This is most easily clarified when looking into case.scf.

Below is an example, similar to yours:

As you can read, the requirement for PG 2/m is to have a 2||z, but in the crystal this 2-axis is || to x. Thus the local coordinate system must be such, that the local z-axis points into the crystal x-direction (your d-z2 orbital points into "x").

 ATOM:           2
Cu         operation #  1     1
Cu         operation #  2     -1
Cu         operation #  3     2 || x
Cu         operation #  8     m n x
  pointgroup is 2/m (neg. iatnr!!)
  axes should be: 2 || z, m n z
  z-rotation vector:  1.0000  0.0000  0.0000
  y-rotation vector:  0.0000  1.0000  0.0000    0
  WARNING: LOCAL ROTATION MATRIX CHANGED
LOCAL ROT MATRIX:       NEW                                OLD
           0.0000000 0.0000000 1.0000000      1.0000000 0.0000000 0.0000000
           1.0000000 0.0000000 0.0000000      0.0000000 1.0000000 0.0000000
           0.0000000 1.0000000 0.0000000      0.0000000 0.0000000 1.0000000


Am 26.04.2016 um 04:20 schrieb 徐远骥:
Dear everyone:
       I am doing the band structure with band character plotting. I
want plot the Mn atom's dz2 character. As we know, in wien2k the  atom's
  orbital are define in its local coordinate system.
       In the .struct file, the crystal is Orthorhombic with lattice
vector a,b,c and  the local matrix of Mn atom are (0 0 1, 1 0 0, 0 1 0).
       My question is the Mn dz2 orbital point to what direction(lattice
vector a or b?) in wien2k program?
   Best wishes!
   Y.J Xu





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