Merge pull request #2144 from pybamm-team/issue-2026-total-reaction

Issue 2026 total reaction

pybamm/models/full_battery_models/base_battery_model.py

@@ -712,33 +712,6 @@ def set_standard_output_variables(self):
                 {"y": var.y, "y [m]": var.y * L_z, "z": var.z, "z [m]": var.z * L_z}
             )
 
-        # Initialize "total reaction" variables
-        # These will get populated by the "get_coupled_variables" methods, and then used
-        # later by "set_rhs" or "set_algebraic", which ensures that we always have
-        # added all the necessary variables by the time the sum is used
-        self.variables.update(
-            {
-                "Sum of electrolyte reaction source terms": 0,
-                "Sum of positive electrode electrolyte reaction source terms": 0,
-                "Sum of x-averaged positive electrode "
-                "electrolyte reaction source terms": 0,
-                "Sum of interfacial current densities": 0,
-                "Sum of positive electrode interfacial current densities": 0,
-                "Sum of x-averaged positive electrode interfacial current densities": 0,
-            }
-        )
-        if not self.half_cell:
-            self.variables.update(
-                {
-                    "Sum of negative electrode electrolyte reaction source terms": 0,
-                    "Sum of x-averaged negative electrode "
-                    "electrolyte reaction source terms": 0,
-                    "Sum of negative electrode interfacial current densities": 0,
-                    "Sum of x-averaged negative electrode interfacial current densities"
-                    "": 0,
-                }
-            )
-
     def build_fundamental_and_external(self):
         # Get the fundamental variables
         for submodel_name, submodel in self.submodels.items():

pybamm/models/full_battery_models/lead_acid/base_lead_acid_model.py

@@ -109,3 +109,8 @@ def set_sei_submodel(self):
     def set_lithium_plating_submodel(self):
 
         self.submodels["lithium plating"] = pybamm.lithium_plating.NoPlating(self.param)
+
+    def set_total_kinetics_submodel(self):
+        self.submodels["total interface"] = pybamm.kinetics.TotalKinetics(
+            self.param, "lead-acid", self.options
+        )

pybamm/models/full_battery_models/lead_acid/full.py

@@ -49,6 +49,7 @@ def __init__(self, options=None, name="Full model", build=True):
         self.set_current_collector_submodel()
         self.set_sei_submodel()
         self.set_lithium_plating_submodel()
+        self.set_total_kinetics_submodel()
 
         if build:
             self.build_model()

pybamm/models/full_battery_models/lead_acid/higher_order.py

@@ -57,6 +57,7 @@ def __init__(self, options=None, name="Composite model", build=True):
         self.set_current_collector_submodel()
         self.set_sei_submodel()
         self.set_lithium_plating_submodel()
+        self.set_total_kinetics_submodel()
 
         if build:
             self.build_model()

pybamm/models/full_battery_models/lead_acid/loqs.py

@@ -48,6 +48,7 @@ def __init__(self, options=None, name="LOQS model", build=True):
         self.set_current_collector_submodel()
         self.set_sei_submodel()
         self.set_lithium_plating_submodel()
+        self.set_total_kinetics_submodel()
 
         if build:
             self.build_model()

pybamm/models/full_battery_models/lithium_ion/base_lithium_ion_model.py

@@ -54,7 +54,6 @@ def set_submodels(self, build):
         self.set_convection_submodel()
         self.set_open_circuit_potential_submodel()
         self.set_intercalation_kinetics_submodel()
-        self.set_other_reaction_submodels_to_zero()
         self.set_particle_submodel()
         self.set_solid_submodel()
         self.set_electrolyte_submodel()
@@ -63,6 +62,7 @@ def set_submodels(self, build):
 
         self.set_sei_submodel()
         self.set_lithium_plating_submodel()
+        self.set_total_kinetics_submodel()
 
         if self.half_cell:
             # This also removes "negative electrode" submodels, so should be done last
@@ -251,16 +251,10 @@ def set_lithium_plating_submodel(self):
                 self.param, self.x_average, self.options
             )
 
-    def set_other_reaction_submodels_to_zero(self):
-        for domain in ["Negative", "Positive"]:
-            self.submodels[
-                f"{domain.lower()} oxygen interface"
-            ] = pybamm.kinetics.NoReaction(self.param, domain, "lithium-ion oxygen")
-            self.submodels[
-                f"{domain.lower()} oxygen open circuit potential"
-            ] = pybamm.open_circuit_potential.SingleOpenCircuitPotential(
-                self.param, domain, "lithium-ion oxygen", self.options
-            )
+    def set_total_kinetics_submodel(self):
+        self.submodels["total interface"] = pybamm.kinetics.TotalKinetics(
+            self.param, "lithium-ion", self.options
+        )
 
     def set_crack_submodel(self):
         for domain in ["Negative", "Positive"]:

pybamm/models/submodels/electrolyte_conductivity/surface_potential_form/explicit_surface_form_conductivity.py

@@ -40,18 +40,13 @@ def get_coupled_variables(self, variables):
         variables.update(
             self._get_standard_surface_potential_difference_variables(delta_phi)
         )
-        if (
-            "X-averaged"
-            + self.domain.lower()
-            + "electrode surface potential difference"
-            not in variables
-        ):
-            delta_phi_av = pybamm.x_average(delta_phi)
-            variables.update(
-                self._get_standard_average_surface_potential_difference_variables(
-                    delta_phi_av
-                )
+
+        delta_phi_av = pybamm.x_average(delta_phi)
+        variables.update(
+            self._get_standard_average_surface_potential_difference_variables(
+                delta_phi_av
             )
+        )
         return variables
 
     def set_boundary_conditions(self, variables):