model):
+    """Test the distribute_surplus method of the Stochiometry class.
+
+    NOTE: This method should have a more robust test with a more deliberate test value.
+    This will be easier to implement once growth is functioning.
+    """
+
+    fxt_stochiometry_model.distribute_surplus(0)
+
+    assert fxt_stochiometry_model.element_surplus[0] >= 0

virtual_ecosystem/models/plants/constants.py

@@ -40,27 +40,33 @@ class PlantsConsts(ConstantsDataclass):
     deadwood_c_n_ratio: float = 56.5
     """Carbon to Nitrogen ratio of deadwood."""
 
-    leaf_turnover_c_n_ratio: float = 25.5
-    """Carbon to Nitrogen ratio of leaf turnover."""
-
-    plant_reproductive_tissue_turnover_c_n_ratio: float = 12.5
-    """Carbon to Nitrogen ratio of plant reproductive tissue turnover."""
-
-    root_turnover_c_n_ratio: float = 45.6
-    """Carbon to Nitrogen ratio of root turnover."""
-
     deadwood_c_p_ratio: float = 856.5
     """Carbon to Phosphorous ratio of deadwood."""
 
+    leaf_turnover_c_n_ratio: float = 25.5
+    """Carbon to Nitrogen ratio of leaf turnover (senesced leaves)."""
+
     leaf_turnover_c_p_ratio: float = 415.0
-    """Carbon to Phosphorous ratio of leaf turnover."""
+    """Carbon to Phosphorous ratio of leaf turnover (senesced leaves)."""
+
+    plant_reproductive_tissue_turnover_c_n_ratio: float = 12.5
+    """Carbon to Nitrogen ratio of plant reproductive tissue turnover."""
 
     plant_reproductive_tissue_turnover_c_p_ratio: float = 125.5
     """Carbon to Phosphorous ratio of plant reproductive tissue turnover."""
 
     root_turnover_c_p_ratio: float = 656.7
     """Carbon to Phosphorous ratio of root turnover."""
 
+    root_turnover_c_n_ratio: float = 45.6
+    """Carbon to Nitrogen ratio of root turnover."""
+
+    foliage_c_n_ratio: float = 15
+    """Carbon to Nitrogen ratio of foliage on trees."""
+
+    foliage_c_p_ratio: float = 300
+    """Carbon to Phosphorous ratio of foliage on trees."""
+
     subcanopy_extinction_coef: float = 0.5
     """The extinction coefficient of subcanopy vegetation (unitless)."""
 
@@ -85,6 +91,7 @@ class PlantsConsts(ConstantsDataclass):
     subcanopy_sprout_yield: float = 0.5
     """The fraction of subcanopy seedbank mass that is realised as subcanopy vegetation
     mass (kg kg-1)."""
+
     root_exudates: float = 0.5
     """Fraction of GPP topslice allocated to root exudates."""