exercises:2017_ethz_mmm:md_slab
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— | exercises:2017_ethz_mmm:md_slab [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== Hot gold ====== | ||
+ | <note warning> | ||
+ | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
+ | you@eulerX ~$ module load courses mmm vmd | ||
+ | |||
+ | you@eulerX ~$ mmm-init | ||
+ | </ | ||
+ | |||
+ | |||
+ | 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 $HOME folder and unzip it: | ||
+ | <code bash> | ||
+ | you@eulerX ~$ wget http:// | ||
+ | you@eulerX ~$ unzip exercises: | ||
+ | you@eulerX ~$ cd exercise_4.2 | ||
+ | </ | ||
+ | <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}} | ||
+ | </ | ||
+ | |||
+ | * First, we simulate the system at 700 K using a thermostat. | ||
+ | <code bash> | ||
+ | you@eulerX exercise_4.2$ bsub cp2k.popt -i 700.inp -o 700.out | ||
+ | </ | ||
+ | * Then, the obtained xyz trajectory can be analyzed using the script **histo_z** available in the directory. | ||
+ | |||
+ | <code bash> | ||
+ | you@eulerX exercise_4.2$ ./histo_z 700-pos-1.xyz | ||
+ | </ | ||
+ | |||
+ | The output is **700-pos-1.xyz.z**, | ||
+ | |||
+ | |||
+ | <note tip> | ||
+ | Assignments: | ||
+ | - Explain the profile, and use the third column to draw conclusions about the surface structure. | ||
+ | - Study the source of the script. Understand its behavior. | ||
+ | - Copy histo_z into another file and modify it to only include the particles from the first 10 frames of the trajectory. | ||
+ | - Run it and see the differences to the first profile. | ||
+ | - Do the same excluding the first 10 frames. | ||
+ | - Explain those differences, | ||
+ | </ | ||
+ | |||
+ | * 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 | ||
+ | </ | ||
+ | |||
+ | * 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> | ||
+ | Assignments: | ||
+ | - 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, | ||
+ | in Tk console you can: | ||
+ | |||
+ | 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> | ||
+ | Assignments: | ||
+ | - Discuss radial distribution function for 700, 1100, and 1300 K. | ||
+ | </ | ||
+ | <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 " | ||
+ | |||
+ | {{: | ||
+ | </ |