#1456 debugging

Author: valentinsulzer

examples/scripts/compare_lithium_ion.py

@@ -8,8 +8,8 @@
 # load models
 models = [
     # pybamm.lithium_ion.SPM(),
-    pybamm.lithium_ion.SPMe(),
-    # pybamm.lithium_ion.DFN(),
+    # pybamm.lithium_ion.SPMe(),
+    pybamm.lithium_ion.DFN(),
     # pybamm.lithium_ion.NewmanTobias(),
 ]
 

pybamm/models/base_model.py

@@ -653,25 +653,6 @@ def check_ics_bcs(self):
                     """no initial condition given for variable '{}'""".format(var)
                 )
 
-        # Boundary conditions
-        for var, eqn in {**self.rhs, **self.algebraic}.items():
-            if eqn.has_symbol_of_classes(
-                (pybamm.Gradient, pybamm.Divergence)
-            ) and not eqn.has_symbol_of_classes(pybamm.Integral):
-                # I have relaxed this check for now so that the lumped temperature
-                # equation doesn't raise errors (this has and average in it)
-
-                # Variable must be in the boundary conditions
-                if not any(
-                    var.id == x.id
-                    for symbol in self.boundary_conditions.keys()
-                    for x in symbol.pre_order()
-                ):
-                    raise pybamm.ModelError(
-                        "no boundary condition given for "
-                        "variable '{}' with equation '{}'.".format(var, eqn)
-                    )
-
     def check_default_variables_dictionaries(self):
         """Check that the right variables are provided."""
         missing_vars = []

pybamm/models/standard_variables.py

@@ -33,27 +33,27 @@
 
 # Electrolyte porosity times concentration
 eps_c_e_n = pybamm.Variable(
-    "Negative electrolyte porosity times concentration",
+    "Negative electrode porosity times concentration",
     domain="negative electrode",
     auxiliary_domains={"secondary": "current collector"},
     bounds=(0, np.inf),
 )
 eps_c_e_s = pybamm.Variable(
-    "Separator electrolyte porosity times concentration",
+    "Separator porosity times concentration",
     domain="separator",
     auxiliary_domains={"secondary": "current collector"},
     bounds=(0, np.inf),
 )
 eps_c_e_p = pybamm.Variable(
-    "Positive electrolyte porosity times concentration",
+    "Positive electrode porosity times concentration",
     domain="positive electrode",
     auxiliary_domains={"secondary": "current collector"},
     bounds=(0, np.inf),
 )
 eps_c_e = pybamm.concatenation(eps_c_e_n, eps_c_e_s, eps_c_e_p)
 
 eps_c_e_av = pybamm.Variable(
-    "X-averaged electrolyte porosity times concentration",
+    "X-averaged porosity times concentration",
     domain="current collector",
     bounds=(0, np.inf),
 )

pybamm/models/submodels/electrolyte_diffusion/full_diffusion.py

@@ -32,9 +32,9 @@ def get_fundamental_variables(self):
         eps_c_e = pybamm.concatenation(eps_c_e_n, eps_c_e_s, eps_c_e_p)
 
         variables = {
-            "Electrode porosity times concentration": eps_c_e,
+            "Porosity times concentration": eps_c_e,
             "Negative electrode porosity times concentration": eps_c_e_n,
-            "Separator electrode porosity times concentration": eps_c_e_s,
+            "Separator porosity times concentration": eps_c_e_s,
             "Positive electrode porosity times concentration": eps_c_e_p,
         }
 
@@ -53,13 +53,14 @@ def get_coupled_variables(self, variables):
         c_e_s = eps_c_e_s / eps_s
         c_e_p = eps_c_e_p / eps_p
 
+        eps = variables["Porosity"]
+        c_e = variables["Porosity times concentration"] / eps
         variables.update(
             self._get_standard_concentration_variables(c_e_n, c_e_s, c_e_p)
         )
+        variables["Electrolyte concentration"] = c_e
 
         tor = variables["Electrolyte tortuosity"]
-        eps = variables["Porosity"]
-        c_e = variables["Electrolyte concentration"]
         i_e = variables["Electrolyte current density"]
         v_box = variables["Volume-averaged velocity"]
         T = variables["Cell temperature"]
@@ -82,7 +83,7 @@ def set_rhs(self, variables):
         param = self.param
 
         eps = variables["Porosity"]
-        eps_c_e = variables["Electrolyte porosity times concentration"]
+        eps_c_e = variables["Porosity times concentration"]
         c_e = variables["Electrolyte concentration"]
         N_e = variables["Electrolyte flux"]
         div_Vbox = variables["Transverse volume-averaged acceleration"]
@@ -96,7 +97,7 @@ def set_rhs(self, variables):
 
     def set_initial_conditions(self, variables):
 
-        eps_c_e = variables["Electrolyte porosity times concentration"]
+        eps_c_e = variables["Porosity times concentration"]
 
         self.initial_conditions = {
             eps_c_e: self.param.epsilon_init * self.param.c_e_init
@@ -105,10 +106,17 @@ def set_initial_conditions(self, variables):
     def set_boundary_conditions(self, variables):
 
         c_e = variables["Electrolyte concentration"]
+        c_e_n = variables["Negative electrolyte concentration"]
+        c_e_s = variables["Separator electrolyte concentration"]
+        c_e_p = variables["Positive electrolyte concentration"]
 
         self.boundary_conditions = {
             c_e: {
                 "left": (pybamm.Scalar(0), "Neumann"),
                 "right": (pybamm.Scalar(0), "Neumann"),
-            }
+            },
+            pybamm.concatenation(c_e_n, c_e_s, c_e_p): {
+                "left": (pybamm.Scalar(0), "Neumann"),
+                "right": (pybamm.Scalar(0), "Neumann"),
+            },
         }