pymatgen.entries.entry_tools module¶
This module implements functions to perform various useful operations on entries, such as grouping entries by structure.
-
class
EntrySet
(entries: Iterable[Union[pymatgen.analysis.phase_diagram.PDEntry, pymatgen.entries.computed_entries.ComputedEntry, pymatgen.entries.computed_entries.ComputedStructureEntry]])[source]¶ Bases:
collections.abc.MutableSet
,monty.json.MSONable
A convenient container for manipulating entries. Allows for generating subsets, dumping into files, etc.
- Parameters
entries – All the entries.
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property
chemsys
[source]¶ Returns: set representing the chemical system, e.g., {“Li”, “Fe”, “P”, “O”}
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classmethod
from_csv
(filename: str)[source]¶ Imports PDEntries from a csv.
- Parameters
filename – Filename to import from.
- Returns
List of Elements, List of PDEntries
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get_subset_in_chemsys
(chemsys: List[str])[source]¶ Returns an EntrySet containing only the set of entries belonging to a particular chemical system (in this definition, it includes all sub systems). For example, if the entries are from the Li-Fe-P-O system, and chemsys=[“Li”, “O”], only the Li, O, and Li-O entries are returned.
- Parameters
chemsys – Chemical system specified as list of elements. E.g., [“Li”, “O”]
- Returns
EntrySet
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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]]