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exercises:2017_ethz_mmm:surface_cu

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exercises:2017_ethz_mmm:surface_cu [2017/03/17 04:24] – dpasseroneexercises:2017_ethz_mmm:surface_cu [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ====== Surface energies of Copper high-symmetry surfaces ====== ====== Surface energies of Copper high-symmetry surfaces ======
  
 +<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>
  
 <note important> **REMEMBER: this is the command to load the  module for the cp2k program:** <note important> **REMEMBER: this is the command to load the  module for the cp2k program:**
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 ---- ----
-  * Download all the necessary files from  from the wiki: {{exercise_4.1.zip|exercise_4.1.zip}} (**all inputs are commented**) in your home directory and unzip it:+  * Download all the necessary files from  from the wiki: {{e4.1.zip|e4.1.zip}} (**all inputs are commented**) in your home directory and unzip it:
 <code bash> <code bash>
-you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:exercise_4.1.zip +you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:e4.1.zip 
-you@eulerX ~$ unzip exercises:2017_ethz_mmm:exercise_4.1.zip+you@eulerX ~$ unzip exercises:2017_ethz_mmm:e4.1.zip
 you@eulerX ~$ cd exercise_4.1 you@eulerX ~$ cd exercise_4.1
 </code> </code>
  
-<note tip>If you cannot download with **wget**, you can copy the zip file directly from my directory +If you cannot download with **wget**, you can copy the zip file directly from my directory 
 <code bash> <code bash>
-you@eulerX ~$ cp /Users/home/danielep/2017/exercise_4.1.zip . +you@eulerX ~$ cp /cluster/home/danielep/2017/e4.1.zip . 
-<code> +you@eulerX ~$ unzip e4.1.zip 
-</note>+you@eulerX ~$ cd exercise_4.1 
 +</code> 
   * Run the optimizations 100.inp, 110.inp, 111.inp and the bulk.   * Run the optimizations 100.inp, 110.inp, 111.inp and the bulk.
 <code bash> <code bash>
-you@eulerX exercise_3.1$ bsub cp2k.popt -i 100.inp -o 100.out +you@eulerX exercise_4.1$ bsub cp2k.popt -i 100.inp -o 100.out 
-you@eulerX exercise_3.1$ bsub cp2k.popt -i 110.inp -o 110.out +you@eulerX exercise_4.1$ bsub cp2k.popt -i 110.inp -o 110.out 
-you@eulerX exercise_3.1$ bsub cp2k.popt -i 111.inp -o 111.out +you@eulerX exercise_4.1$ bsub cp2k.popt -i 111.inp -o 111.out 
-you@eulerX exercise_3.1$ bsub cp2k.popt -i bulk.inp -o bulk.out+you@eulerX exercise_4.1$ bsub cp2k.popt -i bulk.inp -o bulk.out
 </code> </code>
   * While geometry optimization is running you can have a look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. In vmd it is also possible to open a console, and give the command **pbc set { a b c 90 90 90 }**  where a, b, c can be extracted from the cp2k input file. Then you can make several periodic copies for visualization.   * While geometry optimization is running you can have a look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. In vmd it is also possible to open a console, and give the command **pbc set { a b c 90 90 90 }**  where a, b, c can be extracted from the cp2k input file. Then you can make several periodic copies for visualization.
 <code bash> <code bash>
-you@eulerX exercise_3.1$ vmd 100.xyz +you@eulerX exercise_4.1$ vmd 100.xyz 
-you@eulerX exercise_3.1$ vmd 110.xyz +you@eulerX exercise_4.1$ vmd 110.xyz 
-you@eulerX exercise_3.1$ vmd 111.xyz+you@eulerX exercise_4.1$ vmd 111.xyz
 </code> </code>
  
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   * At this point, you can run the sowos program:   * At this point, you can run the sowos program:
 <code bash> <code bash>
-you@eulerX exercise_3.1$ ./sowos.v02.00.02.x+you@eulerX exercise_4.1$ ./sowos.v02.00.02.x
 </code> </code>
   * There will be many output files. Important are:    * There will be many output files. Important are: 
   - the atomistic model **out.atomistic-inside-gnuplot.xyz** which will contain many atoms if you chose a proportionality constant in the file DP which is too large. Unfortunately this file does NOT have a proper structure of an xyz file.    - the atomistic model **out.atomistic-inside-gnuplot.xyz** which will contain many atoms if you chose a proportionality constant in the file DP which is too large. Unfortunately this file does NOT have a proper structure of an xyz file. 
 +  - This can be solved by using a simple m_* function that adds the atomic symbol at the beginning of each line, and adding two lines at the beginning of the resulting file (number of atoms; comment):
 +<code bash>
 +you@eulerX exercise_4.1$ m_addcolumn Au < out.atomistic-inside-gnuplot.xyz > cluster.xyz
 +you@eulerX exercise_4.1$ nano cluster.xyz # Add two lines at the beginning.
 +</code>
   - the **out.plot-gnuplot.plt** file. You can open it with gnuplot   - the **out.plot-gnuplot.plt** file. You can open it with gnuplot
 <code bash> <code bash>
-you@eulerX exercise_3.1$ gnuplot+you@eulerX exercise_4.1$ gnuplot
 gnuplot> load "out.plot-gnuplot.plt" gnuplot> load "out.plot-gnuplot.plt"
 gnuplot> set xrange [-80:80] gnuplot> set xrange [-80:80]
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