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Well, by changing pore/throat diameter, you're essentially changing the porosity, and subsequently the permeability. You can't directly change the permeability of a pore network model (or any other pore-scale method), that's what you do in a volume-averaged continuum model. As for wettability, I'm not very familiar, @jgostick knows more. But, I guess it has to do with the phase properties (ex. you can modify contact angle in your phase, say op.phase.Mercury).

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