This PR starts to touch on the painful world of indices associated to our AtomTypes, relating to #289 and #508.
Here we begin by removing the local index storage from the AtomTypeData class and modify AtomTypeMix to only allow add()ing atom types, prohibiting remove() operations. This indexing is _still_copied over to Atoms making up a Configuration since there is no faster way of accessing the 2D array when computing forces and energies between atoms, but at least we remove one piece of easily-broken storage in a class.
This PR starts to touch on the painful world of indices associated to our
AtomTypes, relating to #289 and #508.Here we begin by removing the local index storage from the
AtomTypeDataclass and modifyAtomTypeMixto only allowadd()ing atom types, prohibitingremove()operations. This indexing is _still_copied over toAtoms making up aConfigurationsince there is no faster way of accessing the 2D array when computing forces and energies between atoms, but at least we remove one piece of easily-broken storage in a class.Works towards #289.