pymatgen.electronic_structure.dos module¶

This module defines classes to represent the density of states, etc.

class CompleteDos(structure: pymatgen.core.structure.Structure, total_dos: pymatgen.electronic_structure.dos.Dos, pdoss: Dict[pymatgen.core.sites.PeriodicSite, Dict[pymatgen.electronic_structure.core.Orbital, Dict[pymatgen.electronic_structure.core.Spin, Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]]]])[source]¶

Bases: pymatgen.electronic_structure.dos.Dos

This wrapper class defines a total dos, and also provides a list of PDos. Mainly used by pymatgen.io.vasp.Vasprun to create a complete Dos from a vasprun.xml file. You are unlikely to try to generate this object manually.

structure[source]¶: Structure associated with the CompleteDos.

pdos[source]¶: Dict of partial densities of the form {Site:{Orbital:{Spin:Densities}}}

Parameters

structure – Structure associated with this particular DOS.
total_dos – total Dos for structure
pdoss – The pdoss are supplied as an {Site:{Orbital:{ Spin:Densities}}}

as_dict() → dict[source]¶: Json-serializable dict representation of CompleteDos.

classmethod from_dict(d) → pymatgen.electronic_structure.dos.CompleteDos [source]¶: Returns CompleteDos object from dict representation.

get_element_dos() → Dict[Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies], pymatgen.electronic_structure.dos.Dos][source]¶

Get element projected Dos.

Returns: Dos}
Return type: dict of {Element

get_element_spd_dos(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → Dict[pymatgen.electronic_structure.core.Orbital, pymatgen.electronic_structure.dos.Dos][source]¶

Get element and spd projected Dos

Parameters: el – Element in Structure.composition associated with CompleteDos
Returns: {“S”: densities, “P”: densities, “D”: densities}}
Return type: dict of {Element

get_site_dos(site: pymatgen.core.sites.PeriodicSite) → pymatgen.electronic_structure.dos.Dos [source]¶

Get the total Dos for a site (all orbitals).

Parameters: site – Site in Structure associated with CompleteDos.
Returns: Dos containing summed orbital densities for site.

get_site_orbital_dos(site: pymatgen.core.sites.PeriodicSite, orbital: pymatgen.electronic_structure.core.Orbital) → pymatgen.electronic_structure.dos.Dos [source]¶

Get the Dos for a particular orbital of a particular site.

Parameters

site – Site in Structure associated with CompleteDos.
orbital – Orbital in the site.

Returns

Dos containing densities for orbital of site.

get_site_spd_dos(site: pymatgen.core.sites.PeriodicSite) → Dict[pymatgen.electronic_structure.core.Orbital, pymatgen.electronic_structure.dos.Dos][source]¶

Get orbital projected Dos of a particular site

Parameters: site – Site in Structure associated with CompleteDos.
Returns: Dos}, e.g. {“s”: Dos object, …}
Return type: dict of {orbital

get_site_t2g_eg_resolved_dos(site: pymatgen.core.sites.PeriodicSite) → Dict[str, pymatgen.electronic_structure.dos.Dos][source]¶

Get the t2g, eg projected DOS for a particular site.

Parameters: site – Site in Structure associated with CompleteDos.
Returns: Dos, “t2g”: Dos} containing summed e_g and t2g DOS for the site.
Return type: A dict {“e_g”

get_spd_dos() → Dict[pymatgen.electronic_structure.core.Orbital, pymatgen.electronic_structure.dos.Dos][source]¶

Get orbital projected Dos.

Returns: Dos}, e.g. {“s”: Dos object, …}
Return type: dict of {orbital

property spin_polarization[source]¶

Calculates spin polarization at Fermi level.

See Sanvito et al., doi: 10.1126/sciadv.1602241 for an example usage.

Return (float): spin polarization in range [0, 1],

will also return NaN if spin polarization ill-defined (e.g. for insulator)

class DOS(energies: Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray], densities: Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray], efermi: float)[source]¶

Bases: pymatgen.core.spectrum.Spectrum

Replacement basic DOS object. All other DOS objects are extended versions of this object. Work in progress.

Parameters

energies – A sequence of energies
densities (ndarray) – Either a Nx1 or a Nx2 array. If former, it is interpreted as a Spin.up only density. Otherwise, the first column is interpreted as Spin.up and the other is Spin.down.
efermi – Fermi level energy.

XLABEL = 'Energy'[source]¶

YLABEL = 'Density'[source]¶

get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin=None)[source]¶

Expects a DOS object and finds the cbm and vbm.

Parameters

tol – tolerance in occupations for determining the gap
abs_tol – An absolute tolerance (True) and a relative one (False)
spin – Possible values are None - finds the gap in the summed densities, Up - finds the gap in the up spin channel, Down - finds the gap in the down spin channel.

Returns

float in eV corresponding to the gap

Return type

(cbm, vbm)

get_gap(tol: float = 0.001, abs_tol: bool = False, spin: pymatgen.electronic_structure.core.Spin = None)[source]¶

Expects a DOS object and finds the gap.

Parameters

tol – tolerance in occupations for determining the gap
abs_tol – An absolute tolerance (True) and a relative one (False)
spin – Possible values are None - finds the gap in the summed densities, Up - finds the gap in the up spin channel, Down - finds the gap in the down spin channel.

Returns

gap in eV

get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: pymatgen.electronic_structure.core.Spin = None)[source]¶

Expects a DOS object and finds the gap

Parameters

tol – tolerance in occupations for determining the gap
abs_tol – Set to True for an absolute tolerance and False for a relative one.
spin – Possible values are None - finds the gap in the summed densities, Up - finds the gap in the up spin channel, Down - finds the gap in the down spin channel.

Returns

Tuple of floats in eV corresponding to the gap, cbm and vbm.

Return type

(gap, cbm, vbm)

class Dos(efermi: float, energies: Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray], densities: Dict[pymatgen.electronic_structure.core.Spin, Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]])[source]¶

Bases: monty.json.MSONable

Basic DOS object. All other DOS objects are extended versions of this object.

Parameters

efermi – Fermi level energy
energies – A sequences of energies
({Spin (densities) – np.array}): representing the density of states for each Spin.

as_dict() → dict[source]¶: Json-serializable dict representation of Dos.

classmethod from_dict(d) → pymatgen.electronic_structure.dos.Dos [source]¶: Returns Dos object from dict representation of Dos.

get_cbm_vbm(tol: float = 0.001, abs_tol: bool = False, spin: pymatgen.electronic_structure.core.Spin = None)[source]¶

Expects a DOS object and finds the cbm and vbm.

Parameters

tol – tolerance in occupations for determining the gap
abs_tol – An absolute tolerance (True) and a relative one (False)
spin – Possible values are None - finds the gap in the summed densities, Up - finds the gap in the up spin channel, Down - finds the gap in the down spin channel.

Returns

float in eV corresponding to the gap

Return type

(cbm, vbm)

get_densities(spin: pymatgen.electronic_structure.core.Spin = None)[source]¶

Returns the density of states for a particular spin.

Parameters: spin – Spin
Returns: Returns the density of states for a particular spin. If Spin is None, the sum of all spins is returned.

get_gap(tol: float = 0.001, abs_tol: bool = False, spin: pymatgen.electronic_structure.core.Spin = None)[source]¶

Expects a DOS object and finds the gap.

Parameters

tol – tolerance in occupations for determining the gap
abs_tol – An absolute tolerance (True) and a relative one (False)
spin – Possible values are None - finds the gap in the summed densities, Up - finds the gap in the up spin channel, Down - finds the gap in the down spin channel.

Returns

gap in eV

get_interpolated_gap(tol: float = 0.001, abs_tol: bool = False, spin: pymatgen.electronic_structure.core.Spin = None)[source]¶

Expects a DOS object and finds the gap

Parameters

tol – tolerance in occupations for determining the gap
abs_tol – Set to True for an absolute tolerance and False for a relative one.
spin – Possible values are None - finds the gap in the summed densities, Up - finds the gap in the up spin channel, Down - finds the gap in the down spin channel.

Returns

Tuple of floats in eV corresponding to the gap, cbm and vbm.

Return type

(gap, cbm, vbm)

get_interpolated_value(energy: float)[source]¶

Returns interpolated density for a particular energy.

Parameters: energy – Energy to return the density for.

get_smeared_densities(sigma: float)[source]¶

Returns the Dict representation of the densities, {Spin: densities}, but with a Gaussian smearing of std dev sigma applied about the fermi level.

Parameters: sigma – Std dev of Gaussian smearing function.
Returns: Dict of Gaussian-smeared densities.

class FermiDos(dos: pymatgen.electronic_structure.dos.Dos, structure: pymatgen.core.structure.Structure = None, nelecs: float = None, bandgap: float = None)[source]¶

Bases: pymatgen.electronic_structure.dos.Dos, monty.json.MSONable

This wrapper class helps relate the density of states, doping levels (i.e. carrier concentrations) and corresponding fermi levels. A negative doping concentration indicates the majority carriers are electrons (n-type doping); a positive doping concentration indicates holes are the majority carriers (p-type doping).

Parameters

dos – Pymatgen Dos object.
structure – A structure. If not provided, the structure of the dos object will be used. If the dos does not have an associated structure object, an error will be thrown.
nelecs – The number of electrons included in the energy range of dos. It is used for normalizing the densities. Default is the total number of electrons in the structure.
bandgap – If set, the energy values are scissored so that the electronic band gap matches this value.

as_dict() → dict[source]¶: Json-serializable dict representation of Dos.

classmethod from_dict(d) → pymatgen.electronic_structure.dos.FermiDos [source]¶: Returns Dos object from dict representation of Dos.

get_doping(fermi_level: float, temperature: float) → float[source]¶

Calculate the doping (majority carrier concentration) at a given fermi level and temperature. A simple Left Riemann sum is used for integrating the density of states over energy & equilibrium Fermi-Dirac distribution.

Parameters

fermi_level – The fermi_level level in eV.
temperature – The temperature in Kelvin.

Returns

The doping concentration in units of 1/cm^3. Negative values indicate that the majority carriers are electrons (n-type doping) whereas positivie values indicates the majority carriers are holes (p-type doping).

get_fermi(concentration: float, temperature: float, rtol: float = 0.01, nstep: int = 50, step: float = 0.1, precision: int = 8)[source]¶

Finds the fermi level at which the doping concentration at the given temperature (T) is equal to concentration. A greedy algorithm is used where the relative error is minimized by calculating the doping at a grid which continually becomes finer.

Parameters

concentration – The doping concentration in 1/cm^3. Negative values represent n-type doping and positive values represent p-type doping.
temperature – The temperature in Kelvin.
rtol – The maximum acceptable relative error.
nstep – THe number of steps checked around a given fermi level.
step – Initial step in energy when searching for the Fermi level.
precision – Essentially the decimal places of calculated Fermi level.

Returns

The fermi level in eV.. Note that this is different from the default dos.efermi.

get_fermi_interextrapolated(concentration: float, temperature: float, warn: bool = True, c_ref: float = 10000000000.0, **kwargs) → float[source]¶

Similar to get_fermi except that when get_fermi fails to converge, an interpolated or extrapolated fermi is returned with the assumption that the fermi level changes linearly with log(abs(concentration)).

Parameters

concentration – The doping concentration in 1/cm^3. Negative values represent n-type doping and positive values represent p-type doping.
temperature – The temperature in Kelvin.
warn – Whether to give a warning the first time the fermi cannot be found.
c_ref – A doping concentration where get_fermi returns a value without error for both c_ref and -c_ref.
**kwargs – Keyword arguments passed to the get_fermi function.

Returns

The Fermi level. Note, the value is possibly interpolated or extrapolated and must be used with caution.

class LobsterCompleteDos(structure: pymatgen.core.structure.Structure, total_dos: pymatgen.electronic_structure.dos.Dos, pdoss: Dict[pymatgen.core.sites.PeriodicSite, Dict[pymatgen.electronic_structure.core.Orbital, Dict[pymatgen.electronic_structure.core.Spin, Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]]]])[source]¶

Bases: pymatgen.electronic_structure.dos.CompleteDos

Extended CompleteDOS for Lobster

Parameters

structure – Structure associated with this particular DOS.
total_dos – total Dos for structure
pdoss – The pdoss are supplied as an {Site:{Orbital:{ Spin:Densities}}}

classmethod from_dict(d) → pymatgen.electronic_structure.dos.LobsterCompleteDos [source]¶: Returns: CompleteDos object from dict representation.

get_element_spd_dos(el: Union[str, pymatgen.core.periodic_table.Element, pymatgen.core.periodic_table.Species, pymatgen.core.periodic_table.DummySpecies]) → Dict[str, pymatgen.electronic_structure.dos.Dos][source]¶

Get element and spd projected Dos

Parameters: el – Element in Structure.composition associated with LobsterCompleteDos
Returns: densities, “P”: densities, “D”: densities}
Return type: dict of {“S”

get_site_orbital_dos(site: pymatgen.core.sites.PeriodicSite, orbital: str) → pymatgen.electronic_structure.dos.Dos [source]¶

Get the Dos for a particular orbital of a particular site.

Parameters

site – Site in Structure associated with CompleteDos.
orbital – principal quantum number and orbital in string format, e.g. “4s”. possible orbitals are: “s”, “p_y”, “p_z”, “p_x”, “d_xy”, “d_yz”, “d_z^2”, “d_xz”, “d_x^2-y^2”, “f_y(3x^2-y^2)”, “f_xyz”, “f_yz^2”, “f_z^3”, “f_xz^2”, “f_z(x^2-y^2)”, “f_x(x^2-3y^2)” In contrast to the Cohpcar and the Cohplist objects, the strings from the Lobster files are used

Returns

Dos containing densities of an orbital of a specific site.

get_site_t2g_eg_resolved_dos(site: pymatgen.core.sites.PeriodicSite) → Dict[str, pymatgen.electronic_structure.dos.Dos][source]¶

Get the t2g, eg projected DOS for a particular site. :param site: Site in Structure associated with CompleteDos.

Returns: Dos, “t2g”: Dos} containing summed e_g and t2g DOS for the site.
Return type: A dict {“e_g”

get_spd_dos() → Dict[str, pymatgen.electronic_structure.dos.Dos][source]¶

Get orbital projected Dos. For example, if 3s and 4s are included in the basis of some element, they will be both summed in the orbital projected DOS

Returns: Dos}, e.g. {“s”: Dos object, …}
Return type: dict of {orbital

add_densities(density1: Dict[pymatgen.electronic_structure.core.Spin, Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]], density2: Dict[pymatgen.electronic_structure.core.Spin, Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]]) → Dict[pymatgen.electronic_structure.core.Spin, Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]][source]¶

Method to sum two densities.

Parameters

density1 – First density.
density2 – Second density.

Returns

density}.

Return type

Dict of {spin

f0(E, fermi, T)[source]¶: Returns the equilibrium fermi-dirac. :param E: energy in eV :type E: float :param fermi: the fermi level in eV :type fermi: float :param T: the temperature in kelvin :type T: float