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The wind does have a z component, but it isn't used within the trochoid calculation itself which just focused on 2D. The z values of the final path are merely linearly interpolated. We point this out in the last paragraph of the methodology section of our paper, and future work could include solving trochoidal paths in 3D.
Very cool paper and thanks for releasing it as open source. I've got some questions about the wind input.
Cheers
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