harpoon
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I have not done such large scale modelling before ... but half the battle is setting up the simulator and the test bench.
I am guessing something like HFSS will do it, probably ADS Momentum (pricey)
Mentor has some 2.5D/3D solvers for PCB ... can't remember what is called.
Probably have something in Cadence as well ...
On the lower end, maybe Eagle ?
And the free ones ... maybe, just maybe ASITIC or FastHenry can give some guidance (they were written for inductor extraction/modelling).
good luck !
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