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"Unpowered omniwheels" are not really going to be useful to MoveIt (or ROS even), and so you probably only need them for simulation. Within MoveIt, you probably only need rough collision data (and if your arm can't hit the wheels, then even that may not be necessary).

I think what you are actually looking for with MoveIt is to create a virtual link which is "planar" type for the mobile base itself. Presumably you have a controller which, given a plan for where to move the mobile base, can control the powered wheels.

Now, as to how you would do this without maintaining both the URDF and SDF, I'm not entirely sure. In the past, I have used XACRO to add simulation-only things (such as sensor plugin XML blocks) to an existing URDF, thereby creating the "simulation-ready" URDF. I'm not sure how the URDF->SDF converter actually works -- perhaps it will simply pass a SDF block through without trying to convert it? It would be a bit of a hack, but it might work...