Is there a way of significantly improving the speed in Perl that involves this kind of math?
Maybe, maybe not. You don't define how the "cutoff" distance is determined, so it's hard to say. Is it related to the lines where the atoms appear? Are X, Y, Z coordinates?
If I have a fortran code (subroutine) that reads three arrays and then give me output, can I use the object file generated by that program to plugin to Perl?
It's not clear what you mean here by "object file". Often, with "object file" we mean a file that can be linked into an executable, that is, the output of a compiler. But your description of how it's made suggests otherwise. If it contains data, then, yes, you can read it. You must know the structure of the data though to make sense out it - you may need
unpack if the data is in some binary format.
Abigail
