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

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

This means that some number you specified is larger than the number of
atoms or the number is negative. Is this your case?

Togo

On Thu, Jan 28, 2016 at 2:22 PM, Mostafa Youssef <myo...@mi...> wrote:
> 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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-- 
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...