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.

2) Download the script:

      File:Ngeom.tgz

and uncompress it.

3) CHANGE IN LINE 14 OF ngeom.sh path=/home/lbellarosa/src/complex/Cell with the path of where you put your directory A.

4) Now you can run the script typing:

      ngeom.sh OUTCAR