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kups.core.neighborlist.fixed

Empty and fixed-edge :class:NeighborList implementations.

These cover graph-construction cases without cutoff search: always-empty edge sets for point clouds and state-provided fixed edge topology for bonded interactions, optionally filtered to a patch-affected subset. They satisfy the standard :class:NeighborList[D] protocol so a unified graph constructor can ask any neighbor list for edges, regardless of how those edges were obtained.

The public call contract treats lh as the self-graph/output table. rh is keyword-only and reserved for true bipartite neighbor-list queries; fixed topology is a self-graph implementation and does not use rh. for_indices is keyword-only, mutually exclusive with rh, and names affected lh ids after the caller has already written updated particle data into lh. FixedEdgesNeighborList returns only fixed topology rows touched by those ids. Its implementation is a normal selector -> mask -> compactor pipeline over the fixed edge rows; shifts are computed from the current particle positions during selection.

EmptyNeighborList

Neighbor list that emits an :class:Edges[D] with zero rows.

The degree field is the runtime arity carried by the emitted edges; it must match the type parameter D.

Attributes:

Name Type Description
degree int

Edge arity (Literal[0] for point clouds, higher for unified graph constructors that need a degree-aware empty NL).
Source code in src/kups/core/neighborlist/fixed.py 
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@dataclass
class EmptyNeighborList[D: int]:
    """Neighbor list that emits an :class:`Edges[D]` with zero rows.

    The ``degree`` field is the runtime arity carried by the emitted edges;
    it must match the type parameter ``D``.

    Attributes:
        degree: Edge arity (``Literal[0]`` for point clouds, higher for
            unified graph constructors that need a degree-aware empty NL).
    """

    degree: int = field(static=True, default=0)

    @jit
    def __call__(
        self,
        lh: Table[ParticleId, NeighborListPoints],
        systems: Table[SystemId, NeighborListSystems],
        *,
        rh: Table[ParticleId, NeighborListPoints] | None = None,
        for_indices: Index[ParticleId] | None = None,
    ) -> Edges[D]:
        assert rh is None or for_indices is None, (
            "Neighbor-list calls cannot combine rh with for_indices."
        )
        del rh, systems, for_indices
        shift_inner = self.degree - 1 if self.degree > 1 else 0
        return Edges(
            indices=Index(lh.keys, jnp.zeros((0, self.degree), dtype=int)),
            shifts=jnp.zeros((0, shift_inner, 3), dtype=int),
        )

FixedEdgesNeighborList

Neighbor list for a fixed topology edge set.

Full self-graph calls return all fixed topology rows with shifts computed from the current particle positions. Affected self-graph calls pass keyword-only for_indices after updated particle data has been written into lh; the neighbor list returns only fixed rows touched by those affected lh ids. rh is reserved for true bipartite neighbor-list implementations and is not a fixed-edge update mechanism.

Attributes:

Name Type Description
indices Index[ParticleId]

Fixed edge topology. Shifts are intentionally not stored; they are computed from the call's current particle positions.
avg_edges Capacity[int] | None

Update-only average affected-edge capacity per affected lh id. Full calls ignore this field and use the stored topology length; affected calls default to the full edge-buffer size when it is not provided.
Source code in src/kups/core/neighborlist/fixed.py 
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@dataclass
class FixedEdgesNeighborList[D: int]:
    """Neighbor list for a fixed topology edge set.

    Full self-graph calls return all fixed topology rows with shifts computed
    from the current particle positions. Affected self-graph calls pass
    keyword-only ``for_indices`` after updated particle data has been written
    into ``lh``; the neighbor list returns only fixed rows touched by those
    affected ``lh`` ids. ``rh`` is reserved for true bipartite neighbor-list
    implementations and is not a fixed-edge update mechanism.

    Attributes:
        indices: Fixed edge topology. Shifts are intentionally not stored;
            they are computed from the call's current particle positions.
        avg_edges: Update-only average affected-edge capacity per affected
            ``lh`` id. Full calls ignore this field and use the stored
            topology length; affected calls default to the full edge-buffer
            size when it is not provided.
    """

    indices: Index[ParticleId]
    avg_edges: Capacity[int] | None = None

    @jit
    def __call__(
        self,
        lh: Table[ParticleId, NeighborListPoints],
        systems: Table[SystemId, NeighborListSystems],
        *,
        rh: Table[ParticleId, NeighborListPoints] | None = None,
        for_indices: Index[ParticleId] | None = None,
    ) -> Edges[D]:
        assert rh is None or for_indices is None, (
            "Neighbor-list calls cannot combine rh with for_indices."
        )
        assert rh is None, "FixedEdgesNeighborList only supports self-graph calls."
        if for_indices is None:
            max_edges = FixedCapacity(len(self.indices))
        else:
            max_edges = (
                self.avg_edges.multiply(for_indices.size)
                if self.avg_edges is not None
                else FixedCapacity(len(self.indices))
            )

        pipeline = Pipeline[D](
            selector=_FixedEdgesSelector(self.indices),
            masks=(TouchesForIndicesMask(),),
            compactor=ReduceCompactor(max_edges),
        )
        return pipeline(lh, systems, for_indices=for_indices)