MoveNiPP

#!/bin/bash
#This script was written by Matt Hannigan 12/19/19
#this script takes all xyz structures in a directory
#finds the Ni and P atoms in the structures 
#and moves the Ni atom to the 3rd line (right after the number of atoms and comment lines)
#and moves the P atoms to the 4th and 5th lines
#This script assumes that there is only 1 Ni and 2 Ps in the structure. This will only capture the 1st and last P atoms
#if there are more P atoms

#This script can be modified to other atoms by modifying the grep commands
#this script can be modified to include more atoms by modifying the number of grep commands
#the order can be modified just by changing the order of the echo commands in the script

array=`ls *.xyz`
for thing in $array
do
	num=`head -n 1 $thing`
	space=`head -n 2 $thing | tail -n 1`
	Ni=`grep "Ni " $thing`
	P1=`grep "P " $thing | head -n 1`
	P2=`grep "P " $thing | tail -n 1`
	sed -i '/Ni/d' $thing
	sed -i '/P /d' $thing
	tail -n +3 $thing > rest.xyz
	echo $num > $thing
	echo $space >> $thing
	echo $Ni >> $thing
	echo $P1 >> $thing
	echo $P2 >> $thing
	cat rest.xyz >> $thing
	rm -rf rest.xyz 
	ls $thing
done