
Calculation of the vibrational spectrum of CH4 from molecular dynamics

1) cg.i: Ground state calculation of CH4 and geometry optimization

2) cgdisp.i: Ground state calculation of CH4 with atoms displaced from their
equilibrium positions, in preparation for a MD run.

3) md1.i: MD simulation of CH4 starting from the cgdisp.xml configuration.

4) Analysis of trajectories

4 a) Create an xyz files from md1.r using: qbox_xyz.py -all md1.r > md1.xyz
4 b) compile the program spectrum.C using: make spectrum
4 c) compute the vibrational spectrum from the trajectories using the spectrum
program:

use: spectrum [-w {h|b|w}] coord.xyz spectrum.dat npoles fmin fmax dt

-w              windowing: Hann, Bartlett or Welsh (optional)
coord.xyz       input: contains the atomic coordinates at all steps
spectrum.dat    output: contains the estimate of the power spectrum
npoles          number of poles used in the maximum entropy algorithm
fmin fmax       bounds of the power spectrum wanted (cm-1)
dt              time step of the simulation (a.u.)

For example: ./spectrum -w h md1.xyz sp.dat 100 0 4000 10

The computed spectrum is in file sp.dat and can be viewed with gnuplot.

