Consistent indices for StructureStorage.get_structures #482
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When not specifying indices when creating an Atoms, the mapping between chemical element and index is not unique and may change. For calculations on single structures this is no problem, but when iterating over a StructureStorage in a single (e.g. interactive) calculation this may cause confusion, since the atomistic jobs generally only save the indices of atoms across multiple steps.
indices is ignored when symbols is given, so instead we provide indices and species, where species is just the set of elements occuring in the structure.
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Previously the index<->chemical element mapping was unspecified for structures returned from a storage. This works ok for single calculations since our jobs remap the indices, but crucially they only do it once for the first structure set on a job. So if you have two structures with an inconsistent mapping and put them through the same interactive job great despair ensues. The structures are passed correctly to lammps, but since the index mapping changed they are incorrectly saved in the HDF and using
get_structureon that job will give from structures (with elements swapped). More details in the commit messages.