hikari.scripts.hkl_completeness

This sub-module contains scripts made to work mainly with .hkl files, containing information from single crystal diffraction experiments. Due to authors interest in the subjects, majority of them aim to analyse or model data from high-pressure experiments, which utilise DAC - diamond anvil cell.

Functions

completeness_statistics(a, b, c, al, be, ga[, ...])

For a given experimental .hkl file calculate basic completeness statistics

dac_statistics(a, b, c, al, be, ga[, space_group, ...])

For a given experimental .hkl file calculate number of experimentally found

reformat_hkl(input_path, input_format, output_path, ...)

simulate_dac(a, b, c, al, be, ga[, opening_angle, ...])

For a given experimental .hkl file simulate a lack of completeness

Module Contents

hikari.scripts.hkl_completeness.completeness_statistics(a, b, c, al, be, ga, space_group='P-1', input_path='shelx.hkl', input_format='shelx_4', input_wavelength='CuKa')[source]

For a given experimental .hkl file calculate basic completeness statistics in ten resolution shells of equal-volume.

Parameters:

  • a (float) – Unit cell parameter a in Angstrom.

  • b (float) – Unit cell parameter b in Angstrom.

  • c (float) – Unit cell parameter c in Angstrom.

  • al (float) – Unit cell parameter alpha in degrees.

  • be (float) – Unit cell parameter alpha in degrees.

  • ga (float) – Unit cell parameter alpha in degrees.

  • space_group (str or int) – Short Hermann-Mauguin name or index of space group. For details see table in hikari.symmetry.space_groups.

  • input_path (str) – Path to the input .hkl file.

  • input_format (str or dict) – Format of the .hkl file. For reference see hikari.dataframes.HklFrame.interpret_hkl_format().

  • input_wavelength (float or str) – Wavelength of radiation utilised in experiment.

Returns:

None

Return type:

None

hikari.scripts.hkl_completeness.dac_statistics(a, b, c, al, be, ga, space_group='P1', opening_angle=35.0, orientation=((1, 0, 0), (0, 1, 0), (0, 0, 1)), input_path='shelx.hkl', input_format=4, input_wavelength='CuKa', resolution=None)[source]

For a given experimental .hkl file calculate number of experimentally found and theoretically possible reflections up to a given resolution.

Parameters:

  • a (float) – Unit cell parameter a in Angstrom.

  • b (float) – Unit cell parameter b in Angstrom.

  • c (float) – Unit cell parameter c in Angstrom.

  • al (float) – Unit cell parameter alpha in degrees.

  • be (float) – Unit cell parameter alpha in degrees.

  • ga (float) – Unit cell parameter alpha in degrees.

  • space_group (str or int) – Short Hermann-Mauguin name or index of space group. For details see table in hikari.symmetry.space_groups.

  • opening_angle (float) – Value of single opening angle as defined in hikari.dataframes.HklFrame.dac().

  • orientation (tuple or numpy.array) – Crystal orientation as defined in hikari.dataframes.BaseFrame

  • input_path (str) – Path to the input .hkl file.

  • input_format (int or str or dict) – Format of the .hkl file. For reference see hikari.dataframes.HklFrame.interpret_hkl_format().

  • input_wavelength (float or str) – Wavelength of radiation utilised in experiment.

  • resolution (float) – If given, calculate statistics only up to this value. Please provide it as a distance in rec. space (twice the resolution in A-1).

Returns:

None

hikari.scripts.hkl_completeness.reformat_hkl(input_path, input_format, output_path, output_format)[source]
Parameters:

  • input_path (str) – Relative or absolute path to the input .hkl file.

  • input_format (str) – Format of the .hkl file. For reference see hikari.dataframes.HklIo.format.

  • output_path (str) – Relative or absolute path to the output .hkl file.

  • output_format (str) – Format of the .hkl file. For reference see hikari.dataframes.HklIo.format.

Returns:

Return type:

hikari.scripts.hkl_completeness.simulate_dac(a, b, c, al, be, ga, opening_angle=35, orientation=((1, 0, 0), (0, 1, 0), (0, 0, 1)), vector=None, resolution=None, input_path='shelx.hkl', input_format=4, input_wavelength='CuKa', output_path='output.hkl', output_format=4)[source]

For a given experimental .hkl file simulate a lack of completeness caused by a presence of high-pressure diamond anvil cell.

Parameters:

  • a (float) – Unit cell parameter a in Angstrom.

  • b (float) – Unit cell parameter b in Angstrom.

  • c (float) – Unit cell parameter c in Angstrom.

  • al (float) – Unit cell parameter alpha in degrees.

  • be (float) – Unit cell parameter alpha in degrees.

  • ga (float) – Unit cell parameter alpha in degrees.

  • opening_angle (float) – Value of single opening angle as defined in hikari.dataframes.HklFrame.dac().

  • orientation (tuple or numpy.array) – Crystal orientation as defined in hikari.dataframes.BaseFrame

  • vector (tuple) – If given, overwrite orientation to provide information about crystal placement in dac, as defined in hikari.dataframes.HklFrame.dac().

  • resolution (float) – If given, additionally limit data resolution to given value. Please provide the resolution as a distance from the origin in reciprocal space (twice the resolution in reciprocal angstrom).

  • input_path (str) – Path to the input .hkl file.

  • input_format (int or str or dict) – Format of the input .hkl file. For reference see hikari.dataframes.HklFrame.interpret_hkl_format().

  • input_wavelength (float or str) – Wavelength of radiation utilised in experiment.

  • output_path (str) – Path to the output .hkl file.

  • output_format (int or str or dict) – Format of the input .hkl file. For reference see hikari.dataframes.HklFrame.interpret_hkl_format().

Returns:

None