This is an old revision of the document!
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
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.
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.
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.
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: