Determination of the melting temperature of copper
In order to be able to run simulations at high priority, today we will work on the Empa Cluster. We have created a personal account for you. Since the cluster is behind a firewall, we must connect to a gate machine (jumphost) to be allowed to access to the cluster. For security reasons, there are two temporary passwords that you should change to a personal password (can be the same for the gate and for the cluster.
Here the instructions to connect. Your username/password (EMPA-USER, TEMP-PASSW1, TEMP-PASSW2) are listed at the end of this message.
1) Decide a password (we will call it EMPA-PASSW )
2) connect to the jumphost:
ssh -X EMPA-USER@jump1.empa.ch Password: TEMP-PASSW1
3) Accept the contract
4) Set a new password (input old password, TEMP-PASSW1, write new password, EMPA-PASSW)
5) Connect to hypatia: ssh -X hypatia password: TEMP-PASSW2
6) Accept the contract
7) Change your password as in point 4) using TMP-PASSW2 as old password and set EMPA-PASSW
User-specific information (note: TMP-PASSW1 ist the password for jump1, that is the FIRST one, but is listed as second):
[you@hypatia ~]$ mmm-init [you@hypatia ~]$ cd exercise_5.1
is then the only thing you need to do in order to initialize the m_* scripts. This time the exercise is already in your home directory, and the cp2k module is already loaded!
[you@hypatia ~]$ cp2k.popt -i file.inp -o file.out
and to submit the job:
[stb@hypatia exercise_5.1]$ qsub -v INP=file run [stb@hypatia exercise_5.1]$ qstat -u stb # checks if it is running
where file is the name of the input file without suffix.
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.
All files of this exercise (all inputs and scripts are commented) can be also downloaded from the wiki: exercise5.1.zip
- First of all, we will test the NOSE-HOOVER thermostat
- Take a look at the file 111.xyz with vmd.
- We will apply a thermostat to half of the cell.
- copy the half_TIMECON.inp into half_20.inp
- Edit the half_20.inp and change _MYTIMECON_ to 20 (two places in the file). This sets the time constant of the thermostat.
- Run the job (interactively): > cp2k.popt -i half_20.inp -o half_20.out
- Plot the temperature behavior with gnuplot, file half_20-1.ener
- Take a look at the half_20.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?
- Repeat by copying half_TIMECON.inp into half_300.inp (TIMECON 300)
- Plot the -growing- half*ener file with gnuplot together with the previous ones. Comment the differences
- Now, run the simulation that should melt your system:
you@hypatia 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.
- 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@hypatia 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@hypatia exercise_5.1$ animate -alpha off -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@hypatia exercise_5.1$ qsub run -v INP=1400nve
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: qsub run -v INP=1300npe.init ; This is a very short simulation to set the temperature using the old velocities. Why do you need it?
- Run the second simulation: qsub run -v INP=1300npe
- 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?