Negative electrode Bruggeman coefficient (electrode)' not found

[ehtec]

• PyBaMM version - latest from Github
• Python version - 3.9

Describe the bug
Some code that is running fine in the latest pip version is not working properly in the latest Github version of Pybamm. This is the error:

KeyError: "'Negative electrode Bruggeman coefficient (electrode)' not found. Best matches are ['Negative electrode Bruggeman coefficient (electrolyte)', 'Positive electrode Bruggeman coefficient (electrolyte)', 'Separator Bruggeman coefficient (electrolyte)']"

To Reproduce
Steps to reproduce the behaviour:

import pybamm as pb
import pybamm
import copy
import numpy as np

# ambient and initial temperature in kelvin
TEMPERATURE = 300.0

# battery type can be cylindric or prismatic
BATTERY_TYPE = "cylindric"

# diameter in m of the cylindric cell. Ignored when another geometry is selected
DIAMETER = 0.02

# widths in m of the prismatic cell. Ignored when another geometry is selected
WIDTH_A = 0.02
WIDTH_B = 0.02

# height
HEIGHT = 0.05

# generator to split list into chunks
def chunks(lst, n):
    if not n:
        raise Exception("n must be a positive integer")

    for i in range(0, len(lst), n):
        yield lst[i:i + n]

def merge_parameter_values(p_A, p_B):
    
    dict_a = dict(p_A)
    dict_b = dict(p_B)
    
    merged_dict = copy.deepcopy(dict_a)
    
    for the_key, the_value in dict_b.items():
        
        if the_key not in merged_dict.keys():
            
            merged_dict.update({the_key: the_value})
    
    return pb.ParameterValues(merged_dict)

def calc_geometry(battery_type=BATTERY_TYPE, diameter=DIAMETER, width_a=WIDTH_A, width_b=WIDTH_B, height=HEIGHT):
    
    if battery_type == 'cylindric':
        
        area = diameter**2 * np.pi / 2 + diameter * np.pi * height
        
        volume = diameter**2 * np.pi * height / 4
    
    elif battery_type == 'prismatic':
        
        area = 2 * (width_a * width_b + width_a * height + width_b * height)
        
        volume = width_a * width_b * height
    
    else:
        
        raise Exception("Unsupported battery type: {0}".format(battery_type))
    
    return area, volume
    
area, volume = calc_geometry()

# lumped with arbitrary geometry specified 
options = {
    "cell geometry": "arbitrary",
    "thermal": "lumped",
    "particle": "Fickian diffusion",
    "particle mechanics": "swelling and cracking"
}

model = pybamm.lithium_ion.DFN(options)

output_variables = [
    "Terminal voltage [V]",
    'Negative particle surface tangential stress [Pa]',
    'Negative particle surface radial stress [Pa]',
    'X-averaged negative particle surface radial stress [Pa]',
    'X-averaged negative particle surface tangential stress [Pa]',
    'Positive particle surface tangential stress [Pa]',
    'Positive particle surface radial stress [Pa]',
    'X-averaged positive particle surface radial stress [Pa]',
    'X-averaged positive particle surface tangential stress [Pa]',
    'Negative particle surface displacement [m]',
    'Positive particle surface displacement [m]'
    ]

param_keys = ['Negative current collector thickness [m]',
 'Negative electrode thickness [m]',
 'Separator thickness [m]',
 'Positive electrode thickness [m]',
 'Positive current collector thickness [m]',
 'Electrode height [m]',
 'Electrode width [m]',
 'Cell cooling surface area [m2]',
 'Cell volume [m3]',
 'Negative current collector density [kg.m-3]',
 'Positive current collector density [kg.m-3]',
 'Negative current collector specific heat capacity [J.kg-1.K-1]',
 'Positive current collector specific heat capacity [J.kg-1.K-1]',
 'Negative current collector thermal conductivity [W.m-1.K-1]',
 'Positive current collector thermal conductivity [W.m-1.K-1]',
 'Nominal cell capacity [A.h]',
 'Typical current [A]',
 'Current function [A]',
 'Negative electrode conductivity [S.m-1]',
 'Maximum concentration in negative electrode [mol.m-3]',
 'Negative electrode diffusivity [m2.s-1]',
 'Negative electrode OCP [V]',
 'Negative electrode porosity',
 'Negative electrode active material volume fraction',
 'Negative particle radius [m]',
 'Negative electrode Bruggeman coefficient (electrolyte)',
 'Negative electrode electrons in reaction',
 'Negative electrode exchange-current density [A.m-2]',
 'Negative electrode density [kg.m-3]',
 'Negative electrode specific heat capacity [J.kg-1.K-1]',
 'Negative electrode thermal conductivity [W.m-1.K-1]',
 'Negative electrode OCP entropic change [V.K-1]',
 'Positive electrode conductivity [S.m-1]',
 'Maximum concentration in positive electrode [mol.m-3]',
 'Positive electrode diffusivity [m2.s-1]',
 'Positive electrode OCP [V]',
 'Positive electrode porosity',
 'Positive electrode active material volume fraction',
 'Positive particle radius [m]',
 'Positive electrode Bruggeman coefficient (electrolyte)',
 'Positive electrode electrons in reaction',
 'Positive electrode exchange-current density [A.m-2]',
 'Positive electrode density [kg.m-3]',
 'Positive electrode specific heat capacity [J.kg-1.K-1]',
 'Positive electrode thermal conductivity [W.m-1.K-1]',
 'Positive electrode OCP entropic change [V.K-1]',
 'Separator porosity',
 'Separator Bruggeman coefficient (electrolyte)',
 'Separator density [kg.m-3]',
 'Separator specific heat capacity [J.kg-1.K-1]',
 'Separator thermal conductivity [W.m-1.K-1]',
 'Typical electrolyte concentration [mol.m-3]',
 'Cation transference number',
 '1 + dlnf/dlnc',
 'Electrolyte diffusivity [m2.s-1]',
 'Electrolyte conductivity [S.m-1]',
 'Reference temperature [K]',
 'Ambient temperature [K]',
 'Total heat transfer coefficient [W.m-2.K-1]',
 'Number of electrodes connected in parallel to make a cell',
 'Number of cells connected in series to make a battery',
 'Lower voltage cut-off [V]',
 'Upper voltage cut-off [V]',
 'Initial concentration in negative electrode [mol.m-3]',
 'Initial concentration in positive electrode [mol.m-3]',
 'Initial concentration in electrolyte [mol.m-3]',
 'Initial temperature [K]'] + ['Inner SEI partial molar volume [m3.mol-1]',
 'Outer SEI partial molar volume [m3.mol-1]',
 'SEI reaction exchange current density [A.m-2]',
 'SEI resistivity [Ohm.m]',
 'Initial inner SEI thickness [m]',
 'Initial outer SEI thickness [m]']

parameter_values_dict = dict(pybamm.ParameterValues(chemistry=pybamm.parameter_sets.Marquis2019))

required_parameter_values_dict = {}

for elem in parameter_values_dict.keys():
    
    if elem in param_keys:
        
        required_parameter_values_dict.update({elem: parameter_values_dict[elem]})

# assert len(required_parameter_values_dict) == len(param_keys)

parameter_values = pb.ParameterValues(required_parameter_values_dict)

ai_params = pb.ParameterValues(chemistry=pb.parameter_sets.Ai2020)

additional_parameter_values_dict = {
    'Negative electrode cracking rate': ai_params['Negative electrode cracking rate'],
    'Negative electrode activation energy for cracking rate [J.mol-1]': ai_params['Negative electrode activation energy for cracking rate [J.mol-1]'],
    "Negative electrode Young's modulus [Pa]": ai_params["Negative electrode Young's modulus [Pa]"],
    "Negative electrode Paris' law constant m": ai_params["Negative electrode Paris' law constant m"],
    "Negative electrode initial crack length [m]": ai_params["Negative electrode initial crack length [m]"],
    "Negative electrode partial molar volume [m3.mol-1]": ai_params["Negative electrode partial molar volume [m3.mol-1]"],
    "Negative electrode Poisson's ratio": ai_params["Negative electrode Poisson's ratio"],
    "Negative electrode Paris' law constant b": ai_params["Negative electrode Paris' law constant b"],
    'Positive electrode cracking rate': ai_params['Positive electrode cracking rate'],
    'Positive electrode activation energy for cracking rate [J.mol-1]': ai_params['Positive electrode activation energy for cracking rate [J.mol-1]'],
    "Positive electrode Young's modulus [Pa]": ai_params["Positive electrode Young's modulus [Pa]"],
    "Positive electrode Paris' law constant m": ai_params["Positive electrode Paris' law constant m"],
    "Positive electrode initial crack length [m]": ai_params["Positive electrode initial crack length [m]"],
    "Positive electrode partial molar volume [m3.mol-1]": ai_params["Positive electrode partial molar volume [m3.mol-1]"],
    "Positive electrode Poisson's ratio": ai_params["Positive electrode Poisson's ratio"],
    "Positive electrode Paris' law constant b": ai_params["Positive electrode Paris' law constant b"],
    'Negative electrode reference concentration for free of deformation [mol.m-3]': ai_params['Negative electrode reference concentration for free of deformation [mol.m-3]'],
    'Positive electrode reference concentration for free of deformation [mol.m-3]': ai_params['Negative electrode reference concentration for free of deformation [mol.m-3]'],
    'Negative electrode number of cracks per unit area [m-2]': ai_params['Negative electrode number of cracks per unit area [m-2]'],
    'Positive electrode number of cracks per unit area [m-2]': ai_params['Positive electrode number of cracks per unit area [m-2]'],
    'Negative electrode initial crack width [m]': ai_params['Negative electrode initial crack width [m]'],
    'Positive electrode initial crack width [m]': ai_params['Positive electrode initial crack width [m]'],
    'Cell thermal expansion coefficient [m.K-1]': ai_params['Cell thermal expansion coefficient [m.K-1]'],
    'Negative electrode volume change': ai_params['Negative electrode volume change'],
    'Positive electrode volume change': ai_params['Positive electrode volume change']
}

additional_parameter_values = pb.ParameterValues(additional_parameter_values_dict)

parameter_values = merge_parameter_values(additional_parameter_values, parameter_values)

parameter_values["Current function [A]"] = 0
parameter_values["Initial temperature [K]"] = TEMPERATURE
parameter_values["Ambient temperature [K]"] = TEMPERATURE
parameter_values["Cell cooling surface area [m2]"] = area
parameter_values["Cell volume [m3]"] = volume

# pick solver 
solver = pybamm.CasadiSolver(mode="fast", atol=1e-3)

sim = pb.Simulation(model, parameter_values=parameter_values, solver=solver)

sim.solve([0, 1000])

for temp_vars in chunks(output_variables, 6):
    sim.plot(temp_vars, n_rows=3, figsize=(8, 12))

Expected behaviour
The simulation should finish without errors and the results should be plotted.

Workaround
This is how the error can be prevented:

This needs to be added to the additional_parameter_values_dict:

'Negative electrode Bruggeman coefficient (electrode)': 0,
'Positive electrode Bruggeman coefficient (electrode)': 0

And this right above the cell throwing the error:

parameter_values['Negative electrode Bruggeman coefficient (electrode)'] = parameter_values['Negative electrode Bruggeman coefficient (electrolyte)']
parameter_values['Positive electrode Bruggeman coefficient (electrode)'] = parameter_values['Positive electrode Bruggeman coefficient (electrolyte)']

[brosaplanella]

There was a bug in the previous version in which the Bruggeman coefficient in the electrode wasn't used. This has now been fixed so when you define the parameters you need to define them too.

This is certainly a very good question, so I will convert it into a discussion.