#933 fix tests except public functions

pybamm-team · Apr 9, 2020 · 4fdf3d8 · 4fdf3d8
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diff --git a/pybamm/input/parameters/lead-acid/anodes/lead_Sulzer2019/parameters.csv b/pybamm/input/parameters/lead-acid/anodes/lead_Sulzer2019/parameters.csv
@@ -18,18 +18,18 @@ Negative electrode morphological parameter,0.6,srinivasan2003mathematical,
 Negative electrode capacity [C.m-3],3473000000,,
 ,,,
 # Interfacial reactions,,,
-Negative electrode cation signed stoichiometry,-1,,
+Negative electrode cation signed stoichiometry,1,,
 Negative electrode electrons in reaction,2,,
 Negative electrode reference exchange-current density [A.m-2],0.06,srinivasan2003mathematical,
-Signed stoichiometry of cations (oxygen reaction),-4,,
-Signed stoichiometry of water (oxygen reaction),1,,
-Signed stoichiometry of oxygen (oxygen reaction),-1,,
+Signed stoichiometry of cations (oxygen reaction),4,,
+Signed stoichiometry of water (oxygen reaction),-1,,
+Signed stoichiometry of oxygen (oxygen reaction),1,,
 Electrons in oxygen reaction,4,,
 Negative electrode reference exchange-current density (oxygen) [A.m-2],2.5E-32,srinivasan2003mathematical,
 Reference oxygen molecule concentration [mol.m-3],1000,srinivasan2003mathematical,
 Oxygen reference OCP vs SHE [V],1.229,srinivasan2003mathematical,
-Signed stoichiometry of cations (hydrogen reaction),-2,,
-Signed stoichiometry of hydrogen (hydrogen reaction),1,,
+Signed stoichiometry of cations (hydrogen reaction),2,,
+Signed stoichiometry of hydrogen (hydrogen reaction),-1,,
 Electrons in hydrogen reaction,2,,
 Negative electrode reference exchange-current density (hydrogen) [A.m-2],1.56E-11,srinivasan2003mathematical,
 Hydrogen reference OCP vs SHE [V],0,srinivasan2003mathematical,

diff --git a/pybamm/input/parameters/lead-acid/cathodes/lead_dioxide_Sulzer2019/parameters.csv b/pybamm/input/parameters/lead-acid/cathodes/lead_dioxide_Sulzer2019/parameters.csv
@@ -18,18 +18,18 @@ Positive electrode morphological parameter,0.6,srinivasan2003mathematical,
 Positive electrode capacity [C.m-3],2745000000,,
 ,,,
 # Interfacial reactions,,,
-Positive electrode cation signed stoichiometry,-3,,
+Positive electrode cation signed stoichiometry,3,,
 Positive electrode electrons in reaction,2,,
 Positive electrode reference exchange-current density [A.m-2],0.004,srinivasan2003mathematical,
-Signed stoichiometry of cations (oxygen reaction),-4,,
-Signed stoichiometry of water (oxygen reaction),1,,
-Signed stoichiometry of oxygen (oxygen reaction),-1,,
+Signed stoichiometry of cations (oxygen reaction),4,,
+Signed stoichiometry of water (oxygen reaction),-1,,
+Signed stoichiometry of oxygen (oxygen reaction),1,,
 Electrons in oxygen reaction,4,,
 Positive electrode reference exchange-current density (oxygen) [A.m-2],2.5E-23,srinivasan2003mathematical,
 Reference oxygen molecule concentration [mol.m-3],1000,srinivasan2003mathematical,
 Oxygen reference OCP vs SHE [V],1.229,srinivasan2003mathematical,
-Signed stoichiometry of cations (hydrogen reaction),-2,,
-Signed stoichiometry of hydrogen (hydrogen reaction),1,,
+Signed stoichiometry of cations (hydrogen reaction),2,,
+Signed stoichiometry of hydrogen (hydrogen reaction),-1,,
 Electrons in hydrogen reaction,2,,
 Positive electrode reference exchange-current density (hydrogen) [A.m-2],0,srinivasan2003mathematical,
 Hydrogen reference OCP vs SHE [V],0,srinivasan2003mathematical,

diff --git a/pybamm/models/full_battery_models/base_battery_model.py b/pybamm/models/full_battery_models/base_battery_model.py
@@ -294,6 +294,24 @@ def set_standard_output_variables(self):
                 {"y": var.y, "y [m]": var.y * L_y, "z": var.z, "z [m]": var.z * L_z}
             )
 
+        # Initialize "total reaction" variables
+        self.variables.update(
+            {
+                "Sum of electrolyte reaction source terms": 0,
+                "Sum of negative electrode electrolyte reaction source terms": 0,
+                "Sum of positive electrode electrolyte reaction source terms": 0,
+                "Sum of x-averaged negative 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 negative electrode interfacial current densities": 0,
+                "Sum of positive electrode interfacial current densities": 0,
+                "Sum of x-averaged negative electrode interfacial current densities": 0,
+                "Sum of x-averaged positive electrode interfacial current densities": 0,
+            }
+        )
+
     def build_fundamental_and_external(self):
         # Get the fundamental variables
         for submodel_name, submodel in self.submodels.items():
@@ -350,11 +368,11 @@ def build_coupled_variables(self):
                         if len(submodels) == 1 or count == 100:
                             # no more submodels to try
                             raise pybamm.ModelError(
-                                """Submodel "{}" requires the variable {}, but it cannot be found.
-                                Check the selected submodels provide all of the required
-                                variables.""".format(
+                                "Submodel '{}' requires the variable {}, ".format(
                                     submodel_name, key
                                 )
+                                + "but it cannot be found. Check the selected "
+                                "submodels provide all of the required variables."
                             )
                         else:
                             # try setting coupled variables on next loop through

diff --git a/pybamm/models/full_battery_models/lead_acid/higher_order.py b/pybamm/models/full_battery_models/lead_acid/higher_order.py
@@ -97,6 +97,24 @@ def set_leading_order_model(self):
             leading_order_model.variables["X-averaged electrolyte concentration"]
         ]
 
+        # Reset sums
+        self.variables.update(
+            {
+                "Sum of electrolyte reaction source terms": 0,
+                "Sum of negative electrode electrolyte reaction source terms": 0,
+                "Sum of positive electrode electrolyte reaction source terms": 0,
+                "Sum of x-averaged negative 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 negative electrode interfacial current densities": 0,
+                "Sum of positive electrode interfacial current densities": 0,
+                "Sum of x-averaged negative electrode interfacial current densities": 0,
+                "Sum of x-averaged positive electrode interfacial current densities": 0,
+            }
+        )
+
     def set_average_interfacial_submodel(self):
         self.submodels[
             "x-averaged negative interface"

diff --git a/pybamm/models/submodels/electrode/ohm/full_ohm.py b/pybamm/models/submodels/electrode/ohm/full_ohm.py
@@ -60,11 +60,10 @@ def set_algebraic(self, variables):
         phi_s = variables[self.domain + " electrode potential"]
         i_s = variables[self.domain + " electrode current density"]
 
-        # All possible reactions. Some of these could be zero
-        j = variables[self.domain + " electrode interfacial current density"]
-        j_ox = variables[self.domain + " electrode oxygen interfacial current density"]
-
-        sum_j = j + j_ox
+        # Variable summing all of the interfacial current densities
+        sum_j = variables[
+            "Sum of " + self.domain.lower() + " electrode interfacial current densities"
+        ]
 
         self.algebraic[phi_s] = pybamm.div(i_s) + sum_j
 

diff --git a/pybamm/models/submodels/electrolyte_conductivity/full_conductivity.py b/pybamm/models/submodels/electrolyte_conductivity/full_conductivity.py
@@ -52,11 +52,8 @@ def set_algebraic(self, variables):
         phi_e = variables["Electrolyte potential"]
         i_e = variables["Electrolyte current density"]
 
-        # All possible reactions. Some of these could be zero
-        j = variables["Interfacial current density"]
-        j_ox = variables["Oxygen interfacial current density"]
-
-        sum_j = j + j_ox
+        # Variable summing all of the interfacial current densities
+        sum_j = variables["Sum of interfacial current densities"]
 
         self.algebraic = {phi_e: pybamm.div(i_e) - sum_j}
 

diff --git a/...bmodels/electrolyte_conductivity/surface_potential_form/full_surface_form_conductivity.py b/...bmodels/electrolyte_conductivity/surface_potential_form/full_surface_form_conductivity.py
@@ -232,11 +232,11 @@ def set_algebraic(self, variables):
         delta_phi = variables[self.domain + " electrode surface potential difference"]
         i_e = variables[self.domain + " electrolyte current density"]
 
-        # All possible reactions. Some of these could be zero
-        j = variables[self.domain + " electrode interfacial current density"]
-        j_ox = variables[self.domain + " electrode oxygen interfacial current density"]
+        # Variable summing all of the interfacial current densities
+        sum_j = variables[
+            "Sum of " + self.domain.lower() + " electrode interfacial current densities"
+        ]
 
-        sum_j = j + j_ox
         self.algebraic[delta_phi] = pybamm.div(i_e) - sum_j
 
 
@@ -270,10 +270,9 @@ def set_rhs(self, variables):
         delta_phi = variables[self.domain + " electrode surface potential difference"]
         i_e = variables[self.domain + " electrolyte current density"]
 
-        # All possible reactions. Some of these could be zero
-        j = variables[self.domain + " electrode interfacial current density"]
-        j_ox = variables[self.domain + " electrode oxygen interfacial current density"]
-
-        sum_j = j + j_ox
+        # Variable summing all of the interfacial current densities
+        sum_j = variables[
+            "Sum of " + self.domain.lower() + " electrode interfacial current densities"
+        ]
 
         self.rhs[delta_phi] = 1 / C_dl * (pybamm.div(i_e) - sum_j)
diff --git a/...dels/electrolyte_conductivity/surface_potential_form/leading_surface_form_conductivity.py b/...dels/electrolyte_conductivity/surface_potential_form/leading_surface_form_conductivity.py
@@ -103,19 +103,11 @@ def set_rhs(self, variables):
 
         param = self.param
 
-        # All possible reactions. Some of these could be zero
-        j = variables[
-            "X-averaged "
+        sum_j = variables[
+            "Sum of x-averaged "
             + self.domain.lower()
-            + " electrode interfacial current density"
+            + " electrode interfacial current densities"
         ]
-        j_ox = variables[
-            "X-averaged "
-            + self.domain.lower()
-            + " electrode oxygen interfacial current density"
-        ]
-
-        sum_j = j + j_ox
 
         sum_j_av = variables[
             "X-averaged "
@@ -157,19 +149,11 @@ def set_algebraic(self, variables):
         if self.domain == "Separator":
             return
 
-        # All possible reactions. Some of these could be zero
-        j = variables[
-            "X-averaged "
+        sum_j = variables[
+            "Sum of x-averaged "
             + self.domain.lower()
-            + " electrode interfacial current density"
+            + " electrode interfacial current densities"
         ]
-        j_ox = variables[
-            "X-averaged "
-            + self.domain.lower()
-            + " electrode oxygen interfacial current density"
-        ]
-
-        sum_j = j + j_ox
 
         sum_j_av = variables[
             "X-averaged "

diff --git a/pybamm/models/submodels/electrolyte_diffusion/composite_diffusion.py b/pybamm/models/submodels/electrolyte_diffusion/composite_diffusion.py
@@ -64,52 +64,26 @@ def set_rhs(self, variables):
         c_e = variables["Electrolyte concentration"]
         N_e = variables["Electrolyte flux"]
         if self.extended is False:
-            source_terms_0 = self._get_source_terms_leading_order(variables)
+            sum_s_j = variables[
+                "Leading-order sum of electrolyte reaction source terms"
+            ]
         elif self.extended == "distributed":
-            source_terms_0 = self._get_source_terms_first_order(variables)
+            sum_s_j = variables["Sum of electrolyte reaction source terms"]
         elif self.extended == "average":
-            source_terms_0 = self._get_source_terms_first_order_average(variables)
+            sum_s_j_0 = variables[
+                "Leading-order sum of electrolyte reaction source terms"
+            ]
+            sum_s_j_1 = variables[
+                "Sum of first-order electrolyte reaction source terms"
+            ]
+            sum_s_j = sum_s_j_0 + param.C_e * sum_s_j_1
+        source_terms_0 = sum_s_j / self.param.gamma_e
 
         self.rhs = {
             c_e: (1 / eps_0)
             * (-pybamm.div(N_e) / param.C_e + source_terms_0 - c_e * deps_0_dt)
         }
 
-    def _get_source_terms_leading_order(self, variables):
-        param = self.param
-
-        # All possible reactions. Some of these could be zero
-        j = variables["Leading-order interfacial current density"]
-        j_ox = variables["Leading-order oxygen interfacial current density"]
-
-        return (-param.s_plus_S * j - param.s_plus_Ox * j_ox) / self.param.gamma_e
-
-    def _get_source_terms_first_order(self, variables):
-        param = self.param
-
-        # All possible reactions. Some of these could be zero
-        j = variables["Interfacial current density"]
-        j_ox = variables["Oxygen interfacial current density"]
-
-        return (-param.s_plus_S * j - param.s_plus_Ox * j_ox) / self.param.gamma_e
-
-    def _get_source_terms_first_order_average(self, variables):
-        param = self.param
-        # All possible reactions. Some of these could be zero
-        j_av = variables["First-order x-averaged interfacial current density"]
-        j_ox_av = variables["First-order x-averaged oxygen interfacial current density"]
-
-        first_order_average = (
-            -param.s_plus_S * j_av - param.s_plus_Ox * j_ox_av
-        ) / param.gamma_e
-
-        return self._get_source_terms_leading_order(
-            variables
-        ) + self.param.C_e * pybamm.PrimaryBroadcast(
-            first_order_average,
-            ["negative electrode", "separator", "positive electrode"],
-        )
-
     def set_initial_conditions(self, variables):
 
         c_e = variables["Electrolyte concentration"]

diff --git a/pybamm/models/submodels/electrolyte_diffusion/first_order_diffusion.py b/pybamm/models/submodels/electrolyte_diffusion/first_order_diffusion.py
@@ -56,39 +56,30 @@ def get_coupled_variables(self, variables):
         d_epsc_p_0_dt = c_e_0 * deps_p_0_dt + eps_p_0 * dc_e_0_dt
 
         # Right-hand sides
-        # All possible reactions. Some of these could be zero
-        j_n_0 = variables[
-            "Leading-order x-averaged negative electrode interfacial current density"
+        sum_j_n_0 = variables[
+            "Leading-order sum of x-averaged "
+            "negative electrode interfacial current densities"
         ]
-        j_p_0 = variables[
-            "Leading-order x-averaged positive electrode interfacial current density"
+        sum_j_p_0 = variables[
+            "Leading-order sum of x-averaged "
+            "positive electrode interfacial current densities"
         ]
-        j_ox_n_0 = variables[
-            "Leading-order x-averaged negative electrode "
-            "oxygen interfacial current density"
+        sum_s_j_n_0 = variables[
+            "Leading-order sum of x-averaged "
+            "negative electrode electrolyte reaction source terms"
         ]
-        j_ox_p_0 = variables[
-            "Leading-order x-averaged positive electrode "
-            "oxygen interfacial current density"
+        sum_s_j_p_0 = variables[
+            "Leading-order sum of x-averaged "
+            "positive electrode electrolyte reaction source terms"
         ]
         rhs_n = (
             d_epsc_n_0_dt
-            - (
-                -param.s_plus_n_S * j_n_0
-                - param.s_plus_Ox * j_ox_n_0
-                - param.t_plus(c_e_0) * (j_n_0 + j_ox_n_0)
-            )
-            / param.gamma_e
+            - (sum_s_j_n_0 - param.t_plus(c_e_0) * sum_j_n_0) / param.gamma_e
         )
         rhs_s = d_epsc_s_0_dt
         rhs_p = (
             d_epsc_p_0_dt
-            - (
-                -param.s_plus_p_S * j_p_0
-                - param.s_plus_Ox * j_ox_p_0
-                - param.t_plus(c_e_0) * (j_p_0 + j_ox_p_0)
-            )
-            / param.gamma_e
+            - (sum_s_j_p_0 - param.t_plus(c_e_0) * sum_j_p_0) / param.gamma_e
         )
 
         # Diffusivities

diff --git a/pybamm/models/submodels/electrolyte_diffusion/full_diffusion.py b/pybamm/models/submodels/electrolyte_diffusion/full_diffusion.py
@@ -61,13 +61,8 @@ def set_rhs(self, variables):
         N_e = variables["Electrolyte flux"]
         div_Vbox = variables["Transverse volume-averaged acceleration"]
 
-        # All possible reactions. Some of these could be zero
-        j = variables["Interfacial current density"]
-        j_ox = variables["Oxygen interfacial current density"]
-
-        source_terms = (
-            -param.s_plus_S * j - param.s_plus_Ox * j_ox
-        ) / self.param.gamma_e
+        sum_s_j = variables["Sum of electrolyte reaction source terms"]
+        source_terms = sum_s_j / self.param.gamma_e
 
         self.rhs = {
             c_e: (1 / eps)

diff --git a/pybamm/models/submodels/electrolyte_diffusion/leading_order_diffusion.py b/pybamm/models/submodels/electrolyte_diffusion/leading_order_diffusion.py
@@ -61,29 +61,21 @@ def set_rhs(self, variables):
             "X-averaged separator transverse volume-averaged acceleration"
         ]
 
-        # All possible reactions. Some of these could be zero
-        j_n_0 = variables["X-averaged negative electrode interfacial current density"]
-        j_p_0 = variables["X-averaged positive electrode interfacial current density"]
-        j_ox_n_0 = variables[
-            "X-averaged negative electrode oxygen interfacial current density"
+        sum_j_n_0 = variables[
+            "Sum of x-averaged negative electrode interfacial current densities"
         ]
-        j_ox_p_0 = variables[
-            "X-averaged positive electrode oxygen interfacial current density"
+        sum_j_p_0 = variables[
+            "Sum of x-averaged positive electrode interfacial current densities"
+        ]
+        sum_s_j_n_0 = variables[
+            "Sum of x-averaged negative electrode electrolyte reaction source terms"
+        ]
+        sum_s_j_p_0 = variables[
+            "Sum of x-averaged positive electrode electrolyte reaction source terms"
         ]
-
         source_terms = (
-            param.l_n
-            * (
-                -param.s_plus_n_S * j_n_0
-                - param.s_plus_Ox * j_ox_n_0
-                - param.t_plus(c_e_av) * (j_n_0 + j_ox_n_0)
-            )
-            + param.l_p
-            * (
-                -param.s_plus_p_S * j_p_0
-                - param.s_plus_Ox * j_ox_p_0
-                - param.t_plus(c_e_av) * (j_p_0 + j_ox_p_0)
-            )
+            param.l_n * (sum_s_j_n_0 - param.t_plus(c_e_av) * sum_j_n_0)
+            + param.l_p * (sum_s_j_p_0 - param.t_plus(c_e_av) * sum_j_p_0)
         ) / param.gamma_e
 
         self.rhs = {