$file = shift@ARGV;
$file2=shift@ARGV;

open (FILE, "<$file");

while (<FILE>) {

( $x, $y, $z) = split (/\s+/, $_);

}

open (FILE2, "<$file2");
while (<FILE2>) {
( $x1, $y1, $z1) = split (/\s+/, $_);
}

open (OUT, ">output");
print OUT $x $y $z $x1 $y1 $z1;

###then do maths
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Looking at what you've done so far, you're basically there. Perhaps you're confused about how to output a properly formatted line? The last print statement you have will create an output file with no separation between the numbers (and no newline at the end). There are a number of ways (of course) to get it properly formatted. Some examples:

print OUT "$a $b $c\n";

printf OUT "%d %d %d\n", $a, $b, $c;

print OUT join(' ',$a, $b, $c), "\n";
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The latter two will work better if you are going to do the addition inline, e.g.:

printf OUT "%d %d %d\n", $x+$x1, $y+$y1, $z+$z1;
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Brad