Fixitt,
You say you don't completely buy into the copper better than aluminum thing. So long as you have access to solid copper and solid aluminum, I've got a couple experiments for you that may help.
First, let me state the common misconception and why it arises. Many people believe that copper is more effective at absorbing heat while aluminum is better at getting rid of it. The simple fact is that materials simply move thermal energy from point A to point B based on temperature differentials. They don't care whether point A or B is warmer, they just move heat from high temperature to low temperature.
The biggest reason people seem to be confused by this is that these materials behave differently under transient conditions. Aluminum actually has a lot higher specific heat than copper. This means that mass for mass, aluminum holds thermal energy a lot more effectively than copper, to the tune of 903 Joules/kg-K vs 385 Joules/kg-K. This means that 903 joules of energy (.856 BTU for us Americans) would raise a one kilogram block of aluminum by 1°C. The same amount of energy would raise a one kilogram block of copper by 2.35°C. Hmmm, sounds like aluminum might actually absorb heat better, right? Well, this is offset by aluminum's lower density. Aluminum's density is 2702 kg/m^3 vs 8933 kg/m^3 for copper. This means that if you take two pieces that are the same size, the aluminum one will weigh only 30% what the copper one weighs. Stuffing that same 903 joules into two equal size blocks would raise the temperature of the copper one by only 71% as much as the aluminum because of copper's higher density.
OK, what's this mean in English? It means that on a volume for volume basis, copper will store heat more compactly than aluminum. This heat storage means that copper will heat more slowly when you turn on your computer and will stay warm longer when you turn off your computer. The real question is what happens in between when the computer runs steady-state?
This situation is perhaps the most confusing of all. Copper has a higher conductivity, 401 W/m-K versus 237. On a purely volumetric basis, copper requires less temperature differential to transmit "X" watts of heat from point A to point B. This is why you'll find it in all high end heat sinks where the sink meets the core. Now, why do many high end heat sinks then use aluminum fins or pins? The density once more plays a role. Getting rid of heat requires convection to air. Convection requires surface area. Aluminum's lower density means that you can make a lot more surface area from a given mass of material. So where convection matters, aluminum has an advantage.
OK, I mentioned some experiments that you can do that may help. What you'll need are two blocks of material of equal dimensions, one of copper and one of aluminum. It's also handy to have another block of identical dimensions made from wood. Place all three blocks in the fridge for a few hours until you're sure they are the same temperature as the fridge interior. Pull all three out and quickly place them on your forearm. Pay attention to hold cold each one feels and for how long. The copper will feel coldest for the longest time. The aluminum will feel cold, but not as long. The wood will scarcely feel cold at all. The sensation of cold comes from how quickly the blocks are transferring heat from your forearm. Copper does the job best of the group while wood does the job poorly.
Take these same blocks and put them in a kettle of water on the stove using the lowest setting. Let them sit there for a couple of hours. Test the water to make sure it isn't too hot to touch. So long as it isn't, take the blocks out and put them on your forearm again. The copper will feel hottest the longest, then the aluminum, then the wood.
Each of these two tests shows the transient properties of the materials and represents what happens when you first turn on (cold test) and finally turn off (hot test) your computer.
Now to know what happens while your computer is running, put a kettle of water on the stove with a lid on it. Set the temperature on the stove fairly low and place the blocks on top of the lid. Wait a while and touch the top of each block. The copper should feel the warmest, the aluminum almost as warm, and the wood probably cool to the touch. This means that copper is getting heat out of the lid most effectively and would make the best material for getting heat off a core. If you think the aluminum would be better because it doesn't feel as warm, then why not use the wood to make a heat sink?
In the end what you'll find is that for identical shape blocks, conductivity rules and copper beats aluminum. For identical material masses, the decreased density of aluminum allows so much more material. This excess of material means a lower overall thermal resistance in conduction and copious surface area for convection. Air heat sinks and water blocks are constrained around the core such that you can't use aluminum's lower density to put a bigger hunk in there. This is why copper rules for inserts and water blocks. In air heat sinks you tend to have all sorts of room for fins/pins, so aluminum does a better here for a given weight.
Honestly, the differences in water blocks are pretty small and you really shouldn't see more than 1-2°C difference between aluminum and copper. Rest assured, however, that for two water blocks of identical geometry the copper one will always win.
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