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In free running mode, the ADC samples and updates automatically and continuously. You can get the highest sampling frequency using this mode. Note that the ADC must be fixed to a channel in free running mode. In other words, you cannot set up the ADC to ``scan'' channels in the free runnung mode.
In manual mode, the ADC only samples and updates after it is ``started'' manually in software. After one conversion, the devices stops. This mode is useful if you need the best resolution (you need to put the rest of the MCU to sleep during conversion), or if you need to reduce power consumption.
Free Running mode is selected when ADFR is set to 1. ADFR is bit 5 of ADCSRA.