Many thanks Javier for your reaction and time, it worked! Just if someone is interested to also have ir intensities computed. One can use vib2xsf if, in the *.vectors file computed setting "Intensities .true." in the *fdf file, the lines "IR Intensity = ..." (one line per each mode) are manually deleted.
Thanks again, ticu On Wed, Apr 27, 2016 at 8:23 PM, Javier Junquera <[email protected]> wrote: > > Hi Ticu: > > Remove from your benzene.ifc.fdf file the line: > > Intensities true > > and run again. > > This line was not included in the fdf files provided by the exercise. > It is responsible for writing extra lines in the benzene.vectors file > that are not properly digested by vib2xsf. > > Hope this helps, > > Javier > > > > > Hi Everybody, > > I performed calculations using siesta-trunk-462 > > siesta < benzene.ifc.fdf > benzene.ifc.out > > vibrator < benzene.ifc.fdf > benzene.vibra.out > > to visualize phonon modes following the example at > > > http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Vibrationalproperties/Vibrational.html > > The resulting files benzene.FC, benzene.vectors, benzene.XV, > benzene.ifc.out, benzene.bands, benzene.vibra.out are in the attached > tarball. Ignoring minor arithmetic differences, they agree with the results > at > > > http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Vibrationalproperties/Benzene/Visualization_phonons.pdf > > The problem I have is to visualize the modes. Executing > > vib2xsf < vib2xsf.dat > > yields: > > "Specify SystemLabel (or 'siesta' if none): dstmin= > 1.1063746327275770 > Now define the grid cell for your XCrysDen plot. > Note that it can be arbitrarily chosen with respect to the Siesta > simulation cell, and it needs not to be orthogonal. We'll define it by the > origin point and three spanning vectors. They can be given in Bohr or Ang. > Would you use Bohr (B) or Ang (A) ? Enter origin point in Bohr : Enter > 1st spanning vector in Bohr : Enter 2nd spanning vector in Bohr : Enter > 3rd spanning vector in Bohr : Specify SystemLabel of vibrator calculation > (or 'siesta' if none): select first and last modes (out of 36 ) for > analysis. > A separate XSF/AXSF file will be created for each mode. > First mode : Last mode : Error reading real part of > eigenvector 1 iat= 1" > > ... presumably a format error. > > Many thanks for your kind help! > > ti-cu cubot > > <bz.tar> > > >
