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?

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I don't use VESTA and there are probably a few tools that can do this.

My suggestion would be to use the open source Python package ASE or "Atomic Simulation Environment." developed in part by the group of Karsten W. Jacobsen.

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()))
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  • $\begingroup$ I checked ASE, but that seems require LINUX. I have only WINDOWS system $\endgroup$ – latra Dec 31 '16 at 9:53
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    $\begingroup$ ASE requires Python (e.g., ASE install instructions ) and certainly Python and ASE can be installed on Windows: python.org/downloads/windows $\endgroup$ – Geoff Hutchison Dec 31 '16 at 16:46
  • $\begingroup$ I have got Pythod under windows....so how should I proceed to install ASE? get Cywin? I have also got it...... $\endgroup$ – latra Jan 1 '17 at 7:16
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    $\begingroup$ As indicated in my comment above, if you have Python installed, you can install ASE using pip install --upgrade --user ase $\endgroup$ – Geoff Hutchison Jan 2 '17 at 0:22
  • $\begingroup$ Where should I run this pip command? Under Python or under window command? or under Cywin? I have tried them all but none successed. $\endgroup$ – latra Jan 4 '17 at 1:21

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