#1456 fix example

Author: valentinsulzer

examples/notebooks/initialize-model-with-solution.ipynb

@@ -23,6 +23,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "\u001b[33mWARNING: You are using pip version 21.0.1; however, version 21.1 is available.\n",
+      "You should consider upgrading via the '/Users/vsulzer/Documents/Energy_storage/PyBaMM/.tox/dev/bin/python -m pip install --upgrade pip' command.\u001b[0m\n",
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
     }
@@ -159,7 +161,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "0b5f9d809e244114b29f527062decbe9",
+       "model_id": "7ad44c260ec446e0bd04a2f7dfbf8c65",
        "version_major": 2,
        "version_minor": 0
       },
@@ -173,7 +175,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x7f3292dc9710>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x1447078e0>"
       ]
      },
      "execution_count": 6,
@@ -240,7 +242,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d1e3967157584ff3802279544b0cc442",
+       "model_id": "aaf63750ed354d1987703fd2fdde83af",
        "version_major": 2,
        "version_minor": 0
       },
@@ -254,7 +256,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x7f32818d1990>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x10437c370>"
       ]
      },
      "execution_count": 8,
@@ -299,6 +301,13 @@
    "source": [
     "pybamm.print_citations()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -317,7 +326,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.8"
   },
   "toc": {
    "base_numbering": 1,

pybamm/models/submodels/electrolyte_diffusion/base_electrolyte_diffusion.py

@@ -78,6 +78,19 @@ def _get_standard_concentration_variables(self, c_e_n, c_e_s, c_e_p):
 
         return variables
 
+    def _get_standard_porosity_times_concentration_variables(
+        self, eps_c_e_n, eps_c_e_s, eps_c_e_p
+    ):
+        eps_c_e = pybamm.concatenation(eps_c_e_n, eps_c_e_s, eps_c_e_p)
+
+        variables = {
+            "Porosity times concentration": eps_c_e,
+            "Negative electrode porosity times concentration": eps_c_e_n,
+            "Separator porosity times concentration": eps_c_e_s,
+            "Positive electrode porosity times concentration": eps_c_e_p,
+        }
+        return variables
+
     def _get_standard_flux_variables(self, N_e):
         """
         A private function to obtain the standard variables which

pybamm/models/submodels/electrolyte_diffusion/constant_concentration.py

@@ -39,6 +39,19 @@ def get_fundamental_variables(self):
         return variables
 
     def get_coupled_variables(self, variables):
+        eps_n = variables["Negative electrode porosity"]
+        eps_s = variables["Separator porosity"]
+        eps_p = variables["Positive electrode porosity"]
+        c_e_n = variables["Negative electrolyte concentration"]
+        c_e_s = variables["Separator electrolyte concentration"]
+        c_e_p = variables["Positive electrolyte concentration"]
+
+        variables.update(
+            self._get_standard_porosity_times_concentration_variables(
+                eps_n * c_e_n, eps_s * c_e_s, eps_p * c_e_p
+            )
+        )
+
         c_e = variables["Electrolyte concentration"]
         eps = variables["Porosity"]
 

pybamm/models/submodels/electrolyte_diffusion/full_diffusion.py

@@ -29,14 +29,9 @@ def get_fundamental_variables(self):
         eps_c_e_s = pybamm.standard_variables.eps_c_e_s
         eps_c_e_p = pybamm.standard_variables.eps_c_e_p
 
-        eps_c_e = pybamm.concatenation(eps_c_e_n, eps_c_e_s, eps_c_e_p)
-
-        variables = {
-            "Porosity times concentration": eps_c_e,
-            "Negative electrode porosity times concentration": eps_c_e_n,
-            "Separator porosity times concentration": eps_c_e_s,
-            "Positive electrode porosity times concentration": eps_c_e_p,
-        }
+        variables = self._get_standard_porosity_times_concentration_variables(
+            eps_c_e_n, eps_c_e_s, eps_c_e_p
+        )
 
         return variables