you@eulerX ~$ module load courses mmm vmd
you@eulerX ~$ 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:
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:e4.1.zip you@eulerX ~$ unzip exercises:2017_ethz_mmm:e4.1.zip you@eulerX ~$ cd exercise_4.1
If you cannot download with wget, you can copy the zip file directly from my directory
you@eulerX ~$ cp /cluster/home/danielep/2017/e4.1.zip . you@eulerX ~$ unzip e4.1.zip you@eulerX ~$ cd exercise_4.1
you@eulerX exercise_4.1$ bsub cp2k.popt -i 100.inp -o 100.out you@eulerX exercise_4.1$ bsub cp2k.popt -i 110.inp -o 110.out you@eulerX exercise_4.1$ bsub cp2k.popt -i 111.inp -o 111.out you@eulerX exercise_4.1$ bsub cp2k.popt -i bulk.inp -o bulk.out
you@eulerX exercise_4.1$ vmd 100.xyz you@eulerX exercise_4.1$ vmd 110.xyz you@eulerX exercise_4.1$ vmd 111.xyz
Now 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: the program takes care of assigning the surface energy to equivalent surfaces (like (010)) but since it was developed for island on surfaces it does not do it automatically in all directions. z direction is treated differently in this program.
you@eulerX exercise_4.1$ ./sowos.v02.00.02.x
you@eulerX exercise_4.1$ m_addcolumn Au < out.atomistic-inside-gnuplot.xyz > cluster.xyz you@eulerX exercise_4.1$ nano cluster.xyz # Add two lines at the beginning.
you@eulerX exercise_4.1$ 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!