I have a few of those waiting to be hooked up, though I did plug one in to see that it worked. Which it did.
Yes, they will shuffle around the "extra" voltage until things are even...within 0.05V or something.
I don't see why an ultra cap would fry it. I had it hooked up to lithium cells - high output, low internal resistance - and those things can kick pretty hard. Not ultra cap hard, but still hard. Not like, say, lead-acid, where there's a certain level of...resistance (not electrical, more like chemical reaction time) that things like simple chargers take advantage of to prevent too much current being drawn.
They're inductive...which leads me to assume they're like little transformers, which allow the output to be isolated from the input, otherwise things start frying when you're trying to pass power from one cell that's already connected to another cell. I'm making a lot of assumptions here, but using induction to isolate the output so it can be sent wherever safely only makes sense, to me.
Presumably each induction circuit on it acts like a boost converter, like you can buy ones for cheap on ebay and such ranging from tiny ones - for use as usb 5V output from a lithium cell - to big 900W beasts (that I only have several of and use often). So it's sucking power from one cell, isolates and boosts it, and sends it to another. (No boost and it probably wouldn't be able to put out any appreciable current with only 0.05V difference)
...and since it is limited to 1 amp or so, I would assume there is either current limiting built in, or else the "transformer" simply can not exceed a certain amount (like a cheap transformer based charger can only output so much before the voltage falls right off.)
I'm saying that I don't see why it wouldn't be safe to use with ultra caps. Great idea, by the way.
If you're really concerned about not frying a $10 item, you could put low-resistance resistors on each lead. You'll lose efficiency, but it will save it from ever drawing too much instantaneously from frying itself. Would only be inefficient while balancing and not piss away power otherwise.
If I'm doing my math right, the battery I tested mine on would have had a total resistance along any one of the parallel strings of ~0.3 milliohms...which is stupid low...if these things can work with that, I doubt capacitors with their stupid low resistance would bother them. Unless there is some weird interaction between using a capacitor with an inductor that I'm not considering. The source isn't AC so I don't think there's any there to be concerned about.
This is starting to hurt my head. Just hook it up. It'll be fine. No, honest, it will! Maybe.
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