SEI on cracks

examples/notebooks/models/SEI-on-cracks.ipynb

@@ -0,0 +1,106 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "eb5375ae",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[33mWARNING: You are using pip version 22.0.4; however, version 22.1.2 is available.\n",
+      "You should consider upgrading via the '/home/sokane/PyBaMM/env/bin/python3 -m pip install --upgrade pip' command.\u001b[0m\u001b[33m\n",
+      "\u001b[0mNote: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
+   "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
+    "import pybamm\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "05c30b49",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "At t = 0.00698581, , mxstep steps taken before reaching tout.\n"
+     ]
+    },
+    {
+     "ename": "SolverError",
+     "evalue": "Could not solve for summary variables, run `sim.solve(calc_esoh=False)` to skip this step",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mSolverError\u001b[0m                               Traceback (most recent call last)",
+      "File \u001b[0;32m~/PyBaMM/pybamm/solvers/solution.py:918\u001b[0m, in \u001b[0;36mget_cycle_summary_variables\u001b[0;34m(cycle_solution, esoh_sim)\u001b[0m\n\u001b[1;32m    917\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 918\u001b[0m     esoh_sol \u001b[38;5;241m=\u001b[39m \u001b[43mesoh_sim\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msolve\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43minputs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43minputs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msolver\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msolver\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    919\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m pybamm\u001b[38;5;241m.\u001b[39mSolverError:  \u001b[38;5;66;03m# pragma: no cover\u001b[39;00m\n",
+      "File \u001b[0;32m~/PyBaMM/pybamm/simulation.py:710\u001b[0m, in \u001b[0;36mSimulation.solve\u001b[0;34m(self, t_eval, solver, check_model, save_at_cycles, calc_esoh, starting_solution, initial_soc, callbacks, **kwargs)\u001b[0m\n\u001b[1;32m    696\u001b[0m                 warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m    697\u001b[0m                     \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    698\u001b[0m \u001b[38;5;124;03m                    The largest timestep in t_eval ({}) is larger than\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    707\u001b[0m                     pybamm\u001b[38;5;241m.\u001b[39mSolverWarning,\n\u001b[1;32m    708\u001b[0m                 )\n\u001b[0;32m--> 710\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_solution \u001b[38;5;241m=\u001b[39m \u001b[43msolver\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msolve\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbuilt_model\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mt_eval\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    712\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39moperating_mode \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mwith experiment\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
+      "File \u001b[0;32m~/PyBaMM/pybamm/solvers/base_solver.py:1083\u001b[0m, in \u001b[0;36mBaseSolver.solve\u001b[0;34m(self, model, t_eval, external_variables, inputs, initial_conditions, nproc, calculate_sensitivities)\u001b[0m\n\u001b[1;32m   1082\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ninputs \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[0;32m-> 1083\u001b[0m     new_solution \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_integrate\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m   1084\u001b[0m \u001b[43m        \u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1085\u001b[0m \u001b[43m        \u001b[49m\u001b[43mt_eval_dimensionless\u001b[49m\u001b[43m[\u001b[49m\u001b[43mstart_index\u001b[49m\u001b[43m:\u001b[49m\u001b[43mend_index\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1086\u001b[0m \u001b[43m        \u001b[49m\u001b[43mext_and_inputs_list\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1087\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m   1088\u001b[0m     new_solutions \u001b[38;5;241m=\u001b[39m [new_solution]\n",
+      "File \u001b[0;32m~/PyBaMM/pybamm/solvers/casadi_algebraic_solver.py:184\u001b[0m, in \u001b[0;36mCasadiAlgebraicSolver._integrate\u001b[0;34m(self, model, t_eval, inputs_dict)\u001b[0m\n\u001b[1;32m    183\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m success:\n\u001b[0;32m--> 184\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m pybamm\u001b[38;5;241m.\u001b[39mSolverError(\n\u001b[1;32m    185\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCould not find acceptable solution: \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(message)\n\u001b[1;32m    186\u001b[0m     )\n\u001b[1;32m    187\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28many\u001b[39m(np\u001b[38;5;241m.\u001b[39misnan(fun)):\n",
+      "\u001b[0;31mSolverError\u001b[0m: Could not find acceptable solution: .../casadi/core/rootfinder.cpp:280: rootfinder process failed. Set 'error_on_fail' option to false to ignore this error.",
+      "\nDuring handling of the above exception, another exception occurred:\n",
+      "\u001b[0;31mSolverError\u001b[0m                               Traceback (most recent call last)",
+      "Input \u001b[0;32mIn [2]\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      8\u001b[0m experiment \u001b[38;5;241m=\u001b[39m pybamm\u001b[38;5;241m.\u001b[39mExperiment([\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mDischarge at 1C until 3 V\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n\u001b[1;32m      9\u001b[0m sim1 \u001b[38;5;241m=\u001b[39m pybamm\u001b[38;5;241m.\u001b[39mSimulation(model1, parameter_values\u001b[38;5;241m=\u001b[39mparameter_values, experiment\u001b[38;5;241m=\u001b[39mexperiment)\n\u001b[0;32m---> 10\u001b[0m sol1 \u001b[38;5;241m=\u001b[39m \u001b[43msim1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msolve\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     11\u001b[0m sim2 \u001b[38;5;241m=\u001b[39m pybamm\u001b[38;5;241m.\u001b[39mSimulation(model2, parameter_values\u001b[38;5;241m=\u001b[39mparameter_values, experiment\u001b[38;5;241m=\u001b[39mexperiment)\n\u001b[1;32m     12\u001b[0m sol2 \u001b[38;5;241m=\u001b[39m sim2\u001b[38;5;241m.\u001b[39msolve()\n",
+      "File \u001b[0;32m~/PyBaMM/pybamm/simulation.py:858\u001b[0m, in \u001b[0;36mSimulation.solve\u001b[0;34m(self, t_eval, solver, check_model, save_at_cycles, calc_esoh, starting_solution, initial_soc, callbacks, **kwargs)\u001b[0m\n\u001b[1;32m    856\u001b[0m \u001b[38;5;66;03m# At the final step of the inner loop we save the cycle\u001b[39;00m\n\u001b[1;32m    857\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(steps) \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m--> 858\u001b[0m     cycle_sol \u001b[38;5;241m=\u001b[39m \u001b[43mpybamm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmake_cycle_solution\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    859\u001b[0m \u001b[43m        \u001b[49m\u001b[43msteps\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    860\u001b[0m \u001b[43m        \u001b[49m\u001b[43mesoh_sim\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    861\u001b[0m \u001b[43m        \u001b[49m\u001b[43msave_this_cycle\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msave_this_cycle\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    862\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    863\u001b[0m     cycle_solution, cycle_sum_vars, cycle_first_state \u001b[38;5;241m=\u001b[39m cycle_sol\n\u001b[1;32m    864\u001b[0m     all_cycle_solutions\u001b[38;5;241m.\u001b[39mappend(cycle_solution)\n",
+      "File \u001b[0;32m~/PyBaMM/pybamm/solvers/solution.py:812\u001b[0m, in \u001b[0;36mmake_cycle_solution\u001b[0;34m(step_solutions, esoh_sim, save_this_cycle)\u001b[0m\n\u001b[1;32m    808\u001b[0m cycle_solution\u001b[38;5;241m.\u001b[39mset_up_time \u001b[38;5;241m=\u001b[39m sum_sols\u001b[38;5;241m.\u001b[39mset_up_time\n\u001b[1;32m    810\u001b[0m cycle_solution\u001b[38;5;241m.\u001b[39msteps \u001b[38;5;241m=\u001b[39m step_solutions\n\u001b[0;32m--> 812\u001b[0m cycle_summary_variables \u001b[38;5;241m=\u001b[39m \u001b[43mget_cycle_summary_variables\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcycle_solution\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mesoh_sim\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    814\u001b[0m cycle_first_state \u001b[38;5;241m=\u001b[39m cycle_solution\u001b[38;5;241m.\u001b[39mfirst_state\n\u001b[1;32m    816\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m save_this_cycle:\n",
+      "File \u001b[0;32m~/PyBaMM/pybamm/solvers/solution.py:920\u001b[0m, in \u001b[0;36mget_cycle_summary_variables\u001b[0;34m(cycle_solution, esoh_sim)\u001b[0m\n\u001b[1;32m    918\u001b[0m     esoh_sol \u001b[38;5;241m=\u001b[39m esoh_sim\u001b[38;5;241m.\u001b[39msolve([\u001b[38;5;241m0\u001b[39m], inputs\u001b[38;5;241m=\u001b[39minputs, solver\u001b[38;5;241m=\u001b[39msolver)\n\u001b[1;32m    919\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m pybamm\u001b[38;5;241m.\u001b[39mSolverError:  \u001b[38;5;66;03m# pragma: no cover\u001b[39;00m\n\u001b[0;32m--> 920\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m pybamm\u001b[38;5;241m.\u001b[39mSolverError(\n\u001b[1;32m    921\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCould not solve for summary variables, run \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    922\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m`sim.solve(calc_esoh=False)` to skip this step\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    923\u001b[0m     )\n\u001b[1;32m    924\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m var \u001b[38;5;129;01min\u001b[39;00m esoh_sim\u001b[38;5;241m.\u001b[39mbuilt_model\u001b[38;5;241m.\u001b[39mvariables:\n\u001b[1;32m    925\u001b[0m     cycle_summary_variables[var] \u001b[38;5;241m=\u001b[39m esoh_sol[var]\u001b[38;5;241m.\u001b[39mdata[\u001b[38;5;241m0\u001b[39m]\n",
+      "\u001b[0;31mSolverError\u001b[0m: Could not solve for summary variables, run `sim.solve(calc_esoh=False)` to skip this step"
+     ]
+    }
+   ],
+   "source": [
+    "parameter_values = pybamm.ParameterValues(\"Ai2020\")\n",
+    "model1 = pybamm.lithium_ion.DFN({\"SEI\": \"solvent-diffusion limited\"})\n",
+    "model2 = pybamm.lithium_ion.DFN({\n",
+    "    \"particle mechanics\": \"swelling and cracking\",\n",
+    "    \"SEI\": \"solvent-diffusion limited\",\n",
+    "    \"SEI on cracks\": \"true\",\n",
+    "})\n",
+    "experiment = pybamm.Experiment([\"Discharge at 1C until 3 V\"])\n",
+    "sim1 = pybamm.Simulation(model1, parameter_values=parameter_values, experiment=experiment)\n",
+    "sol1 = sim1.solve()\n",
+    "sim2 = pybamm.Simulation(model2, parameter_values=parameter_values, experiment=experiment)\n",
+    "sol2 = sim2.solve()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c3884817",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

pybamm/models/full_battery_models/base_battery_model.py

@@ -140,6 +140,9 @@ class BatteryModelOptions(pybamm.FuzzyDict):
                     .. math::
                         \\eta_r = \\frac{F}{RT}
                         * (\\phi_s - \\phi_e - U - R_{sei} * L_{sei} * \\frac{I}{aL})
+            * "SEI on cracks" : str
+                Whether to include SEI growth on particle cracks, can be "false"
+                (default) or "true".
             * "SEI porosity change" : str
                 Whether to include porosity change due to SEI formation, can be "false"
                 (default) or "true".
@@ -237,6 +240,7 @@ def __init__(self, extra_options):
                 "ec reaction limited",
             ],
             "SEI film resistance": ["none", "distributed", "average"],
+            "SEI on cracks": ["false", "true"],
             "SEI porosity change": ["false", "true"],
             "stress-induced diffusion": ["false", "true"],
             "surface form": ["false", "differential", "algebraic"],
@@ -332,6 +336,17 @@ def __init__(self, extra_options):
                     "current density as a state' must be 'true'"
                 )
 
+        if options["SEI on cracks"] == "true":
+            if options["particle mechanics"] != "swelling and cracking":
+                raise pybamm.OptionError(
+                    "To model SEI on cracks, 'particle mechanics' must be set to "
+                    "'swelling and cracking'."
+                )
+            elif options["working electrode"] == "positive":
+                raise NotImplementedError(
+                    "SEI on cracks not yet implemented for lithium metal eleectrode."
+                )
+
         # Options not yet compatible with particle-size distributions
         if options["particle size"] == "distribution":
             if options["lithium plating"] != "none":

pybamm/models/full_battery_models/lithium_ion/base_lithium_ion_model.py

@@ -137,11 +137,13 @@ def set_degradation_variables(self):
         # Different way of measuring LLI but should give same value
         LLI_sei = self.variables["Loss of lithium to SEI [mol]"]
         if self.half_cell:
+            LLI_sei_cracks = pybamm.Scalar(0)
             LLI_pl = pybamm.Scalar(0)
         else:
+            LLI_sei_cracks = self.variables["Loss of lithium to SEI on cracks [mol]"]
             LLI_pl = self.variables["Loss of lithium to lithium plating [mol]"]
 
-        LLI_reactions = LLI_sei + LLI_pl
+        LLI_reactions = LLI_sei + LLI_sei_cracks + LLI_pl
         self.variables.update(
             {
                 "Total lithium lost to side reactions [mol]": LLI_reactions,
@@ -199,12 +201,26 @@ def set_sei_submodel(self):
 
         if self.options["SEI"] == "none":
             self.submodels["sei"] = pybamm.sei.NoSEI(self.param, self.options)
+            self.submodels["sei on cracks"] = pybamm.sei.NoSEI(
+                self.param, self.options, cracks=True
+            )
         elif self.options["SEI"] == "constant":
             self.submodels["sei"] = pybamm.sei.ConstantSEI(self.param, self.options)
+            self.submodels["sei on cracks"] = pybamm.sei.NoSEI(
+                self.param, self.options, cracks=True
+            )
         else:
             self.submodels["sei"] = pybamm.sei.SEIGrowth(
-                self.param, reaction_loc, self.options
+                self.param, reaction_loc, self.options, cracks=False
             )
+            if self.options["SEI on cracks"] == "true":
+                self.submodels["sei on cracks"] = pybamm.sei.SEIGrowth(
+                    self.param, reaction_loc, self.options, cracks=True
+                )
+            else:
+                self.submodels["sei on cracks"] = pybamm.sei.NoSEI(
+                    self.param, self.options, cracks=True
+                )
 
     def set_lithium_plating_submodel(self):
         if self.options["lithium plating"] == "none":
@@ -228,7 +244,9 @@ def set_crack_submodel(self):
         for domain in ["Negative", "Positive"]:
             crack = getattr(self.options, domain.lower())["particle mechanics"]
             if crack == "none":
-                pass
+                self.submodels[
+                    domain.lower() + " particle mechanics"
+                ] = pybamm.particle_mechanics.NoMechanics(self.param, domain)
             elif crack == "swelling only":
                 self.submodels[
                     domain.lower() + " particle mechanics"

pybamm/models/submodels/interface/base_interface.py

@@ -41,6 +41,9 @@ def __init__(self, param, domain, reaction, options=None):
         elif reaction == "SEI":
             self.reaction_name = " SEI"
             self.Reaction_icd = "SEI interfacial current density"
+        elif reaction == "SEI on cracks":
+            self.reaction_name = " SEI on cracks"
+            self.Reaction_icd = "SEI on cracks interfacial current density"
         elif reaction == "lithium plating":
             self.reaction_name = " lithium plating"
             self.Reaction_icd = "Lithium plating interfacial current density"