Re: [Phonopy-users] Pdos for larg number of atoms

[Mostafa Y. <myo...@mi...>]

Thank you for your reply, Dr. Togo.  The problem I have with PDOS with large number of atoms is that phonopy (v 1.9.6.3 )   stops with error message:


Calculating partial DOS...
Your specified atom number is out of range.
Traceback (most recent call last):
  File "/phonopy-1.9.6.3/bin/phonopy", line 1069, in <module>
    legend=([np.array(x) + 1 for x in pdos_indices]))
  File "//phonopy-1.9.6.3/lib/python/phonopy/api_phonopy.py", line 722, in plot_partial_DOS
    legend=legend)
  File "/phonopy-1.9.6.3/lib/python/phonopy/phonon/dos.py", line 406, in plot
    flip_xy=flip_xy)
  File "/phonopy-1.9.6.3/lib/python/phonopy/phonon/dos.py", line 117, in plot_partial_dos
    raise ValueError
ValueError



Regards,
Mostafa
________________________________________
From: Atsushi Togo [atz...@gm...]
Sent: Monday, January 25, 2016 8:28 PM
To: phonopy-users
Subject: Re: [Phonopy-users] Pdos for larg number of atoms

Hi,

For the first, no shorthand is prepared. I usually use a shell one-liner, e.g.,
for i in {1..50};do echo -n "$i ";done
and copy and paste it.

For the second, I couldn't understand what you wrote. How did the
phonopy complain?

Togo



On Mon, Jan 25, 2016 at 3:55 PM, Mostafa Youssef <myo...@mi...> wrote:
> Dear all,
>
> I have a very asymmetric structure with more than 120 non-equivalent atoms.
> I'm trying to calculate the partial phonon density of states using the PDOS
> tag.
>
>
> First, is there a quick way to specify atoms from 1 to 50 rather than
> explicitly listing all of them. For example something like PDOS= 1 - 50
> instead of PDOS = 1 2 3 4 5 ....and so on ?
>
>
> Second ,  phononpy (v 1.9.6.3 )   complains that there is a maximum limit
> for the number of atoms I'm listing in the PDOS tag.  Is there a way to
> increase this maximum limit ?
>
>
> Thank you,
> Mostafa
>
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--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...

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