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.
- 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.
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:
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:
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:
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:
Returns: The list of defect studies stored on the object. Return type: list of
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
- material_specifications (
SubstitutionalList creates directory names with a structure
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.
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) nlprint(substitutionals) substitutionals.update() nlsave('defects.hdf5', substitutionals)