So I'm thinking of building a Flanger 301 from tonepad.com, and I saw that it needed an 18V supply. After looking around for a bit, I found a few methods, and I just wanted a second opinion on which method is better, the ICL7660 Voltage Doubler or the MAX1044 Voltage Multipler method.

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To be honest, the best way is to just use 2 9v batteries in series.

With things like voltage doublers, the higher up you go the lower the quality and stability of the voltage is. When you increase a voltage, it's available current decreases proportionately.

Double the voltage and you'll half the current that you can draw. Say you have a 9v battery capable of giving you 100mA. If you double the voltage from that single battery, you can only draw 50mA.

You could fix this by putting 2 9v batteries in parallel to double the available current, but then you might as well just hook them in series and be done with it.
...or just use an ac adapter. no batteries necessary and you can get ones that will give you 18v, but thats just what i would do since i really hate wasting money on 9v batteries.

but to answer your question, both methods will work. as for which is better, i dunno. i guess it all matters on what parts you already have on hand.
you could always build and 18V supply as well. i saw a link on how to do a 9V supply a while ago, and it gave the part # for the transformer if you wanted to do 18V instead. it was great because you could build a brick will completly isolated outputs and could do a good job filtering if you wanted. im thinking phase shift of +90 degrees then full wave rectification on all of your three "phases" would do it. yes expensive, but it would be good. worth it for the price? maybe not if you did the phase shifts, but otherwise it would be good if you set up the propper filtering.