Adding a column in table A when using condition in table B

remove your ORDER BY :), so the sql like this :)

SELECT SUM(calories) FROM foods a, user_foods b WHERE a.id = b.foodid AND b.username LIKE '$user' AND b.day='$day' AND b.month LIKE '$month' AND b.year LIKE '$year'

If you are looking for exact match then use equal to operator. Try this query:

SELECT SUM(calories) FROM foods a INNER JOIN
user_foods b ON a.id = b.foodid AND b.username LIKE '$user' 
AND b.day='$day' AND b.month LIKE '$month' AND b.year LIKE '$year' 

Since you create an associative array $calories[0] won't work. Give that sum a name in your query and use that as array index.