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exercises:2017_ethz_mmm:md_slab [2017/02/22 10:01] (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: 2017/02/22 10:01 (external edit)