Half Cell model

[sklein-ise]

Hello,

I am trying to use the new half cell model of the new release

options = {"working electrode" : "positive"}
model = pybamm.lithium_ion.DFN(options = options)
param = model.default_parameter_values
#param.update( param_dic)   
sim =  pybamm.Simulation(model, 
                     parameter_values=param)
sim.solve(
    t_eval=np.linspace(0, 1000, 200),
    solver=pybamm.CasadiSolver(mode="safe"),
    )
sol= sim.solution 

but I get the error:

KeyError: KeyError("'Typical plated lithium concentration [mol.m-3]' not found. Best matches are ['Typical electrolyte concentration [mol.m-3]', 'Bulk solvent concentration [mol.m-3]', 'Lithium interstitial reference concentration [mol.m-3]']")

Am I using it wrong?

Best regards

[brosaplanella]

The reason is that the parameter set you are using does not have a lithium plating parameter set. You can either add it to a parameter set by doing:

chemistry = pybamm.parameter_sets.Chen2020
chemistry["lithium plating"] = "okane2020_Li_plating"
param = pybamm.ParameterValues(chemistry=chemistry)

or you can use a parameter set that already has it (e.g. Chen2020_plating)

param = pybamm.ParameterValues(chemistry=pybamm.parameter_sets.Chen2020_plating)

[brosaplanella]

Note that this will also cause another error if you try to do

sim.plot()

as by default will try to plot the negative particle concentrations which in this case are not applicable. You can instead choose which variables to plot by doing

sim.plot(output_variables=["Terminal voltage [V]"]

and add as many variables as you want to plot in the list.

[brosaplanella]

I have opened an issue for each one (#1719 and #1720). If you would like to contribute to PyBaMM, #1720 is a very good first issue to start with. If you want to tackle it, feel free to assign it to yourself.

[sklein-ise]

Thanks! I added the lithium parameter set and now it works. I'd also love to contribute but I won't have time to do it until january since I am in the final stages of my master thesis.

There is also another error when using the Half cell model with the experiment class:

experiment = pybamm.Experiment(
    [(
      "Discharge at 0.5C for 30 seconds (0.01 second period)")],
    )
options = {"working electrode" : "positive"}


model = pybamm.lithium_ion.DFN(options = options)
chemistry = pybamm.parameter_sets.Chen2020
chemistry["lithium plating"] = "okane2020_Li_plating"
param = pybamm.ParameterValues(chemistry=chemistry)


sim =  pybamm.Simulation(model, parameter_values=param, experiment=experiment)

sim.solve( solver=pybamm.CasadiSolver(mode="safe"))

KeyError: "'Negative electrode capacity [A.h]' not found. Best matches are ['Positive electrode capacity [A.h]', 'Negative electrode temperature [K]', 'Negative electrode exchange current density [A.m-2]']"

**edit for clarity
I was trying to fix it by adding the "'Negative electrode capacity [A.h]' value to the parameter set but it says it cannot be updated because there is no default value.

Is the experiment class not compatible with the Halfcell model yet?

[sklein-ise]

I was using the Code snippet from above. Last part of the debug information:

...
2021-10-13 14:55:33,834 - [VERBOSE] base_solver.step(1329): Finish stepping Doyle-Fuller-Newman model (the solver successfully reached the end of the integration interval)
2021-10-13 14:55:33,835 - [VERBOSE] base_solver.step(1330): Set-up time: 127.013 ms, Step time: 1.030 s (of which integration time: 85.768 ms), Total time: 1.157 s
2021-10-13 14:55:33,836 - [DEBUG] solution.update(441): Post-processing Discharge capacity [A.h]
2021-10-13 14:55:34,011 - [DEBUG] solution.update(441): Post-processing Negative electrode capacity [A.h]

and the error:

KeyError                                  Traceback (most recent call last)
C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\util.py in __getitem__(self, key)
     89         try:
---> 90             return super().__getitem__(key)
     91         except KeyError:

KeyError: 'Negative electrode capacity [A.h]'

During handling of the above exception, another exception occurred:

KeyError                                  Traceback (most recent call last)
<ipython-input-4-7d46ab997494> in <module>
     15 sim =  pybamm.Simulation(model, parameter_values=param, experiment=experiment)
     16 
---> 17 sim.solve( solver=pybamm.CasadiSolver(mode="safe"))

C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\simulation.py in solve(self, t_eval, solver, check_model, save_at_cycles, calc_esoh, starting_solution, initial_soc, **kwargs)
    894 
    895                 # At the final step of the inner loop we save the cycle
--> 896                 cycle_solution, cycle_summary_variables = pybamm.make_cycle_solution(
    897                     steps,
    898                     esoh_sim,

C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\solvers\solution.py in make_cycle_solution(step_solutions, esoh_sim, save_this_cycle)
    784     cycle_solution.steps = step_solutions
    785 
--> 786     cycle_summary_variables = get_cycle_summary_variables(cycle_solution, esoh_sim)
    787 
    788     if save_this_cycle:

C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\solvers\solution.py in get_cycle_summary_variables(cycle_solution, esoh_sim)
    837     last_state = cycle_solution.last_state
    838     for var in degradation_variables:
--> 839         data_first = first_state[var].data
    840         data_last = last_state[var].data
    841         cycle_summary_variables[var] = data_last[0]

C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\solvers\solution.py in __getitem__(self, key)
    509         else:
    510             # otherwise create it, save it and then return it
--> 511             self.update(key)
    512             return self._variables[key]
    513 

C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\solvers\solution.py in update(self, variables)
    449             # Otherwise a standard ProcessedVariable is ok
    450             else:
--> 451                 vars_pybamm = [model.variables[key] for model in self.all_models]
    452 
    453                 # Iterate through all models, some may be in the list several times and

C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\solvers\solution.py in <listcomp>(.0)
    449             # Otherwise a standard ProcessedVariable is ok
    450             else:
--> 451                 vars_pybamm = [model.variables[key] for model in self.all_models]
    452 
    453                 # Iterate through all models, some may be in the list several times and

C:\ProgramData\Anaconda3\envs\ISE_1\lib\site-packages\pybamm\util.py in __getitem__(self, key)
    102                 )
    103             best_matches = self.get_best_matches(key)
--> 104             raise KeyError(f"'{key}' not found. Best matches are {best_matches}")
    105 
    106     def search(self, key, print_values=False):

KeyError: "'Negative electrode capacity [A.h]' not found. Best matches are ['Positive electrode capacity [A.h]', 'Negative electrode temperature [K]', 'Negative electrode exchange current density [A.m-2]']"

[brosaplanella]

I think it is because in a half cell the capacity is not calculated for the lithium counter electrode (the model takes it as an infinite source of lithium). Why do you want to plot the capacity of the negative electrode?

[sklein-ise]

I wasn't trying to plot the capacity of the negative electrode. I wanted to test the experiment class with the half cell model:

import pybamm
experiment = pybamm.Experiment(
    [(
      "Discharge at 0.5C for 30 seconds (0.01 second period)")],
    )
options = {"working electrode" : "positive"}


model = pybamm.lithium_ion.DFN(options = options)
chemistry = pybamm.parameter_sets.Chen2020
chemistry["lithium plating"] = "okane2020_Li_plating"
param = pybamm.ParameterValues(chemistry=chemistry)


sim =  pybamm.Simulation(model, parameter_values=param, experiment=experiment)

sim.solve( solver=pybamm.CasadiSolver(mode="safe"))

And got the error that I mentioned above.

[brosaplanella]

I think this should be fixed in the most recent version. When we release it (at some point this week) can you check again and see if the error persists? Otherwise you can test it now if you install the develop version.

[sklein-ise]

It works with the new release! Thank you!