Is there any software can give me the information of nearest neighbour, nest nearest neighbour,....(and their distance) from an atom within a crystal (described by a .cif file)? Perhaps some visualization software like VESTA?
I don't use VESTA and there are probably a few tools that can do this.
There are several algorithms available for generating neighbor lists and iterating through them: https://wiki.fysik.dtu.dk/ase/ase/neighborlist.html
Here's an example from the documentation:
# get neighbors of atom 42 indices, offsets = nl.get_neighbors(42) for i, offset in zip(indices, offsets): print(atoms.positions[i] + dot(offset, atoms.get_cell()))