#247 fix processed variable

pybamm/processed_variable.py

@@ -149,22 +149,24 @@ def initialise_2D(self):
         self.entries = entries
         self.dimensions = 2
         if self.domain[0] in ["negative particle", "positive particle"]:
-            self.spatial_var_name = "r"
+            self.first_dimension = "r"
             self.r_sol = space
         elif self.domain[0] in [
             "negative electrode",
             "separator",
             "positive electrode",
         ]:
-            self.spatial_var_name = "x"
+            self.first_dimension = "x"
             self.x_sol = space
         elif self.domain == ["current collector"]:
-            self.spatial_var_name = "z"
+            self.first_dimension = "z"
             self.z_sol = space
         else:
-            self.spatial_var_name = "x"
+            self.first_dimension = "x"
             self.x_sol = space
 
+        self.first_dim_pts = space
+
         # set up interpolation
         # note that the order of 't' and 'space' is the reverse of what you'd expect
 
@@ -242,6 +244,8 @@ def initialise_3D(self):
         # assign attributes for reference
         self.entries = entries
         self.dimensions = 3
+        self.first_dim_pts = first_dim_pts
+        self.second_dim_pts = second_dim_pts
 
         # set up interpolation
         self._interpolation_function = interp.RegularGridInterpolator(
@@ -335,7 +339,7 @@ def __call__(self, t=None, x=None, r=None, y=None, z=None, warn=True):
 
     def call_2D(self, t, x, r, z):
         "Evaluate a 2D variable"
-        spatial_var = eval_dimension_name(self.spatial_var_name, x, r, None, z)
+        spatial_var = eval_dimension_name(self.first_dimension, x, r, None, z)
         return self._interpolation_function(t, spatial_var)
 
     def call_3D(self, t, x, r, y, z):

tests/integration/test_models/standard_output_comparison.py

@@ -51,9 +51,9 @@ def test_all(self, skip_first_timestep=False):
         self.run_test_class(VariablesComparison, skip_first_timestep)
 
         if self.chemistry == "Lithium-ion":
-            self.run_test_class(ParticleConcentrationComparison)
+            self.run_test_class(ParticleConcentrationComparison, skip_first_timestep)
         elif self.chemistry == "Lead-acid":
-            self.run_test_class(PorosityComparison)
+            self.run_test_class(PorosityComparison, skip_first_timestep)
 
 
 class BaseOutputComparison(object):
@@ -67,13 +67,14 @@ def compare(self, var, tol=1e-2):
         model_variables = [solution[var] for solution in self.solutions]
         var0 = model_variables[0]
 
-        if var0.mesh is None:
-            x = None
-        else:
-            x = var0.mesh[0].nodes
+        spatial_pts = {}
+        if var0.dimensions >= 2:
+            spatial_pts[var0.first_dimension] = var0.first_dim_pts
+        if var0.dimensions >= 3:
+            spatial_pts[var0.second_dimension] = var0.second_dim_pts
 
         # Calculate tolerance based on the value of var0
-        maxvar0 = np.max(abs(var0(self.t, x)))
+        maxvar0 = np.max(abs(var0(self.t, **spatial_pts)))
         if maxvar0 < 1e-14:
             decimal = -int(np.log10(tol))
         else:
@@ -82,7 +83,7 @@ def compare(self, var, tol=1e-2):
         for model_var in model_variables[1:]:
             np.testing.assert_equal(var0.dimensions, model_var.dimensions)
             np.testing.assert_array_almost_equal(
-                model_var(self.t, x), var0(self.t, x), decimal
+                model_var(self.t, **spatial_pts), var0(self.t, **spatial_pts), decimal
             )
 
 
@@ -123,7 +124,6 @@ def test_all(self):
         self.compare("X-averaged negative electrode open circuit potential")
         self.compare("X-averaged positive electrode open circuit potential")
         self.compare("Terminal voltage")
-        self.compare("X-averaged electrolyte overpotential")
         self.compare("X-averaged solid phase ohmic losses")
         self.compare("Negative electrode reaction overpotential")
         self.compare("Positive electrode reaction overpotential")

tests/integration/test_models/test_full_battery_models/test_lithium_ion/test_compare_outputs.py

@@ -42,7 +42,7 @@ def test_compare_outputs_surface_form(self):
 
             # solve model
             solutions = []
-            t_eval = np.linspace(0, 0.2, 100)
+            t_eval = np.linspace(0, 3600, 100)
             for i, model in enumerate(models):
                 solution = pybamm.CasadiSolver().solve(model, t_eval)
                 solutions.append(solution)
@@ -58,5 +58,4 @@ def test_compare_outputs_surface_form(self):
 
     if "-v" in sys.argv:
         debug = True
-    pybamm.set_logging_level("DEBUG")
     unittest.main()