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FAQ
We have tried to put fixed joint inside the current architecture, and we failed. The main reason is that the eigen release for the Ubuntu 12.04 LTS is not able to handle matrix of size 0. As in addition, this will induce useless computation in the system if you are mainly interested by generating a control law taking care of the dynamical effects.
Either you have a hyper-redundant robot with a backbone, and then you should modify the hard-coded limitation here: https://github.com/laas/metapod/blob/cd4372403e3061f6073bb6ef3b7e6e30123cedf5/include/metapod/tools/constants.hh#L29 Or you have a robot with fingers which are likely to be control only by one degree-of-freedom as in Romeo and in HRP-2 and we strongly recommend that you remove them from your URDF file.
We strongly suggest that you create a xacro version of your robot URDF model to build a reduced version. The dynamic involved by the fingers has almost not impact on the overall robot.