Tools to operate on CifData nodes.
aiida.tools.data.cif.
InvalidOccupationsError
Bases: Exception
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__
__weakref__
list of weak references to the object (if defined)
_get_aiida_structure_ase_inline
Creates aiida.orm.nodes.data.structure.StructureData using ASE.
aiida.orm.nodes.data.structure.StructureData
Note
unable to correctly import structures of alloys.
requires ASE module.
_get_aiida_structure_pymatgen_inline
Creates aiida.orm.nodes.data.structure.StructureData using pymatgen.
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.
requires pymatgen module.
refine_inline
Refine (reduce) the cell of aiida.orm.nodes.data.cif.CifData, find and remove symmetrically equivalent atoms.
aiida.orm.nodes.data.cif.CifData
node – a aiida.orm.nodes.data.cif.CifData instance.
dict with aiida.orm.nodes.data.cif.CifData
can be used as inline calculation.
symop_string_from_symop_matrix_tr
Construct a CIF representation of symmetry operator plus translation. See International Tables for Crystallography Vol. A. (2002) for definition.
matrix – 3x3 matrix, representing the symmetry operator
tr – translation vector of length 3 (default 0)
eps – epsilon parameter for fuzzy comparison x == 0
CIF representation of symmetry operator