pymatgen.analysis.defects.thermodynamics module¶

class
DefectPhaseDiagram
(entries, vbm, band_gap, filter_compatible=True)[source]¶ Bases:
monty.json.MSONable
This is similar to a PhaseDiagram object in pymatgen, but has ability to do quick analysis of defect formation energies when fed DefectEntry objects
uses many of the capabilities from PyCDT’s DefectsAnalyzer class…
 This class is able to get:
 stability of charge states for a given defect,
 list of all formation ens
c) transition levels in the gap d)
Parameters: dentries ([DefectEntry]) – A list of DefectEntry objects 
all_stable_entries
¶ List all stable entries (defect+charge) in the DefectPhaseDiagram

all_unstable_entries
¶ List all unstable entries (defect+charge) in the DefectPhaseDiagram

defect_concentrations
(chemical_potentials, temperature=300, fermi_level=0.0)[source]¶ Give list of all concentrations at specified efermi in the DefectPhaseDiagram :param chemical_potentials = {Element: number} is dictionary of chemical potentials to provide formation energies for :param temperature = temperature to produce concentrations from: :param fermi_level: (float) is fermi level relative to valence band maximum
Default efermi = 0 = VBM energyReturns: list of dictionaries of defect concentrations

defect_types
¶ List types of defects existing in the DefectPhaseDiagram

find_stable_charges
()[source]¶ Sets the stable charges and transition states for a series of defect entries. This function uses scipy’s HalfspaceInterection to oncstruct the polygons corresponding to defect stability as a function of the Fermilevel. The Halfspace Intersection constructs Ndimensional hyperplanes, in this case N=2, based on the equation of defect formation energy with considering chemical potentials:
E_form = E_0^{Corrected} + Q_{defect}*(E_{VBM} + E_{Fermi})Extra hyperplanes are constructed to bound this space so that the algorithm can actually find enclosed region.
This code was modeled after the Halfspace Intersection code for the Pourbaix Diagram

solve_for_fermi_energy
(temperature, chemical_potentials, bulk_dos)[source]¶ Solve for the Fermi energy selfconsistently as a function of T and p_O2 Observations are Defect concentrations, electron and hole conc :param bulk_dos: bulk system dos (pymatgen Dos object) :param gap: Can be used to specify experimental gap.
Will be useful if the self consistent Fermi level is > DFT gapReturns: Fermi energy