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--- exercises:2015_ethz_mmm:md_slab [2015/03/09 16:39] – yakutovich
+++ exercises:2015_ethz_mmm:md_slab [2015/03/19 22:13] – yakutovich
@@ Line 2: / Line 2: @@
-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 $HOME folder and unzip it:
@@ Line 11: / Line 11: @@
 </code>
 <note tip>
-All files of this exercise (**input and scripts are all commented**) can be also downloaded from the wiki: {{exercise_4.2.zip|exercise_4.2.zip}}
+All files of this exercise (** input and scripts are all commented**) can be also downloaded from the wiki: {{exercise_4.2.zip|exercise_4.2.zip}}
 </note>
-As usual, create a new directory and download the files from the wiki: {{exercise_4.2.tar.gz|exercise_4.2.tar.gz}}
-First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat.
+  * First, we simulate the system at 700 K using a thermostat.
-Then, the obtained xyz trajectory can be analyzed using the script **histo_z** available in the directory.
+<code bash>
+you@eulerX exercise_4.2$ bsub cp2k.popt -i 700.inp -o 700.out
+</code>
+  * Then, the obtained xyz trajectory can be analyzed using the script **histo_z** available in the directory.
-<code>
+<code bash>
-./histo_z 700-pos-1.xyz
+you@eulerX exercise_4.2$ ./histo_z 700-pos-1.xyz
 </code>
@@ Line 25: / Line 27: @@
-<note important>
+<note tip>
   - Explain the profile, and use the third column to draw conclusions about the surface structure.
   - Study the source of the script. Understand its behavior.
@@ Line 34: / Line 36: @@
 </note>
-Perform a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp).
+  * Perform **consequently** a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp):
+<code bash>
+you@eulerX exercise_4.2$ bsub cp2k.popt -i 1100.inp -o 1100.out
+you@eulerX exercise_4.2$ bsub cp2k.popt -i 1300.inp -o 1300.out
+</code>
-<note important>Discuss the differences in the density profile. What do you expect to see in vmd?
+  * And again analyze these trajectories using the script histo_z:
+<code bash>
+you@eulerX exercise_4.2$ ./histo_z 1100-1-pos.xyz
+you@eulerX exercise_4.2$ ./histo_z 1300-1-pos.xyz
+</code>
+<note tip>
+Discuss the differences in the density profile. What do you expect to see in vmd?
 </note>
-Now, use vmd to look at the trajectories. As you launch vmd,
+  * Now, use vmd to look at the trajectories. As you launch vmd,
-you can (assignment):
+in Tk console you can:
+Load a pbc.vmd file which includes the definition of the periodic box
+<code tcl>
+vmd> source pbc.vmd
+</code>
+Draw the box:
+<code tcl>
+vmd> draw pbcbox
+</code>
+Wrap all atoms in the periodic box:
+<code tcl>
+vmd> pbc wrap -first first -last last
+</code>
+  * 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 (Extensions>Analysis>Radial Pair Distribution Function g( r ) ), draw the g( r ) of the system.
+<note tip>
+ Discuss radial distribution function for 700, 1100, and 1300 K.
+</note>
 <note important>
-- source a pbc.vmd file which includes the definition of the periodic box
+Hint: how to use the g( r ) module:
-- draw the box: **draw pbcbox** in the Tk console
+  - First apply pbcs (see above)
-- wrap all atoms in the periodic box: **pbc wrap -first first -last last**
+  - 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)
-- "play" with representations: try to color the surface atoms in one color, the bulk ones in another color.
+  - Click "Compute g( r )"
-- Using the "radial distribution function" plugin from the extension menu, draw the g(r) of the system. Discuss it for 700, 1100, and 1300 K.
+  - 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>