orgdisord.merge.merge_structures#

orgdisord.merge.merge_structures(images, algo='symm', symops=None, use_disordered_only=True, symprec=0.001, oxidation_states=None, return_group_indices=False, quiet=False, check_species=True)[source]#

Merge a list of ASE atoms objects to the symmetry inequivalent ones.

Parameters

  • images (list) – A list of ASE atoms objects.

  • algo (str) – The merging algorithm. Default is ‘symm’.

  • symops (list) – A list of tuples: (rotation, translation). Note: we skip the first one assuming it’s the identity.

  • use_disordered_only (bool) – If True, use the disordered atoms (tag != 0) instead of the full structure when comparing.

  • symprec (float) – The tolerance for symmetry equivalence.

  • oxidation_states (dict) – A dictionary of oxidation states for each element. (Only needed for the ‘ewald’ algorithm.)

  • return_group_indices (bool) – If True, return the indices of the merged structures in addition to the merged structures.

  • quiet (bool) – If True, suppress progress bar.

  • check_species (bool) – If True, check that the species match before comparing the coordinates.

Returns

Tuple of one structure per group and the group multiplicity. If return_group_indices is True, the indices of the merged structures in the original list are also returned.