graph2mat.AtomicTableWithEdges

class graph2mat.AtomicTableWithEdges(atoms: Sequence[Atom])[source]

Bases: BasisTableWithEdges

Variant of BasisTableWithEdges for the case in which points are atoms.

This class mostly just adds a few aliases to the methods of BasisTableWithEdges by replacing “point” to “atom” in the method names. It also provides some methods to create a table from atomic basis.

See also

BasisTableWithEdges: The class that actually does the work.

Methods

`atom_block_pointer`(atom_types)
`atom_type_to_edge_type`(atom_type)
`from_basis_dir`(basis_dir[, basis_ext, ...])	Generates a table from a directory containing basis files.
`from_basis_glob`(basis_glob[, no_basis_atoms])	Generates a table from basis files that match a glob pattern.

Attributes

`atom_block_shape`
`atom_block_size`
`atomic_DM`
`zs`
`atoms`
`file_names`	If the basis was read from files, this might store the names of the files.
`file_contents`	If the basis was read from files, this might store the contents of the files.
`basis`	List of `PointBasis` objects that this table knows about.
`basis_convention`	The spherical harmonics convention used for the basis (same for all `PointBasis`).
`types`	Type identifier for each point basis.
`point_matrix`	The matrix that is constant for each type of point.
`edge_type`	The edge type for each pair of point types.
`R`	Shape (n_point_types,).
`basis_size`	Shape (n_point_types,).
`point_block_shape`	Shape (n_point_types, 2).
`point_block_size`	Shape (n_point_types,).
`edge_block_shape`	Shape (n_edge_types, 2).
`edge_block_size`	Shape (n_edge_types,).
`edge_type_to_point_types`	Shape (n_edge_types, 2).
`change_of_basis`	Shape (3, 3).
`change_of_basis_inv`	Shape (3, 3).

atom_block_pointer(atom_types: Sequence[int])[source]

property atom_block_shape

property atom_block_size

atom_type_to_edge_type(atom_type: ndarray)[source]

property atomic_DM

atoms: List[Atom]

file_contents: List[str] | None: If the basis was read from files, this might store the contents of the files. For saving/loading purposes.

file_names: List[str] | None: If the basis was read from files, this might store the names of the files. For saving/loading purposes.

classmethod from_basis_dir(basis_dir: str, basis_ext: str = 'ion.xml', no_basis_atoms: dict | None = None) → AtomicTableWithEdges[source]

Generates a table from a directory containing basis files.

Parameters:

basis_dir – The directory containing the basis files.
basis_ext – The extension of the basis files.

classmethod from_basis_glob(basis_glob: str | Generator, no_basis_atoms: dict | None = None) → AtomicTableWithEdges[source]

Generates a table from basis files that match a glob pattern.

Parameters:: basis_glob – The glob pattern to match the basis files.

property zs