SpeciesInfo and Atom lists, any reason for mot keeping more details than pos?
Joint Density Functional Theory
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It looks like you made a lot of code changes but there is still the
creation of local Atom lists from the species lists. Some of this
information, like forces or other derivaatives, may be useful to retain with the atoms info and does not seem to be that large. You make the atom list by traversing all the species and then discard it. You could just keep the atom class including a position in the speciesinfo and making iterators, or maybe some kind of linked struct, that traverse over all atoms or just a given species. The atom descriptors could infact have maps like you apparently did with the Energies. I think in my earlier playing this species-atom thing generated a lot of confusing code :)