`aim2dat.strct.mixin`¶

Mixin classes for the Structure and StructureOperations classes.

Module Contents¶

Classes¶

`AnalysisMixin`	Mixin class to perform structural analysis tasks.
`ConstraintsMixin`	Mixin to implement structural constraints.
`ManipulationMixin`	Mixin class to perform structural manipulation tasks.

Functions¶

`analysis_method`(func)	Mark function as calculation function.
`manipulates_structure`(func)	Mark structure manipulating functions.

exception aim2dat.strct.mixin.ConstraintError[source]¶

Bases: Exception

Constraint error.

class args¶

Overview

Methods¶
`with_traceback`()	Exception.with_traceback(tb) –

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class aim2dat.strct.mixin.AnalysisMixin[source]¶

Mixin class to perform structural analysis tasks.

Overview

Properties¶
`analysis_methods`	class Return calculation methods.

Methods¶
`calculate_angle`(key, site_index1, site_index2, site_index3, backfold_positions)	Calculate angle between three atoms.
`calculate_coordination`(key, r_max, method, min_dist_delta, n_nearest_neighbours, econ_tolerance, econ_conv_threshold, voronoi_weight_type, voronoi_weight_threshold, okeeffe_weight_threshold)	Calculate coordination environment of each atomic site.
`calculate_dihedral_angle`(key, site_index1, site_index2, site_index3, site_index4, backfold_positions)	Calculate dihedral angle between four atoms.
`calculate_distance`(key, site_index1, site_index2, backfold_positions, use_supercell, r_max)	Calculate distance between two atoms.
`calculate_ffingerprint`(key, r_max, delta_bin, sigma, use_legacy_smearing, distinguish_kinds)	Calculate f-fingerprint function for each element-pair and atomic site.
`calculate_voronoi_tessellation`(key, r_max)	Calculate voronoi polyhedron for each atomic site.
`determine_point_group`(key, threshold_distance, threshold_angle, threshold_inertia)	Determine the point group of a molecule.
`determine_space_group`(key, symprec, angle_tolerance, hall_number, return_sym_operations, return_primitive_structure, return_standardized_structure, no_idealize)	Determine the space group of the structure using spglib as backend.

class property analysis_methods : list¶

Return calculation methods.

Type:¶: list

calculate_angle(key: str | int | tuple | list = None, site_index1: int = 0, site_index2: int = 1, site_index3: int = 2, backfold_positions: bool = True) → float[source]¶

Calculate angle between three atoms.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
site_index1 (int) – Index of the site.
site_index2 (int) – Index of the site.
site_index3 (int) – Index of the site.
backfold_positions (bool) – Whether to backfold the atomic sites and return the smallest distance.

Returns:¶

float – Angle calculated via the vectors from atom 2 to atom 1 and atom 3.

calculate_coordination(key: str | int | tuple | list = None, r_max: float = 10.0, method: str = 'minimum_distance', min_dist_delta: float = 0.1, n_nearest_neighbours: int = 5, econ_tolerance: float = 0.5, econ_conv_threshold: float = 0.001, voronoi_weight_type: float = 'rel_solid_angle', voronoi_weight_threshold: float = 0.5, okeeffe_weight_threshold: float = 0.5) → dict[source]¶

Calculate coordination environment of each atomic site.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.
method (str (optional)) – Method used to calculate the coordination environment. The default value is 'minimum_distance'.
min_dist_delta (float (optional)) – Tolerance parameter that defines the relative distance from the nearest neighbour atom for the 'minimum_distance' method.
n_nearest_neighbours (int (optional)) – Number of neighbours that are considered coordinated for the 'n_neighbours' method.
econ_tolerance (float (optional)) – Tolerance parameter for the econ method.
econ_conv_threshold (float (optional)) – Convergence threshold for the econ method.
voronoi_weight_type (str (optional)) – Weight type of the Voronoi facets. Supported options are 'covalent_atomic_radius', 'area' and 'solid_angle'. The prefix 'rel_' specifies that the relative weights with respect to the maximum value of the polyhedron are calculated.
voronoi_weight_threshold (float (optional)) – Weight threshold to consider a neighbouring atom coordinated.
okeeffe_weight_threshold (float (optional)) – Threshold parameter to distinguish indirect and direct neighbour atoms for the 'okeeffe'.

This parameter is depreciated and will be removed in a future version. The original results can be obtained by using the voronoi_weight_threshold parameter and setting voronoi_weight_type to 'rel_solid_angle'.

Returns:¶

dict – Dictionary containing the coordination information of the structure.

calculate_dihedral_angle(key: str | int | tuple | list = None, site_index1: int = 0, site_index2: int = 1, site_index3: int = 2, site_index4: int = 3, backfold_positions: bool = True) → float[source]¶

Calculate dihedral angle between four atoms.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
site_index1 (int) – Index of the site.
site_index2 (int) – Index of the site.
site_index3 (int) – Index of the site.
site_index4 (int) – Index of the site.
backfold_positions (bool) – Whether to backfold the atomic sites and return the smallest distance.

Returns:¶

float – Dihedral angle.

Calculate distance between two atoms.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
site_index1 (int) – Index of the site.
site_index2 (int) – Index of the site.
backfold_positions (bool) – Whether to backfold the atomic sites and return the smallest distance.
use_supercell (bool) – User supercell to calculate all distances between the two atomic sites up to the radius r_max.
r_max (float) – Cut-off value for the maximum distance between two atoms in angstrom.

Returns:¶

float – Distance between the two atoms or a list of distances (if use_super_cell is set to True).

calculate_ffingerprint(key: str | int | tuple | list = None, r_max: float = 20.0, delta_bin: float = 0.005, sigma: float = 0.05, use_legacy_smearing: bool = False, distinguish_kinds: bool = False) → tuple[dict, dict][source]¶

Calculate f-fingerprint function for each element-pair and atomic site.

The calculation is based on equation (3) in doi:10.1063/1.3079326.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.
delta_bin (float (optional)) – Bin size to descritize the function in angstrom.
sigma (float (optional)) – Smearing parameter for the Gaussian function.
use_legacy_smearing (bool) – Use the depreciated smearing method.
distinguish_kinds (bool (optional)) – Whether different kinds should be distinguished e.g. Ni0 and Ni1 would be considered as different elements if True.

Returns:¶

element_fingerprints (dict) – Dictionary containing all fingerprint functions of the structure summed over all atoms of the same element.
atomic_fingerprints (dict) – Dictionary containing all individual fingerprint functions for each atomic site.

calculate_voronoi_tessellation(key: str | int | tuple | list = None, r_max: float = 10.0) → list[list[dict]][source]¶

Calculate voronoi polyhedron for each atomic site.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.

Returns:¶

list – List of voronoi details for each atomic site.

determine_point_group(key: str | int | tuple | list = None, threshold_distance: float = 0.1, threshold_angle: float = 1.0, threshold_inertia: float = 0.1) → dict[source]¶

Determine the point group of a molecule.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
threshold_distance (float (optional)) – Tolerance parameter for distances.
threshold_angle (float (optional)) – Tolerance parameter for angles.
threshold_inertia (float (optional)) – Tolerance parameter for inertia.

Returns:¶

dict – Dictionary containing the point group and symmetry elements of the structure.

determine_space_group(key: str | int | tuple | list = None, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0, return_sym_operations: bool = False, return_primitive_structure: bool = False, return_standardized_structure: bool = False, no_idealize: bool = False) → dict[source]¶

Determine the space group of the structure using spglib as backend.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
symprec (float (optional)) – Tolerance parameter for spglib
angle_tolerance (float (optional)) – Tolerance parameter for spglib.
hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it.
return_sym_operations (bool (optional)) – Additionally, return all symmetry elements.
return_primitive_structure (bool (optional)) – Whether to return the primitive standardized structure.
return_standardized_structure (bool (optional)) – Whether to the non-primitive standardized structure.
no_idealize (bool (optional)) – Whether to idealize unit cell vectors and angles.

Returns:¶

dict – Dictionary containing the internal space group number and labels.

class aim2dat.strct.mixin.ConstraintsMixin[source]¶

Mixin to implement structural constraints.

Overview

Properties¶
`attribute_constraints`	Attribute constraints.
`chem_formula_constraints`	Constraints on the chemical formula.
`concentration_constraints`	Elemental concentration constraints.
`neglect_elemental_structures`	Whether to neglect elemental phases.

Methods¶
`add_chem_formula_constraint`(chem_formula, reduced_formula)	Add a chemical formula as a constraint.
`remove_constraints`()	Remove all constraints.
`set_attribute_constraint`(attribute, min_value, max_value)	Set a constraint on attributes.
`set_concentration_constraint`(element, min_conc, max_conc)	Set a constraint on the concentration of an element in the structure.

property attribute_constraints¶: Attribute constraints.

property chem_formula_constraints¶: Constraints on the chemical formula.

property concentration_constraints¶: Elemental concentration constraints.

property neglect_elemental_structures¶: Whether to neglect elemental phases.

add_chem_formula_constraint(chem_formula, reduced_formula=True)[source]¶

Add a chemical formula as a constraint.

The formula can be given as a string, dictionary or list of strings or dictionaries.

Parameters:¶

chem_formula (list, dict or str) – Chemical formula given as list, dict or str.
reduced_formula (bool (optional)) – If set to True the reduced formulas are compared. The default value is True.

remove_constraints()[source]¶: Remove all constraints.

set_attribute_constraint(attribute, min_value=None, max_value=None)[source]¶

Set a constraint on attributes.

Parameters:¶

attribute (str) – Attribute to be constraint.
min_value (float) – Minimum value of the attribute. In case of no limit the variable can be set to 0.0.
max_value (float) – Maximum value of the attribute. In case of no limit the variable can be set to 1.0.

set_concentration_constraint(element, min_conc=0.0, max_conc=1.0)[source]¶

Set a constraint on the concentration of an element in the structure.

The minimum and maximum values have to be set between 0.0 and 1.0.

Parameters:¶

element (str) – Element to be constraint.
min_conc (float) – Minimum concentration. In case of no limit the variable can be set to 0.0.
max_conc (float) – Maximum concentration. In case of no limit the variable can be set to 1.0.

class aim2dat.strct.mixin.ManipulationMixin[source]¶

Mixin class to perform structural manipulation tasks.

Overview

Properties¶
`manipulation_methods`	class Return manipulation methods.

Methods¶
`delete_atoms`(key, elements, site_indices, change_label)	Delete atoms by element, list of elements, site index or list of site indices.
`scale_unit_cell`(key, scaling_factor, change_label)	Scale unit cell of the structure.
`substitute_elements`(key, elements, radius_type, change_label)	Substitute all atoms of one or several elements.

class property manipulation_methods : list¶

Return manipulation methods.

Type:¶: list

Delete atoms by element, list of elements, site index or list of site indices.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
elements (str, list or tuple) – Element or tuple or list of the elements to be deleted.
site_indices (list or tuple) – Site index or tuple or list of site indices to be deleted.

Returns:¶

aim2dat.strct.Structure – Structure with deleted atoms.

scale_unit_cell(key: str | int | tuple | list = None, scaling_factor: float = 1.0, change_label: bool = False) → aim2dat.strct.Structure | aim2dat.strct.StructureCollection[source]¶

Scale unit cell of the structure.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
scaling_factor (float) – Scaling factor.

Returns:¶

aim2dat.strct.Structure – Structure with scaled unit cell.

Substitute all atoms of one or several elements.

Parameters:¶

key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.
elements (list or tuple) – Tuple or list of tuples of the elements that are substituted.
radius_type (str or None (optional)) – Radius type used to calculate the scaling factor for the unit cell. If set to None no scaling is applied. The default value is covalent.

Returns:¶

aim2dat.strct.Structure – Structure with substituted elements.

aim2dat.strct.mixin.analysis_method(func)[source]¶: Mark function as calculation function.

aim2dat.strct.mixin.manipulates_structure(func)[source]¶: Mark structure manipulating functions.

aim2dat.strct.mixin¶

Module Contents¶

Classes¶

Functions¶

`aim2dat.strct.mixin`¶