Analysis of the binary files from LAMMPS outputs.

LAMMPS LAMMPS Mailing List Mirror
1

Hello all,

I have got binary files after executing the LAMMPS input scripts for QUARTZ. I have used PHANA for the analysis of the binary output file. But 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 for the analysis of the binary output files. So can you suggest any better software for the post processing of the binary output files for QUARTZ (charged system)?

Thanks in advance
Santunu

2

Hello all,

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

what kind of binary files with what content?

QUARTZ. I have used PHANA for the analysis of the binary output file. But

i don't know PHANA. does it have a home page? what is it good for?

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

why so?

work well for the analysis of the binary output files. So can you suggest
any better software for the post processing of the binary output files for
QUARTZ (charged system)?

why is would quartz have to be "charged" or rather what do you mean by that?
typically, you won't have to have a charged unit cell, if you set it
up properly.

also, what *kind* of analysis are you talking about?
there is a lot of stuff that can be done with LAMMPS
on the fly while running a simulation. since LAMMPS,
if compiled properly, supports many output formats,
you can use its trajectory files with many different
existing tools. it all is a matter to setting things up.

in general, if you ask such a generic and unspecific
question, it is near impossible to provide any kind of advice.
you have to keep in mind, that people here don't know
*anything* that you are doing or what your intentions are.

... and crystal balls are in extremely short supply these days.

cheers,
     axel.

3

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)

4

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.

fix phonon is not an official part of lammps.
you have to contact the author of the plugin
for help. i never used it and thus have no idea.

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.

your problem is specific to fix phonon and thus
you have to talk to him not us.

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?"

no. again, this is a fix phonon specific question and should be
discussed with the author of that fix.

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?

no. the author of fix phonon *did* give you a
recommendation, why don't you follow it?

i repeat, you problems are specific to this
feature and not LAMMPS in general and
thus you have to get help from the author
and should follow the advice that your are
given by him.

axel.

5

Hello Axel,

Thank you very much. I am not talking about the problems of fix-phonon. The authour of the fix phonon has told to use another software. My problem is to get a another software for the analysis of the binary output files to get the phonon dispersion curve. Can you just suggest any software for the post processing of the LAMMPS binary output files to get the phonon dispersion curves?

sincerely
Santunu

6

Hello Axel,

  Thank you very much. I am not talking about the problems of fix-phonon.
The authour of the fix phonon has told to use another software. My problem
is to get a another software for the analysis of the binary output files to
get the phonon dispersion curve. Can you just suggest any software for the
post processing of the LAMMPS binary output files to get the phonon
dispersion curves?

you are *still* talking about an output that is
created by fix phonon and *not* by lammps.

this is not a lammps problem. full stop.

axel.