Adding subcanopy transpiration to transpiration

tests/models/plants/test_plants_model.py

@@ -277,6 +277,7 @@ def test_PlantsModel_estimate_gpp(fxt_plants_model):
     fxt_plants_model.set_shortwave_absorption()
 
     # Calculate GPP
+    fxt_plants_model.reset_update_vars()
     fxt_plants_model.calculate_light_use_efficiency()
     fxt_plants_model.estimate_gpp(time_index=0)
 

tests/models/plants/test_subcanopy.py

@@ -171,6 +171,7 @@ def test_subcanopy_vegetation_dynamics(
     plants_data["shortwave_absorption"] = template.copy()
     plants_data["leaf_area_index"] = template.copy()
     plants_data["layer_fapar"] = template.copy()
+    plants_data["transpiration"] = template.copy()
 
     subcanopy = Subcanopy(
         data=plants_data,
@@ -186,6 +187,7 @@ def test_subcanopy_vegetation_dynamics(
 
     # Set the subcanopy shortwave absorption - don't need finesse here - either
     # vegetation present or not
+
     subcanopy.set_light_capture(below_canopy_light_fraction=np.ones(4))
 
     subcanopy.calculate_dynamics(

virtual_ecosystem/data_variables.toml

@@ -154,7 +154,7 @@ variable_type = "float"
 
 [[variable]]
 axis = ["spatial"]
-description = "Transpiration from canopy"
+description = "Transpiration from the canopy and subcanopy"
 name = "transpiration"
 unit = "mm"
 variable_type = "float"
@@ -1517,13 +1517,6 @@ name = "subcanopy_phosphorus_uptake"
 unit = "kg"
 variable_type = "float"
 
-[[variable]]
-axis = ["spatial"]
-description = "Transpiration from subcanopy vegetation"
-name = "subcanopy_transpiration"
-unit = "mm"
-variable_type = "float"
-
 [[variable]]
 axis = ["spatial"]
 description = "C, N, and P masses for stem turnover in a given timestep"
@@ -1627,4 +1620,4 @@ axis = ["spatial"]
 description = "Average C, N, and P masses of each seed in a PFT"
 name = "fallen_seeds_cnp"
 unit = "kg"
-variable_type = "float"
+variable_type = "float"

virtual_ecosystem/models/plants/plants_model.py

@@ -149,7 +149,6 @@ class PlantsModel(
         "subcanopy_ammonium_uptake",
         "subcanopy_nitrate_uptake",
         "subcanopy_phosphorus_uptake",
-        "subcanopy_transpiration",
     ),
     vars_populated_by_first_update=(
         "stem_turnover_cnp",
@@ -217,7 +216,6 @@ class PlantsModel(
         "subcanopy_ammonium_uptake",
         "subcanopy_nitrate_uptake",
         "subcanopy_phosphorus_uptake",
-        "subcanopy_transpiration",
     ),
 ):
     """Representation of plants in the Virtual Ecosystem.
@@ -654,6 +652,9 @@ def reset_update_vars(self) -> None:
         for var in pft_cnp_vars:
             self.data[var] = self.data_object_templates["cnp_pft"].copy()
 
+        # Initialise transpiration array to collect per grid cell values
+        self.data["transpiration"] = self.layer_structure.from_template("transpiration")
+
     def _update(self, time_index: int, **kwargs: Any) -> None:
         """Update the plants model.
 
@@ -1006,8 +1007,10 @@ def estimate_gpp(self, time_index: int) -> None:
                 community.cohorts.n_individuals * per_layer_transpiration_mm
             ).sum(axis=1)
 
-        # Pass values to data object
-        self.data["transpiration"] = transpiration
+        # Write canopy layers to transpiration data array
+        self.data["transpiration"][self.layer_structure.index_filled_canopy] = (
+            transpiration[self.layer_structure.index_filled_canopy]
+        )
 
     def allocate_gpp(self) -> None:
         """Calculate the allocation of GPP to growth and respiration.

virtual_ecosystem/models/plants/subcanopy.py

@@ -470,15 +470,17 @@ def calculate_dynamics(
             self.data["cell_id"], self.model_constants.subcanopy_seedbank_lignin
         )
 
-        # Write nutrient uptakes and transpiration - one m3 is 1000 mm/m2
+        # Write nutrient uptakes
         for name, values in (
             ("subcanopy_ammonium_uptake", ammonium_uptake_kg),
             ("subcanopy_nitrate_uptake", nitrate_uptake_kg),
             ("subcanopy_phosphorus_uptake", phosphorus_uptake_kg),
-            ("subcanopy_transpiration", subcanopy_volume_m3 / 1000),
         ):
             self.data[name] = DataArray(values, coords=coords)
 
+        # Write transpiration
+        self.data["transpiration"][self.layer_index] = subcanopy_volume_m3 / 1000
+
     def set_light_capture(self, below_canopy_light_fraction: NDArray) -> None:
         r"""Calculate the leaf area index and absorption of subcanopy vegetation.