qc2xyz.sh

#!/bin/bash
# created by Jan Mewes Sep 2017 www.janmewes.de

file=$1
output=$(echo $file | sed s/out/xyz/)
natoms=0
quiet=""
otherout=$2

if [ ! $quiet ]; then
  echo "### Q-CHEM OPTIMIZED XYZ MAKER V1.0 ###"
  echo
  echo "Usage: 1st argument output file (has to be an optimization)"
  echo "       2nd optional argument: name of desired output file. Default is outputfile.xyz"
  echo
  echo "Now doing $1..."
fi

if [ $1 ]; then

  if [ $otherout ] && [ -n $otherout ]; then
    output=$otherout
    echo "... using non default outputfile $output"
  else
    echo "Using default outputfile $output"
  fi

  for i in $file; do
    if [ $(cat $1 | grep -c "OPTIMIZATION CONVERGED") -eq 1 ]; then
      natoms=$(grep "NAtoms," $1 -A1 | tail -n1 | awk '{print $1}')
      nlines=$((natoms + 4))
      [ ! $quiet ] && echo "Found $natoms atoms..."

      if [ -e $output ]; then
        cp $output "$output"_bkup
        echo "Desired output file already exists, backing up..."
      fi

      echo "$natoms" >$output
      grep "Final energy is" $file >>$output
      grep "OPTIMIZATION CONVERGED" -A $nlines $file | tail -n $natoms | cut -c 10- >>$output

      [ ! $quiet ] && echo "### All done, sweetas!"

    else
      echo "Optimization not converged, exiting"
    fi
  done

else

  echo "No additional input parameters provided, doing all .out files in folder... "

  for i in *out; do
    echo "... now doing $i"
    output=$(echo $i | sed s/out/xyz/)
    if [ $(cat $1 | grep -c "OPTIMIZATION CONVERGED") -eq 1 ]; then
      natoms=$(grep "NAtoms," $i -A1 | tail -n1 | awk '{print $1}')
      nlines=$((natoms + 4))
      [ ! $quiet ] && echo "Found $natoms atoms..."

      if [ -e $output ]; then
        cp $output "$output"_bkup
        echo "Desired output file already exists, backing up..."
      fi

      echo "$natoms" >$output
      grep "Final energy is" $i >>$output
      grep "OPTIMIZATION CONVERGED" -A $nlines $i | tail -n $natoms | cut -c 10- >>$output

    else
      echo "Optimization not converged, exiting"
    fi
  done

  [ ! $quiet ] && echo "### All done, sweetas!"

fi