pymatgen.electronic_structure.dos module

class CompleteDos(structure, total_dos, pdoss)[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.

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}}}

structure

Structure associated with the CompleteDos.

pdos

Dict of partial densities of the form {Site:{Orbital:{Spin:Densities}}}

as_dict()[source]

Json-serializable dict representation of CompleteDos.

classmethod from_dict(d)[source]

Returns CompleteDos object from dict representation.

get_element_dos()[source]

Get element projected Dos.

Returns

Dos}

Return type

dict of {Element

get_element_spd_dos(el)[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)[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, orbital)[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)[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)[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()[source]

Get orbital projected Dos.

Returns

Dos}, e.g. {“s”: Dos object, …}

Return type

dict of {orbital

spin_polarization

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, densities, efermi)[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'
YLABEL = 'Density'
get_cbm_vbm(tol=0.001, abs_tol=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=0.001, abs_tol=False, 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=0.001, abs_tol=False, 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, energies, densities)[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()[source]

Json-serializable dict representation of Dos.

classmethod from_dict(d)[source]

Returns Dos object from dict representation of Dos.

get_cbm_vbm(tol=0.001, abs_tol=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_densities(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=0.001, abs_tol=False, 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=0.001, abs_tol=False, 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)[source]

Returns interpolated density for a particular energy.

Parameters

energy – Energy to return the density for.

get_smeared_densities(sigma)[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, structure=None, nelecs=None, bandgap=None)[source]

Bases: pymatgen.electronic_structure.dos.Dos

This wrapper class helps relates the density of states, doping levels (i.e. carrier concentrations) and corresponding fermi levels. A negative doping concentration (c) means that the majority carriers are electrons (n-type doping) and positive c represents holes or p-type doping.

Parameters
  • dos (pymatgen Dos class) – density of states at corresponding energy levels

  • structure (pymatgen Structure class) – provided either as input or inside Dos (e.g. if CompleteDos used)

  • nelecs (float) – 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 (float) – if set, the energy values are scissored so that the electronic band gap matches this value.

get_doping(fermi, T)[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 (float) – the fermi level in eV

  • T (float) – the temperature in Kelvin

Returns (float): in units 1/cm3. If negative it means that the majority

carriers are electrons (n-type doping) and if positive holes/p-type

get_fermi(c, T, rtol=0.01, nstep=50, step=0.1, precision=8)[source]

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

Parameters
  • c (float) – doping concentration. c<0 represents n-type doping and c>0 represents p-type doping (i.e. majority carriers are holes)

  • T (float) – absolute temperature in Kelvin

  • rtol (float) – maximum acceptable relative error

  • nstep (int) – number of steps checked around a given fermi level

  • step (float) – initial step in fermi level when searching

  • precision (int) – essentially the decimal places of calculated fermi

Returns (float): the fermi level. Note that this is different from the

default dos.efermi.

get_fermi_interextrapolated(c, T, warn=True, c_ref=10000000000.0, **kwargs)[source]

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

Parameters
  • c (float) – doping concentration in 1/cm3. c<0 represents n-type doping and c>0 p-type doping (i.e. majority carriers are holes)

  • T (float) – absolute temperature in Kelvin

  • warn (bool) – whether to warn for the first time when no fermi can be found.

  • c_ref (float) – a doping concentration where get_fermi returns a value without error for both c_ref and -c_ref

  • **kwargs – see keyword arguments of the get_fermi function

Returns (float): the fermi level that is possibly interapolated or

extrapolated and must be used with caution.

class LobsterCompleteDos(structure, total_dos, pdoss)[source]

Bases: pymatgen.electronic_structure.dos.CompleteDos

Extended CompleteDOS for Lobster

classmethod from_dict(d)[source]

Returns: CompleteDos object from dict representation.

get_element_spd_dos(el)[source]

Get element and spd projected Dos

Parameters

el – Element in Structure.composition associated with LobsterCompleteDos

Returns

{“S”: densities, “P”: densities, “D”: densities}}

Return type

dict of {Element

get_site_orbital_dos(site, orbital)[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)[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()[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, density2)[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