Re: [Phonopy-users] Polarization vectors, Phonopy-1.6.4-pre

[Iyad AL-Q. <iy...@gm...>]

Thank you very much,

This is helpful, and good to know.

Many Thanks,
IYAD

On Tue, Feb 26, 2013 at 12:17 AM, Atsushi Togo <atz...@gm...> wrote:

> Hi,
>
> You have to transpose eigenvectors, they are the column vectors.
> Internally phonopy uses numpy.linalg.eigh. eigh uses LAPACK. So
> eigenvectors follow the convention of LAPACK.
> http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.eigh.html
>
> The code example is as follows:
>
> for pol in eigvecs[0].T:
>     print pol
>
> Then you can obtain consistent results. This seems not written in the
> manual, but I got a similar question and replied before. Anyway I'm
> sorry for this lack of information and I will write this somewhere in
> the manual.
>
> Togo
>
>
> On Tue, Feb 26, 2013 at 1:52 PM, Iyad AL-QASIR <iy...@gm...> wrote:
> > Dear Dr. Togo,
> >
> > Please find the attached files for polarization vectors for the qpoint
> [0.2,
> > 0.2, 0], these files are:
> > qpoints.yaml produced using the command line ( note that in band.conf,
> > FORCE_CONSTANT=READ), and  the other file was produced using python
> module
> > and reading the force_constants.
> >
> > Please note that, the NaCl case we study  is the example available in
> > phonopy directory, where POSCAR file is already there and the
> FORCE_CONSTANT
> > as you know can be written from there.
> >
> > Thank you,
> > IYAD
> >
> >
> >
> > On Mon, Feb 25, 2013 at 9:57 PM, Atsushi Togo <atz...@gm...>
> wrote:
> >>
> >> Hi,
> >>
> >> > A. Nb system:
> >> >
> >> > 1- The polarization vectors for certain q-vectors have imaginary
> >> > components.0.2, 0.2, 0]
> >>
> >> > For Bravais lattice ( one atom per unit cell) the polarization vectors
> >> > should be real ( see A. Maradudin et al, " Theory of Lattice Dynamics
> in
> >> > the
> >> > Harmonic Approximation", 1963, page 13.)
> >>
> >> I don't have Maradudin's book.
> >> "Certain q-vectors" is not clear for me but I think, in general,
> >> polarization vectors have to be complex. Do you know the reason why
> >> the polarization vectors become real?
> >>
> >> > B. NaCl system:
> >> >
> >> > 1- We were testing the polarization vectors for NaCl ( using the
> example
> >> > provided, and setting is_nac=False) using both the command line, and
> >> > phonopy
> >> > module and we noticed different numerical values for the polarization
> >> > vectors for the same q-vector. The origin of this difference is not
> >> > clear to
> >> > us.
> >> >
> >> > 2- I am attaching the Python script(NaCl_test.py that used phonopy
> >> > module to
> >> > calculate the polarization vectors, for example, for q=[0.2, 0.2, 0]
> >> >
> >> > also I am attaching the band.conf file, and QPOINTS file so you can
> run
> >> > (./phonopy band.conf) and compare with results we get using the
> phonopy
> >> > module.
> >>
> >> I could not reproduce your calculations because no POSCAR and
> >> FORCE_CONSTANTS.
> >> But if the point is clear, you can just show eigenvectors.
> >>
> >> Togo
> >>
> >> >
> >> >
> >> > ** We think great improvements have been achieved in the latest
> version
> >> > of
> >> > phonopy and we are excited to see it more more and advanced, We really
> >> > appreciate your efforts in this regard.
> >> >
> >> >
> >> > We will be more than happy to assist you in solving this issue.
> >> >
> >> >
> >> > Thank you for your support and interest.
> >> >
> >> >
> >> > Kindest Regards,
> >> > _________________________
> >> > 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...
> >
> >
> >
> >
> > --
> > ___________________________
> >
> > 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...
>



-- 
___________________________
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