First, the easiest but most important part: change your IDs to classes. IDs must be unique per page so jQuery's ID selector and JavaScript's document.getElementById() function are only going to give you the first matching element:
Each id value must be used only once within a document. If more than one element has been assigned the same ID, queries that use that ID will only select the first matched element in the DOM.
Change
<div id="container">
...
<div id="element">
to
<div class="container">
...
<div class="element">
and change
$('#element')
to
$('.element')
Next, the more difficult part: you are currently issuing one centerDiv() call to your elements with coordinates from center of 0, 0. That's going to take all your .elements and position them at the exact same spot.
If that's not what you intend, you're going to have to loop through them using .each() and decide the xPosFromCenter and yPosFromCenter in each iteration. It's not clear to me yet how your function works so you may have to explore on your own and see what you can come up with.
Scratch that, see Jamiec's working example for the solution.