That's typically what we suggest as well: run the 2.5D optimization first as it is much faster, then use its results as the initial guess for the full 3D optimization. This allows to reduce the number of iterations needed to reach the optimized design.
Using the structure imported from a GDS is a bit difficult: for the optimization, the structure is defined with a limited number of parameters (in our example we use 10 parameters):
Then we use an interpolation on a higher number of points to get a smoother shape. The issue we're investigating is related to this interpolation that gives some weird shapes!
Set aside the interpolation issue, to use the GDS, you need to extract from the polygon the y values at x_i to get the initial parameters.
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