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In most cases the right solution is to not include those structures. You can inspect them manually to determine the cause. Often it is due to a very large relaxation to a different structure (i.e. an ordering on HCP relaxing to a Laves phase, or HCP to BCC, etc.) which means there is no good mapping, or perhaps an atom has relaxed to an interstitial site that is equally far from multiple prim sites.
Ok thanks. Just one thing, if we have layered structure, and one of the supercells ( say 211) when constructed corresponds to just one layer of atoms, is it good idea to have that supercell in the CE model? of course there are other supercells in my model.
If you are saying "just one layer", meaning it is periodic system of just layer "A" corresponding to "...AAA...", then I would expect it should be included.
I am not able to import some structures because there are multiple optimal mappings possible, what is the possible fix for this?