Hi Axel

Thank you very much for your reply.

**I have got binary files after executing the LAMMPS input scripts for**

**what kind of binary files with what content?**

I am sending you the LAMMPS input script for alpha quartz to get the phonon dispersion curve. After executing the input script we are getting the binary output files. The analysis of this binary files by Fix-Phonon it results the datas for wave vectors and frequency to obtain the phonon dispersion curves.

**Your question was: " i don’t know PHANA. does it have a home page? what is it good for?"**

Fix-phonon presents an implementation of the method to evaluate the phonon dispersion directly from molecular dynamics simulations. The basic algorithm is to construct the dynamical matrices by observing the displacement fluctuations.

Yes it has homepage: http://code.google.com/p/fix-phonon/

and the developer is Prof. L. T Kong.

**Another question was:" PHANA is not a good software for the analysis of the binary output files**

**for any charged system. Since QUARTZ is a charged system so PHANA doesn’t work well**

**why so?** **"**

We sent an email to the developer L.T. Kong of the fix-phonon PHANA by mentioning our problem.

**Our email was**:

"We have trouble getting the dispersion curves of quartz with LAMMPS/fix-phonon: The lowest branches are OK but all the upper branches clutter between 9 and 10 Thz at the gamma point, whereas it should go up to 30 THz. Furthermore, it is the same for various values of the number of unit cells included in the simulation box (we have also tried with a tilted and a non tilted simulation box and find essentially the same thing.

However, in the fix phonon line, we sample every 10 time steps (of duration 0.0005 ps), so that if I understand well we have a sampling frequency of 200 THz that should be enough to reproduce phonon frequencies up to 30 Thz.

(fix 2 all phonon 10 50000 500000 quartz$nwtf.map.in Quartz$n-nontilted)

Do you have any idea why it seems we cannot get more than 10 Thz?"

**And his reply was**:

" I don’t know what kind of potential you are using for quartz, generally it will contain Coulombic interaction. Fix-phonon is however known to have problem for systems with charges, as I don’t have a solution to account for the contribution from the Born effective charge tensor due

to the long range nature of the Coulombic interaction. As a result, frequencies at the gamma point are generally inaccurate. Nevertheless one can

use a large simulation box and derive the frequencies at the gamma point by extrapolating data obtained for small q-points, such as the q-point corresponds

to (1/Nx, 0, 0).

In my understanding, the phonon frequencies are however not related to the sampling frequency.

"

So can you suggest anything better than fix-phonon for the analysis of the binary files?

Sincerely

Santunu

quartz input file.txt (2.57 KB)