Grass-BRIDGES CNW

src/openalea/cnwgrass/gasexchange/simulation.py

@@ -104,7 +104,7 @@ def run(self, Ta, ambient_CO2, RH, Ur):
         the results in :attr:`outputs`.
 
         :param float Ta: air temperature at t (degree Celsius)
-        :param float ambient_CO2: air CO2 at t (µmol mol-1)
+        :param float ambient_CO2: air CO2 at t (µmol mol-1)
         :param float RH: relative humidity at t (decimal fraction)
         :param float Ur: wind speed at the top of the canopy at t (m s-1)
         """
@@ -126,11 +126,11 @@ def run(self, Ta, ambient_CO2, RH, Ur):
                 Ts = self.inputs['axes'][axis_id]['SAM_temperature']
 
             else:
-                Ts = Ta # Initial value of Ts (°C)
+                Ts = Ta # Initial value of Ts (°C)
                 if element_inputs['Ci'] is None or np.isnan(element_inputs['Ci']):
                     Ci = ambient_CO2
                 else:
-                    Ci = element_inputs['Ci']      #: previous organ internal CO2 concentration (µmol mol-1) todo Ci = parameters.Ci_init_ratio * ambient_CO2 see with Victoria if we keep this
+                    Ci = element_inputs['Ci']      #: previous organ internal CO2 concentration (µmol mol-1) todo Ci = parameters.Ci_init_ratio * ambient_CO2 see with Victoria if we keep this
                 height_canopy = self.inputs['axes'][axis_id]['height_canopy']
                 water_potential = element_inputs.get('water_potential', None)
 

src/openalea/cnwgrass/growth/simulation.py

@@ -29,7 +29,7 @@ class Simulation(object):
     """The Simulation class permits to initialize and run a simulation.
     """
 
-    def __init__(self, delta_t=1, hydraulics=False, update_parameters=None):
+    def __init__(self, delta_t=1, hydraulics=False, update_parameters=None, cnwgrass_roots=True):
         """
         :param int delta_t: the delta t of the simulation (in seconds)
         :param bool hydraulics: if True the model will assume the coupling to the turgor-driven growth model
@@ -81,6 +81,8 @@ def __init__(self, delta_t=1, hydraulics=False, update_parameters=None):
                 else:
                     warnings.warn(f"Parameter '{key}' is not defined in class self.self.model.parameters.")
 
+        self.cnwgrass_roots = cnwgrass_roots
+
     def initialize(self, inputs):
         """
         Initialize :attr:`inputs` from `inputs`.
@@ -260,13 +262,13 @@ def run(self, postflowering_stages=False):
                 curr_hiddenzone_outputs['AA_consumption_mstruct'] = self.model.calculate_s_Nstruct_amino_acids((delta_leaf_enclosed_Nstruct + delta_internode_enclosed_Nstruct),
                                                                                                           delta_lamina_Nstruct,
                                                                                                           delta_sheath_Nstruct,
-                                                                                                          delta_internode_Nstruct)  #: Consumption of amino acids due to mstruct growth (µmol N)
+                                                                                                          delta_internode_Nstruct)  #: Consumption of amino acids due to mstruct growth (µmol N)
                 curr_hiddenzone_outputs['sucrose_consumption_mstruct'] = self.model.calculate_s_mstruct_sucrose((delta_leaf_enclosed_mstruct + delta_internode_enclosed_mstruct),
                                                                                                            delta_lamina_mstruct,
                                                                                                            delta_sheath_mstruct,
                                                                                                            curr_hiddenzone_outputs[
-                                                                                                               'AA_consumption_mstruct'])  #: Consumption of sucrose due to mstruct growth (µmol C)
-                curr_hiddenzone_outputs['Respi_growth'] = RespirationModel.R_growth(curr_hiddenzone_outputs['sucrose_consumption_mstruct'])  #: Respiration growth (µmol C)
+                                                                                                               'AA_consumption_mstruct'])  #: Consumption of sucrose due to mstruct growth (µmol C)
+                curr_hiddenzone_outputs['Respi_growth'] = RespirationModel.R_growth(curr_hiddenzone_outputs['sucrose_consumption_mstruct'])  #: Respiration growth (µmol C)
 
                 # -- Update of hiddenzone outputs
                 curr_hiddenzone_outputs['leaf_enclosed_mstruct'] += delta_leaf_enclosed_mstruct
@@ -407,32 +409,33 @@ def run(self, postflowering_stages=False):
         # --------------------------------
         # -------------- Roots -----------
         # --------------------------------
-        for root_id, root_inputs in all_roots_inputs.items():
-            curr_root_outputs = all_roots_outputs[root_id]
-
-            axis_id = root_id[:2]
-            curr_axis_outputs = all_axes_outputs[axis_id]
-
-            # Temperature-compensated time (delta_teq)
-            delta_teq = all_axes_inputs[axis_id]['delta_teq_roots']
-
-            # Growth
-            xylem_water_potential = all_axes_inputs[axis_id].get('xylem_water_potential')  # Set at None if hydraulics is False
-            mstruct_C_growth, mstruct_growth, Nstruct_growth, Nstruct_N_growth = self.model.calculate_roots_mstruct_growth(root_inputs['sucrose'], root_inputs['amino_acids'],
-                                                                                                                      root_inputs['mstruct'], delta_teq, postflowering_stages,
-                                                                                                                      all_axes_inputs[axis_id]['nb_leaves'], xylem_water_potential)
-            # Respiration growth
-            curr_root_outputs['Respi_growth'] = RespirationModel.R_growth(mstruct_C_growth)
-
-            # Update of root outputs
-            curr_root_outputs['mstruct'] += mstruct_growth
-            curr_root_outputs['AA_consumption_mstruct'] = Nstruct_N_growth
-            curr_root_outputs['sucrose_consumption_mstruct'] = self.model.calculate_roots_s_mstruct_sucrose(mstruct_growth, Nstruct_N_growth)
-            curr_root_outputs['sucrose'] -= (curr_root_outputs['sucrose_consumption_mstruct'] + curr_root_outputs['Respi_growth'])
-            curr_root_outputs['Nstruct'] += Nstruct_growth
-            curr_root_outputs['amino_acids'] -= curr_root_outputs['AA_consumption_mstruct']
-            curr_root_outputs['delta_mstruct_growth'] = mstruct_growth
-            self.outputs['roots'][root_id] = curr_root_outputs
-
-            # Update of axis outputs
-            self.outputs['axes'][axis_id] = curr_axis_outputs
+        if self.cnwgrass_roots:
+            for root_id, root_inputs in all_roots_inputs.items():
+                curr_root_outputs = all_roots_outputs[root_id]
+
+                axis_id = root_id[:2]
+                curr_axis_outputs = all_axes_outputs[axis_id]
+
+                # Temperature-compensated time (delta_teq)
+                delta_teq = all_axes_inputs[axis_id]['delta_teq_roots']
+
+                # Growth
+                xylem_water_potential = all_axes_inputs[axis_id].get('xylem_water_potential')  # Set at None if hydraulics is False
+                mstruct_C_growth, mstruct_growth, Nstruct_growth, Nstruct_N_growth = self.model.calculate_roots_mstruct_growth(root_inputs['sucrose'], root_inputs['amino_acids'],
+                                                                                                                        root_inputs['mstruct'], delta_teq, postflowering_stages,
+                                                                                                                        all_axes_inputs[axis_id]['nb_leaves'], xylem_water_potential)
+                # Respiration growth
+                curr_root_outputs['Respi_growth'] = RespirationModel.R_growth(mstruct_C_growth)
+
+                # Update of root outputs
+                curr_root_outputs['mstruct'] += mstruct_growth
+                curr_root_outputs['AA_consumption_mstruct'] = Nstruct_N_growth
+                curr_root_outputs['sucrose_consumption_mstruct'] = self.model.calculate_roots_s_mstruct_sucrose(mstruct_growth, Nstruct_N_growth)
+                curr_root_outputs['sucrose'] -= (curr_root_outputs['sucrose_consumption_mstruct'] + curr_root_outputs['Respi_growth'])
+                curr_root_outputs['Nstruct'] += Nstruct_growth
+                curr_root_outputs['amino_acids'] -= curr_root_outputs['AA_consumption_mstruct']
+                curr_root_outputs['delta_mstruct_growth'] = mstruct_growth
+                self.outputs['roots'][root_id] = curr_root_outputs
+
+                # Update of axis outputs
+                self.outputs['axes'][axis_id] = curr_axis_outputs