Use the vector option to define the orientation of the local coordinate system of the cross section of the beam. Then use the ztol command with a tolerance of around .0001 to compensate for numerical errors.
This is needed because TrueGrid®'s internal data structure for a beam includes its orientation point (not vector). When the output file is written for ABAQUS, TrueGrid® converts the points to vectors, and sorts them to get a unique list. This can be the source of numerical errors, and is the reason for the tolerance parameter.
