generate_optimization_traj_adf

#!/bin/bash

echo "Enter the number of atoms: "
read num_atoms
num_out_file=`ls *.out | wc -l`
if [ "$num_out_file" -gt 1 ]
then
        echo "More than one .out file found in the directory, please provide the .out file explicitly below: "
        ls *.out
        read file
else
        file=`ls *.out`
fi

`grep -n "Coordinates (Cartesian)" $file | cut -d':' -f1 > line_nums.tmp`
num_cyc=`cat line_nums.tmp | wc -l`
for i in `seq 2 $num_cyc`
do
        start_1=`head -$i line_nums.tmp | tail -1`
        start_l=$((start_1+6))
        finish=$((start_l+num_atoms-1))
        echo $start_l,$finish
        energy_line=$((start_1-11))
        energy=`sed "${energy_line}q;d" $file`
        echo $energy
        echo $num_atoms >> traj.xyz
        echo $energy >> traj.xyz
        #head -$finish $file | tail -$num_atoms >> traj.xyz
        #echo $ghost >> traj.xyz
        `head -$finish $file | tail -$num_atoms | tr -s ' ' | cut -d' ' -f3,7-9 >> traj.xyz`     #to generate only standard xyz file in Angstrom units
        #sed -n ${start_l},${finish}p $2 >> traj.xyz
        wait
done