Re: [Phonopy-users] Interface of Phono3py to Abinit

[tangdaosheng17 <tan...@16...>]

Dear Prof. Togo,


When I used Phono3py for third IFC calculation with file unitcell.in from Abinit and command
$phono3py --cutoff-pair-distance=15 -d --dim="4 4 4" -c run.in --abinit
the output in screen is
"
        _                      _____
  _ __ | |__   ___  _ __   ___|___ / _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
 | |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
 |_|                                |_|    |___/ 
                                          1.18.1


Python version 3.6.5
Spglib version 1.13.0


Displacement distance: 0.06
Traceback (most recent call last):
  File "/home/opt/anaconda352/bin/phono3py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/home/phono3py/scripts/phono3py", line 479, in <module>
    log_level=log_level)
  File "/home/phono3py/phono3py/cui/create_supercells.py", line 109, in create_phono3py_supercells
    width=5)
  File "/home/opt/anaconda352/lib/python3.6/site-packages/phonopy/interface/abinit.py", line 113, in write_supercells_with_displacements
    write_abinit(filename, cell)
  File "/home/opt/anaconda352/lib/python3.6/site-packages/phonopy/interface/abinit.py", line 100, in write_abinit
    f.write(get_abinit_structure(cell))
  File "/home/opt/anaconda352/lib/python3.6/site-packages/phonopy/interface/abinit.py", line 118, in get_abinit_structure
    numbers = cell.get_atomic_numbers()
AttributeError: 'NoneType' object has no attribute 'get_atomic_numbers'
"
94 supercells are created, however, the 94th supercell (supercell-00094.in) is an empty file with nothing in it. 
Is there something wrong?


Thanks,
Daosheng




--

Dao-Sheng Tang
PhD student of Engineering Thermophysics
School of Aerospace Engineering
Tsinghua University, Beijing, China
Email: tan...@ma...





At 2020-07-19 21:03:11, "Atsushi Togo" <atz...@gm...> wrote:
>Hi,
>
>User interfaces of phonopy and phono3py are similar. Have you tried
>phonopy with abinit? In case not, please start from using phonopy.
>
>Togo
>
>On Sun, Jul 19, 2020 at 7:15 PM tangdaosheng17 <tan...@16...> wrote:
>>
>>
>> Dear all,
>>
>> I find the brief introduction of Phono3py-Abinit interface in the website of Phono3py. However, in the example of silicon, number of supercell files created from the phono3py for VASP and Abinit POSCAR (unitcell.in) are different. I wonder whether the phono3py can be used with Abinit for thermal conductivity calculations.
>>
>> Thanks,
>> Daosheng
>>
>>
>> --
>>
>> Dao-Sheng Tang
>> PhD student of Engineering Thermophysics
>> School of Aerospace Engineering
>> Tsinghua University, Beijing, China
>> Email: tan...@ma...
>> _______________________________________________
>> Phonopy-users mailing list
>> Pho...@li...
>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
>
>
>-- 
>Atsushi Togo
>
>
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