Warning for overlapping sites

[AstyLavrinenko]

When creating transitions and manually setting the site_radius, there is currently no check to ensure sites do not overlap. Could you please introduce a warning or error message when two or more sites overlap? 1-5% of overlap is fine, so there could be a threshold to return a warning or error message.

Additionally, it would be helpful if the site_radius could be extracted as a parameter directly from transitions or states objects, especially in cases where the radius is automatically calculated by the code rather than manually specified.

[stefsmeets]

So, basically the following:

1. If manually setting the site radius (in Transitions.from_trajectory), check if sites overlap. This can be done in a quite rudimentary way, see snippet below. I will have a look if this can be included.
2. Extract site radius from Transitions or States object. Site radius is not a proporty of either of those, need to think a bit for how to make this work.

site_coords = sites.frac_coords

pdist = lattice.get_all_distances(site_coords, site_coords)
min_dist = np.min(pdist[np.triu_indices_from(pdist, k=1)])
print(min_dist < site_radius)