RDF

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Description

This program computes the Radial Distribution Function (RDF) for a given system, being it a single geometry, an optimization, or a dynamics. For more infos about what the RDF is, please check: [1].

Setting up the program

First, we download the following file:

Tar/zipped directory: File:RDF.tgz

and we untar and unzip it with the following command:

user@computer: tar -xvzf RDF.tgz

A directory called ( quite unoriginally ¬¬ ) "RDF" will appear in your current directory. You enter the directory and do the following commands:

user@computer: a=`ls *.f`
user@computer: f95 $a -o x.RDF [NOTE: if you don't have f95, try using ifort or g95, otherwise download and install a proper compiler for the program.]

#!/bin/bash
#BSUB -J name_of_job_1
#BSUB -q class_c 
#BSUB -n 64 
#BSUB -W 23:59
#BSUB -o o_name_of_job_1.%J
#BSUB -e e_name_of_job_1.%J
#BSUB -u youremail@iciq.es
#BSUB -R"span[ptile=16]"

### Load environment variables ###########
module load VASP/5.3.3

### Run job ##############################
resurrection_timecontrol 23 30 r_name_of_job_1 &
mpirun vasp.complex ; touch stopflag ; resurrection name_of_job_ 1 16c 64 23 30 ; echo the dynamics has been resurrected >> r_name_of_job_1 ; exit

Explanation:

• In this example, you are running with 64 processors on class_c queue.
• You have three quickly accesible log files: o_* is the standard output, e_* contains the errors, and r_* contains the information related to the resurrection process.
• Your time limit will be 23:59 hours, the maximum allowed by class_c is 24:00
• Before starting VASP, you will lauch resurrection_timecontrol, which will stop the calculation after 23:30 hours, via STOPCAR (LSTOP = .TRUE.).
• Then the script will execute VASP on your local folder.
• If the VASP calculation ends abruptly before the time limit, it will deliver a signal (stopflag) that will kill "resurrection_timecontrol", avoiding a phantom job to stay on the line for hours.
• Now the calculation will be resurrected with the name name_of_job_2, on folder 2 (see script 1 for more details) on the same queue with the same number of processors and the same time control. This script will call internally to rungen_resurrection, but you can merge them if you prefer.
• This set of scripts is totally self-contained.
• Tested and debugged.

Now that you know how this work, begin to calculate by typing:

you@login1:~/my_dynamics/1> bsub < run.sh 

Do not forget to baby-sit your calculations every day, and verify that all your electronic cycles have been converged.

Script 2: rungen_resurrection

• Input