I've looked at the input files, and I agree that it seems odd that two-st-refNode2.in doesn't produce the same nodal values, as Iz == Iy.
refangle = 0 produces a switch of the y and z axis in the local c.s.
so at this point, it's not surprising that those two cases produces the same results.
I've checked that the D-matrix is invariant of this rotation, but rotating the K matrix with this rotation yields a different result. As far as I can tell, there is something wrong with the B-matrix.
Numerically checking the B matrix reveals
octave:80> B([1, 3, 2, 4, 6, 5], [1, 3, 2, 4, 6, 5, 7, 9, 8, 10, 12, 11]) - B
ans =
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 -9.01400 0.00000 0.00000 0.00000 0.00000 0.00000 9.01400 0.00000 0.00000 0.00000
0.00000 9.01400 0.00000 0.00000 0.00000 0.00000 0.00000 -9.01400 0.00000 0.00000 0.00000 0.00000
though, it's possible that I haven't thought this through properly.
The sources for these lines are
answer.at(5, 3) = ( 6. - 12. * ksi ) / ( l * l * c1y );
...
answer.at(6, 2) = -( 6. - 12. * ksi ) / ( l * l * c1z ); // new
Are those signs correct?
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a) I suppose the output from the element (the beam element does it's own thing here, compared to what most other elements do) if the reaction forces, which would explain the sign maybe?
b) Yes, the beam only prints the local number. It should be fixed to include the global number (5). A few other elements also do this (incorrectly) and they should be fixed.
c) Well, the cross-section only knows about Iy and Iz. It does not know anything about the shape other than through the cross-sections properties. It should be invariant to a 90 degree rotation around the x-axis as far as I can tell.