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Fix ase_to_atom_lattice due to changes in ASE atoms object

Magnus Nord requested to merge fix_ase_changes into master

In previous versions of ASE (at least 3.20.1), it does not seem like atoms.positions returns negative numbers:

from ase.cluster import Octahedron
atoms = Octahedron("Ag", 5, cutoff=2)
print(atoms.positions.min(), atoms.positions.max())

0.0 8.18

However, in the newest version (3.21.1), the structure seems to be centred around 0, leading to negative values. Running the same script as above returns:

-4.09 4.09

This lead to the unit test for this failing: https://gitlab.com/atomap/atomap/-/jobs/982545214#L3624

This merge request fixes this, essentially by offsetting the negative coordinates back to positive values, and also adding a little bit of padding around the structure.

However, I haven't used the ASE functionality that much myself, so I'm unsure if this will break people's workflows.

@TomSlater, @PinkShnack, @thomasaarholt

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