\(\newcommand{\AA}{\text{Å}}\)

CRYSTALpytools.spectra module

Classes and methods for spectra.

class XRD(theta, spectra)

Bases: object

The class for X-ray diffraction spectra.

Parameters:

  • theta (array) – 2:math:`theta` values in degree.

  • spectra (array) – Spectra intensities.

classmethod from_file(output, option='LP')

Read XRD spectra from the standard screen output of properties calculation.

Parameters:

  • output (str) – Output filename.

  • option (str) – ‘NC’ for no correction (The ‘INTENS’ col); ‘LP’ for Lorentz and polarization effects (‘INTENS-LP’) and ‘DW’ for LP with Debye-Waller thermal factors (‘INTENS-LP-DW’).

Returns:

cls (XRD)

plot(theta_range=[], normalize=True, title=None, figsize=[6.4, 4.8], fontsize=14, **kwargs)

Plot XRD spectra.

Parameters:

  • theta_range (list) – 1*2 list of theta range in degree.

  • normalize (bool) – Normalize the maximum intensity to 100.

  • title (str|None) – The title of the plot. ‘None’ for no title.

  • figsize (list) – Matplotlib figure size.

  • fontsize (int) – Fontsize of the axis label and title.

  • **kwargs – Other parameters passed to matplotlib Axes.plot() method.

Returns:

fig (Figure) – Matplotlib figure.

class IR(freq, absorb, reflec, type, unit='cm-1')

Bases: object

The class for infrared spectrum. Unit: in principle, should always in ‘cm \(^{-1}\)’.

Parameters:

  • freq (array) – Frequencies. Must be commensurate with unit.

  • absorb (array) – Absorbance spectrum, nType*nFreq array.

  • reflec (array) – Reflectance spectrum along inequivalent polarization directions (periodic systems only), nDir*nFreq array.

  • type (str) – ‘molecule’ or ‘crystal’

  • unit (str) – ‘cm-1’ or ‘THz’.

classmethod from_file(specfile, output=None)

Generate an IR object from output and ‘IRSPEC.DAT’ files of CRYSTAL.

Parameters:

specfile (str) – The ‘IRSPEC.DAT’ file.

Returns:

cls (IR)

plot(unit='cm-1', option='LG', normalize=True, REFL_overlap=True, shift=0, label=None, color=None, linestyle=None, linewidth=None, x_range=[], title=None, figsize=[6.4, 4.8], legend='upper left', sharey=True, fontsize=14, fig=None, **kwargs)

Plot IR spectra into the same axis.

Parameters:

  • unit (str) – X axis unit. ‘cm \(^{-1}\)’ or ‘nm’.

  • option (str) – Broadening method. ‘LG’ for Lorentzian-Gaussian, ‘V’ for Voigt, ‘RS’ for Rayleigh spherical particles, ‘RE’ for Rayleigh with elipsoid particles, ‘REFL’ for reflectance spectra with ‘LG’. Periodic systems only.

  • normalize (bool) – Normalize the maximum intensity to 100.

  • REFL_overlap (bool) – For ``option=’REFL’`` only If more than 1 inequivalent directions exists, whether to plot REFL data into the same plot or into subplots.

  • shift (float) – For ``option=’REFL’`` and ``REFL_overlap=False`` only If multiple spectra are plotted, shift them up by the given value. Shift length is the value after normalization if normalize=True.

  • label (list|str|None) – For ``option=’REFL’`` only List of plot labels. ‘None’ for the default values (’# <number>’) and string for prefix the string before number. Otherwise should be a 1*nPlot list.

  • color (list|str|None) – For ``option=’REFL’`` only If str, use the same color for all the plot lines. If 1*nPlot, use the color defined for every plot line. ‘None’ for default values (matplotlib Tableau Palette).

  • linestyle (list|str|None) – For ``option=’REFL’`` only See explanations of color.

  • linewidth (list|float|None) – For ``option=’REFL’`` only See explanations of color.

  • x_range (list) – 1*2 list of x axis range.

  • title (str|None) – The title of the plot. ‘None’ for no title.

  • figsize (list) – Matplotlib figure size.

  • legend (str|None) – Location of legend. None for not adding legend.

  • sharey (bool) – Whether to share the y-axis among subplots. Share x is enforced.

  • fontsize (int) – Fontsize of the axis label and title.

  • fig (Figure) – Developer Only Matplotlib figure object.

  • **kwargs – Other parameters passed to matplotlib Axes.plot() method.

Returns:

fig (Figure) – Matplotlib figure.

_set_unit(unit)

Set unit of frequency.

Parameters:

unit (str) – ‘cm-1’ or ‘THz’

class Raman(freq, poly, single, unit='cm-1')

Bases: object

The class for Raman spectrum. Unit: in principle, should always in ‘cm \(^{-1}\)’.

Parameters:

  • freq (array) – Frequencies. Must be commensurate with unit.

  • poly (array) – Polycrystalline isotropic spectrum, 3*nFreq array for total, parallel and perpendicular directions.

  • single (array) – Single crystal spectrum, 6*nFreq array for xx, xy, xz, yy, yz, zz directions.

  • unit (str) – ‘cm-1’ or ‘THz’.

classmethod from_file(specfile, output=None)

Generate an Raman object from output and ‘RAMSPEC.DAT’ files of CRYSTAL.

Parameters:

specfile (str) – The ‘RAMSPEC.DAT’ file.

Returns:

cls (IR)

plot(option='poly', normalize=True, overlap=True, direction=['xx', 'xy', 'xz', 'yy', 'yz', 'zz'], shift=0, label=None, color=None, linestyle=None, linewidth=None, x_range=[], title=None, figsize=[6.4, 4.8], legend='upper left', sharey=True, fontsize=14, fig=None, ax_index=None, **kwargs)

Plot Raman spectra into the same axis.

Parameters:

  • option (str) – ‘tot’, ‘poly’ or ‘single’. ‘tot’ plots the total raman spectrum of polycrystalline material. ‘poly’ plots total, parallel and perpendicular spectra. ‘single’ plots spectra along xx, xy, xz, yy, yz, zz directions.

  • normalize (bool) – Normalize the maximum intensity to 100.

  • overlap (bool) – If more than 1 inequivalent directions exists, whether to plot spectra into the same plot or into subplots.

  • direction (list|str) – ``option=’single’`` only Specify the directions of single crystal spectra to plot.

  • shift (float) – If multiple spectra are plotted, shifting them up by the given value.

  • label (list|str|None) – List of plot labels. ‘None’ for the default values (‘total’, ‘parallel’ series or ‘xx’ ‘yy’ series) and string for prefix the string before default values. Otherwise should be a 1*nPlot list.

  • color (list|str|None) – If str, use the same color for all the plot lines. If 1*nPlot, use the color defined for every plot line. ‘None’ for default values (matplotlib Tableau Palette).

  • linestyle (list|str|None) – See explanations of color.

  • linewidth (list|float|None) – See explanations of color.

  • x_range (list) – 1*2 list of x axis range.

  • title (str|None) – The title of the plot. ‘None’ for no title.

  • figsize (list) – Matplotlib figure size.

  • legend (str|None) – Location of legend. None for not adding legend.

  • sharey (bool) – Whether to share the y-axis among subplots. Share x is enforced.

  • fontsize (int) – Fontsize of the axis label and title.

  • fig (Figure) – Developer Only Matplotlib figure object.

  • ax_index (int) – Developer Only Index of the Axes object in fig.

  • **kwargs – Other parameters passed to matplotlib Axes.plot() method.

Returns:

fig (Figure) – Matplotlib figure.

_set_unit(unit)

Set unit of frequency.

Parameters:

unit (str) – ‘cm-1’ or ‘THz’