DefectEntry

class DefectEntry(defect, energy_diff=None, corrections={}, data=None, formation_energy_function=None, defect_concentration_function=None)

Bases: MSONable

Object to store the results of a defect calculation. This object is usually created automatically when importing results, either from directories or DataFrame.

Parameters:

• defect (Defect) – Defect object (Vacancy, Interstitial, Substitution, Polaron or DefectComplex)

• energy_diff (float) – Difference btw energy of defect structure and energy of pristine (bulk) structure in eV.

• corrections (dict) – Dictionary of corrections in eV to apply to defect formation energy. All values will be added to the defect formation energy. Keys indicate the correction type.

• data (dict) – Store additional data in dict format.

• label (str) – Additional label to add to defect specie.

• formation_energy_function (function) – Custom function for calculation of defect formation energy. Check documentation in formation_energy function for more details.

• defect_concentration_function (function) – Custom function for calculation of defect concentration. Check documentation in defect_concentration function for more details.

Methods

as_dict
defect_concentration	Compute the defect concentration.
formation_energy	Compute the formation energy of the defect.
from_computed_entries	Generate DefectEntry object from Pymatgen's ComputedStructureEntry objects.
from_dict	Reconstitute a DefectEntry object from a dict representation created using as_dict().
from_structures	Generate DefectEntry object from Structure objects.
from_vasp_directories	Generate DefectEntry object from VASP directories read with Pymatgen.
load	Load an instance from a JSON file written by save().
relaxation_volume	Calculate relaxation volume from stresses.
reset_defect_concentration_function	Reset formation energy function to default.
reset_formation_energy_function	Reset formation energy function to default.
save	Serialize the instance to JSON on disk, pickling fields if needed.
set_charge	Set defect charge
set_corrections	Set defect corrections.
set_data	Set data dictionary
set_defect_concentration_function	Set custom defect concentration function.
set_formation_energy_function	Set custom defect concentrations function.
set_label	Set defect label.
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 of pristine material.
charge
corrections	Dictionary with corrections to the defect energy.
data	Dictionary containing additional data.
defect	Defect object.
defect_concentration_function
defect_specie	Species involved in defect.
defect_type	Defect type.
delta_atoms	Dictionary with Element as keys and particle difference between defect structure and bulk structure as values.
energy_diff
formation_energy_function
label
multiplicity
name
structure
symbol
symbol_charge	Defect symbol with charge formatted with numbers.
symbol_kroger	Defect symbol with charge formatted with Kröger-Vink notation.

as_dict()

Returns:

Json-serializable dict representation of DefectEntry.

property bulk_structure

Structure of pristine material.

property charge

property corrections

Dictionary with corrections to the defect energy. Its values will be added to the formation energy.

property data

Dictionary containing additional data.

property defect

Defect object.

defect_concentration(vbm=0, chemical_potentials=None, temperature=300, fermi_level=0.0, per_unit_volume=True, eform_kwargs={}, **kwargs)

Compute the defect concentration. If defect_concentration_function is set, the custom function is called, otherwise, the concentration is computed in the dilute limit as:

n = N * (1 / e^(Ef/kT) + 1), where:

• N is the site multiplicity (in cm^-3 or per unit cell)

• Ef is the formation energy of the defect.

• k is the Boltzmann constant.

• T is the temperature.

A custom function can be set when initializing the DefectEntry or by using the ‘set_defect_concentration_function` method. Use reset_defect_concentration_function to restore the default behaviour. If a custom function is given, the input must have the same args as this function, with the possibility to add more kwargs.

Parameters:

• vbm (float) – Valence band maximum of bulk calculation in eV

• chemical_potentials (dict) – Chemical potentials of the elements involved in the defect.

• temperature (float) – Temperature in Kelvin.

• fermi_level (float) – Fermi level in eV (with respect to the VBM).

• per_unit_volume (bool) – Compute concentrations per unit volume using self.defect.bulk_volume.

• eform_kwargs (dict) – Kwargs to pass to self.formation_energy.

• kwargs (dict) – Kwargs to pass to custom function.

• Returns

• --------

• conc (float) – Defect concentration in cm^-3 or per unit cell.

property defect_concentration_function

property defect_specie

Species involved in defect.

property defect_type

Defect type.

property delta_atoms

Dictionary with Element as keys and particle difference between defect structure and bulk structure as values.

property energy_diff

formation_energy(vbm=0, chemical_potentials=None, fermi_level=0, temperature=0, **kwargs)

Compute the formation energy of the defect. If formation_energy_function is set, the custom function is called, otherwise, the formation energy is computed as:

Ef = E_D - E_B + q(eVBM + fermi_level) + Ecorr - sum_i [(ni(D) - ni(B))* mu_i]

where:

• E_D is the energy of the defective cell

• E_B is the energy of the pristine (bulk) cell

  Note: E_D - E_B is self.energy_diff

• eVBM is the valence band maximum energy

• fermi_level is the chemical potential of electrons

• Ecorr are correction terms

• ni are the number of particles in the defective and pristine cells

• mu_i are the chemical potentials of the elements.

A custom function can be set when initializing the DefectEntry or by using the ‘set_formation_energy_function` method. Use reset_formation_energy_function to restore the default behaviour. If a custom function is given, the input must have the same args as this function, with the possibility to add more kwargs.

Parameters:

• vbm (float) – Valence band maximum of bulk calculation in eV

• chemical_potentials (dict) – Chemical potentials of the elements involved in the defect.

• fermi_level (float) – Fermi level in eV (with respect to the VBM).

• temperature (float) – Temperature in Kelvin. If a custom function is not passed, this parameter has no effect.

• kwargs (dict) – Kwargs to pass to custom function.

Returns:

formation_energy – Formation energy in eV.

Return type:

float

property formation_energy_function

static from_computed_entries(computed_entry_defect, computed_entry_bulk, corrections, multiplicity=1, data=None, label=None, initial_structure=False, **kwargs)

Generate DefectEntry object from Pymatgen’s ComputedStructureEntry objects.

Parameters:

• computed_entry_defect (VaspJob) – ComputedStructureEntry of the defect calculation.

• computed_entry_bulk (VaspJob) – ComputedStructureEntry of the bulk calculation.

• corrections (dict) – Dict of corrections for defect formation energy. All values will be summed and added to the defect formation energy.

• multiplicity (int) – Multiplicity of defect within the supercell. If set to None is attempted to be determined automatically.

• data (dict) – Store additional data in dict format.

• label (str) – Additional label to add to defect specie. Does not influence non equilibrium calculations.

• initial_structure (bool) – Use initial structure for defect recognition. Useful when relaxations are large and defect_finder struggles to find the right defects.

• kwargs (dict) – Kwargs to pass to defect_finder.

Returns:

entry – DefectEntry object

Return type:

DefectEntry

classmethod from_dict(d)

Reconstitute a DefectEntry object from a dict representation created using as_dict().

Parameters:

d (dict) – Dictionary representation of DefectEntry.

Returns:

entry – DefectEntry object

Return type:

DefectEntry

static from_structures(defect_structure, bulk_structure, energy_diff, corrections, charge=0, multiplicity=1, data=None, label=None, **kwargs)

Generate DefectEntry object from Structure objects.

Parameters:

• defect_structure (Structure) – Defect structure.

• bulk_structure (Structure) – Bulk structure.

• energy_diff (float) – Difference btw energy of defect structure and energy of pristine structure

• corrections (dict) – Dict of corrections in eV for defect formation energy. All values will be summed and added to the defect formation energy.

• charge (int or float) – Charge of the defect system. The default is 0.

• multiplicity (int) – multiplicity of defect within the supercell. If set to None is attempted to be determined automatically with Pymatgen. The default is 1.

• data (dict) – Store additional data in dict format.

• label (str) – Additional label to add to defect specie. Does not influence non equilibrium calculations.

• kwargs (dict) – Kwargs to pass to defect_finder. ‘verbose’ is set to True by default.

Returns:

entry – DefectEntry object

Return type:

DefectEntry

static from_vasp_directories(path_defect, computed_entry_bulk=None, path_bulk=None, corrections={}, multiplicity=1, data=None, label=None, initial_structure=False, function=None, function_kwargs={}, computed_entry_kwargs={}, finder_kwargs={})

Generate DefectEntry object from VASP directories read with Pymatgen.

Parameters:

• path_defect (str) – Path of VASP defect calculation.

• computed_entry_bulk (VaspJob) – ComputedStructureEntry of the bulk calculation.

• path_bulk (str) – If computed_entry_bulk is not provided, read directly from VASP directory.

• corrections (dict) – Dict of corrections for defect formation energy. All values will be summed and added to the defect formation energy.

• multiplicity (int) – Multiplicity of defect within the supercell. If set to None is attempted to be determined automatically with Pymatgen. The default is 1.

• data (dict) – Store additional data in dict format.

• label (str) – Additional label to add to defect specie. Does not influence non equilibrium calculations.

• initial_structure (bool) – Use initial structure for defect recognition. Useful when relaxations are large and defect_finder struggles to find the right defects.

• function (function) – Function to apply to DefectEntry. Useful to automate custom entry modification. The function can modify entry attributes and returns None.

• function_kwargs (dict) – Kwargs to pass to custom function.

• computed_entr_kwargs (dict) – Kwargs to pass to Vasprun.get_computed_entry.

• finder_kwargs (dict) – Kwargs to pass to defect_finder.

Returns:

entry – DefectEntry object

Return type:

DefectEntry

property label

property multiplicity

property name

relaxation_volume(stress_bulk, bulk_modulus, stress_defect=None, corrections={})

Calculate relaxation volume from stresses. Stress of defect calculation needs to be provided either directly or in data dict with “stress” key.

Parameters:

• stress_bulk (np.array) – Stresses from bulk calculation in kbar (units of VASP output)

• bulk_volume (float) – Cell volume of bulk calculation in A°^3.

• bulk_modulus (float) – Bulk modulus in GPa.

• stress_defect (np.array) – Stresses from defect calculation in kbar (units of VASP output)

• corrections (bool) – Add correction terms to the residual stress tensor.

Returns:

rel_volume – Relaxation volume in A°^3.

Return type:

float

reset_defect_concentration_function()

Reset formation energy function to default.

reset_formation_energy_function()

Reset formation energy function to default.

set_charge(new_charge=0)

Set defect charge

set_corrections(**kwargs)

Set defect corrections. Pass either dict or kwargs.

set_data(new_data)

Set data dictionary

set_defect_concentration_function(new_function)

Set custom defect concentration function.

set_formation_energy_function(new_function)

Set custom defect concentrations function.

set_label(new_label)

Set defect label.

set_multiplicity(new_multiplicity=None)

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

property structure

property symbol

property symbol_charge

Defect symbol with charge formatted with numbers.

property symbol_kroger

Defect symbol with charge formatted with Kröger-Vink notation.