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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
REMEMBER: this is the command to load the module for the cp2k program:
you@eulerX ~$ module load new cp2k

and to submit the job:

you@eulerX ~$ bsub < jobname

Generation of slab with high symmetry surfaces

Surface energies of Copper high-symmetry surfaces

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:

http://example.com|External Link


  • 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:
  1. 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.
  2. 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!
Assignment: 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/2015_ethz_mmm/surface_cu.1425637504.txt.gz · Last modified: 2015/03/06 10:25 by yakutovich