\(\newcommand{\AA}{\text{Å}}\)

CRYSTALpytools.phonons module

A post-processing module for phonon properties

class PhononBand(tick_pos, tick_label, bands, k_path, geometry=None, reciprocal_latt=None, tick_pos3d=None, k_path3d=None, unit='THz')

Bases: object

Phonon band object. Frequency unit: THz.

Note

Even though this class is not directly inherited from the electronics.ElectronBand class, its bands attribute still has the same, nBand*nKpoint*nSpin dimentionalities for using the shared plotting functions. nSpin is always 1 here.

Parameters:

  • tick_pos (array) – 1*nTick array of 1D tick coordinates. Unit: Angstrom

  • tick_label (list) – 1*nTick of default tick labels

  • bands (array) – nBand*nKpoint*1 array of frequency. Unit: THz

  • k_path (array) – 1D coordinates of k points. Unit: Angstrom

  • geometry (Structure) – Pymatgen structure

  • reciprocal_latt (array) – 3*3 array of reciprocal lattice matrix. Not valid if geometry is specified.

  • tick_pos3d (array) – 1*nTick 3D fractional tick coordinates

  • k_path3d (array) – nKpoints*3 3D fractional coordinates of k points

  • unit (str) – In principle, should always be ‘THz’: THz-Angstrom.

classmethod from_file(output, q_overlap_tol=0.0001)

Generate an PhononBand object from the output file of CRYSTAL.

Note

Currently only the screen output (‘.out’) file is supported.

Parameters:

  • output (str) – CRYSTAL output file

  • q_overlap_tol (float) – The threshold for overlapped k points. Only used for getting tick positions.

Returns:

cls (PhononBand)

plot(**kwargs)

A wrapper to plot band structure of a single system using matplotlib. For input arguments or plotting multiple systems, check plot.plot_phonon_bands().

Parameters:

**kwargs – Plot setting parameters (i.e., except the variable for PhononBand object). Check documents for plot.plot_electron_bands().

Returns:

fig (Figure) – Matplotlib figure object

_set_unit(unit)

Set units of data of PhononBand object. Internal method.

Parameters:

unit (str) – ‘THz’ or ‘cm-1’. Length unit is always in \(\AA\).

class PhononDOS(doss, frequency, unit='THz')

Bases: object

Phonon DOS object. Frequency unit: THz.

Note

Even though this class is not directly inherited from the electronics.ElectronDOS class, its doss attribute still has the same, nProj*nFrequency*nSpin dimentionalities for using the shared plotting functions. nSpin is always 1 here.

Parameters:

  • doss (array) – nProj*nFrequency*1 array of DOS.

  • frequency (array) – Positions of DOS peaks (x axis)

  • unit (str) – In principle, should always be ‘THz’: THz-Angstrom.

classmethod from_file(output, read_INS=False, atom_prj=[], element_prj=[])

Generate an PhononDOS object from the output file of CRYSTAL.

Note

Currently only the screen output (‘.out’) file is supported.

Parameters:

  • output (str) – CRYSTAL output file

  • read_INS (bool) – Read the inelastic neutron scattering spectra.

  • atom_prj (list) – Read the projections of atoms with specified labels.

  • element_prj (list) – Read projections of elements with specified conventional atomic numbers.

Returns:

cls (PhononDOS)

plot(**kwargs)

A wrapper to plot density of states of a single system with matplotlib. For input arguments or plotting multiple systems, check plot.plot_phonon_doss().

Parameters:

**kwargs – Plot setting parameters (i.e., except the variable for PhononDOS object). Check documents for plot.plot_phonon_doss().

Returns:

fig (Figure) – Matplotlib figure object

_set_unit(unit)

Set units of data of PhononDOS object.

Parameters:

unit (str) – ‘THz’ or ‘cm-1’. Length unit is always in \(\AA\).

class PhononBandDOS(band, dos)

Bases: object

Phonon band + dos object. Frequency unit: THz.

Parameters:
classmethod from_file(*output, q_overlap_tol=0.0001, read_INS=False, atom_prj=[], element_prj=[])

Get PhononBandDOS object from files

Parameters:

  • *output (str) – CRYSTAL screen output file. 2 files, the first one is for band the second one is for DOS. Or a single output file file with both band and DOS.

  • q_overlap_tol (float) – The threshold for overlapped k points. Only used for getting tick positions.

  • read_INS (bool) – Read the inelastic neutron scattering spectra.

  • atom_prj (list) – Read the projections of atoms with specified labels.

  • element_prj (list) – Read projections of elements with specified conventional atomic numbers.

Returns:

cls (PhononBandDOS)

plot(**kwargs)

A wrapper to plot phonon band structure + density of states of a single system with matplotlib. For input arguments, check plot.plot_phonon_banddos().

Parameters:

**kwargs – Plot setting parameters (i.e., except the variable for PhononBandDOS object). Check documents for plot.plot_phonon_banddos().

Returns:

fig (Figure) – Matplotlib figure object

_set_unit()

Set units of data of PhononBandDOS object.

Parameters:

unit (str) – ‘THz’ or ‘cm-1’. Length unit is always in \(\AA\).