[lammps-users] Vibrational analysis

Hi,

I’m studying the mechanical behavior of a polymeric sample using LAMMPS.

I’d like to calculate the vibrational information (frequency and intensity) of my molecular model, and then I will compare that with the FT-IR spectroscopic data (experimental data).

Would you inform me of the useful code or the script compatible with LAMMPS for this calculation?

Thanks,

Jae-Hyun

Jae-Hyun,

Other users may have such a code or script that they’d point you to, but if you don’t hear back from anyone, here are a few ideas for you:

  1. You could write your own. This may sound difficult, but if you used the Pizza.py toolkit, it should be quite easy. See this URL: http://www.cs.sandia.gov/~sjplimp/pizza.html

  2. You could convert your LAMMPS dump files into a format readable by other software that have more post-processing capabilities, like CHARMM. If you have and use CHARMM, it is really easy to tell LAMMPS to dump trajectories into CHARMM-compatible *.dcd files. CHARMM might have a module to calculate the vibrational information.

Paul

Hi Jae-Hyun,

For your problem you may want to dump the velocities from the atoms you’re simulating. you can then use a Fourier transform of the velocity autocorrelation function as a function of a particular wavevector; that will give you the power spectrum that you can compare to experiment.

Here’s a reference that might help you

Surf. Sci. 446 (2000) 17-30

hope this helps,
Jaime

Hi Jae-Hyun,