printf OUT "%s to %s Distance=%.5f\n",
$data[$i][0], $data[$j][0],
$data[$i][2], $data[$j][2],
distance(\@coords_i, \@coords_j);
Your printf statement has three placeholders, but you supply five elements of data to be printed.
return sqrt(($x - $x)**2 + ($y - $y)**2 + ($z - $z)**2);
The expression $x - $x will always be zero, as will the others.
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