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exercises:2017_ethz_mmm:surface_cu

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exercises:2017_ethz_mmm:surface_cu [2017/03/17 04:39] – 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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 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/e4.1.zip .+you@eulerX ~$ cp /cluster/home/danielep/2017/e4.1.zip . 
 +you@eulerX ~$ unzip e4.1.zip 
 +you@eulerX ~$ cd exercise_4.1
 </code> </code>
  
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   * 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]
exercises/2017_ethz_mmm/surface_cu.1489725564.txt.gz · Last modified: (external edit)