Clarify relative energies for 3dSets

[ghutchis]

When creating 3dSets (e.g., conformers, molecular dynamics, following an optimization or IRC) it is useful to retain multiple properties - particularly relative energies.

It's not clear the best way to do handle this.

[ghutchis]

After some thought, I'd like to nest this in properties:

'properties': {
    'totalCharge': 0,
    'spinMultiplicity': 1,
    'sets': {
        'totalEnergies': [ … ]
    }
}

This mirrors sets in orbitals and 3dsets in coords

[ghutchis]

Thoughts @cryos ? - I'd like to implement this soon (to enable conformers)

[ghutchis]

I was actually thinking about how to implement this, and I'd much rather have this second option:

'properties': {
    'totalCharge': 0,
    'spinMultiplicity': 1,
    'energies': [ … ]
}

The difference is that if we avoid nested objects (dictionaries, maps) in properties the parsing code just handles properties as one key/value store (e.g. energies is an array of numbers).

Thus properties would be a VariantMap for Avogadro:

• booleans
• numbers
• strings
• numeric arrays
• 2D matrices (e.g., polarizabilities or lists of numeric arrays)

The schema can then specify a few well-defined keys (e.g., totalCharge, spinMultiplicity, energies, totalEnergy, etc.)