this is exactly the issue, the voltage and current at low rpm's are just too low to be picked..
An Arduino ADC could easily read a 100 mV signal, and it would be no problem to deduce the frequency. But why would you care?
Unless you used a transformer that was rated for the frequency, that is part of your problem. Transformers designed for 50-60Hz need to work at those frequencies. The amount and type of iron core material needs to match the frequency.
Use an oscilloscope to actually look at the signal you have at the very low frequency. I would suggest that at very low RPM your generator produces NO measurable voltage.
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Another problem at low RPM, even if voltage is high enough to read, is slow rise and fall time, maybe a Schmitt trigger or comparator to make a square wave would work
I'd use an optocoupler with a constant current device (JFET) in place of a resistor. Should be good down to a few volts as the LED in optocouplers is normally IR and so fairly low voltage.
The problem with using a transformer is that, as the frequency gets lower, it becomes much less efficient at coupling the signal.
Connect the gate to the source of the JFET and use it as a 2 terminal device.
There's already a solution
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