amd.periodicset module

Implements the PeriodicSet class representing a periodic set, defined by a motif and unit cell. This models a crystal with a point at the center of each atom.

This is the object type yielded by the readers io.CifReader and io.CSDReader. The PeriodicSet can be passed as the first argument to calculate.AMD() or calculate.PDD() to calculate its invariants.

class amd.periodicset.PeriodicSet(motif: numpy.ndarray, cell: numpy.ndarray, name: Optional[str] = None, asymmetric_unit: Optional[numpy.ndarray] = None, wyckoff_multiplicities: Optional[numpy.ndarray] = None, types: Optional[numpy.ndarray] = None)

Bases: object

A periodic set is the mathematical representation of a crystal by putting a single point in the center of every atom. It is defined by a basis (unit cell) and collection of points (motif) which repeats according to the basis.

PeriodicSet s are returned by the readers in the io module. Instances of this object can be passed to calculate.AMD() or calculate.PDD() to calculate the invariant.

Parameters

  • motif (numpy.ndarray) – Cartesian (orthogonal) coordinates of the motif, shape (no points, dims).

  • cell (numpy.ndarray) – Cartesian (orthogonal) square array representing the unit cell, shape (dims, dims). Use utils.cellpar_to_cell() to convert 6 cell parameters to an orthogonal square matrix.

  • name (str, optional) – Name of the periodic set.

  • asymmetric_unit (numpy.ndarray, optional) – Indices for the asymmetric unit, pointing to the motif.

  • wyckoff_multiplicities (numpy.ndarray, optional) – Wyckoff multiplicities of each atom in the asymmetric unit (number of unique sites generated under all symmetries).

  • types (numpy.ndarray, optional) – Array of atomic numbers of motif points.