aiida_atomistic.data.structure.getter_mixin

aiida_atomistic.data.structure.getter_mixin#

Attributes#

`has_ase`
`has_pymatgen`
`_MASS_THRESHOLD`
`_SUM_THRESHOLD`
`_DEFAULT_CELL`
`_valid_symbols`
`_atomic_masses`
`_atomic_numbers`
`_DEFAULT_THRESHOLDS`

Classes#

GetterMixin

Module Contents#

aiida_atomistic.data.structure.getter_mixin.has_ase = True[source]#

aiida_atomistic.data.structure.getter_mixin.has_pymatgen = True[source]#

aiida_atomistic.data.structure.getter_mixin._MASS_THRESHOLD = 0.001[source]#

aiida_atomistic.data.structure.getter_mixin._SUM_THRESHOLD = 1e-06[source]#

aiida_atomistic.data.structure.getter_mixin._DEFAULT_CELL = ((0, 0, 0), (0, 0, 0), (0, 0, 0))[source]#

aiida_atomistic.data.structure.getter_mixin._valid_symbols[source]#

aiida_atomistic.data.structure.getter_mixin._atomic_masses[source]#

aiida_atomistic.data.structure.getter_mixin._atomic_numbers[source]#

aiida_atomistic.data.structure.getter_mixin._DEFAULT_THRESHOLDS[source]#

class aiida_atomistic.data.structure.getter_mixin.GetterMixin[source]#

Bases: aiida_atomistic.data.structure.hubbard_mixin.HubbardGetterMixin

property cell[source]#

property pbc[source]#

property sites[source]#

property kinds[source]#

property is_alloy[source]#

property has_vacancies[source]#

property formula[source]#

static get_supported_properties()[source]#: Get a dictionary of global and site properties that can be set for this structure.

get_defined_properties()[source]#

Retrieve the defined properties of the structure, categorized into direct, computed, and site-specific properties.

Args:: exclude_computed (bool): If False, all properties will be returned, including those computed after the initialization (the pydantic computed fields). exclude_defaults (bool): If True, properties with default values will be excluded from the result.

get_kind_names()[source]#: Return a list of the kind names defined in this structure.

get_kind(kind_name: str = None)[source]#: Return a given kind.

property is_collinear[source]#

classmethod from_ase(aseatoms: ASE_ATOMS_TYPE, detect_kinds: bool = False)[source]#: Load the structure from a ASE object

classmethod from_file(filename, format='cif', detect_kinds: bool = False, **kwargs)[source]#: Load the structure from a file.

classmethod from_pymatgen(pymatgen_obj: PYMATGEN_MOLECULE | PYMATGEN_STRUCTURE, detect_kinds: bool = False, **kwargs)[source]#: Load the structure from a pymatgen object.

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).

classmethod _from_pymatgen_molecule(mol: PYMATGEN_MOLECULE, margin=5, detect_kinds: bool = False)[source]#

Load the structure from a pymatgen Molecule object.

Parameters:: margin – the margin to be added in all directions of the bounding box of the molecule.

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).

classmethod _from_pymatgen_structure(struct: PYMATGEN_STRUCTURE, detect_kinds: bool = False)[source]#

Load the structure from a pymatgen Structure object.

Note

periodic boundary conditions are set to True in all three directions.

Note

Requires the pymatgen module (version >= 3.3.5, usage of earlier versions may cause errors).

Raises:: ValueError – if there are partial occupancies together with spins.

generate_kinds(tolerance: dict | float = 0.001)[source]#

validate_kinds()[source]#

to_dict(exclude_kinds=False)[source]#

Convert the structure to a dictionary representation.

Parameters:: detect_kinds (bool, optional) – Whether to detect and include the kinds of the structure.
Returns:: The structure as a dictionary.
Return type:: dict

to_kinds_based(tolerance: dict | float = 0.001)[source]#

Convert the structure to a kinds-based representation.

Parameters:: tolerance (float or dict, optional) – Tolerance for grouping sites into kinds. Can be a float or a dictionary specifying tolerances for specific properties.
Returns:: The structure as a dictionary with kinds.
Return type:: dict

get_cif(converter='ase', store=False, **kwargs)[source]#

Creates aiida.orm.nodes.data.cif.CifData.

Parameters:

converter – specify the converter. Default ‘ase’.
store – If True, intermediate calculation gets stored in the AiiDA database for record. Default False.

Returns:

aiida.orm.nodes.data.cif.CifData node.

get_description()[source]#

Returns a string with infos retrieved from StructureData node’s properties

Parameters:: self – the StructureData node
Returns:: retsrt: the description string

get_composition(mode='full')[source]#

Returns the chemical composition of this structure as a dictionary, where each key is the kind symbol (e.g. H, Li, Ba), and each value is the number of occurences of that element in this structure.

Parameters:: mode – Specify the mode of the composition to return. Choose from full, reduced or fractional. For example, given the structure with formula Ba2Zr2O6, the various modes operate as follows. full: The default, the counts are left unnnormalized. reduced: The counts are renormalized to the greatest common denominator. fractional: The counts are renormalized such that the sum equals 1.
Returns:: a dictionary with the composition

to_ase()[source]#

Get the ASE object. Requires to be able to import ase.

Returns:: an ASE object corresponding to this

StructureData object.

Note

If any site is an alloy or has vacancies, a ValueError is raised (from the site.to_ase() routine).

to_pymatgen(**kwargs)[source]#

Get pymatgen object. Returns pymatgen Structure for structures with periodic boundary conditions (in 1D, 2D, 3D) and Molecule otherwise. :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).

Note

The spins are set according to the following rule:

if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).

to_file(filename=None, format='cif')[source]#

Writes the structure to a file.

Args:: filename (_type_, optional): defaults to None. format (str, optional): defaults to “cif”.
Raises:: ValueError: should provide a filename different from None.

get_pymatgen_structure(**kwargs)[source]#

Get the pymatgen Structure object with any PBC, provided the cell is not singular. :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).

Note

The spins are set according to the following rule:

if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).

Returns:: a pymatgen Structure object corresponding to this

StructureData object. :raise ValueError: if the cell is singular, e.g. when it has not been set.

Use get_pymatgen_molecule instead, or set a proper cell.

get_pymatgen_molecule()[source]#

Get the pymatgen Molecule object.

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).

Returns:: a pymatgen Molecule object corresponding to this

StructureData object.

_prepare_xsf(main_file_name='')[source]#: Write the given structure to a string of format XSF (for XCrySDen).

_prepare_cif(main_file_name='')[source]#: Write the given structure to a string of format CIF.

_prepare_chemdoodle(main_file_name='')[source]#: Write the given structure to a string of format required by ChemDoodle.

_prepare_xyz(main_file_name='')[source]#: Write the given structure to a string of format XYZ.

_parse_xyz(inputstring)[source]#: Read the structure from a string of format XYZ.

_adjust_default_cell(vacuum_factor=1.0, vacuum_addition=10.0, pbc=(False, False, False))[source]#: If the structure was imported from an xyz file, it lacks a cell. This method will adjust the cell

_get_object_phonopyatoms()[source]#

Converts StructureData to PhonopyAtoms

Returns:: a PhonopyAtoms object

_get_object_ase()[source]#

Converts StructureData to ase.Atoms

Returns:: an ase.Atoms object

_get_object_pymatgen(**kwargs)[source]#

Converts StructureData to pymatgen object

Returns:: a pymatgen Structure for structures with periodic boundary conditions (in three dimensions) and Molecule otherwise

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).

_get_object_pymatgen_structure(**kwargs)[source]#

Converts StructureData to pymatgen Structure object :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).

Note

The spins are set according to the following rule:

if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1

Returns:: a pymatgen Structure object corresponding to this StructureData object
Raises:: ValueError – if the cell is not set (i.e. is the default one); if there are partial occupancies together with spins (defined by kind names ending with ‘1’ or ‘2’).

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors)

_get_object_pymatgen_molecule(**kwargs)[source]#

Converts StructureData to pymatgen Molecule object

Returns:: a pymatgen Molecule object corresponding to this StructureData object.

Note

Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors)

_get_dimensionality()[source]#

Return the dimensionality of the structure and its length/surface/volume.

Zero-dimensional structures are assigned “volume” 0.

Returns:: returns a dictionary with keys “dim” (dimensionality integer), “label” (dimensionality label) and “value” (numerical length/surface/volume).

_validate_dimensionality()[source]#: Check whether the given pbc and cell vectors are consistent.

get_symbols_set()[source]#: Return the set of unique chemical symbols in the structure.

__len__()[source]#