Clarify the Stepper motor doubt

Hi all,

Am driving bipolar stepper motor using DRV8821 driver..Without chopping, the motor current waveforms are good without any noise...But, if i chopped the current to 1A or 1.2A my current waveforms has much high frequency noise..

can anyone clarify about this???

Its not "noise" it is the chopped voltage output from the chopper/PWM. Should be around 20kHz, or the upper audio range.

Will this effect the efficiency of the motor???

No, at ~20kHz the motor won't even know its happening. That is the beauty of "chopping", the voltage is not affected only the amperage.