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

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

It would be useful if a wrong number out of range is displayed. I will
update phonopy so.

Thanks.

Togo

On Thu, Jan 28, 2016 at 2:49 PM, Mostafa Youssef <myo...@mi...> wrote:
> 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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>
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-- 
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...