Bug fix: added SEI on cracks to total_kinetics.py

CHANGELOG.md

@@ -4,8 +4,15 @@
 
 -   For experiments, the simulation now automatically checks and skips steps that cannot be performed (e.g. "Charge at 1C until 4.2V" from 100% SOC) ([#2212](https://github.com/pybamm-team/PyBaMM/pull/2212))
 
+## Bug fixes
+
+-   Added `SEI on cracks` to loop over all interfacial reactions ([#2262](https://github.com/pybamm-team/PyBaMM/pull/2262))
+-   Fixed `X-averaged SEI on cracks concentration` so it's an average over x only, not y and z ([#2262](https://github.com/pybamm-team/PyBaMM/pull/2262))
+-   Corrected initial state for SEI on cracks ([#2262](https://github.com/pybamm-team/PyBaMM/pull/2262))
+
 ## Optimizations
 
+-   Default options for `particle mechanics` now dealt with differently in each electrode ([#2262](https://github.com/pybamm-team/PyBaMM/pull/2262))
 -   Sped up calculations of Electrode SOH variables for summary variables ([#2210](https://github.com/pybamm-team/PyBaMM/pull/2210))
 
 ## Breaking changes

pybamm/models/full_battery_models/base_battery_model.py

@@ -299,17 +299,21 @@ def __init__(self, extra_options):
         # The "SEI film resistance" option will still be overridden by extra_options if
         # provided
 
-        # Change the default for particle mechanics based on which SEI on cracks option
-        # is provided
-        # return "false" if option not given
+        # Change the default for particle mechanics based on which SEI on cracks and LAM
+        # options are provided
+        # return "false" and "none" respectively if options not given
         SEI_cracks_option = extra_options.get("SEI on cracks", "false")
+        LAM_opt = extra_options.get("loss of active material", "none")
         if SEI_cracks_option == "true":
-            default_options["particle mechanics"] = "swelling and cracking"
+            if "stress-driven" in LAM_opt or "stress and reaction-driven" in LAM_opt:
+                default_options["particle mechanics"] = (
+                    "swelling and cracking", "swelling only"
+                )
+            else:
+                default_options["particle mechanics"] = (
+                    "swelling and cracking", "none"
+                )
         else:
-            # Change the default for particle mechanics based on which LAM option is
-            # provided
-            # return "none" if option not given
-            LAM_opt = extra_options.get("loss of active material", "none")
             if "stress-driven" in LAM_opt or "stress and reaction-driven" in LAM_opt:
                 default_options["particle mechanics"] = "swelling only"
             else:

pybamm/models/submodels/interface/base_interface.py

@@ -301,16 +301,25 @@ def _get_standard_volumetric_current_density_variables(self, variables):
         a_j_av = pybamm.x_average(a_j)
         a_j_scale = self.param.i_typ / self.param.L_x
 
+        if reaction_name == "SEI on cracks ":
+            roughness = variables["Negative electrode roughness ratio"] - 1
+            roughness_av = variables[
+                "X-averaged negative electrode roughness ratio"
+            ] - 1
+        else:
+            roughness = 1
+            roughness_av = 1
+
         variables.update(
             {
                 f"{Domain} electrode {reaction_name}volumetric "
-                "interfacial current density": a_j,
+                "interfacial current density": a_j * roughness,
                 f"X-averaged {domain} electrode {reaction_name}volumetric "
-                "interfacial current density": a_j_av,
+                "interfacial current density": a_j_av * roughness_av,
                 f"{Domain} electrode {reaction_name}volumetric "
-                "interfacial current density [A.m-3]": a_j_scale * a_j,
-                f"X-averaged {domain} electrode {reaction_name}volumetric "
-                "interfacial current density [A.m-3]": a_j_scale * a_j_av,
+                "interfacial current density [A.m-3]": a_j_scale * a_j * roughness,
+                f"X-averaged {domain} electrode {reaction_name}volumetric interfacial "
+                "current density [A.m-3]": a_j_scale * a_j_av * roughness_av,
             }
         )
         return variables

pybamm/models/submodels/interface/sei/base_sei.py

@@ -206,7 +206,8 @@ def _get_standard_concentration_variables(self, variables):
             n_outer_av = pybamm.x_average(n_outer)
 
             n_SEI = n_inner + n_outer / v_bar  # SEI concentration
-            n_SEI_av = pybamm.yz_average(pybamm.x_average(n_SEI))
+            n_SEI_xav = pybamm.x_average(n_SEI)
+            n_SEI_av = pybamm.yz_average(n_SEI_xav)
 
             # Calculate change in SEI concentration with respect to initial state
             delta_n_SEI = n_SEI_av - (L_inner_0 + L_outer_0 / v_bar)
@@ -230,7 +231,7 @@ def _get_standard_concentration_variables(self, variables):
                     "X-averaged outer SEI concentration [mol.m-3]": n_outer_av
                     * n_outer_scale,
                     "SEI concentration [mol.m-3]": n_SEI * n_scale,
-                    "X-averaged SEI concentration [mol.m-3]": n_SEI_av * n_scale,
+                    "X-averaged SEI concentration [mol.m-3]": n_SEI_xav * n_scale,
                     "Loss of lithium to SEI [mol]": Q_sei,
                     "Loss of capacity to SEI [A.h]": Q_sei * self.param.F / 3600,
                 }
@@ -248,11 +249,13 @@ def _get_standard_concentration_variables(self, variables):
             n_outer_cr_av = pybamm.x_average(n_outer_cr)
 
             n_SEI_cr = n_inner_cr + n_outer_cr / v_bar  # SEI on cracks concentration
-            n_SEI_cr_av = pybamm.yz_average(pybamm.x_average(n_SEI_cr))
+            n_SEI_cr_xav = pybamm.x_average(n_SEI_cr)
+            n_SEI_cr_av = pybamm.yz_average(n_SEI_cr_xav)
 
-            # Calculate change in SEI cracks concentration with respect to initial state
-            rho_cr = param.n.rho_cr
-            n_SEI_cr_init = 2 * rho_cr * (L_inner_0 + L_outer_0 / v_bar) / 10000
+            # Calculate change in SEI cracks concentration
+            # Initial state depends on roughness (to avoid division by zero)
+            roughness_av = pybamm.x_average(roughness)
+            n_SEI_cr_init = (L_inner_0 + L_outer_0 / v_bar) * (roughness_av - 1) / 10000
             delta_n_SEI_cr = n_SEI_cr_av - n_SEI_cr_init
 
             # Q_sei_cr in mol
@@ -275,7 +278,7 @@ def _get_standard_concentration_variables(self, variables):
                     "X-averaged outer SEI on cracks "
                     "concentration [mol.m-3]": n_outer_cr_av * n_outer_scale,
                     "SEI on cracks concentration [mol.m-3]": n_SEI_cr * n_scale,
-                    "X-averaged SEI on cracks concentration [mol.m-3]": n_SEI_cr_av
+                    "X-averaged SEI on cracks concentration [mol.m-3]": n_SEI_cr_xav
                     * n_scale,
                     "Loss of lithium to SEI on cracks [mol]": Q_sei_cr,
                     "Loss of capacity to SEI on cracks [A.h]": Q_sei_cr

tests/unit/test_models/test_full_battery_models/test_base_battery_model.py

@@ -280,12 +280,15 @@ def test_options(self):
                     )
                 }
             )
+
         # check default options change
-        model = pybamm.BaseBatteryModel({"loss of active material": "stress-driven"})
-        self.assertEqual(model.options["particle mechanics"], "swelling only")
-        self.assertEqual(model.options["stress-induced diffusion"], "true")
-        model = pybamm.BaseBatteryModel({"SEI on cracks": "true"})
-        self.assertEqual(model.options["particle mechanics"], "swelling and cracking")
+        model = pybamm.BaseBatteryModel({
+            "loss of active material": "stress-driven",
+            "SEI on cracks": "true"
+        })
+        self.assertEqual(model.options["particle mechanics"], (
+            "swelling and cracking", "swelling only"
+        ))
         self.assertEqual(model.options["stress-induced diffusion"], "true")
 
         # crack model