def test_topography_analyzer(self):
# check interstitial sites for FePO4 using Voronoi Tessellation
vor_feo4 = TopographyAnalyzer(self.feo4,
framework_ions=["O"],
cations=["P", "Fe"],
check_volume=False)
vor_feo4.cluster_nodes(tol=1.2)
vor_feo4.remove_collisions(1.2)
s_feo4 = vor_feo4.get_structure_with_nodes()
sites_feo4 = np.array([
s_feo4[i].frac_coords for i in range(len(s_feo4))
if s_feo4[i].species_string == "X0+"
])
# check total number of vnodes
self.assertAlmostEqual(len(vor_feo4.vnodes), 24)
# check four sites that match Li sites in LiFePO4(mp-19017)
site_predicted = [[0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0, 0.5],
[0, 0.5, 0]]
for i in range(0, 4):
is_site_matched = False
for site in sites_feo4:
distance = s_feo4.lattice. \
get_distance_and_image(site, site_predicted[i])
if distance[0] < 0.01:
is_site_matched = True
else:
continue
self.assertTrue(is_site_matched)
def test_topography_analyzer(self):
# check interstitial sites for FePO4 using Voronoi Tessellation
vor_feo4 = TopographyAnalyzer(self.feo4, framework_ions=["O"],
cations=["P", "Fe"], check_volume=False)
vor_feo4.cluster_nodes(tol=1.2)
vor_feo4.remove_collisions(1.2)
s_feo4 = vor_feo4.get_structure_with_nodes()
sites_feo4 = np.array(
[s_feo4[i].frac_coords for i in range(len(s_feo4)) if
s_feo4[i].species_string == "X0+"])
# check total number of vnodes
self.assertAlmostEqual(len(vor_feo4.vnodes), 24)
# check four sites that match Li sites in LiFePO4(mp-19017)
site_predicted = [[0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0, 0.5],
[0, 0.5, 0]]
for i in range(0, 4):
is_site_matched = False
for site in sites_feo4:
distance = s_feo4.lattice. \
get_distance_and_image(site, site_predicted[i])
if distance[0] < 0.01:
is_site_matched = True
else:
continue
self.assertTrue(is_site_matched)
def __init__(self, structure, element):
"""
Initializes an Interstitial generator using Voronoi sites
Args:
structure (Structure): pymatgen structure object
element (str or Element or Specie): element for the interstitial
"""
self.structure = structure
self.element = element
framework = list(self.structure.symbol_set)
get_voronoi = TopographyAnalyzer(self.structure,
framework, [],
check_volume=False)
get_voronoi.cluster_nodes()
get_voronoi.remove_collisions()
# trim equivalent nodes with symmetry analysis
struct_to_trim = self.structure.copy()
for poss_inter in get_voronoi.vnodes:
struct_to_trim.append(self.element,
poss_inter.frac_coords,
coords_are_cartesian=False)
symmetry_finder = SpacegroupAnalyzer(struct_to_trim, symprec=1e-1)
equiv_sites_list = symmetry_finder.get_symmetrized_structure(
).equivalent_sites
self.equiv_site_seq = []
for poss_site_list in equiv_sites_list:
if poss_site_list[0] not in self.structure:
self.equiv_site_seq.append(poss_site_list)
self.count_def = 0 # for counting the index of the generated defect
def __init__(self, structure, element):
"""
Initializes an Interstitial generator using Voronoi sites
Args:
structure (Structure): pymatgen structure object
element (str or Element or Specie): element for the interstitial
"""
self.structure = structure
self.element = element
framework = list(self.structure.symbol_set)
get_voronoi = TopographyAnalyzer(self.structure, framework, [], check_volume=False)
get_voronoi.cluster_nodes()
get_voronoi.remove_collisions()
# trim equivalent nodes with symmetry analysis
struct_to_trim = self.structure.copy()
for poss_inter in get_voronoi.vnodes:
struct_to_trim.append(self.element, poss_inter.frac_coords, coords_are_cartesian=False)
symmetry_finder = SpacegroupAnalyzer(struct_to_trim, symprec=1e-1)
equiv_sites_list = symmetry_finder.get_symmetrized_structure().equivalent_sites
self.equiv_site_seq = []
for poss_site_list in equiv_sites_list:
if poss_site_list[0] not in self.structure:
self.equiv_site_seq.append(poss_site_list)
self.count_def = 0 # for counting the index of the generated defect
def __init__(self, structure, element):
"""
Initializes an Interstitial generator using Voronoi sites
Args:
structure (Structure): pymatgen structure object
element (str or Element or Species): element for the interstitial
"""
self.structure = structure
self.element = element
framework = list(self.structure.symbol_set)
get_voronoi = TopographyAnalyzer(self.structure,
framework, [],
check_volume=False)
get_voronoi.cluster_nodes()
get_voronoi.remove_collisions()
# trim equivalent nodes with symmetry analysis
struct_to_trim = self.structure.copy()
for poss_inter in get_voronoi.vnodes:
struct_to_trim.append(self.element,
poss_inter.frac_coords,
coords_are_cartesian=False)
symmetry_finder = SpacegroupAnalyzer(struct_to_trim, symprec=1e-1)
equiv_sites_list = symmetry_finder.get_symmetrized_structure(
).equivalent_sites
# do additional screening for sublattice equivalent
# defects which may have slipped through
pdc = PointDefectComparator()
self.unique_defect_seq = []
for poss_site_list in equiv_sites_list:
poss_site = poss_site_list[0]
if poss_site not in self.structure:
now_defect = Interstitial(self.structure, poss_site)
append_defect = True
for unique_defect in self.unique_defect_seq:
if pdc.are_equal(now_defect, unique_defect):
append_defect = False
if append_defect:
self.unique_defect_seq.append(now_defect)
self.count_def = 0 # for counting the index of the generated defect
def __init__(self, structure, element):
"""
Initializes an Interstitial generator using Voronoi sites
Args:
structure (Structure): pymatgen structure object
element (str or Element or Specie): element for the interstitial
"""
self.structure = structure
self.element = element
framework = list(self.structure.symbol_set)
get_voronoi = TopographyAnalyzer(self.structure, framework, [], check_volume=False)
get_voronoi.cluster_nodes()
get_voronoi.remove_collisions()
# trim equivalent nodes with symmetry analysis
struct_to_trim = self.structure.copy()
for poss_inter in get_voronoi.vnodes:
struct_to_trim.append(self.element, poss_inter.frac_coords, coords_are_cartesian=False)
symmetry_finder = SpacegroupAnalyzer(struct_to_trim, symprec=1e-1)
equiv_sites_list = symmetry_finder.get_symmetrized_structure().equivalent_sites
# do additional screening for sublattice equivalent
# defects which may have slipped through
pdc = PointDefectComparator()
self.unique_defect_seq = []
for poss_site_list in equiv_sites_list:
poss_site = poss_site_list[0]
if poss_site not in self.structure:
now_defect = Interstitial( self.structure, poss_site)
append_defect = True
for unique_defect in self.unique_defect_seq:
if pdc.are_equal( now_defect, unique_defect):
append_defect = False
if append_defect:
self.unique_defect_seq.append( now_defect)
self.count_def = 0 # for counting the index of the generated defect