exercises:2015_ethz_mmm:surface_cu

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TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
you@eulerX ~$ module load courses mmm vmd ; mmm-init

`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 the 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:2015_ethz_mmm:exercise_3.1.zip you@eulerX ~$ unzip exercises:2015_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

- Compute the three surface energies: you need to compute the area, subtract bulk contribution, take care of the units.
- Unordered List ItemIn the class we will learn how to compute the Wulff crystal from these three numbers.
- Basically, you should edit the input file “DP”, replacing
**“PUT_HERE_THE_XXX_SURFACE_ENERGY”**with corresponding surface energy. Note that for the {100} and {110} surfaces you need to edit**TWO**lines each, since the**z**direction is treated differently in this program. - 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. If you appropriately modify it (how?) you can have a xyz file to be opened in vmd. - 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!

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

exercises/2015_ethz_mmm/surface_cu.1425637504.txt.gz · Last modified: 2015/03/06 10:25 by yakutovich

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