for my $one (0..$#@dist-1) {
    my $two = $one;
    while (++$two < @dist && $dist[$two]-$dist[$one] <= $cutoff) {
        print "found pair: ($x[$one],$y[$one],$z[$one]) and
($x[$two],$y[$two],$z[$two])\n"
            if sqrt(($x[$one]-$x[$two])**2+($y[$one]-$y[$two])**2+($z[$one]-$z[$two])**2) <= $cutoff;
    }
}