Issue 1245 active material

[valentinsulzer]

Description

Set up active material models ready to model loss of active material
Fixes #1245

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: $ flake8
• All tests pass: $ python run-tests.py --unit
• The documentation builds: $ cd docs and then $ make clean; make html

You can run all three at once, using $ python run-tests.py --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

Merging #1262 (41284b7) into develop (0d34872) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #1262      +/-   ##
===========================================
+ Coverage    98.06%   98.07%   +0.01%     
===========================================
  Files          265      270       +5     
  Lines        14900    15030     +130     
===========================================
+ Hits         14611    14741     +130     
  Misses         289      289              

Impacted Files	Coverage Δ
pybamm/models/submodels/porosity/base_porosity.py	100.00% <ø> (ø)
...m/models/full_battery_models/base_battery_model.py	99.68% <100.00%> (+<0.01%)	⬆️
...l_battery_models/lead_acid/base_lead_acid_model.py	100.00% <100.00%> (ø)
...ybamm/models/full_battery_models/lead_acid/full.py	100.00% <100.00%> (ø)
...dels/full_battery_models/lead_acid/higher_order.py	98.09% <100.00%> (+0.01%)	⬆️
...ybamm/models/full_battery_models/lead_acid/loqs.py	100.00% <100.00%> (ø)
...ttery_models/lithium_ion/base_lithium_ion_model.py	100.00% <100.00%> (ø)
...bamm/models/full_battery_models/lithium_ion/dfn.py	100.00% <100.00%> (ø)
...bamm/models/full_battery_models/lithium_ion/spm.py	100.00% <100.00%> (ø)
...amm/models/full_battery_models/lithium_ion/spme.py	100.00% <100.00%> (ø)
... and 39 more

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[rtimms]

thanks @tinosulzer !

[rtimms]

If you set a model for LAM then the variable corresponding to epsislon_s_n and the parameter epsilon_s_n will be different (I think?) - the latter will just give the initial parameter value/function provided. Will this cause confusion? What you really provide as a parameter is the initial active material volume fraction, but I think it would be messy to append "Initial" everywhere. The same is true for porosity.

I don't think this needs changing here, but something to think about in the future. I think my opinion is to leave it as is, and that it is understood that if you have a model describing how a parameter changes then that parameter should be treated as a variable.

[valentinsulzer]

Yes, this is something we should mention when we put together the workflow for degradation modeling. I agree putting "Initial" into the parameter names would be messy

[weilongai]

Hi, I have made a loss of active material submodel in pybamm. It is based on the LAM model (Eq. 25) in Reniers et al. Would you mind if I push it here?
Reniers, J. M., Mulder, G., & Howey, D. A. (2019). Review and performance comparison of mechanical-chemical degradation models for lithium-ion batteries. Journal of The Electrochemical Society, 166(14), A3189.

[valentinsulzer]

Yes, go for it! This branch has now been merged though so you'll need to open a PR to develop

[weilongai]

I see there is a place holder already, but my implementation is not based on this. How do you think is the best way to do? Is it good to push my current version (tracing back to the last commit on Nov 17, 2020) to develop anyway?