oekosheri/GB_code: Bug fix on gb_generator.Find_overlapping_Atoms

1- Bug fix on atoms removed on the image boundary. There should now be no problem in the atom removal. In general as written in Readme, I would be careful about atom removal with the overlap distance and when possible find the minimum energy by translation only.

2- I noticed there are some Tilt GBs for which there maybe a small gap difference between the main GB and the periodic image. As this happens in particular orientations I could not solve it quickly without damaging the rest of GBs. So I just added a little tolerance in gb_generator.CSL_Bicrystal_Atom_generator which reads as:

# tol = 0.01
self.atoms2[:, 0] = self.atoms2[:, 0] - norm(Or_2[0, :])  # - tol

If this is the case, uncomment the tol, change the number as you see fit.

2- I made some pep8 changes.