Tools to operate on CifData nodes.


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__ = ''

list of weak references to the object (if defined), **kwargs)[source]

Creates using ASE.


unable to correctly import structures of alloys.


requires ASE module., **kwargs)[source]

Creates 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.[source]

Refine (reduce) the cell of, find and remove symmetrically equivalent atoms.

Parameters:node – a instance.
Returns:dict with


can be used as inline calculation., 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.

  • 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