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Parametric Surfaces to 3D object

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I've been attempting to use two parametric surfaces from interpolations to define the shape of a 3D solid domain. I'm following steps similar to those used in this previous thread www.comsol.dk/community/forums/general/thread/20848/.

I use tab-delimited text data (x, y, and z) to define two interpolation functions ('top' and 'bottom'); both files have the same x and y points (though these are not uniformly gridded). I then make two parametric functions from these. I make a union of those two (which isn't really necessary, I think), make a solid block, convert everything to a solid, delete entities, then form union.

I've tried a variety of combinations of relative tolerances and max. number of knots in the parametric surface settings. Unfortunately, I get an "Internal error in geometry decomposition" when I make the union (or if I don't make the union, then when I convert everything to solid). Or, the union produces just one of the surfaces along with some connections on the sides that seem to connect with whichever surface is no longer there.

I think that the problem comes from the interpolation of the files. When I limit my domain to just regions (x and y) where the top is very far from bottom, this works fine. However, over the full xy domain, all of the z values in the top are not always above the bottom, in some cases they are equal. However, while they might be the same in some places, the top never has a lower z value then the bottom. Here's where I think the problem comes in: when I look at the parametric surfaces, top and bottom often overlap. My file size apparently too big to attach; I'll try to find a work around at some point.

A couple questions:
Has anyone else encountered something like this? Have any solutions been found?
Even if I can get the weird overlapping to go away, will the top and the bottom having equal z values be a problem? Could I do something like just add a very small value (like 0.1% of the thickness) to the top to circumvent this problem? Such a small value would not greatly affect the final results.

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