Multispecies support

[jhdark]

Proposed changes

With these series of changes, festim will support multispecies transport. This also will provide the foundation for future festim.Reactions() class to be implemented. With this, users can simulate the simultaneous transport of multiple mobile species.

The species being modelled will have to be given as a list of festim.species objects:

mobile_H = F.Species("H")
mobile_D = F.Species("D")
my_model.species = [mobile_H, mobile_D]

The diffusion properties of each species will need to be given as a dictionary within the festim.Material object.

my_material = F.Material(
        D_0={"H": 1.9e-7, mobile_D : 1.9e-07}, E_D={"H": 0.2, mobile_D : 0.2}, name="my_mat"
)

Keys within this dictionary can either be the name of the species as a string, or the species object.

The species will also have to be defined within the boundary conditions and exports:

my_model.boundary_conditions = [
        F.DirichletBC(subdomain=left_surface, value=1e18, species="H"),
        F.DirichletBC(subdomain=right_surface, value=1e18, species="D"),
    ]
    my_model.exports = [
        F.XDMFExport("mobile_H.xdmf", field=mobile_H),
        F.XDMFExport("mobile_D.xdmf", field=mobile_D),
        F.VTXExport("mobile_H.bp", field="H"),
        F.VTXExport("mobile_D.bp", field=mobile_D),
    ]

Again, species can either be given as the string name assigned or the species object itself.

Types of changes

What types of changes does your code introduce to FESTIM?

• 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

• Black formatted
• 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

All modified and coverable lines are covered by tests ✅

Comparison is base (6f627cd) 97.47% compared to head (3376833) 98.17%.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #617      +/-   ##
===========================================
+ Coverage    97.47%   98.17%   +0.70%     
===========================================
  Files           16       16              
  Lines          475      549      +74     
===========================================
+ Hits           463      539      +76     
+ Misses          12       10       -2     

Files	Coverage Δ
festim/__init__.py	75.00% <100.00%> (ø)
festim/boundary_conditions/dirichlet_bc.py	100.00% <ø> (ø)
festim/exports/vtx.py	100.00% <100.00%> (ø)
festim/exports/xdmf.py	100.00% <100.00%> (ø)
festim/hydrogen_transport_problem.py	99.47% <100.00%> (+1.67%)	⬆️
festim/material.py	100.00% <100.00%> (ø)
festim/species.py	97.56% <100.00%> (+0.59%)	⬆️
festim/subdomain/surface_subdomain.py	100.00% <100.00%> (ø)

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