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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…). </note> Perform a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp). <note important>Discuss the differences in the density profile. What do you expect to see in vmd? </note> Now, use vmd to look at the trajectories. As you launch vmd, you can (assignment): <note important>- source a pbc.vmd file which includes the definition of the periodic box - draw the box: draw pbcbox in the Tk console - wrap all atoms in the periodic box: pbc wrap -first first -last last**
- “play” with representations: try to 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. Discuss it for 700, 1100, and 1300 K.