coloration of atoms--cna/atom

Dear all,

The attached is two pictures visualized by VMD, and the model is built by lammps. My purpose is to show the atoms by different colors based on the results obtained by command of cna/atom. You can see the structure of the middle column of atoms in white region is different from others with consideration of common neighbours (Picture 1). It should be a hcp structure while others are fcc structure. This is what I mean twin plane. But the display of coloration is not reasonable based on cna/atom (Picture 2).
I hope I’ve described the problem clearly!
Looking forward to your reply! Thanks!

Best regards,
Sun Ligang



I can't tell if you are asking a question about VMD or about
the output of cna/atom in LAMMPS. If the latter are you
saying that cna/atom is not tagging the atoms correctly?


Dear Steve and all,

I visualize based on the data in dump file. I check the dump file and find the results output are incorrect. That’s why the picture shown in VMD is not reasonable. So I ask a question about of cna/atom in Lammps.Thanks!

Best regards,
Sun Ligang

2013/1/12 Steve Plimpton <[email protected]>

From the doc page of compute cna/atom, this calculation can be

sensitive to the cutoff. It appears your specified cutoff is exactly
0.8536 * a_0, but you might want to try experimenting with slightly
larger numbers. Also make sure the condition of "Rc + Rs > 2 *
cutoff" is met.