Fix vtx outputs zero

[RemDelaporteMathurin]

Proposed changes

This PR fixes #622

Turns out using .collapse() for the output function of a VTXWriter produces zeros when writing. This doesn't occur with XDMFFile.

I removed it and manually tested that the expected output was produced.
I cannot add test for this as dolfinx doesn't have checkpointing yet.

Also removed some un-necessary code here and there.

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)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (1dbe47d) 98.19% compared to head (3ce66cd) 98.18%.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #624      +/-   ##
===========================================
- Coverage    98.19%   98.18%   -0.01%     
===========================================
  Files           16       16              
  Lines          610      607       -3     
===========================================
- Hits           599      596       -3     
  Misses          11       11              

Files	Coverage Δ
festim/hydrogen_transport_problem.py	99.19% <100.00%> (-0.01%)	⬇️

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[jhdark]

Looks great, cleans up the code nicely