def test_connectivity_description(self):
"""Test Routine Connectivity Description on BCC Fe"""
central_species = ['Fe']
peripheral_species = ['Fe']
fe_matrix, fe_polyhedra, supercell = \
connectivity.get_connectivity_matrix(self.fe_structure, False, 2.8, peripheral_species, central_species)
fe_descriptions = connectivity.get_connectivity_description(fe_matrix, fe_polyhedra, self.fe_structure, False)
for cation in fe_descriptions.keys():
self.assertIn(cation, fe_matrix.keys())
self.assertTrue(isinstance(fe_descriptions[cation], str)
or isinstance(fe_descriptions[cation], unicode),
"Descriptions are not type str or unicode")
def test_connectivity_description_sites_diff(self):
"""Test Routine Connectivity Description on LiCoO2"""
licoo2_matrix, licoo2_polyhedra, supercell = \
connectivity.get_connectivity_matrix(self.licoo2_structure, True)
licoo2_descriptions = connectivity.get_connectivity_description(licoo2_matrix, licoo2_polyhedra, self.licoo2_structure, True)
for cation in licoo2_descriptions.keys():
in_matrix_keys = False
for keys in licoo2_matrix.keys():
if cation in keys:
in_matrix_keys = True
self.assertTrue(in_matrix_keys, "Cation being described not in connectivity matrix")
self.assertTrue(isinstance(licoo2_descriptions[cation], str)
or isinstance(licoo2_descriptions[cation], unicode),
"Descriptions are not type str or unicode")
__author__ = 'Tina_Chen'
__contributor__ = 'Anubhav Jain'
if __name__ == '__main__':
# path to structure file
path = 'LiCoO2.cif'
# optional list of strings with central/target species abbreviations
# (i.e. we aim to find connectivity between polyhedra with these species at the center)
central_species = ['Li']
# optional list of strings with peripheral species abbreviations
# (i.e. we aim to find connectivity where these species are surrounding the central/target species)
peripheral_species = None
# radius from the central/target sites to which we look for peripheral species
# only needs to be changed if central species is very large (eg: Ba, Sr)
radius = 2.6
structure = Structure.from_file(path, True, True)
print structure
connectivity_matrix, all_polyhedra, supercell = \
connectivity.get_connectivity_matrix(structure, True, radius, peripheral_species, central_species)
descriptions = connectivity.get_connectivity_description(connectivity_matrix, all_polyhedra, structure, True, anions=peripheral_species)
for cation in descriptions:
print ""
print descriptions[cation]
