#!/bin/bash
d0=0.0002                                       #definition of a step multiplicator

nmax=11                                         # number of steps
rm curve.a.c2h2                                 # delete file curve.a.c2h2 if it exists
for n in $(eval echo "{1..$nmax}")              # loop, where n changes from 1 to 11 (nmax)
do
delta=`echo \( $n \- 6 \)  \* $d0  | bc -l `    # This command performs delta=n-6*d0
                                                # Where "bc" is a linux calculator.
                                                # symbol "\" says to bash that next symbol is a text symbol not a command
awk -v delta=$delta '{if (($1 == "H" || $1 == "C" ))
{
if (ind<=1)
 {printf "%s %10.8f %10.8f %10.8f \n", $1,$2-delta,$3,$4; ind=ind+1}
else
 {printf "%s %10.8f %10.8f %10.8f \n", $1,$2+delta,$3,$4; ind=ind+1}
}
else 
{print $0}
}' < c2h2.amber.inp > c2h2.$n.inp               # awk reads file c2h2.amber.inp line by line and prints output in the file cp2k.1.inp (if n equals 1)
                                                # If the firs word of a line is H or C, then x coordinate is decreased (for the first and the second atom) or increased
                                                # (for the third and the fourth atom) by the value of "delta"
cp2k.popt -i c2h2.$n.inp > c2h2.$n.out          # running cp2k
dist=`grep -A 4 '&COORD' c2h2.$n.inp | grep ^C | awk '{x[NR]=$2;y[NR]=$3;z[NR]=$4} END {dx=x[1]-x[2]; dy=y[1]-y[2]; dz=z[1]-z[2];print sqrt(dx*dx+dy*dy+dz*dz)}'  `
        #       ^ 
        # reading the cp2k ouput file
        # and printing line which 
        # contains the world 
        # "&COORD" + 4 lines below
                                #      ^
                                # printing only
                                # the lines
                                # which begins
                                # from C
                                        #          ^
                                        # NR is the number of current line (in our case it can be only 1 or 2, because there are only two carbon atoms in C2H2)
                                        # When awk finished reading the input file it performs directives, which are written in END { ... }
                                        # in our case it's simply calculation the distance between two carbon atoms
# ^ finally the variable dist is equal to the distance between two carbon atoms
grep 'ENERGY|' c2h2.$n.out | grep -v Run | awk -v dist=$dist '{print dist,$9}'  >> curve.a.c2h2
# ^
# print lines from the file c2h2.1.inp (if n equals 1) , which contains the word "ENERGY|"
                        #   ^ 
                        # don't print lines, which contains the word "Run"
                                        #   ^
                                        # print distance between two atoms and 9th word from the line which correspond to the value of energy in the file curve.a.c2h2
done                                    # finishing the loop
mkdir Logs                              # creating directory Logs
mv c2h2.?.inp c2h2.??.inp c2h2.*.out Logs
rm RUN* *restart*                       # removing all the files, which has name starting from "RUN.." or contains word "restart"