You didn't say what should happen if a coord triple is only in one file. And probably needs a lot of safety checks, if these are big files.

#!/usr/bin/env perl

# Store X,Y,Z coordinates from one file, along with a number and press
+ure.
# Find a matching coord in a second file, subtract pressure1 from pres
+sure2.
# Output with the number from the first file.

# Sample data:
# 0, 4.38336420e+00, -2.47429684e-01, 6.79128885e+00, 1.51447906e+05
# 1, 4.38336420e+00, -2.78662264e-01, 6.79128885e+00, 1.58727812e+05
# 2, 4.38336420e+00, -2.78662264e-01, 6.69878864e+00, 1.61132406e+05
# 3, 4.38336420e+00, -2.47429684e-01, 6.69878864e+00, 1.54500719e+05

# Assume there are 2 filenames on the command line, in the correct ord
+er.

use strict;
use warnings;

our $key_format = '%16.8f'; # Fixed decimals for use in keys
our $out_format = '%e'; # scientific notation

sub read_it {
    my $line = shift;
    chomp($line);
    my ($n, $x, $y, $z, $p) = split /,\s+/, $line;
    my $key = sprintf "$key_format,$key_format,$key_format", $x, $y, $
+z;    
    return($n, $x, $y, $z, $key, $p);
}

our %press;

# File 1
while (<>) {
    my ($n, $x, $y, $z, $key, $p) = read_it($_);
    $press{$key}{num} = $n;
    $press{$key}{press} = $p;
} continue {
    # If this is the end of the first file, close it and escape the lo
+op
    if (eof) { # "eof", not "eof()"!
        close ARGV;
        last;
    }
}

# File 2
while (<>) {
    my ($n, $x, $y, $z, $key, $p2) = read_it($_);
    if (exists($press{$key})) {
        my $pdiff = $p2 - $press{$key}{press};
        my $n1 = $press{$key}{n};
        print "%d, $out_format, $out_format, $out_format, $out_format\
+n", $n1, $x, $y, $z, $pdiff;
    }
}

exit;
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