Re: [Phonopy-users] ERROR Creating supercell by Phonop3y

[Atsushi T. <atz...@gm...>]

Hi,

Please read https://phonopy.github.io/phonopy/symmetry.html.

Togo

On Wed, Jul 12, 2023 at 6:50 PM Seyed Vahid Hosseini
<vah...@gm...> wrote:
>
> Hello dear phono3py users:
> I have problem creating supercell for my structure.
> this is my input file:
> ###############################################
> &control
>  calculation='scf',
>  verbosity = 'low',
>  restart_mode = 'from_scratch',
>  prefix = 'input-kappa',
>  tstress = .true.,
>  tprnfor = .true.,
>  forc_conv_thr = 1.0D-4
>     pseudo_dir ='./',
>     outdir= './',
>  nstep=3000,
>  wf_collect=.true.
> /
>
> &SYSTEM
>  ibrav=0,
>  nat=10,
>  ntyp=2,
>  ecutwfc=40,
>  ecutrho=400,
>  occupations='smearing',
>  degauss=0.002,
>  smearing='mv',
> /
> &electrons
>  diagonalization='cg',
>  mixing_mode = 'plain',
>  mixing_beta = 0.4,
>  conv_thr =  1.0d-6,
>  electron_maxstep=600
> /
> &IONS
>  ion_dynamics = 'bfgs',
> /
> &CELL
> cell_dynamics = 'bfgs',
> /
>
> ATOMIC_SPECIES
>  Ti  47.867    Ti.pbe-sp-van_ak.UPF
>  O   15.9994   O.pbe-van_ak.UPF
>
> K_POINTS {automatic}
> 4 4 4 0 0 0
>
> CELL_PARAMETERS (bohr)
>    8.777485583  -3.914331818  -0.006161821
>    8.777485583   3.914331818  -0.006161821
>   -3.276301914   0.000000000  10.503396064
>
> ATOMIC_POSITIONS (crystal)
> Ti            0.3514812176        0.3514812176        0.6762452335
> Ti            0.6485187824        0.6485187824        0.3237547665
> Ti            0.3370406879        0.3370406879        0.1732195302
> Ti            0.6629593121        0.6629593121        0.8267804698
> Ti           -0.0000000000       -0.0000000000        0.5000000000
> O             0.5000000000        0.5000000000        0.0000000000
> O             0.1715541780        0.1715541780        0.8319048573
> O             0.8284458220        0.8284458220        0.1680951427
> O             0.1711642338        0.1711642338        0.3451210511
> O             0.8288357662        0.8288357662        0.6548789489
>
> ##########################################################
>
>
> phono3py --qe -d --dim="2 2 2" --pa="F" -c input.in
>         _                      _____
>   _ __ | |__   ___  _ __   ___|___ / _ __  _   _
>  | '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
>  | |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
>  | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
>  |_|                                |_|    |___/
>                                        2.7.0
>
> -------------------------[time 2023-07-12 13:14:32]-------------------------
> Compiled with OpenMP support (max 4 threads).
> Python version 3.9.17
> Spglib version 2.0.2
> Traceback (most recent call last):
>   File "/home/cpg/.local/bin/phono3py", line 45, in <module>
>     main(**argparse_control)
>   File "/home/cpg/dev/phono3py/phono3py/cui/phono3py_script.py", line 1164, in main
>     phono3py = create_phono3py_supercells(
>   File "/home/cpg/dev/phono3py/phono3py/cui/create_supercells.py", line 73, in create_phono3py_supercells
>     phono3py = Phono3py(
>   File "/home/cpg/dev/phono3py/phono3py/api_phono3py.py", line 279, in __init__
>     self._build_primitive_cell()
>   File "/home/cpg/dev/phono3py/phono3py/api_phono3py.py", line 2442, in _build_primitive_cell
>     self._primitive = self._get_primitive_cell(
>   File "/home/cpg/dev/phono3py/phono3py/api_phono3py.py", line 2547, in _get_primitive_cell
>     return get_primitive(
>   File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 849, in get_primitive
>     return Primitive(
>   File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 389, in __init__
>     self._run(supercell, positions_to_reorder=positions_to_reorder)
>   File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 526, in _run
>     self._p2s_map = self._create_primitive_cell(
>   File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 538, in _create_primitive_cell
>     trimmed_cell, p2s_map, _ = _trim_cell(
>   File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 1008, in _trim_cell
>     tcell = TrimmedCell(
>   File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 669, in __init__
>     self._run(cell, relative_axes, positions_to_reorder, check_overlap, symprec)
>   File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 754, in _run
>     raise RuntimeError("Remapping of atoms by TrimmedCell failed.")
> RuntimeError: Remapping of atoms by TrimmedCell failed.
> cpg@cpg-MS-7693:~/Desktop/Vahid/kappa/m-TiO/scf$
>
> Any help would be appreciated.
>
> Best regards
> Vahid
>
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-- 
Atsushi Togo