Scylla&charybdis.tgz: Difference between revisions
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appear green on your screen). If not, run the command ''chmod u+x'' on each of them. | appear green on your screen). If not, run the command ''chmod u+x'' on each of them. | ||
The installation is ready | The installation is ready! | ||
== SETUP STEPS == | == SETUP STEPS == | ||
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1) Be sure to be on mn1/mn2 or whatever in marenostrum. | 1) Be sure to be on mn1/mn2 or whatever in marenostrum. | ||
2) In your home directory (~), create all the | 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'' | |||
= REMARKS = | |||
Revision as of 15:56, 9 January 2013
go back to Main Page, Computational Resources, Scripts, Scripts for VASP
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