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STL Geometry & Meshing

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I have been working on importing a geometry from an STL file; it's a thing 3-D object, where the length and width are on the order of 10^5 m and the thickness is 10^3 m. I originally had problems where the finalized geometry contained strange overlaps that came from some interpolation within COMSOL. I have finally figured out how to import without these problems.* Now I have another concern.

The intent of this is to build a Java file that I can run within a Fortran model with a variety of geometries, so I ideally want something that is very general and not gui-based. The import geometries will always have a top surface, a bottom surface, and some side faces that are perpendicular to the y-axis.

If you look at the model, you can see that the imported geometry still contains all of the faces defined within the stl file. I cannot get rids of this segmentation, which is the problem now for meshing and for setting boundary conditions.

Is there a way to combine all of these segments together? They are all treated as one domain within the geometry. I have tried converting to solid and a variety of other processes dealing with the geometry. But it seems that when I go to mesh, the mesh is over each small unit and really takes quite a bit of time to get going.

Second question, is there a way to write in the face number when I create the geometry. Since I want something that can be generalized, but I will always know the number of faces/facets, numbering them would allow me to easily group them into the surface necessary for the boundary conditions that I want to apply.

Unfortunately, my file is too large. I'll try to figure this out so that i can attach it. Probably clearing the mesh will solve that problem.

*Just for your information, I have attempted a variety of other methods to bring in this geometry, including an interpolation function (from a file) with a block & parametric surfaces for the geometry. I never got this to work successfully to make something 3D, though it worked for either the top or bottom just fine (see the mention of the interpolation in the first paragraph). I've also gone through many, many permutations of stl files, and this seems to be the best.

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