Tutorial:Vibrational modes

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Warning: this tutorial requires feautures not available in Octopus 3.0.1, the development version should be used.

This tutorial will show you how to obtain vibrational modes in Octopus by using Sternheimer linear response. We will use the water molecule as example. To start we will need the geometry, copy the following in a file called h2o.xyz:

3

O                    0.008165   -0.658276    0.215737
H                    1.508729    0.441434    0.259102
H                   -1.419465    0.543189    0.243811

Since to obtained proper vibrational modes we need to be as close as possible to the minimum of energy, first we will optimize the geometry under the parameters we have defined for the simulation. For that we use the following input file:

CalculationMode = go

XYZCoordinates = "h2o.xyz"

Spacing = 0.3
Radius = 12
BoxShape = sphere
 
FilterPotentials = filter_ts

ConvForce = 1e-8

As you see we will use a smaller than usual spacing and a larger spherical box, this is required since forces require more precision than other quantities, of course for production runs this values should be properly converged. Also to increase the precision of the forces and the total energy we will use the variable FilterPotentials, it specifies that a filter should be applied to the ionic potentials that removes the Fourier components that are higher than what we can represent on our grid. Finally, as dictated by the ConvForce variable, the criterion to stop the self-consistency process will be given by the change in the force.

Now run Octopus, once the calculation is finished you should get the optimized geometry in mix.xyz, modify your the value of XYZCoordinates to point to this file.

To perform a calculation of the vibrational modes we need a ground state calculation, so change the CalculationMode to gs and run Octopus again. Once done, check that the forces in the static/info file are reasonably small (<0.01).

Now we are ready for the actual calculation of vibrational modes, to do it, change CalculationMode to vib_modes and run Octopus. This calculation will take a while, since 3N_atoms response calculations are required.