Add geometry optimisation

[ElliottKasoar]

Resolves #32

This will require rebasing once #31 is merged.

To do:

• Check atoms returned correctly
• Add functionality to return intermediate structures
• Add functionality to save optimised structure

[oerc0122]

Mostly stylistic, but some over-generalisations on type-hints which would be nice to address.

[ElliottKasoar]

• Add functionality to return intermediate structures

This was actually already possible via opt_kwargs (see example in unit tests), which I think is sufficient, rather than adding another argument.

As with single point calculations, we need to document this soon and add examples (#34), even more so now the tests are a little harder to read off.

[ElliottKasoar]

Mostly stylistic, but some over-generalisations on type-hints which would be nice to address.

Thanks for the suggestions! I think I've addressed most of them, with a couple of slightly open questions/comments.

One thing you may notice is that there's now a mix of Union and x | y typing. When we include from __future__ import annotations, pyupgrade prefers x | y where possible.

However, this seemed to break linking to ASE's documentation via intersphinx_mapping, so I've reverted back to Union where necessary.

[ElliottKasoar]

One additional option I've realised that @alinelena included in lavello/md.py is to read the saved trajectory (a pickled file) and rewrite e.g. as an extxyz:

  x = read(traj, index=":")
  write(opt_traj, x, format="extxyz")
  try:
     p = pathlib.Path(traj)
     p.unlink()
  except:
     pass

Do we want to add this in as well, or is the current option of saving the .traj binary file enough?

[oerc0122]

One additional option I've realised that @alinelena included in lavello/md.py is to read the saved trajectory (a pickled file) and rewrite e.g. as an extxyz:

  x = read(traj, index=":")
  write(opt_traj, x, format="extxyz")
  try:
     p = pathlib.Path(traj)
     p.unlink()
  except:
     pass

Do we want to add this in as well, or is the current option of saving the .traj binary file enough?

Why is the Path creation in the try? Also, never use a bare except, unlink also has missing_ok=True for this situation.

[ElliottKasoar]

Why is the Path creation in the try? Also, never use a bare except, unlink also has missing_ok=True for this situation.

I was mostly just quoting the code that was in md.py for the gist, but good points, I'll fix those if we decide it's worth adding.

[ElliottKasoar]

One additional option I've realised that @alinelena included in lavello/md.py is to read the saved trajectory (a pickled file) and rewrite e.g. as an extxyz:

The way this is done isn't quite a neat as I'd like, as you specify both the .traj file and the .xyz file, but I thought it's probably safer to require both be specified since the former is deleted after creation of the latter.

I also changed saving the optimised structure to act in the same way as I've implemented this - requiring filename in the kwargs rather than its own variable, so it's slightly more condensed.