This piece of code may do something similar what you need.

use strict;
use warnings;
use diagnostics;

sub distance {
    my ($aa, $bb) = @_;
    return sqrt(($aa->[0] - $bb->[0])**2 +
                ($aa->[1] - $bb->[1])**2 +
                ($aa->[2] - $bb->[2])**2);
}

my $source = "./CONTCAR";

open(IN, '<', $source) or die "Couldn't open $source: $!\n";

my @data = map [ split ], grep /\S/, <IN>;

foreach my $d1 (@data) {
    foreach my $d2 (@data) {
        printf "($d1->[0],$d1->[1],$d1->[2]) <-> ($d2->[0],$d2->[1],$d
+2->[2]) = %f\n", distance($d1, $d2);
    }
}

close IN;

print "Done.\n";
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