From a Dusty MechEng
A Simplified Generalization:
If I'm applying the flow formula correctly: m=pAV, where m is flow rate, p is 'rho' which is the density of water (ignore in this case), A is cross sectional area of the tube, and V is velocity.
Flow is constant throughout the system, that is, you don't have a greater amount of water flowing out of the pump than you have flowing in to it and the same for any component. Since the flow is constant and the density is (basically) constant, the above formula can be reduced to AV=c so that the Area times the Velocity equals some constant. Therefore, as the area increases, the velocity decreases and vice versa.
The point is this, the arrangement of components, Pump->HC->CPU or Pump->CPU->HC, is irrelevant on velocity. It is the cross sectional area of the Block the governs velocity.
It's been a little while since I've used my engineering background but here's what I think really matters. Since you want to draw heat off of the CPU, a "convective heat transfer process", the basic formula is: Q=hA(dT), where Q is the rate of heat transfer (bigger is better), h and A are dependent on the block characteristics, and (dT) is delta T or temperature difference. The only thing that you can control by your setup is the delta T. The bigger the delta T, the better. Now, what is delta T? It is the temperature difference between the surface temperature of the CPU block and the water flowing across it. Specifically it is t(s) minus t(w) where t(s) is the temperature of the surface and t(w) is the temperature of the water. To make this number bigger, our goal, we can make the CPU hotter, not what we want, or make the water cooler!
Therefore, in my old, rusty, dusty, mind - Pump->HC->CPU would be preferred because it puts the lowest possible water temperature into contact with the CPU.
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