writeGauInp

#!/bin/bash
#####################################################################
#   Program :                                                       #
#           Extract the coordinate and then write the input file    #
#           for Gaussian program                                    #
#   Input   :                                                       #
#           $1 = header.txt ; record the route section              #
#           *.log                                                   #
#   Output  :                                                       #
#           *.com                                                   #
#####################################################################

#2015/11/30, Grace, 1st. ver.
#2016/11/11, Grace, 2nd. ver. change the extension 

# Step 1. Check the input argument
test -f $1 || echo $1 is not exist
test -f $1 || exit
# Step 2. Creat the list 
nfile=$(ls | grep -c .out )
ls | grep .out > list.txt
# Step 3. Extract the partial optimized coordinate and write the input
testfile=$(ls | grep .log| head -n 1)
NAtoms=$(grep NAtoms $testfile| head -n 1| awk '{print $2}')
for ((i=1; i<=$nfile; i=i+1))
do 
name=$(head -n $i list.txt | tail -n 1)
inp=$(echo $name | sed 's/.log/.com/g')
grep -A $(($NAtoms+4)) orientation $name | tail -n $NAtoms \
| awk '{print $2,$4,$5,$6}' > coord.txt
cat $1 > $inp
cat coord.txt >> $inp
echo ' ' >> $inp
done

rm -f list.txt coord.txt