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.Figure

How can I reconcile both of these?

  • $\begingroup$ I gave my +1 long ago, but can you update us now that it has been 6+ months since you asked this question? Have you found the answer? Are you still actively in need of an answer? $\endgroup$ Nov 5, 2023 at 15:47
  • $\begingroup$ I am still looking for an answer $\endgroup$ Nov 5, 2023 at 19:49


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