DefectComplex

DefectComplex#

class DefectComplex(defects, bulk_structure=None, charge=None, multiplicity=None, bulk_volume=None, label=None)[source]#

Bases: MSONable

Class to describe defect complexes

Parameters:

defects (list) – List of Defect objects.
bulk_structure (Structure) – Pymatgen Structure of the bulk material.
charge (int or float) – Charge of the defect.
multiplicity (int) – Multiplicity of the defect.

Methods

`as_dict`	A JSON serializable dict representation of an object.
`from_dict`	Reconstruct an MSONable object from a dict.
`from_string`	Get DefectComplex object from string.
`generate_defect_structure`	Generate a structure containing the defect starting from a bulk structure.
`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_charge`	Sets the charge of the defect.
`set_label`	Sets the label of the defect
`set_multiplicity`	Sets the charge 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`	Composition of defect structure.
`defect_names`	List of names of the single defects.
`defect_structure`	Structure containing the defect.
`defects`	List of single defects consituting the complex.
`delta_atoms`	Dictionary with Element as keys and particle difference between defect structure and bulk structure as values.
`label`	Defect label.
`multiplicity`	Multiplicity of a defect site within the structure
`name`	Name of the defect.
`site_concentration_in_cm3`	Site concentration (multiplicity/volume) expressed in cm^-3.
`sites`	Site objects of single defects.
`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 kroger 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.

property defect_composition#: Composition of defect structure.

property defect_names#: List of names of the single defects.

property defect_structure#: Structure containing the defect.

property defects#: List of single defects consituting the complex.

property delta_atoms#: Dictionary with Element as keys and particle difference between defect structure and bulk structure as values.

static from_string(string, **kwargs)[source]#: Get DefectComplex object from string.

generate_defect_structure(bulk_structure=None)[source]#: Generate a structure containing the defect starting from a bulk structure. If not provided self.bulk_structure is used.

get_multiplicity()[source]#

property label#: Defect label.

property multiplicity#: Multiplicity of a defect site within the structure

property name#: Name of the defect. Behaves like a string with additional attributes.

set_charge(new_charge)[source]#: Sets the charge of the defect.

set_label(new_label)[source]#: Sets the label of the defect

set_multiplicity(new_multiplicity)[source]#: Sets the charge of the defect.

property site_concentration_in_cm3#: Site concentration (multiplicity/volume) expressed in cm^-3.

property sites#: Site objects of single defects.

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 kroger and vink notation.

property type#: Defect type.