def test_pbc_all_distances(self):
fcoords = np.array([[0.3, 0.3, 0.5], [0.1, 0.1, 0.3], [0.9, 0.9, 0.8],
[0.1, 0.0, 0.5], [0.9, 0.7, 0.0]])
lattice = Lattice.from_lengths_and_angles([8, 8, 4], [90, 76, 58])
expected = np.array([[0.000, 3.015, 4.072, 3.519, 3.245],
[3.015, 0.000, 3.207, 1.131, 4.453],
[4.072, 3.207, 0.000, 2.251, 1.788],
[3.519, 1.131, 2.251, 0.000, 3.852],
[3.245, 4.453, 1.788, 3.852, 0.000]])
output = pbc_all_distances(lattice, fcoords, fcoords)
self.assertArrayAlmostEqual(output, expected, 3)
#test just one input point
output2 = pbc_all_distances(lattice, fcoords[0], fcoords)
self.assertArrayAlmostEqual(output2, [expected[0]], 2)
#test distance when initial points are not in unit cell
f1 = [0, 0, 17]
f2 = [0, 0, 10]
self.assertEqual(pbc_all_distances(lattice, f1, f2)[0, 0], 0)
def test_pbc_all_distances(self):
fcoords = np.array([[0.3, 0.3, 0.5],
[0.1, 0.1, 0.3],
[0.9, 0.9, 0.8],
[0.1, 0.0, 0.5],
[0.9, 0.7, 0.0]])
lattice = Lattice.from_lengths_and_angles([8, 8, 4],
[90, 76, 58])
expected = np.array([[0.000, 3.015, 4.072, 3.519, 3.245],
[3.015, 0.000, 3.207, 1.131, 4.453],
[4.072, 3.207, 0.000, 2.251, 1.788],
[3.519, 1.131, 2.251, 0.000, 3.852],
[3.245, 4.453, 1.788, 3.852, 0.000]])
output = pbc_all_distances(lattice, fcoords, fcoords)
self.assertArrayAlmostEqual(output, expected, 3)
#test just one input point
output2 = pbc_all_distances(lattice, fcoords[0], fcoords)
self.assertArrayAlmostEqual(output2, [expected[0]], 2)
#test distance when initial points are not in unit cell
f1 = [0, 0, 17]
f2 = [0, 0, 10]
self.assertEqual(pbc_all_distances(lattice, f1, f2)[0, 0], 0)
def test_subset(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=False,
allow_subset=True)
l = Lattice.orthorhombic(10, 20, 30)
s1 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0,0.1],[0,0,0.2],[.7,.4,.5]])
s2 = Structure(l, ['Si', 'Ag'],
[[0,0.1,0],[-.7,.5,.4]])
result = sm.get_s2_like_s1(s1, s2)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0,0,0.1])), 1)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0.7,0.4,0.5])), 1)
#test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Si'],
[[0,0,0.1],[0,0,0.2],[.7,.4,.5]])
s2 = Structure(l, ['Si', 'Si'],
[[0,0.1,0],[-.7,.5,.4]])
result = sm.get_s2_like_s1(s1, s2)
mindists = np.min(pbc_all_distances(s1.lattice, s1.frac_coords,
result.frac_coords), axis=0)
self.assertLess(np.max(mindists), 1e-6)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0,0,0.1])), 1)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0.7,0.4,0.5])), 1)
#test with not enough sites in s1
#test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Cl'],
[[0,0,0.1],[0,0,0.2],[.7,.4,.5]])
s2 = Structure(l, ['Si', 'Si'],
[[0,0.1,0],[-.7,.5,.4]])
self.assertEqual(sm.get_s2_like_s1(s1, s2), None)
def parse_oxide(self):
"""
Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide
Returns:
oxide_type:
Type of oxide - ozonide/peroxide/superoxide/hydroxide/None
nbonds:
Number of peroxide/superoxide/hydroxide bonds in structure
"""
structure = self.structure
relative_cutoff = self.relative_cutoff
o_sites_frac_coords = []
h_sites_frac_coords = []
lattice = structure.lattice
if isinstance(structure.composition.elements[0], Element):
comp = structure.composition
elif isinstance(structure.composition.elements[0], Specie):
elmap = collections.defaultdict(float)
for site in structure:
for species, occu in site.species_and_occu.items():
elmap[species.element] += occu
comp = Composition(elmap)
if Element("O") not in comp or comp.is_element:
return "None", 0
for site in structure:
syms = [sp.symbol for sp in site.species_and_occu.keys()]
if "O" in syms:
o_sites_frac_coords.append(site.frac_coords)
if "H" in syms:
h_sites_frac_coords.append(site.frac_coords)
if h_sites_frac_coords:
dist_matrix = pbc_all_distances(lattice, o_sites_frac_coords,
h_sites_frac_coords)
if np.any(dist_matrix < relative_cutoff * 0.93):
return "hydroxide", len(
np.where(dist_matrix < relative_cutoff * 0.93)[0]) / 2.0
dist_matrix = pbc_all_distances(lattice, o_sites_frac_coords,
o_sites_frac_coords)
np.fill_diagonal(dist_matrix, 1000)
is_superoxide = False
is_peroxide = False
is_ozonide = False
if np.any(dist_matrix < relative_cutoff * 1.35):
bond_atoms = np.where(dist_matrix < relative_cutoff * 1.35)[0]
is_superoxide = True
elif np.any(dist_matrix < relative_cutoff * 1.49):
is_peroxide = True
bond_atoms = np.where(dist_matrix < relative_cutoff * 1.49)[0]
if is_superoxide:
if len(bond_atoms) > len(set(bond_atoms)):
is_superoxide = False
is_ozonide = True
try:
nbonds = len(set(bond_atoms))
except UnboundLocalError:
nbonds = 0.0
if is_ozonide:
str_oxide = "ozonide"
elif is_superoxide:
str_oxide = "superoxide"
elif is_peroxide:
str_oxide = "peroxide"
else:
str_oxide = "oxide"
return str_oxide, nbonds
def parse_oxide(self):
"""
Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide
Returns:
oxide_type:
Type of oxide - ozonide/peroxide/superoxide/hydroxide/None
nbonds:
Number of peroxide/superoxide/hydroxide bonds in structure
"""
structure = self.structure
relative_cutoff = self.relative_cutoff
o_sites_frac_coords = []
h_sites_frac_coords = []
lattice = structure.lattice
if isinstance(structure.composition.elements[0], Element):
comp = structure.composition
elif isinstance(structure.composition.elements[0], Specie):
elmap = collections.defaultdict(float)
for site in structure:
for species, occu in site.species_and_occu.items():
elmap[species.element] += occu
comp = Composition(elmap)
if Element("O") not in comp or comp.is_element:
return "None", 0
for site in structure:
syms = [sp. symbol for sp in site.species_and_occu.keys()]
if "O" in syms:
o_sites_frac_coords.append(site.frac_coords)
if "H" in syms:
h_sites_frac_coords.append(site.frac_coords)
if h_sites_frac_coords:
dist_matrix = pbc_all_distances(lattice, o_sites_frac_coords,
h_sites_frac_coords)
if np.any(dist_matrix < relative_cutoff * 0.93):
return "hydroxide", len(np.where(dist_matrix < relative_cutoff * 0.93)[0]) / 2.0
dist_matrix = pbc_all_distances(lattice, o_sites_frac_coords,
o_sites_frac_coords)
np.fill_diagonal(dist_matrix, 1000)
is_superoxide = False
is_peroxide = False
is_ozonide = False
if np.any(dist_matrix < relative_cutoff * 1.35):
bond_atoms = np.where(dist_matrix < relative_cutoff * 1.35)[0]
is_superoxide = True
elif np.any(dist_matrix < relative_cutoff * 1.49):
is_peroxide = True
bond_atoms = np.where(dist_matrix < relative_cutoff * 1.49)[0]
if is_superoxide:
if len(bond_atoms) > len(set(bond_atoms)):
is_superoxide = False
is_ozonide = True
try:
nbonds = len(set(bond_atoms))
except UnboundLocalError:
nbonds = 0.0
if is_ozonide:
str_oxide = "ozonide"
elif is_superoxide:
str_oxide = "superoxide"
elif is_peroxide:
str_oxide = "peroxide"
else:
str_oxide = "oxide"
return str_oxide, nbonds
def oxide_type(structure, relative_cutoff=1.2):
"""
Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide
Args:
structure:
Input structure.
relative_cutoff:
Relative_cutoff * act. cutoff stipulates the max. distance two
O atoms must be from each other.
"""
o_sites_frac_coords = []
h_sites_frac_coords = []
lattice = structure.lattice
# Check if H2O/O2/H2O2/non-oxide is being checked
el_other_than_OH = [el.symbol for el in structure.composition.elements if el.symbol not in ["H", "O"]]
if (not el_other_than_OH) | (len(el_other_than_OH) == len(structure.composition.elements)):
return "None"
for site in structure:
syms = [sp. symbol for sp in site.species_and_occu.keys()]
if "O" in syms:
o_sites_frac_coords.append(site.frac_coords)
if "H" in syms:
h_sites_frac_coords.append(site.frac_coords)
# We are not correcting hydrides
if not o_sites_frac_coords:
return "None"
if h_sites_frac_coords:
dist_matrix = pbc_all_distances(lattice, o_sites_frac_coords, h_sites_frac_coords)
if np.any(dist_matrix < relative_cutoff * 0.93):
return "hydroxide"
dist_matrix = pbc_all_distances(lattice, o_sites_frac_coords, o_sites_frac_coords)
np.fill_diagonal(dist_matrix, 1000)
is_superoxide = False
is_peroxide = False
is_ozonide = False
if np.any(dist_matrix < relative_cutoff * 1.35):
is_superoxide = True
elif np.any(dist_matrix < relative_cutoff * 1.49):
is_peroxide = True
if is_superoxide:
if (int(structure.composition["O"] / structure.composition.get_reduced_composition_and_factor()[1]) % 3 == 0):
sum = 0
for elt in [el for el in structure.composition.elements if el is not Element("O")]:
sum += structure.composition[elt.symbol]
if sum / structure.composition.get_reduced_composition_and_factor()[1] <= 1:
is_superoxide = False
is_ozonide = True
if is_ozonide:
return "ozonide"
elif is_superoxide:
return "superoxide"
elif is_peroxide:
return "peroxide"
else:
return "oxide"