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|
:py:mod:`aiida.tools`
=====================
.. py:module:: aiida.tools
.. autodoc2-docstring:: aiida.tools
:allowtitles:
Package Contents
----------------
Classes
~~~~~~~
.. list-table::
:class: autosummary longtable
:align: left
* - :py:obj:`CalculationTools <aiida.tools.calculations.base.CalculationTools>`
- .. autodoc2-docstring:: aiida.tools.calculations.base.CalculationTools
:summary:
* - :py:obj:`Graph <aiida.tools.visualization.graph.Graph>`
- .. autodoc2-docstring:: aiida.tools.visualization.graph.Graph
:summary:
* - :py:obj:`GroupPath <aiida.tools.groups.paths.GroupPath>`
- .. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath
:summary:
* - :py:obj:`Orbital <aiida.tools.data.orbital.orbital.Orbital>`
- .. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital
:summary:
* - :py:obj:`RealhydrogenOrbital <aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital>`
- .. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital
:summary:
Functions
~~~~~~~~~
.. list-table::
:class: autosummary longtable
:align: left
* - :py:obj:`default_link_styles <aiida.tools.visualization.graph.default_link_styles>`
- .. autodoc2-docstring:: aiida.tools.visualization.graph.default_link_styles
:summary:
* - :py:obj:`default_node_styles <aiida.tools.visualization.graph.default_node_styles>`
- .. autodoc2-docstring:: aiida.tools.visualization.graph.default_node_styles
:summary:
* - :py:obj:`default_node_sublabels <aiida.tools.visualization.graph.default_node_sublabels>`
- .. autodoc2-docstring:: aiida.tools.visualization.graph.default_node_sublabels
:summary:
* - :py:obj:`delete_group_nodes <aiida.tools.graph.deletions.delete_group_nodes>`
- .. autodoc2-docstring:: aiida.tools.graph.deletions.delete_group_nodes
:summary:
* - :py:obj:`delete_nodes <aiida.tools.graph.deletions.delete_nodes>`
- .. autodoc2-docstring:: aiida.tools.graph.deletions.delete_nodes
:summary:
* - :py:obj:`get_explicit_kpoints_path <aiida.tools.data.array.kpoints.main.get_explicit_kpoints_path>`
- .. autodoc2-docstring:: aiida.tools.data.array.kpoints.main.get_explicit_kpoints_path
:summary:
* - :py:obj:`get_kpoints_path <aiida.tools.data.array.kpoints.main.get_kpoints_path>`
- .. autodoc2-docstring:: aiida.tools.data.array.kpoints.main.get_kpoints_path
:summary:
* - :py:obj:`pstate_node_styles <aiida.tools.visualization.graph.pstate_node_styles>`
- .. autodoc2-docstring:: aiida.tools.visualization.graph.pstate_node_styles
:summary:
* - :py:obj:`spglib_tuple_to_structure <aiida.tools.data.structure.spglib_tuple_to_structure>`
- .. autodoc2-docstring:: aiida.tools.data.structure.spglib_tuple_to_structure
:summary:
* - :py:obj:`structure_to_spglib_tuple <aiida.tools.data.structure.structure_to_spglib_tuple>`
- .. autodoc2-docstring:: aiida.tools.data.structure.structure_to_spglib_tuple
:summary:
Data
~~~~
.. list-table::
:class: autosummary longtable
:align: left
* - :py:obj:`DELETE_LOGGER <aiida.tools.graph.deletions.DELETE_LOGGER>`
- .. autodoc2-docstring:: aiida.tools.graph.deletions.DELETE_LOGGER
:summary:
API
~~~
.. py:class:: CalculationTools(node)
:canonical: aiida.tools.calculations.base.CalculationTools
.. autodoc2-docstring:: aiida.tools.calculations.base.CalculationTools
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.calculations.base.CalculationTools.__init__
.. py:data:: DELETE_LOGGER
:canonical: aiida.tools.graph.deletions.DELETE_LOGGER
:value: None
.. autodoc2-docstring:: aiida.tools.graph.deletions.DELETE_LOGGER
.. py:class:: Graph(engine=None, graph_attr=None, global_node_style=None, global_edge_style=None, include_sublabels=True, link_style_fn=None, node_style_fn=None, node_sublabel_fn=None, node_id_type='pk', backend: typing.Optional[aiida.orm.implementation.StorageBackend] = None)
:canonical: aiida.tools.visualization.graph.Graph
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.__init__
.. py:property:: backend
:canonical: aiida.tools.visualization.graph.Graph.backend
:type: aiida.orm.implementation.StorageBackend
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.backend
.. py:property:: graphviz
:canonical: aiida.tools.visualization.graph.Graph.graphviz
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.graphviz
.. py:property:: nodes
:canonical: aiida.tools.visualization.graph.Graph.nodes
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.nodes
.. py:property:: edges
:canonical: aiida.tools.visualization.graph.Graph.edges
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.edges
.. py:method:: _load_node(node)
:canonical: aiida.tools.visualization.graph.Graph._load_node
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph._load_node
.. py:method:: _default_link_types(link_types)
:canonical: aiida.tools.visualization.graph.Graph._default_link_types
:staticmethod:
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph._default_link_types
.. py:method:: add_node(node, style_override=None, overwrite=False)
:canonical: aiida.tools.visualization.graph.Graph.add_node
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.add_node
.. py:method:: add_edge(in_node, out_node, link_pair=None, style=None, overwrite=False)
:canonical: aiida.tools.visualization.graph.Graph.add_edge
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.add_edge
.. py:method:: _convert_link_types(link_types)
:canonical: aiida.tools.visualization.graph.Graph._convert_link_types
:staticmethod:
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph._convert_link_types
.. py:method:: add_incoming(node, link_types=(), annotate_links=None, return_pks=True)
:canonical: aiida.tools.visualization.graph.Graph.add_incoming
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.add_incoming
.. py:method:: add_outgoing(node, link_types=(), annotate_links=None, return_pks=True)
:canonical: aiida.tools.visualization.graph.Graph.add_outgoing
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.add_outgoing
.. py:method:: recurse_descendants(origin, depth=None, link_types=(), annotate_links=False, origin_style=MappingProxyType(_OVERRIDE_STYLES_DICT['origin_node']), include_process_inputs=False, highlight_classes=None)
:canonical: aiida.tools.visualization.graph.Graph.recurse_descendants
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.recurse_descendants
.. py:method:: recurse_ancestors(origin, depth=None, link_types=(), annotate_links=False, origin_style=MappingProxyType(_OVERRIDE_STYLES_DICT['origin_node']), include_process_outputs=False, highlight_classes=None)
:canonical: aiida.tools.visualization.graph.Graph.recurse_ancestors
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.recurse_ancestors
.. py:method:: add_origin_to_targets(origin, target_cls, target_filters=None, include_target_inputs=False, include_target_outputs=False, origin_style=(), annotate_links=False)
:canonical: aiida.tools.visualization.graph.Graph.add_origin_to_targets
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.add_origin_to_targets
.. py:method:: add_origins_to_targets(origin_cls, target_cls, origin_filters=None, target_filters=None, include_target_inputs=False, include_target_outputs=False, origin_style=(), annotate_links=False)
:canonical: aiida.tools.visualization.graph.Graph.add_origins_to_targets
.. autodoc2-docstring:: aiida.tools.visualization.graph.Graph.add_origins_to_targets
.. py:exception:: GroupNotFoundError(grouppath)
:canonical: aiida.tools.groups.paths.GroupNotFoundError
Bases: :py:obj:`Exception`
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupNotFoundError
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupNotFoundError.__init__
.. py:exception:: GroupNotUniqueError(grouppath)
:canonical: aiida.tools.groups.paths.GroupNotUniqueError
Bases: :py:obj:`Exception`
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupNotUniqueError
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupNotUniqueError.__init__
.. py:class:: GroupPath(path: str = '', cls: aiida.orm.groups.GroupMeta = orm.Group, warn_invalid_child: bool = True)
:canonical: aiida.tools.groups.paths.GroupPath
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__init__
.. py:method:: _validate_path(path)
:canonical: aiida.tools.groups.paths.GroupPath._validate_path
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath._validate_path
.. py:method:: __repr__() -> str
:canonical: aiida.tools.groups.paths.GroupPath.__repr__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__repr__
.. py:method:: __eq__(other: typing.Any) -> bool
:canonical: aiida.tools.groups.paths.GroupPath.__eq__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__eq__
.. py:method:: __lt__(other: typing.Any) -> bool
:canonical: aiida.tools.groups.paths.GroupPath.__lt__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__lt__
.. py:property:: path
:canonical: aiida.tools.groups.paths.GroupPath.path
:type: str
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.path
.. py:property:: path_list
:canonical: aiida.tools.groups.paths.GroupPath.path_list
:type: typing.List[str]
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.path_list
.. py:property:: key
:canonical: aiida.tools.groups.paths.GroupPath.key
:type: typing.Optional[str]
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.key
.. py:property:: delimiter
:canonical: aiida.tools.groups.paths.GroupPath.delimiter
:type: str
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.delimiter
.. py:property:: cls
:canonical: aiida.tools.groups.paths.GroupPath.cls
:type: aiida.orm.groups.GroupMeta
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.cls
.. py:property:: parent
:canonical: aiida.tools.groups.paths.GroupPath.parent
:type: typing.Optional[aiida.tools.groups.paths.GroupPath]
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.parent
.. py:method:: __truediv__(path: str) -> aiida.tools.groups.paths.GroupPath
:canonical: aiida.tools.groups.paths.GroupPath.__truediv__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__truediv__
.. py:method:: __getitem__(path: str) -> aiida.tools.groups.paths.GroupPath
:canonical: aiida.tools.groups.paths.GroupPath.__getitem__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__getitem__
.. py:method:: get_group() -> typing.Optional[aiida.tools.groups.paths.GroupPath]
:canonical: aiida.tools.groups.paths.GroupPath.get_group
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.get_group
.. py:property:: group_ids
:canonical: aiida.tools.groups.paths.GroupPath.group_ids
:type: typing.List[int]
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.group_ids
.. py:property:: is_virtual
:canonical: aiida.tools.groups.paths.GroupPath.is_virtual
:type: bool
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.is_virtual
.. py:method:: get_or_create_group() -> typing.Tuple[aiida.orm.Group, bool]
:canonical: aiida.tools.groups.paths.GroupPath.get_or_create_group
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.get_or_create_group
.. py:method:: delete_group()
:canonical: aiida.tools.groups.paths.GroupPath.delete_group
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.delete_group
.. py:property:: children
:canonical: aiida.tools.groups.paths.GroupPath.children
:type: typing.Iterator[aiida.tools.groups.paths.GroupPath]
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.children
.. py:method:: __iter__() -> typing.Iterator[aiida.tools.groups.paths.GroupPath]
:canonical: aiida.tools.groups.paths.GroupPath.__iter__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__iter__
.. py:method:: __len__() -> int
:canonical: aiida.tools.groups.paths.GroupPath.__len__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__len__
.. py:method:: __contains__(key: str) -> bool
:canonical: aiida.tools.groups.paths.GroupPath.__contains__
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.__contains__
.. py:method:: walk(return_virtual: bool = True) -> typing.Iterator[aiida.tools.groups.paths.GroupPath]
:canonical: aiida.tools.groups.paths.GroupPath.walk
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.walk
.. py:method:: walk_nodes(filters: typing.Optional[dict] = None, node_class: typing.Optional[aiida.orm.Node] = None, query_batch: typing.Optional[int] = None) -> typing.Iterator[aiida.tools.groups.paths.WalkNodeResult]
:canonical: aiida.tools.groups.paths.GroupPath.walk_nodes
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.walk_nodes
.. py:property:: browse
:canonical: aiida.tools.groups.paths.GroupPath.browse
.. autodoc2-docstring:: aiida.tools.groups.paths.GroupPath.browse
.. py:exception:: InvalidPath()
:canonical: aiida.tools.groups.paths.InvalidPath
Bases: :py:obj:`Exception`
.. autodoc2-docstring:: aiida.tools.groups.paths.InvalidPath
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.groups.paths.InvalidPath.__init__
.. py:exception:: NoGroupsInPathError(grouppath)
:canonical: aiida.tools.groups.paths.NoGroupsInPathError
Bases: :py:obj:`Exception`
.. autodoc2-docstring:: aiida.tools.groups.paths.NoGroupsInPathError
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.groups.paths.NoGroupsInPathError.__init__
.. py:class:: Orbital(**kwargs)
:canonical: aiida.tools.data.orbital.orbital.Orbital
.. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital
.. rubric:: Initialization
.. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital.__init__
.. py:attribute:: _base_fields_required
:canonical: aiida.tools.data.orbital.orbital.Orbital._base_fields_required
:value: (('position',),)
.. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital._base_fields_required
.. py:attribute:: _base_fields_optional
:canonical: aiida.tools.data.orbital.orbital.Orbital._base_fields_optional
:value: None
.. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital._base_fields_optional
.. py:method:: __repr__()
:canonical: aiida.tools.data.orbital.orbital.Orbital.__repr__
.. py:method:: __str__() -> str
:canonical: aiida.tools.data.orbital.orbital.Orbital.__str__
.. py:method:: _validate_keys(input_dict)
:canonical: aiida.tools.data.orbital.orbital.Orbital._validate_keys
.. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital._validate_keys
.. py:method:: set_orbital_dict(init_dict)
:canonical: aiida.tools.data.orbital.orbital.Orbital.set_orbital_dict
.. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital.set_orbital_dict
.. py:method:: get_orbital_dict()
:canonical: aiida.tools.data.orbital.orbital.Orbital.get_orbital_dict
.. autodoc2-docstring:: aiida.tools.data.orbital.orbital.Orbital.get_orbital_dict
.. py:class:: RealhydrogenOrbital
:canonical: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital
Bases: :py:obj:`aiida.tools.data.orbital.orbital.Orbital`
.. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital
.. py:attribute:: _base_fields_required
:canonical: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital._base_fields_required
:value: None
.. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital._base_fields_required
.. py:attribute:: _base_fields_optional
:canonical: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital._base_fields_optional
:value: None
.. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital._base_fields_optional
.. py:method:: __str__()
:canonical: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital.__str__
.. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital.__str__
.. py:method:: _validate_keys(input_dict)
:canonical: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital._validate_keys
.. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital._validate_keys
.. py:method:: get_name_from_quantum_numbers(angular_momentum, magnetic_number=None)
:canonical: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital.get_name_from_quantum_numbers
:classmethod:
.. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital.get_name_from_quantum_numbers
.. py:method:: get_quantum_numbers_from_name(name)
:canonical: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital.get_quantum_numbers_from_name
:classmethod:
.. autodoc2-docstring:: aiida.tools.data.orbital.realhydrogen.RealhydrogenOrbital.get_quantum_numbers_from_name
.. py:function:: default_link_styles(link_pair: aiida.orm.utils.links.LinkPair, add_label: bool, add_type: bool) -> dict
:canonical: aiida.tools.visualization.graph.default_link_styles
.. autodoc2-docstring:: aiida.tools.visualization.graph.default_link_styles
.. py:function:: default_node_styles(node)
:canonical: aiida.tools.visualization.graph.default_node_styles
.. autodoc2-docstring:: aiida.tools.visualization.graph.default_node_styles
.. py:function:: default_node_sublabels(node)
:canonical: aiida.tools.visualization.graph.default_node_sublabels
.. autodoc2-docstring:: aiida.tools.visualization.graph.default_node_sublabels
.. py:function:: delete_group_nodes(pks: typing.Iterable[int], dry_run: typing.Union[bool, typing.Callable[[typing.Set[int]], bool]] = True, backend=None, **traversal_rules: bool) -> typing.Tuple[typing.Set[int], bool]
:canonical: aiida.tools.graph.deletions.delete_group_nodes
.. autodoc2-docstring:: aiida.tools.graph.deletions.delete_group_nodes
.. py:function:: delete_nodes(pks: typing.Iterable[int], dry_run: typing.Union[bool, typing.Callable[[typing.Set[int]], bool]] = True, backend=None, **traversal_rules: bool) -> typing.Tuple[typing.Set[int], bool]
:canonical: aiida.tools.graph.deletions.delete_nodes
.. autodoc2-docstring:: aiida.tools.graph.deletions.delete_nodes
.. py:function:: get_explicit_kpoints_path(structure, method='seekpath', **kwargs)
:canonical: aiida.tools.data.array.kpoints.main.get_explicit_kpoints_path
.. autodoc2-docstring:: aiida.tools.data.array.kpoints.main.get_explicit_kpoints_path
.. py:function:: get_kpoints_path(structure, method='seekpath', **kwargs)
:canonical: aiida.tools.data.array.kpoints.main.get_kpoints_path
.. autodoc2-docstring:: aiida.tools.data.array.kpoints.main.get_kpoints_path
.. py:function:: pstate_node_styles(node)
:canonical: aiida.tools.visualization.graph.pstate_node_styles
.. autodoc2-docstring:: aiida.tools.visualization.graph.pstate_node_styles
.. py:function:: spglib_tuple_to_structure(structure_tuple, kind_info=None, kinds=None)
:canonical: aiida.tools.data.structure.spglib_tuple_to_structure
.. autodoc2-docstring:: aiida.tools.data.structure.spglib_tuple_to_structure
.. py:function:: structure_to_spglib_tuple(structure)
:canonical: aiida.tools.data.structure.structure_to_spglib_tuple
.. autodoc2-docstring:: aiida.tools.data.structure.structure_to_spglib_tuple
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