Sometimes ICSD structures contain duplicate atoms…I learned the hard way. I was recently running some VASP calculations and was getting errors like WARNING: CNORMN: search vector ill defined. Additionally, I was finding that changing ALGO to All was producing the same error, leading to my conclusion that I likely had a problematic structure. Using pymatgen, you can quickly check if a structure contains duplicate atoms.

from pymatgen.core.structure import Structure
s = Structure.from_file('POSCAR')

With that said and to the best of my knowledge, pymatgen doesn’t have a method for removing duplicate atoms. For that, I turned to atomsk, is a tool to convert and manipulate atomic data files. atomsk has an option for removing duplicate atoms (; it’s really easy to use and it works great! What worked for me was

atomsk POSCAR -rmd 0.2 pos

which gave

 |              ___________                          |
 |     o---o    A T O M S K                          |
 |    o---o|    Version master                       |
 |    |   |o    (C) 2010 Pierre Hirel                |
 |    o---o         |
 >>> Opening the input file: POSCAR
 ..> Input file was read successfully (54 atoms).
 >>> Removing atoms that are closer than 0.200 A.
 >>> Constructing neighbor list...
 ..> 18 atoms were removed, 36 atoms left.
 >>> Writing output file(s) (36 atoms):
 <?> This file already exists: POSCAR
     Do you want to overwrite it (y/n) (Y=overwrite all)?

to which I answered n and gave as a filename. The final message was

 ..> Successfully wrote POSCAR file:
 \o/ Program terminated successfully!
     Total time: 12.311 s.; CPU time: 0.007 s.

Bye bye duplicate atoms!