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There's an explanation on the effort and velocity safety limits here. As far as I know, these safety limits are only taken into account if you use the pr2_controller_manager as a Gazebo controller plugin (don't be fooled by the name, the controller manager is also very useful for non-PR2 robots). If you write your own controller, you can of course also write it such that it respects those limits.

Now that I think about it, it would be illogical for apply_joint_effort to respect those limits: they represent desired limits on effort and velocity that you don't want the controller to exceed. They are not physical limits on the joints. The service apply_joint_effort simulates the effect of some "external" subject other than the controller taking the joint and twisting it.