script to monitor VASP run

#!/bin/bash
##Read the OUTCAR and print distances between atoms atA and atB
atA=1
atB=5


########################## routines ###########################
distance()
{
 x1=$1 ; y1=$2 ; z1=$3
 x2=$4 ; y2=$5 ; z2=$6

 dist=`echo "scale=6; sqrt( ($x1-$x2)^2+($y1-$y2)^2+($z1-$z2)^2 )" | bc`
 echo $dist
}
###############
findelem()
{
 filename=$3
 element=`awk -v i=$1 -v j=$2 'FNR == i {print $j}' $filename`
 echo $element
}
###############################################################

if [[ -e tempZc.dat ]]; then
 rm tempZc.dat
fi
if [[ -e tempZh.dat ]]; then
 rm tempZh.dat
fi
if [[ -e tempchdist.dat ]]; then
 rm tempchdist.dat
fi

iternum=`cat OUTCAR | grep -c "TOTAL-FORCE"`
vacref=286.87753

dist=0

cat OUTCAR | grep "without entropy=" | awk -v p=$vacref '{print $7*1+p}' > tempener.dat


for index in `seq 1 $iternum`;
do
  cat OUTCAR | grep -m$index -A15 "TOTAL-FORCE" | tail -14 > tempcoord.dat
  ptzco=`tail -9 tempcoord.dat | awk '{i=3;{sum[i]+=$i}} END {printf sum[i]/NR "\t"}'`

  xh=`findelem $atA 1 tempcoord.dat`
  yh=`findelem $atA 2 tempcoord.dat`
  zh=`findelem $atA 3 tempcoord.dat`

  xc=`findelem $atB 1 tempcoord.dat`
  yc=`findelem $atB 2 tempcoord.dat`
  zc=`findelem $atB 3 tempcoord.dat`

  chdist=`distance $xh $yh $zh $xc $yc $zc`
  echo $chdist >> tempchdist.dat
  echo "scale=6; $zc-$ptzco " | bc  >> tempZc.dat
  echo "scale=6; $zh-$ptzco " | bc  >> tempZh.dat
done

paste tempener.dat tempZc.dat tempZh.dat tempchdist.dat> values.dat
nl values.dat > temp.dat
sed -e 's/\t/      /g' < temp.dat > values.dat


rm tempchdist.dat
rm tempcoord.dat
rm tempener.dat
rm tempZc.dat
rm tempZh.dat
rm temp.dat