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to control a differential drive robot, and using the "profiled position" drive mode

I don't think that profiled position mode is suitable for controlling a diffential drive. It is is setpoint-based, so the timing might vary between different modules.

I used schunk_lwa4p as a template

While you can reuse some parts of it, I don't think that it is helpful to use it as template. It is meant for schunk hardware with highly specific settings.

This is very noticeable because I am having to run at a very slow sync interval of 200ms

You should really try reduce this, I would target at least 20ms.

Checking my logs, I found that sometimes one motor will begin moving one sync interval later than the other.

The motion should get commanded in the same sync slot. How do you determine the start of the motion?

as a result of this ROS_CANOpen issue: https://github.com/ipa320/schunk_robots/issues/59

That's a non-issue, and quite specific the Schunk LWA hardware.