aiida.tools.data package

Submodules

Tools to operate on CifData nodes.

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

__module__ = 'aiida.tools.data.cif'
__weakref__

list of weak references to the object (if defined)

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.

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.

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.

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