Distortion index

Functions

The calculation of the distortion index as defined in the article: Baur WH. Acta Crystallogr Sect B Struct Crystallogr Cryst Chem. 1974;30(5):1195–215. is implemented in the functions

import montecarlo.analysis.distorsion as distorsion
distorsion.get_distortion_indices_angles(structure [Structure], 'A', 'B', 'C')
    Return distortion_index [Float]

distorsion.get_distortion_indices_distances(structure [Structure] , 'A', 'B')
    Return distortion_index [Float]

where structure is a Structure type object and ‘A’, ‘B’, and ‘C’ are the chemical symbol of the elements to analyze.

These functions can be called from a list of Structure type objects to return a dictionary with statistic data

dist_OPO = distorsion.get_distortion_statistic_analysis(structures [List of Structure],
                                                        distorsion.get_distortion_indices_angles [Distorsion function],
                                                        ['A', 'B', 'C'],
                                                        show_plots=False)
        return {'average': average [Float],
                'deviation': deviation [Float]}

dist_OP = distorsion.get_distortion_statistic_analysis(structures [List of Structure],
                                                       distorsion.get_distortion_indices_distances [Distorsion function],
                                                       ['A', 'B'],
                                                       show_plots=False)
        return {'average': average [Float],
                'deviation': deviation [Float]}

Example

import montemodes.functions.reading as io_monte
molecule1 = io_monte.reading_from_xyz_file('PO4_1.xyz')
molecule2 = io_monte.reading_from_xyz_file('PO4_2.xyz')
molecule3 = io_monte.reading_from_xyz_file('PO4_3.xyz')

import montemodes.analysis.distortion as distortion

di_OPO = distorsion.get_distortion_indices_angles(molecule1, 'P', 'O', 'P')
di_OP = distorsion.get_distortion_indices_distances(molecule2, 'P', 'O')

print 'results: {} {}'.format(di_OPO, di_OP)

####
structures = [molecule1, molecule2, molecule3]
stat_OPO = distorsion.get_distortion_statistic_analysis(structures,
                                                        distorsion.get_distortion_indices_angles,
                                                        ['O', 'P', 'O'],
                                                        show_plots=False)

stat_OP = distorsion.get_distortion_statistic_analysis(structures,
                                                       distorsion.get_distortion_indices_distances,
                                                       ['O', 'P'],
                                                       show_plots=False)

print 'averages: {} {} and deviations: {} {}'.format(stat_OP['average'], stat_OPO['average'],
                                                     stat_OP['deviation'], stat_OPO['deviation'])

Symmetry classification

Classify the symmetry of a list of structures is symmetry categories defined by the user

import montecarlo.analysis.symmetry_analysis
get_symmetry_analysis(structures [List of Structure Objects],
                                   symmetry_to_analyze=None [List of Strings],
                                   shape_to_analyze=1 [Integer],
                                   central_atom=0 [Integer],
                                   symmetry_threshold=0.1 [Float],
                                   cutoff_shape=3.0 [Float],
                                   show_plots=True [Boolean])

    return {symmetry_label : percentage} [Dictionary]

• structures: List of Structure type objects to be analyzed
• symmetry_to_analyze : List of symmetry operations to classify the structures into.
• shape_to_analyze: Ideal shape of the structures
• cutoff_shape: Maximum value of shape measurement (defined in shape_to_analyze) to be accepted. Structures with a higher value will be discarded.
• symmetry_threshold: Maximum value of a symmetry measurement of a structure to consider that the structure has the measured symmetry.
• show_plots: If True, graphical data is shown. This includes histrograms showing the distribution of symmetry and shape measurements.

Exemple

import montemodes.functions.reading as io_monte
import montecarlo.analysis.symmetry_analysis

molecule1 = io_monte.reading_from_xyz_file('PO4_1.xyz')
molecule2 = io_monte.reading_from_xyz_file('PO4_2.xyz')
molecule3 = io_monte.reading_from_xyz_file('PO4_3.xyz')

structures = [molecule1, molecule2, molecule3]

percentage_dict = get_symmetry_analysis(structures [List of Structure Objects],
                                        symmetry_to_analyze=['c 2', 'c 3', 's 4', 'r'],
                                        shape_to_analyze=2,
                                        central_atom=5,
                                        symmetry_threshold=0.15,
                                        cutoff_shape=5.0,
                                        show_plots=False)

for key in percentage_dict:
    print '{} : {} '.format(key, percentage_dict[key])