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Hot gold
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® 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
- 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.
- Explain the profile, and use the third column to draw conclusions about the surface structure.
- Study the source of the script. Understand its behavior.
- Copy histo_z into another file and modify it to only include the particles from the first 10 frames of the trajectory.
- Run it and see the differences to the first profile.
- Do the same excluding the first 10 frames.
- Explain those differences, based on what you see in the *.ener file (energies, temperature…).
Perform 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
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
source pbc.vmd
Draw the box:
draw pbcbox
Wrap all atoms in the periodic box:
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, draw the g® of the system.