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

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

Then, I have no idea.
It is difficult to see what is happening without reproducing it.

Togo

On Fri, Jan 21, 2022 at 1:21 PM Amir Behbahanian
<ami...@gm...> wrote:
>
> Hi Dr. Togo,
>
> I did as you suggested and the problem with getting errors doing the wavevector analysis is somehow solved but now I get the following error with both wavevector and frequency analyses.
>
> /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--cutooff=0.001 and --cutoff=1 but still get the same error. I would appreciate your suggestions solving this issue.
>
> Best regards,
> Amir
>
> On Thu, Jan 20, 2022 at 3:51 PM Atsushi Togo <atz...@gm...> wrote:
>>
>> 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
>> > _______________________________________________
>> > Phonopy-users mailing list
>> > Pho...@li...
>> > https://lists.sourceforge.net/lists/listinfo/phonopy-users
>>
>>
>>
>> --
>> Atsushi Togo
>>
>>
>> _______________________________________________
>> Phonopy-users mailing list
>> Pho...@li...
>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
> _______________________________________________
> Phonopy-users mailing list
> Pho...@li...
> https://lists.sourceforge.net/lists/listinfo/phonopy-users



-- 
Atsushi Togo