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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.

As usual, create a new directory and copy the files from:

/cluster/home03/matl/danielep/LECTURE4/EXERCISE_4.2/

First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat. Then, the obtained xyz trajectory can be analyzed using the script histo_z available in the directory.

./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).