Enable cylindrical and platelet particle shape options

[d-cogswell]

Description

Enables cylindrical and platelet as model options for particle shape. A 2-tuple can also now be provided to assign different particle shapes at the anode and cathode. Cylindrical particles are discretized in cylindrical polar coordinates and given an area/volume ratio of 2/R. Platelet particles are discretized in cartesian coordinates and given an area/volume ratio of 1/R.

The coordinate change is applied to copies of r_n and r_p to avoid the bad programming practice of modifying global variables in pybamm.standard_spatial_vars. This requires a minimal number of code changes while also insuring that changes made during the creation of a model are not accidentally inherited by subsequent models.

The model options documentation for particle shape has been updated.

Fixes #1072

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 -m pytest (or $ nox -s tests)
• The documentation builds: $ python -m pytest --doctest-plus src (or $ nox -s doctests)

You can run integration tests, unit tests, and doctests together at once, using $ 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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.71%. Comparing base (10a404e) to head (a33a7d7).
Report is 81 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4827   +/-   ##
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  Coverage    98.71%   98.71%           
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  Files          304      304           
  Lines        23478    23496   +18     
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+ Hits         23176    23194   +18     
  Misses         302      302           

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[DrSOKane]

In terms of the coding, this is flawless.

In terms of how useful this upgrade will be, I am not sure. While supervising a summer project with @katiezzzzz, I discovered that GITT measurements of diffusivity presuppose the particle to have a particular shape (usually spherical), which limits the utility of this feature. @brosaplanella I believe you looked into this but not sure if you ever published your findings.

Despite this, I would like to thank @d-cogswell for the code and strongly recommend its inclusion in PyBaMM. The question around diffusivity could be the subject of future work, by yourself of another PyBaMM user who can now hit the ground running.

[valentinsulzer]

I'm not sure this would work as is since standard_spatial_vars.r_n will still be used in other places with the spherical coordinates (e.g. in the geometry, and in r_average). Have you tested that this works?

[valentinsulzer]

See #4857

[d-cogswell]

I'm not sure this would work as is since standard_spatial_vars.r_n will still be used in other places with the spherical coordinates (e.g. in the geometry, and in r_average). Have you tested that this works?

After some more testing, I'm noticing my solution here does not produce the same results as when the global variable is modified. This must be because the global variable is still being used in other places.

[d-cogswell]

I'm working on a modification that uses factory functions for r_n and r_p instead of global variables.

[valentinsulzer]

I think it would be easier to just do #4857

[d-cogswell]

I agree, #4857 is a better solution. With my approach, there isn't a good solution for the calls to pybamm.standard_spatial_vars from the Mesh classes.