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Different fan headers

CPU fan should be used for CPU as it often has safety features i.e. auto shutdown and warning. PSU fan is for your PSU and for monitoring purposes only if your PSU has a fan cable. System/Chasis is usually for case fans often controllable by the motherboard, PWR fan is usually for auxiliary power (or it is synonymous with PSU fan) and is typically a constant 12v uncontrolled if not used for monitoring. PWM is pulse width modulation, it's a different type of fan control that supplies a fan with 12v but at burst periods to sustain a specific speed without changing a voltage, it also circumvents the issue of fan start up voltages.

 

I think there are some differences in the labeling based on manufacturer, if your board is not common you should look in the manual if you're not sure. The online manual that is, I'm pretty sure you, like everyone else, has thrown the paper one away.

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3-Pin fan header consists of 12V, ground, and tachometer (RPM monitor).  4-Pin fan header adds PWM speed controls.  3-pin or 4-pin fans can plug into either 3-pin or 4-pin headers but if you mix them you won't have PWM speed control and they will just run at full speed (12V).

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3-Pin fan header consists of 12V, ground, and tachometer (RPM monitor).  4-Pin fan header adds PWM speed controls.  3-pin or 4-pin fans can plug into either 3-pin or 4-pin headers but if you mix them you won't have PWM speed control and they will just run at full speed (12V).

You can control 3-pin fans though.

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3-Pin fan header consists of 12V, ground, and tachometer (RPM monitor).  4-Pin fan header adds PWM speed controls.  3-pin or 4-pin fans can plug into either 3-pin or 4-pin headers but if you mix them you won't have PWM speed control and they will just run at full speed (12V).

I believe the PWM fan can still be voltage controlled and most boards can differentiate a 3 pin on a 4 pin header and control by voltage accordingly.

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As pointed out before, the difference lies in how the fan's speed is controlled. 3-pin fans are controlled using voltage modulation, 4-pin fans are controlled using pulse width modulation (PWM).

 

Voltage modulation

This is very straightforward and probably something you'll already know. When controlling the fan via voltage modulation, you simply lower the voltage applied to the fan motor to lower it's speed. Lowering the voltage will lower the power the motor produces (P=V²/R). Lowering the power output will lower the speed.

 

Pulse width modulation

PWM is a technique that has been used for decades to 'simulate' a varying voltage in digital systems. It consists of applying a high frequency pulse train in which the pulse width is variabel. For example: as pulse train that is 10µs on and 30µs off has a duty cycle of 25% (and operates at a frequency of 25 kHz). What this means is that a quarter of the time (10µs), the maximum voltage (in case of a fan, this is 12V) is applied. The other 75% (30µs), no voltage is applied and the motor is left freewheeling. Inertia will make sure that the motor moves smooth instead of in bursts.

Practically, the fan always gets fed 12V, and a a little control circuit inside the fan hub mixes the high frequency PWM signal into the power going to the motor.

 

Voltage modulation vs PWM

Now, why are there two different standards? Simple: voltage modulation made the fans cheap (no controlling circuit on-board). However, PWM does have some advantages. The biggest one being the lower starting speed. Because PWM fans always get 12V, the motor will always start spinning during the 'on time' of the duty cycle (it always delivers full power). This means that -theoretically- PWM fans are capable of running at 1rpm. The reason this isn't completely the case is that, at very low duty cycles, the bursts of power it puts out aren't enough to overcome inertia and the magnetic resistance to move one pole position further (this has to do with brushless DC motor design).

 

One of the problems with PWM fans, however is that, due to the extra controller circuit needed, they are susceptible to coil whine if that circuit isn't design very well or different frequencies for the PWM signal are used.

 

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TL;DR: 3-pins are controlled via variable voltage, 4-pins are controlled via PWM. PWM is better because it gives a lower starting speed

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