aiida_pseudo.groups.family.pseudo ================================= .. py:module:: aiida_pseudo.groups.family.pseudo .. autoapi-nested-parse:: Subclass of ``Group`` that serves as a base class for representing pseudo potential families. Classes ------- .. autoapisummary:: aiida_pseudo.groups.family.pseudo.PseudoPotentialFamily Module Contents --------------- .. py:class:: PseudoPotentialFamily(*args, **kwargs) Bases: :py:obj:`aiida.orm.Group` Group to represent a pseudo potential family. This is a base class that provides most of the functionality but does not actually define what type of pseudo potentials can be contained. If ``_pseudo_types`` is not defined, any pseudo potential type is accepted in this family, as long as it is a subclass of ``PseudoPotentialData``. Subclasses can limit which pseudo types can be hosted by setting ``_pseudo_types`` to a tuple of ``PseudoPotentialData`` subclasses. .. py:attribute:: _key_pseudo_type :value: '_pseudo_type' .. py:attribute:: _pseudo_types .. py:attribute:: _pseudos :value: None .. py:method:: __repr__() Represent the instance for debugging purposes. .. py:method:: __str__() Represent the instance for human-readable purposes. .. py:method:: pseudo_types() Return the pseudo potential types that this family accepts. :return: the tuple of subclasses of ``PseudoPotentialData`` that this family can host nodes of. If it returns ``None``, that means all subclasses are supported. .. py:method:: _validate_pseudo_type(pseudo_type) :classmethod: Validate the ``pseudo_type`` passed to ``parse_pseudos_from_directory``. :return: the pseudo type to be used. .. py:method:: _validate_dirpath(dirpath) :classmethod: Validate the ``dirpath`` passed to ``parse_pseudos_from_directory``. :return: the directory path to be used. .. py:method:: parse_pseudos_from_directory(dirpath, pseudo_type=None, deduplicate=True) :classmethod: Parse the pseudo potential files in the given directory into a list of data nodes. .. note:: The directory pointed to by `dirpath` should only contain pseudo potential files. Optionally, it can contain just a single directory, that contains all the pseudo potential files. If any other files are stored in the basepath or the subdirectory, that cannot be successfully parsed as pseudo potential files the method will raise a ``ValueError``. :param dirpath: absolute path to a directory containing pseudo potentials. :param pseudo_type: subclass of ``PseudoPotentialData`` to be used for the parsed pseudos. If not specified and the family only defines a single supported pseudo type in ``_pseudo_types`` then that will be used otherwise a ``ValueError`` is raised. :param deduplicate: if True, will scan database for existing pseudo potentials of same type and with the same md5 checksum, and use that instead of the parsed one. :return: list of data nodes :raises ValueError: if ``dirpath`` is not a directory or contains anything other than files. :raises ValueError: if ``dirpath`` contains multiple pseudo potentials for the same element. :raises ValueError: if ``pseudo_type`` is explicitly specified and is not supported by this family class. :raises ValueError: if ``pseudo_type`` is not specified and the class supports more than one pseudo type. :raises ParsingError: if the constructor of the pseudo type fails for one of the files in the ``dirpath``. .. py:method:: create_from_folder(dirpath, label, *, description='', pseudo_type=None, deduplicate=True) :classmethod: Create a new ``PseudoPotentialFamily`` from the pseudo potentials contained in a directory. :param dirpath: absolute path to the folder containing the UPF files. :param label: label to give to the ``PseudoPotentialFamily``, should not already exist. :param description: description to give to the family. :param pseudo_type: subclass of ``PseudoPotentialData`` to be used for the parsed pseudos. If not specified and the family only defines a single supported pseudo type in ``_pseudo_types`` then that will be used otherwise a ``ValueError`` is raised. :param deduplicate: if True, will scan database for existing pseudo potentials of same type and with the same md5 checksum, and use that instead of the parsed one. :raises ValueError: if a ``PseudoPotentialFamily`` already exists with the given name. :raises ValueError: if ``dirpath`` is not a directory or contains anything other than files. :raises ValueError: if ``dirpath`` contains multiple pseudo potentials for the same element. :raises ValueError: if ``pseudo_type`` is explicitly specified and is not supported by this family class. :raises ValueError: if ``pseudo_type`` is not specified and the class supports more than one pseudo type. :raises ParsingError: if the constructor of the pseudo type fails for one of the files in the ``dirpath``. .. py:property:: pseudo_type Return the type of the pseudopotentials that are hosted by this family. :return: the pseudopotential type or ``None`` if none has been set yet. .. py:method:: update_pseudo_type() Update the pseudo type, stored as an extra, based on the current nodes in the family. .. py:method:: add_nodes(nodes) Add a node or a set of nodes to the family. .. note: Each family instance can only contain a single pseudo potential for each element. :param nodes: a single or list of ``Node`` instances of type that is in ``PseudoPotentialFamily._pseudo_types``. :raises ModificationNotAllowed: if the family is not stored. :raises TypeError: if nodes are not an instance or list of instance of any of the classes listed by ``PseudoPotentialFamily._pseudo_types``. :raises ValueError: if any of the nodes are not stored or their elements already exist in this family. .. py:method:: remove_nodes(nodes) Remove a pseudopotential or a set of pseudopotentials from the family. :param nodes: a single or list of ``PseudoPotentialData`` instances or subclasses thereof. .. py:method:: clear() Remove all the pseudopotentials from this family. .. py:property:: pseudos Return the dictionary of pseudo potentials of this family indexed on the element symbol. :return: dictionary of element symbol mapping pseudo potentials .. py:property:: elements Return the list of elements for which this family defines a pseudo potential. :return: list of element symbols .. py:method:: get_pseudo(element) Return the pseudo potential for the given element. :param element: the element for which to return the corresponding pseudo potential. :return: pseudo potential instance if it exists :raises ValueError: if the family does not contain a pseudo potential for the given element .. py:method:: get_pseudos(*, elements: Optional[Union[List[str], Tuple[str]]] = None, structure: Union[structures_classes] = None) -> Mapping[str, Union[structures_classes]] Return the mapping of kind names on pseudo potential data nodes for the given list of elements or structure. :param elements: list of element symbols. :param structure: the ``StructureData`` or ``LegacyStructureData`` node. :return: dictionary mapping the kind names of a structure on the corresponding pseudo potential data nodes. :raises ValueError: if the family does not contain a pseudo for any of the elements of the given structure.