aiida_atomistic.data.structure.models

Classes

StructureBaseModel	A base model representing a structure in atomistic simulations.
MutableStructureModel	A mutable structure model that extends the StructureBaseModel class.
ImmutableStructureModel	A class representing an immutable structure model.

Module Contents

class aiida_atomistic.data.structure.models.StructureBaseModel(/, **data: Any)

Bases: pydantic.BaseModel

A base model representing a structure in atomistic simulations.

Attributes:

pbc (Optional[List[bool]]): Periodic boundary conditions in the x, y, and z directions. cell (Optional[List[List[float]]]): The cell vectors defining the unit cell of the structure.

_mutable: ClassVar[bool] = True

pbc: list[bool] = None

cell: numpy.ndarray[float] = None

sites: list[aiida_atomistic.data.structure.site.Site] = None

tot_magnetization: float | None = None

tot_charge: float | None = None

hubbard: aiida_quantumespresso.common.hubbard.Hubbard | None = None

custom: dict | None = None

class Config

from_attributes = True

frozen = False

arbitrary_types_allowed = True

classmethod validate_cell_shape(v)

Ensure cell is always a 3x3 array.

check_minimal_requirements(data)

Validate the minimal requirements of the structure.

Args:

data (dict): The input data for the structure. This is automatically passed by pydantic.

Returns:

dict: The validated input data.

Raises:

ValueError: If the structure does not meet the minimal requirements.

validate_sites(v)

Validate the list of sites.

freeze_sites(v)

Freeze the list of sites if the structure is immutable.

cell_volume() → float

Compute the volume of the unit cell.

Returns:

float: The volume of the unit cell in cubic Angstroms.

dimensionality() → dict

Determine the dimensionality of the structure.

Returns:

dict: A dictionary indicating the dimensionality of the structure.

formula() → str

Get the chemical formula of the structure.

Returns:

str: The chemical formula of the structure.

is_alloy() → dict

Computed field to determine if the structure is an alloy.

has_vacancies() → bool

Computed field to determine if the structure has vacancies.

positions() → numpy.ndarray

Return the positions of all sites in the structure as a numpy array.

Returns:

np.ndarray: An array of shape (N, 3) where N is the number of sites.

kind_names() → List[str]

Return the list of kind names for all sites in the structure.

Returns:

List[str]: A list of kind names corresponding to each site.

symbols() → List[str]

Return the list of chemical symbols for all sites in the structure.

Returns:

List[str]: A list of chemical symbols corresponding to each site.

masses() → numpy.ndarray

Return the masses of all sites in the structure as a numpy array.

Returns:

np.ndarray: An array of masses corresponding to each site.

charges() → numpy.ndarray

Return the charges of all sites in the structure as a numpy array.

Returns:

np.ndarray: An array of charges corresponding to each site.

magmoms() → numpy.ndarray

Return the magnetic moments of all sites in the structure as a numpy array.

Returns:

np.ndarray: An array of magnetic moments corresponding to each site.

magnetizations() → numpy.ndarray

Return the magnetizations of all sites in the structure as a numpy array.

Returns:

np.ndarray: An array of magnetizations corresponding to each site.

weights() → List[Tuple[float, Ellipsis]]

Return the weights of all sites in the structure as a list of tuples.

Returns:

List[Tuple[float, …]]: A list of weight tuples corresponding to each site.

kinds() → aiida_atomistic.data.structure.site.FrozenList[aiida_atomistic.data.structure.kind.Kind]

Return the reduced set of kinds, grouping sites that share all properties except positions and site_indices.

class aiida_atomistic.data.structure.models.MutableStructureModel(/, **data: Any)

Bases: StructureBaseModel

A mutable structure model that extends the StructureBaseModel class.

Attributes:

_mutable (bool): Flag indicating whether the structure is mutable or not. sites (List[Site]): List of immutable sites in the structure.

_mutable = True

class aiida_atomistic.data.structure.models.ImmutableStructureModel(/, **data: Any)

Bases: StructureBaseModel

A class representing an immutable structure model.

This class inherits from StructureBaseModel and provides additional functionality for handling immutable structures.

Attributes:

_mutable (bool): Flag indicating whether the structure is mutable or not. sites (List[Site]): List of immutable sites in the structure.

Config:

from_attributes (bool): Flag indicating whether to load attributes from the input data. frozen (bool): Flag indicating whether the model is frozen or not. arbitrary_types_allowed (bool): Flag indicating whether arbitrary types are allowed or not.

_mutable = False

sites: list[aiida_atomistic.data.structure.site.FrozenSite] | None = None

class Config

from_attributes = True

frozen = True

arbitrary_types_allowed = True

__setattr__(key, value)