Re: [Phonopy-users] Runtime Error running phonopy-gruneisen

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

Hi,

For your second problem, I guess you have to specify --qe option.
For your first question, you may try adjusting the --cutoff option
value to eliminate phonons whose frequencies are close to zero.

Togo

On Fri, Jan 21, 2022 at 6:02 AM Amir Behbahanian
<ami...@gm...> wrote:
>
> Hi All,
>
> I ran tests on a copper in its primitive structure using quantum espresso. I was able to calculate all the possible properties using phonopy except the modal gruneisen parameters.
>
> I ran the reciprocal space command;
>
> phonopy-gruneisen --qe orig plus minus --dim="3 3 3" --pa="auto"  --mesh="30 30 30" -p -c Cu-primitive.in
>
> and got the following error:
>
> Unit cell was read from "orig/Cu-primitive.in".
> Force sets were read from "orig/FORCE_SETS".
>
> Unit cell was read from "plus/Cu-primitive.in".
> Force sets were read from "plus/FORCE_SETS".
>
> Unit cell was read from "minus/Cu-primitive.in".
> Force sets were read from "minus/FORCE_SETS".
>
> /home/amir/.local/lib/python3.8/site-packages/phonopy/gruneisen/core.py:135: RuntimeWarning: invalid value encountered in true_divide
>   self._gruneisen = -edDe / self._delta_strain / self._eigenvalues / 2
>
> I also tried the command that is based on wavevectors;
>
> phonopy-gruneisen orig plus minus --dim="3 3 3" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="0.0 0.0 0.0  0.0 0.5 0.5  0.25 0.75 0.5  0.0 0.5 0.5  0.0 0.0 0.0" -p -c Cu-primitive.in
>
> and got this set of errors:
>
> Unit cell was read from "orig/Cu-primitive.in".
> Force sets were read from "orig/FORCE_SETS".
> Traceback (most recent call last):
>   File "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load_helper.py", line 264, in _read_crystal_structure
>     return read_crystal_structure(filename=filename, interface_mode=interface_mode)
>   File "/home/amir/.local/lib/python3.8/site-packages/phonopy/interface/calculator.py", line 391, in read_crystal_structure
>     unitcell = read_vasp(cell_filename)
>   File "/home/amir/.local/lib/python3.8/site-packages/phonopy/interface/vasp.py", line 203, in read_vasp
>     return _get_atoms_from_poscar(lines, symbols)
>   File "/home/amir/.local/lib/python3.8/site-packages/phonopy/interface/vasp.py", line 216, in _get_atoms_from_poscar
>     scale = float(lines[1])
> ValueError: could not convert string to float: '  ibrav = 0\n'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
>   File "/home/amir/.local/bin/phonopy-gruneisen", line 409, in <module>
>     main(get_options())
>   File "/home/amir/.local/bin/phonopy-gruneisen", line 304, in main
>     phonon = phonopy.load(
>   File "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load.py", line 211, in load
>     cell, smat, pmat = load_helper.get_cell_settings(
>   File "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load_helper.py", line 75, in get_cell_settings
>     cell, optional_structure_info = _read_crystal_structure(
>   File "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load_helper.py", line 274, in _read_crystal_structure
>     raise RuntimeError("\n".join(msg))
> RuntimeError: ============================ phonopy.load ============================
>   Reading crystal structure file failed in phonopy.load.
>   Maybe phonopy.load(..., calculator='<calculator name>') expected?
> ============================ phonopy.load ============================
>
> I would appreciate your comment on the problem. Please also find the related files attached.
>
> Regards,
> Amir
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-- 
Atsushi Togo