DefectPairList

class DefectPairList(substitutional_defect, native_defect, cutoff_distances, charge_states=None, processes_per_defect=None, processes_per_task=None, processes_per_displacement=None, resume=None)

A class which describes the list of possible pair defects in a material.

Parameters:
  • substitutional_defect (SubstitutionalList) – List substitutional defects that will constitute the first defect in the pair. The list does not require being updated (by using update()). The main objective of pairs is to simulate impurity or dopant diffusion driven by native defects. This defect must be the substitutional one and cannot be a native element.
  • native_defect (VacancyList | SplitInterstitialList | InterstitialList) – List of vacancies or interstitials that will constitute the second defect in the pair and will be responsible for paired diffusion. If interstitial must be a native element. The list does not require being updated (by using update()).
  • cutoff_distances (tuple of two PhysicalQuantity of type length.) – Minimum and maximum distance between the specified defects to be considered valid. Pairs where any point defect is at a distance not in between these specified distances to the other point defect in the pair will be considered to just be 2 isolated point defects, and will be discarded. For the case of SplitInterstitialList, it checks minimum distance to both atoms of the dumbbell, and maximum distance to the center of the dumbbell.
  • charge_states (int | sequence of int) – The charge states to calculate for each defect pair.
    Default: 0
  • processes_per_defect (int) – The number of processes assigned to calculating a single defect.
    Default: All available processes.
  • processes_per_task (int) – The number of processes assigned to each task. The number of processes per defect divided by the processes per task determines the number of tasks to be computed in parallel for each defect. If more than 1 task is computed in parallel, 1 processor will be devoted to synchronize all tasks, so that in practice the number of parallel tasks will be (processes_per_defect - 1) / processes_per_task
    Default: Each charge will be run in parallel, i.e.: processes_per_task = (processes_per_defect - 1) / len(charge_states)
  • processes_per_displacement (int) – The number of processes assigned to calculating a single displacement in a dynamical matrix (used for phonon calculations).
    Default: Use all available processes.
  • resume (bool) – Whether reruning the simulation will resume non converged results
    Default: True
chargeStates()
Returns:The charge states to calculate for each defect.
Return type:list of int
cutoffDistances()
Returns:The cut off distances
Return type:tuple of two PhysicalQuantity of type length
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 out. After filtering, the wyckoff indices with no defects will be erased.

Parameters:
  • 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
Returns:

A filtered defect list.

Return type:

rtype:VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList

filterByEquivalentEnvironments(num_groups, r_cut=PhysicalQuantity(6.0, Ang))
Parameters:
  • num_groups – The number of unique defect types. This will cause defects to be grouped into num_groups types where the defects in each group are the most similar to one another.
  • r_cut (PhysicalQuantity of type length) – The cut-off distance for the local atomic environment. Atoms outside of this radius are not included when comparing/grouping defects together.
    Default: 6.0 * Angstrom
Returns:

A filtered defect list.

Return type:

VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList

filterByFormationEnergy(charge=0, minimum_energy=None, maximum_energy=None)

Method for filtering defects by formation energy. This method only works on defects that are updated. Given a minimum and maximum energy, only defects between those values will be kept, the rest being discarded. A value of None means that the particular limit is not applied.

Parameters:
  • charge (int) – Charge state for the filtering.
    Default: 0
  • minimum_energy (PhysicalQuantity of type energy) – Defects with energies lower than this will be discarded.
  • maximum_energy (PhysicalQuantity of type energy) – Defects with energies higher than this will be discarded.
Returns:

a filtered defect list.

Return type:

VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList

filterByInterface(interface_index, distance)
Parameters:
  • interface_index (int) – The index of the interface to filter by.
  • distance (PhysicalQuantity of type length) – The distance from the interfaces to include.
Returns:

A filtered defect list.

Return type:

VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList

filterByLatticeSpecies(element_list)

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:
rtype:VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList
filterByLayer(layer_index, distance=None)
Parameters:
  • layer_index (int) – The index of the layer to filter by.
  • distance (PhysicalQuantity of type length) – The distance from the interfaces to exclude.
    Default: 0.0*Angstrom
Returns:

A filtered defect list.

Return type:

VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList

filterByMostStable(how_many, charge=0)

Method for filtering the most stable (by formation energy) converged defects.

Parameters:
  • how_many (int) – Maximum number of filtered defects.
  • charge (int) – Charge state for the formation energies
    Default: 0
Returns:

a filtered defect list.

Return type:

VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList

filterByWyckoffIndex(wyckoff_indices)

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:VacancyList | SubstitutionalList | InterstitialList SplitInterstitialList | DefectPairList | DefectClusterList
materialSpecifications()
Returns:The descriptor of a bulk material, plus the information needed to perform the calculations.
Return type:MaterialSpecifications
nativeDefectList()
Returns:The list of vacancies or interstitials that will constitute the second defect in the pair.
Return type:VacancyList | SplitInterstitialList | InterstitialList
nlprint(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)

Prints a summary of the wyckoff indices created and equivalent defects

pointDefects()
Returns:The list of inequivalent point defects.
Return type:Vacancy | Substitutional | Interstitial | DefectCluster | SplitInterstitial
processesPerDefect()
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
processesPerDisplacement()
Returns:Number of processes assigned per displacement in dynamical matrix calculations.
Return type:int
processesPerItem()
Returns:Processes per item
Return type:int
processesPerTask()
Returns:Number of processes assigned per task and per defect.
Return type:int | None
results(discard_faulty=True)

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
resume()
Returns:Whether running it again will resume unconverged simulations
Return type:bool
substitutionalDefectList()
Returns:The list of substitutional defects which constitute the first defect in the pair.
Return type:SubstitutionalList
update()

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

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

Directory name

DefectPairList creates directory names with a structure

pair/compact/constituents/sites/hash

For instance,

pair/CV/C^Si_0+Si_0/001+000/8510ca94d3b960045791f06a3741606f
  • All pair defects are stored in a directory called pair.
  • compact shows the usual cluster notation in TCAD, with I or V meaning interstitial/vacancy and the rest denoting the non-native defect.
  • constituent shows the names of the two constituent defects.
  • sites contains the indices for the two sites occupied by the constituent defects.
  • hash is a hash string represents 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 *
from SentaurusMaterialsWorkbench.MaterialSpecifications.TestMaterials import SiGe_64_tersoff

reference = SiGe_64_tersoff
vacancies = VacancyList(reference)
substitutionals = SubstitutionalList(reference, Germanium)
pairs = DefectPairList(substitutionals, vacancies, (2.2 * Angstrom, 3.2 * Angstrom))

nlprint(pairs)
pairs.update()

nlsave('defects.hdf5', vacancies)
nlsave('defects.hdf5', substitutionals)
nlsave('defects.hdf5', pairs)

pairlist_example.py