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== Code == <nowiki> #!/bin/bash # Script for extracting the displacement vector of the (lowest) imaginary frequency # from an OUTCAR file in order to setup IDM (Improved Dimer Method) calculation. # David Karhanek, 2011-03-10 @ ICIQ Tarragona # Get basic data from OUTCAR printf " Checking for OUTCAR file... " if [[ -f OUTCAR ]] ; then printf "present, OK.\n" ; else printf "NOT PRESENT! Bye-bye.\n" ; exit ; fi IBRION=`grep IBRION OUTCAR | awk '{print $3}'` if [[ $IBRION -gt "8" || $IBRION -lt "5" ]] ; then printf " However, it is not a frequency job. Bye-Bye.\n" ; exit ; fi VASPVER=`head -1 OUTCAR | cut -c 7` # VASP version check NIONS=`grep NIONS OUTCAR | awk '{print $12}'` # Number of atoms grep -A $(($NIONS+1)) 'cm-1' OUTCAR > temp.tmp # Snip eigenvectors parts of OUTCAR only NVIBS=`grep 'cm-1' temp.tmp | wc -l` # Total nr. of printed frequencies NIMAG=`grep 'f/i' temp.tmp | wc -l` # ... of which so many are imaginary if [[ $VASPVER -lt "5" ]] || [[ $VASPVER -ge "5" && $NWRITE -lt "3" ]] ; then NVIBS=$(($NVIBS/2)) ; NIMAG=$(($NIMAG/2)) ; fi NWRITE=`grep NWRITE OUTCAR | awk '{print $3}'` # Verbosity check - v 5.* needs NWRITE=3 printf " VASP version %1g.*. Total of %3g atoms, %3g vibration modes, %3g imaginary mode(s).\n" $VASPVER $NIONS $NVIBS $NIMAG if [[ $VASPVER -gt "4" && $NWRITE -lt "3" ]] ; then printf " Restart your calculation with NWRITE=3 tag in INCAR! Bye-Bye.\n" ; rm temp.tmp ; exit ; fi # Parse the lowest imaginary mode displacement vector if [[ ! -d ../TS ]] ; then mkdir ../TS ; fi tail -$NIONS temp.tmp | awk '{printf " %12.6f%12.6f%12.6f\n",$4,$5,$6}' > ../TS/DIMERDIRECTION # The file DIMERDIRECTION may be needed for some obsolete implementations of the IDM. cp POSCAR ../TS/ ; echo >> ../TS/POSCAR ; cat ../TS/DIMERDIRECTION >> ../TS/POSCAR rm temp.tmp printf " The POSCAR for IDM was saved into 'TS' up-dir.\n" </nowiki>
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