Thanks a lot bakunin! I knew I should be more clear.
1. Yes, the bottom 2 layers are the atoms whose z coordinates start with 0.***** & 2.*****. There are two more layer of atoms above these.
2. I just made up the pivot atoms keyword, what it means is I have some adsorbed species on surface of the catalyst layer. Pivot atoms are those directly under the adsorbed species.
3. You're right, nearest neighbor distance is

Code:

sqrt[(a1-a2)^2 + (b1-b2)^2 +(c1-c2)^2]

For Pt it's 2.82 angstrom. My thinking if the above value is in between 2.82, then the code should copy those coordinates. About more than one nearest neighbors, think of it like this, I have 2 layers of atoms and on the top layer is one of my pivot atom. I'm looking for all the atoms that are in between 2.82 angstrom radius, that also includes the atoms of the bottom layer which are within 2.82 angstrom of the pivot atom. Now when I choose the second atom,(which is itself also a neighbor of 1st pivot atom) some of it's nearest neighbors might be already copied cause they were the nearest neighbor of the 1st pivot atom.

doom=($(grep Pt cluster.xyz | awk '{ print $4 }' | grep '[0]\.[0-9]\{14\}')); sed 's/"${doom[*]}"//g' cluster.xyzIn this line of code what I was trying to do was storing those coordinates into the "doom" array and replace them with blank spaces. But now I think of it, it's not what I wanted, I wanted to remove those lines on whole, not those coordinates only.

The thing I am trying to do is I do the aqueous phase calculations on a cluster of atoms, not on periodic systems. Every time I have to do this cluster building manually which is very time consuming. I also have to extend this line of thought for my MD simulation but that's for later. I guess I'm stuck in the very first step i.e deleting the bottom two layers of atoms. Sorry if I made my thinking more complex. Thanks a lot man! Really appreciate it!