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 theio
module. Instances of this object can be passed tocalculate.AMD()
orcalculate.PDD()
.- copy()
Return copy of the PeriodicSet.
- astype(dtype)
Returns copy of the
PeriodicSet
with.motif
and.cell
casted todtype
.