pymatgen.phonon.dos module

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

Bases: pymatgen.phonon.dos.PhononDos

This wrapper class defines a total dos, and also provides a list of PDos.

Parameters
  • structure – Structure associated with this particular DOS.

  • total_dos – total Dos for structure

  • pdoss – The pdoss are supplied as an {Site: Densities}

pdos

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

as_dict()[source]

Json-serializable dict representation of CompletePhononDos.

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_site_dos(site)[source]

Get the Dos for a site.

Parameters

site – Site in Structure associated with CompletePhononDos.

Returns

PhononDos containing summed orbital densities for site.

class PhononDos(frequencies, densities)[source]

Bases: monty.json.MSONable

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

Parameters
  • frequencies – A sequences of frequencies in THz

  • densities – A list representing the density of states.

as_dict()[source]

Json-serializable dict representation of PhononDos.

cv(t, structure=None)[source]

Constant volume specific heat C_v at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/(K*mol)

Parameters
  • t – a temperature in K

  • structure – the structure of the system. If not None it will be used to determine the numer of formula units

Returns

Constant volume specific heat C_v

entropy(t, structure=None)[source]

Vibrational entropy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/(K*mol)

Parameters
  • t – a temperature in K

  • structure – the structure of the system. If not None it will be used to determine the numer of formula units

Returns

Vibrational entropy

classmethod from_dict(d)[source]

Returns PhononDos object from dict representation of PhononDos.

get_interpolated_value(frequency)[source]

Returns interpolated density for a particular frequency.

Parameters

frequency – frequency to return the density for.

get_smeared_densities(sigma)[source]

Returns the densities, but with a Gaussian smearing of std dev sigma applied.

Parameters

sigma – Std dev of Gaussian smearing function.

Returns

Gaussian-smeared densities.

helmholtz_free_energy(t, structure=None)[source]

Phonon contribution to the Helmholtz free energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol

Parameters
  • t – a temperature in K

  • structure – the structure of the system. If not None it will be used to determine the numer of formula units

Returns

Phonon contribution to the Helmholtz free energy

ind_zero_freq[source]

Index of the first point for which the freqencies are equal or greater than zero.

internal_energy(t, structure=None)[source]

Phonon contribution to the internal energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol

Parameters
  • t – a temperature in K

  • structure – the structure of the system. If not None it will be used to determine the numer of formula units

Returns

Phonon contribution to the internal energy

zero_point_energy(structure=None)[source]

Zero point energy energy of the system. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol

Parameters
  • t – a temperature in K

  • structure – the structure of the system. If not None it will be used to determine the numer of formula units

Returns

Phonon contribution to the internal energy

coth(x)[source]