aiida.tools.data package¶
Subpackages¶
Submodules¶
Tools to operate on CifData nodes.
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exception
aiida.tools.data.cif.
InvalidOccupationsError
[source]¶ Bases:
Exception
An exception that will be raised if pymatgen fails to parse the structure from a cif because some site occupancies exceed the occupancy tolerance. This often happens for structures that have attached species, such as hydrogen, and specify a placeholder position for it, leading to occupancies greater than one. Pymatgen only issues a warning in this case and simply does not return a structure
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__module__
= 'aiida.tools.data.cif'¶
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__weakref__
¶ list of weak references to the object (if defined)
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aiida.tools.data.cif.
_get_aiida_structure_ase_inline
(cif, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.structure.StructureData
using ASE.Note
unable to correctly import structures of alloys.
Note
requires ASE module.
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aiida.tools.data.cif.
_get_aiida_structure_pymatgen_inline
(cif, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.structure.StructureData
using pymatgen.- Parameters
occupancy_tolerance – If total occupancy of a site is between 1 and occupancy_tolerance, the occupancies will be scaled down to 1.
site_tolerance – This tolerance is used to determine if two sites are sitting in the same position, in which case they will be combined to a single disordered site. Defaults to 1e-4.
Note
requires pymatgen module.
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aiida.tools.data.cif.
refine_inline
(node)[source]¶ Refine (reduce) the cell of
aiida.orm.nodes.data.cif.CifData
, find and remove symmetrically equivalent atoms.- Parameters
node – a
aiida.orm.nodes.data.cif.CifData
instance.- Returns
dict with
aiida.orm.nodes.data.cif.CifData
Note
can be used as inline calculation.
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aiida.tools.data.cif.
symop_string_from_symop_matrix_tr
(matrix, tr=(0, 0, 0), eps=0)[source]¶ Construct a CIF representation of symmetry operator plus translation. See International Tables for Crystallography Vol. A. (2002) for definition.
- Parameters
matrix – 3x3 matrix, representing the symmetry operator
tr – translation vector of length 3 (default 0)
eps – epsilon parameter for fuzzy comparison x == 0
- Returns
CIF representation of symmetry operator