class SubstitutionalList(material_specifications, substitutional_element, charge_states=None, processes_per_defect=None)

A class which describes the list of possible substitutional defects for a given host material.

  • material_specifications (MaterialSpecifications) – A descriptor of a bulk material, plus the information needed to perform the calculations.
  • substitutional_element (PeriodicTableElement) – The element to set as substitutional defect.
  • charge_states (int | sequence of int) – The charge states to calculate for each defect.
    Default: 0
  • processes_per_defect (int) – The number of processes assigned to calculating a single defect.
    Default: All available processes.
Returns:The charge states to calculate for each defect.
Return type:list of int
filterByDistance(distance, cartesian_coordinates=None, fractional_coordinates=None)

Method for filtering defects by distance. Given a origin in the supercell and a distance, all defects within a bigger distance will be filtered. After filtering, the wyckoff indices with no defects will be erased.

  • distance (PhysicalQuantity of type length) – Maximum distance
  • cartesian_coordinates (sequence (size 3) of PhysicalQuantity of type length) – The position of the reference to measure distances, given in absolute coordinates. This option is mutually exclusive to fractional_coordinates.
    Default: None
  • fractional_coordinates (sequence (size 3) of float) – The position of the reference to measure distances, given in fractional coordinates of the bulk unit cell. This option is mutually exclusive to cartesian_coordinates.
    Default: None

A filtered defect list.

Return type:

VacancyList | SubstitutionalList | SplitInterstitialList


Method for selecting inequivalent defects by element name. Valid only for defect types that are associated with a lattice site, e. g. Vacancies, but not Interstitials.

Parameters:element_list (PeriodicTableElement | list of PeriodicTableElement) – List of elements to keep after filtering.
Returns:A filtered defect list.
Return type:VacancyList | SubstitutionalList | SplitInterstitialList

Method for filtering the list of inequivalent point defects by selecting specific Wyckoff indices.

Parameters:wyckoff_indices (int | list of int) – The list of Wyckoff indices to keep after filtering.
Returns:A filtered defect list.
Return type:The same type as the unfiltered list.
Returns:The descriptor of a bulk material, plus the information needed to perform the calculations.
Return type:MaterialSpecifications
nlprint(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)

Prints a summary of the wyckoff indices created and equivalent defects

Returns:The list of inequivalent point defects.
Return type:Vacancy | Substitutional | Interstitial | DefectCluster
Returns:The number of processes to be assigned to calculating each defect. If None, all available processes should perform the calculation for each defect collaboratively.
Return type:int | None

Method for retrieving calculated defect studies.

Parameters:discard_faulty (bool) – Flag to determine whether faulty defect studies should be discarded.
Default: True
Returns:The list of defect studies stored on the object.
Return type:list of HarmonicChargedPointDefect
Returns:The substitutional element.
Return type:PeriodicTableElement

Update all the harmonic charged point defect studies contained in the defect list.

Returns:The Wyckoff indices for the current defect list.
Return type:list of int

Directory name

SubstitutionalList creates directory names with a structure


For instance


for a carbon substitutional replacing a Silicon site, with Wyckoff index 0, at the site 4.

  • All substitutionals are stored in a directory call substitutional
  • The first element represents the substitutional element.
  • The second element shows the element being replaced at the lattice site where the substitutional sits.
  • wyckoff is the Wyckoff number for the defect, different for all inequivalent positions..
  • site contains the particular lattice site occupied by the defect. Different for all equivalent and inequivalent positions.
  • A hash string representing the material specifications.

Usage example

The following shows an example of use. It assumes there is an already defined Si_64Ge_tersoff specification in MaterialSpecifications that support Ge as a substitutional element.

from SMW import *

reference = MaterialSpecificationsDatabase.SiGe_64_tersoff
substitutionals = SubstitutionalList(reference, Germanium)


nlsave('defects.hdf5', substitutionals)