httk.atomistic.structure_comparison

Comparing structures as crystals rather than as lists of atoms.

Structure.__eq__ compares the site list element by element, which is the right default for a data object but is stricter than crystallographic identity: the same crystal written with its atoms in a different order, or with a site represented by a different lattice translate, is a different Structure and the same crystal.

That distinction matters for the asymmetric-unit round trip. Structure -> ASUStructure -> Structure reproduces the crystal exactly — the coordinates are exact rationals throughout, with no numerical drift — but site ordering and the choice of lattice representative follow the canonical expansion order rather than the original input. same_crystal() is the predicate that guarantee is stated in.

Functions

same_crystal(→ bool)

Whether two structures describe the same crystal.

Module Contents

httk.atomistic.structure_comparison.same_crystal(first: httk.atomistic.structure_like.StructureLike, second: httk.atomistic.structure_like.StructureLike) → bool

Whether two structures describe the same crystal.

True when they have the same cell and the same multiset of occupied sites, comparing each site by its species and its reduced coordinate wrapped into [0, 1). Site order is ignored, and so is which lattice translate of a site was written down.

The comparison is exact, not approximate: reduced coordinates are exact rationals and cell bases are exact, so two structures that differ by any amount at all compare unequal. There is deliberately no tolerance parameter — a tolerant comparison belongs with the recognition step that snaps a measured structure onto an idealised one, not here.

Periodicity takes part in two ways. Cells must agree on it, so a slab is never the same crystal as the bulk with the same lattice vectors. And only the periodic directions are wrapped, since along the others there is no lattice translate to be indifferent about — an atom at 1.05 really is somewhere else than one at 0.05. The comparison stays exact in the frame as written: two descriptions of the same slab that differ in their non-periodic frame vector compare unequal, because reconciling them would need an origin convention this function deliberately does not have.

Accepts anything structure-like on either side, so a Structure may be compared directly against an ASUStructure without expanding it by hand.