#2418 integration tests

examples/scripts/compare_lithium_ion.py

@@ -6,9 +6,9 @@
 pybamm.set_logging_level("INFO")
 # load models
 models = [
-    pybamm.lithium_ion.SPM(),
-    pybamm.lithium_ion.SPMe(),
-    pybamm.lithium_ion.DFN(),
+    # pybamm.lithium_ion.SPM(),
+    # pybamm.lithium_ion.SPMe(),
+    pybamm.lithium_ion.DFN({"dimensionality": 1}),
     # pybamm.lithium_ion.DFN(
     #     {"particle": "uniform profile"}
     # ),

pybamm/models/standard_variables.py

@@ -6,26 +6,6 @@
 
 class StandardVariables:
     def __init__(self):
-        # Discharge capacity and energy
-        self.Q_Ah = pybamm.Variable("Discharge capacity [A.h]")
-        self.Q_Wh = pybamm.Variable("Discharge energy [W.h]")
-
-        # Throughput capacity and energy (cumulative)
-        self.Qt_Ah = pybamm.Variable("Throughput capacity [A.h]")
-        self.Qt_Wh = pybamm.Variable("Throughput energy [W.h]")
-
-        # Electrode potential
-        self.phi_s_n = pybamm.Variable(
-            "Negative electrode potential [V]",
-            domain="negative electrode",
-            auxiliary_domains={"secondary": "current collector"},
-        )
-        self.phi_s_p = pybamm.Variable(
-            "Positive electrode potential [V]",
-            domain="positive electrode",
-            auxiliary_domains={"secondary": "current collector"},
-        )
-
         # Potential difference
         self.delta_phi_n = pybamm.Variable(
             "Negative electrode surface potential difference [V]",
@@ -47,29 +27,6 @@ def __init__(self):
             domain="current collector",
         )
 
-        # current collector variables
-        self.phi_s_cn = pybamm.Variable(
-            "Negative current collector potential [V]", domain="current collector"
-        )
-        self.phi_s_cp = pybamm.Variable(
-            "Positive current collector potential [V]", domain="current collector"
-        )
-        self.i_boundary_cc = pybamm.Variable(
-            "Current collector current density [A.m-2]", domain="current collector"
-        )
-        self.phi_s_cn_composite = pybamm.Variable(
-            "Composite negative current collector potential [V]",
-            domain="current collector",
-        )
-        self.phi_s_cp_composite = pybamm.Variable(
-            "Composite positive current collector potential [V]",
-            domain="current collector",
-        )
-        self.i_boundary_cc_composite = pybamm.Variable(
-            "Composite current collector current density [A.m-2]",
-            domain="current collector",
-        )
-
     def __setattr__(self, name, value):
         value.print_name = name
         super().__setattr__(name, value)

pybamm/models/submodels/current_collector/potential_pair.py

@@ -32,14 +32,20 @@ def __init__(self, param):
         pybamm.citations.register("Timms2021")
 
     def get_fundamental_variables(self):
-
-        phi_s_cn = pybamm.standard_variables.phi_s_cn
+        param = self.param
+        phi_s_cn = pybamm.Variable(
+            "Negative current collector potential [V]", domain="current collector"
+        )
 
         variables = self._get_standard_negative_potential_variables(phi_s_cn)
 
         # TODO: grad not implemented for 2D yet
         i_cc = pybamm.Scalar(0)
-        i_boundary_cc = pybamm.standard_variables.i_boundary_cc
+        i_boundary_cc = pybamm.Variable(
+            "Current collector current density [A.m-2]",
+            domain="current collector",
+            scale=param.Q / (param.A_cc * param.n_electrodes_parallel),
+        )
 
         variables.update(self._get_standard_current_variables(i_cc, i_boundary_cc))
 

pybamm/models/submodels/current_collector/quite_conductive_potential_pair.py

@@ -28,13 +28,19 @@ def __init__(self, param):
 
     def get_fundamental_variables(self):
 
-        phi_s_cn = pybamm.standard_variables.phi_s_cn
+        phi_s_cn = pybamm.Variable(
+            "Negative current collector potential [V]", domain="current collector"
+        )
 
         variables = self._get_standard_negative_potential_variables(phi_s_cn)
 
         # TODO: grad not implemented for 2D yet
         i_cc = pybamm.Scalar(0)
-        i_boundary_cc = pybamm.standard_variables.i_boundary_cc
+        i_boundary_cc = pybamm.Variable(
+            "Current collector current density [A.m-2]",
+            domain="current collector",
+            scale=param.Q / (param.A_cc * param.n_electrodes_parallel),
+        )
 
         variables.update(self._get_standard_current_variables(i_cc, i_boundary_cc))
 

pybamm/models/submodels/external_circuit/base_external_circuit.py

@@ -11,13 +11,15 @@ def __init__(self, param, options):
         super().__init__(param, options=options)
 
     def get_fundamental_variables(self):
-        Q_Ah = pybamm.standard_variables.Q_Ah
+        Q_Ah = pybamm.Variable("Discharge capacity [A.h]")
 
         variables = {"Discharge capacity [A.h]": Q_Ah}
         if self.options["calculate discharge energy"] == "true":
-            Q_Wh = pybamm.standard_variables.Q_Wh
-            Qt_Wh = pybamm.standard_variables.Qt_Wh
-            Qt_Ah = pybamm.standard_variables.Qt_Ah
+            Q_Wh = pybamm.Variable("Discharge energy [W.h]")
+
+            # Throughput capacity and energy (cumulative)
+            Qt_Ah = pybamm.Variable("Throughput capacity [A.h]")
+            Qt_Wh = pybamm.Variable("Throughput energy [W.h]")
             variables.update(
                 {
                     "Discharge energy [W.h]": Q_Wh,

pybamm/models/submodels/interface/lithium_plating/plating.py

@@ -41,6 +41,7 @@ def get_fundamental_variables(self):
             c_plated_Li_av = pybamm.Variable(
                 "X-averaged lithium plating concentration [mol.m-3]",
                 domain="current collector",
+                scale=self.param.c_plated_Li_0,
             )
             c_plated_Li = pybamm.PrimaryBroadcast(c_plated_Li_av, "negative electrode")
             c_dead_Li_av = pybamm.Variable(
@@ -53,6 +54,7 @@ def get_fundamental_variables(self):
                 "Lithium plating concentration [mol.m-3]",
                 domain="negative electrode",
                 auxiliary_domains={"secondary": "current collector"},
+                scale=self.param.c_plated_Li_0,
             )
             c_dead_Li = pybamm.Variable(
                 "Dead lithium concentration [mol.m-3]",

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

@@ -69,35 +69,38 @@ def compare_outputs_two_phase_graphite_graphite(self, model_class):
             # Compare two phase model to standard model
             for variable in [
                 "X-averaged negative electrode active material volume fraction",
-                "X-averaged negative electrode volumetric interfacial current density [A.m-3]",
+                "X-averaged negative electrode volumetric "
+                "interfacial current density [A.m-3]",
                 "Terminal voltage [V]",
             ]:
-                np.testing.assert_array_almost_equal(
-                    sol[variable].entries, sol_two_phase[variable].entries, decimal=2
+                np.testing.assert_allclose(
+                    sol[variable].entries, sol_two_phase[variable].entries, rtol=1e-2
                 )
 
             # Compare each phase in the two-phase model
-            np.testing.assert_array_almost_equal(
+            np.testing.assert_allclose(
                 sol_two_phase[
                     "Negative primary particle concentration [mol.m-3]"
                 ].entries,
                 sol_two_phase[
                     "Negative secondary particle concentration [mol.m-3]"
                 ].entries,
-                decimal=6,
+                rtol=1e-6,
             )
-            np.testing.assert_array_almost_equal(
+            np.testing.assert_allclose(
                 sol_two_phase[
-                    "Negative electrode primary volumetric interfacial current density [A.m-3]"
+                    "Negative electrode primary volumetric "
+                    "interfacial current density [A.m-3]"
                 ].entries
                 / x,
                 sol_two_phase[
-                    "Negative electrode secondary volumetric interfacial current density [A.m-3]"
+                    "Negative electrode secondary volumetric "
+                    "interfacial current density [A.m-3]"
                 ].entries
                 / (1 - x),
-                decimal=6,
+                rtol=1e-6,
             )
-            np.testing.assert_array_almost_equal(
+            np.testing.assert_allclose(
                 sol_two_phase[
                     "Negative electrode primary active material volume fraction"
                 ].entries
@@ -106,7 +109,7 @@ def compare_outputs_two_phase_graphite_graphite(self, model_class):
                     "Negative electrode secondary active material volume fraction"
                 ].entries
                 / (1 - x),
-                decimal=6,
+                rtol=1e-6,
             )
 
     def test_compare_SPM_graphite_graphite(self):
@@ -151,8 +154,8 @@ def compare_outputs_two_phase_silicon_graphite(self, model_class):
             "Average negative primary particle concentration",
             "Average negative secondary particle concentration",
         ]:
-            np.testing.assert_array_almost_equal(
-                sol1[var].data[:20], sol2[var].data[:20], decimal=2
+            np.testing.assert_allclose(
+                sol1[var].data[:20], sol2[var].data[:20], rtol=1e-2
             )
 
         # More silicon means longer sim

tests/unit/test_expression_tree/test_binary_operators.py

@@ -237,7 +237,9 @@ def test_sparse_divide(self):
     def test_inner(self):
         model = pybamm.lithium_ion.BaseModel()
 
-        phi_s = pybamm.standard_variables.phi_s_n
+        phi_s = pybamm.Variable(
+            "Negative electrode potential [V]", domain="negative electrode"
+        )
         i = pybamm.grad(phi_s)
 
         model.rhs = {phi_s: pybamm.inner(i, i)}

tests/unit/test_expression_tree/test_operations/test_jac.py

@@ -283,7 +283,9 @@ def test_jac_of_binary_operator(self):
         a = pybamm.Symbol("a")
         b = pybamm.Symbol("b")
 
-        phi_s = pybamm.standard_variables.phi_s_n
+        phi_s = pybamm.Variable(
+            "Negative electrode potential [V]", domain="negative electrode"
+        )
         i = pybamm.grad(phi_s)
 
         inner = pybamm.inner(2, i)

tests/unit/test_solvers/test_idaklu_solver.py

@@ -341,7 +341,7 @@ def test_set_atol(self):
         disc.process_model(model)
         solver = pybamm.IDAKLUSolver()
 
-        variable_tols = {"Porosity times concentration [mol.m-3]": 1e-3}
+        variable_tols = {"Negative electrode potential [V]": 1e-3}
         solver.set_atol_by_variable(variable_tols, model)
 
         model = pybamm.BaseModel()

tests/unit/test_solvers/test_scikits_solvers.py

@@ -886,8 +886,12 @@ def nonsmooth_rate(t):
                 dindex = np.searchsorted(solution.t, discontinuity)
                 value_before = solution.t[dindex - 1]
                 value_after = solution.t[dindex]
-                self.assertEqual(value_before + sys.float_info.epsilon, discontinuity)
-                self.assertEqual(value_after - sys.float_info.epsilon, discontinuity)
+                self.assertEqual(
+                    value_before / (1 - sys.float_info.epsilon), discontinuity
+                )
+                self.assertEqual(
+                    value_after / (1 + sys.float_info.epsilon), discontinuity
+                )
 
             # both solution time vectors should have same number of points
             self.assertEqual(len(solution1.t), len(solution2.t))