====== Hot gold ======
<note warning>
TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:

you@eulerX ~$ module load courses mmm vmd
 
you@eulerX ~$ mmm-init
</note>


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 $HOME folder and unzip it:
<code bash>
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2016_ethz_mmm:exercise_4.2.zip
you@eulerX ~$ unzip exercises:2016_ethz_mmm:exercise_4.2.zip
you@eulerX ~$ cd exercise_4.2
</code>
<note tip>
All files of this exercise (** input and scripts are all commented**) can be also downloaded from the wiki: {{exercise_4.2.zip|exercise_4.2.zip}}
</note>

  * First, we simulate the system at 700 K using a thermostat.
<code bash>
you@eulerX exercise_4.2$ bsub cp2k.popt -i 700.inp -o 700.out
</code>
  * Then, the obtained xyz trajectory can be analyzed using the script **histo_z** available in the directory. 

<code bash>
you@eulerX exercise_4.2$ ./histo_z 700-pos-1.xyz
</code>

The output is **700-pos-1.xyz.z**, a file with three columns: z, dn/dz, and the progressive integral of this quantity.


<note tip>
Assignments: 
  - 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 **consequently** a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp):
<code bash>
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
</code>

  * And again analyze these trajectories using the script histo_z:
<code bash>
you@eulerX exercise_4.2$ ./histo_z 1100-1-pos.xyz
you@eulerX exercise_4.2$ ./histo_z 1300-1-pos.xyz
</code>


<note tip>
Assignments: 
  - 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, 
in Tk console you can:

Load a pbc.vmd file which includes the definition of the periodic box
<code tcl>
vmd> source pbc.vmd
</code>
Draw the box: 
<code tcl> 
vmd> draw pbcbox
</code>
Wrap all atoms in the periodic box:
<code tcl>
vmd> pbc wrap -first first -last last
</code>
  * 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 (Extensions>Analysis>Radial Pair Distribution Function g( r ) ), draw the g( r ) of the system.

<note tip>
Assignments: 
  - Discuss radial distribution function for 700, 1100, and 1300 K. 
</note>
<note important>
Hint: how to use the g( r ) module:
  - First apply pbcs (see above)
  - Open the radial distribution function plugin and enter the parameters as shown (**note: in the example below we excluded the first 10 frames**) (from "Utilities" you can check that your unit cell is OK)
  - Click "Compute g( r )"
  - From the "File" menu of the graph window, you can save as postscript file or other formats.

{{:exercises:2015_ethz_mmm:screen_shot_2015-03-19_at_23.03.32.png?600|}}
</note>