Update to pyrealm 2.0.0rc2, add reproductive tissue and carbon servicing

pyproject.toml

@@ -38,7 +38,7 @@ netcdf4 = "^1.6.5"
 numpy = "~2.1" # Pinning numpy less than 2.2.0 until this resolves: https://github.com/numpy/numpy/issues/27957
 openpyxl = "^3.1.5" 
 pint = "^0.24.1" 
-pyrealm = {version = "^2.0.0rc1", allow-prereleases = true} 
+pyrealm = {version = "^2.0.0rc2", allow-prereleases = true}
 python = ">=3.10,<3.14" 
 scipy = "^1.9.0" 
 tomli = {version = "^2.0.1", python = "<3.11"} 

tests/conftest.py

@@ -217,12 +217,16 @@ def fixture_config(microbial_groups_cfg):
         resp_f = 0.1
         resp_r = 0.913
         resp_s = 0.044
+        resp_rt = 0.05
         rho_s = 200.0
         sla = 14.0
         tau_f = 4.0
         tau_r = 1.04
-        yld = 0.17
+        tau_rt = 1
+        yld = 0.6
         zeta = 0.17
+        gpp_topslice = 0.1
+        p_foliage_for_reproductive_tissue = 0.05
 
         [[plants.pft_definition]]
         a_hd = 116.0
@@ -237,12 +241,16 @@ def fixture_config(microbial_groups_cfg):
         resp_f = 0.1
         resp_r = 0.913
         resp_s = 0.044
+        resp_rt = 0.05
         rho_s = 200.0
         sla = 14.0
         tau_f = 4.0
         tau_r = 1.04
-        yld = 0.17
+        tau_rt = 1
+        yld = 0.6
         zeta = 0.17
+        gpp_topslice = 0.1
+        p_foliage_for_reproductive_tissue = 0.05
 
         [[animal.functional_groups]]
         name = "carnivorous_bird"

tests/core/data/all_config.toml

@@ -38,6 +38,10 @@ tau_f = 4.0
 tau_r = 1.04
 yld = 0.17
 zeta = 0.17
+resp_rt = 0.05
+tau_rt = 1
+gpp_topslice = 0.1
+p_foliage_for_reproductive_tissue = 0.05
 
 [[plants.pft_definition]]
 a_hd = 116.0
@@ -58,6 +62,10 @@ tau_f = 4.0
 tau_r = 1.04
 yld = 0.17
 zeta = 0.17
+resp_rt = 0.05
+tau_rt = 1
+gpp_topslice = 0.1
+p_foliage_for_reproductive_tissue = 0.05
 
 [[animal.functional_groups]]
 name = "carnivorous_bird"

tests/models/animals/conftest.py

@@ -127,6 +127,10 @@ def animal_fixture_config():
         tau_r = 1.04
         yld = 0.17
         zeta = 0.17
+        resp_rt = 0.05
+        tau_rt = 1
+        gpp_topslice = 0.1
+        p_foliage_for_reproductive_tissue = 0.05
 
         [[plants.pft_definition]]
         a_hd = 116.0
@@ -147,6 +151,10 @@ def animal_fixture_config():
         tau_r = 1.04
         yld = 0.17
         zeta = 0.17
+        resp_rt = 0.05
+        tau_rt = 1
+        gpp_topslice = 0.1
+        p_foliage_for_reproductive_tissue = 0.05
 
         [[animal.functional_groups]]
         name = "carnivorous_bird"

tests/models/litter/conftest.py

@@ -66,7 +66,7 @@ def dummy_litter_data(fixture_core_components):
         "c_p_ratio_below_structural": [550.5, 595.6, 773.1, 651.2],
         "deadwood_production": [0.075, 0.099, 0.063, 0.033],
         "leaf_turnover": [0.027, 0.0003, 0.021, 0.0285],
-        "plant_reproductive_tissue_turnover": [0.003, 0.0075, 0.00255, 0.00375],
+        "fallen_non_propagule_c_mass": [0.003, 0.0075, 0.00255, 0.00375],
         "root_turnover": [0.027, 0.021, 0.0003, 0.0249],
         "stem_lignin": [0.233, 0.545, 0.612, 0.378],
         "senesced_leaf_lignin": [0.05, 0.25, 0.3, 0.57],

tests/models/plants/data/pfts.csv

@@ -1,3 +1,3 @@
-name,a_hd,ca_ratio,h_max,lai,par_ext,resp_f,resp_r,resp_s,rho_s,sla,tau_f,tau_r,yld,zeta,f_g,m,n
-test1,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5
-test2,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5
+name,a_hd,ca_ratio,h_max,lai,par_ext,resp_f,resp_r,resp_s,rho_s,sla,tau_f,tau_r,yld,zeta,f_g,m,n,tau_rt,resp_rt,gpp_topslice,p_foliage_for_reproductive_tissue
+test1,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05
+test2,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05

tests/models/plants/test_plants_model.py

@@ -187,6 +187,14 @@ def test_PlantsModel_allocate_gpp(fxt_plants_model, fixture_core_components):
         # Ensure that leaf and root turnover exist and are > 0
         assert fxt_plants_model.data["leaf_turnover"][cell_id] > 0
         assert fxt_plants_model.data["root_turnover"][cell_id] > 0
+        assert np.all(fxt_plants_model.data["fallen_n_propagules"][cell_id] >= 0)
+        assert fxt_plants_model.data["fallen_non_propagule_c_mass"][cell_id] > 0
+        assert np.all(fxt_plants_model.data["canopy_n_propagules"][cell_id] >= 0)
+        assert np.all(
+            fxt_plants_model.data["canopy_non_propagule_c_mass"][cell_id] >= 0
+        )  # For cell_id = 1, only one of the two PFTs is present.
+        assert fxt_plants_model.data["root_carbohydrate_exudation"][cell_id] > 0
+        assert fxt_plants_model.data["plant_symbiote_carbon_supply"][cell_id] > 0
 
 
 def test_PlantsModel_update(
@@ -228,9 +236,6 @@ def test_PlantsModel_calculate_turnover(fxt_plants_model, fixture_config):
     consts = fxt_plants_model.model_constants
 
     # Check that all expected variables are generated and have the correct value
-    assert np.allclose(
-        fxt_plants_model.data["plant_reproductive_tissue_turnover"], 0.003
-    )
     assert np.allclose(fxt_plants_model.data["stem_lignin"], consts.stem_lignin)
     assert np.allclose(
         fxt_plants_model.data["senesced_leaf_lignin"], consts.senesced_leaf_lignin
@@ -322,3 +327,18 @@ def test_PlantsModel_apply_mortality(fxt_plants_model):
             >= fxt_plants_model.communities[cell_id].cohorts.n_individuals
         )
         assert fxt_plants_model.data["deadwood_production"][cell_id] == deadwood_mass
+
+
+def test_partition_reproductive_tissue(fxt_plants_model):
+    """Tests the partition reproductive tissue function."""
+
+    n_propagules, mass_non_propagules = fxt_plants_model.partition_reproductive_tissue(
+        reproductive_tissue_mass=10.5
+    )
+
+    assert n_propagules == 5
+    assert mass_non_propagules == 5.5
+    assert (
+        n_propagules * fxt_plants_model.model_constants.carbon_mass_per_propagule
+        + mass_non_propagules
+    )

virtual_ecosystem/data_variables.toml

@@ -973,8 +973,8 @@ variable_type = "float"
 
 [[variable]]
 axis = ["spatial"]
-description = "Plant reproductive tissue (fruits and flowers) turnover since last update"
-name = "plant_reproductive_tissue_turnover"
+description = "Plant reproductive tissue non-propagule turnover since last update"
+name = "fallen_non_propagule_c_mass"
 unit = "kg C m^-2"
 variable_type = "float"
 

virtual_ecosystem/example_data/data/plant_pfts.csv

@@ -1,3 +1,3 @@
-name,a_hd,ca_ratio,h_max,lai,par_ext,resp_f,resp_r,resp_s,rho_s,sla,tau_f,tau_r,yld,zeta,f_g,m,n
-broadleaf,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5
-shrub,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5
+name,a_hd,ca_ratio,h_max,lai,par_ext,resp_f,resp_r,resp_s,rho_s,sla,tau_f,tau_r,yld,zeta,f_g,m,n,tau_rt,resp_rt,gpp_topslice,p_foliage_for_reproductive_tissue
+broadleaf,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05
+shrub,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05

virtual_ecosystem/models/litter/inputs.py

@@ -135,7 +135,7 @@ def combine_input_sources(data: Data) -> dict[str, NDArray[np.float32]]:
     ).to_numpy()
     root_total = data["root_turnover"]
     deadwood_total = data["deadwood_production"]
-    reprod_total = data["plant_reproductive_tissue_turnover"]
+    reprod_total = data["fallen_non_propagule_c_mass"]
 
     # Calculate lignin concentrations for each combined pool
     leaf_lignin = merge_input_chemical_proportions(

virtual_ecosystem/models/litter/litter_model.py

@@ -94,7 +94,7 @@ class LitterModel(
         "c_p_ratio_below_structural",
         "deadwood_production",
         "leaf_turnover",
-        "plant_reproductive_tissue_turnover",
+        "fallen_non_propagule_c_mass",
         "root_turnover",
         "stem_lignin",
         "senesced_leaf_lignin",

virtual_ecosystem/models/plants/constants.py

@@ -59,3 +59,12 @@ class PlantsConsts(ConstantsDataclass):
 
     root_turnover_c_p_ratio: float = 656.7
     """Carbon to Phosphorous ratio of root turnover."""
+
+    root_exudates: float = 0.5
+    """Fraction of GPP topslice allocated to root exudates."""
+
+    propagule_mass_portion: float = 0.5
+    """Fraction of reprodutive tissue allocated to propagules."""
+
+    carbon_mass_per_propagule: float = 1
+    """Mass of carbon per propagule in g."""

virtual_ecosystem/models/plants/module_schema.json

@@ -47,6 +47,9 @@
                      "resp_r": {
                         "type": "number"
                      },
+                     "resp_rt": {
+                        "type": "number"
+                     },
                      "resp_s": {
                         "type": "number"
                      },
@@ -62,6 +65,9 @@
                      "tau_r": {
                         "type": "number"
                      },
+                     "tau_rt": {
+                        "type": "number"
+                     },
                      "yld": {
                         "type": "number"
                      },
@@ -76,6 +82,12 @@
                      },
                      "n": {
                         "type": "number"
+                     },
+                     "gpp_topslice": {
+                        "type": "number"
+                     },
+                     "p_foliage_for_reproductive_tissue": {
+                        "type": "number"
                      }
                   },
                   "required": [
@@ -96,7 +108,9 @@
                      "zeta",
                      "f_g",
                      "m",
-                     "n"
+                     "n",
+                     "gpp_topslice",
+                     "p_foliage_for_reproductive_tissue"
                   ]
                }
             },