Stir plate magnet orientation

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I've not been successful using stirbars that big on my DIY plates, but I used your bottom configuration. I'd be inclined to try the first configuration - I might revisit that on my two plates.
 
I don't know how that style of magnet is magnetized, but you want a N up on one side, and a S up on the other. Stir bars have an N end and a S end so the opposing polarities will couple together. Whether that takes 1 magnet or 2 depends on how it was magnetized.

This is pretty easy to test with 2 magnets. Put 2 ends together, if they attract, then you have a N-S pair. If they repel you either have N-N or S-S. Check a few more orientations and you should know the how the poles are aligned.

I bought my magnets from this company, and they have a really good diagram showing some possibilities: https://www.kjmagnetics.com/magdir.asp

This link shows how hard drive magnets are configured: http://physics.stackexchange.com/qu...um-hard-drive-magnet-it-appears-to-vibrate-in
 
Ditto on the one magnet in a cigar box. It does work great, but remember there are different size magnets that come with different drives. I had some fairly old drives that had relatively small magnets. I had a newer larger capacity drive that had a much larger magnet. You might put everything together in whatever box you are going to use, without the glue, and see how well the bar stays put with one magnet.
 
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