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@indices = sort {$dist[$a]<=>$dist[$b]} 0..$#dist;
@dist = @dist[@indices];
@x = @x[@indices];
@y = @y[@indices];
@z = @z[@indices];
@name = @name[@incides];

for my $one (0..$#@dist-1) {
    my $two = $one;
    while (++$two < @dist && $dist[$two]-$dist[$one] <= $cutoff) {
...
            if sqrt(($x[$one]-$x[$two])**2+($y[$one]-$y[$two])**2+($z[
+$one]-$z[$two])**2) <= $cutoff;
    }
}