aiida_atomistic.data.structure.site

aiida_atomistic.data.structure.site#

Attributes#

NumpyArray

Classes#

`FrozenList`	A subclass of list that represents an immutable list.
`Site`	This class contains the core information about a given site of the system.
`FrozenSite`	This class contains the core information about a given site of the system.

Functions#

`_validate_array`(v)	Convert input to numpy array if it isn't already.
`_serialize_array`(v)	Serialize numpy array to list.
`freeze_nested`(obj)	Recursively freezes a nested dictionary or list by converting it into an immutable object.

Module Contents#

aiida_atomistic.data.structure.site._validate_array(v)[source]#: Convert input to numpy array if it isn’t already.

aiida_atomistic.data.structure.site._serialize_array(v)[source]#: Serialize numpy array to list.

aiida_atomistic.data.structure.site.NumpyArray[source]#

aiida_atomistic.data.structure.site.freeze_nested(obj)[source]#

Recursively freezes a nested dictionary or list by converting it into an immutable object.

Args:: obj (dict or list): The nested dictionary or list to be frozen.
Returns:: AttributesFrozendict or FrozenList: The frozen version of the input object.

class aiida_atomistic.data.structure.site.FrozenList[source]#

Bases: list

A subclass of list that represents an immutable list.

This class overrides the __setitem__ method to raise a ValueError when attempting to modify the list.

Usage: >>> my_list = FrozenList([1, 2, 3]) >>> my_list[0] = 4 ValueError: This list is immutable…

__setitem__(index, value)[source]#: Set self[key] to value.

class aiida_atomistic.data.structure.site.Site(/, **data: Any)[source]#

Bases: pydantic.BaseModel

This class contains the core information about a given site of the system.

It can be a single atom, or an alloy, or even contain vacancies.

_mutable: ClassVar[bool] = True[source]#

model_config[source]#: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

symbol: str | List[str][source]#

position: NumpyArray = None[source]#

mass: float | None = None[source]#

charge: float | None = None[source]#

magmom: NumpyArray | None = None[source]#

magnetization: float | None = None[source]#

weight: Tuple[float, Ellipsis] | None = None[source]#

kind_name: str | None = None[source]#

classmethod ensure_numpy_array(v)[source]#: We want to ensure that the input is a numpy array.

check_minimal_requirements(data)[source]#

__repr__() → str[source]#: Return a string representation of the Site.

property is_alloy[source]#

Return whether the Site is an alloy, i.e. contains more than one element

Returns:: boolean, True if the kind has more than one element, False otherwise.

property alloy_list[source]#: Return the list of elements in the given site which is defined as an alloy

property has_vacancies[source]#

Return whether the Structure contains vacancies, i.e. when the sum of the weight is less than one.

Note

the property uses the internal variable _SUM_THRESHOLD as a threshold.

Returns:: boolean, True if the sum of the weight is less than one, False otherwise

classmethod get_default_tolerances() → dict[source]#

Extract default tolerances from field metadata.

Returns a dictionary mapping property names to their default tolerance values as defined in the json_schema_extra metadata of each field.

Returns:: dictionary with property names as keys and tolerance values as floats

Example:

>>> Site.get_default_tolerances()
{'position': 1e-06, 'mass': 0.001, 'charge': 0.0001, 'magmom': 0.01, 'magnetization': 0.01, 'weight': 0.0001}

classmethod from_ase_atom(aseatom: ase.Atom | None = None, **kwargs) → dict[source]#: Convert an ASE atom or dictionary to a dictionary object which the correct format to describe a Site.

update(**new_data)[source]#

Update the attributes of the SiteCore instance with new values.

Parameters:: new_data – keyword arguments representing the attributes to be updated

get_magmom_coord(coord='spherical')[source]#

Get magnetic moment in given coordinate.

Returns:: spherical theta and phi in unit rad cartesian x y and z in unit ang

set_automatic_kind_name(tag=None)[source]#

Set the type to a string obtained with the symbol appended one after the other, without spaces, in alphabetical order; if the site has a vacancy, a X is appended at the end too.

Parameters:: tag – optional tag to be appended to the kind name

to_ase()[source]#

Return a ase.Atom object for this site.

Parameters:: kind_name – the list of kind_name from the StructureData object.
Returns:: ase.Atom object representing this site
Raises:: ValueError – if any site is an alloy or has vacancies

class aiida_atomistic.data.structure.site.FrozenSite(/, **data: Any)[source]#

Bases: Site

This class contains the core information about a given site of the system.

It can be a single atom, or an alloy, or even contain vacancies.

_mutable: ClassVar[bool] = False[source]#

model_config[source]#: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].