Issue 1115 surface area

[rtimms]

Description

Computes surface area per unit volume a as a function of particle shape. A major change is that the modules that contained the standard parameters are now classes (so they can take options, such as particle shape).

Also fixes some bugs in the models when R=R(x). For now we don't allow active material volume fraction to be a function of x (see #1119), so we only have a(x) when we have R(x).

Fixes #1115

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 #1120 into develop will increase coverage by 0.05%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #1120      +/-   ##
===========================================
+ Coverage    97.82%   97.87%   +0.05%     
===========================================
  Files          245      245              
  Lines        13281    13382     +101     
===========================================
+ Hits         12992    13098     +106     
+ Misses         289      284       -5     

Impacted Files	Coverage Δ
pybamm/parameters/parameter_values.py	99.29% <ø> (ø)
pybamm/expression_tree/unary_operators.py	100.00% <100.00%> (ø)
pybamm/geometry/battery_geometry.py	100.00% <100.00%> (+6.25%)	⬆️
...er2019/lead_exchange_current_density_Sulzer2019.py	100.00% <100.00%> (ø)
...ead_dioxide_exchange_current_density_Sulzer2019.py	100.00% <100.00%> (ø)
...2019/oxygen_exchange_current_density_Sulzer2019.py	100.00% <100.00%> (ø)
...0_electrolyte_exchange_current_density_Chen2020.py	100.00% <100.00%> (ø)
..._electrolyte_exchange_current_density_Ecker2015.py	100.00% <100.00%> (ø)
...te_electrolyte_exchange_current_density_Kim2011.py	100.00% <100.00%> (ø)
..._electrolyte_exchange_current_density_PeymanMPM.py	100.00% <100.00%> (ø)
... and 33 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4e4e1ab...5f3c713. Read the comment docs.

[valentinsulzer]

Looks good to me, thanks @rtimms ! I might have missed it, but is there an example for setting particle shape to "user"?

[valentinsulzer]

Shouldn't this return variables? Otherwise it is just quietly updating them.

[rtimms]

yep, good point, thanks.

[rtimms]

thanks @tinosulzer will add an example for "user" then merge