pymatgen.entries.entry_tools module

group_entries_by_structure(entries, species_to_remove=None, ltol=0.2, stol=0.4, angle_tol=5, primitive_cell=True, scale=True, comparator=<pymatgen.analysis.structure_matcher.SpeciesComparator object>, ncpus=None)[source]

Given a sequence of ComputedStructureEntries, use structure fitter to group them by structural similarity.

Parameters:
  • entries – Sequence of ComputedStructureEntries.
  • species_to_remove – Sometimes you want to compare a host framework (e.g., in Li-ion battery analysis). This allows you to specify species to remove before structural comparison.
  • ltol (float) – Fractional length tolerance. Default is 0.2.
  • stol (float) – Site tolerance in Angstrom. Default is 0.4 Angstrom.
  • angle_tol (float) – Angle tolerance in degrees. Default is 5 degrees.
  • primitive_cell (bool) – If true: input structures will be reduced to primitive cells prior to matching. Defaults to True.
  • scale – Input structures are scaled to equivalent volume if true; For exact matching, set to False.
  • comparator – A comparator object implementing an equals method that declares equivalency of sites. Default is SpeciesComparator, which implies rigid species mapping.
  • ncpus – Number of cpus to use. Use of multiple cpus can greatly improve fitting speed. Default of None means serial processing.
Returns:

Sequence of sequence of entries by structural similarity. e.g, [[ entry1, entry2], [entry3, entry4, entry5]]