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I don't think you will need to even lock the rotor. The motor won't have time to even try to turn in 0.02 seconds. And you won't need the encoder for the PI loop tuning. It won't hurt anything though. But don't expect it to turn at all. You may just hear an instantaneous bump or something each time you type run-pi-test. You should be able to tell from the streaming data if it is converging to zero without graphing it, but you could just cut and paste it into excel if you want.
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