This exercise deals with heating a gold slab, namely the (100) reconstructed that you already simulated last time. The goal is to plot a density profile in the direction orthogonal to the slab, and to compute (using vmd) the radial distribution function g( r ) at various temperatures.

Download the 4.2 exercise into your $HOME folder and unzip it:

you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2016_ethz_mmm:exercise_4.2.zip
you@eulerX ~$ unzip exercises:2016_ethz_mmm:exercise_4.2.zip
you@eulerX ~$ cd exercise_4.2

• First, we simulate the system at 700 K using a thermostat.

you@eulerX exercise_4.2$ bsub cp2k.popt -i 700.inp -o 700.out

• Then, the obtained xyz trajectory can be analyzed using the script histo_z available in the directory.

you@eulerX exercise_4.2$ ./histo_z 700-pos-1.xyz

The output is 700-pos-1.xyz.z, a file with three columns: z, dn/dz, and the progressive integral of this quantity.

• Perform consequently a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp):

you@eulerX exercise_4.2$ bsub cp2k.popt -i 1100.inp -o 1100.out
you@eulerX exercise_4.2$ bsub cp2k.popt -i 1300.inp -o 1300.out

• And again analyze these trajectories using the script histo_z:

you@eulerX exercise_4.2$ ./histo_z 1100-1-pos.xyz
you@eulerX exercise_4.2$ ./histo_z 1300-1-pos.xyz

• Now, use vmd to look at the trajectories. As you launch vmd,

in Tk console you can:

Load a pbc.vmd file which includes the definition of the periodic box

vmd> source pbc.vmd

Draw the box:

vmd> draw pbcbox

Wrap all atoms in the periodic box:

vmd> pbc wrap -first first -last last

• Try to play with representations: color the surface atoms in one color, the bulk ones in another color.
• Using the “radial distribution function” plugin from the extension menu (Extensions>Analysis>Radial Pair Distribution Function g( r ) ), draw the g( r ) of the system.