pymatgen.analysis.defects.corrections module¶
Implementation of defect correction methods.

class
BandEdgeShiftingCorrection
[source]¶ Bases:
pymatgen.analysis.defects.core.DefectCorrection
A class for BandEdgeShiftingCorrection class. Largely adapted from PyCDT code
Initializes the BandEdgeShiftingCorrection class

get_correction
(entry)[source]¶ Gets the BandEdge correction for a defect entry :param entry: defect entry to compute BandFilling correction on.
 Requires some parameters in the DefectEntry to properly function:
 hybrid_cbm (float)
CBM of HYBRID bulk calculation one wishes to shift to
 hybrid_vbm (float)
VBM of HYBRID bulk calculation one wishes to shift to
 cbm (float)
CBM of bulk calculation (or band structure calculation of bulk); calculated on same level of theory as the defect (ex. GGA defects > requires GGA cbm)
 vbm (float)
VBM of bulk calculation (or band structure calculation of bulk); calculated on same level of theory as the defect (ex. GGA defects > requires GGA vbm)
 Returns
BandfillingCorrection value as a dictionary


class
BandFillingCorrection
(resolution=0.01)[source]¶ Bases:
pymatgen.analysis.defects.core.DefectCorrection
A class for BandFillingCorrection class. Largely adapted from PyCDT code
Initializes the Bandfilling correction
 Parameters
resolution (float) – energy resolution to maintain for gap states

get_correction
(entry)[source]¶ Gets the BandFilling correction for a defect entry :param entry: defect entry to compute BandFilling correction on.
 Requires following parameters in the DefectEntry to exist:
 eigenvalues
dictionary of defect eigenvalues, as stored in a Vasprun object
 kpoint_weights (list of floats)
kpoint weights corresponding to the dictionary of eigenvalues, as stored in a Vasprun object
 potalign (float)
potential alignment for the defect calculation Only applies to nonzero charge, When using potential alignment correction (freysoldt or kumagai), need to divide by q
 cbm (float)
CBM of bulk calculation (or band structure calculation of bulk); calculated on same level of theory as the defect (ex. GGA defects > requires GGA cbm)
 vbm (float)
VBM of bulk calculation (or band structure calculation of bulk); calculated on same level of theory as the defect (ex. GGA defects > requires GGA vbm)
 Returns
Bandfilling Correction value as a dictionary

perform_bandfill_corr
(eigenvalues, kpoint_weights, potalign, vbm, cbm)[source]¶ This calculates the band filling correction based on excess of electrons/holes in CB/VB…
 Note that the total free holes and electrons may also be used for a “shallow donor/acceptor”
 correction with specified band shifts:
+num_elec_cbm * Delta E_CBM (or num_hole_vbm * Delta E_VBM)

class
FreysoldtCorrection
(dielectric_const, q_model=None, energy_cutoff=520, madetol=0.0001, axis=None)[source]¶ Bases:
pymatgen.analysis.defects.core.DefectCorrection
A class for FreysoldtCorrection class. Largely adapated from PyCDT code
If this correction is used, please reference Freysoldt’s original paper. doi: 10.1103/PhysRevLett.102.016402
Initializes the FreysoldtCorrection class :param dielectric_const: Dielectric constant for the structure :type dielectric_const: float or 3x3 matrix :param q_model: instantiated QModel object or None.
Uses default parameters to instantiate QModel if None supplied
 Parameters
energy_cutoff (int) – Maximum energy in eV in reciprocal space to perform integration for potential correction.
madeltol (float) – Convergence criteria for the Madelung energy for potential correction
axis (int) – Axis to calculate correction. If axis is None, then averages over all three axes is performed.

get_correction
(entry)[source]¶ Gets the Freysoldt correction for a defect entry :param entry: defect entry to compute Freysoldt correction on.
Requires following keys to exist in DefectEntry.parameters dict:
axis_grid (3 x NGX where NGX is the length of the NGX grid in the x,y and z axis directions. Same length as planar average lists):
A list of 3 numpy arrays which contain the cartesian axis values (in angstroms) that correspond to each planar avg potential supplied.
bulk_planar_averages (3 x NGX where NGX is the length of the NGX grid in the x,y and z axis directions.):
A list of 3 numpy arrays which contain the planar averaged electrostatic potential for the bulk supercell.
defect_planar_averages (3 x NGX where NGX is the length of the NGX grid in the x,y and z axis directions.):
A list of 3 numpy arrays which contain the planar averaged electrostatic potential for the defective supercell.
 initial_defect_structure (Structure) structure corresponding to
initial defect supercell structure (uses Lattice for charge correction)
 defect_frac_sc_coords (3 x 1 array) Fractional coordinates of
defect location in supercell structure
 Returns
FreysoldtCorrection values as a dictionary

perform_es_corr
(lattice, q, step=0.0001)[source]¶ Peform Electrostatic Freysoldt Correction :param lattice: Pymatgen lattice object :param q: Charge of defect :type q: int :param step: step size for numerical integration :type step: float
 Returns
Electrostatic Point Charge contribution to Freysoldt Correction (float)

perform_pot_corr
(axis_grid, pureavg, defavg, lattice, q, defect_frac_position, axis, widthsample=1.0)[source]¶ For performing planar averaging potential alignment :param axis_grid (1 x NGX where NGX is the length of the NGX grid:
 in the axis direction. Same length as pureavg list):
A numpy array which contain the cartesian axis values (in angstroms) that correspond to each planar avg potential supplied.
 Parameters
(1 x NGX where NGX is the length of the NGX grid in (defavg) –
 the axis direction.):
A numpy array for the planar averaged electrostatic potential of the bulk supercell.
(1 x NGX where NGX is the length of the NGX grid in –
 the axis direction.):
A numpy array for the planar averaged electrostatic potential of the defect supercell.
lattice – Pymatgen Lattice object of the defect supercell
q (float or int) – charge of the defect
defect_frac_position – Fracitional Coordinates of the defect in the supercell
axis (int) – axis for performing the freysoldt correction on
widthsample (float) – width (in Angstroms) of the region in between defects where the potential alignment correction is averaged. Default is 1 Angstrom.
 Returns
Potential Alignment contribution to Freysoldt Correction (float)

plot
(axis, title=None, saved=False)[source]¶ Plots the planar average electrostatic potential against the Long range and short range models from Freysoldt. Must run perform_pot_corr or get_correction (to load metadata) before this can be used. :param axis: axis to plot :type axis: int :param title: Title to be given to plot. Default is no title. :type title: str :param saved: Whether to save file or not. If False then returns plot
object. If True then saves plot as str(title) + “FreyplnravgPlot.pdf”

class
KumagaiCorrection
(dielectric_tensor, sampling_radius=None, gamma=None)[source]¶ Bases:
pymatgen.analysis.defects.core.DefectCorrection
A class for KumagaiCorrection class. Largely adapated from PyCDT code
If this correction is used, please reference Kumagai and Oba’s original paper (doi: 10.1103/PhysRevB.89.195205) as well as Freysoldt’s original paper (doi: 10.1103/PhysRevLett.102.016402)
NOTE that equations 8 and 9 from Kumagai et al. reference are divided by (4 pi) to get SI units
Initializes the Kumagai Correction :param dielectric_tensor: Dielectric constant for the structure :type dielectric_tensor: float or 3x3 matrix :param optional data that can be tuned:
 sampling_radius (float): radius (in Angstrom) which sites must be outside
of to be included in the correction. Publication by Kumagai advises to use WignerSeitz radius of defect supercell, so this is default value.
 gamma (float): convergence parameter for gamma function.
Code will automatically determine this if set to None.

get_correction
(entry)[source]¶ Gets the Kumagai correction for a defect entry :param entry: defect entry to compute Kumagai correction on.
Requires following parameters in the DefectEntry to exist:
 bulk_atomic_site_averages (list): list of bulk structure”s atomic site averaged ESPs * charge,
in same order as indices of bulk structure note this is list given by VASP’s OUTCAR (so it is multiplied by a test charge of 1)
 defect_atomic_site_averages (list): list of defect structure”s atomic site averaged ESPs * charge,
in same order as indices of defect structure note this is list given by VASP’s OUTCAR (so it is multiplied by a test charge of 1)
 site_matching_indices (list): list of corresponding site index values for
bulk and defect site structures EXCLUDING the defect site itself (ex. [[bulk structure site index, defect structure”s corresponding site index], … ]
 initial_defect_structure (Structure): Pymatgen Structure object representing unrelaxed defect
structure
 defect_frac_sc_coords (array): Defect Position in fractional coordinates of the supercell
given in bulk_structure
 Returns
KumagaiCorrection values as a dictionary

get_potential_shift
(gamma, volume)[source]¶  Parameters
gamma (float) – Gamma
volume (float) – Volume.
 Returns
Potential shift for defect.

get_real_summation
(gamma, real_vectors)[source]¶ Get real summation term from list of realspace vectors

get_recip_summation
(gamma, recip_vectors, volume, r=[0.0, 0.0, 0.0])[source]¶ Get Reciprocal summation term from list of reciprocalspace vectors

get_self_interaction
(gamma)[source]¶  Parameters
() (gamma) –
 Returns
Selfinteraction energy of defect.

perform_es_corr
(gamma, prec, lattice, charge)[source]¶ Peform Electrostatic Kumagai Correction :param gamma: Ewald parameter :type gamma: float :param prec: Precision parameter for reciprical/real lattice vector generation :type prec: int :param lattice: Pymatgen Lattice object corresponding to defect supercell :param charge: Defect charge :type charge: int
 Returns
Electrostatic Point Charge contribution to Kumagai Correction (float)

perform_pot_corr
(defect_structure, defect_frac_coords, site_list, sampling_radius, q, r_vecs, g_vecs, gamma)[source]¶ For performing potential alignment in manner described by Kumagai et al. :param defect_structure: Pymatgen Structure object corrsponding to the defect supercell :param defect_frac_coords: Defect Position in fractional coordinates of the supercell
given in bulk_structure
 Parameters
site_list – list of corresponding site index values for bulk and defect site structures EXCLUDING the defect site itself (ex. [[bulk structure site index, defect structure”s corresponding site index], … ]
sampling_radius (float) – radius (in Angstrom) which sites must be outside of to be included in the correction. Publication by Kumagai advises to use WignerSeitz radius of defect supercell, so this is default value.
q (int) – Defect charge
r_vecs – List of real lattice vectors to use in summation
g_vecs – List of reciprocal lattice vectors to use in summation
gamma (float) – Ewald parameter
 Returns
Potential alignment contribution to Kumagai Correction (float)