def _get_coord_no_sites_chrg(self, site):
"""
Compute the coordination number and coordination charge
Args:
site:
pymatgen.core.sites.Site
"""
struct = self._structure.copy()
struct.append(site.species_string, site.frac_coords)
coord_finder = VoronoiCoordFinder(struct)
coord_no = coord_finder.get_coordination_number(-1)
coord_sites = coord_finder.get_coordinated_sites(-1)
# In some cases coordination sites to interstitials include
# interstitials also.
sites_to_be_deleted = []
for i in range(len(coord_sites)):
if coord_sites[i].species_string == 'X':
sites_to_be_deleted.append(i)
sites_to_be_deleted.reverse() # So index won't change in between
for ind in sites_to_be_deleted:
del coord_sites[ind]
coord_chrg = 0
for site, weight in coord_finder.get_voronoi_polyhedra(-1).items():
if not site.species_string == 'X':
coord_chrg += weight * self._valence_dict[site.species_string]
return coord_no, coord_sites, coord_chrg
def _get_coord_no_sites_chrg(self, site):
"""
Compute the coordination number and coordination charge
Args:
site:
pymatgen.core.sites.Site
"""
struct = self._structure.copy()
struct.append(site.specie.symbol, site.frac_coords)
coord_finder = VoronoiCoordFinder(struct)
coord_no = coord_finder.get_coordination_number(-1)
coord_sites = coord_finder.get_coordinated_sites(-1)
# In some cases coordination sites to interstitials include
# interstitials also. Filtering them.
def no_inter(site):
return not site.specie.symbol == 'X'
coord_sites = filter(no_inter, coord_sites)
coord_chrg = 0
for site, weight in coord_finder.get_voronoi_polyhedra(-1).items():
if not site.specie.symbol == 'X':
coord_chrg += weight * self._valence_dict[site.species_string]
return coord_no, coord_sites, coord_chrg
def _get_coord_no_sites_chrg(self, site):
"""
Compute the coordination number and coordination charge
Args:
site:
pymatgen.core.sites.Site
"""
struct = self._structure.copy()
struct.append(site.specie.symbol, site.frac_coords)
coord_finder = VoronoiCoordFinder(struct)
coord_no = coord_finder.get_coordination_number(-1)
coord_sites = coord_finder.get_coordinated_sites(-1)
# In some cases coordination sites to interstitials include
# interstitials also. Filtering them.
def no_inter(site):
return not site.specie.symbol == 'X'
coord_sites = filter(no_inter, coord_sites)
coord_chrg = 0
for site, weight in coord_finder.get_voronoi_polyhedra(-1).items():
if not site.specie.symbol == 'X':
coord_chrg += weight * self._valence_dict[site.species_string]
return coord_no, coord_sites, coord_chrg
def get_atom_ofms(self, struct, symm=False):
"""
Calls get_single_ofm for every site in struct. If symm=True,
get_single_ofm is called for symmetrically distinct sites, and
counts is constructed such that ofms[i] occurs counts[i] times
in the structure
Args:
struct (Structure): structure for find ofms for
symm (bool): whether to calculate ofm for only symmetrically
distinct sites
Returns:
ofms ([32 X 32 matrix] X len(struct)): ofms for struct
if symm:
ofms ([32 X 32 matrix] X number of symmetrically distinct sites):
ofms for struct
counts: number of identical sites for each ofm
"""
ofms = []
vcf = VCF(struct, allow_pathological=True)
if symm:
symm_struct = SpacegroupAnalyzer(struct).get_symmetrized_structure()
indices = [lst[0] for lst in symm_struct.equivalent_indices]
counts = [len(lst) for lst in symm_struct.equivalent_indices]
else:
indices = [i for i in range(len(struct.sites))]
for index in indices:
ofms.append(self.get_single_ofm(struct.sites[index], \
vcf.get_voronoi_polyhedra(index)))
if symm:
return ofms, counts
return ofms
def _get_coord_no_sites_chrg(self, site):
"""
Compute the coordination number and coordination charge
Args:
site:
pymatgen.core.sites.Site
"""
struct = self._structure.copy()
struct.append(site.species_string, site.frac_coords)
coord_finder = VoronoiCoordFinder(struct)
coord_no = coord_finder.get_coordination_number(-1)
coord_sites = coord_finder.get_coordinated_sites(-1)
# In some cases coordination sites to interstitials include
# interstitials also.
sites_to_be_deleted = []
for i in range(len(coord_sites)):
if coord_sites[i].species_string == 'X':
sites_to_be_deleted.append(i)
sites_to_be_deleted.reverse() # So index won't change in between
for ind in sites_to_be_deleted:
del coord_sites[ind]
coord_chrg = 0
for site, weight in coord_finder.get_voronoi_polyhedra(-1).items():
if not site.species_string == 'X':
coord_chrg += weight * self._valence_dict[site.species_string]
return coord_no, coord_sites, coord_chrg
def compute(self, structure, n):
params = self._params
vor = VoronoiCoordFinder(structure, **params)
vorp = vor.get_voronoi_polyhedra(n)
cdict = {}
for i in vorp:
if i.species_string not in cdict:
cdict[i.species_string] = vorp[i]
else:
cdict[i.species_string] += vorp[i]
return cdict
class VoronoiCoordFinderTest(PymatgenTest):
def setUp(self):
s = self.get_structure('LiFePO4')
self.finder = VoronoiCoordFinder(s, [Element("O")])
def test_get_voronoi_polyhedra(self):
self.assertEqual(len(self.finder.get_voronoi_polyhedra(0).items()), 8)
def test_get_coordination_number(self):
self.assertAlmostEqual(self.finder.get_coordination_number(0),
5.809265748999465, 7)
def test_get_coordinated_sites(self):
self.assertEqual(len(self.finder.get_coordinated_sites(0)), 8)
def _coord_find(self):
"""
calls VoronoiCoordFinder to compute the coordination number,
coordination charge
"""
for i in range(self.defect_count()):
struct = self._structs[i].copy()
coord_finder = VoronoiCoordFinder(struct)
self._coord_no.append(coord_finder.get_coordination_number(-1))
self._coord_sites.append(coord_finder.get_coordinated_sites(-1))
coord_chrg = 0
for site, weight in coord_finder.get_voronoi_polyhedra(-1).items():
coord_chrg += weight * self._valence_dict[site.species_string]
self._coord_charge_no.append(coord_chrg)
class VoronoiCoordFinderTest(PymatgenTest):
def setUp(self):
s = self.get_structure('LiFePO4')
self.finder = VoronoiCoordFinder(s, [Element("O")])
def test_get_voronoi_polyhedra(self):
self.assertEqual(len(self.finder.get_voronoi_polyhedra(0).items()), 8)
def test_get_coordination_number(self):
self.assertAlmostEqual(self.finder.get_coordination_number(0),
5.809265748999465, 7)
def test_get_coordinated_sites(self):
self.assertEqual(len(self.finder.get_coordinated_sites(0)), 8)
def _coord_find(self):
"""
calls VoronoiCoordFinder to compute the coordination number,
coordination charge
"""
for i in range(self.defect_count()):
struct = self._structs[i].copy()
coord_finder = VoronoiCoordFinder(struct)
self._coord_no.append(coord_finder.get_coordination_number(-1))
self._coord_sites.append(coord_finder.get_coordinated_sites(-1))
coord_chrg = 0
for site, weight in coord_finder.get_voronoi_polyhedra(-1).items():
coord_chrg += weight * self._valence_dict[site.species_string]
self._coord_charge_no.append(coord_chrg)
class VoronoiCoordFinderTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'vasprun.xml')
reader = Vasprun(filepath)
s = reader.final_structure
self.finder = VoronoiCoordFinder(s,[Element("O")])
def test_get_voronoi_polyhedra(self):
self.assertEqual(len(self.finder.get_voronoi_polyhedra(0).items()),10, "Incorrect number of results returned for get_voronoi_polyhedra")
def test_get_coordination_number(self):
print self.finder.get_coordination_number(0)
self.assertAlmostEqual(self.finder.get_coordination_number(0), 5.60588600732, 7, "Incorrect coordination number returned!")
def test_get_coordinated_sites(self):
self.assertEqual(len(self.finder.get_coordinated_sites(0)), 10)
def substructures_from_structure(structure, weight_cutoff=1e-2):
"""
Helper method to calculate substructural components from a
pymatgen structure object.
Args:
structure (Structure): Input structure
weight_cutoff (float): minimum solid angle weight for
inclusion in a substructure
Returns:
A list of Substructure objects for the given structure
"""
vcf = VoronoiCoordFinder(structure)
substructures = []
for i, site in enumerate(structure):
charge = sum([getattr(specie, "oxi_state", 0) * amt
for specie, amt in site.species_and_occu.items()])
central_subspecies = SubStructureSpecie(site.specie.symbol,
oxidation_state=charge,
properties=site.properties,
weight=1.0)
peripheral_subspecies = []
for peripheral_site, weight in vcf.get_voronoi_polyhedra(i).iteritems():
if weight > weight_cutoff:
charge = sum([getattr(specie, "oxi_state", 0) * amt
for specie, amt in
peripheral_site.species_and_occu.items()])
peripheral_subspecies.append(
SubStructureSpecie(peripheral_site.specie.symbol,
oxidation_state=charge,
properties=peripheral_site.properties,
weight=weight))
substructures.append(SubStructure(peripheral_subspecies, central_sub_species=central_subspecies))
return substructures
class VoronoiCoordFinderTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'LiFePO4.cif')
parser = CifParser(filepath)
s = parser.get_structures()[0]
self.finder = VoronoiCoordFinder(s, [Element("O")])
def test_get_voronoi_polyhedra(self):
self.assertEqual(len(self.finder.get_voronoi_polyhedra(0).items()), 8,
"Incorrect number of results returned for " +
"get_voronoi_polyhedra")
def test_get_coordination_number(self):
self.assertAlmostEqual(self.finder.get_coordination_number(0),
5.809265748999465, 7)
def test_get_coordinated_sites(self):
self.assertEqual(len(self.finder.get_coordinated_sites(0)), 8)
class VoronoiCoordFinderTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'LiFePO4.cif')
parser = CifParser(filepath)
s = parser.get_structures()[0]
self.finder = VoronoiCoordFinder(s, [Element("O")])
def test_get_voronoi_polyhedra(self):
self.assertEqual(
len(self.finder.get_voronoi_polyhedra(0).items()), 8,
"Incorrect number of results returned for " +
"get_voronoi_polyhedra")
def test_get_coordination_number(self):
self.assertAlmostEqual(self.finder.get_coordination_number(0),
5.809265748999465, 7)
def test_get_coordinated_sites(self):
self.assertEqual(len(self.finder.get_coordinated_sites(0)), 8)
spacegroup1 = SpacegroupAnalyzer(s1)
spacegroup2 = SpacegroupAnalyzer(s2)
print('space group symbol of structure1:',
spacegroup1.get_space_group_symbol())
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)
def featurize(self, struct, idx):
"""
Get crystal fingerprint of site with given index in input
structure.
Args:
struct (Structure): Pymatgen Structure object.
idx (int): index of target site in structure.
Returns:
list of weighted order parameters of target site.
"""
cn_fingerprint_array = defaultdict(
list
) # dict where key = CN, val is array that contains each OP for that CN
total_weight = math.pi / 4 # 1/4 unit circle area
target = None
if self.cation_anion:
target = []
m_oxi = struct[idx].specie.oxi_state
for site in struct:
if site.specie.oxi_state * m_oxi <= 0: # opposite charge
target.append(site.specie)
if not target:
raise ValueError(
"No valid targets for site within cation_anion constraint!"
)
vcf = VoronoiCoordFinder(struct,
cutoff=self.cutoff_radius,
target=target)
n_w = vcf.get_voronoi_polyhedra(idx)
dist_sorted = (sorted(n_w.values(), reverse=True))
if self.override_cn1:
cn1 = 1
for d in dist_sorted[1:]:
cn1 = cn1 * (dist_sorted[0]**2 - d**2) / dist_sorted[0]**2
cn_fingerprint_array[1] = [round(cn1, 6)]
dist_sorted[0] = dist_sorted[1]
dist_norm = [d / dist_sorted[0] for d in dist_sorted if d > 0]
dist_bins = [] # bin numerical tolerances (~error bar of measurement)
for d in dist_norm:
if not dist_bins or (d > self.tol and dist_bins[-1] /
(1 + self.tol) > d):
dist_bins.append(d)
for dist_idx, dist in enumerate(dist_bins):
neigh_sites = [
n for n, w in n_w.items()
if w > 0 and w / dist_sorted[0] >= dist / (1 + self.tol)
]
cn = len(neigh_sites)
if cn in self.ops:
for opidx, op in enumerate(self.ops[cn]):
if self.optypes[cn][opidx] == "wt":
opval = 1
else:
opval = \
op.get_order_parameters([struct[idx]] + neigh_sites, 0,
indices_neighs=[i for i in
range(1, len(
neigh_sites) + 1)])[
0]
opval = opval or 0 # handles None
if self.optypes[cn][
opidx] == 'bcc': # TODO: remove after pymatgen update
opval = opval / 0.976
# figure out the weight for this opval based on semicircle integration method
x1 = 1 - dist
x2 = 1 if dist_idx == len(dist_bins) - 1 else \
1 - dist_bins[dist_idx + 1]
weight = self._semicircle_integral(x2) - \
self._semicircle_integral(x1)
opval = opval * weight / total_weight
cn_fingerprint_array[cn].append(opval)
# convert dict to list
cn_fingerprint = []
for cn in sorted(self.optypes):
for op_idx, _ in enumerate(self.optypes[cn]):
try:
cn_fingerprint.append(cn_fingerprint_array[cn][op_idx])
except IndexError: # no OP value computed
cn_fingerprint.append(0)
return cn_fingerprint
