Editing Intensities.sh (section)

== CODE ==

 #!/bin/bash
 # A utility for calculating the vibrational intensities from VASP output (OUTCAR)
 # (C) David Karhanek, 2009-08-05
 
 # extract Born effective charges tensors
 printf "..reading OUTCAR"
 BORN_NROWS=`grep NIONS OUTCAR | awk '{print $12*4+1}'`
 grep "in e, cummulative" -A $BORN_NROWS OUTCAR > born.txt
 
 # extract Eigenvectors and eigenvalues
 EIG_NVIBS=`grep cm-1 OUTCAR | wc -l`
 EIG_NIONS=`grep NIONS OUTCAR | awk '{print $12}'`
 EIG_NROWS=`echo "($EIG_NIONS+3)*$EIG_NVIBS+3" | bc`
 grep "Eigenvectors and eigenvalues" -A $EIG_NROWS OUTCAR | sed 's/f\/i/fi /g' > eigenvectors.txt
 printf " ..done\n"
 
 # set up a new directory, split files - prepare for parsing
 printf "..splitting files"
 mkdir intensities ; mv born.txt eigenvectors.txt intensities/
 cd intensities/
 let NBORN_NROWS=BORN_NROWS-1
 let NEIG_NROWS=EIG_NROWS-3
 let NBORN_STEP=4
 let NEIG_STEP=EIG_NIONS+3
 tail -n $NBORN_NROWS born.txt > temp.born.txt
 tail -n $NEIG_NROWS eigenvectors.txt > temp.eige.txt
 mkdir inputs ; mv born.txt eigenvectors.txt inputs/
 split -a 3 -d -l $NEIG_STEP temp.eige.txt temp.ei.
 split -a 3 -d -l $NBORN_STEP temp.born.txt temp.bo.
 mkdir temps01 ; mv temp.born.txt temp.eige.txt temps01/
 for nu in `seq 1 $EIG_NVIBS` ; do
  let nud=nu-1 ; ei=`printf "%03u" $nu` ; eid=`printf "%03u" $nud` ; mv temp.ei.$eid eigens.vib.$ei 
 done
 for s in `seq 1 $EIG_NIONS` ; do
  let sd=s-1 ; bo=`printf "%03u" $s` ; bod=`printf "%03u" $sd` ; mv temp.bo.$bod borncs.$bo 
 done
 printf " ..done\n"
 
 # parse deviation vectors (eig)
 printf "..parsing eigenvectors"
 let sad=$EIG_NIONS+1
 for nu in `seq 1 $EIG_NVIBS` ; do
  nuu=`printf "%03u" $nu`
  tail -n $sad eigens.vib.$nuu | head -n $EIG_NIONS | awk '{print $4,$5,$6}' > e.vib.$nuu.allions
  split -a 3 -d -l 1 e.vib.$nuu.allions temp.e.vib.$nuu.ion.
  for s in `seq 1 $EIG_NIONS` ; do
   let sd=s-1; bo=`printf "%03u" $s`; bod=`printf "%03u" $sd`; mv temp.e.vib.$nuu.ion.$bod e.vib.$nuu.ion.$bo
  done
 done
 printf " ..done\n"
 
 # parse born effective charge matrices (born)
 printf "..parsing eff.charges"
 for s in `seq 1 $EIG_NIONS` ; do
  ss=`printf "%03u" $s`
  awk '{print $2,$3,$4}' borncs.$ss | tail -3 > bornch.$ss
 done
 mkdir temps02 ; mv eigens.* borncs.* temps02/
 printf " ..done\n"
 
 # parse matrices, multiply them and collect squares (giving intensities)
 printf "..multiplying matrices, summing "
 for nu in `seq 1 $EIG_NVIBS` ; do
  nuu=`printf "%03u" $nu`
  int=0.0
  for alpha in 1 2 3 ;  do            # summing over alpha coordinates
   sumpol=0.0
   for s in `seq 1 $EIG_NIONS` ; do   # summing over atoms
    ss=`printf "%03u" $s`
    awk -v a="$alpha" '(NR==a){print}' bornch.$ss > z.ion.$ss.alpha.$alpha
    # summing over beta coordinates and multiplying Z(s,alpha)*e(s) done by the following awk script
    paste z.ion.$ss.alpha.$alpha  e.vib.$nuu.ion.$ss | \
    awk '{pol=$1*$4+$2*$5+$3*$6; print $0,"  ",pol}' > matr-vib-${nuu}-alpha-${alpha}-ion-${ss}
   done
   sumpol=`cat matr-vib-${nuu}-alpha-${alpha}-ion-* | awk '{sum+=$7} END {print sum}'`
   int=`echo "$int+($sumpol^2)" | bc -l`
  done
  freq=`awk '(NR==1){print $8}' temps02/eigens.vib.$nuu`
  printf "%3u %11.6f %16.14f\n" $nuu $freq $int >> exact.res.txt
  printf "."
 done
 printf " ..done\n"
 
 # format results, normalize intensities
 printf "..normalizing intensities"
 max=`awk '(NR==1){max=$3} $3>=max {max=$3} END {print max}' exact.res.txt`
 awk -v max="$max" '{printf "%3u %11.6f %16.14f\n",$1,$2,$3/max}' exact.res.txt > results.txt
 printf " ..done\n"
 
 # clean up, display results
 printf "..finalizing:\n"
 mkdir temps03; mv bornch.* e.vib.*.allions temps03/
 mkdir temps04; mv z.ion* e.vib.*.ion.* temps04/
 mkdir temps05; mv matr-* temps05/
 mkdir results; mv *res*txt results/
 let NMATRIX=$EIG_NVIBS**2
 printf "%5u atoms found\n%5u vibrations found\n%5u matrices evaluated" \
        $EIG_NIONS $EIG_NVIBS $NMATRIX > results/statistics.txt
 # fast switch to clean up all temporary files
 rm -r temps*
 
 # list results
 cat results/results.txt

--[[User:Dkarhanek|Dkarhanek]] 16:44, 30 September 2010 (CEST)