amd.periodicset module

Implements the PeriodicSet class representing a periodic set, defined by a motif (collection of points) and unit cell (basis). 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[Any, numpy.dtype[numpy.floating]], cell: numpy.ndarray[Any, numpy.dtype[numpy.floating]], name: Optional[str] = None, asym_unit: Optional[numpy.ndarray[Any, numpy.dtype[numpy.integer]]] = None, multiplicities: Optional[numpy.ndarray[Any, numpy.dtype[numpy.floating]]] = None, types: Optional[numpy.ndarray[Any, numpy.dtype[numpy.integer]]] = 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 (amd.CifReader and amd.CSDReader). They can be passed to amd.AMD() or amd.PDD() to calculate their invariants.

Parameters

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

  • cell (numpy.ndarray) – Square array representing the unit cell in Cartesian (orthogonal) coordinates, shape (dims, dims). Use amd.cellpar_to_cell to convert a vector of 6 conventional cell parameters a,b,c,α,β,γ to a 3x3 matrix.

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

  • asym_unit (numpy.ndarray, optional) – Indices of motif points constituting an asymmetric unit, so that motif[asym_unit] are points in an asymmetric unit. Used in AMD/PDD calculation.

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

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

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

Return 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. Implemented for dimensions 2 and 3 only.