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--- exercises:2017_ethz_mmm:surface_cu [2017/03/17 04:39] – dpasserone
+++ exercises:2017_ethz_mmm:surface_cu [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 2: / Line 2: @@
 ====== 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:**
@@ Line 34: / Line 41: @@
 If you cannot download with **wget**, you can copy the zip file directly from my directory
 <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>
@@ Line 65: / Line 74: @@
   * 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.
+  - 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
 <code bash>
-you@eulerX exercise_3.1$ gnuplot
+you@eulerX exercise_4.1$ gnuplot
 gnuplot> load "out.plot-gnuplot.plt"
 gnuplot> set xrange [-80:80]