`aim2dat.strct`¶

Modules to analyze the chemical environment and the coordination of atoms.

Subpackages¶

Package Contents¶

Classes¶

`Structure`	Represents a structure and contains methods to calculate properties of a structure
`StructureCollection`	The StructureCollection class is a container for one or multiple atomic structures. It
`StructureOperations`	Serves as a wrapper to make the methods defined on a single
`SurfaceGeneration`	Generates a surfaces and surface slabs based on a bulk crystal structure.

class aim2dat.strct.Structure(elements: list[str], positions: list[list[float]], pbc: list[bool], is_cartesian: bool = True, wrap: bool = False, cell: list[list[float]] = None, kinds: list[str] = None, label: str = None, store_calculated_properties: bool = True, attributes: dict = None, extras: dict = None, function_args: dict = None)[source]¶

Bases: aim2dat.strct.mixin.AnalysisMixin, aim2dat.strct.mixin.ManipulationMixin

Represents a structure and contains methods to calculate properties of a structure (molecule or crystal) or to manipulate a structure.

Overview

Properties¶
`analysis_methods`	class Return calculation methods.
`attributes`	Return the specified attributes.
`cell`	Return the cell of the structure.
`cell_angles`	Cell angles.
`cell_lengths`	cell lengths.
`cell_volume`	cell volume.
`chem_formula`	Return chemical formula.
`elements`	Return the elements of the structure.
`export_methods`	class Return export methods.
`extras`	Return the specified extras.
`function_args`	Return function arguments for stored extras.
`import_methods`	class Return import methods.
`kinds`	Return the kinds of the structure.
`label`	Return label of the structure (especially relevant in StructureCollection).
`manipulation_methods`	class Return manipulation methods.
`pbc`	Return the pbc of the structure.
`positions`	Return the cartesian positions of the structure.
`scaled_positions`	Return the scaled positions of the structure.
`store_calculated_properties`	Store calculated properties to reuse them later.

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.
`copy`()	Return copy of Structure object.
`delete_atoms`(key, elements, site_indices, change_label)	Delete atoms by element, list of elements, site index or list of site indices.
`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.
`from_aiida_structuredata`(structure_node, use_uuid, label)	class Append structure from AiiDA structure node.
`from_ase_atoms`(ase_atoms, attributes, label)	class Get structure from ase atoms object.
`from_file`(file_path, attributes, label)	class Get structure from file using the ase read-function.
`from_pymatgen_structure`(pymatgen_structure, attributes, label)	class Get structure from pymatgen structure or molecule object.
`get`(key, value)	Get attribute by key and return default if not present.
`get_positions`(cartesian, wrap)	Return positions of atoms.
`iter_sites`(get_kind, get_cart_pos, get_scaled_pos, wrap)	Iterate through the sites of the structure.
`keys`()	Return property names to create the structure.
`scale_unit_cell`(key, scaling_factor, change_label)	Scale unit cell of the structure.
`set_attribute`(key, value)	Set attribute.
`set_positions`(positions, is_cartesian, wrap)	Set postions of atoms.
`substitute_elements`(key, elements, radius_type, change_label)	Substitute all atoms of one or several elements.
`to_aiida_structuredata`(label)	Create AiiDA structuredata.
`to_ase_atoms`()	Create ase Atoms object.
`to_file`(file_path)	Export structure to file using the ase interface.
`to_pymatgen_structure`()	Create pymatgen Structure (if cell is not None) or Molecule (if cell is None) object.

class property analysis_methods : list¶

Return calculation methods.

Type:¶: list

property attributes : dict¶: Return the specified attributes.

property cell : tuple | None¶: Return the cell of the structure.

property cell_angles : tuple | None¶

Cell angles.

Type:¶: tuple

property cell_lengths : tuple | None¶

cell lengths.

Type:¶: tuple

property cell_volume : float | None¶

cell volume.

Type:¶: tuple

property chem_formula : dict¶: Return chemical formula.

property elements : tuple¶: Return the elements of the structure.

class property export_methods : list¶

Return export methods.

Type:¶: list

property extras : dict¶: Return the specified extras.

property function_args : dict¶: Return function arguments for stored extras.

class property import_methods : list¶

Return import methods.

Type:¶: list

property kinds : tuple | None¶: Return the kinds of the structure.

property label : str | None¶: Return label of the structure (especially relevant in StructureCollection).

class property manipulation_methods : list¶

Return manipulation methods.

Type:¶: list

property pbc : tuple¶: Return the pbc of the structure.

property positions : tuple¶

Return the cartesian positions of the structure.

Type:¶: tuple

property scaled_positions : tuple | None¶

Return the scaled positions of the structure.

Type:¶: tuple or None

property store_calculated_properties : bool¶: Store calculated properties to reuse them later.

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¶

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¶

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¶

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]¶

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]]¶

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.

copy() → Structure[source]¶: Return copy of Structure object.

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.

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¶

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¶

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.

classmethod from_aiida_structuredata(structure_node: int | str | aiida.orm.StructureData, use_uuid: bool = False, label: str = None) → Structure[source]¶

Append structure from AiiDA structure node.

Parameters:¶

label (str) – Label used internally to store the structure in the object.
structure_node (int, str or aiida.orm.nodes.data.structure.StructureData) – Primary key, UUID or AiiDA structure node.
use_uuid (bool (optional)) – Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key (int).

Returns:¶

aiida_scripst.strct.Structure – Structure.

classmethod from_ase_atoms(ase_atoms: ase.Atoms, attributes: dict = None, label: str = None) → Structure[source]¶

Get structure from ase atoms object.

Parameters:¶

ase_atoms (ase.Atoms) – ase Atoms object.
attributes (dict) – Additional information about the structure.
label (str) – Label used internally to store the structure in the object.

Returns:¶

aiida_scripst.strct.Structure – Structure.

classmethod from_file(file_path: str, attributes: dict = None, label: str = None) → Structure[source]¶

Get structure from file using the ase read-function.

Parameters:¶

file_path (str) – File path.
attributes (dict)
label (str) – Label used internally to store the structure in the object.

Returns:¶

aiida_scripst.strct.Structure – Structure.

classmethod from_pymatgen_structure(pymatgen_structure: pymatgen.core.Molecule | pymatgen.core.Structure, attributes: dict = None, label: str = None) → Structure[source]¶

Get structure from pymatgen structure or molecule object.

Parameters:¶

pymatgen_structure (pymatgen.core.Structure or pymatgen.core.Molecule) – pymatgen structure or molecule object.
attributes (dict) – Additional information about the structure.
label (str) – Label used internally to store the structure in the object.

Returns:¶

aiida_scripst.strct.Structure – Structure.

get(key, value=None)[source]¶: Get attribute by key and return default if not present.

get_positions(cartesian: bool = True, wrap: bool = False)[source]¶

Return positions of atoms.

Parameters:¶

cartesian (bool (optional)) – Get cartesian positions. If set to False scaled positions are returned.
wrap (bool (optional)) – Wrap atomic positions into the unit cell.

iter_sites(get_kind: bool = False, get_cart_pos: bool = False, get_scaled_pos: bool = False, wrap: bool = False)[source]¶

Iterate through the sites of the structure.

Parameters:¶

get_kind (bool (optional)) – Include kind in tuple.
get_cart_pos (bool (optional)) – Include cartesian position in tuple.
get_scaled_pos (bool (optional)) – Include scaled position in tuple.
wrap (bool (optional)) – Wrap atomic positions back into the unit cell.

Yields:¶

str or tuple – Either element symbol or tuple containing the element symbol, kind string, cartesian position or scaled position.

keys() → list[source]¶: Return property names to create the structure.

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

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.

set_attribute(key: str, value)[source]¶

Set attribute.

Parameters:¶

key (str) – Key of the attribute.
value – Value of the attribute.

set_positions(positions: list | tuple, is_cartesian: bool = True, wrap: bool = False)[source]¶

Set postions of atoms.

Parameters:¶

positions (list or tuple) – Nested list or tuple of the coordinates (n atoms x 3).
is_cartesian (bool (optional)) – Whether the coordinates are cartesian or scaled.
wrap (bool (optional)) – Wrap atomic positions into the 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.

to_aiida_structuredata(label=None)[source]¶

Create AiiDA structuredata.

Returns:¶: aiida.orm.StructureData – AiiDA structure node.

to_ase_atoms() → ase.Atoms[source]¶

Create ase Atoms object.

Returns:¶: ase.Atoms – ase Atoms object of the structure.

to_file(file_path: str) → None[source]¶: Export structure to file using the ase interface.

to_pymatgen_structure() → pymatgen.core.Molecule | pymatgen.core.Structure[source]¶

Create pymatgen Structure (if cell is not None) or Molecule (if cell is None) object.

Returns:¶: pymatgen.core.Structure or pymatgen.core.Molecule – pymatgen structure or molecule object.

class aim2dat.strct.StructureCollection(structures: list | None = None)[source]¶

The StructureCollection class is a container for one or multiple atomic structures. It implements several import_* and append_* functions to add new data to the object.

Parameters:¶: structures (list) – List of Structure or dict objects.

Overview

Properties¶
`labels`	Labels assigened to the structures.

Methods¶
`append`(label, elements, positions, pbc, cell, is_cartesian, wrap, kinds, attributes, extras)	Append structure.
`append_from_aiida_structuredata`(aiida_node, use_uuid, label)	Append structure from aiida structuredata.
`append_from_ase_atoms`(label, ase_atoms, attributes)	Append structure from ase atoms object.
`append_from_file`(label, file_path, attributes)	Append structure from file using the ase read-function.
`append_from_pymatgen_structure`(label, pymatgen_structure, attributes)	Append structure from pymatgen structure or molecule object.
`append_structure`(structure, label)	Append `Structure` object to collection. The label of the structure needs to be
`copy`()	Return copy of `StructureCollection` object.
`create_pandas_df`(exclude_columns)	Create a pandas data frame of the object.
`duplicate_structure`(key, new_label)	Duplicate structure.
`get_all_attribute_keys`()	Get all attribute keys.
`get_all_elements`()	Get the element symbols of all structures.
`get_all_kinds`()	Get the kind strings of all structures.
`get_all_structures`()	Return a list of all structures.
`get_structure`(key, return_index_label)	Get structure by key.
`import_from_aiida_db`(group_label, use_uuid, raise_error)	Import from the AiiDA database.
`import_from_hdf5_file`(file_path, raise_error)	Import from hdf5-file. Calculated extras are not yet supported.
`import_from_pandas_df`(data_frame, structure_column, exclude_columns, use_uuid, raise_error)	Import from pandas data frame.
`index`(label)	Return index of label. If the label is not present, `None` is returned.
`items`()	Return a list of label, value tuples.
`pop`(key)	Pop structure.
`store_in_aiida_db`(group_label, group_description)	Store structures into the AiiDA-database.
`store_in_hdf5_file`(file_path)	Store structures in hdf5-file. Calculated extras are not yet supported.

property labels : list[str]¶: Labels assigened to the structures.

append(label: str, elements: list, positions: list, pbc: list, cell: list = None, is_cartesian: bool = True, wrap: bool = False, kinds: list = None, attributes: dict = None, extras: dict = None)[source]¶

Append structure.

Parameters:¶

label (str) – String used to identify the structure.
elements (list) – List of element symbols or their atomic numbers.
positions (list) – List of the atomic positions, either cartesian or scaled coordinates.
pbc (list or bool) – Periodic boundary conditions.
cell (list or np.array) – Nested 3x3 list of the cell vectors.
is_cartesian (bool (optional)) – Whether the coordinates are cartesian or scaled.
wrap (bool (optional)) – Wrap atomic positions back into the unit cell.
kinds (list) – List of kind names (this allows custom kinds like Ni0, Ni1, …). If None, the elements will be used as the kind names.
attributes (dict) – Additional information about the structure.
extras (dict) – Extras of the structure.

append_from_aiida_structuredata(aiida_node: int | str | aiida.orm.StructureData, use_uuid: bool = False, label: str = None)[source]¶

Append structure from aiida structuredata.

Parameters:¶

aiida_node (int, str or aiida.orm.StructureData) – Primary key, UUID or AiiDA structure node.
use_uuid (bool (optional)) – Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key (int).
label (str) – String used to identify the structure. Overwrites label property of the structure.

append_from_ase_atoms(label: str, ase_atoms: ase.Atoms, attributes: dict = None)[source]¶

Append structure from ase atoms object.

Parameters:¶

label (str) – String used to identify the structure.
ase_atoms (ase.Atoms) – ase Atoms object.
attributes (dict) – Additional information about the structure.

append_from_file(label: str, file_path: str, attributes: dict = None)[source]¶

Append structure from file using the ase read-function.

Parameters:¶

label (str) – String used to identify the structure.
file_path (str) – File path.
attributes (dict) – Additional information about the structure.

append_from_pymatgen_structure(label: str, pymatgen_structure: pymatgen.core.Molecule | pymatgen.core.Structure, attributes: dict = None)[source]¶

Append structure from pymatgen structure or molecule object.

Parameters:¶

label (str) – String used to identify the structure.
pymatgen_structure (pymatgen.core.Structure or pymatgen.core.Molecule) – pymatgen structure or molecule object.
attributes (dict) – Additional information about the structure.

append_structure(structure: aim2dat.strct.strct.Structure, label: str = None)[source]¶

Append Structure object to collection. The label of the structure needs to be either given via the structures’s property or as keyword argument.

Parameters:¶

structure (Structure) – Structure object.
label (str (optional)) – String used to identify the structure. Overwrites label property of the structure.

copy() → StructureCollection[source]¶: Return copy of StructureCollection object.

create_pandas_df(exclude_columns: list = []) → pandas.DataFrame[source]¶

Create a pandas data frame of the object.

Parameters:¶: exclude_columns (list (optional)) – Columns that are not shown in the pandas data frame.
Returns:¶: pandas.DataFrame – Pandas data frame.

duplicate_structure(key: str | int, new_label: str)[source]¶

Duplicate structure.

Parameters:¶

key (str or int) – Key of the structure.
new_label (str) – Label of the copied structure.

get_all_attribute_keys() → list[source]¶

Get all attribute keys.

Returns:¶: list – All attribute keys.

get_all_elements() → list[str][source]¶

Get the element symbols of all structures.

Returns:¶: list – List of all element symbols .

get_all_kinds() → list[source]¶

Get the kind strings of all structures.

Returns:¶: list – List of all kinds.

get_all_structures() → list[aim2dat.strct.strct.Structure][source]¶

Return a list of all structures.

Returns:¶: list – List of all structures stored in the object.

get_structure(key: str | int, return_index_label: bool = False) → aim2dat.strct.strct.Structure[source]¶

Get structure by key.

Parameters:¶: key (str or int) – Key of the structure.
Returns:¶: Structure – structure.

import_from_aiida_db(group_label: str = None, use_uuid: bool = False, raise_error: bool = True)[source]¶

Import from the AiiDA database.

Parameters:¶

group_label (str or list (optional)) – Constrains query to structures that are member of the group(s).
use_uuid (bool (optional)) – Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key (int).
raise_error (bool (optional)) – Whether to raise an error if one of the constraints is not met.

import_from_hdf5_file(file_path: str, raise_error: bool = True)[source]¶

Import from hdf5-file. Calculated extras are not yet supported.

Parameters:¶

file_path (str) – File path.
raise_error (bool (optional)) – Whether to raise an error if one of the constraints is not met.

import_from_pandas_df(data_frame: pandas.DataFrame, structure_column: str = 'optimized_structure', exclude_columns: list = [], use_uuid: bool = False, raise_error: bool = True)[source]¶

Import from pandas data frame.

Parameters:¶

data_frame (pd.DataFrame) – Pandas data frame containing at least one column with the AiiDA structure nodes.
structure_column (str (optional)) – Column containing AiiDA structure nodes used to determine structural and compositional properties. The default value is 'optimized_structure'.
exclude_columns (list (optional)) – Columns of the data frame that are excluded. The default value is [].
use_uuid (bool (optional)) – Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key (int).
raise_error (bool (optional)) – Whether to raise an error if one of the constraints is not met.

index(label: str)[source]¶

Return index of label. If the label is not present, None is returned.

Parameters:¶: str – Label of the structure.

items() → list[tuple[str, aim2dat.strct.strct.Structure]][source]¶: Return a list of label, value tuples.

pop(key: str | int) → aim2dat.strct.strct.Structure[source]¶

Pop structure.

Parameters:¶: str – Key of the structure.

store_in_aiida_db(group_label: str = None, group_description: str = None)[source]¶

Store structures into the AiiDA-database.

Parameters:¶

group_label (str (optional)) – Label of the AiiDA group.
group_description (str (optional)) – Description of the AiiDA group.

Returns:¶

list – List containing dictionary of all structure nodes.

store_in_hdf5_file(file_path: str)[source]¶

Store structures in hdf5-file. Calculated extras are not yet supported.

Parameters:¶: file_path (str) – File path.

class aim2dat.strct.StructureOperations(structures: aim2dat.strct.StructureCollection, append_to_coll: bool = True, output_format: str = 'dict', n_procs: int = 1, chunksize: int = 50, verbose: bool = True)[source]¶

Bases: aim2dat.strct.mixin.AnalysisMixin, aim2dat.strct.mixin.ManipulationMixin

Serves as a wrapper to make the methods defined on a single Structure object accessible for a StructureCollection.

Overview

Properties¶
`analysis_methods`	class Return calculation methods.
`append_to_coll`	Whether to append manipulated structures also to the internal `StructureCollection`
`chunksize`	Number of tasks handed to each process at once.
`manipulation_methods`	class Return manipulation methods.
`n_procs`	Number of parallel processes.
`output_format`	Specify the output format of calculation methods. Supported options are `'dict'`
`structures`	Return the internal `StructureCollection` object.
`supported_output_formats`	Return the supported output formats.
`verbose`	Print progress bar.

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_stabilities`(unit, exclude_keys)	Calculate the formation energies and stabilities of all structures.
`calculate_voronoi_tessellation`(key, r_max)	Calculate voronoi polyhedron for each atomic site.
`compare_sites_via_coordination`(key1, key2, site_index1, site_index2, r_max, cn_method, min_dist_delta, n_nearest_neighbours, econ_tolerance, econ_conv_threshold, voronoi_weight_type, voronoi_weight_threshold, okeeffe_weight_threshold, distinguish_kinds, threshold)	Compare two atomic sites based on their coordination and the distances to their neighbour
`compare_sites_via_ffingerprint`(key1, key2, site_index1, site_index2, r_max, delta_bin, sigma, use_weights, use_legacy_smearing, distinguish_kinds)	Calculate similarity of two atom sites.
`compare_structures_via_comp_sym`(key1, key2, symprec, angle_tolerance, hall_number)	Compare two structures merely based on the composition and space group.
`compare_structures_via_direct_comp`(key1, key2, symprec, angle_tolerance, hall_number, no_idealize, length_threshold, angle_threshold, position_threshold, distinguish_kinds)	Compare structures by comparing lattice vectors, angles and scaled positions.
`compare_structures_via_ffingerprint`(key1, key2, r_max, delta_bin, sigma, use_weights, use_legacy_smearing, distinguish_kinds)	Calculate similarity of two structures.
`copy`()	Return copy of `StructureCollection` object.
`delete_atoms`(key, elements, site_indices, change_label)	Delete atoms by element, list of elements, site index or list of site indices.
`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.
`find_duplicates_via_comp_sym`(confined, remove_structures, symprec, angle_tolerance, hall_number)	Find duplicate structures coimparing the composition and space group.
`find_duplicates_via_direct_comp`(confined, remove_structures, symprec, angle_tolerance, hall_number, no_idealize, length_threshold, angle_threshold, position_threshold, distinguish_kinds)	Find duplicate structures comparing directly the lattice parameters and positions of the
`find_duplicates_via_ffingerprint`(confined, remove_structures, threshold, r_max, delta_bin, sigma, use_weights, use_legacy_smearing, distinguish_kinds)	Find duplicate structures using the FFingerprint method.
`find_eq_sites_via_coordination`(key, r_max, cn_method, min_dist_delta, n_nearest_neighbours, econ_tolerance, econ_conv_threshold, voronoi_weight_type, voronoi_weight_threshold, okeeffe_weight_threshold, distinguish_kinds, threshold)	Find equivalent sites by comparing the coordination of each site and its distance to the
`find_eq_sites_via_ffingerprint`(key, r_max, delta_bin, sigma, use_weights, use_legacy_smearing, distinguish_kinds, threshold)	Find equivalent sites by comparing the F-Fingerprint of each site.
`perform_analysis`(key, method, kwargs)	Perform structure analaysis using an external method.
`perform_manipulation`(key, method, kwargs)	Perform structure manipulation using an external method.
`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 analysis_methods : list¶

Return calculation methods.

Type:¶: list

property append_to_coll : bool¶

Whether to append manipulated structures also to the internal StructureCollection object.

Type:¶: bool

property chunksize : int¶

Number of tasks handed to each process at once.

Type:¶: int

class property manipulation_methods : list¶

Return manipulation methods.

Type:¶: list

property n_procs : int¶

Number of parallel processes.

Type:¶: int

property output_format : str¶

Specify the output format of calculation methods. Supported options are 'dict' and 'DataFrame'.

Type:¶: str

property structures : aim2dat.strct.StructureCollection¶: Return the internal StructureCollection object.

property supported_output_formats : list[str]¶: Return the supported output formats.

property verbose : bool¶

Print progress bar.

Type:¶: bool

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¶

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 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 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 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_stabilities(unit: str = 'eV', exclude_keys: list = []) → tuple[list, list][source]¶

Calculate the formation energies and stabilities of all structures.

The stabilities are only valid for binary systems.

Parameters:¶

unit (str (optional)) – Energy unit.
exclude_keys (list) – List of keys of structures that are not included in the detection of the convex hull. This means that the stability of these structures may have a negative sign.

Returns:¶

formation_energies (list) – List of the formation energies of all structures.
stabilities (list) – List of the stabilities of all structures.

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

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.

compare_sites_via_coordination(key1: str | int, key2: str | int, site_index1: int, site_index2: int, r_max: float = 10.0, cn_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, distinguish_kinds: bool = False, threshold: float = 0.01)[source]¶

Compare two atomic sites based on their coordination and the distances to their neighbour atoms.

Parameters:¶

key1 (str or int) – Index or label of the first structure.
key2 (str or int) – Index or label of the second structure.
site_index1 (int) – Index of the site.
site_index2 (int) – Index of the site.
r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.
cn_method (str (optional)) – Method used to calculate the coordination environment.
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'.
distinguish_kinds (bool (optional)) – Whether different kinds should be distinguished e.g. Ni0 and Ni1 would be considered as different elements if True.
threshold (float (optional)) – Threshold to consider two sites equivalent.

Returns:¶

bool – Whether the two sites are equivalent or not.

compare_sites_via_ffingerprint(key1: str | int, key2: str | int, site_index1: int, site_index2: int, r_max: float = 15.0, delta_bin: float = 0.005, sigma: float = 10.0, use_weights: bool = True, use_legacy_smearing: bool = False, distinguish_kinds: bool = False)[source]¶

Calculate similarity of two atom sites.

The cosine-distance is used to compare the two structures.

Parameters:¶

key1 (str or int) – Index or label of the first structure.
key2 (str or int) – Index or label of the second structure.
site_index1 (int) – Index of the site.
site_index2 (int) – Index of the site.
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_weights (bool (optional)) – Whether to use importance weights for the element pairs.
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:¶

distance (float) – Measure for the similarity of the two sites.

compare_structures_via_comp_sym(key1: str | int, key2: str | int, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0) → bool[source]¶

Compare two structures merely based on the composition and space group.

Parameters:¶

key1 (str or int) – Index or label of the first structure.
key2 (str or int) – Index or label of the second structure.
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.

Returns:¶

bool – Returns True if the structures match and otherwise False.

compare_structures_via_direct_comp(key1: str | int, key2: str | int, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: float = 0, no_idealize: bool = False, length_threshold: float = 0.08, angle_threshold: float = 0.03, position_threshold: float = 0.025, distinguish_kinds: bool = False) → bool[source]¶: Compare structures by comparing lattice vectors, angles and scaled positions.

compare_structures_via_ffingerprint(key1: str | int, key2: str | int, r_max: float = 15.0, delta_bin: float = 0.005, sigma: float = 0.05, use_weights: bool = True, use_legacy_smearing: bool = False, distinguish_kinds: bool = False) → float[source]¶

Calculate similarity of two structures.

The cosine-distance is used to compare the two structures.

Parameters:¶

key1 (str or int) – Index or label of the first structure.
key2 (str or int) – Index or label of the second structure.
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_weights (bool (optional)) – Whether to use importance weights for the element pairs.
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:¶

distance (float) – Measure for the similarity of the two structures.

copy() → StructureOperations[source]¶: Return copy of StructureCollection object.

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.

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¶

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 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.

find_duplicates_via_comp_sym(confined: list = None, remove_structures: bool = False, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0) → list[tuple[str]][source]¶

Find duplicate structures coimparing the composition and space group.

Parameters:¶

confined (list or None (optional)) – Confine comparison to a subset of the structure collection by giving a minimum and maximum index.
remove_structures (bool (optional)) – Whether to remove the duplicate structures.
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.

Returns:¶

list – List of tuples containing the indices of the found duplicate pairs.

find_duplicates_via_direct_comp(confined: list = None, remove_structures: bool = False, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0, no_idealize: bool = False, length_threshold: float = 0.08, angle_threshold: float = 0.03, position_threshold: float = 0.025, distinguish_kinds: bool = False) → list[tuple[str]][source]¶

Find duplicate structures comparing directly the lattice parameters and positions of the: standardized structures..

Parameters:¶

confined (list or None (optional)) – Confine comparison to a subset of the structure collection by giving a minimum and maximum index.
remove_structures (bool (optional)) – Whether to remove the duplicate structures.
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.

Returns:¶

list – List of tuples containing the indices of the found duplicate pairs.

find_duplicates_via_ffingerprint(confined: list = None, remove_structures: bool = False, threshold: float = 0.001, r_max: float = 15.0, delta_bin: float = 0.005, sigma: float = 0.05, use_weights: bool = True, use_legacy_smearing: bool = False, distinguish_kinds: bool = False) → list[tuple[str]][source]¶

Find duplicate structures using the FFingerprint method.

Parameters:¶

confined (list or None (optional)) – Confine comparison to a subset of the structure collection by giving a minimum and maximum index.
remove_structures (bool (optional)) – Whether to remove the duplicate structures.
threshold (float (optional)) – Threshold of the FFingerprint to detect duplicate structures.
r_max (float (optional)) – Maximum distance between two atoms used to construct the super cell.
delta_bin (float (optional)) – Bin size to discretize the function in angstrom.
sigma (float (optional)) – Smearing parameter for the Gaussian function.
use_weights (bool (optional)) – Whether to use importance weights for the element pairs.
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:¶

list – List of tuples containing the indices of the found duplicate pairs.

find_eq_sites_via_coordination(key: str | int, r_max: float = 10.0, cn_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, distinguish_kinds: bool = False, threshold: float = 0.01)[source]¶

Find equivalent sites by comparing the coordination of each site and its distance to the neighbour atoms.

Parameters:¶

key (str or int) – Index or label of the structure.
r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.
cn_method (str (optional)) – Method used to calculate the coordination environment.
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.
okeeffe_weight_threshold (float (optional)) – Threshold parameter to distinguish indirect and direct neighbour atoms for the 'okeeffe'.
distinguish_kinds (bool (optional)) – Whether different kinds should be distinguished e.g. Ni0 and Ni1 would be considered as different elements if True.
threshold (float (optional)) – Threshold to consider two sites equivalent.

Returns:¶

dict – Dictionary grouping equivalent sites.

find_eq_sites_via_ffingerprint(key: str | int, r_max: float = 20.0, delta_bin: float = 0.005, sigma: float = 0.05, use_weights: bool = True, use_legacy_smearing: bool = False, distinguish_kinds: bool = False, threshold: float = 0.001)[source]¶

Find equivalent sites by comparing the F-Fingerprint of each site.

Parameters:¶

key (str or int) – Index or label of the structure.
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_weights (bool) – Whether to use importance weights for the element pairs.
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.
threshold (float (optional)) – Threshold to consider two sites equivalent.

Returns:¶

dict – Dictionary grouping equivalent sites.

perform_analysis(key: str | int | tuple | list, method: collections.abc.Callable, kwargs: dict = {})[source]¶

Perform structure analaysis using an external method.

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.
method (function) – Analysis function.
kwargs (dict) – Arguments to be passed to the function.

Returns:¶

output – Output of the analysis.

perform_manipulation(key: str | int | tuple | list, method: collections.abc.Callable, kwargs: dict = {})[source]¶

Perform structure manipulation using an external method.

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.
method (function) – Function which manipulates the structure(s).
kwargs (dict) – Arguments to be passed to the function.

Returns:¶

aim2dat.strct.Structure or
aim2dat.strct.StructureCollection – Manipulated structure(s).

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

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.

class aim2dat.strct.SurfaceGeneration(structure: aim2dat.strct.strct.Structure)[source]¶

Generates a surfaces and surface slabs based on a bulk crystal structure.

Overview

Methods¶
`create_surface`(miller_indices, termination, tolerance, symprec, angle_tolerance, hall_number)	Create surface from a bulk crystal structure.
`generate_surface_slabs`(miller_indices, nr_layers, periodic, vacuum, vacuum_factor, symmetrize, tolerance, symprec, angle_tolerance, hall_number)	Generate surface slabs with all terminations for a certain direction given by its
`store_surfaces_in_aiida_db`(miller_indices, tolerance, symprec, angle_tolerance, hall_number, group_label, group_description)	Store surfaces into the AiiDA-database.
`to_aiida_surfacedata`(miller_indices, termination, tolerance, symprec, angle_tolerance, hall_number)	Create surface from a bulk crystal structure.

create_surface(miller_indices: tuple[int] | list[int] = (1, 0, 0), termination: int = 1, tolerance: float = 0.005, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0) → dict[source]¶

Create surface from a bulk crystal structure.

Parameters:¶

miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).
termination (int (optional)) – Determine termination of the surface.
tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.
symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.
angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.
hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.

Returns:¶

dict – Dictionary containing the surface data.

generate_surface_slabs(miller_indices: tuple[int] | list[int] = (1, 0, 0), nr_layers: int = 5, periodic: bool = False, vacuum: float = 10.0, vacuum_factor: float = 0.0, symmetrize: bool = True, tolerance: float = 0.01, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0) → aim2dat.strct.structure_collection.StructureCollection | None[source]¶

Generate surface slabs with all terminations for a certain direction given by its miller indices.

Parameters:¶

miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).
nr_layers (int (optional)) – Number of repititions of the underlying periodic surface cell. The default value is 5.
periodic (bool (optional)) – Whether to apply periodic boundary conditions in the direction normal to the surface plane. The default value is False.
vacuum (float (optional)) – Vacuum space added at the top and bottom of the slab. The default value is 10.0.
vacuum_factor (float (optional)) – Alternatively to the vacuum-parameter the amount of vacuum can be set as a multiple of the slab size. The method is only applied if the parameter is larger than zero. The default value is 0.0.
symmetrize (bool (optional)) – Create slabs that have the same termination on both sides. The default value is True.
tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.
symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.
angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.
hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.

Returns:¶

StructureCollection – Collection of the generated surface slabs.

store_surfaces_in_aiida_db(miller_indices: tuple[int] = (1, 0, 0), tolerance: float = 0.005, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0, group_label: str = None, group_description: str = None)[source]¶

Store surfaces into the AiiDA-database.

Parameters:¶

miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).
tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.
symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.
angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.
hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.
group_label (str (optional)) – Label of the AiiDA group.
group_description (str (optional)) – Description of the AiiDA group.

Returns:¶

list – List containing dictionary of all surface nodes.

to_aiida_surfacedata(miller_indices: tuple[int] | list[int] = (1, 0, 0), termination: int = 1, tolerance: float = 0.005, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0)[source]¶

Create surface from a bulk crystal structure.

Parameters:¶

miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).
termination (int (optional)) – Determine termination of the surface.
tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.
symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.
angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.
hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.

Returns:¶

SurfaceData – AiiDA surface data node.

aim2dat.strct¶

Subpackages¶

Package Contents¶

Classes¶

`aim2dat.strct`¶