graph2mat.OrbitalConfiguration

class graph2mat.OrbitalConfiguration(point_types: ndarray, positions: ndarray, basis: Atoms, cell: ndarray | None = None, pbc: tuple | None = None, matrix: OrbitalMatrix | None = None, weight: float = 1.0, config_type: str | None = 'Default', metadata: Dict[str, Any] | None = None, _cls_format: str = 'orbitalconfiguration')

Bases: BasisConfiguration

Stores a distribution of atoms in space, with associated orbitals.

Optionally, it can also store an associated matrix.

In a typical case, your configurations will contain the matrix as a label for training, validating or testing. When doing inference, the configurations will not have an associated matrix, since the matrix is what you are trying to calculate.

This is a version of BasisConfiguration for atomic systems, where points are atoms.

Parameters:

• point_types (numpy.ndarray) – Shape (n_points,). The type of each point. Each type can be either a string or an integer, and it should be the type key of a PointBasis object in the basis list.

• positions (numpy.ndarray) – Shape (n_points, 3). The positions of each point in cartesian coordinates.

• basis (sisl.Atoms) – Atoms that are (possibly) present in the system.

• cell (numpy.ndarray | None) – Shape (3, 3). The cell vectors that delimit the system, in cartesian coordinates.

• pbc (tuple | None) – Shape (3,). Whether the system is periodic in each cell direction.

• matrix (graph2mat.core.data.matrices.physics.orbital_matrix.OrbitalMatrix | None) –

  The matrix associated to the configuration.

  It can be a numpy or scipy sparse matrix, which will be converted to a BasisMatrix object.

• weight (float) – The weight of the configuration in the loss.

• config_type (str | None) – A string that indicates the type of configuration.

• metadata (Dict[str, Any] | None) – A dictionary with additional metadata related to the configuration.

Methods

Attributes

atom_types	Alias for point_types.
atoms	Alias for basis.
cell	Shape (3, 3).
config_type	A string that indicates the type of configuration.
matrix	The matrix associated to the configuration.
metadata	A dictionary with additional metadata related to the configuration.
pbc	Shape (3,).
weight	The weight of the configuration in the loss.
point_types	Shape (n_points,).
positions	Shape (n_points, 3).
basis	Atoms that are (possibly) present in the system.

property atom_types: ndarray

Alias for point_types.

property atoms: Atoms

Alias for basis.

basis: Atoms

Atoms that are (possibly) present in the system.

cell: ndarray | None = None

Shape (3, 3). The cell vectors that delimit the system, in cartesian coordinates.

config_type: str | None = 'Default'

A string that indicates the type of configuration.

matrix: OrbitalMatrix | None = None

The matrix associated to the configuration.

metadata: Dict[str, Any] | None = None

A dictionary with additional metadata related to the configuration.

pbc: tuple | None = None

Shape (3,). Whether the system is periodic in each cell direction.

point_types: ndarray

Shape (n_points,). The type of each point. Each type can be either a string or an integer, and it should be the type key of a PointBasis object in the basis list.

positions: ndarray

Shape (n_points, 3). The positions of each point in cartesian coordinates.

weight: float = 1.0

The weight of the configuration in the loss.