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exercises:2015_ethz_mmm:surface_au

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exercises:2015_ethz_mmm:surface_au [2015/03/06 10:44] – yakutovichexercises:2015_ethz_mmm:surface_au [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 Take the above table as reference for the orders of magnitude of surface energies.  Take the above table as reference for the orders of magnitude of surface energies. 
-You can download the ** commented **  inputs by downloading from the wiki: {{exercise_3.2.zip|exercise_3.2.zip}}) the necessary files for computing the surface energies of all 3 high symmetry faces of gold.+  * Download all the necessary files for computing the surface energies of all 3 high symmetry faces of gold from  from the wiki: {{exercise_3.2.zip|exercise_3.2.zip}} (**all inputs are commented**) in your home directory and unzip it: 
 +<code bash> 
 +you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_3.2.zip 
 +you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_3.2.zip 
 +you@eulerX ~$ cd exercise_3.2 
 +</code>
 In principle all reconstructed phases should be with a lower surface energy, but this EAM potential fails for some of them. In principle all reconstructed phases should be with a lower surface energy, but this EAM potential fails for some of them.
 The input files are: The input files are:
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 Run the cp2k code as  Run the cp2k code as 
  
-<code> +<code bash> 
-you@eulerxx $ cp2k.popt -i 100_unr.inp > 100_unr.out +you@eulerxx $ bsub cp2k.popt -i 100_unr.inp -o 100_unr.out 
-you@eulerxx $ cp2k.popt -i 110_unr.inp > 110_unr.out +you@eulerxx $ bsub cp2k.popt -i 110_unr.inp -o 110_unr.out 
-you@eulerxx $ cp2k.popt -i 111_unr.inp > 111_unr.out+you@eulerxx $ bsub cp2k.popt -i 111_unr.inp -o 111_unr.out
 </code> </code>
  
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-<code> +<code bash> 
-you@eulerxx $ cp2k.popt -i 100_rec.inp > 100_rec.out +you@eulerxx $ bsub cp2k.popt -i 100_rec.inp -o 100_rec.out 
-you@eulerxx $ cp2k.popt -i 110_rec.inp > 110_rec.out+you@eulerxx $ bsub cp2k.popt -i 110_rec.inp -o 110_rec.out
 </code> </code>
 +<note tip>
 Assignments: Assignments:
  
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   - Try to color the surfaces in vmd in a way that makes the height evident (ask the assistant) and produce snapshots (render)   - Try to color the surfaces in vmd in a way that makes the height evident (ask the assistant) and produce snapshots (render)
   - Comment on the (2x1) reconstruction: what do you see?   - Comment on the (2x1) reconstruction: what do you see?
-  - Copy the 100_unr.xyz into a new file 110_my_rec.xyz +  - Copy the 110_unr.xyz into a new file 110_my_rec.xyz 
   - Edit the file and remove one line each two on the two surfaces   - Edit the file and remove one line each two on the two surfaces
   - Check that the result is the same as in 110_rec.xyz   - Check that the result is the same as in 110_rec.xyz
   - Plot the same slabs, but adding periodic images in vmd: remember pbc set { a b c 90 90 90 }.   - Plot the same slabs, but adding periodic images in vmd: remember pbc set { a b c 90 90 90 }.
- +</note> 
-<note tip>Hint: you can save a configuration file in vmd and reuse it for a new sample! Ask the assistant!</note>+<note important>Hint: you can save a configuration file in vmd and reuse it for a new sample! Ask the assistant!</note>
exercises/2015_ethz_mmm/surface_au.1425638653.txt.gz · Last modified: 2020/08/21 10:14 (external edit)