We describe a technique for initializing the flux state of an inductively isolated Josephson junction, fulfilling an essential requirement for using the device as a qubit. By oscillating the applied magnetic flux with a specified amplitude and offset, we can select any of the allowed long-lived metastable flux states. We applied this technique to $\mathrm{Nb}\text{\ensuremath{-}}{\mathrm{Al}}_{2}{\mathrm{O}}_{3}\text{\ensuremath{-}}\mathrm{Nb}$ and $\mathrm{Al}\text{\ensuremath{-}}{\mathrm{Al}}_{2}{\mathrm{O}}_{3}\text{\ensuremath{-}}\mathrm{Al}$ devices with from 10 to over 100 distinct flux states at temperatures as low as $25\phantom{\rule{0.3em}{0ex}}\mathrm{mK}$. In a ten-state system with an initial probability $p=0.13$ to be in the desired flux state, we achieved $p=0.999\phantom{\rule{0.2em}{0ex}}96$ after 50 oscillations at $22.6\phantom{\rule{0.3em}{0ex}}\mathrm{kHz}$. The technique is generally applicable to other systems with multiple metastable wells (including rf SQUIDs), requires no additional readout or bias lines, involves minimal energy dissipation, and appears to scale favorably with the number of qubits.
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