Please bear with me, but my Unix skills are better then my rudimentary knowledge of condensed matter physics.

1) What is - in terms of dsitinguishing text elements - a "bottom layer"? Can it be described in terms like all lines with "0.0000000" in the fourth field or something such?

2) In the same way of description: what is a "pivot atom"? I guess your table lists platinum atoms and their coordinates, but what makes an atom a "pivot atom"?

3) I guess "nearest neighbor" is probably the one where the absolute value of the sum of the 3 coordinate differences is minimal, yes? Something like

min( || a1 - a2 || + || b1 - b2 || + || c1 - c2 || )

How can there be more than one "nearest neighbors" and how should they be calculated?

I cannot even guess what you are trying to accomplish here. Let me tell you what this thing does:

You filter all the lines containing "Pt" from a file, the use awk to only output the fourth field of these lines. You end up with a stream of lines all consisting of one coordinate. This stream is piped into a another grep, which filters out all lines starting with "0.", followed by 14 other digits. You do nothing further with this result. Then you call "sed" and try to remove a double quote, followed by the lines end, followed (sic!) by the string '{doom[*]}"'. The "g" at the end has no significance because i promise there is only one line end in every line. Therefore the whole file comes out unchanged.

Finally you use "( ... )" to construct an array "doom" in which every word (separated by blanks) is one element. The first elements will be the filtered fourth columns from your first pipeline, then your input file is cut in separate words and these take the next places. Depending on the shell you use it might even run out of space, because i.e. ksh88 has a limitation of 1024 elements in an array.


No. It won't delete anything, just declare an array variable.

I am aware you had a few more questions, but please specify your requirements first. It makes sense to talk about implementation specifics only after this is covered.

I hope this helps.

bakunin