EMC calls the conversion between cartesian coordinates and motor
positions "kinematics".  To define a machine with a novel motor
configuration, a new kinematics module must be written.  You can find a
description of the necessary functions in our documentation:
    http://linuxcnc.org/docs/2.2/html/motion_kinematics.html

One limitation of emc's kinematics is that it currently only imposes
velocity and acceleration limits on individual cartesian axes.  In
machines with nontrivial kinematics, there are also "joint limits", the
acceleration and velocity limitations for a particular motor.
Presently, the only way to ensure that these limits are met is to set
the machine's axis limits low enough that the joint limits are met at
any point within the work volume.

Jeff

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