Determination of the melting temperature of copper
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.
- Download the 5.1 exercise into your $HOME folder and unzip it:
you@eulerX ~$ 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
- Now, run the first simulation, that should melt your system:
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.
- Take a look at the file 111.xyz with vmd. Visualize it on the screen, and try to reproduce the figure similar to the one on the last slide of the lectures of today. Include the pbc box, create a representation with vdw, periodic images, rotate the sample, etc. Produce a snapshot and include the file in your assignment.
- Take a look at the half.inp file. How is the temperature controlled? Are all particles moving? Why? Which are the relevant sections for MD? Which kind of MD is it?
- Plot the -growing- half*ener file with gnuplot. How is temperature changing? Is there a conserved quantity?
- 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:
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.
- Describe the profile you have obtained. What do you see?
- Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles:
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.
SIMULATIONS AT DIFFERENT TOTAL ENERGIES FOR DETERMINING THE MELTING TEMPERATURE
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:
- Copy the files TEMPnpe.init.inp and TEMPnpe.inp into 1300npe.init.inp and 1300npe.inp (for T=1300) and then edit them in the appropriate points: PROJECT name, INITIAL temperature and RESTART filename.
- Run the first simulation: bsub cp2k.popt -i 1300npe.init.inp > 1300npe.init.out ; This is a very short simulation to set the temperature using the old velocities. Why do you need it?
- Run the second simulation: bsub cp2k.popt -i 1300npe.inp > 1300npe.out
- Observe the temperature and the z profile. Can you find the melting temperature? How do you choose temperatures?
- What is the melting temperature of copper that you have found using this potential?