Add file prefix options to singlepoint and geomopt

[k-harris27]

Adds the option to provide a file prefix that is used for all of the files produced by single point and geometry optimisations. Since this can include a directory, it helps to allow the option to create a results directory for #359 (comment).

[ElliottKasoar]

Do we want to set a (partial?) default file prefix, as part of this PR or otherwise e.g. to save everything to ./results?

In that case, we may want an additional option, to specify the output directory, which prepends the file prefix?

Otherwise we'd lose the more descriptive part of the file prefix.

[k-harris27]

In that case, we may want an additional option, to specify the output directory, which prepends the file prefix?

I feel like an output directory option that doesn't affect the file name would be a good addition. I was thinking that making sure all the files work consistently with file_prefix should help make a directory option relatively easy to add.

[ElliottKasoar]

Thanks, @k-harris27!

Could you:

• Summarise the changes to how the trajectory file can now be saved (in the comments here)
• Update the CLI docs (docs/source/user_guide/command_line.rst) to make sure the example is correct

[k-harris27]

Summarise the changes to how the trajectory file can now be saved (in the comments here)

In geomopt, the trajectory is now written if the write_traj option is True.

By default, the trajectory filename is inferred from file_prefix as with other output files, and only a .extxyz file is written.

The filename can be specified manually by setting traj_kwargs["filename"].

The binary .traj file written by ASE can be retained by manually setting its output path using opt_kwargs["trajectory"].

If traj_kwargs["filename"] or opt_kwargs["trajectory"] are given when write_traj is False, an error is raised.