Support for 2D cylindrical and 1D spherical

[RemDelaporteMathurin]

Proposed changes

This PR adds the possibility to run simulations in cylindrical and spherical coordinates.

Usage:

    my_materials = FESTIM.Materials(
        [
            FESTIM.Material(id=1, D_0=1, E_D=0)
        ]
    )

    my_mesh = FESTIM.MeshFromVertices(np.linspace(1, 2, 500), type="cylindrical")

    my_bcs = [
        FESTIM.DirichletBC(surfaces=1, value=1),
        FESTIM.DirichletBC(surfaces=2, value=0),
    ]

    my_temp = FESTIM.Temperature(100)

    my_sources = [
        FESTIM.Source(f, 1, "0"),
    ]

    my_settings = FESTIM.Settings(
        absolute_tolerance=1e-10,
        relative_tolerance=1e-9,
        maximum_iterations=50,
        transient=False
    )


    my_sim = FESTIM.Simulation(
        mesh=my_mesh, materials=my_materials,
        boundary_conditions=my_bcs,
        temperature=my_temp, sources=my_sources, settings=my_settings)

    my_sim.initialise()
    my_sim.run()

Todo:

• Add feature to heat transfer

Types of changes

What types of changes does your code introduce to FESTIM?
Put an x in the boxes that apply

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Code refactoring
• Documentation Update (if none of the other choices apply)
• New tests

Checklist

Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before merging your code.

• Pep8 applied
• Unit tests pass locally with my changes
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)

Further comments

If this is a relatively large or complex change, kick off the discussion by explaining why you chose the solution you did and what alternatives you considered, etc...

[codecov]

Codecov Report

Merging #410 (3c3f63b) into dev (a52452b) will increase coverage by 0.01%.
The diff coverage is 98.47%.

@@            Coverage Diff             @@
##              dev     #410      +/-   ##
==========================================
+ Coverage   98.85%   98.86%   +0.01%     
==========================================
  Files          49       49              
  Lines        1923     1943      +20     
==========================================
+ Hits         1901     1921      +20     
  Misses         22       22              

Impacted Files	Coverage Δ
FESTIM/temperature/temperature_solver.py	97.91% <97.91%> (+0.16%)	⬆️
FESTIM/concentration/mobile.py	100.00% <100.00%> (ø)
FESTIM/h_transport_problem.py	100.00% <100.00%> (ø)
FESTIM/meshing/mesh.py	100.00% <100.00%> (ø)
FESTIM/meshing/mesh_1d.py	100.00% <100.00%> (ø)
FESTIM/meshing/mesh_from_refinements.py	100.00% <100.00%> (ø)
FESTIM/meshing/mesh_from_vertices.py	100.00% <100.00%> (ø)
FESTIM/meshing/mesh_from_xdmf.py	100.00% <100.00%> (ø)

---

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 a52452b...3c3f63b. Read the comment docs.

[RemDelaporteMathurin]

The failing patch coverage is due to a vsc bug which stagged the whole temperature_solver.py file as changed...