exercises:2015_ethz_mmm:md_slab
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exercises:2015_ethz_mmm:md_slab [2015/03/09 17:03] – yakutovich | exercises:2015_ethz_mmm:md_slab [2015/03/19 22:13] – yakutovich | ||
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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 $HOME folder and unzip it: | ||
Line 36: | Line 36: | ||
</ | </ | ||
- | Perform a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp): | + | * Perform |
<code bash> | <code bash> | ||
you@eulerX exercise_4.2$ bsub cp2k.popt -i 1100.inp -o 1100.out | you@eulerX exercise_4.2$ bsub cp2k.popt -i 1100.inp -o 1100.out | ||
you@eulerX exercise_4.2$ bsub cp2k.popt -i 1300.inp -o 1300.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 | ||
+ | </ | ||
+ | |||
<note tip> | <note tip> | ||
Line 46: | Line 53: | ||
</ | </ | ||
- | Now, use vmd to look at the trajectories. As you launch vmd, | + | * Now, use vmd to look at the trajectories. As you launch vmd, |
in Tk console you can: | in Tk console you can: | ||
+ | |||
Load a pbc.vmd file which includes the definition of the periodic box | Load a pbc.vmd file which includes the definition of the periodic box | ||
- | < | + | < |
- | source pbc.vmd | + | vmd> |
</ | </ | ||
Draw the box: | Draw the box: | ||
- | < | + | < |
- | draw pbcbox | + | vmd> |
</ | </ | ||
Wrap all atoms in the periodic box: | Wrap all atoms in the periodic box: | ||
- | < | + | < |
- | pbc wrap -first first -last last | + | vmd> |
</ | </ | ||
- | Try to play with representations: | + | * Try to play with representations: |
- | Using the " | + | |
<note tip> | <note tip> | ||
| | ||
+ | </ | ||
+ | <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 " | ||
+ | - Click " | ||
+ | - From the " | ||
+ | |||
+ | {{: | ||
</ | </ |
exercises/2015_ethz_mmm/md_slab.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1