Re: [Phonopy-users] freq vs q-distance as a table

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Hi,

I don't understand what you want exactly, but if you mean you want to
combine all segments, you can use numpy.concatenate, numpy.vstack and
numpy.hstack. I attach an example for Al2O3 that can run on the
directory of example/Al2O3.

phonon.set_band_structure(bands,
                          is_eigenvectors=True)
bands = phonon.get_band_structure()
distances = bands[1]
frequencies = bands[2]
eigvecs = bands[3]
qpoints = bands[0]

all_freqs = np.vstack(frequencies)
all_qs = np.vstack(qpoints)
all_dists = np.hstack(distances)
all_eigvecs = np.concatenate(eigvecs)

Togo

On Fri, Oct 12, 2012 at 9:22 AM, Iyad AL-QASIR <iy...@gm...> wrote:
> Dear Dr. Togo,
>
> Using Phonopy-1.5 gives points, distances, frequencies, and polarization
> vectors as a tuple.
>
> How can I get the frequencies and polarization vectors as array, so I can
> define each frequency by two indices, one for q number ( let us say i) and
> the other for branch number ( let us say j), such that freq[i][j], That is,
> in similar way to older versions. I need that so I can make direct
> comparison with measured data or calculating differences.
>
> Indeed, I highly apprecatie and aknowldge the new modiications and updates
> in the latest version of phonopy.
>
>
> Thanks a lot,
> IYAD
>
>
>
>
>
> On Wed, Oct 3, 2012 at 11:47 PM, Atsushi Togo <atz...@gm...> wrote:
>>
>> Hi,
>>
>> I'm sorry for that I didn't mention in detail about it. Currently,
>> get_band_structure is defined as follows:
>>
>>     def get_band_structure(self):
>>         band = self._band_structure
>>         return (band.get_qpoints(),
>>                 band.get_distances(),
>>                 band.get_frequencies(),
>>                 band.get_eigenvectors())
>>
>> So, you would obtain a list (tuple) of qpoints, distances,
>> frequencies, eigenvectors.
>> Now each element of this list is a set of quantities of band segments.
>> The unit conversion factor is multiplied in the phonopy module.
>> VasptoTHz is the default value of it, so you don't need to multiply by
>> yourself if your unit conversion factor is this.
>>
>> An example of code script is shown below.
>>
>> bands = phonon.get_band_structure()
>> distances = bands[1]
>> frequencies = bands[2]
>> qpoints = bands[0]
>> for (qs_at_segments,
>>      dists_at_segments,
>>      freqs_at_segments) in zip(qpoints, distances, frequencies):
>>
>>     for q, d, f in zip(qs_at_segments,
>>                        dists_at_segments,
>>                        freqs_at_segments):
>>         print "# %f %f %f" % tuple(q)
>>         print d, ("%f " * len(f)) % tuple(f)
>>
>> I attach an example for workable with example/Al2O3, too.
>>
>> Togo
>>
>>
>> On Thu, Oct 4, 2012 at 4:40 AM, Iyad AL-QASIR <iy...@gm...> wrote:
>> > Dear Phonopy Users,
>> >
>> > Moving from Phonpy-1.3 to Phonopy-1.5 some changes ( toward better) have
>> > been made.
>> >
>> > I am using mainly phonopy as a python module. In my *.py file to get the
>> > phonon dispersions ( Freq vs q-distance), I had this part of code do
>> > that
>> > (Thanks to A. Togo he helped in that),
>> >
>> > phonon.set_band_structure(bands,is_eigenvectors=True)
>> > dispersion=phonon.get_band_structure()
>> > phonon.write_yaml_band_structure()
>> > distances=dispersion[0]
>> > eigenvalues=dispersion[2]
>> > for eigs_at_index in eigenvalues.T:
>> >     freq=[-np.sqrt(-x) if x<0 else np.sqrt(x) for x in eigs_at_index]
>> >     for d,f in zip(distances, freq):
>> >         print d,f*VasptoTHz
>> >     print
>> >     print
>> >
>> >
>> > However, in Phonopy-1.5 this will not work since some changes made in
>> > order
>> > of distances, eigen values, ...
>> >
>> > It would be grate if the above piece of code is corrected so it will
>> > give me
>> > the dispersions in a table as a function of q-distance.
>> >
>> > Thanks,
>> > ___________________________
>> > IYAD I. AL-QASIR, PhD
>> > Postdoc Research Associate
>> >
>> > X-Ray and Neutron Scattering and Spectroscopy Group
>> > Materials Science and Technology Division
>> > Oak Ridge National Lab
>> > Oak Ridge, TN
>> >
>> >
>> >
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>> >
>>
>>
>>
>> --
>> Atsushi Togo
>> http://atztogo.users.sourceforge.net/
>> atz...@gm...
>
>
>
>
> --
> ___________________________
> IYAD I. AL-QASIR, PhD
> Postdoc Research Associate
>
> X-Ray and Neutron Scattering and Spectroscopy Group
> Materials Science and Technology Division
> Oak Ridge National Lab
> Oak Ridge, TN
>

-- 
Atsushi Togo
http://atztogo.users.sourceforge.net/
atz...@gm...