#579 add docs and fix tests

pybamm-team · Nov 13, 2019 · 9903249 · 9903249
1 parent da30127
commit 9903249
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Showing 12 changed files with 55 additions and 9 deletions.
diff --git a/docs/source/models/submodels/index.rst b/docs/source/models/submodels/index.rst
@@ -14,3 +14,4 @@ Submodels
     particle/index
     porosity/index
     thermal/index
+    tortuosity/index
diff --git a/docs/source/models/submodels/tortuosity/base_tortuosity.rst b/docs/source/models/submodels/tortuosity/base_tortuosity.rst
@@ -0,0 +1,6 @@
+Base Model
+===========
+
+.. autoclass:: pybamm.tortuosity.BaseModel
+    :members:
+
diff --git a/docs/source/models/submodels/tortuosity/bruggeman_tortuosity.rst b/docs/source/models/submodels/tortuosity/bruggeman_tortuosity.rst
@@ -0,0 +1,8 @@
+Bruggeman Model 
+===============
+
+.. autoclass:: pybamm.tortuosity.Bruggeman
+    :members:
+
+
+
diff --git a/docs/source/models/submodels/tortuosity/index.rst b/docs/source/models/submodels/tortuosity/index.rst
@@ -0,0 +1,9 @@
+Tortuosity
+==========
+
+.. toctree::
+  :maxdepth: 1
+
+  base_tortuosity
+  bruggeman_tortuosity
+
diff --git a/.../electrolyte/stefan_maxwell/conductivity/base_higher_order_stefan_maxwell_conductivity.py b/.../electrolyte/stefan_maxwell/conductivity/base_higher_order_stefan_maxwell_conductivity.py
@@ -44,9 +44,9 @@ def get_coupled_variables(self, variables):
             "X-averaged negative electrode surface potential difference"
         ]
         phi_s_n_av = variables["X-averaged negative electrode potential"]
-        tor_n_av = variables["Leading-order x-averaged negative electrode tortuosity"]
+        tor_n_av = variables["Leading-order x-averaged negative electrolyte tortuosity"]
         tor_s_av = variables["Leading-order x-averaged separator tortuosity"]
-        tor_p_av = variables["Leading-order x-averaged positive electrode tortuosity"]
+        tor_p_av = variables["Leading-order x-averaged positive electrolyte tortuosity"]
 
         T_av = variables["X-averaged cell temperature"]
         T_av_n = pybamm.PrimaryBroadcast(T_av, "negative electrode")

diff --git a/...ls/submodels/electrolyte/stefan_maxwell/diffusion/first_order_stefan_maxwell_diffusion.py b/...ls/submodels/electrolyte/stefan_maxwell/diffusion/first_order_stefan_maxwell_diffusion.py
@@ -40,9 +40,9 @@ def get_coupled_variables(self, variables):
         eps_n_0 = variables["Leading-order x-averaged negative electrode porosity"]
         eps_s_0 = variables["Leading-order x-averaged separator porosity"]
         eps_p_0 = variables["Leading-order x-averaged positive electrode porosity"]
-        tor_n_0 = variables["Leading-order x-averaged negative electrode tortuosity"]
+        tor_n_0 = variables["Leading-order x-averaged negative electrolyte tortuosity"]
         tor_s_0 = variables["Leading-order x-averaged separator tortuosity"]
-        tor_p_0 = variables["Leading-order x-averaged positive electrode tortuosity"]
+        tor_p_0 = variables["Leading-order x-averaged positive electrolyte tortuosity"]
         deps_n_0_dt = variables[
             "Leading-order x-averaged negative electrode porosity change"
         ]

diff --git a/pybamm/models/submodels/oxygen_diffusion/first_order_oxygen_diffusion.py b/pybamm/models/submodels/oxygen_diffusion/first_order_oxygen_diffusion.py
@@ -38,7 +38,9 @@ def get_coupled_variables(self, variables):
 
         # Unpack
         tor_s_0_av = variables["Leading-order x-averaged separator tortuosity"]
-        tor_p_0_av = variables["Leading-order x-averaged positive electrode tortuosity"]
+        tor_p_0_av = variables[
+            "Leading-order x-averaged positive electrolyte tortuosity"
+        ]
 
         # Diffusivities
         D_ox_s = tor_s_0_av * param.curlyD_ox

diff --git a/...olyte/test_stefan_maxwell/test_conductivity/test_composite_stefan_maxwell_conductivity.py b/...olyte/test_stefan_maxwell/test_conductivity/test_composite_stefan_maxwell_conductivity.py
@@ -22,6 +22,9 @@ def test_public_functions(self):
             "Leading-order x-averaged negative electrode porosity": a,
             "Leading-order x-averaged separator porosity": a,
             "Leading-order x-averaged positive electrode porosity": a,
+            "Leading-order x-averaged negative electrolyte tortuosity": a,
+            "Leading-order x-averaged separator tortuosity": a,
+            "Leading-order x-averaged positive electrolyte tortuosity": a,
             "X-averaged cell temperature": a,
         }
         submodel = pybamm.electrolyte.stefan_maxwell.conductivity.Composite(param)

diff --git a/...test_conductivity/test_surface_form/test_full_surface_form_stefan_maxwell_conductivity.py b/...test_conductivity/test_surface_form/test_full_surface_form_stefan_maxwell_conductivity.py
@@ -23,6 +23,8 @@ def test_public_functions(self):
                 a, "current collector"
             ),
             "Negative electrode porosity": a_n,
+            "Negative electrolyte tortuosity": a_n,
+            "Negative electrode tortuosity": a_n,
             "Negative electrolyte concentration": a_n,
             "Negative electrode interfacial current density": a_n,
             "Electrolyte potential": pybamm.Concatenation(a_n, a_s, a_p),
@@ -55,6 +57,8 @@ def test_public_functions(self):
             "Separator electrolyte potential": a_s,
             "Separator electrolyte current density": a_s,
             "Positive electrode porosity": a_p,
+            "Positive electrolyte tortuosity": a_p,
+            "Positive electrode tortuosity": a_p,
             "Positive electrolyte concentration": a_p,
             "Positive electrode interfacial current density": a_p,
             "Positive electrode temperature": a_p,

diff --git a/tests/unit/test_models/test_submodels/test_oxygen_diffusion/test_full_oxygen_diffusion.py b/tests/unit/test_models/test_submodels/test_oxygen_diffusion/test_full_oxygen_diffusion.py
@@ -17,6 +17,11 @@ def test_public_functions(self):
                 pybamm.FullBroadcast(a, "separator", "current collector"),
                 pybamm.FullBroadcast(a, "positive electrode", "current collector"),
             ),
+            "Electrolyte tortuosity": pybamm.Concatenation(
+                pybamm.FullBroadcast(a, "negative electrode", "current collector"),
+                pybamm.FullBroadcast(a, "separator", "current collector"),
+                pybamm.FullBroadcast(a, "positive electrode", "current collector"),
+            ),
             "Porosity change": pybamm.Concatenation(
                 pybamm.FullBroadcast(a, "negative electrode", "current collector"),
                 pybamm.FullBroadcast(a, "separator", "current collector"),

diff --git a/tests/unit/test_models/test_submodels/test_porosity/test_base_porosity.py b/tests/unit/test_models/test_submodels/test_porosity/test_base_porosity.py
@@ -9,8 +9,10 @@
 
 class TestBaseModel(unittest.TestCase):
     def test_public_functions(self):
+        a = pybamm.Scalar(0)
+        variables = {"Negative electrode porosity": a, "Positive electrode porosity": a}
         submodel = pybamm.porosity.BaseModel(None)
-        std_tests = tests.StandardSubModelTests(submodel)
+        std_tests = tests.StandardSubModelTests(submodel, variables)
         std_tests.test_all()
 
 

diff --git a/tests/unit/test_parameters/test_standard_parameters_lead_acid.py b/tests/unit/test_parameters/test_standard_parameters_lead_acid.py
@@ -157,9 +157,15 @@ def test_update_initial_state_of_charge(self):
         # Test that relevant parameters have changed as expected
         self.assertLess(param_eval_update["q_init"], param_eval["q_init"])
         self.assertLess(param_eval_update["c_e_init"], param_eval["c_e_init"])
-        self.assertLess(param_eval_update["eps_n_init"], param_eval["eps_n_init"])
-        self.assertEqual(param_eval_update["eps_s_init"], param_eval["eps_s_init"])
-        self.assertLess(param_eval_update["eps_p_init"], param_eval["eps_p_init"])
+        self.assertLess(
+            param_eval_update["epsilon_n_init"], param_eval["epsilon_n_init"]
+        )
+        self.assertEqual(
+            param_eval_update["epsilon_s_init"], param_eval["epsilon_s_init"]
+        )
+        self.assertLess(
+            param_eval_update["epsilon_p_init"], param_eval["epsilon_p_init"]
+        )
         self.assertGreater(
             param_eval_update["curlyU_n_init"], param_eval["curlyU_n_init"]
         )