exercises:2015_ethz_mmm:md_slab
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exercises:2015_ethz_mmm:md_slab [2015/03/09 16:56] – yakutovich | exercises:2015_ethz_mmm:md_slab [2015/03/19 22:05] – dpasserone | ||
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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> | ||
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</ | </ | ||
- | 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 |
- | <note important> | + | Load a pbc.vmd file which includes the definition of the periodic box |
- | - source | + | <code tcl> |
- | - draw the box: **draw pbcbox** in the Tk console | + | vmd> source pbc.vmd |
- | - wrap all atoms in the periodic box: **pbc wrap -first first -last last** | + | </ |
- | - "play" | + | Draw the box: |
- | - Using the " | + | <code tcl> |
+ | vmd> | ||
+ | </ | ||
+ | Wrap all atoms in the periodic box: | ||
+ | <code tcl> | ||
+ | vmd> | ||
+ | </ | ||
+ | * Try to play with representations: | ||
+ | | ||
+ | |||
+ | <note tip> | ||
+ | Discuss | ||
+ | Here how to use the g(r) module: | ||
+ | 1) First apply pbcs (see above) | ||
+ | 2) Open the radial distribution function plugin and enter the parameters as shown (from " | ||
+ | 3) Click " | ||
+ | 4) From the " | ||
</ | </ |
exercises/2015_ethz_mmm/md_slab.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1