exercises:2015_ethz_mmm:md_slab
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exercises:2015_ethz_mmm:md_slab [2015/03/09 16:39] – yakutovich | exercises: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 $HOME folder and unzip it: | ||
Line 11: | Line 11: | ||
</ | </ | ||
<note tip> | <note tip> | ||
- | All files of this exercise (**input and scripts are all commented**) can be also downloaded from the wiki: {{exercise_4.2.zip|exercise_4.2.zip}} | + | All files of this exercise (** input and scripts are all commented**) can be also downloaded from the wiki: {{exercise_4.2.zip|exercise_4.2.zip}} |
</ | </ | ||
- | As usual, create a new directory and download the files from the wiki: {{exercise_4.2.tar.gz|exercise_4.2.tar.gz}} | ||
- | First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat. | + | * First, we simulate the system at 700 K using a thermostat. |
- | Then, the obtained xyz trajectory can be analyzed using the script **histo_z** available in the directory. | + | <code bash> |
+ | you@eulerX exercise_4.2$ bsub cp2k.popt -i 700.inp | ||
+ | </ | ||
+ | | ||
- | < | + | < |
- | ./histo_z 700-pos-1.xyz | + | you@eulerX exercise_4.2$ |
</ | </ | ||
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- | < | + | < |
- Explain the profile, and use the third column to draw conclusions about the surface structure. | - Explain the profile, and use the third column to draw conclusions about the surface structure. | ||
- Study the source of the script. Understand its behavior. | - Study the source of the script. Understand its behavior. | ||
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</ | </ | ||
- | Perform a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp). | + | * Perform |
+ | <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 | ||
+ | </ | ||
- | < | + | * 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 | ||
+ | </ | ||
+ | |||
+ | |||
+ | < | ||
+ | Discuss the differences in the density profile. What do you expect to see in vmd? | ||
</ | </ | ||
- | 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 |
+ | Load a pbc.vmd file which includes the definition of the periodic box | ||
+ | <code tcl> | ||
+ | vmd> source pbc.vmd | ||
+ | </ | ||
+ | Draw the box: | ||
+ | <code tcl> | ||
+ | vmd> draw pbcbox | ||
+ | </ | ||
+ | Wrap all atoms in the periodic box: | ||
+ | <code tcl> | ||
+ | vmd> pbc wrap -first first -last last | ||
+ | </ | ||
+ | * Try to play with representations: | ||
+ | * Using the " | ||
+ | |||
+ | <note tip> | ||
+ | | ||
+ | </ | ||
<note important> | <note important> | ||
- | - source a pbc.vmd file which includes | + | 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 |
- | - "play" | + | - Click "Compute g( r )" |
- | - Using the "radial distribution function" | + | - From the "File" menu of the graph window, you can save as postscript file or other formats. |
+ | |||
+ | {{: | ||
</ | </ |
exercises/2015_ethz_mmm/md_slab.1425919198.txt.gz · Last modified: 2020/08/21 10:14 (external edit)