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exercises:2017_ethz_mmm:md_slab [2017/02/22 10:01]
exercises:2017_ethz_mmm:md_slab [2020/08/21 10:15] (current)
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 +====== 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>
exercises/2017_ethz_mmm/md_slab.txt ยท Last modified: 2020/08/21 10:15 (external edit)