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The 3-phase permanent magnet BLDC motors come in two types, internal rotor and external rotor. Mostly the external rotor types are called Hub motors as they are used in electric bikes. Both types of motors use Hall sensors inside them for position sensing and commutation of currents.

I wonder if the controller of these two types of motors are same or not? Let us say I have a controller for BLDC internal rotor type motor. Will it be possible to use the same controller with a BLDC external rotor type motor? Let us say all other specs of both motors are matching.

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The quick answer is: yes of course. There is no difference in control between these two types of motors.

However there are few notable differences. The pancake motor is designed for high torque & low speed, while the classic type can be high speed & low torque. Thus, the pancake motor usually has a quite large winding inductance, compared to the other. If you want to drive a motor with low inductance and expect high speed, then the PWM frequency shall be high. For high inductance motor, the PWM doesn't have to be such high, so reducing the frequency you get the nasty noise from motor, but it greatly reduces the switching loss thus maintaining the driver cool.

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