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:2015_ethz_mmm:exercise_4.2.zip you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_4.2.zip you@eulerX ~$ cd exercise_4.2
you@eulerX exercise_4.2$ bsub cp2k.popt -i 700.inp -o 700.out
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.
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
you@eulerX exercise_4.2$ ./histo_z 1100-1-pos.xyz you@eulerX exercise_4.2$ ./histo_z 1300-1-pos.xyz
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