Merge branch 'develop' into black_action

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Features
 
 -   Added function `pybamm.get_git_commit_info()`, which returns information about the last git commit, useful for reproducibility ([#2293](https://github.com/pybamm-team/PyBaMM/pull/2293))
+-   Added SEI model for composite electrodes ([#2290](https://github.com/pybamm-team/PyBaMM/pull/2290))
 -   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

examples/notebooks/models/using-submodels.ipynb

@@ -490,8 +490,8 @@
     "model.submodels[\n",
     "    \"Positive particle mechanics\"\n",
     "] = pybamm.particle_mechanics.NoMechanics(model.param, \"Positive\", model.options)\n",
-    "model.submodels[\"sei\"] = pybamm.sei.NoSEI(model.param)\n",
-    "model.submodels[\"sei on cracks\"] = pybamm.sei.NoSEI(model.param, cracks=True)\n",
+    "model.submodels[\"sei\"] = pybamm.sei.NoSEI(model.param, model.options)\n",
+    "model.submodels[\"sei on cracks\"] = pybamm.sei.NoSEI(model.param, model.options, cracks=True)\n",
     "model.submodels[\"lithium plating\"] = pybamm.lithium_plating.NoPlating(model.param)"
    ]
   },
@@ -632,7 +632,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.13"
   },
   "toc": {
    "base_numbering": 1,

examples/scripts/custom_model.py

@@ -98,8 +98,10 @@
 model.submodels["Positive particle mechanics"] = pybamm.particle_mechanics.NoMechanics(
     model.param, "Positive", model.options
 )
-model.submodels["sei"] = pybamm.sei.NoSEI(model.param)
-model.submodels["sei on cracks"] = pybamm.sei.NoSEI(model.param, cracks=True)
+model.submodels["sei"] = pybamm.sei.NoSEI(model.param, model.options)
+model.submodels["sei on cracks"] = pybamm.sei.NoSEI(
+    model.param, model.options, cracks=True
+)
 model.submodels["lithium plating"] = pybamm.lithium_plating.NoPlating(model.param)
 
 # build model

pybamm/expression_tree/concatenations.py

@@ -117,7 +117,7 @@ def _concatenation_new_copy(self, children):
 
     def _concatenation_jac(self, children_jacs):
         """Calculate the jacobian of a concatenation."""
-        return NotImplementedError
+        raise NotImplementedError
 
     def _evaluate_for_shape(self):
         """See :meth:`pybamm.Symbol.evaluate_for_shape`"""

pybamm/expression_tree/operations/evaluate_python.py

@@ -38,7 +38,7 @@ class JaxCooMatrix:
     """
 
     def __init__(self, row, col, data, shape):
-        if not pybamm.have_jax():
+        if not pybamm.have_jax():  # pragma: no cover
             raise ModuleNotFoundError(
                 "Jax or jaxlib is not installed, please see https://pybamm.readthedocs.io/en/latest/install/GNU-linux.html#optional-jaxsolver"  # noqa: E501
             )
@@ -413,7 +413,7 @@ def to_python(symbol, debug=False, output_jax=False):
 
     line_format = "{} = {}"
 
-    if debug:
+    if debug:  # pragma: no cover
         variable_lines = [
             "print('{}'); ".format(
                 line_format.format(id_to_python_variable(symbol_id, False), symbol_line)
@@ -540,7 +540,7 @@ class EvaluatorJax:
     """
 
     def __init__(self, symbol):
-        if not pybamm.have_jax():
+        if not pybamm.have_jax():  # pragma: no cover
             raise ModuleNotFoundError(
                 "Jax or jaxlib is not installed, please see https://pybamm.readthedocs.io/en/latest/install/GNU-linux.html#optional-jaxsolver"  # noqa: E501
             )

pybamm/expression_tree/symbol.py

@@ -811,14 +811,16 @@ def evaluate_ignoring_errors(self, t=0):
                 return None
             elif error.args[0] == "StateVectorDot cannot evaluate input 'y_dot=None'":
                 return None
-            else:
+            else:  # pragma: no cover
                 raise error
-        except ValueError as e:
+        except ValueError as error:
             # return None if specific ValueError is raised
             # (there is a e.g. Time in the tree)
-            if e.args[0] == "t must be provided":
+            if error.args[0] == "t must be provided":
                 return None
-            raise pybamm.ShapeError("Cannot find shape (original error: {})".format(e))
+            raise pybamm.ShapeError(
+                f"Cannot find shape (original error: {error})"
+            )  # pragma: no cover
         return result
 
     def evaluates_to_number(self):
@@ -891,7 +893,7 @@ def create_copy(self):
         """
         raise NotImplementedError(
             """method self.new_copy() not implemented
-               for symbol {!s} of type {}""".format(
+            for symbol {!s} of type {}""".format(
                 self, type(self)
             )
         )

pybamm/input/discharge_data/Ecker2015/README.md

@@ -2,7 +2,7 @@
 
 Experimental data (Time [s], Terminal voltage [V]) for a 1C and 5C constant current discharge of a Kokam SLPB 75106100 cell at a temperature of 25°C from
 
->Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
+> Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
 
 The data were collected from Figure 8 of
 

pybamm/input/parameters/lithium_ion/cells/kokam_Ecker2015/README.md

@@ -4,7 +4,7 @@ Parameters for a Kokam SLPB 75106100 cell, from the papers
 
 > Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery I. determination of parameters." Journal of the Electrochemical Society 162.9 (2015): A1836-A1848.
 
->Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
+> Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
 
 The tab placement parameters are taken from measurements in
 

pybamm/input/parameters/lithium_ion/experiments/1C_discharge_from_full_Ecker2015/README.md

@@ -2,5 +2,5 @@
 
 Discharge lithium-ion battery from full charge at 1C, using the initial conditions from the paper
 
->Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857..
+> Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857..
 

pybamm/input/parameters/lithium_ion/negative_electrodes/graphite_Ecker2015/README.md

@@ -4,7 +4,7 @@ Parameters for a graphite negative electrode, from the papers:
 
 > Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery I. determination of parameters." Journal of the Electrochemical Society 162.9 (2015): A1836-A1848.
 
->Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
+> Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
 
 The fits to data for the electrode and electrolyte properties are those provided
 by Dr. Simon O’Kane in the paper:

pybamm/input/parameters/lithium_ion/positive_electrodes/LiNiCoO2_Ecker2015/README.md

@@ -4,7 +4,7 @@ Parameters for a Lithium Nickel Cobalt Oxide positive electrode, from the papers
 
 > Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery i. determination of parameters." Journal of the Electrochemical Society 162.9 (2015): A1836-A1848.
 
->Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
+> Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
 
 The fits to data for the electrode and electrolyte properties are those provided
 by Dr. Simon O’Kane in the paper:

pybamm/input/parameters/lithium_ion/seis/example_composite/README.md

@@ -0,0 +1,5 @@
+# SEI parameters
+
+Example parameters for composite SEI on silicon/graphite. Both phases use the same values, from the paper
+
+> Yang, X., Leng, Y., Zhang, G., Ge, S., Wang, C. (2017). Modeling of lithium plating induced aging of lithium-ion batteries: Transition from linear to nonlinear aging. Journal of Power Sources, 360, 28-40.

pybamm/input/parameters/lithium_ion/seis/example_composite/parameters.csv

@@ -0,0 +1,28 @@
+Name [units],Value,Reference,Notes
+# Empty rows and rows starting with ‘#’ will be ignored,,,
+,,,
+# SEI properties,,,
+Primary: Ratio of lithium moles to SEI moles,2,,Assume SEI made of LEDC and/or Li2CO3
+Primary: Inner SEI partial molar volume [m3.mol-1],9.585e-5, Safari paper,
+Primary: Outer SEI partial molar volume [m3.mol-1],9.585e-5, Safari paper,
+Primary: SEI resistivity [Ohm.m],2e5, Safari paper,
+Primary: Initial inner SEI thickness [m], 2.5E-9, 2.5E-9 1/2 of initial thickness in Safari paper,
+Primary: Initial outer SEI thickness [m], 2.5E-9, 1/2 of initial thickness in Safari paper,
+Primary: EC initial concentration in electrolyte [mol.m-3], 4.541E3, Safari paper,
+Primary: EC diffusivity [m2.s-1], 2E-18, adjusted parameter in Yang paper,
+Primary: SEI kinetic rate constant [m.s-1], 1e-12, adjusted parameter in Yang paper,
+Primary: SEI open-circuit potential [V], 0.4, Safari paper,
+Primary: SEI growth activation energy [J.mol-1], 0,,
+,,,
+Secondary: Ratio of lithium moles to SEI moles,2,,Assume SEI made of LEDC and/or Li2CO3
+Secondary: Inner SEI partial molar volume [m3.mol-1],9.585e-5, Safari paper,
+Secondary: Outer SEI partial molar volume [m3.mol-1],9.585e-5, Safari paper,
+Secondary: SEI resistivity [Ohm.m],2e5, Safari paper,
+Secondary: Initial inner SEI thickness [m], 2.5E-9, 2.5E-9 1/2 of initial thickness in Safari paper,
+Secondary: Initial outer SEI thickness [m], 2.5E-9, 1/2 of initial thickness in Safari paper,
+Secondary: EC initial concentration in electrolyte [mol.m-3], 4.541E3, Safari paper,
+Secondary: EC diffusivity [m2.s-1], 2E-18, adjusted parameter in Yang paper,
+Secondary: SEI kinetic rate constant [m.s-1], 1e-12, adjusted parameter in Yang paper,
+Secondary: SEI open-circuit potential [V], 0.4, Safari paper,
+Secondary: SEI growth activation energy [J.mol-1], 0,,
+,,,

pybamm/input/parameters/lithium_ion/separators/separator_Ecker2015/README.md

@@ -4,7 +4,7 @@ Parameters for the separator from the papers
 
 > Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery i. determination of parameters." Journal of the Electrochemical Society 162.9 (2015): A1836-A1848.
 
->Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
+> Ecker, Madeleine, et al. "Parameterization of a physico-chemical model of a lithium-ion battery II. Model validation." Journal of The Electrochemical Society 162.9 (2015): A1849-A1857.
 
 The thermal material properties are for a 5 Ah power pouch cell by Kokam. The data are extracted from
 

pybamm/models/event.py

@@ -12,6 +12,10 @@ class EventType(Enum):
     should return the time that the discontinuity occurs. The solver will integrate up
     to the discontinuity and then restart just after the discontinuity.
 
+    INTERPOLANT_EXTRAPOLATION indicates that a pybamm.Interpolant object has been
+    evaluated outside of the range.
+
+    SWITCH indicates an event switch that is used in CasADI "fast with events" model.
     """
 
     TERMINATION = 0
@@ -29,12 +33,11 @@ class Event:
     ----------
 
     name: str
-        A string giving the name of the event
-    event_type: :class:`pybamm.EventType`
-        An enum defining the type of event
+        A string giving the name of the event.
     expression: :class:`pybamm.Symbol`
-        An expression that defines when the event occurs
-
+        An expression that defines when the event occurs.
+    event_type: :class:`pybamm.EventType` (optional)
+        An enum defining the type of event. By default it is set to TERMINATION.
 
     """
 

pybamm/models/full_battery_models/base_battery_model.py

@@ -510,7 +510,6 @@ def __init__(self, extra_options):
                 options["surface form"] != "false"
                 and options["particle size"] == "single"
                 and options["particle"] == "Fickian diffusion"
-                and options["SEI"] == "none"
                 and options["particle mechanics"] == "none"
                 and options["loss of active material"] == "none"
                 and options["lithium plating"] == "none"
@@ -519,7 +518,7 @@ def __init__(self, extra_options):
                     "If there are multiple particle phases: 'surface form' cannot be "
                     "'false', 'particle size' must be 'false', 'particle' must be "
                     "'Fickian diffusion'. Also the following must "
-                    "be 'none': 'SEI', 'particle mechanics', "
+                    "be 'none': 'particle mechanics', "
                     "'loss of active material', 'lithium plating'"
                 )
 
@@ -1256,8 +1255,10 @@ def set_voltage_variables(self):
             eta_sei_av = self.variables["SEI film overpotential"]
             eta_sei_av_dim = self.variables["SEI film overpotential [V]"]
         else:
-            eta_sei_av = self.variables["X-averaged SEI film overpotential"]
-            eta_sei_av_dim = self.variables["X-averaged SEI film overpotential [V]"]
+            eta_sei_av = self.variables[f"X-averaged {phase_n}SEI film overpotential"]
+            eta_sei_av_dim = self.variables[
+                f"X-averaged {phase_n}SEI film overpotential [V]"
+            ]
 
         # TODO: add current collector losses to the voltage in 3D
 

pybamm/models/full_battery_models/lead_acid/base_lead_acid_model.py

@@ -104,7 +104,7 @@ def set_active_material_submodel(self):
 
     def set_sei_submodel(self):
 
-        self.submodels["sei"] = pybamm.sei.NoSEI(self.param)
+        self.submodels["sei"] = pybamm.sei.NoSEI(self.param, self.options)
 
     def set_lithium_plating_submodel(self):