Substitution

class Substitution(specie=None, bulk_specie=None, defect_site=None, bulk_structure=None, charge=None, multiplicity=None, bulk_volume=None, label=None, site_in_bulk=None)

Bases: Defect

Subclass of Defect for substitutional defects.

Parameters:

site_in_bulk (PeriodicSite) – Original Site in bulk structure were substitution took place.

Methods

as_dict	A JSON serializable dict representation of an object.
from_dict	Reconstruct an MSONable object from a dict.
from_string
generate_defect_structure	Generate a structure containing the defect starting from a bulk structure.
get_multiplicity	Get multiplicity of the defect in the structure
get_site_in_bulk
load	Load an instance from a JSON file written by save().
save	Serialize the instance to JSON on disk, pickling fields if needed.
set_bulk_volume	Sets the volume of bulk cell
set_charge	Sets the charge of the defect.
set_label	Sets the label of the defect
set_multiplicity	Sets the Multiplicity of the defect.
to_json	Returns a json string representation of the MSONable object.
unsafe_hash	Return a hash of the current object.
validate_monty_v1	Pydantic validator with correct signature for pydantic v1.x.
validate_monty_v2	Pydantic validator with correct signature for pydantic v2.x.

Attributes

REDIRECT
bulk_specie
bulk_structure	Structure without defects.
bulk_volume	Volume of bulk cell in A°^3.
charge	Charge of the defect.
defect_composition	Composition of the defect.
defect_site_index	Index of the defect site in the bulk structure.
defect_structure	Structure of the defect.
defects
delta_atoms	Dictionary with element symbol as keys and difference in particle number between defect and bulk structure as values
label	Defect label.
multiplicity	Multiplicity of a defect site within the structure
name	Name for this defect.
site	Defect position as a Site object
site_concentration_in_cm3	Site concentration (multiplicity/volume) expressed in cm^-3.
site_in_bulk
specie	Defect species.
symbol	Latex formatted name of the defect.
symbol_with_charge	Name in latex format with charge written as a number.
symbol_with_charge_kv	Name in latex format with charge written with Kröger and Vink notation.
type	Defect type.

property bulk_specie

property defect_composition

Composition of the defect.

property defect_site_index

Index of the defect site in the bulk structure.

property delta_atoms

Dictionary with element symbol as keys and difference in particle number between defect and bulk structure as values

generate_defect_structure(bulk_structure=None, defect_site_index=None)

Generate a structure containing the defect starting from a bulk structure.

Parameters:

• bulk_structure (Structure) – Bulk Structure. If not provided self.bulk_structure is used.

• defect_site_index (Structure) – Index of the defect site in the bulk structure. If not provided self.defect_site_index is used.

Returns:

structure – Structure containing the defect.

Return type:

Structure

get_multiplicity(**kwargs)

Get multiplicity of the defect in the structure

Parameters:

**kwargs (dict) – Kwargs to pass to SpacegroupAnalyzer (“symprec”, “angle_tolerance”)

get_site_in_bulk()

property name

Name for this defect.

property site_in_bulk

property symbol

Latex formatted name of the defect.