Defect

class Defect(specie=None, defect_site=None, bulk_structure=None, charge=None, multiplicity=None, bulk_volume=None, label=None)

Bases: MSONable

Abstract class for a single point defect

Base class for defect objets.

Parameters:

• specie (str) – Defect element symbol.

• defect_site (Site) – Pymatgen Site object of the defect.

• bulk_structure (Structure) – Pymatgen Structure without defects.

• charge (int or float) – Charge of the defect.

• multiplicity (int) – Multiplicity of defect within the simulation cell.

• bulk_volume (float) – Volume of bulk cell in A°^3.

• label (str) – Defect label.

Methods

as_dict	A JSON serializable dict representation of an object.
from_dict	Reconstruct an MSONable object from a dict.
from_string
get_multiplicity
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_structure	Structure without defects.
bulk_volume	Volume of bulk cell in A°^3.
charge	Charge of the defect.
defect_composition	Defect composition as a Composition object
defect_site_index	Index of the defect site in the structure
defect_structure	Structure of the defect.
defects
delta_atoms	Dictionary with defect 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 of the defect.
site	Defect position as a Site object
site_concentration_in_cm3	Site concentration (multiplicity/volume) expressed in cm^-3.
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_structure

Structure without defects.

property bulk_volume

Volume of bulk cell in A°^3.

property charge

Charge of the defect.

abstract property defect_composition

Defect composition as a Composition object

abstract property defect_site_index

Index of the defect site in the structure

property defect_structure

Structure of the defect.

property defects

property delta_atoms

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

static from_string(string, **kwargs)

abstractmethod get_multiplicity()

property label

Defect label.

property multiplicity

Multiplicity of a defect site within the structure

abstract property name

Name of the defect.

set_bulk_volume(new_volume)

Sets the volume of bulk cell

set_charge(new_charge=0.0)

Sets the charge of the defect.

set_label(new_label)

Sets the label of the defect

set_multiplicity(new_multiplicity=None)

Sets the Multiplicity of the defect. If new_multiplicity is not provided it is determined with self.get_multiplicity

property site

Defect position as a Site object

property site_concentration_in_cm3

Site concentration (multiplicity/volume) expressed in cm^-3.

property specie

Defect species.

property symbol

Latex formatted name of the defect.

property symbol_with_charge

Name in latex format with charge written as a number.

property symbol_with_charge_kv

Name in latex format with charge written with Kröger and Vink notation.

property type

Defect type.