class IStructureTest(PymatgenTest):
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_matches(self):
ss = self.struct * 2
self.assertTrue(ss.matches(self.struct))
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_volume_and_density(self):
self.assertAlmostEqual(self.struct.volume, 40.04, 2, "Volume wrong!")
self.assertAlmostEqual(self.struct.density, 2.33, 2,
"Incorrect density")
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(s.composition.formula, 'Mg0.8 O1')
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_get_spacegroup_data(self):
self.assertEqual(self.struct.get_spacegroup_info(), ('Fd-3m', 227))
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(s.composition.formula, 'Mg0.8 O1')
self.assertFalse(s.is_ordered)
def test_get_distance(self):
self.assertAlmostEqual(self.struct.get_distance(0, 1), 2.35, 2,
"Distance calculated wrongly!")
pt = [0.9, 0.9, 0.8]
self.assertAlmostEqual(self.struct[0].distance_from_point(pt),
1.50332963784, 2,
"Distance calculated wrongly!")
def test_as_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.as_dict())
self.assertIn("sites", struct.as_dict())
d = self.propertied_structure.as_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.as_dict()
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
self.assertEqual(d['sites'][0]['species'][0]['properties']['spin'], 3)
d = s.as_dict(0)
self.assertNotIn("volume", d['lattice'])
self.assertNotIn("xyz", d['sites'][0])
def test_from_dict(self):
d = self.propertied_structure.as_dict()
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
d = self.propertied_structure.as_dict(0)
s2 = IStructure.from_dict(d)
self.assertEqual(s, s2)
d = {'lattice': {'a': 3.8401979337, 'volume': 40.044794644251596,
'c': 3.8401979337177736, 'b': 3.840198994344244,
'matrix': [[3.8401979337, 0.0, 0.0],
[1.9200989668, 3.3257101909, 0.0],
[0.0, -2.2171384943, 3.1355090603]],
'alpha': 119.9999908639842, 'beta': 90.0,
'gamma': 60.000009137322195},
'sites': [{'properties': {'magmom': 5}, 'abc': [0.0, 0.0, 0.0],
'occu': 1.0, 'species': [{'occu': 1.0,
'oxidation_state': -2,
'properties': {'spin': 3},
'element': 'O'}],
'label': 'O2-', 'xyz': [0.0, 0.0, 0.0]},
{'properties': {'magmom': -5},
'abc': [0.75, 0.5, 0.75],
'occu': 0.8, 'species': [{'occu': 0.8,
'oxidation_state': 2,
'properties': {'spin': 2},
'element': 'Mg'}],
'label': 'Mg2+:0.800',
'xyz': [3.8401979336749994, 1.2247250003039056e-06,
2.351631795225]}]}
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
self.assertEqual(s[0].specie.spin, 3)
self.assertEqual(type(s), IStructure)
def test_site_properties(self):
site_props = self.propertied_structure.site_properties
self.assertEqual(site_props['magmom'], [5, -5])
self.assertEqual(self.propertied_structure[0].magmom, 5)
self.assertEqual(self.propertied_structure[1].magmom, -5)
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 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 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_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_primitive_cell_site_merging(self):
l = Lattice.cubic(10)
coords = [[0, 0, 0], [0, 0, 0.5],
[0, 0, 0.26], [0, 0, 0.74]]
sp = ['Ag', 'Ag', 'Be', 'Be']
s = Structure(l, sp, coords)
dm = s.get_primitive_structure().distance_matrix
self.assertArrayAlmostEqual(dm, [[0, 2.5], [2.5, 0]])
def test_primitive_on_large_supercell(self):
coords = [[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5]]
fcc_ag = Structure(Lattice.cubic(4.09), ["Ag"] * 4, coords)
fcc_ag.make_supercell([2, 2, 2])
fcc_ag_prim = fcc_ag.get_primitive_structure()
self.assertEqual(len(fcc_ag_prim), 1)
self.assertAlmostEqual(fcc_ag_prim.volume, 17.10448225)
def test_primitive_positions(self):
coords = [[0, 0, 0], [0.3, 0.35, 0.45]]
s = Structure(Lattice.from_parameters(1,2,3,50,66,88), ["Ag"] * 2, coords)
a = [[-1,2,-3], [3,2,-4], [1,0,-1]]
b = [[4, 0, 0], [1, 1, 0], [3, 0, 1]]
c = [[2, 0, 0], [1, 3, 0], [1, 1, 1]]
for sc_matrix in [c]:
sc = s.copy()
sc.make_supercell(sc_matrix)
prim = sc.get_primitive_structure(0.01)
self.assertEqual(len(prim), 2)
self.assertAlmostEqual(prim.distance_matrix[0,1], 1.0203432356739286)
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_get_all_neighbors_and_get_neighbors(self):
s = self.struct
nn = s.get_neighbors_in_shell(s[0].frac_coords, 2, 4,
include_index=True)
self.assertEqual(len(nn), 47)
self.assertEqual(nn[0][-1], 0)
r = random.uniform(3, 6)
all_nn = s.get_all_neighbors(r, True)
for i in range(len(s)):
self.assertEqual(len(all_nn[i]), len(s.get_neighbors(s[i], r)))
for site, nns in zip(s, all_nn):
for nn in nns:
self.assertTrue(nn[0].is_periodic_image(s[nn[2]]))
d = sum((site.coords - nn[0].coords) ** 2) ** 0.5
self.assertAlmostEqual(d, nn[1])
s = Structure(Lattice.cubic(1), ['Li'], [[0,0,0]])
s.make_supercell([2,2,2])
self.assertEqual(sum(map(len, s.get_all_neighbors(3))), 976)
def test_get_all_neighbors_outside_cell(self):
s = Structure(Lattice.cubic(2), ['Li', 'Li', 'Li', 'Si'],
[[3.1] * 3, [0.11] * 3, [-1.91] * 3, [0.5] * 3])
all_nn = s.get_all_neighbors(0.2, True)
for site, nns in zip(s, all_nn):
for nn in nns:
self.assertTrue(nn[0].is_periodic_image(s[nn[2]]))
d = sum((site.coords - nn[0].coords) ** 2) ** 0.5
self.assertAlmostEqual(d, nn[1])
self.assertEqual(list(map(len, all_nn)), [2, 2, 2, 0])
def test_get_dist_matrix(self):
ans = [[0., 2.3516318],
[2.3516318, 0.]]
self.assertArrayAlmostEqual(self.struct.distance_matrix, ans)
def test_to_from_file_string(self):
for fmt in ["cif", "json", "poscar", "cssr"]:
s = self.struct.to(fmt=fmt)
self.assertIsNotNone(s)
ss = IStructure.from_str(s, fmt=fmt)
self.assertArrayAlmostEqual(
ss.lattice.lengths_and_angles,
self.struct.lattice.lengths_and_angles, decimal=5)
self.assertArrayAlmostEqual(ss.frac_coords, self.struct.frac_coords)
self.assertIsInstance(ss, IStructure)
self.struct.to(filename="POSCAR.testing")
self.assertTrue(os.path.exists("POSCAR.testing"))
os.remove("POSCAR.testing")
self.struct.to(filename="Si_testing.yaml")
self.assertTrue(os.path.exists("Si_testing.yaml"))
s = Structure.from_file("Si_testing.yaml")
self.assertEqual(s, self.struct)
os.remove("Si_testing.yaml")
class IStructureTest(PymatgenTest):
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_matches(self):
ss = self.struct * 2
self.assertTrue(ss.matches(self.struct))
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_volume_and_density(self):
self.assertAlmostEqual(self.struct.volume, 40.04, 2, "Volume wrong!")
self.assertAlmostEqual(self.struct.density, 2.33, 2,
"Incorrect density")
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(s.composition.formula, 'Mg0.8 O1')
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_get_space_group_data(self):
self.assertEqual(self.struct.get_space_group_info(), ('Fd-3m', 227))
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(s.composition.formula, 'Mg0.8 O1')
self.assertFalse(s.is_ordered)
def test_get_distance(self):
self.assertAlmostEqual(self.struct.get_distance(0, 1), 2.35, 2,
"Distance calculated wrongly!")
pt = [0.9, 0.9, 0.8]
self.assertAlmostEqual(self.struct[0].distance_from_point(pt),
1.50332963784, 2,
"Distance calculated wrongly!")
def test_as_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.as_dict())
self.assertIn("sites", struct.as_dict())
d = self.propertied_structure.as_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.as_dict()
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
self.assertEqual(d['sites'][0]['species'][0]['properties']['spin'], 3)
d = s.as_dict(0)
self.assertNotIn("volume", d['lattice'])
self.assertNotIn("xyz", d['sites'][0])
def test_from_dict(self):
d = self.propertied_structure.as_dict()
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
d = self.propertied_structure.as_dict(0)
s2 = IStructure.from_dict(d)
self.assertEqual(s, s2)
d = {
'lattice': {
'a':
3.8401979337,
'volume':
40.044794644251596,
'c':
3.8401979337177736,
'b':
3.840198994344244,
'matrix': [[3.8401979337, 0.0, 0.0],
[1.9200989668, 3.3257101909, 0.0],
[0.0, -2.2171384943, 3.1355090603]],
'alpha':
119.9999908639842,
'beta':
90.0,
'gamma':
60.000009137322195
},
'sites': [{
'properties': {
'magmom': 5
},
'abc': [0.0, 0.0, 0.0],
'occu':
1.0,
'species': [{
'occu': 1.0,
'oxidation_state': -2,
'properties': {
'spin': 3
},
'element': 'O'
}],
'label':
'O2-',
'xyz': [0.0, 0.0, 0.0]
}, {
'properties': {
'magmom': -5
},
'abc': [0.75, 0.5, 0.75],
'occu':
0.8,
'species': [{
'occu': 0.8,
'oxidation_state': 2,
'properties': {
'spin': 2
},
'element': 'Mg'
}],
'label':
'Mg2+:0.800',
'xyz':
[3.8401979336749994, 1.2247250003039056e-06, 2.351631795225]
}]
}
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
self.assertEqual(s[0].specie.spin, 3)
self.assertEqual(type(s), IStructure)
def test_site_properties(self):
site_props = self.propertied_structure.site_properties
self.assertEqual(site_props['magmom'], [5, -5])
self.assertEqual(self.propertied_structure[0].magmom, 5)
self.assertEqual(self.propertied_structure[1].magmom, -5)
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 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 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_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_primitive_cell_site_merging(self):
l = Lattice.cubic(10)
coords = [[0, 0, 0], [0, 0, 0.5], [0, 0, 0.26], [0, 0, 0.74]]
sp = ['Ag', 'Ag', 'Be', 'Be']
s = Structure(l, sp, coords)
dm = s.get_primitive_structure().distance_matrix
self.assertArrayAlmostEqual(dm, [[0, 2.5], [2.5, 0]])
def test_primitive_on_large_supercell(self):
coords = [[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5]]
fcc_ag = Structure(Lattice.cubic(4.09), ["Ag"] * 4, coords)
fcc_ag.make_supercell([2, 2, 2])
fcc_ag_prim = fcc_ag.get_primitive_structure()
self.assertEqual(len(fcc_ag_prim), 1)
self.assertAlmostEqual(fcc_ag_prim.volume, 17.10448225)
def test_primitive_positions(self):
coords = [[0, 0, 0], [0.3, 0.35, 0.45]]
s = Structure(Lattice.from_parameters(1, 2, 3, 50, 66, 88), ["Ag"] * 2,
coords)
a = [[-1, 2, -3], [3, 2, -4], [1, 0, -1]]
b = [[4, 0, 0], [1, 1, 0], [3, 0, 1]]
c = [[2, 0, 0], [1, 3, 0], [1, 1, 1]]
for sc_matrix in [c]:
sc = s.copy()
sc.make_supercell(sc_matrix)
prim = sc.get_primitive_structure(0.01)
self.assertEqual(len(prim), 2)
self.assertAlmostEqual(prim.distance_matrix[0, 1],
1.0203432356739286)
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_get_all_neighbors_and_get_neighbors(self):
s = self.struct
nn = s.get_neighbors_in_shell(s[0].frac_coords,
2,
4,
include_index=True)
self.assertEqual(len(nn), 47)
self.assertEqual(nn[0][-1], 0)
r = random.uniform(3, 6)
all_nn = s.get_all_neighbors(r, True)
for i in range(len(s)):
self.assertEqual(len(all_nn[i]), len(s.get_neighbors(s[i], r)))
for site, nns in zip(s, all_nn):
for nn in nns:
self.assertTrue(nn[0].is_periodic_image(s[nn[2]]))
d = sum((site.coords - nn[0].coords)**2)**0.5
self.assertAlmostEqual(d, nn[1])
s = Structure(Lattice.cubic(1), ['Li'], [[0, 0, 0]])
s.make_supercell([2, 2, 2])
self.assertEqual(sum(map(len, s.get_all_neighbors(3))), 976)
def test_get_all_neighbors_outside_cell(self):
s = Structure(Lattice.cubic(2), ['Li', 'Li', 'Li', 'Si'],
[[3.1] * 3, [0.11] * 3, [-1.91] * 3, [0.5] * 3])
all_nn = s.get_all_neighbors(0.2, True)
for site, nns in zip(s, all_nn):
for nn in nns:
self.assertTrue(nn[0].is_periodic_image(s[nn[2]]))
d = sum((site.coords - nn[0].coords)**2)**0.5
self.assertAlmostEqual(d, nn[1])
self.assertEqual(list(map(len, all_nn)), [2, 2, 2, 0])
def test_get_dist_matrix(self):
ans = [[0., 2.3516318], [2.3516318, 0.]]
self.assertArrayAlmostEqual(self.struct.distance_matrix, ans)
def test_to_from_file_string(self):
for fmt in ["cif", "json", "poscar", "cssr"]:
s = self.struct.to(fmt=fmt)
self.assertIsNotNone(s)
ss = IStructure.from_str(s, fmt=fmt)
self.assertArrayAlmostEqual(ss.lattice.lengths_and_angles,
self.struct.lattice.lengths_and_angles,
decimal=5)
self.assertArrayAlmostEqual(ss.frac_coords,
self.struct.frac_coords)
self.assertIsInstance(ss, IStructure)
self.struct.to(filename="POSCAR.testing")
self.assertTrue(os.path.exists("POSCAR.testing"))
os.remove("POSCAR.testing")
self.struct.to(filename="Si_testing.yaml")
self.assertTrue(os.path.exists("Si_testing.yaml"))
s = Structure.from_file("Si_testing.yaml")
self.assertEqual(s, self.struct)
os.remove("Si_testing.yaml")
self.struct.to(filename="POSCAR.testing.gz")
s = Structure.from_file("POSCAR.testing.gz")
self.assertEqual(s, self.struct)
os.remove("POSCAR.testing.gz")
