TSImaginaries

#!/bin/bash

#this script was written by Matt Hannigan on 4/19/2018
#run this script in a directory containing .out files from qchem. Works for qchemmay142015.
#purpose: for a linked job of the form "Job 1 = frequency calc, Job 2= OPT or TSOpt, Job 3=frequency calc"
#this script will tell you how many imagninary frequencies the frequency calc in Job 3 calculated
#and print it into an output named imginaryfrequencies.out file
#Tells you if the Opt or TSOpt was good by saying the file has 0 or 1 imaginary freq, respectively

#Notes: this script can be adapted to other styles of linked jobs by changing the sed command 

list=`ls *.out`
for item in $list
do
	sed -n '/Job 3 of 3/,/END OF MOLDEN-FORMATTED INPUT FILE/p' <$item >$item's'
#prints the lines between the string "Job 3 of 3" and "END OF MOLDEN..." in the $item file to a new file with the same name and with 
#an s appended to the end. If you want to search between different strings, change the stuff between the "/"s (do not remove the "/"s)
done
lists=`ls *.outs`
touch imaginaryfrequencies.out
for item in $lists
do
  ls $item
  echo $item `grep Imaginary $item | tail -n 1` >> imaginaryfrequencies.out 
#grabs the line that contained the string "Imaginary" and then puts it into an the imgaginaryfrequencies file, along with the file name
done
rm -rf *.outs