Arduino Due has 54 pins. It says that it has 12 PWM pins. I know it uses a more powerful chip than other Arduinos.
Can the number of PWM be increased?
Can any of its pin be used for PWM?
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According to the manual:
"The Arduino Due supports analogWrite() on pins 2 through 13, plus pins DAC0 and DAC1. Unlike the PWM pins, DAC0 and DAC1 are Digital to Analog converters, and act as true analog outputs."
You could do software pwm but the frequency will be several orders of magnitude less than the clock frequency.
The hardware pwm pins have a counter a register and a comparator where every tick it increments the counter, compares the value of the counter to the value in the register and setting the pin to the corresponding value.
If you need more analogue outputs then it's easier to use an external DAC module.