matador.orm.spectral package¶
This submodule implements some useful classes for manipulating DOS and dispersion data.
- class matador.orm.spectral.VibrationalDOS(*args, **kwargs)[source]¶
Bases:
DensityOfStates
Specific class for phonon DOS data, including free energy integration.
Initialise the DOS and trim the DOS data arrays.
- Parameters
data (dict/Dispersion) – dictionary containing the phonon dos data, or a dispersion object to convert.
- gaussian_width = 0.0012398419840000002¶
- property debye_temperature¶
Returns the Debye temperature in K.
- property debye_freq¶
Returns the Debye frequency in eV.
- property zpe¶
The zero-point energy per atom as computed from frequency data.
- vibrational_free_energy(temperatures=None)[source]¶
Computes and returns the vibrational contribution to the free energy, including zero-point energy, from the phonon frequencies.
- Parameters
temperatures (list) – list or array of temperatures to compute G(T) at.
- Returns
temperature and energy array.
- Return type
(np.ndarray, np.ndarray)
- compute_free_energy(temperature)[source]¶
Compute the vibrational free energy at the given temperature, using lru_cache to avoid doing much extra work. Uses minimum temperature cutoff of 1e-9, below which it returns just the ZPE (unless T < 0 K).
- Raises
RuntimeError – if temperature is < 0 K.
- Returns
vibrational free energy per atom, including ZP correction.
- Return type
- vibrational_free_energy_from_dos(temperatures=None)[source]¶
Computes the vibrational contribution to the free energy at a given set of temperatures.
- Keyword Arguments
temperature (list) – list, array or float of temperatures.
- property vdos_function¶
From the data arrays
sample_energies
andsample_dos
, return an interpolated function to integrate.
- plot_free_energy(temperatures=None, ax=None, **kwargs)[source]¶
Plot G(T) on the array of given temperatures. Default T is [0, 800].
- Keyword Arguments
temperatures (list/np.ndarray) – list or array of temperatures to plot. If the array/list has length 2, use these as the start and endpoints with 21 plotting points.
ax (matplotlib.pyplot.Axis) – axis object to plot onto.
- class matador.orm.spectral.ElectronicDOS(*args, **kwargs)[source]¶
Bases:
DensityOfStates
Specific class for electronic DOS data.
Initialise the DOS and trim the DOS data arrays.
- Parameters
data (dict/Dispersion) – dictionary containing the phonon dos data, or a dispersion object to convert.
- gaussian_width = 0.01¶
- class matador.orm.spectral.DensityOfStates(*args, **kwargs)[source]¶
Bases:
Dispersion
,DataContainer
Generic class for density of states.
Initialise the DOS and trim the DOS data arrays.
- Parameters
data (dict/Dispersion) – dictionary containing the phonon dos data, or a dispersion object to convert.
- required_keys = ['dos', 'energies']¶
- property sample_dos¶
Return the calculated density of states, trimmed at each end to only include non-zero values.
- property sample_energies¶
Return the energies corresponding to the trimmed DOS.
- class matador.orm.spectral.VibrationalDispersion(*args, **kwargs)[source]¶
Bases:
Dispersion
Class that stores vibrational dispersion data. Attributes are all implemented as properties based on underlying raw data.
- eigs¶
eigenvalue array of shape (1, num_modes, num_kpoints), in frequency units below, with first index denoting the single “spin channel” for phonons.
- Type
- kpoint_path¶
array of shape (num_kpoints, 3) containing the k-point path in fractional coordinates.
- Type
- kpoint_path_cartesian¶
as above, in Cartesian coordinates.
- Type
Initalise copy of raw data.
- required_keys = ['num_kpoints', 'num_modes', 'eigs_q', 'kpoint_path']¶
- property num_atoms¶
Number of atoms in cell.
- property num_modes¶
Number of phonon modes.
- property num_bands¶
Alias for number of modes.
- property eigs_q¶
Eigenvalues in frequency units
self.freq_unit
, with shape (1, num_modes, num_kpoints).
- property softest_mode_freq¶
The frequency of the softest mode in the calculation. Negative modes correspond to imaginary frequencies.
- property debye_temperature¶
Returns the Debye temperature in K.
- property debye_freq¶
Returns the Debye frequency in cm^-1.
- class matador.orm.spectral.ElectronicDispersion(*args, **kwargs)[source]¶
Bases:
Dispersion
Class that stores electronic dispersion data. Attributes are all implemented as properties based on underlying raw data.
- eigs_s_k¶
eigenvalue array of shape (num_spins, num_bands, num_kpoints).
- Type
- kpoint_path¶
array of shape (num_kpoints, 3) containing the k-point path in fractional coordinates.
- Type
- kpoint_path_cartesian¶
as above, in Cartesian coordinates.
- Type
- fermi_energy¶
Fermi energy in eV (takes average of spin channels if more than one is present).
- Type
- projector_weights¶
array of projector_weights with shape (num_kpoints, num_bands, num_projectors)
- Type
Note
projector_weights will only work with one spin channel.
Initalise copy of raw data.
- required_keys = ['num_kpoints', 'num_spins', 'num_bands', 'num_electrons', 'eigs_s_k', 'kpoint_path', 'lattice_cart', 'fermi_energy']¶
- property num_spins¶
Number of spin channels in spectrum.
- property num_electrons¶
Number of electrons.
- property eigs_s_k¶
Array of electronic eigenvalues with shape (num_spins, num_bands, num_kpoints).
- property eigs¶
Alias for
self.eigs_s_k
.
- property fermi_energy¶
Return the Fermi energy as described in the raw data.
- property spin_fermi_energy¶
Return the Fermi energy as described in the raw data.
- property band_gap¶
Return the band gap of the system.
- property band_gap_path_inds¶
Return the indices of the k-points that comprise the smallest band gap.
- property spin_band_gap¶
Return the band gap for each spin channel.
- property spin_band_gap_path_inds¶
Return the indices of the k-points that comprise the smallest band gap for each spin channel.
- class matador.orm.spectral.Dispersion(data=None, mutable=False, **kwargs)[source]¶
Bases:
Spectral
Parent class for continuous spectra in reciprocal space, i.e. electronic and vibrational bandstructures.
Note
This class speaks of “k-points” as general reciprocal space points used to display the dispersion curves; these correspond to CASTEP’s phonon_kpoints or spectral_kpoints, and not the k-points used to generate the underlying wavefunction or dynamical matrix.
Initalise copy of raw data.
- linearise_path(preserve_kspace_distance=False)[source]¶
For a given k-point path, normalise the spacing between points, mapping it onto [0, 1].
- Keyword Arguments
preserve_kspace_distance (bool) – if True, point separation will be determined by their actual separation in reciprocal space, otherwise they will be evenly spaced.
- Returns
3xN array containing k-points mapped onto [0, 1].
- Return type
np.ndarray
- static get_band_reordering(eigs, kpoint_branches)[source]¶
Recursively reorder eigenvalues such that bands join up correctly, based on local gradients.
- Parameters
dispersion (numpy.ndarray) – array containing eigenvalues as a function of q/k
branches (
list
ofint
) – list containing branches of k/q-point path
- Returns
reordered branches.
- Return type
- class matador.orm.spectral.Spectral(data=None, mutable=False, **kwargs)[source]¶
Bases:
DataContainer
Note
This class speaks of “k-points” as general reciprocal space points used to display the dispersion curves; these correspond to CASTEP’s phonon_kpoints or spectral_kpoints, and not the k-points used to generate the underlying wavefunction or dynamical matrix.
Initalise copy of raw data.
- property eigs¶
Alias for the correct eigenvalue array.
- property lattice_cart¶
The Cartesian lattice vectors of the real space lattice.
- property num_kpoints¶
Number of dispersion k-points sampled.
- property num_qpoints¶
Alias for number of kpoints.
- property projectors¶
Return list of projector labels in the format
(element, l-channel)
.
- property num_modes¶
Number of eigenvalues per q/k-point.
- property num_bands¶
Number of eigenvalues per q/k-point.
- property projector_weights¶
Return the array of projector weights per eigval, with shape (num_projectors, num_kpoints, num_bands).
- property num_projectors¶
Return the number of projectors.
- property kpoint_branches¶
Return the k-point branches in the older format, which contained a list of lists of continous indices.
- property kpoint_branch_start¶
Return the indices of the start of branches.
- property kpoint_path_spacing¶
An estimated kpoint spacing.
- property kpoint_path¶
The fractional sampling path in reciprocal space.
- property kpoint_weights¶
- property kpoint_path_cartesian¶
The reicprocal space sampling path in Cartesian coordinates.
- property num_spins¶
Dummy number of spins.
- property spin_fermi_energy¶
Dummy Fermi energy per spin channel.
Submodules¶
matador.orm.spectral.dispersion module¶
This file implements classes to store and manipulate electronic and vibrational bandstructures, with or without projection data.
- class matador.orm.spectral.dispersion.Dispersion(data=None, mutable=False, **kwargs)[source]¶
Bases:
Spectral
Parent class for continuous spectra in reciprocal space, i.e. electronic and vibrational bandstructures.
Note
This class speaks of “k-points” as general reciprocal space points used to display the dispersion curves; these correspond to CASTEP’s phonon_kpoints or spectral_kpoints, and not the k-points used to generate the underlying wavefunction or dynamical matrix.
Initalise copy of raw data.
- linearise_path(preserve_kspace_distance=False)[source]¶
For a given k-point path, normalise the spacing between points, mapping it onto [0, 1].
- Keyword Arguments
preserve_kspace_distance (bool) – if True, point separation will be determined by their actual separation in reciprocal space, otherwise they will be evenly spaced.
- Returns
3xN array containing k-points mapped onto [0, 1].
- Return type
np.ndarray
- static get_band_reordering(eigs, kpoint_branches)[source]¶
Recursively reorder eigenvalues such that bands join up correctly, based on local gradients.
- Parameters
dispersion (numpy.ndarray) – array containing eigenvalues as a function of q/k
branches (
list
ofint
) – list containing branches of k/q-point path
- Returns
reordered branches.
- Return type
- class matador.orm.spectral.dispersion.ElectronicDispersion(*args, **kwargs)[source]¶
Bases:
Dispersion
Class that stores electronic dispersion data. Attributes are all implemented as properties based on underlying raw data.
- eigs_s_k¶
eigenvalue array of shape (num_spins, num_bands, num_kpoints).
- Type
- kpoint_path¶
array of shape (num_kpoints, 3) containing the k-point path in fractional coordinates.
- Type
- kpoint_path_cartesian¶
as above, in Cartesian coordinates.
- Type
- fermi_energy¶
Fermi energy in eV (takes average of spin channels if more than one is present).
- Type
- projector_weights¶
array of projector_weights with shape (num_kpoints, num_bands, num_projectors)
- Type
Note
projector_weights will only work with one spin channel.
Initalise copy of raw data.
- required_keys = ['num_kpoints', 'num_spins', 'num_bands', 'num_electrons', 'eigs_s_k', 'kpoint_path', 'lattice_cart', 'fermi_energy']¶
- property num_spins¶
Number of spin channels in spectrum.
- property num_electrons¶
Number of electrons.
- property eigs_s_k¶
Array of electronic eigenvalues with shape (num_spins, num_bands, num_kpoints).
- property eigs¶
Alias for
self.eigs_s_k
.
- property fermi_energy¶
Return the Fermi energy as described in the raw data.
- property spin_fermi_energy¶
Return the Fermi energy as described in the raw data.
- property band_gap¶
Return the band gap of the system.
- property band_gap_path_inds¶
Return the indices of the k-points that comprise the smallest band gap.
- property spin_band_gap¶
Return the band gap for each spin channel.
- property spin_band_gap_path_inds¶
Return the indices of the k-points that comprise the smallest band gap for each spin channel.
- class matador.orm.spectral.dispersion.VibrationalDispersion(*args, **kwargs)[source]¶
Bases:
Dispersion
Class that stores vibrational dispersion data. Attributes are all implemented as properties based on underlying raw data.
- eigs¶
eigenvalue array of shape (1, num_modes, num_kpoints), in frequency units below, with first index denoting the single “spin channel” for phonons.
- Type
- kpoint_path¶
array of shape (num_kpoints, 3) containing the k-point path in fractional coordinates.
- Type
- kpoint_path_cartesian¶
as above, in Cartesian coordinates.
- Type
Initalise copy of raw data.
- required_keys = ['num_kpoints', 'num_modes', 'eigs_q', 'kpoint_path']¶
- property num_atoms¶
Number of atoms in cell.
- property num_modes¶
Number of phonon modes.
- property num_bands¶
Alias for number of modes.
- property eigs_q¶
Eigenvalues in frequency units
self.freq_unit
, with shape (1, num_modes, num_kpoints).
- property softest_mode_freq¶
The frequency of the softest mode in the calculation. Negative modes correspond to imaginary frequencies.
- property debye_temperature¶
Returns the Debye temperature in K.
- property debye_freq¶
Returns the Debye frequency in cm^-1.
matador.orm.spectral.dos module¶
This file implements classes to store and manipulate electronic and vibrational DOS, with or without projection data.
- class matador.orm.spectral.dos.DensityOfStates(*args, **kwargs)[source]¶
Bases:
Dispersion
,DataContainer
Generic class for density of states.
Initialise the DOS and trim the DOS data arrays.
- Parameters
data (dict/Dispersion) – dictionary containing the phonon dos data, or a dispersion object to convert.
- required_keys = ['dos', 'energies']¶
- property sample_dos¶
Return the calculated density of states, trimmed at each end to only include non-zero values.
- property sample_energies¶
Return the energies corresponding to the trimmed DOS.
- class matador.orm.spectral.dos.VibrationalDOS(*args, **kwargs)[source]¶
Bases:
DensityOfStates
Specific class for phonon DOS data, including free energy integration.
Initialise the DOS and trim the DOS data arrays.
- Parameters
data (dict/Dispersion) – dictionary containing the phonon dos data, or a dispersion object to convert.
- gaussian_width = 0.0012398419840000002¶
- property debye_temperature¶
Returns the Debye temperature in K.
- property debye_freq¶
Returns the Debye frequency in eV.
- property zpe¶
The zero-point energy per atom as computed from frequency data.
- vibrational_free_energy(temperatures=None)[source]¶
Computes and returns the vibrational contribution to the free energy, including zero-point energy, from the phonon frequencies.
- Parameters
temperatures (list) – list or array of temperatures to compute G(T) at.
- Returns
temperature and energy array.
- Return type
(np.ndarray, np.ndarray)
- compute_free_energy(temperature)[source]¶
Compute the vibrational free energy at the given temperature, using lru_cache to avoid doing much extra work. Uses minimum temperature cutoff of 1e-9, below which it returns just the ZPE (unless T < 0 K).
- Raises
RuntimeError – if temperature is < 0 K.
- Returns
vibrational free energy per atom, including ZP correction.
- Return type
- vibrational_free_energy_from_dos(temperatures=None)[source]¶
Computes the vibrational contribution to the free energy at a given set of temperatures.
- Keyword Arguments
temperature (list) – list, array or float of temperatures.
- property vdos_function¶
From the data arrays
sample_energies
andsample_dos
, return an interpolated function to integrate.
- plot_free_energy(temperatures=None, ax=None, **kwargs)[source]¶
Plot G(T) on the array of given temperatures. Default T is [0, 800].
- Keyword Arguments
temperatures (list/np.ndarray) – list or array of temperatures to plot. If the array/list has length 2, use these as the start and endpoints with 21 plotting points.
ax (matplotlib.pyplot.Axis) – axis object to plot onto.
- class matador.orm.spectral.dos.ElectronicDOS(*args, **kwargs)[source]¶
Bases:
DensityOfStates
Specific class for electronic DOS data.
Initialise the DOS and trim the DOS data arrays.
- Parameters
data (dict/Dispersion) – dictionary containing the phonon dos data, or a dispersion object to convert.
- gaussian_width = 0.01¶
matador.orm.spectral.spectral module¶
- class matador.orm.spectral.spectral.Spectral(data=None, mutable=False, **kwargs)[source]¶
Bases:
DataContainer
Note
This class speaks of “k-points” as general reciprocal space points used to display the dispersion curves; these correspond to CASTEP’s phonon_kpoints or spectral_kpoints, and not the k-points used to generate the underlying wavefunction or dynamical matrix.
Initalise copy of raw data.
- property eigs¶
Alias for the correct eigenvalue array.
- property lattice_cart¶
The Cartesian lattice vectors of the real space lattice.
- property num_kpoints¶
Number of dispersion k-points sampled.
- property num_qpoints¶
Alias for number of kpoints.
- property projectors¶
Return list of projector labels in the format
(element, l-channel)
.
- property num_modes¶
Number of eigenvalues per q/k-point.
- property num_bands¶
Number of eigenvalues per q/k-point.
- property projector_weights¶
Return the array of projector weights per eigval, with shape (num_projectors, num_kpoints, num_bands).
- property num_projectors¶
Return the number of projectors.
- property kpoint_branches¶
Return the k-point branches in the older format, which contained a list of lists of continous indices.
- property kpoint_branch_start¶
Return the indices of the start of branches.
- property kpoint_path_spacing¶
An estimated kpoint spacing.
- property kpoint_path¶
The fractional sampling path in reciprocal space.
- property kpoint_weights¶
- property kpoint_path_cartesian¶
The reicprocal space sampling path in Cartesian coordinates.
- property num_spins¶
Dummy number of spins.
- property spin_fermi_energy¶
Dummy Fermi energy per spin channel.