Composite model for particle mechanics

[mohammedasher]

Description

Implementing the composite model for particle mechanics: The phase in the current particle mechanics implementation is set to 'primary' by default. This is being updated to support independent phases (e.g., primary/secondary such as Gr/Si). To accommodate these changes, the associated files in full_battery_models, interface, SEI, and particle modules have been updated, along with modifications to the Chen2020 parameter set.

This is part of the work by Bonkile et al.

Fixes # (issue)

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist:

• No style issues: $ pre-commit run (or $ nox -s pre-commit) (see CONTRIBUTING.md for how to set this up to run automatically when committing locally, in just two lines of code)
• All tests pass: $ python run-tests.py --all (or $ nox -s tests)
• The documentation builds: $ python run-tests.py --doctest (or $ nox -s doctests)

You can run integration tests, unit tests, and doctests together at once, using $ python run-tests.py --quick (or $ nox -s quick).

Further checks:

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[mohammedasher]

@brosaplanella Unable to request specific reviewer in draft mode.

[brosaplanella]

Hi Asher! The style tests are failing, this is because you have some defined variables/function that are not used. This is an issue it can't be automatically fixed by the pre-commit bot, so you will need to do it manually. You can find what's causing the issue if you check the failing test (https://github.com/pybamm-team/PyBaMM/actions/runs/11345431722/job/31553629641?pr=4516) and scroll down (you need to start reading at line 46).

[mohammedasher]

Hi @brosaplanella,
I've addressed the style issues, and now the remaining problem is with the unit tests. Although multiple tests are failing, they all stem from two types of errors:

1. AttributeError: 'set' object has no attribute 'values'
2. AttributeError: 'ReactionDriven' object has no attribute 'phase_name'
   Could you advise on how I should proceed with resolving these? Thank you!

[brosaplanella]

Hi! The latter is because the ReactionDriven porosity model (reaction_driven_porosity.py) is not available for composite materials, that's why it breaks. I need to dig a bit more regarding the first issue.

BTW, it's better to not force push. I believe the issue you encountered is that the pre-commit bot made some style changes. In those cases you have to pull first and then push.

[DrSOKane]

Hi! The latter is because the ReactionDriven porosity model (reaction_driven_porosity.py) is not available for composite materials, that's why it breaks.

I made a PR that fixes this, which Sunil is already using (he requested it). @mohammedasher you can go to this branch of my fork of PyBaMM and merge the changes into your branch.

[mohmdasher]

Thank you @DrSOKane; merging reaction_driven_porosity from your branch significantly reduced the number of failed tests.
Now, the errors are:

• AttributeError: 'set' object has no attribute 'values'
• AttributeError: 'ReactionDriven' object has no attribute 'phase_name'
  Can this be re-scoped to self.phase_name??
• pybamm.expression_tree.exceptions.ModelError: Missing variable for submodel 'porosity': 'Negative total SEI thick...'
• Failed: DID NOT RAISE <class 'pybamm.expression_tree.exceptions.OptionError'>

[brosaplanella]

Some comments that should help fix the bugs. Regarding the one about the "Negative total SEI thickness [m]" I have not been able to find where the issue is. Maybe @DrSOKane knows, as he has been working with the model recently.

[brosaplanella]

I think this one is causing the set has no values attribute, as you forgot to pass the variable in the inputs.

[brosaplanella]

These two are repository specific, I would suggest to remove them

[brosaplanella]

The issue with the phase_name is that this class does not take a phase as argument (see for example how loss_active_material.py does it. However, I don't understand how this model works: you have different values for different phases for the roughness, but the SEI on cracks thickness is only one. Shouldn't you just have one roughness ratio overall?