class VoronoiIndex(BaseFeaturizer):
"""
The Voronoi indices n_i and the fractional Voronoi indices n_i/sum(n_i) that
reflects the i-fold symmetry in the local sites.
n_i denotes the number of the i-edged faces, and i is in the range of 3-10 here.
e.g. for bcc lattice, the Voronoi indices are [0,6,0,8,0,0...]
for fcc/hcp lattice, the Voronoi indices are [0,12,0,0,...]
for icosahedra, the Voronoi indices are [0,0,12,0,...]
"""
def __init__(self, cutoff=6.0):
"""
Args:
cutoff (float): cutoff distance in determining the potential
neighbors for Voronoi tessellation analysis
"""
self.cutoff = cutoff
self.voronoi_analyzer = VoronoiAnalyzer(cutoff=self.cutoff)
def featurize(self, struct, idx):
"""
Args:
struct (Structure): Pymatgen Structure object.
idx (int): index of target site in structure.
Returns:
list including Voronoi indices, sum of Voronoi indices, and
fractional Voronoi indices
"""
voro_index_result = []
voro_index_list = self.voronoi_analyzer.analyze(struct, n=idx)
for voro_index in voro_index_list:
voro_index_result.append(voro_index)
voro_index_sum = sum(voro_index_list)
voro_index_result.append(voro_index_sum)
voro_index_frac_list = voro_index_list / voro_index_sum
for voro_index_frac in voro_index_frac_list:
voro_index_result.append(voro_index_frac)
return voro_index_result
def feature_labels(self):
labels = []
for i in range(3, 11):
labels.append('voro_index_%d' % i)
labels.append('voro_index_sum')
for i in range(3, 11):
labels.append('voro_index_frac_%d' % i)
return labels
def citations(self):
citation = ('@book{okabe1992spatial, '
'title={Spatial tessellations}, '
'author={Okabe, Atsuyuki}, '
'year={1992}, '
'publisher={Wiley Online Library}}')
return citation
def implementors(self):
return ['Qi Wang']
class VoronoiAnalyzerTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
self.ss = Xdatcar(
os.path.join(PymatgenTest.TEST_FILES_DIR, "XDATCAR.MD")).structures
self.s = self.ss[1]
self.va = VoronoiAnalyzer(cutoff=4.0)
def test_analyze(self):
# Check for the Voronoi index of site i in Structure
single_structure = self.va.analyze(self.s, n=5)
self.assertIn(
single_structure.view(),
np.array([4, 3, 3, 4, 2, 2, 1, 0]).view(),
"Cannot find the right polyhedron.",
)
# Check for the presence of a Voronoi index and its frequency in
# a ensemble (list) of Structures
ensemble = self.va.analyze_structures(self.ss,
step_freq=2,
most_frequent_polyhedra=10)
self.assertIn(
("[1 3 4 7 1 0 0 0]", 3),
ensemble,
"Cannot find the right polyhedron in ensemble.",
)
class VoronoiAnalyzerTest(PymatgenTest):
def setUp(self):
self.ss = Xdatcar(os.path.join(test_dir, 'XDATCAR.MD')).structures
self.s = self.ss[1]
self.va = VoronoiAnalyzer(cutoff=4.0)
def test_analyze(self):
# Check for the Voronoi index of site i in Structure
single_structure = self.va.analyze(self.s, n=5)
self.assertIn(single_structure.view(),
np.array([4, 3, 3, 4, 2, 2, 1, 0]).view(),
"Cannot find the right polyhedron.")
# Check for the presence of a Voronoi index and its frequency in
# a ensemble (list) of Structures
ensemble = self.va.analyze_structures(self.ss, step_freq=2,
most_frequent_polyhedra=10)
self.assertIn(('[1 3 4 7 1 0 0 0]', 3),
ensemble, "Cannot find the right polyhedron in ensemble.")
class VoronoiAnalyzerTest(PymatgenTest):
def setUp(self):
self.ss = Xdatcar(os.path.join(test_dir, 'XDATCAR.MD')).structures
self.s = self.ss[19]
self.va = VoronoiAnalyzer(cutoff=4.0)
def test_analyze(self):
# Check for the Voronoi index of site i in Structure
single_structure = self.va.analyze(self.s, n=5)
self.assertIn(single_structure.view(),
np.array([5, 4, 2, 5, 3, 1, 0, 2]).view(),
"Cannot find the right polyhedron.")
# Check for the presence of a Voronoi index and its frequency in
# a ensemble (list) of Structures
ensemble = self.va.analyze_structures(self.ss, step_freq=2,
most_frequent_polyhedra=10)
self.assertIn(('[2 3 3 3 1 1 0 0]', 6),
ensemble, "Cannot find the right polyhedron in ensemble.")
print('space group number of structure1:',
spacegroup1.get_space_group_number())
print('space group symbol of structure2:',
spacegroup2.get_space_group_symbol())
print('space group number of structure2:',
spacegroup2.get_space_group_number())
Voronoi = VoronoiCoordFinder(s2, target=None)
site = s2.num_sites
#print("s2[0]:",s2.sites)
print("s2_cart_coords[0]", s2.cart_coords[0])
#print("s2_distance_(0,1)",s2.get_distance(0,1))
polyhedra = Voronoi.get_voronoi_polyhedra(1)
coordinate = Voronoi.get_coordination_number(1)
coordinate_sites = Voronoi.get_coordinated_sites(1)
Voronoi_Analyzer = VoronoiAnalyzer()
anay = Voronoi_Analyzer.analyze(s1, n=0)
strucs = [s1, s2]
anays = Voronoi_Analyzer.analyze_structures(strucs)
print("Voronoi_Analyzer.analyze(s1,n=0):", anay)
#plt = Voronoi_Analyzer.plot_vor_analysis(anays)
relax = RelaxationAnalyzer(s1, s2)
volume_change = relax.get_percentage_volume_change()
lattice_parameter_changes = relax.get_percentage_lattice_parameter_changes()
print('initial volume:', s1.volume)
print('final volume:', s2.volume)
print("percent_volume_change:", volume_change)
print("percent_lattice_change:", lattice_parameter_changes)
bond_dist = relax.get_percentage_bond_dist_changes(max_radius=6)
print("percent_bond_distance_change:", bond_dist)
connec = VoronoiConnectivity(s2)
#print("connec.get_connections():",connec.get_connections())
