Editing Gaussian2molden

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<nowiki>#### copy this text and put it in ~/bin/gaussian2molden.sh, then type "chmod 777 *" , restart your terminal and you can use it</nowiki>

<nowiki>#### This program reads a gaussian output file to create a xyz file, easy to read with molden.</nowiki>

<nowiki>#### Be careful the file "temp" will be used and removed</nowiki>

<nowiki>#### first argument $1 is the gaussian output file you want to convert</nowiki>

<nowiki>#### second argument $2 is the xyz file you want to create</nowiki>

<nowiki>#### type in the console </nowiki>

<nowiki>#### "gaussian2molden.sh file1.out file2.xyz"</nowiki>

<nowiki>if test -z "$1"</nowiki>

<nowiki>	then echo "Error: This program needs two arguments"</nowiki>

<nowiki>	exit 1</nowiki>

<nowiki>fi</nowiki>

<nowiki>if [! -f ${1} ] ;then</nowiki>

<nowiki>	echo "Error : File \"$1\" doesnt exist" </nowiki>

<nowiki>	exit 1</nowiki>

<nowiki>fi	</nowiki>

<nowiki>if test -z $2</nowiki>

<nowiki>    then echo "Error : This program needs two arguments"</nowiki>

<nowiki>    exit 1</nowiki>

<nowiki>fi</nowiki>

<nowiki>if [ $1 = $2 ] ; then</nowiki>

<nowiki>	echo "Error: your new file cannot be same as the argument file."</nowiki>

<nowiki>	echo "your files wont be changed"</nowiki>

<nowiki>	exit 1</nowiki>

<nowiki>fi</nowiki>

<nowiki>if [ -f  $2 ]; then</nowiki>

<nowiki>	echo "Error new file: $2 arleady exists! type ctrl c to quit or enter to continue"</nowiki>

<nowiki>	read rien</nowiki>

<nowiki>fi </nowiki>

<nowiki>natoms=$(fgrep NAtoms $1 | awk '{print $2}' | tail -1 )</nowiki>

<nowiki>total=$(echo "$natoms+4" | bc )</nowiki>

<nowiki>fgrep -A""$total"" 'orientation' $1 | awk '{print $2,$4,$5,$6}' > $2</nowiki>

<nowiki>sed -i "s/orientation:/$natoms/g"  $2</nowiki>

<nowiki>sed -i '/Atomic/d' $2</nowiki>

<nowiki>sed -i '/Number/d' $2</nowiki>

<nowiki>fgrep  Done $1 | cut -d" " -f 8  >temp</nowiki>

<nowiki>i=0</nowiki>

<nowiki>for line in $(cat temp)</nowiki>

<nowiki>        do </nowiki>

<nowiki>        n=$(echo $i*$total+2 | bc )</nowiki>

<nowiki>        sed -i "$n s/.*/E= $line/g" $2</nowiki>

<nowiki>        i=$(echo $i+1 | bc) </nowiki>

<nowiki>        done</nowiki>

<nowiki>  awk 'NF' $2 > temp</nowiki>

<nowiki>  cat temp > $2</nowiki>

<nowiki> </nowiki>

<nowiki># ADD MORE LINES HERE FOR PROCESSING DIFFERENT ATOMS </nowiki>

<nowiki>#Hydrogens</nowiki>

<nowiki>sed -i "1,$ s/^1\ /H\ /g" $2 </nowiki>

<nowiki>#Carbons</nowiki>

<nowiki>sed -i "1,$ s/^6\ /C\ /g" $2</nowiki>

<nowiki></nowiki>

<nowiki>#Nitrogens</nowiki>

<nowiki>sed -i "1,$ s/^7\ /N\ /g" $2</nowiki>

<nowiki></nowiki>

<nowiki>#Oxygens</nowiki>

<nowiki>sed -i "1,$ s/^8\ /O\ /g" $2</nowiki>

<nowiki></nowiki>

<nowiki></nowiki>

<nowiki>echo -en '\E[0;31m'"\033[1mK\033[0m"'\E[0;32m'"\033[1mA\033[0m"'\E[0;34m'"\033[1mR\033[0m"'\E[0;35m'"\033[1mL\033[0m"</nowiki>

<nowiki>echo "                                                                       "</nowiki>

<nowiki>echo "                                                                       "</nowiki>

<nowiki>rm temp</nowiki>