amd.periodicset module

Implements the class PeriodicSet representing a periodic set, defined by a motif and unit cell.

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. They can be written to a file with io.SetWriter which can be read with io.SetReader.

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

Bases: object

A periodic set is the mathematical representation of a crystal by putting a single point in the center of every atom. A periodic set is defined by a basis (unit cell) and collection of points (motif) which repeats according to the basis. Has attributes motif, cell and name (which can be None).

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

copy()

Return copy of the PeriodicSet.

astype(dtype)

Returns copy of the PeriodicSet with .motif and .cell casted to dtype.