def get_connectivity_description(connectivity_matrix, polyhedra, structure, sites_diff, radius=2.6, anions=None):
"""
Writes a verbal description of the connectivity between cations in a structure; connections between cation
polyhedra and reflections of itself (and reflections of other cation polyhedra) are also counted; different
sites of the same species are not differentiated (that is, connectivity for cations with different sites, not
including reflections, are not counted separately)
:param connectivity_matrix: (dict) dictionary of dictionaries containing connectivities between different cation
polyhedra (should be output from get_connectivity_matrix)
:param polyhedra: (List of Polyhedra) list of all Polyhedra in the supercell structure
:param structure: (Structure) target structure
:param sites_diff: (Boolean) whether sites with the same cation species should be differentiated
:param radius: (float) radius within which to determine whether a nearby atom is a peripheral ion
:param anions: (List of Strings) list of species strings of what we consider anions in the structure
:return: (dict) dictionary of strings containing verbal descriptions of connectivites between cations in the given
structure; keys = cation tag (eg: Li1, Na2, where the letters represent the species and the number distinguishes
the species from the other instances of that same species in the unit cell); dict values = String descriptions of
connectivity
"""
if anions is None:
anions = ['O2-', 'O', 'F-', 'F', 'Cl-', 'Cl', 'I-', 'I', 'Br-', 'Br', 'S2-', 'S', 'N', 'N3-']
cn_list = EffectiveCoordFinder(structure).get_avg_cn(radius, anions)
descriptions = {}
for cation_1 in connectivity_matrix.keys():
descriptions[cation_1] = ""
for cation_1 in connectivity_matrix.keys():
if sites_diff:
cn1 = get_effective_cn(get_ex_poly(polyhedra, cation_1))
else:
cn1 = cn_list[cation_1]
descriptions[cation_1] += cation_1 + " are " + get_cn_description(cn1) + ". \n"
for cation_2 in connectivity_matrix[cation_1].keys():
connected = False
for connectivity_type in connectivity_matrix[cation_1][cation_2].keys():
if connectivity_matrix[cation_1][cation_2][connectivity_type] != 0:
connected = True
if connected:
descriptions[cation_1] += "They are "
first = True
for connectivity_type in connectivity_matrix[cation_1][cation_2].keys():
if connectivity_matrix[cation_1][cation_2][connectivity_type] != 0:
if first:
descriptions[cation_1] += connectivity_type + "-connected "
first = False
else:
descriptions[cation_1] += "and " + connectivity_type + "-connected "
if sites_diff:
cn2 = get_effective_cn(get_ex_poly(polyhedra, cation_2))
else:
cn2 = cn_list[cation_2]
descriptions[cation_1] += "to " + get_cn_description(cn2) + " " + cation_2 + ". "
return descriptions
def test_econ_on_polyhedra(self):
"""Test Routine econ for single Polyhedra"""
licoo2_matrix, licoo2_polyhedra = connectivity.get_connectivity_matrix(self.licoo2_structure, False)
for polyhedra in licoo2_polyhedra:
if polyhedra.central_ion_name == "Li":
test_poly = polyhedra
break
cn = econ.get_effective_cn(test_poly)
self.assertAlmostEqual(cn, 6.0, 2, "Li polyhedra should be 6-fold coordinated")