giovannipizzi/seekpath

Issue creating primitive cell for F-centred cubic cells

Emberx opened this issue · 0 comments

I've got a set of structures for which SeeK Path cannot generate primitive cells. They're all face centred cubic cells of space group F m -3 m. The website also failed to yield an outcome with a warning message of "Unable to process the structure"

The error message is listed below:

File "/home/uccazxi/.python2local/lib/python2.7/site-packages/matools/prim.py", line 44, in main
  seek_data = seekpath.get_path(std)
File "/home/uccazxi/.python2local/lib/python2.7/site-packages/seekpath/getpaths.py", line 95, in get_path
  res = hpkot.get_path(structure, with_time_reversal, threshold)
File "/home/uccazxi/.python2local/lib/python2.7/site-packages/seekpath/hpkot/__init__.py", line 423, in get_path
  bravais_lattice=bravais_lattice)
File "/home/uccazxi/.python2local/lib/python2.7/site-packages/seekpath/hpkot/spg_mapping.py", line 312, in get_primitive
  volume_ratio, ", ".join(str(_) for _ in wrong_count)))
ValueError: Problem creating primitive cell, I found the following group of atoms with len != 4: (0, 1, 3, 4, 6, 7, 9, 10)

And one of the POSCAR looks like this:

Bi1 Na1 Se2
1.0
5.9879999161 0.0000000000 0.0000000000
0.0000000000 5.9879999161 0.0000000000
0.0000000000 0.0000000000 5.9879999161
Bi Na Se
4 4 4
Direct
0.000000000 0.000000000 0.000000000
0.000000000 0.500000000 0.500000000
0.500000000 0.000000000 0.500000000
0.500000000 0.500000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.500000000 0.500000000
0.500000000 0.000000000 0.500000000
0.500000000 0.500000000 0.000000000
0.500000000 0.500000000 0.500000000
0.500000000 0.000000000 0.000000000
0.000000000 0.500000000 0.000000000
0.000000000 0.000000000 0.500000000

Thank you.

Sorry I just realized that when VESTA was generating the unit cell it makes the occupancy from 0.5 to 1, making two cations on the same site. That's why it got wrong.