# Open SourceMolecular Dynamics

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exercises:2017_ethz_mmm:md_slab

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 — exercises:2017_ethz_mmm:md_slab [2017/02/22 10:01] (current) Line 1: Line 1: + ====== Hot gold ====== + + 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 $HOME folder and unzip it: + + you@eulerX ~$ wget http://​www.cp2k.org/​_media/​exercises:​2016_ethz_mmm:​exercise_4.2.zip + you@eulerX ~$unzip exercises:​2016_ethz_mmm:​exercise_4.2.zip + you@eulerX ~$ cd exercise_4.2 + ​ + + 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. + + you@eulerX exercise_4.2$bsub cp2k.popt -i 700.inp -o 700.out + ​ + * Then, the obtained xyz trajectory can be analyzed using the script **histo_z** available in the directory. ​ + + + you@eulerX exercise_4.2$ ./histo_z 700-pos-1.xyz + ​ + + The output is **700-pos-1.xyz.z**,​ a file with three columns: z, dn/dz, and the progressive integral of this quantity. + + + + 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,​ based on what you see in the *.ener file (energies, temperature...). + ​ + + * Perform **consequently** a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp): + + 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: + + you@eulerX exercise_4.2$./histo_z 1100-1-pos.xyz + you@eulerX exercise_4.2$ ./histo_z 1300-1-pos.xyz + ​ + + + + 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 + + vmd> source pbc.vmd + ​ + Draw the box: +  ​ + vmd> draw pbcbox + ​ + Wrap all atoms in the periodic box: + + vmd> pbc wrap -first first -last last + ​ + * 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. + + + Assignments: ​ + - Discuss radial distribution function for 700, 1100, and 1300 K. + ​ + ​ + 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 "​Utilities"​ you can check that your unit cell is OK) + - Click "​Compute g( r )" + - 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|}} +