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 use a slab geometry (without vacuum region, so without a surface) with full periodic boundary conditions to study the melting behavior of copper.
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_5.1.zip you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_5.1.zip you@eulerX ~$ cd exercise_5.1
you@eulerX exercise_5.1$ cp2k.popt -i half.inp -o half.out
It is a 3000 step molecular dynamics. While it is running you can complete the first assignments.
you@eulerX exercise_5.1$ ./doprof half-pos-1.xyz
The script calls the histogram script of last time, with a modification: a running window of configurations is averaged to produce a single frame. First, step 1-10, then step 10-20, and so on. At the end, the file movie.half-pos-1.xyz.gif, an animated gif is produced. If it works, you can run the command:
you@eulerX exercise_5.1$ animate -loop 0 -delay 100 movie.half-pos-1.xyz.gif
or download the file to your local machine and open in your internet browser. It will run the animation.
you@eulerX exercise_5.1$ bsub cp2k.popt -i 1400nve.inp -o 1400nve.out
The resulting configuration (check) will be an equilibrated system (which profile?).
Now we have a file called “1400nve-1.restart”. Do not delete it !!! It will be used as a restart file for all simulations.
As explained in the class, we will run NPE (that is, constant energies but variable cell) simulations at energies which are above and below the supposed “melting energy” (energy corresponding to melting temperature).
THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN
For EACH temperature you should: