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I’ve been struggling to run PWM fans with a Megasquirt for a few years now. The closest I have come to making it work was documented in a different thread where I was able to make it work using a Lincoln Zephyr fan controller and a single 2d PWM table. That would have worked fine but Megasquirt cannot control running PWM fans with an override for AC on firmware 1.4 that I previously had.
Megasquirt FW 1.60 (the public release) and FW 1.5.3 (beta) both offer native fan control for a PWM based fan with proper ac override now.
I don’t know how you have your Megasquirt wired up but on my Megasquirt I had an extra PWM output called PWM output 3. PWM output 2 was the normal output to control the oem cooling fan but that is connected to the fan relay which is not a solid state relay and trying to control a pwm fan from the oem fan connector will quickly fry the oem fan relay hence me running a dedicated PWMoutput 3.
In short, to get the wiring sorted for the FM Spal brushless fan the red wire on the fan goes to the breaker that FM supplies and the power for the breaker is direct from the alternator lug. The negative is direct to any chassis negative that you like and the white wire (not yellow wire) goes directly to the PWM output of your choice on the ecu.
The Spal fans are controlled backward from conventional wisdom. 0-5% duty cycle turns them off 7-10% is full steam ahead and 90% is low.
In Tuner Studio under fan control, you can select for the outputs to be inverted as shown in the photo below so that 7% is now treated as the minimum speed % and 90 is the max output speed. I will keep tweaking these specific numbers but so far this is working well for me.
What is nice is now when AC is turned on it brings the fan to full speed independent of coolant temperature. It also slowly ramps up fan speed automatically from the on temp until full-speed temp.