Why there are two sets of primitive vectors in str.out file? When I define the unit cell with a set of a, b, c, alpha, beta, gamma why do the unit vectors have to follow in the three lines after this set? I pretty sure the explanation is trivial and I am missing something, but could you please comment on this.
The first set of axes defines the coordinate system.
The 2nd defines the unit cell. It is useful to allow them to differ. Example: for FCC using cubic coordinate is easier even though the unit cell (with one atom not four) is not a cube.