Wrong ordering of energy levels

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Multiple possible reasons
Hi Chloe,
I think there can be multiple possible reasons for the behavior you are seeing. Whatever the reason is at convergence the total energy is a minimum for the corresponding orbital occupations. Possible reasons include: the choice of density functional, the use of level shifters, the symmetry of the system, etc.
With regards to the choice of functional this sort of thing is less likely to happen if you pick a functional including exact exchange. Alternatively I would guess that the quasi Newton-Raphson solver is also less likely to produce these kinds of answers.
If you are willing to send me you input I can have a look to see if I can give you some more detailed answers.
Hubertus dot vanDam at PNNL dot gov.

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