DefectsParameters¶

class DefectsParameters(defect_type=None, defect_element=None, include_voronoi_faces=None, include_voronoi_vertices=None, include_voronoi_ridges=None, miller_indices=None, split_distance=None, fractional_position=None, symmetry_tolerance=None, group_distance=None, filter_by_z_position=None, z_start=None, z_end=None, filter_by_distinct_configurations=None, top_n_configurations=None, filter_by_lattice_sites=None, filter_elements=None)¶

A class which describes the list of defects.

Parameters:

defect_type (int) – The type of defect.
Default: 0 (DefectType.SUBSTITUTIONAL)
defect_element (PeriodicTableElement) – The element added as an interstitial or substitutional defect.
include_voronoi_faces (bool) – Generate defects using Voronoi faces.
include_voronoi_vertices (bool) – Generate defects using Voronoi vertices.
include_voronoi_ridges (bool) – Generate defects using Voronoi ridges.
miller_indices (tuple) – The Miller indices that define the direction of split interstitials.
split_distance (PhysicalQuantity of type length) – The distance form the lattice position of split interstitial atoms.
fractional_position (sequence (size 3) of float) – The position at which to insert the interstitial atom, given in fractional coordinates of the bulk unit cell.
symmetry_tolerance (PhysicalQuantity of type length) – The tolerance to be used when determining the symmetries.
Default: 0.1 * Angstrom.
group_distance (PhysicalQuantity of type length) – The tolerance to be used when determining groups of defects.
Default: 0.1 * Angstrom.
filter_by_z_position (bool) – Activate the filtering by Z position.
z_start (PhysicalQuantity of type length) – The start of the position interval.
z_end (PhysicalQuantity of type length) – The end of the position interval.
filter_by_distinct_configurations (bool) – Activate the filtering using the MTP structural descriptor.
top_n_configurations (int) – Number of most distinct configurations.
filter_by_lattice_sites (bool) – Activate the filtering by lattice site elements.
filter_elements (iterable) – The set of lattice elements that should be replaced.

defectGenerator(host_configuration)¶

The defect generator

Parameters:: host_configuration (BulkConfiguration) – The host configuration.
Returns:: Returns a generator of the defects stored in the collection.
Return type:: BaseDefectGenerator based

uniqueDefects(host_configuration)¶

Return all symmetrically unique defects

Parameters:: host_configuration (BulkConfiguration) – The host configuration.
Returns:: Returns a list of the defects stored in the collection.
Return type:: list of NamedPointDefect

uniqueString()¶: Return a unique string representing the state of the object.

classmethod voronoiTypes(include_voronoi_vertices, include_voronoi_faces, include_voronoi_ridges)¶

Returns:: A list of the types of Voronoi points to use to generate interstitial defects.
Return type:: list of VoronoiVertices, VoronoiFaces and VoronoiRidges

Notes¶

The DefectsParameters object enables the creation of an abstract defect definition. While defect generators such as VacancyGenerator or InterstitialGenerator require a specific pristine material, the DefectsParameters object only stores the parameters required to define a kind of point defect. This can be useful when applying the same kinds of defects across a number of configurations, such as when studying amorphous materials or materials with the same lattice.

The first required argument is the defect type. The type is represented by an integer as shown in the table below. Once the parameters are defined, the defect generator for a specific configuration can be obtained using the defectGenerator method. The unique defects for a given configuration can also be directly accessed using the uniqueDefects method.

Table 16 Generator types.¶
Argument	Defect Type
0	SubstitutionalGenerator
1	VacancyGenerator
2	InterstitialGenerator
3	SplitInterstitialGenerator
4	CustomInterstitialGenerator