Scylla&charybdis.tgz

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The coupled scripts scylla.sh and charybdis.sh are used to run iteratively molecular dynamics simulations.

Launching: charybdis.sh name nproc final_time (check the running steps for more details)

Output file: directories with prefix prfx

INSTALLATION STEPS

First of all, download the package of scripts:

      File:Scripts.tgz

Place it in the directory of Mare Nostrum ~/bin. If this directory does not exist, create it.

1) If YOU DO NOT HAVE a directory called ~/bin/scripts, put scripts.tgz inside ~/bin and uncompress it with the command: tar -xvzf scripts.tgz and remove scripts.tgz.

2) If YOU HAVE already a directory called ~/bin/scripts, create a new directory exp, put scripts.tgz inside ~/bin/exp and uncompress it with the command: tar -xvzf scripts.tgz and remove scripts.tgz. Now move the files adjust.sh, charybdis.sh, copy.sh and scylla.sh in the directory ~/bin/scripts; remove ~/bin/exp.

Plese, check that all the scripts adjust.sh, charybdis.sh, copy.sh and scylla.sh are executables (they should appear green on your screen). If not, run the command chmod u+x on each of them.

The installation is ready!

SETUP STEPS

Before running a calculation with scylla and charybdis, a special care is needed in the preparation of the input DIRECTORIES.

1) Be sure to be on mn1/mn2 or whatever in marenostrum.

2) In your home directory (~), create all the tree of directories where you want to store your results. For example, create the directories ~/Work/h2o_on_Pt/Gamma_point/Ecut_500/Tr1.

3) In the scratch directory /gpfs/scratch/GROUP/USER, you will create the same tree of directories. In this case, we will have /gpfs/scratch/GROUP/USER/Work/h2o_on_Pt/Gamma_point/Ecut_500/Tr1. Here, we will put in a directory called dyn_00 our initial (un)optimized geometry... Remember! We need an INCAR, KPOINTS, POSCAR AND POTCAR at least!!! You can simply copy the directory with all the optimization here: scylla.sh and charybdis.sh are smart enough to realize that there is a CONTCAR file and to move it to a POSCAR.

RUNNING STEPS

You are ready to run scylla.sh and charybdis.sh. The command is:

charybdis.sh name proc final_time

An example of the paraters will clear things up. Let suppose I want to simulate 17 ps of water on Pt(100). name (the name of the command sub file for the queues) can be h2o_on_Pt100, proc (the number of processors; up to date, it is better to put it = to an integer multiple of 16) can be set to 80, and finally final_time = 17. So, the command will be:

charybdis.sh h2o_on_Pt100 80 17