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 nobel gases.
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2016_ethz_mmm:exercise_5.1.tar.gz you@eulerX ~$ tar -zxvf exercises:2016_ethz_mmm:exercise_5.1.tar.gz you@eulerX ~$ cd exercise_5.1
Before you run any simulations you should do the following things:
To do the last step you can use the template provided in the exercise folder (111_unit.xyz). The file contains positions of dummy atoms (named with X) in the unit cell oriented along  axis. All the positions are given in the units of first neighbor distance. Therefore you should rescale the unit cell using the correct first neighbor distance for your nobel gas and change atom names from X to the one you have chosen. Use the following command to do it (FND and ELEMENT must be changed by approximate first neighborg distance and element type respectively):
you@eulerX exercise_5.1$ m_xyzrescale FND < 111_unit.xyz | sed 's/X/ELEMENT/' > ELEMENT_unit.xyz
Open the file cell.inp and specify all the missing settings indicated as X. Unit cell parameters will be given to you in the second line of a freshly created file ELEMENT_unit.xyz. Now it is time to do the fist simulation, which is an optimization of the unit cell:
you@eulerX exercise_5.1$ bsub cp2k.popt -i cell.inp -o cell.out
MULTIPLE_UNIT_CELL 4 2 2
This means that:
This run should not take too much time, because you should have provided first neighbor distance value as the minimum energy of Lennard-Jones potential which is basically the same for the nobel gases at 0 K. Use the optimized geometry from the file opt_cell-pos-1.xyz as the initial geometry for the next run:
you@eulerX exercise_5.1$ tail -n 98 opt_cell-pos-1.xyz > ./ELEMENT_opt_unit.xyz
For the next simulation you will need the file called half.inp. Open it and again provide all the necessary parameters. Note, that unit cell for this run can be found in the file opt_cell-1.restart (section CELL)
Now, run the simulation, that should melt your system:
you@eulerX exercise_5.1$ cp2k.popt -i half.inp -o half.out
It is a 10000 step molecular dynamics. While it is running you can complete the folowing 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.
Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles. But again some parameters needs to be specified in the file nve.inp. Use the simulation cell from the file half-1.restart. Also file with coordinates (X_init_nve.xyz) needs to be created. Use the coordinates from the last frame of the previous run.
And run the simulations:
you@eulerX exercise_5.1$ bsub cp2k.popt -i nve.inp -o nve.out
The resulting configuration (check) will be an equilibrated system (which profile?).
Now we have a file called “nve-1.restart”. Do not delete it !!! It will be used as a restart file for all simulations.
As explained in the class, we should 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). To make the exercise easier, we will run at constant volume (NVE) in this case.
THE TEMPERATURE WILL NOT BE CONTROLLED DURING THE RUN
For EACH temperature you should: