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lines changed Original file line number Diff line number Diff line change @@ -418,17 +418,6 @@ def _generate_coordinates(self, fix_surface_sites=True):
418418 coordinates [i1 , 1 ] -= 0.2
419419 coordinates [i2 , 1 ] += 0.2
420420
421- # If two atoms lie on top of each other, push them apart a bit
422- # This is ugly, but at least the mess you end up with isn't as misleading
423- # as leaving everything piled on top of each other at the origin
424- for atom1 , atom2 in itertools .combinations (backbone , 2 ):
425- i1 , i2 = atoms .index (atom1 ), atoms .index (atom2 )
426- if np .linalg .norm (coordinates [i1 , :] - coordinates [i2 , :]) < 0.5 :
427- coordinates [i1 , 0 ] -= 0.3
428- coordinates [i2 , 0 ] += 0.3
429- coordinates [i1 , 1 ] -= 0.2
430- coordinates [i2 , 1 ] += 0.2
431-
432421 # Center backbone at origin
433422 xmin = np .min (coordinates [:, 0 ])
434423 xmax = np .max (coordinates [:, 0 ])
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