def test_get_primitive_structure(self):
coords = [[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5]]
fcc_ag = IStructure(Lattice.cubic(4.09), ["Ag"] * 4, coords)
self.assertEqual(len(fcc_ag.get_primitive_structure()), 1)
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
bcc_li = IStructure(Lattice.cubic(4.09), ["Li"] * 2, coords)
self.assertEqual(len(bcc_li.get_primitive_structure()), 1)
def test_to_dict(self):
si = Specie("Si", 4)
mn = Element("Mn")
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, [{
si: 0.5,
mn: 0.5
}, {
si: 0.5
}], coords)
self.assertIn("lattice", struct.to_dict)
self.assertIn("sites", struct.to_dict)
d = self.propertied_structure.to_dict
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice,
[{
Specie('O', -2, properties={"spin": 3}): 1.0
}, {
Specie('Mg', 2, properties={"spin": 2}): 0.8
}],
coords,
site_properties={'magmom': [5, -5]})
d = s.to_dict
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
self.assertEqual(d['sites'][0]['species'][0]['properties']['spin'], 3)
def test_interpolate_lattice_rotation(self):
l1 = Lattice([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
l2 = Lattice([[-1.01, 0, 0], [0, -1.01, 0], [0, 0, 1]])
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
struct1 = IStructure(l1, ["Si"] * 2, coords)
struct2 = IStructure(l2, ["Si"] * 2, coords)
int_s = struct1.interpolate(struct2, 2, interpolate_lattices=True)
# Assert that volume is monotonic
self.assertTrue(struct2.lattice.volume >= int_s[1].lattice.volume)
self.assertTrue(int_s[1].lattice.volume >= struct1.lattice.volume)
def test_get_primitive_structure(self):
coords = [[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5]]
fcc_ag = IStructure(Lattice.cubic(4.09), ["Ag"] * 4, coords)
self.assertEqual(len(fcc_ag.get_primitive_structure()), 1)
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
bcc_li = IStructure(Lattice.cubic(4.09), ["Li"] * 2, coords)
bcc_prim = bcc_li.get_primitive_structure()
self.assertEqual(len(bcc_prim), 1)
self.assertAlmostEqual(bcc_prim.lattice.alpha, 109.47122, 3)
coords = [[0] * 3, [0.5] * 3, [0.25] * 3, [0.26] * 3]
s = IStructure(Lattice.cubic(4.09), ["Ag"] * 4, coords)
self.assertEqual(len(s.get_primitive_structure()), 4)
def test_bad_structure(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
coords.append([0.75, 0.5, 0.75])
self.assertRaises(StructureError,
IStructure,
self.lattice, ["Si"] * 3,
coords,
validate_proximity=True)
#these shouldn't raise an error
IStructure(self.lattice, ["Si"] * 2, coords[:2], True)
IStructure(self.lattice, ["Si"], coords[:1], True)
def test_interpolate(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 10)
for s in int_s:
self.assertIsNotNone(s, "Interpolation Failed!")
self.assertEqual(int_s[0].lattice, s.lattice)
self.assertArrayEqual(int_s[1][1].frac_coords, [0.725, 0.5, 0.725])
badlattice = [[1, 0.00, 0.00], [0, 1, 0.00], [0.00, 0, 1]]
struct2 = IStructure(badlattice, ["Si"] * 2, coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si", "Fe"], coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
# Test autosort feature.
s1 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
s1.pop(0)
s2 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
s2.pop(2)
random.shuffle(s2)
for s in s1.interpolate(s2, autosort_tol=0.5):
self.assertArrayAlmostEqual(s1[0].frac_coords, s[0].frac_coords)
self.assertArrayAlmostEqual(s1[2].frac_coords, s[2].frac_coords)
# Make sure autosort has no effect on simpler interpolations,
# and with shuffled sites.
s1 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
s2 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
s2[0] = "Fe", [0.01, 0.01, 0.01]
random.shuffle(s2)
for s in s1.interpolate(s2, autosort_tol=0.5):
self.assertArrayAlmostEqual(s1[1].frac_coords, s[1].frac_coords)
self.assertArrayAlmostEqual(s1[2].frac_coords, s[2].frac_coords)
self.assertArrayAlmostEqual(s1[3].frac_coords, s[3].frac_coords)
def get_pymatgen_formula(compound):
"""
given a string of 'A2B1Bp1X6' return its pymatgen standard formula
Args:
compound: a string of form 'A2B1Bp1X6'
Returns:
formula : a formula style defined in pymatgen
"""
m = re.match(
"([A-Za-z]+)([0-9])([A-Za-z]+)([0-9])([A-Za-z]+)([0-9])([A-Za-z]+)([0-9])",
compound)
A, B, Bp, X = m.group(1), m.group(3), m.group(5), m.group(7)
struc = IStructure(lattice=[[1, 0.000000, 0.000000],
[0.5, sqrt(3) / 2, 0.000000],
[0.5, 1 / 2.0 / sqrt(3.0),
sqrt(2.0 / 3.0)]],
species=[A, A, B, Bp, X, X, X, X, X, X],
coords=[[0.2500, 0.2500, 0.2500],
[0.7500, 0.7500, 0.7500],
[0.5000, 0.5000, 0.5000],
[0.0000, 0.0000, 0.0000],
[0.2550, 0.7450, 0.2550],
[0.7450, 0.7450, 0.2550],
[0.7450, 0.2550, 0.7450],
[0.7450, 0.2550, 0.2550],
[0.2550, 0.7450, 0.7450],
[0.2550, 0.2550, 0.7450]])
return struc.formula
def test_primitive_structure_volume_check(self):
l = Lattice.tetragonal(10, 30)
coords = [[0.5, 0.8, 0], [0.5, 0.2, 0], [0.5, 0.8, 0.333],
[0.5, 0.5, 0.333], [0.5, 0.5, 0.666], [0.5, 0.2, 0.666]]
s = IStructure(l, ["Ag"] * 6, coords)
sprim = s.get_primitive_structure(tolerance=0.1)
self.assertEqual(len(sprim), 6)
def test_fractional_occupations(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, [{'O': 1.0}, {'Mg': 0.8}], coords)
self.assertEqual(str(s.composition), 'Mg0.8 O1')
self.assertFalse(s.is_ordered)
def test_get_sorted_structure(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, ["O", "Li"],
coords,
site_properties={'charge': [-2, 1]})
sorted_s = s.get_sorted_structure()
self.assertEqual(sorted_s[0].species_and_occu, Composition("Li"))
self.assertEqual(sorted_s[1].species_and_occu, Composition("O"))
self.assertEqual(sorted_s[0].charge, 1)
self.assertEqual(sorted_s[1].charge, -2)
s = IStructure(self.lattice, ["Se", "C", "Se", "C"],
[[0] * 3, [0.5] * 3, [0.25] * 3, [0.75] * 3])
self.assertEqual(
[site.specie.symbol for site in s.get_sorted_structure()],
["C", "C", "Se", "Se"])
def test_specie_init(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, [{
Specie('O', -2): 1.0
}, {
Specie('Mg', 2): 0.8
}], coords)
self.assertEqual(str(s.composition), 'Mg2+0.8 O2-1')
def setUp(self):
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
self.lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.struct = IStructure(self.lattice, ["Si"] * 2, coords)
self.assertEqual(len(self.struct), 2,
"Wrong number of sites in structure!")
self.assertTrue(self.struct.is_ordered)
self.assertTrue(self.struct.ntypesp == 1)
coords = list()
coords.append([0, 0, 0])
coords.append([0., 0, 0.0000001])
self.assertRaises(StructureError, IStructure, self.lattice, ["Si"] * 2,
coords, True)
self.propertied_structure = IStructure(
self.lattice, ["Si"] * 2,
coords,
site_properties={'magmom': [5, -5]})
def test_interpolate_lattice(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
l2 = Lattice.from_lengths_and_angles([3, 4, 4], [100, 100, 70])
struct2 = IStructure(l2, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 2, interpolate_lattices=True)
self.assertArrayAlmostEqual(struct.lattice.abc, int_s[0].lattice.abc)
self.assertArrayAlmostEqual(struct.lattice.angles,
int_s[0].lattice.angles)
self.assertArrayAlmostEqual(struct2.lattice.abc, int_s[2].lattice.abc)
self.assertArrayAlmostEqual(struct2.lattice.angles,
int_s[2].lattice.angles)
int_angles = [(a + struct2.lattice.angles[i]) / 2
for i, a in enumerate(struct.lattice.angles)]
self.assertArrayAlmostEqual(int_angles, int_s[1].lattice.angles)
def test_interpolate(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 10)
for s in int_s:
self.assertIsNotNone(s, "Interpolation Failed!")
self.assertArrayEqual(int_s[1][1].frac_coords, [0.725, 0.5, 0.725])
badlattice = [[1, 0.00, 0.00], [0, 1, 0.00], [0.00, 0, 1]]
struct2 = IStructure(badlattice, ["Si"] * 2, coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si", "Fe"], coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
def test_interpolate_lattice(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
l2 = Lattice.from_lengths_and_angles([3, 4, 4], [100, 100, 70])
struct2 = IStructure(l2, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 2, interpolate_lattices=True)
self.assertArrayAlmostEqual(struct.lattice.abc, int_s[0].lattice.abc)
self.assertArrayAlmostEqual(struct.lattice.angles,
int_s[0].lattice.angles)
self.assertArrayAlmostEqual(struct2.lattice.abc, int_s[2].lattice.abc)
self.assertArrayAlmostEqual(struct2.lattice.angles,
int_s[2].lattice.angles)
int_angles = [110.3976469, 94.5359731, 64.5165856]
self.assertArrayAlmostEqual(int_angles, int_s[1].lattice.angles)
# Assert that volume is monotonic
self.assertTrue(struct2.lattice.volume >= int_s[1].lattice.volume)
self.assertTrue(int_s[1].lattice.volume >= struct.lattice.volume)
def test_copy(self):
new_struct = self.propertied_structure.copy(
site_properties={'charge': [2, 3]})
self.assertEqual(new_struct[0].magmom, 5)
self.assertEqual(new_struct[1].magmom, -5)
self.assertEqual(new_struct[0].charge, 2)
self.assertEqual(new_struct[1].charge, 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0., 0, 0.0000001])
structure = IStructure(self.lattice, ["O", "Si"],
coords,
site_properties={'magmom': [5, -5]})
new_struct = structure.copy(site_properties={'charge': [2, 3]},
sanitize=True)
self.assertEqual(new_struct[0].magmom, -5)
self.assertEqual(new_struct[1].magmom, 5)
self.assertEqual(new_struct[0].charge, 3)
self.assertEqual(new_struct[1].charge, 2)
self.assertAlmostEqual(new_struct.volume, structure.volume)
def simple_cubic():
lattice = Lattice.cubic(1.0)
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
def construct_graph(self, traj_coords, lattices, atom_types, target_index):
if self.backend == 'kdtree':
nbr_lists, diag_lattices = [], []
for coord, lattice in tqdm(zip(traj_coords, lattices),
total=len(traj_coords),
disable=not self.verbose):
# take the diagonal part of the lattice matrix
lattice = np.diagonal(lattice)
diag_lattices.append(lattice)
pkdt = PeriodicCKDTree(lattice, coord)
all_nbrs_idxes = pkdt.query_ball_point(coord, self.radius)
nbr_list = []
for idx, nbr_idxes in enumerate(all_nbrs_idxes):
nbr_dists = distance_pbc(coord[idx], coord[nbr_idxes],
lattice)
nbr_idx_dist = sorted(zip(nbr_idxes, nbr_dists),
key=lambda x: x[1])
assert nbr_idx_dist[0][1] == 0 and\
nbr_idx_dist[0][0] == idx and\
len(nbr_idx_dist) >= self.n_nbrs + 1
nbr_list.append(
[idx for idx, dist in nbr_idx_dist[1:self.n_nbrs + 1]])
nbr_lists.append(np.stack(np.array(nbr_list, dtype='int32')))
nbr_lists = np.stack(nbr_lists)
diag_lattices = np.stack(diag_lattices)
return {
'traj_coords': traj_coords,
'lattices': diag_lattices,
'atom_types': atom_types,
'target_index': target_index,
'nbr_lists': nbr_lists
}
elif self.backend == 'direct':
nbr_lists, nbr_dists = [], []
for coord, lattice in tqdm(zip(traj_coords, lattices),
total=len(traj_coords),
disable=not self.verbose):
crystal = IStructure(lattice=lattice,
species=atom_types,
coords=coord,
coords_are_cartesian=True)
all_nbrs = crystal.get_all_neighbors(r=self.radius,
include_index=True)
all_nbrs = [
sorted(nbrs, key=lambda x: x[1]) for nbrs in all_nbrs
]
nbr_list, nbr_dist = [], []
for nbr in all_nbrs:
assert len(nbr) >= self.n_nbrs, 'not find enough neighbors'
nbr_list.append(
list(map(lambda x: x[2], nbr[:self.n_nbrs])))
nbr_dist.append(
list(map(lambda x: x[1], nbr[:self.n_nbrs])))
nbr_lists.append(np.array(nbr_list, dtype='int32'))
nbr_dists.append(np.array(nbr_dist, dtype='float32'))
nbr_lists, nbr_dists = np.stack(nbr_lists), np.stack(nbr_dists)
return {
'traj_coords': traj_coords,
'atom_types': atom_types,
'target_index': target_index,
'nbr_lists': nbr_lists,
'nbr_dists': nbr_dists
}
def construct_graph(self, traj_coords, lattices, atom_types, target_index):
if self.backend == 'kdtree':
nbr_lists, diag_lattices = [], []
for coord, lattice in tqdm(zip(traj_coords, lattices),
total=len(traj_coords),
disable=not self.verbose):
# take the diagonal part of the lattice matrix
lattice = np.diagonal(lattice)
diag_lattices.append(lattice)
pkdt = PeriodicCKDTree(lattice, coord)
all_nbrs_idxes = pkdt.query_ball_point(coord, self.radius)
nbr_list = []
for idx, nbr_idxes in enumerate(all_nbrs_idxes):
nbr_dists = distance_pbc(coord[idx], coord[nbr_idxes],
lattice)
nbr_idx_dist = sorted(zip(nbr_idxes, nbr_dists),
key=lambda x: x[1])
assert nbr_idx_dist[0][1] == 0 and\
nbr_idx_dist[0][0] == idx and\
len(nbr_idx_dist) >= self.n_nbrs + 1
nbr_list.append(
[idx for idx, dist in nbr_idx_dist[1:self.n_nbrs + 1]])
nbr_lists.append(np.stack(np.array(nbr_list, dtype='int32')))
nbr_lists = np.stack(nbr_lists)
diag_lattices = np.stack(diag_lattices)
return {
'traj_coords': traj_coords,
'lattices': diag_lattices,
'atom_types': atom_types,
'target_index': target_index,
'nbr_lists': nbr_lists
}
elif self.backend == 'direct':
nbr_lists, nbr_dists = [], []
for coord, lattice in tqdm(zip(traj_coords, lattices),
total=len(traj_coords),
disable=not self.verbose):
crystal = IStructure(lattice=lattice,
species=atom_types,
coords=coord,
coords_are_cartesian=True)
all_nbrs = crystal.get_all_neighbors(r=self.radius,
include_index=True)
all_nbrs = [
sorted(nbrs, key=lambda x: x[1]) for nbrs in all_nbrs
]
nbr_list, nbr_dist = [], []
for nbr in all_nbrs:
assert len(nbr) >= self.n_nbrs, 'not find enough neighbors'
nbr_list.append(
list(map(lambda x: x[2], nbr[:self.n_nbrs])))
nbr_dist.append(
list(map(lambda x: x[1], nbr[:self.n_nbrs])))
nbr_lists.append(np.array(nbr_list, dtype='int32'))
nbr_dists.append(np.array(nbr_dist, dtype='float32'))
nbr_lists, nbr_dists = np.stack(nbr_lists), np.stack(nbr_dists)
return {
'traj_coords': traj_coords,
'atom_types': atom_types,
'target_index': target_index,
'nbr_lists': nbr_lists,
'nbr_dists': nbr_dists
}
elif self.backend == 'ndirect':
stcs = [
Structure(lattice=lattices[i],
species=atom_types,
coords=traj_coords[i],
coords_are_cartesian=True)
for i in tqdm(range(len(traj_coords)),
desc='Generating structure...',
disable=not self.verbose)
]
a, b, c = [
np.ceil(2 * self.radius / d).astype('int')
for d in stcs[0].lattice.abc
]
if [a, b, c] != [1, 1, 1]:
_ = [
stc.make_supercell([
np.ceil(2 * self.radius / d).astype('int')
for d in stc.lattice.abc
]) for stc in tqdm(stcs,
desc='Building supercell...',
disable=not self.verbose)
]
nbr_lists = np.array([
stc.distance_matrix.argsort()[:, 1:1 + self.n_nbrs]
for stc in tqdm(stcs,
desc='Generating neighbor index...',
disable=not self.verbose)
],
dtype='int32')
nbr_dists = np.array([
np.sort(stc.distance_matrix)[:, 1:1 + self.n_nbrs]
for stc in tqdm(stcs,
desc='Generating neighbor distance...',
disable=not self.verbose)
],
dtype='float32')
nbr_lists, nbr_dists = np.stack(nbr_lists), np.stack(nbr_dists)
if not np.all((nbr_dists < self.radius) & (nbr_dists > 0)):
raise ('not find enough neighbors')
return {
'traj_coords': traj_coords,
'atom_types': atom_types,
'target_index': target_index,
'nbr_lists': nbr_lists,
'nbr_dists': nbr_dists
}
