defects

defects#

Core defect objects

Classes

`Defect`([specie, defect_site, ...])	Abstract class for a single point defect
`DefectComplex`(defects[, bulk_structure, ...])	Class to describe defect complexes
`Interstitial`([specie, defect_site, ...])	Subclass of Defect for interstitial defects.
`Polaron`([specie, defect_site, ...])	Subclass of Defect for polarons.
`Substitution`([specie, bulk_specie, ...])	Subclass of Defect for substitutional defects.
`Vacancy`([specie, defect_site, ...])	Subclass of Defect for single vacancies.

Functions

`format_legend_with_charge_kv`	Get label in latex format with charge written with Kröger and Vink notation.
`format_legend_with_charge_number`	Get label in latex format with charge written as a number.
`get_defect_from_string`	Get defect object from a string (Defect or DefectComplex).
`get_delta_atoms`	Build delta_atoms dictionary starting from Pymatgen Structure objects.
`get_delta_atoms_from_comp`	Build delta_atoms dictionary starting from Composition objects.

class Defect(specie=None, defect_site=None, bulk_structure=None, charge=None, multiplicity=None, bulk_volume=None, label=None)[source]#

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.

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)[source]#

abstractmethod get_multiplicity()[source]#

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)[source]#: Sets the volume of bulk cell

set_charge(new_charge=0.0)[source]#: Sets the charge of the defect.

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

set_multiplicity(new_multiplicity=None)[source]#: 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.

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.

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.

class Interstitial(specie=None, defect_site=None, bulk_structure=None, charge=None, multiplicity=None, bulk_volume=None, label=None)[source]#

Bases: Defect

Subclass of Defect for interstitial defects.

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.

property defect_composition#: Composition of the defect.

property defect_site_index#: Index of the defect site in the defect 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)[source]#

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.
Returns:: structure – Structure containing the defect.
Return type:: Structure

get_multiplicity()[source]#

property name#: Name of the defect.

property symbol#: Latex formatted name of the defect.

class Polaron(specie=None, defect_site=None, bulk_structure=None, charge=None, multiplicity=None, label=None, bulk_volume=None, defect_structure=None)[source]#

Bases: Defect

Subclass of Defect for polarons.

defect_structure: Structure: Structure containing the polaron. If not provided the site index is searched in the bulk structure, and defect_structure is set equal to the bulk structure.

property defect_composition#: Composition of the defect.

property defect_site_index#: Index of the defect site in the structure.

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

generate_defect_structure(bulk_structure=None)[source]#: Structure containing the polaron. If not provided the site index is searched in the bulk structure, and defect_structure is set equal to the bulk structure.

get_multiplicity(**kwargs)[source]#

Get multiplicity of the defect in the structure.

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

property name#: Name of the defect.

property symbol#: Latex formatted name of the defect.

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)[source]#

Bases: Defect

Subclass of Defect for substitutional defects.

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

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)[source]#

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)[source]#

Get multiplicity of the defect in the structure

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

get_site_in_bulk()[source]#

property name#: Name for this defect.

property site_in_bulk#

property symbol#: Latex formatted name of the defect.

class Vacancy(specie=None, defect_site=None, bulk_structure=None, charge=None, multiplicity=None, bulk_volume=None, label=None)[source]#

Bases: Defect

Subclass of Defect for single vacancies.

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.

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)[source]#

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)[source]#

Get multiplicity of the defect in the structure.

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

property name#: Name of the defect.

property symbol#: Latex formatted name of the defect.

format_legend_with_charge_kv(label, charge)[source]#

Get label in latex format with charge written with Kröger and Vink notation.

Parameters:

label (str) – Original name of the defect.
charge (int or float) – Charge of the defect. Floats are converted to integer.

Returns:

string – Formatted defect name with Kröger and Vink notation.

Return type:

str

format_legend_with_charge_number(label, charge)[source]#

Get label in latex format with charge written as a number.

Parameters:

label (str) – Original name of the defect.
charge (int or float) – Charge of the defect. Floats are converted to integers.

Returns:

string – Formatted defect name with charge.

Return type:

str

get_defect_from_string(string, **kwargs)[source]#: Get defect object from a string (Defect or DefectComplex).

get_delta_atoms(structure_defect, structure_bulk)[source]#

Build delta_atoms dictionary starting from Pymatgen Structure objects.

Parameters:

structure_defect (Structure) – Defect structure.
structure_bulk (Structure) – Bulk structure.

Returns:

delta_atoms – Dictionary with Element as keys and delta n as values.

Return type:

dict

get_delta_atoms_from_comp(comp_defect, comp_bulk)[source]#

Build delta_atoms dictionary starting from Composition objects.

Parameters:

comp_defect (Composition) – Defect structure.
comp_bulk (Composition) – Bulk structure.

Returns:

delta_atoms – Dictionary with Element as keys and delta n as values.

Return type:

dict

defects

Contents

defects#