Fix BPX bug when activation energies not provided (#4634)

* fix bpx bug when activation energies not provided

* update BPX tests

* Move function and rename variable

---------

Co-authored-by: Eric G. Kratz <[email protected]>
Co-authored-by: kratman <[email protected]>

src/pybamm/parameters/bpx.py

@@ -108,7 +108,7 @@ def _get_phase_names(domain):
         )
 
 
-def _bpx_to_param_dict(bpx: BPX) -> dict:
+def bpx_to_param_dict(bpx: BPX) -> dict:
     """
     Turns a BPX object in to a dictionary of parameters for PyBaMM
     """
@@ -222,6 +222,9 @@ def _bpx_to_param_dict(bpx: BPX) -> dict:
             domain.pre_name + "transport efficiency"
         ] ** (1.0 / 1.5)
 
+    def _get_activation_energy(var_name):
+        return pybamm_dict.get(var_name) or 0.0
+
     # define functional forms for pybamm parameters that depend on more than one
     # variable
 
@@ -294,11 +297,15 @@ def _conductivity(c_e, T, Ea, sigma_ref, constant=False):
             k_norm = pybamm_dict[
                 phase_domain_pre_name + "reaction rate constant [mol.m-2.s-1]"
             ]
-            Ea_k = pybamm_dict.get(
+            Ea_k = _get_activation_energy(
                 phase_domain_pre_name
-                + "reaction rate constant activation energy [J.mol-1]",
-                0.0,
+                + "reaction rate constant activation energy [J.mol-1]"
             )
+            pybamm_dict[
+                phase_domain_pre_name
+                + "reaction rate constant activation energy [J.mol-1]"
+            ] = Ea_k
+
             # Note that in BPX j = 2*F*k_norm*sqrt((ce/ce0)*(c/c_max)*(1-c/c_max))...
             # *sinh(),
             # and in PyBaMM j = 2*k*sqrt(ce*c*(c_max - c))*sinh()
@@ -308,9 +315,8 @@ def _conductivity(c_e, T, Ea, sigma_ref, constant=False):
             )
 
             # diffusivity
-            Ea_D = pybamm_dict.get(
-                phase_domain_pre_name + "diffusivity activation energy [J.mol-1]",
-                0.0,
+            Ea_D = _get_activation_energy(
+                phase_domain_pre_name + "diffusivity activation energy [J.mol-1]"
             )
             pybamm_dict[
                 phase_domain_pre_name + "diffusivity activation energy [J.mol-1]"
@@ -335,8 +341,11 @@ def _conductivity(c_e, T, Ea, sigma_ref, constant=False):
                 )
 
     # electrolyte
-    Ea_D_e = pybamm_dict.get(
-        electrolyte.pre_name + "diffusivity activation energy [J.mol-1]", 0.0
+    Ea_D_e = _get_activation_energy(
+        electrolyte.pre_name + "diffusivity activation energy [J.mol-1]"
+    )
+    pybamm_dict[electrolyte.pre_name + "diffusivity activation energy [J.mol-1]"] = (
+        Ea_D_e
     )
     D_e_ref = pybamm_dict[electrolyte.pre_name + "diffusivity [m2.s-1]"]
 
@@ -358,8 +367,11 @@ def _conductivity(c_e, T, Ea, sigma_ref, constant=False):
         )
 
     # conductivity
-    Ea_sigma_e = pybamm_dict.get(
-        electrolyte.pre_name + "conductivity activation energy [J.mol-1]", 0.0
+    Ea_sigma_e = _get_activation_energy(
+        electrolyte.pre_name + "conductivity activation energy [J.mol-1]"
+    )
+    pybamm_dict[electrolyte.pre_name + "conductivity activation energy [J.mol-1]"] = (
+        Ea_sigma_e
     )
     sigma_e_ref = pybamm_dict[electrolyte.pre_name + "conductivity [S.m-1]"]
 

src/pybamm/parameters/parameter_values.py

@@ -88,11 +88,11 @@ def create_from_bpx(filename, target_soc: float = 1):
 
         from bpx import parse_bpx_file, get_electrode_concentrations
         from bpx.schema import ElectrodeBlended, ElectrodeBlendedSPM
-        from .bpx import _bpx_to_param_dict
+        from .bpx import bpx_to_param_dict
 
         # parse bpx
         bpx = parse_bpx_file(filename)
-        pybamm_dict = _bpx_to_param_dict(bpx)
+        pybamm_dict = bpx_to_param_dict(bpx)
 
         if "Open-circuit voltage at 0% SOC [V]" not in pybamm_dict:
             pybamm_dict["Open-circuit voltage at 0% SOC [V]"] = pybamm_dict[

tests/unit/test_parameters/test_bpx.py

@@ -475,11 +475,28 @@ def test_bpx_user_defined(self):
 
             param = pybamm.ParameterValues.create_from_bpx(tmp.name)
 
-            assert param["User-defined scalar parameter"] == 1.0
+            assert param["User-defined scalar parameter"] == pytest.approx(
+                1.0, rel=1e-12
+            )
             var = pybamm.Variable("var")
             assert isinstance(
                 param["User-defined parameter data"](var), pybamm.Interpolant
             )
             assert isinstance(
                 param["User-defined parameter data function"](var), pybamm.Power
             )
+
+    def test_bpx_activation_energy_default(self):
+        bpx_obj = copy.copy(self.base)
+        bpx_obj["Parameterisation"]["Negative electrode"][
+            "Diffusivity activation energy [J.mol-1]"
+        ] = None
+        with tempfile.NamedTemporaryFile(
+            suffix="test.json", delete=False, mode="w"
+        ) as test_file:
+            json.dump(copy.copy(bpx_obj), test_file)
+            test_file.flush()
+            param = pybamm.ParameterValues.create_from_bpx(test_file.name)
+            assert param[
+                "Negative electrode diffusivity activation energy [J.mol-1]"
+            ] == pytest.approx(0.0, rel=1e-12)