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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. As usual, connect to brutus and enter the following commands:
module load cp2k/trunk.2.5.13191 module load open_mpi/1.6.5 ! THIS IS NEEDED IF YOU WANT TO RUN AN MPI PARALLEL RUN --- NOT CONVENIENT IN THIS CASE module load vmd mkdir EX_5.1 cd EX_5.1
Now, run the first simulation, that should melt your system.
bsub cp2k.popt -i half.inp > half.out
It is a 3000 step molecular dynamics. During this time (about 20 minutes) you can complete the first assignments.
At the end of the first dynamics (hint: tail -f half*ener) , you can examine the half-pos-1.xyz file by performing z-profiles using the script doprof .
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:
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.
Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles:
bsub cp2k.popt -i 1400nve.inp > 1400nve.out
The resulting configuration (check) will be an equilibrated system (which profile?).
Now we have a file called 1400nve-1.restart
THIS WILL BE USED AS RESTART FILE FOR ALL SIMULATIONS! DO NOT DELETE IT!
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).
For EACH temperature you have to: