[Phonopy-users] RuntimeError: Remapping of atoms by TrimmedCell failed.

[MUKESH S. <gkp...@gm...>]

Dear Phonopy users and Prof. Togo,

I am trying to calculate the phonon spectrum with finite difference methods.

I used the following to generate all the structures:
phonopy -d --dim='2 2 1' -c POSCAR

where my POSCAR is a tightly relaxed file.

After completing the vasp calculations.

I am using the following to generate the phonon-band structure:
phonopy -p band.conf

where
*band.conf:*

DIM = 2 2 1
BAND = 0.000000 0.000000 0.000000   0.500000 0.000000 0.000000   0.500000
0.500000 0.000000   0.000000 0.500000 0.000000  0.000000 0.000000 0.000000
BAND_LABELS = $\Gamma$ X S Y $\Gamma$
PRIMITIVE_AXES= 1/2 0 0   0 1/2 0  0 0 1

On running this, I am getting the following error:
------------------------------------------------
        _
  _ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_|                            |_|    |___/
                                      2.14.0

Python version 3.9.12
Spglib version 1.16.3

Phonopy configuration was read from "band.conf".
Traceback (most recent call last):
  File "/home/mukesh/miniforge3/envs/phono3py/bin/phonopy", line 7, in
<module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/home/mukesh/phono23_dev/phonopy/scripts/phonopy", line 45, in
<module>
    main(**argparse_control)
  File "/home/mukesh/phono23_dev/phonopy/phonopy/cui/phonopy_script.py",
line 1732, in main
    phonon = init_phonopy(settings, cell_info, symprec, log_level)
  File "/home/mukesh/phono23_dev/phonopy/phonopy/cui/phonopy_script.py",
line 1601, in init_phonopy
    phonon = Phonopy(
  File "/home/mukesh/phono23_dev/phonopy/phonopy/api_phonopy.py", line 175,
in __init__
    self._build_primitive_cell()
  File "/home/mukesh/phono23_dev/phonopy/phonopy/api_phonopy.py", line
3523, in _build_primitive_cell
    self._primitive = get_primitive(
  File "/home/mukesh/phono23_dev/phonopy/phonopy/structure/cells.py", line
827, in get_primitive
    return Primitive(
  File "/home/mukesh/phono23_dev/phonopy/phonopy/structure/cells.py", line
386, in __init__
    self._run(supercell, positions_to_reorder=positions_to_reorder)
  File "/home/mukesh/phono23_dev/phonopy/phonopy/structure/cells.py", line
523, in _run
    self._p2s_map = self._create_primitive_cell(
  File "/home/mukesh/phono23_dev/phonopy/phonopy/structure/cells.py", line
535, in _create_primitive_cell
    trimmed_cell, p2s_map, _ = _trim_cell(
  File "/home/mukesh/phono23_dev/phonopy/phonopy/structure/cells.py", line
930, in _trim_cell
    tcell = TrimmedCell(
  File "/home/mukesh/phono23_dev/phonopy/phonopy/structure/cells.py", line
658, in __init__
    self._run(cell, relative_axes, positions_to_reorder, symprec)
  File "/home/mukesh/phono23_dev/phonopy/phonopy/structure/cells.py", line
735, in _run

*    raise RuntimeError("Remapping of atoms by TrimmedCell
failed.")RuntimeError: Remapping of atoms by TrimmedCell failed.*
------------------------------------------------


How if I *change **PRIMITIVE_AXES= 1 0 0   0 1 0  0 0 1,* I am getting
phonon band-structure.

*Any comments of the reasons why PRIMITIVE_AXES=1/2 0 0      0 1/2 0      0
0 1  is showing error would be highly appreciable?*

Note: I chose PRIMITIVE_AXES=1/2 0 0    0 1/2 0   0 0 1 because of during
finite difference structure generation, I choose 2 2 1 super cell.



Thanks and regards
Mukesh Singh
Research Scholar
Department of Physics,
IIT BOMBAY(400076)