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I've found 2 reasons (empirically) for this problem so far. After resolving both issues, I have not seen any problems (tested under ROS Groovy + Gazebo 1.2.5)
All my meshes were made in sketchup or blender, and I managed to invert a few faces and the mesh did not close properly. This affects Gazebo in weird ways. Some of these errors may not be visible in sketchup/blender, but were visible in meshlab.
The erratic differential drive plugin changes the location of the model in the simulator instead of simply imparting the appropriate velocity to the wheel. Consequently the robot would overlap a tiny amount with a wall and bad things happen.
Somebody familiar with Gazebo might be able to provide a better explanation on why an incomplete mesh failed.