getNM

#!/bin/bash
#########################################################################
#	Program :															#
#		Extract the normal mode eigenvector	from Gaussian/QChem job		#
#	Input :																#
#		$1 = test.out or test.log							            #
#	Output :															#
#		NM.txt															#
#                                                                       #
# History:                                                              #
# 2016/04/12, Grace, 1st. ver.                                          #
# 2017/10/23, Grace, 2nd. ver.                                          #
#########################################################################

#Step0. check
[ "$1" == "" ] && echo 'No file, you must key-in the name of qchem output file' && exit
judge=$(grep 'VIBRATIONAL ANALYSIS' $1)
[ "$judge" == "" ] && echo 'Not calculate the frequency successfully' && exit

#Step2. select the number of normal mode; stdin
read -p 'Select the nimber of normal mode: ' mode

#Step3. extract the normal mode vector
rm -f rawdata.txt tmp.txt NM.txt
num=$(grep -a1 'NAtoms' $1 | tail -n 1 | awk '{print $1}' ) #count the number of atom
dof=$(grep 'Number of degrees of freedom' $1| tail -n 1 | awk '{print $9}') 
grep -A $((7+$num)) 'Mode:' $1 | grep -v '\-\-' | grep -v 'Mode' \
| grep -v 'Frequency'| grep -v 'Force Cnst'| grep -v 'Red. Mass' \
| grep -v 'IR Active' | grep -v 'IR Intens' | grep -v 'Raman Active' \
| grep -v 'X      Y      Z' > rawdata.txt 
row=$(($mode/3+1))
column=$(($mode%3))
head -n $(($num*$row)) rawdata.txt | tail -n $num > tmp.txt
case $column in
	"1")
	awk '{print $2,$3,$4}' tmp.txt > NM.txt
	;;
	"2")
	awk '{print $5,$6,$7}' tmp.txt > NM.txt
	;;
	"0")
	awk '{print $8,$9,$10}' tmp.txt > NM.txt
	;;
esac

#Step3. print the result
echo 'The extract normal mode vector is '
cat NM.txt
rm -f rawdata.txt tmp.txt