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exercises:2015_ethz_mmm:md_slab [2015/03/11 14:00] yakutovichexercises:2015_ethz_mmm:md_slab [2020/08/21 10:15] (current) – external edit 127.0.0.1
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-This exercise deals with heating a gold slab, namely the (100) reconstructed that you already simulated last time. The goal is to plot a density profile in the direction orthogonal to the slab, and to compute (using vmd) the radial distribution function g(r) at various temperatures.+This exercise deals with heating a gold slab, namely the (100) reconstructed that you already simulated last time. The goal is to plot a density profile in the direction orthogonal to the slab, and to compute (using vmd) the radial distribution function g( r ) at various temperatures.
  
 Download the 4.2 exercise into your $HOME folder and unzip it: Download the 4.2 exercise into your $HOME folder and unzip it:
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 </code> </code>
   * Try to play with representations: color the surface atoms in one color, the bulk ones in another color.   * Try to play with representations: color the surface atoms in one color, the bulk ones in another color.
-  * Using the "radial distribution function" plugin from the extension menu, draw the g(r) of the system.+  * Using the "radial distribution function" plugin from the extension menu (Extensions>Analysis>Radial Pair Distribution Function g( r ) ), draw the g( r ) of the system.
  
 <note tip> <note tip>
  Discuss radial distribution function for 700, 1100, and 1300 K.   Discuss radial distribution function for 700, 1100, and 1300 K. 
 +</note>
 +<note important>
 +Hint: how to use the g( r ) module:
 +  - First apply pbcs (see above)
 +  - Open the radial distribution function plugin and enter the parameters as shown (**note: in the example below we excluded the first 10 frames**) (from "Utilities" you can check that your unit cell is OK)
 +  - Click "Compute g( r )"
 +  - From the "File" menu of the graph window, you can save as postscript file or other formats.
 +
 +{{:exercises:2015_ethz_mmm:screen_shot_2015-03-19_at_23.03.32.png?600|}}
 </note> </note>
exercises/2015_ethz_mmm/md_slab.1426082418.txt.gz · Last modified: 2020/08/21 10:14 (external edit)