topo_metrics.io.cgd#

Functions#

parse_cgd(→ tuple[pymatgen.core.lattice.Lattice, ...)

Parses a CGD file and extracts lattice, atoms, and edges.

process_neighbour_list(→ numpy.typing.NDArray[numpy.int_])

Processes edges and determines node connectivity.

Module Contents#

topo_metrics.io.cgd.parse_cgd(filename: pathlib.Path | str) → tuple[pymatgen.core.lattice.Lattice, list[str], numpy.typing.NDArray[numpy.floating] | None, list[list[Any]]][source]#

Parses a CGD file and extracts lattice, atoms, and edges.

Parameters:

filename – The path to the CGD file.

Returns:

  • - lattice (The lattice of the network.)

  • - atom_labels (The labels of the atoms.)

  • - all_coords (The fractional coordinates of the atoms.)

  • - edges (The list of edges in the network.)

topo_metrics.io.cgd.process_neighbour_list(edges: list[list[Any]], atom_frac_coords: numpy.typing.NDArray[numpy.floating] | None, atom_labels: list[str]) → numpy.typing.NDArray[numpy.int_][source]#

Processes edges and determines node connectivity.

Parameters:

  • edges – The list of edges in the network.

  • atom_frac_coords – The fractional coordinates of the atoms.

  • atom_labels – The labels of the atoms.

Returns:

  • The neighbour list of the network, where each row corresponds to a pair of

  • connected nodes and the applied image shift to the second node.