Use isclose over == for overlap position check in SlabGenerator.get_slabs

[DanielYang59]

Summary

Follow up #3748.

• Use isclose over == for overlap check in SlabGenerator.get_slabs
• Add a new ztol arg to control the behavior of get_slabs, default to 0 to keep consistency with previous behavior

Use isclose over == for overlap check in SlabGenerator.get_slabs

Previously a z_range is neglected only when two coordinates are exactly the same.

pymatgen/pymatgen/core/surface.py

Lines 1317 to 1321 in 578d29c

	# Neglect overlapping positions
	elif z_range[0] != z_range[1]:
	# TODO (@DanielYang59): use the following for equality check
	# elif not isclose(z_range[0], z_range[1], abs_tol=tol):
	z_ranges.append(z_range)

Need discussion

However I'm not quite sure if checking the z_range really make much sense, as it's not possible to know whether terminating at a specific z-coordinate really breaks a bond (cannot calculate bond-distance just by z-distance).

It might be good to implement a method to detect bond broken by distance?

[DanielYang59]

@janosh Would appreciate it if I could get this reviewed. Thanks!