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 download the files from the wiki: exercise_4.2.tar.gz
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.
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).
Now, use vmd to look at the trajectories. As you launch vmd, you can (assignment):