InterstitialGenerator

class InterstitialGenerator(host_configuration, interstitial_element, interstitial_types=None, symmetry_tolerance=None, group_distance=None)

A class which describes the possible interstitial defects for a given host material.

Parameters:

  • host_configuration (BulkConfiguration) – The host configuration.

  • interstitial_element (PeriodicTableElement) – The element to add as interstitial defect.

  • interstitial_types (VoronoiVertices | VoronoiFaces | VoronoiRidges | sequence of VoronoiVertices, VoronoiFaces, VoronoiRidges) – How the interstitials in the material should be automatically created.
    Default: VoronoiVertices.

  • 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.

filterByDefectGenerators(defect_generators)

Method for filtering a defect generator by keeping the defects that are in one or more other defect generators.

Parameters:

defect_generators (list of BaseDefectGenerator) – The list of defect generators containing the defects to keep after filtering.

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

filterByDistinctConfigurations(top_n_configurations)

Method for selecting a number of distinct unique defects using the MTP structural descriptor.

Parameters:

top_n_configurations (int) – Number of most distinct configurations.

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

filterByLatticeSpecies(element_list)

This method is not implemented

filterByPointDefect(point_defects, keep_defects=True)

Method for filtering the generator of unique point defects by selecting a specific defects.

Parameters:

  • point_defects (Sequence of BasePointDefect) – The sequence of point defects to filter.

  • keep_defects (bool) – Whether or not the given defects are to be kept and all other removed (True) or removed from the generator and all other defect kept (False).
    Default: True

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

filterByPositionInZSlices(start=None, end=None, resolution=None, in_plane_position=None)

Select defects along the Z-axis of the cell. This method is intended to be used for configurations that are anisotropic along one direction, such as interfaces or surfaces.

Parameters:

  • start (PhysicalQuantity of type length) – The start of the position interval.
    Default: 0 * Angstrom.

  • end (PhysicalQuantity of type length) – The end of the position interval.
    Default: length of the cell in z direction.

  • resolution (PhysicalQuantity of type length) – The size of each slice of the interface profile.
    Default: 2.0 * Angstrom

  • in_plane_position (Sequence (2) of type float) – The selected defect in each slice is as close as possible to this fractional coordinate. Mutually exclusive with parameter select_distinct.
    Default: [0.5, 0.5]

  • select_distinct (bool) – Select the most distinct defects per slice. This can be used to sample a diverse configuration space with a minimal number of defects. Mutually exclusive with parameter in_plane_position.
    Default: False

  • defects_per_slice (int) – The number of defects to select per slice. This parameter is only used together with the parameter select_distinct.
    Default: 1

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

filterBySimilarityInZSlices(start=None, end=None, resolution=None, defects_per_slice=None)

Select defects along the Z-axis of the cell. This method is intended to be used for configurations that are anisotropic along one direction, such as interfaces or surfaces.

Parameters:

  • start (PhysicalQuantity of type length) – The start of the position interval.
    Default: 0 * Angstrom.

  • end (PhysicalQuantity of type length) – The end of the position interval.
    Default: length of the cell in z direction.

  • resolution (PhysicalQuantity of type length) – The size of each slice of the interface profile.
    Default: 2.0 * Angstrom

  • defects_per_slice (int) – The number of defects to select per slice. This parameter is only used together with the parameter select_distinct.
    Default: 1

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

filterBySphere(center, radius)

Method for filtering unique defects by their position in a sphere.

Parameters:

  • center (PhysicalQuantity of type position) – The center of the sphere in Cartesian coordinates.

  • radius (PhysicalQuantity of type length) – The radius of the sphere.

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

filterBySymmetryIndex(symmetry_indices)

Method for filtering the list of unique point defects by selecting specific symmetry indices.

Parameters:

symmetry_indices (int | list of int) – The list of symmetry indices to keep after filtering.

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

filterByZPositionInterval(start=None, end=None)

Method for selecting unique defects by their position in an interval of the z axis. Note: The

Parameters:

  • start (PhysicalQuantity of type length) – The start of the position interval.
    Default: 0 * Angstrom.

  • end (PhysicalQuantity of type length) – The end of the position interval.
    Default: length of the cell in z direction.

Returns:

A filtered defect generator.

Return type:

VacancyGenerator | SubstitutionalGenerator | InterstitialGenerator SplitInterstitialGenerator

groupDistance()
Returns:

The tolerance to be used when determining groups of defects.

Return type:

PhysicalQuantity of type length

hostConfiguration()
Returns:

The host configuration.

Return type:

BulkConfiguration

indices()
Returns:

The defect indices for the current defect generator.

Return type:

list of int

interstitialElement()
Returns:

The element to add as interstitial defect.

Return type:

PeriodicTableElement

interstitialTypes()
Returns:

How the interstitials in the material should be automatically created.

Return type:

VoronoiVertices | VoronoiFaces | VoronoiRidges

pointDefects()
Returns:

The list of unique point defects.

Return type:

Vacancy | Substitutional | Interstitial | DefectCluster | SplitInterstitial

symmetryTolerance()
Returns:

The symmetry tolerance.

Return type:

PhysicalQuantity of type length

uniqueDefects()
Returns:

The list of symmetrically unique point defects with their names and symmetry indices, ordered by increasing index.

Return type:

list of NamedPointDefect

uniqueString()

Return a unique string representing the state of the object.

Notes

The InterstitialGenerator object generates the symmetrically unique interstitial defects for a given host material. Possible sites for adding interstitial atoms are determined by calculating the Voronoi volume of each atom. Interstitial atoms can then be added at the vertices, the faces, or between the vertices of the Voronoi volume. Using symmetry analysis, these points are then reduced to a symetrically unique set of points. The InterstitialGenerator object is derived from the BaseDefectGenerator object, and thus contains the common methods from that object.

To create a InterstitialGenerator object, a specific host configuration must be given along with the interstitial element. Optionally, the kinds of Voronoi positions can also be specified. This is done using the argument interstitial_types``argument which can take one or a list of the ``VoronoiFaces, VoronoiVertices or VoronoiRidges keywords. Once the generator is created filters can be added so that only only a desired subset of defects can be generated.

The unique defects can be returned with the uniqueDefects method as NamedPointDefect objects, which can be used as input for a ChargedPointDefectConfiguration object. The defects and generators can also be given to a Defects object to create the basic defect configurations.