def test_get_inequivalent_site_indices(self):
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=False)
inequiv_indices = sa.get_inequivalent_site_indices(list(range(6)))
self.assertEqual(inequiv_indices, [0, 0, 0, 0, 4, 4])
# test using symmetry to determine inequivalent sites.
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=True)
inequiv_indices = sa.get_inequivalent_site_indices(list(range(6)))
self.assertEqual(inequiv_indices, [0, 0, 0, 0, 4, 4])
# test symprec option
sa = SiteAnalyzer(self.ba_n,
use_symmetry_equivalent_sites=True,
symprec=0.000001)
inequiv_indices = sa.get_inequivalent_site_indices(list(range(6)))
self.assertEqual(inequiv_indices, [0, 1, 1, 0, 4, 4])
def _condense_components(
self,
components: List[Component],
spacegroup_analyzer: SpacegroupAnalyzer,
site_analyzer: SiteAnalyzer,
) -> Tuple[Dict[int, Any], List[int]]:
"""Condenses the component data.
Args:
components: A list of structure components, generated using
:obj:`pymatgen.analysis.dimensionality.get_structure_components`
site_analyzer: A site analyzer object for the structure containing
the components.
spacegroup_analyzer: A space group analyzer object for the structure
containing the components.
Returns:
The condensed component data and the component makeup of the
structure. The condensed components have the form::
{
0: {
'formula': 'MoS2',
'sites': [0, 2]
'dimensionality': 2,
'molecule_name': None,
'orientation': (0, 0, 1)
}
}
Where the ``0`` key is the component identifier. The ``sites``
key gives a :obj:`list` of the indexes of the inequivalent sites
in the structure. If the component is zero-dimensional and
is a known molecule, the ``molecule_name`` key will be a :obj:`str`
with the molecule name. The ``orientation`` key is the miller
index (for two-dimensional components) or direction of propagation
(for one-dimensional components).
"""
if self.use_symmetry_equivalent_sites:
inequiv_components = get_sym_inequiv_components(
components, spacegroup_analyzer)
else:
inequiv_components = get_structure_inequiv_components(components)
molecule_namer = MoleculeNamer()
components = {}
component_makeup = []
for i, component in enumerate(inequiv_components):
formula = get_component_formula(
component,
use_iupac_formula=self.use_iupac_formula,
use_common_formulas=self.use_common_formulas,
)
sites = site_analyzer.get_inequivalent_site_indices(
component["site_ids"])
if component["dimensionality"] == 0:
molecule_name = molecule_namer.get_name_from_molecule_graph(
component["molecule_graph"])
else:
molecule_name = None
components[i] = {
"formula": formula,
"dimensionality": component["dimensionality"],
"orientation": component["orientation"],
"molecule_name": molecule_name,
"sites": sites,
}
component_makeup.extend([i] * component["count"])
return components, component_makeup
