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 type yielded by amd.CifReader and amd.CSDReader. A PeriodicSet can be passed as the first argument to amd.AMD() or amd.PDD() to calculate its invariants.

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

Bases: object

A periodic set is a collection of points (motif) which periodically repeats according to a lattice (unit cell), often representing a crystal.

PeriodicSet s are returned by the readers in the io module. They can be passed to amd.AMD() or amd.PDD() to calculate their invariants.

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 amd.cellpar_to_cell to convert 6 cell parameters to an orthogonal square matrix.

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

  • asym_unit (numpy.ndarray, optional) – Indices for the asymmetric unit, pointing to the motif. Used in calculating AMD and PDD.

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

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

property ndim: int
static cubic(scale: float = 1.0, dims: int = 3) → amd.periodicset.PeriodicSet

Returns a PeriodicSet representing a cubic lattice.

static hexagonal(scale: float = 1.0, dims: int = 3) → amd.periodicset.PeriodicSet

Return a PeriodicSet representing a hexagonal lattice. Dimensions 2 and 3 only.