"how does one use them as a crystal?"
I think that part of the conundrum is explained in this paragraph:
"However, there’s an escape clause at the quantum level: the ions can be given a push with a weak magnetic field, to get them rotating, and since they lose no energy to the outside world, that rotation should continue forever – even, according to research leader Xiang Zhang, after the “heat death” of the universe. And since there is no energy output from the crystal, it doesn’t break the rules to offer a perpetual motion machine."
However, what is not clear to me is how one is meant to "read" this clock. The action in so doing would surely impart energy to the system, a sort of "observer effect"? If by observing one imparts energy to the system is it not then above the zero state referred in the article? It is of course highly likely that I am missing something here because this is not my field. Is there a physicist in the house?