I am trying to generate the unit cell for a material from the optimized coordinates of a molecule. I am able to generate an orthorhombic unit cell from the coordinates using utilities in Avogadro. However, it is unable to reduce the orthorhombic cell to the primitive cell which is hexagonal. The cell that I am trying to build is (a) in the attached figure.
The cell that was identified by Avogadro is attached below.
How can I reconcile both of these?
