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exercises:2016_ethz_mmm:surface_cu [2016/03/09 22:37] – yakutovichexercises:2016_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> 
  
  
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 </note>  </note> 
  
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 </code> </code>
  
-  * Compute the three surface energies: you need to compute the area, subtract bulk contribution, take care of the units. + 
-  * Unordered List ItemIn the class we will learn how to compute the Wulff crystal from these three numbers. +<note tip> 
-  * Basically, you should edit the input file "DP", replacing  **"PUT_HERE_THE_XXX_SURFACE_ENERGY"** with corresponding surface energy. Note that for the {100} and {110} surfaces you need to edit **TWO** lines each: the program takes care of assigning the surface energy to equivalent surfaces (like (010)) but since it was developed for island on surfaces it does not do it automatically in all directions. **z** direction is treated differently in this program. +Assignments:  
 +  - Without calculating the surface energies but just looking at the structures, could you guess which surface will be the most stable one? And the least stable one? Why? (Quite often a simple logic could tell you already how your results should look like.) 
 +  - Have a look into the files, containing the optimization trajectory (100-pos-1.xyz, 110-pos-1.xyz, 111-pos-1.xyz). Along the optimization procedure all the surface structures make a similar movement. Could you describe it and explain why it is happening? Take into account that all the geometries were taking from the bulk structure. 
 +  - Compute the three surface energies: you need to compute the area, subtract bulk contribution, take care of the units. 
 +</note> 
 +Now we will learn how to compute the Wulff crystal from these three numbers. Basically, you should edit the input file "DP", replacing  **"PUT_HERE_THE_XXX_SURFACE_ENERGY"** with corresponding surface energy. Note that for the {100} and {110} surfaces you need to edit **TWO** lines each: the program takes care of assigning the surface energy to equivalent surfaces (like (010)) but since it was developed for island on surfaces it does not do it automatically in all directions. **z** direction is treated differently in this program. 
   * At this point, you can run the sowos program:   * At this point, you can run the sowos program:
 <code bash> <code bash>
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 </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. If you appropriately modify it (how?) you can have a xyz file to be opened in vmd.   +  - 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 **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_3.1$ gnuplot
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 gnuplot> replot gnuplot> replot
 </code> </code>
-  * you can rotate with the mouse!+you can rotate with the mouse! 
 + 
 + 
  
 <note tip> <note tip>
-Assignment: use the cluster generated with SOWOS as an input configuration for a cluster optimization with cp2k. Comment on the final geometry. BEWARE OF THE CELL! It is not a periodic system!+Assignments:  
 +  - What is the proper structure of a XYZ file? Try to appropriately modify **out.atomistic-inside-gnuplot.xyz** and open it in vmd. Make a nice snapshot and add it to your report.   
 +  - Use the cluster generated with SOWOS as an input configuration for a cluster optimization with cp2k. Comment on the final geometry. BEWARE OF THE CELL! It is not a periodic system!
 </note> </note>
  
  
 <note tip>documentation on **SOWOS** can be found at [[http://www.danielescopece84.altervista.org/sowos.html|the web site of Daniele Scopece]]</note> <note tip>documentation on **SOWOS** can be found at [[http://www.danielescopece84.altervista.org/sowos.html|the web site of Daniele Scopece]]</note>
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