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

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

Thank you very much, Dr. Togo.  Indeed 55 and 56 were written next to each there making them 5556 and this caused the error. 


Regards,
Mostafa 
________________________________________
From: Atsushi Togo [atz...@gm...]
Sent: Thursday, January 28, 2016 12:33 AM
To: phonopy-users
Subject: Re: [Phonopy-users] Pdos for larg number of atoms

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...

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