algorithmic modeling for Rhino
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StructDrawRhino has a feature to inflate a mesh, I think Daniel also added this feature to Kangaroo.
http://www.grasshopper3d.com/group/geometrygym/forum/topics/install...
If you have access to the circle on the surface and can calculate its diameter (s) then you could use the formula for the segment of a circle. r= h/2 + (s^2)/8h where r is the radius and h is the height above the surface you want your dome to be.
With the results of r, the radius of the circle you can create a sphere below the surface that would only protrude above the desired dome shape. This could then be boolean differenced away from the sphere by the surface.
See attached
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