crystal_torture.node.Node

class crystal_torture.node.Node(index: int, element: str, uc_index: int, is_halo: bool, neighbours_ind: set[int] | None = None, neighbours: set[Node] | None = None)

Bases: object

A node representing an atomic site in a crystal structure for percolation analysis.

Each Node represents one atomic site from the input crystal structure. To properly handle periodic boundary conditions, the analysis uses a 3×3×3 supercell containing the original unit cell surrounded by 26 periodic images. This creates nodes for both the original sites and their periodic copies.

Every Node has a unique index in the supercell. Multiple nodes share the same uc_index because they represent the same original unit cell site in different locations. The is_halo flag distinguishes between sites in the central unit cell (is_halo=False) and their periodic images (is_halo=True). Only unit cell sites are used to seed cluster formation during the percolation analysis.

Nodes are connected to other nodes within a cutoff distance, forming the graph used for percolation analysis. The tortuosity value represents the minimum number of edges traversed for a unit cell node to reach one of its periodic images.

index

Unique node identifier in the supercell.

element

Chemical element symbol (‘Li’, ‘Mg’, ‘O’, etc.).

uc_index

Original unit cell site index this node represents.

is_halo

True if periodic image, False if central unit cell site.

neighbours_ind

Set of connected node indices.

neighbours

Set of connected Node objects.

tortuosity

Minimum edges traversed to reach a periodic image (set by analysis).

dist

Temporary distance for graph algorithms.

dist: int

element

index

is_halo: bool

property labels: dict

Legacy labels interface for backward compatibility.

Deprecated:

The labels interface is deprecated and will be removed in v2.0. Use node.uc_index and node.is_halo directly instead.

Returns:

Dictionary containing UC_index and Halo values for compatibility with legacy code.

neighbours

neighbours_ind

tortuosity: float | None

uc_index: int