getMixedBasis

#!/bin/bash

#This script is for automating adding a mixed basis into a QChem Script
#Do not forget to remove the basis set and replace with "GEN"
#This script was created on 9-18-2019 by Kevin Skinner

X="example.xyz"                                 #This is for defining the .xyz file, needs to be updated to relevant file
Y="6-311++G**"                                  #This defines the first basis set
Z="6-311G**"                                    #This defines the second basis set

for a in $X
do
        awk '{ print $1 }' $a > allatoms        #This prints the first column in a new file to get atoms types
done

for b in "H" "C" "N" "O"                        #This is for defining all atoms in a molecule, needs to be updated to relevant atoms
do
        c=$b                                    #This looks for defined atoms in the file 
        echo "$c"                               #This is a check to make sure all atoms are defined
        grep "$c" allatoms > $c.atoms

        awk 'END {print NR}' $c.atoms > $c.num  #Count the number of lines and print in a new file for each atom type

        d=`cat $b.num`                          #Call number for each atom type
        for ((e=1; e<$d+1; e++))                #Define range for adding number
        do
                echo " $b $e" >> new.txt        #Create file containing atoms and numbers into a new file
        done

        cp new.txt NEW.txt                      #This is so that if script is used more than once, then only one version is printed
        rm -f $c.atoms $c.num new.txt

        sed "/$b/a\ $Y\n ****" NEW.txt >> set1  #This adds the basis set in the correct formatting to each atom
done

        cp set1 Set1
        rm -f set1

for f in "I"
do
        g=$f
        echo "$g"
        grep "$g" allatoms > $g.atoms

        awk 'END {print NR}' $g.atoms > $g.num

        h=`cat $f.num`
        for ((i=1; i<$h+1; i++))
        do
                echo " $f $i" >> new.txt
        done

        cp new.txt NEW.txt
        rm -f $g.atoms $g.num new.txt

        sed "/$f/a\ $Z\n ****" NEW.txt >> set2
done

        cp set2 Set2
        rm -f allatoms set2

        echo '$basis' > basis                   #This is for defining the beginning of the mixed basis definintion
        echo '$end' > end                       #This is for defining the end of the mixed basis definintion

        cat basis Set1 Set2 end > MixedBasisSet #This prints the mixed basis into a new file, just copy into relevant file

        rm -f basis end Set1 Set2 NEW.txt