exercises:2016_ethz_mmm:surface_cu

`you@eulerX ~$ module load new cp2k`

**and to submit the job:**

you@eulerX ~$ bsub < jobname

In this exercise we will compute the surface energies of Cu using the EAM potential. As a reference, we report the table from the Gross book:

- Download all the necessary files from from the wiki: exercise_3.1.zip (
**all inputs are commented**) in your home directory and unzip it:

you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2016_ethz_mmm:exercise_3.1.zip you@eulerX ~$ unzip exercises:2016_ethz_mmm:exercise_3.1.zip you@eulerX ~$ cd exercise_3.1

- Run the optimizations 100.inp, 110.inp, 111.inp and the bulk.

you@eulerX exercise_3.1$ bsub cp2k.popt -i 100.inp -o 100.out you@eulerX exercise_3.1$ bsub cp2k.popt -i 110.inp -o 110.out you@eulerX exercise_3.1$ bsub cp2k.popt -i 111.inp -o 111.out you@eulerX exercise_3.1$ bsub cp2k.popt -i bulk.inp -o bulk.out

- While geometry optimization is running you can have a look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. In vmd it is also possible to open a console, and give the command
**pbc set { a b c 90 90 90 }**where a, b, c can be extracted from the cp2k input file. Then you can make several periodic copies for visualization.

you@eulerX exercise_3.1$ vmd 100.xyz you@eulerX exercise_3.1$ vmd 110.xyz you@eulerX exercise_3.1$ vmd 111.xyz

Assignments:

Now we will learn how to compute the Wulff crystal from these three numbers. Basically, you should edit the input file “DP”, replacing - Without calculating the surface energies but just looking at the structures, could you guess which surface will be the most stable one? And the least stable one? Why? (Quite often a simple logic could tell you already how your results should look like.)
- Have a look into the files, containing the optimization trajectory (100-pos-1.xyz, 110-pos-1.xyz, 111-pos-1.xyz). Along the optimization procedure all the surface structures make a similar movement. Could you describe it and explain why it is happening? Take into account that all the geometries were taking from the bulk structure.
- Compute the three surface energies: you need to compute the area, subtract bulk contribution, take care of the units.

- At this point, you can run the sowos program:

you@eulerX exercise_3.1$ ./sowos.v02.00.02.x

- There will be many output files. Important are:

- the atomistic model
**out.atomistic-inside-gnuplot.xyz**which will contain many atoms if you chose a proportionality constant in the file DP which is too large. Unfortunately this file does NOT have a proper structure of an xyz file. - the
**out.plot-gnuplot.plt**file. You can open it with gnuplot

you@eulerX exercise_3.1$ gnuplot gnuplot> load "out.plot-gnuplot.plt" gnuplot> set xrange [-80:80] gnuplot> set yrange [-80:80] gnuplot> set view equal xyz gnuplot> replot

you can rotate with the mouse!

Assignments:

- What is the proper structure of a XYZ file? Try to appropriately modify
**out.atomistic-inside-gnuplot.xyz**and open it in vmd. Make a nice snapshot and add it to your report. - Use the cluster generated with SOWOS as an input configuration for a cluster optimization with cp2k. Comment on the final geometry. BEWARE OF THE CELL! It is not a periodic system!

documentation on **SOWOS** can be found at the web site of Daniele Scopece

exercises/2016_ethz_mmm/surface_cu.txt · Last modified: 2016/03/11 11:20 by yakutovich

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