Settings and Stepsize classes

[jhdark]

Proposed changes

With this change, users can directly alter the parameters of the solver: the absolute and relative tolerance, the maximum iterations and final time of a transient simulations. The stepsize will be defined in its own class stepsize as this will likely evolve to something very similar to festim in its current version (v0.11.0). Stepsize will be an attribute of F.Settings.

Usage:

my_model.settings = F.Settings(
        absolute_tolerance=1e10,
        relative_tolerance=1e-10,
        max_iterations=30,
        final_time=50,
    )

and for stepsize:

my_model.settings.stepsize = F.Stepsize(initial_value=1 / 20)

Additional solver modifications can be made after the initialisation of the simulation for more niche cases:

   my_model.settings = F.Settings(
        absolute_tolerance=1e10,
        relative_tolerance=1e-10,
        max_iterations=30,
        final_time=50,
    )

  my_model.initialise()

  my_model.solver.convergence_criterion = "incremental"
  ksp = my_model.solver.krylov_solver
  opts = PETSc.Options()
  option_prefix = ksp.getOptionsPrefix()
  opts[f"{option_prefix}ksp_type"] = "cg"
  opts[f"{option_prefix}pc_type"] = "gamg"
  opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
  ksp.setFromOptions()

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 (b26c407) 96.98% compared to head (bf61b3a) 97.47%.
Report is 11 commits behind head on fenicsx.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #616      +/-   ##
===========================================
+ Coverage    96.98%   97.47%   +0.48%     
===========================================
  Files           13       16       +3     
  Lines          398      475      +77     
===========================================
+ Hits           386      463      +77     
  Misses          12       12              

Files	Coverage Δ
festim/__init__.py	75.00% <100.00%> (+3.00%)	⬆️
festim/hydrogen_transport_problem.py	97.79% <100.00%> (+0.01%)	⬆️
festim/reaction.py	100.00% <100.00%> (ø)
festim/settings.py	100.00% <100.00%> (ø)
festim/species.py	96.96% <100.00%> (+8.08%)	⬆️
festim/stepsize.py	100.00% <100.00%> (ø)

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[RemDelaporteMathurin]

First round of comments