mlcolvar.data.graph.Configuration

class mlcolvar.data.graph.Configuration(atomic_numbers: ndarray, positions: ndarray, cell: ndarray, pbc: tuple | None, node_labels: ndarray | None, graph_labels: ndarray | None, weight: float | None = 1.0, system: ndarray | None = None, environment: ndarray | None = None, subsystem: ndarray | None = None)[source]

Bases: object

Internal helper class that describe a given configuration of the system.

Parameters:

  • atomic_numbers (np.ndarray) – Atomic numbers of the atoms in the system. Shape: [n_atoms]

  • positions (np.ndarray) – Positions of the atoms in the system. Shape: [n_atoms, 3], units: Ang

  • cell (np.ndarray) – Cell of the system. Shape: [n_atoms, 3], units: Ang

  • pbc (Optional[tuple]) – Periodic boundary conditions of the system. Shape: [3]

  • node_labels (Optional[np.ndarray]) – Node labels of the graph. Shape: [n_atoms, n_node_labels]

  • graph_labels (Optional[np.ndarray]) – Graph-level labels of the configuration. Shape: [n_graph_labels, 1]

  • weight (Optional[float]) – Weight of the configuration. Shape: []

  • system (Optional[np.ndarray]) – Indices of the system atoms. Shape: [n_system_atoms]

  • environment (Optional[np.ndarray]) – Indices of the environment atoms. Shape: [n_environment_atoms]

  • subsystem (Optional[np.ndarray]) – Indices of the subsystem atoms for long-range interactions. Shape: [n_subsystem_atoms]

__init__(atomic_numbers: ndarray, positions: ndarray, cell: ndarray, pbc: tuple | None, node_labels: ndarray | None, graph_labels: ndarray | None, weight: float | None = 1.0, system: ndarray | None = None, environment: ndarray | None = None, subsystem: ndarray | None = None) → None

Methods

__init__(atomic_numbers, positions, cell, ...)

Attributes

environment

subsystem

system

weight

atomic_numbers

positions

cell

pbc

node_labels

graph_labels