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 = Structure(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 = Structure(Lattice.cubic(4.09), ["Li"] * 2, coords)
self.assertEqual(len(bcc_li.get_primitive_structure()), 1)
def test_get_xrd_data(self):
a = 4.209
latt = Lattice.cubic(a)
structure = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
c = XRDCalculator()
data = c.get_xrd_data(structure, two_theta_range=(0, 90))
#Check the first two peaks
self.assertAlmostEqual(data[0][0], 21.107738329639844)
self.assertAlmostEqual(data[0][1], 36.483184003748946)
self.assertEqual(data[0][2], {(1, 0, 0): 6})
self.assertAlmostEqual(data[0][3], 4.2089999999999996)
self.assertAlmostEqual(data[1][0], 30.024695921112777)
self.assertAlmostEqual(data[1][1], 100)
self.assertEqual(data[1][2], {(1, 1, 0): 12})
self.assertAlmostEqual(data[1][3], 2.976212442014178)
s = read_structure(os.path.join(test_dir, "LiFePO4.cif"))
data = c.get_xrd_data(s, two_theta_range=(0, 90))
self.assertAlmostEqual(data[1][0], 17.03504233621785)
self.assertAlmostEqual(data[1][1], 50.400928948337075)
s = read_structure(os.path.join(test_dir, "Li10GeP2S12.cif"))
data = c.get_xrd_data(s, two_theta_range=(0, 90))
self.assertAlmostEqual(data[1][0], 14.058274883353876)
self.assertAlmostEqual(data[1][1], 4.4111123641667671)
# Test a hexagonal structure.
s = read_structure(os.path.join(test_dir, "Graphite.cif"),
primitive=False)
data = c.get_xrd_data(s, two_theta_range=(0, 90))
self.assertAlmostEqual(data[0][0], 7.929279053132362)
self.assertAlmostEqual(data[0][1], 100)
self.assertAlmostEqual(len(list(data[0][2].keys())[0]), 4)
#Add test case with different lengths of coefficients.
#Also test d_hkl.
coords = [[0.25, 0.25, 0.173], [0.75, 0.75, 0.827], [0.75, 0.25, 0],
[0.25, 0.75, 0], [0.25, 0.25, 0.676], [0.75, 0.75, 0.324]]
sp = ["Si", "Si", "Ru", "Ru", "Pr", "Pr"]
s = Structure(Lattice.tetragonal(4.192, 6.88), sp, coords)
data = c.get_xrd_data(s)
self.assertAlmostEqual(data[0][0], 12.86727341476735)
self.assertAlmostEqual(data[0][1], 31.448239816769796)
self.assertAlmostEqual(data[0][3], 6.88)
self.assertEqual(len(data), 42)
data = c.get_xrd_data(s, two_theta_range=[0, 60])
self.assertEqual(len(data), 18)
#Test with and without Debye-Waller factor
tungsten = Structure(Lattice.cubic(3.1653), ["W"] * 2,
[[0, 0, 0], [0.5, 0.5, 0.5]])
data = c.get_xrd_data(tungsten, scaled=False)
self.assertAlmostEqual(data[0][0], 40.294828554672264)
self.assertAlmostEqual(data[0][1], 2414237.5633093244)
self.assertAlmostEqual(data[0][3], 2.2382050944897789)
c = XRDCalculator(debye_waller_factors={"W": 0.1526})
data = c.get_xrd_data(tungsten, scaled=False)
self.assertAlmostEqual(data[0][0], 40.294828554672264)
self.assertAlmostEqual(data[0][1], 2377745.2296686019)
self.assertAlmostEqual(data[0][3], 2.2382050944897789)
def test_get_slabs(self):
gen = SlabGenerator(self.get_structure("CsCl"), [0, 0, 1], 10, 10)
#Test orthogonality of some internal variables.
a, b, c = gen.oriented_unit_cell.lattice.matrix
self.assertAlmostEqual(np.dot(a, gen._normal), 0)
self.assertAlmostEqual(np.dot(b, gen._normal), 0)
self.assertEqual(len(gen.get_slabs()), 1)
s = self.get_structure("LiFePO4")
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
self.assertEqual(len(gen.get_slabs()), 5)
self.assertEqual(len(gen.get_slabs(bonds={("P", "O"): 3})), 2)
# There are no slabs in LFP that does not break either P-O or Fe-O
# bonds for a miller index of [0, 0, 1].
self.assertEqual(len(gen.get_slabs(
bonds={("P", "O"): 3, ("Fe", "O"): 3})), 0)
#If we allow some broken bonds, there are a few slabs.
self.assertEqual(len(gen.get_slabs(
bonds={("P", "O"): 3, ("Fe", "O"): 3},
max_broken_bonds=2)), 2)
# At this threshold, only the origin and center Li results in
# clustering. All other sites are non-clustered. So the of
# slabs is of sites in LiFePO4 unit cell - 2 + 1.
self.assertEqual(len(gen.get_slabs(tol=1e-4)), 15)
LiCoO2=Structure.from_file(get_path("icsd_LiCoO2.cif"),
primitive=False)
gen = SlabGenerator(LiCoO2, [0, 0, 1], 10, 10)
lco = gen.get_slabs(bonds={("Co", "O"): 3})
self.assertEqual(len(lco), 1)
a, b, c = gen.oriented_unit_cell.lattice.matrix
self.assertAlmostEqual(np.dot(a, gen._normal), 0)
self.assertAlmostEqual(np.dot(b, gen._normal), 0)
scc = Structure.from_spacegroup("Pm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
gen = SlabGenerator(scc, [0, 0, 1], 10, 10)
slabs = gen.get_slabs()
self.assertEqual(len(slabs), 1)
gen = SlabGenerator(scc, [1, 1, 1], 10, 10, max_normal_search=1)
slabs = gen.get_slabs()
self.assertEqual(len(slabs), 1)
# Test whether using units of hkl planes instead of Angstroms for
# min_slab_size and min_vac_size will give us the same number of atoms
natoms = []
for a in [1, 1.4, 2.5, 3.6]:
s = Structure.from_spacegroup("Im-3m", Lattice.cubic(a), ["Fe"], [[0,0,0]])
slabgen = SlabGenerator(s, (1,1,1), 10, 10, in_unit_planes=True,
max_normal_search=2)
natoms.append(len(slabgen.get_slab()))
n = natoms[0]
for i in natoms:
self.assertEqual(n, i)
def test_get_slab(self):
s = self.get_structure("LiFePO4")
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
s = gen.get_slab(0.25)
self.assertAlmostEqual(s.lattice.abc[2], 20.820740000000001)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10)
slab = gen.get_slab()
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10, primitive=False)
slab_non_prim = gen.get_slab()
self.assertEqual(len(slab), 6)
self.assertEqual(len(slab_non_prim), len(slab) * 4)
#Some randomized testing of cell vectors
for i in range(1, 231):
i = random.randint(1, 230)
sg = SpaceGroup.from_int_number(i)
if sg.crystal_system == "hexagonal" or (sg.crystal_system == \
"trigonal" and sg.symbol.endswith("H")):
latt = Lattice.hexagonal(5, 10)
else:
#Cubic lattice is compatible with all other space groups.
latt = Lattice.cubic(5)
s = Structure.from_spacegroup(i, latt, ["H"], [[0, 0, 0]])
miller = (0, 0, 0)
while miller == (0, 0, 0):
miller = (random.randint(0, 6), random.randint(0, 6),
random.randint(0, 6))
gen = SlabGenerator(s, miller, 10, 10)
a, b, c = gen.oriented_unit_cell.lattice.matrix
self.assertAlmostEqual(np.dot(a, gen._normal), 0)
self.assertAlmostEqual(np.dot(b, gen._normal), 0)
def setUp(self):
zno1 = Structure.from_file(get_path("ZnO-wz.cif"), primitive=False)
zno55 = SlabGenerator(zno1, [1, 0, 0], 5, 5, lll_reduce=False,
center_slab=False).get_slab()
Ti = Structure(Lattice.hexagonal(4.6, 2.82), ["Ti", "Ti", "Ti"],
[[0.000000, 0.000000, 0.000000],
[0.333333, 0.666667, 0.500000],
[0.666667, 0.333333, 0.500000]])
Ag_fcc = Structure(Lattice.cubic(4.06), ["Ag", "Ag", "Ag", "Ag"],
[[0.000000, 0.000000, 0.000000],
[0.000000, 0.500000, 0.500000],
[0.500000, 0.000000, 0.500000],
[0.500000, 0.500000, 0.000000]])
laue_groups = ["-1", "2/m", "mmm", "4/m",
"4/mmm", "-3", "-3m", "6/m",
"6/mmm", "m-3", "m-3m"]
self.ti = Ti
self.agfcc = Ag_fcc
self.zno1 = zno1
self.zno55 = zno55
self.h = Structure(Lattice.cubic(3), ["H"],
[[0, 0, 0]])
self.libcc = Structure(Lattice.cubic(3.51004), ["Li", "Li"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
self.laue_groups = laue_groups
def setUp(self):
l = Lattice.cubic(3.51)
species = ["Ni"]
coords = [[0,0,0]]
self.Ni = Structure.from_spacegroup("Fm-3m", l, species, coords)
self.Si = Structure.from_spacegroup("Fd-3m", Lattice.cubic(5.430500),
["Si"], [(0, 0, 0.5)])
def setUp(self):
zno1 = Structure.from_file(get_path("ZnO-wz.cif"), primitive=False)
zno55 = SlabGenerator(zno1, [1, 0, 0], 5, 5, lll_reduce=False,
center_slab=False).get_slab()
self.zno1 = zno1
self.zno55 = zno55
self.h = Structure(Lattice.cubic(3), ["H"],
[[0, 0, 0]])
self.libcc = Structure(Lattice.cubic(3.51004), ["Li", "Li"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
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_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 setUp(self):
self.cscl = Structure.from_spacegroup(
"Pm-3m", Lattice.cubic(4.2), ["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
self.Fe = Structure.from_spacegroup(\
"Im-3m", Lattice.cubic(2.82), ["Fe"],
[[0, 0, 0]])
self.lifepo4 = self.get_structure("LiFePO4")
self.tei = Structure.from_file(get_path("icsd_TeI.cif"),
primitive=False)
self.LiCoO2 = Structure.from_file(get_path("icsd_LiCoO2.cif"),
primitive=False)
self.p1 = Structure(Lattice.from_parameters(3, 4, 5, 31, 43, 50),
["H", "He"], [[0, 0, 0], [0.1, 0.2, 0.3]])
self.graphite = self.get_structure("Graphite")
def test_get_miller_index_from_sites(self):
# test on a cubic system
m = Lattice.cubic(1)
s1 = np.array([0.5, -1.5, 3])
s2 = np.array([0.5, 3., -1.5])
s3 = np.array([2.5, 1.5, -4.])
self.assertEqual(m.get_miller_index_from_coords([s1, s2, s3]),
(2, 1, 1))
# test on a hexagonal system
m = Lattice([[2.319, -4.01662582, 0.],
[2.319, 4.01662582, 0.],
[0., 0., 7.252]])
s1 = np.array([2.319, 1.33887527, 6.3455])
s2 = np.array([1.1595, 0.66943764, 4.5325])
s3 = np.array([1.1595, 0.66943764, 0.9065])
hkl = m.get_miller_index_from_coords([s1, s2, s3])
self.assertEqual(hkl, (2, -1, 0))
# test for previous failing structure
m = Lattice([10, 0, 0, 0, 10, 0, 0, 0, 10])
sites = [[0.5, 0.8, 0.8], [0.5, 0.4, 0.2], [0.5, 0.3, 0.7]]
hkl = m.get_miller_index_from_coords(sites, coords_are_cartesian=False)
self.assertEqual(hkl, (1, 0, 0))
# test for more than 3 sites
sites = [[0.5, 0.8, 0.8], [0.5, 0.4, 0.2], [0.5, 0.3, 0.7],
[0.5, 0.1, 0.2]]
hkl = m.get_miller_index_from_coords(sites, coords_are_cartesian=False)
self.assertEqual(hkl, (1, 0, 0))
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", np.array([0.25, 0.35, 0.45]), self.lattice)
self.site2 = PeriodicSite({"Si":0.5}, np.array([0, 0, 0]), self.lattice)
self.assertEquals(self.site2.species_and_occu, {Element('Si'): 0.5}, "Inconsistent site created!")
self.propertied_site = PeriodicSite(Specie("Fe", 2), [0.25, 0.35, 0.45], self.lattice, properties={'magmom':5.1, 'charge':4.2})
def test_is_compatible(self):
cubic = Lattice.cubic(1)
hexagonal = Lattice.hexagonal(1, 2)
rhom = Lattice.rhombohedral(3, 80)
tet = Lattice.tetragonal(1, 2)
ortho = Lattice.orthorhombic(1, 2, 3)
sg = SpaceGroup("Fm-3m")
self.assertTrue(sg.is_compatible(cubic))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("R-3mH")
self.assertFalse(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(hexagonal))
sg = SpaceGroup("R-3m")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(rhom))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("Pnma")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(tet))
self.assertTrue(sg.is_compatible(ortho))
self.assertFalse(sg.is_compatible(rhom))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("P12/c1")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(tet))
self.assertTrue(sg.is_compatible(ortho))
self.assertFalse(sg.is_compatible(rhom))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("P-1")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(tet))
self.assertTrue(sg.is_compatible(ortho))
self.assertTrue(sg.is_compatible(rhom))
self.assertTrue(sg.is_compatible(hexagonal))
def setUp(self):
lattice = Lattice.cubic(3.010)
frac_coords = [[0.00000, 0.00000, 0.00000],
[0.00000, 0.50000, 0.50000],
[0.50000, 0.00000, 0.50000],
[0.50000, 0.50000, 0.00000],
[0.50000, 0.00000, 0.00000],
[0.50000, 0.50000, 0.50000],
[0.00000, 0.00000, 0.50000],
[0.00000, 0.50000, 0.00000]]
species = ['Mg', 'Mg', 'Mg', 'Mg', 'O', 'O', 'O', 'O']
self.MgO = Structure(lattice, species, frac_coords)
self.MgO.add_oxidation_state_by_element({"Mg": 2, "O": -6})
lattice_Dy = Lattice.hexagonal(3.58, 25.61)
frac_coords_Dy = [[0.00000, 0.00000, 0.00000],
[0.66667, 0.33333, 0.11133],
[0.00000, 0.00000, 0.222],
[0.66667, 0.33333, 0.33333],
[0.33333, 0.66666, 0.44467],
[0.66667, 0.33333, 0.55533],
[0.33333, 0.66667, 0.66667],
[0.00000, 0.00000, 0.778],
[0.33333, 0.66667, 0.88867]]
species_Dy = ['Dy', 'Dy', 'Dy', 'Dy', 'Dy', 'Dy', 'Dy', 'Dy', 'Dy']
self.Dy = Structure(lattice_Dy, species_Dy, frac_coords_Dy)
def test_merge_sites(self):
species = [{'Ag': 0.5}, {'Cl': 0.25}, {'Cl': 0.1},
{'Ag': 0.5}, {'F': 0.15}, {'F': 0.1}]
coords = [[0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0.5, 0.5],
[0, 0, 0], [0.5, 0.5, 1.501], [0.5, 0.5, 1.501]]
s = Structure(Lattice.cubic(1), species, coords)
s.merge_sites(mode="s")
self.assertEqual(s[0].specie.symbol, 'Ag')
self.assertEqual(s[1].species_and_occu,
Composition({'Cl': 0.35, 'F': 0.25}))
self.assertArrayAlmostEqual(s[1].frac_coords, [.5, .5, .5005])
# Test for TaS2 with spacegroup 166 in 160 setting.
l = Lattice.from_lengths_and_angles([3.374351, 3.374351, 20.308941],
[90.000000, 90.000000, 120.000000])
species = ["Ta", "S", "S"]
coords = [[0.000000, 0.000000, 0.944333], [0.333333, 0.666667, 0.353424],
[0.666667, 0.333333, 0.535243]]
tas2 = Structure.from_spacegroup(160, l, species, coords)
assert len(tas2) == 13
tas2.merge_sites(mode="d")
assert len(tas2) == 9
l = Lattice.from_lengths_and_angles([3.587776, 3.587776, 19.622793],
[90.000000, 90.000000, 120.000000])
species = ["Na", "V", "S", "S"]
coords = [[0.333333, 0.666667, 0.165000], [0.000000, 0.000000, 0.998333],
[0.333333, 0.666667, 0.399394], [0.666667, 0.333333, 0.597273]]
navs2 = Structure.from_spacegroup(160, l, species, coords)
assert len(navs2) == 18
navs2.merge_sites(mode="d")
assert len(navs2) == 12
def test_get_vertices_dist_ang_indices(self):
cubic_lattice = Lattice.cubic(10.0)
species = ['Cu', 'O', 'O', 'O', 'O', 'O', 'O']
valences = 'undefined'
#First fake structure
coords = [[5.0, 5.0, 5.0],
[6.01, 5.0, 5.0],
[5.0, 5.0, 3.96],
[4.0, 5.0, 5.0],
[5.0, 6.03, 5.0],
[5.0, 3.98, 5.0],
[5.0, 5.0, 6.05]]
fake_structure = Structure(cubic_lattice, species, coords, coords_are_cartesian=True)
#First fake structure with a given normalized_distance_tolerance of 0.0100001
detailed_voronoi_container = DetailedVoronoiContainer(structure=fake_structure, valences=valences,
normalized_distance_tolerance=0.0100001, isites=[0])
fake_parameter_indices_list = []
for ii in range(2, 5):
for jj in range(7, 14):
fake_parameter_indices_list.append((ii, jj))
for ii in range(5, 7):
for jj in range(10, 14):
fake_parameter_indices_list.append((ii, jj))
points = detailed_voronoi_container._get_vertices_dist_ang_indices(fake_parameter_indices_list)
self.assertEqual(points[0], (2, 7))
self.assertEqual(points[1], (4, 7))
self.assertEqual(points[2], (4, 10))
self.assertEqual(points[3], (6, 10))
self.assertEqual(points[4], (6, 13))
self.assertEqual(points[5], (2, 13))
def test_kpath_generation(self):
triclinic = [1, 2]
monoclinic = range(3, 16)
orthorhombic = range(16, 75)
tetragonal = range(75, 143)
rhombohedral = range(143, 168)
hexagonal = range(168, 195)
cubic = range(195, 231)
species = ['K', 'La', 'Ti']
coords = [[.345, 5, .77298], [.1345, 5.1, .77298], [.7, .8, .9]]
for i in range(230):
sg_num = i + 1
if sg_num in triclinic:
lattice = Lattice([[3.0233057319441246,0,0], [0,7.9850357844548681,0], [0,0,8.1136762279561818]])
elif sg_num in monoclinic:
lattice = Lattice.monoclinic(2, 9, 1, 99)
elif sg_num in orthorhombic:
lattice = Lattice.orthorhombic(2, 9, 1)
elif sg_num in tetragonal:
lattice = Lattice.tetragonal(2, 9)
elif sg_num in rhombohedral:
lattice = Lattice.hexagonal(2, 95)
elif sg_num in hexagonal:
lattice = Lattice.hexagonal(2, 9)
elif sg_num in cubic:
lattice = Lattice.cubic(2)
struct = Structure.from_spacegroup(sg_num, lattice, species, coords)
kpath = HighSymmKpath(struct) #Throws error if something doesn't work, causing test to fail.
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_normal_search(self):
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
for miller in [(1, 0, 0), (1, 1, 0), (1, 1, 1), (2, 1, 1)]:
gen = SlabGenerator(fcc, miller, 10, 10)
gen_normal = SlabGenerator(fcc, miller, 10, 10,
max_normal_search=max(miller))
slab = gen_normal.get_slab()
self.assertAlmostEqual(slab.lattice.alpha, 90)
self.assertAlmostEqual(slab.lattice.beta, 90)
self.assertGreaterEqual(len(gen_normal.oriented_unit_cell),
len(gen.oriented_unit_cell))
graphite = self.get_structure("Graphite")
for miller in [(1, 0, 0), (1, 1, 0), (0, 0, 1), (2, 1, 1)]:
gen = SlabGenerator(graphite, miller, 10, 10)
gen_normal = SlabGenerator(graphite, miller, 10, 10,
max_normal_search=max(miller))
self.assertGreaterEqual(len(gen_normal.oriented_unit_cell),
len(gen.oriented_unit_cell))
sc = Structure(Lattice.hexagonal(3.32, 5.15), ["Sc", "Sc"],
[[1/3, 2/3, 0.25], [2/3, 1/3, 0.75]])
gen = SlabGenerator(sc, (1, 1, 1), 10, 10, max_normal_search=1)
self.assertAlmostEqual(gen.oriented_unit_cell.lattice.angles[1], 90)
def setUp(self):
l = Lattice.cubic(3.51)
species = ["Ni"]
coords = [[0, 0, 0]]
self.Ni = Structure.from_spacegroup("Fm-3m", l, species, coords)
l = Lattice.cubic(2.819000)
species = ["Fe"]
coords = [[0, 0, 0]]
self.Fe = Structure.from_spacegroup("Im-3m", l, species, coords)
self.Si = Structure.from_spacegroup("Fd-3m", Lattice.cubic(5.430500),
["Si"], [(0, 0, 0.5)])
with open(os.path.join(os.path.abspath(os.path.dirname(__file__)), "..",
"reconstructions_archive.json")) as data_file:
self.rec_archive = json.load(data_file)
def test_get_pattern(self):
s = self.get_structure("CsCl")
c = XRDCalculator()
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertTrue(xrd.to_json()) # Test MSONAble property
# Check the first two peaks
self.assertAlmostEqual(xrd.x[0], 21.107738329639844)
self.assertAlmostEqual(xrd.y[0], 36.483184003748946)
self.assertEqual(xrd.hkls[0], [{'hkl': (1, 0, 0), 'multiplicity': 6}])
self.assertAlmostEqual(xrd.d_hkls[0], 4.2089999999999996)
self.assertAlmostEqual(xrd.x[1], 30.024695921112777)
self.assertAlmostEqual(xrd.y[1], 100)
self.assertEqual(xrd.hkls[1], [{"hkl": (1, 1, 0), "multiplicity": 12}])
self.assertAlmostEqual(xrd.d_hkls[1], 2.976212442014178)
s = self.get_structure("LiFePO4")
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[1], 17.03504233621785)
self.assertAlmostEqual(xrd.y[1], 50.400928948337075)
s = self.get_structure("Li10GeP2S12")
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[1], 14.058274883353876)
self.assertAlmostEqual(xrd.y[1], 4.4111123641667671)
# Test a hexagonal structure.
s = self.get_structure("Graphite")
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[0], 26.21057350859598)
self.assertAlmostEqual(xrd.y[0], 100)
self.assertAlmostEqual(len(xrd.hkls[0][0]["hkl"]), 4)
# Add test case with different lengths of coefficients.
# Also test d_hkl.
coords = [[0.25, 0.25, 0.173], [0.75, 0.75, 0.827], [0.75, 0.25, 0],
[0.25, 0.75, 0], [0.25, 0.25, 0.676], [0.75, 0.75, 0.324]]
sp = ["Si", "Si", "Ru", "Ru", "Pr", "Pr"]
s = Structure(Lattice.tetragonal(4.192, 6.88), sp, coords)
xrd = c.get_pattern(s)
self.assertAlmostEqual(xrd.x[0], 12.86727341476735)
self.assertAlmostEqual(xrd.y[0], 31.448239816769796)
self.assertAlmostEqual(xrd.d_hkls[0], 6.88)
self.assertEqual(len(xrd), 42)
xrd = c.get_pattern(s, two_theta_range=[0, 60])
self.assertEqual(len(xrd), 18)
# Test with and without Debye-Waller factor
tungsten = Structure(Lattice.cubic(3.1653), ["W"] * 2,
[[0, 0, 0], [0.5, 0.5, 0.5]])
xrd = c.get_pattern(tungsten, scaled=False)
self.assertAlmostEqual(xrd.x[0], 40.294828554672264)
self.assertAlmostEqual(xrd.y[0], 2414237.5633093244)
self.assertAlmostEqual(xrd.d_hkls[0], 2.2382050944897789)
c = XRDCalculator(debye_waller_factors={"W": 0.1526})
xrd = c.get_pattern(tungsten, scaled=False)
self.assertAlmostEqual(xrd.x[0], 40.294828554672264)
self.assertAlmostEqual(xrd.y[0], 2377745.2296686019)
self.assertAlmostEqual(xrd.d_hkls[0], 2.2382050944897789)
c.get_plot(tungsten).show()
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
with open(
os.path.join(module_dir, "surface_samples.json")) as data_file:
surface_properties = json.load(data_file)
surface_energies, miller_indices = {}, {}
for mpid in surface_properties.keys():
e_surf_list, miller_list = [], []
for surface in surface_properties[mpid]["surfaces"]:
e_surf_list.append(surface["surface_energy"])
miller_list.append(surface["miller_index"])
surface_energies[mpid] = e_surf_list
miller_indices[mpid] = miller_list
# In the case of a high anisotropy material
# Nb: mp-8636
latt_Nb = Lattice.cubic(2.992)
# In the case of an fcc material
# Ir: mp-101
latt_Ir = Lattice.cubic(3.8312)
# In the case of a hcp material
# Ti: mp-72
latt_Ti = Lattice.hexagonal(4.6000, 2.8200)
self.ucell_Nb = Structure(latt_Nb, ["Nb", "Nb", "Nb", "Nb"],
[[0, 0, 0], [0, 0.5, 0.5],
[0.5, 0, 0.5], [0.5, 0.5, 0]])
self.wulff_Nb = WulffShape(latt_Nb, miller_indices["mp-8636"],
surface_energies["mp-8636"])
self.ucell_Ir = Structure(latt_Nb, ["Ir", "Ir", "Ir", "Ir"],
[[0, 0, 0], [0, 0.5, 0.5],
[0.5, 0, 0.5], [0.5, 0.5, 0]])
self.wulff_Ir = WulffShape(latt_Ir, miller_indices["mp-101"],
surface_energies["mp-101"])
self.ucell_Ti = Structure(latt_Ti, ["Ti", "Ti", "Ti"],
[[0, 0, 0], [0.333333, 0.666667, 0.5],
[0.666667, 0.333333, 0.5]])
self.wulff_Ti = WulffShape(latt_Ti, miller_indices["mp-72"],
surface_energies["mp-72"])
self.cube = WulffShape(Lattice.cubic(1), [(1,0,0)], [1])
self.hex_prism = WulffShape(Lattice.hexagonal(2.63, 5.21),
[(0,0,1), (1,0,0)], [0.35, 0.53])
self.surface_properties = surface_properties
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_disordered_supercell_primitive_cell(self):
l = Lattice.cubic(2)
f = [[0.5, 0.5, 0.5]]
sp = [{'Si': 0.54738}]
s = Structure(l, sp, f)
#this supercell often breaks things
s.make_supercell([[0,-1,1],[-1,1,0],[1,1,1]])
self.assertEqual(len(s.get_primitive_structure()), 1)
def test_mapping_symmetry(self):
l = Lattice.cubic(1)
l2 = Lattice.orthorhombic(1.1001, 1, 1)
self.assertEqual(l.find_mapping(l2, ltol=0.1), None)
self.assertEqual(l2.find_mapping(l, ltol=0.1), None)
l2 = Lattice.orthorhombic(1.0999, 1, 1)
self.assertNotEqual(l2.find_mapping(l, ltol=0.1), None)
self.assertNotEqual(l.find_mapping(l2, ltol=0.1), None)
def test_merge_sites(self):
species = [{'Ag': 0.5}, {'Cl': 0.35}, {'Ag': 0.5}, {'F': 0.25}]
coords = [[0, 0, 0], [0.5, 0.5, 0.5], [0, 0, 0], [0.5, 0.5, 1.501]]
s = Structure(Lattice.cubic(1), species, coords)
s.merge_sites()
self.assertEqual(s[0].specie.symbol, 'Ag')
self.assertEqual(s[1].species_and_occu,
Composition({'Cl': 0.35, 'F': 0.25}))
self.assertArrayAlmostEqual(s[1].frac_coords, [.5, .5, .5005])
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", [0.25, 0.35, 0.45], self.lattice)
self.site2 = PeriodicSite({"Si": 0.5}, [0, 0, 0], self.lattice)
self.assertEquals(self.site2.species_and_occu, Composition({Element("Si"): 0.5}), "Inconsistent site created!")
self.propertied_site = PeriodicSite(
Specie("Fe", 2), [0.25, 0.35, 0.45], self.lattice, properties={"magmom": 5.1, "charge": 4.2}
)
def setUp(self):
si = Element("Si")
fe = Element("Fe")
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice.cubic(10)
s = Structure(lattice, [si, fe], coords)
self.mod = SupercellMaker(s, [[1, 1, 0], [-1, 1, 0], [0, 0, 2]])
def test_init(self):
a = 9.026
lattice = Lattice.cubic(a)
self.assertIsNotNone(lattice, "Initialization from new_cubic failed")
lattice2 = Lattice([[a, 0, 0], [0, a, 0], [0, 0, a]])
for i in range(0, 3):
for j in range(0, 3):
self.assertAlmostEqual(lattice.matrix[i][j],
lattice2.matrix[i][j], 5,
"Inconsistent matrix from two inits!")
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_no_oxidation(self):
specie = {"Cu1+": 0.5, "Au2+": 0.5}
cuau = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.677),
[specie], [[0, 0, 0]])
trans = OrderDisorderedStructureTransformation()
ss = trans.apply_transformation(cuau, return_ranked_list=100)
self.assertEqual(ss[0]["structure"].composition["Cu+"], 2)
trans = OrderDisorderedStructureTransformation(no_oxi_states=True)
ss = trans.apply_transformation(cuau, return_ranked_list=100)
self.assertEqual(ss[0]["structure"].composition["Cu+"], 0)
self.assertEqual(ss[0]["structure"].composition["Cu"], 2)
def test_attributes(self):
"""docstring for test_attributes"""
lattice = Lattice.cubic(10.0)
self.assertEqual(lattice.a, 10.0)
self.assertEqual(lattice.b, 10.0)
self.assertEqual(lattice.c, 10.0)
self.assertAlmostEqual(lattice.volume, 1000.0)
xyz = lattice.get_cartesian_coords([0.25, 0.35, 0.45])
self.assertEqual(xyz[0], 2.5)
self.assertEqual(xyz[1], 3.5)
self.assertEqual(xyz[2], 4.5)
def test_cell_scattering_factors(self):
# Test that fcc structure gives 0 intensity for mixed even, odd hkl.
c = TEMCalculator()
nacl = Structure.from_spacegroup("Fm-3m", Lattice.cubic(5.692),
["Na", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(2, 1, 0)]
spacings = c.get_interplanar_spacings(nacl, point)
angles = c.bragg_angles(spacings)
cellscatt = c.cell_scattering_factors(nacl, angles)
self.assertAlmostEqual(cellscatt[(2, 1, 0)], 0)
def test_get_s2(self):
# Tests that the appropriate s2 factor is returned.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(-10, 3, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
angles = c.bragg_angles(spacings)
s2 = c.get_s2(angles)
for p in s2:
self.assertAlmostEqual(s2[p], 1.5381852947115047)
def test_get_points_in_sphere_pbc(self):
latt = Lattice.cubic(1)
pts = []
for a, b, c in itertools.product(xrange(10), xrange(10), xrange(10)):
pts.append([a / 10, b / 10, c / 10])
self.assertEqual(
len(get_points_in_sphere_pbc(latt, pts, [0, 0, 0], 0.1)), 7)
self.assertEqual(
len(get_points_in_sphere_pbc(latt, pts, [0.5, 0.5, 0.5], 0.5)),
515)
def setUp(self):
l = Lattice.cubic(3.51)
species = ["Ni"]
coords = [[0, 0, 0]]
self.Ni = Structure.from_spacegroup("Fm-3m", l, species, coords)
l = Lattice.cubic(2.819000)
species = ["Fe"]
coords = [[0, 0, 0]]
self.Fe = Structure.from_spacegroup("Im-3m", l, species, coords)
self.Si = Structure.from_spacegroup("Fd-3m", Lattice.cubic(5.430500),
["Si"], [(0, 0, 0.5)])
with open(
os.path.join(
os.path.abspath(os.path.dirname(__file__)),
"..",
"reconstructions_archive.json",
)) as data_file:
self.rec_archive = json.load(data_file)
def test_get_slab(self):
s = self.get_structure("LiFePO4")
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
s = gen.get_slab(0.25)
self.assertAlmostEqual(s.lattice.abc[2], 20.820740000000001)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10, max_normal_search=1)
slab = gen.get_slab()
self.assertEqual(len(slab), 6)
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10, primitive=False, max_normal_search=1)
slab_non_prim = gen.get_slab()
self.assertEqual(len(slab_non_prim), len(slab) * 4)
# Some randomized testing of cell vectors
for i in range(1, 231):
i = random.randint(1, 230)
sg = SpaceGroup.from_int_number(i)
if sg.crystal_system == "hexagonal" or (sg.crystal_system == "trigonal" and (sg.symbol.endswith("H") or
sg.int_number in [
143, 144, 145,
147, 149, 150,
151, 152,
153, 154, 156,
157, 158, 159,
162, 163,
164, 165])):
latt = Lattice.hexagonal(5, 10)
else:
# Cubic lattice is compatible with all other space groups.
latt = Lattice.cubic(5)
s = Structure.from_spacegroup(i, latt, ["H"], [[0, 0, 0]])
miller = (0, 0, 0)
while miller == (0, 0, 0):
miller = (random.randint(0, 6), random.randint(0, 6),
random.randint(0, 6))
gen = SlabGenerator(s, miller, 10, 10)
a, b, c = gen.oriented_unit_cell.lattice.matrix
self.assertAlmostEqual(np.dot(a, gen._normal), 0)
self.assertAlmostEqual(np.dot(b, gen._normal), 0)
def test_properties(self):
self.assertEqual(self.kpoint.frac_coords[0], 0.1)
self.assertEqual(self.kpoint.frac_coords[1], 0.4)
self.assertEqual(self.kpoint.frac_coords[2], -0.5)
self.assertEqual(self.kpoint.a, 0.1)
self.assertEqual(self.kpoint.b, 0.4)
self.assertEqual(self.kpoint.c, -0.5)
self.assertEqual(self.lattice, Lattice.cubic(10.0))
self.assertEqual(self.kpoint.cart_coords[0], 1.0)
self.assertEqual(self.kpoint.cart_coords[1], 4.0)
self.assertEqual(self.kpoint.cart_coords[2], -5.0)
self.assertEqual(self.kpoint.label, "X")
def test_from_spacegroup(self):
s1 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Li", "O"],
[[0.25, 0.25, 0.25], [0, 0, 0]])
self.assertEqual(s1.formula, "Li8 O4")
s2 = Structure.from_spacegroup(225, Lattice.cubic(3), ["Li", "O"],
[[0.25, 0.25, 0.25], [0, 0, 0]])
self.assertEqual(s1, s2)
s2 = Structure.from_spacegroup(225,
Lattice.cubic(3), ["Li", "O"],
[[0.25, 0.25, 0.25], [0, 0, 0]],
site_properties={"charge": [1, -2]})
self.assertEqual(sum(s2.site_properties["charge"]), 0)
s = Structure.from_spacegroup("Pm-3m", Lattice.cubic(3), ["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
self.assertEqual(s.formula, "Cs1 Cl1")
self.assertRaises(ValueError, Structure.from_spacegroup, "Pm-3m",
Lattice.tetragonal(1, 3), ["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
def test_merge_sites(self):
species = [{'Ag': 0.5}, {'Cl': 0.35}, {'Ag': 0.5}, {'F': 0.25}]
coords = [[0, 0, 0], [0.5, 0.5, 0.5], [0, 0, 0], [0.5, 0.5, 1.501]]
s = Structure(Lattice.cubic(1), species, coords)
s.merge_sites()
self.assertEqual(s[0].specie.symbol, 'Ag')
self.assertEqual(s[1].species_and_occu,
Composition({
'Cl': 0.35,
'F': 0.25
}))
self.assertArrayAlmostEqual(s[1].frac_coords, [.5, .5, .5005])
def test_max_disordered_sites(self):
l = Lattice.cubic(4)
s_orig = Structure(
l,
[{"Li": 0.2, "Na": 0.2, "K": 0.6}, {"O": 1}],
[[0, 0, 0], [0.5, 0.5, 0.5]],
)
est = EnumerateStructureTransformation(max_cell_size=None, max_disordered_sites=5)
dd = est.apply_transformation(s_orig, return_ranked_list=100)
self.assertEqual(len(dd), 9)
for d in dd:
self.assertEqual(len(d["structure"]), 10)
def test_sulfide_type(self):
# NaS2 -> polysulfide
latt = Lattice.tetragonal(9.59650, 11.78850)
species = ["Na"] * 2 + ["S"] * 2
coords = [
[0.00000, 0.00000, 0.17000],
[0.27600, 0.25000, 0.12500],
[0.03400, 0.25000, 0.29600],
[0.14700, 0.11600, 0.40000],
]
struct = Structure.from_spacegroup(122, latt, species, coords)
self.assertEqual(sulfide_type(struct), "polysulfide")
# NaCl type NaS -> sulfide
latt = Lattice.cubic(5.75)
species = ["Na", "S"]
coords = [[0.00000, 0.00000, 0.00000], [0.50000, 0.50000, 0.50000]]
struct = Structure.from_spacegroup(225, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# Na2S2O3 -> None (sulfate)
latt = Lattice.monoclinic(6.40100, 8.10000, 8.47400, 96.8800)
species = ["Na"] * 2 + ["S"] * 2 + ["O"] * 3
coords = [
[0.29706, 0.62396, 0.08575],
[0.37673, 0.30411, 0.45416],
[0.52324, 0.10651, 0.21126],
[0.29660, -0.04671, 0.26607],
[0.17577, 0.03720, 0.38049],
[0.38604, -0.20144, 0.33624],
[0.16248, -0.08546, 0.11608],
]
struct = Structure.from_spacegroup(14, latt, species, coords)
self.assertEqual(sulfide_type(struct), None)
# Na3PS3O -> sulfide
latt = Lattice.orthorhombic(9.51050, 11.54630, 5.93230)
species = ["Na"] * 2 + ["S"] * 2 + ["P", "O"]
coords = [
[0.19920, 0.11580, 0.24950],
[0.00000, 0.36840, 0.29380],
[0.32210, 0.36730, 0.22530],
[0.50000, 0.11910, 0.27210],
[0.50000, 0.29400, 0.35500],
[0.50000, 0.30300, 0.61140],
]
struct = Structure.from_spacegroup(36, latt, species, coords)
self.assertEqual(sulfide_type(struct), "sulfide")
# test for unphysical cells
struct.scale_lattice(struct.volume * 10)
self.assertEqual(sulfide_type(struct), "sulfide")
def test_remove_oxidation_states(self):
co_elem = Element("Co")
o_elem = Element("O")
co_specie = Specie("Co", 2)
o_specie = Specie("O", -2)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice.cubic(10)
s_elem = Structure(lattice, [co_elem, o_elem], coords)
s_specie = Structure(lattice, [co_specie, o_specie], coords)
s_specie.remove_oxidation_states()
self.assertEqual(s_elem, s_specie, "Oxidation state remover " "failed")
def test_init(self):
a = 9.026
lattice = Lattice.cubic(a)
self.assertIsNotNone(lattice, "Initialization from new_cubic failed")
lattice2 = Lattice([[a, 0, 0], [0, a, 0], [0, 0, a]])
for i in range(0, 3):
for j in range(0, 3):
self.assertAlmostEqual(
lattice.matrix[i][j],
lattice2.matrix[i][j],
5,
"Inconsistent matrix from two inits!",
)
def test_electron_scattering_factors(self):
# Test the electron atomic scattering factor, values approximate with
# international table of crystallography volume C. Rounding error when converting hkl to sin(theta)/lambda.
# Error increases as sin(theta)/lambda is smaller.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
nacl = Structure.from_spacegroup("Fm-3m", Lattice.cubic(5.692),
["Na", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(2, 1, 3)]
point_nacl = [(4, 2, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
spacings_nacl = c.get_interplanar_spacings(nacl, point_nacl)
angles = c.bragg_angles(spacings)
angles_nacl = c.bragg_angles(spacings_nacl)
elscatt = c.electron_scattering_factors(cubic, angles)
elscatt_nacl = c.electron_scattering_factors(nacl, angles_nacl)
self.assertAlmostEqual(elscatt["Cs"][(2, 1, 3)], 2.890, places=1)
self.assertAlmostEqual(elscatt["Cl"][(2, 1, 3)], 1.138, places=1)
self.assertAlmostEqual(elscatt_nacl["Na"][(4, 2, 0)], 0.852, places=1)
self.assertAlmostEqual(elscatt_nacl["Cl"][(4, 2, 0)], 1.372, places=1)
def setUp(self):
self.cscl = Structure.from_spacegroup("Pm-3m", Lattice.cubic(4.2),
["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
self.Fe = Structure.from_spacegroup( \
"Im-3m", Lattice.cubic(2.82), ["Fe"],
[[0, 0, 0]])
self.lifepo4 = self.get_structure("LiFePO4")
self.tei = Structure.from_file(get_path("icsd_TeI.cif"),
primitive=False)
self.LiCoO2 = Structure.from_file(get_path("icsd_LiCoO2.cif"),
primitive=False)
self.p1 = Structure(Lattice.from_parameters(3, 4, 5, 31, 43, 50),
["H", "He"], [[0, 0, 0], [0.1, 0.2, 0.3]])
self.graphite = self.get_structure("Graphite")
self.trigBi = Structure(
Lattice.from_parameters(3, 3, 10, 90, 90,
120), ["Bi", "Bi", "Bi", "Bi", "Bi", "Bi"],
[[0.3333, 0.6666, 0.39945113], [0.0000, 0.0000, 0.26721554],
[0.0000, 0.0000, 0.73278446], [0.6666, 0.3333, 0.60054887],
[0.6666, 0.3333, 0.06611779], [0.3333, 0.6666, 0.93388221]])
def test_get_chemsys(self):
# Test with structure
struct = Structure.from_spacegroup('Fm-3m', Lattice.cubic(5.0),
['Ni', 'O'],
[[0, 0, 0], [0.75, 0.25, 0.75]])
self.assertEqual(get_chemsys(struct), 'Ni-O')
# Test sorting
test_val = get_chemsys("TiO2")
self.assertEqual(test_val, "O-Ti")
test_val = get_chemsys("BaNiO3")
self.assertEqual(test_val, "Ba-Ni-O")
def test_md(self):
s = Structure.from_spacegroup(225, Lattice.cubic(3.62126), ["Cu"],
[[0, 0, 0]])
ld = LammpsData.from_structure(s, atom_style="atomic")
ff = "\n".join(["pair_style eam", "pair_coeff * * Cu_u3.eam"])
md = LammpsRun.md(data=ld,
force_field=ff,
temperature=1600.0,
nsteps=10000)
md.write_inputs(output_dir="md")
with open(os.path.join("md", "in.md")) as f:
md_script = f.read()
script_string = """# Sample input script template for MD
# Initialization
units metal
atom_style atomic
# Atom definition
read_data md.data
#read_restart md.restart
# Force field settings (consult official document for detailed formats)
pair_style eam
pair_coeff * * Cu_u3.eam
# Create velocities
velocity all create 1600.0 142857 mom yes rot yes dist gaussian
# Ensemble constraints
#fix 1 all nve
fix 1 all nvt temp 1600.0 1600.0 0.1
#fix 1 all npt temp 1600.0 1600.0 0.1 iso $pressure $pressure 1.0
# Various operations within timestepping
#fix ...
#compute ...
# Output settings
#thermo_style custom ... # control the thermo data type to output
thermo 100 # output thermo data every N steps
#dump 1 all atom 100 traj.*.gz # dump a snapshot every 100 steps
# Actions
run 10000
"""
self.assertEqual(md_script, script_string)
self.assertTrue(os.path.exists(os.path.join("md", "md.data")))
def setUp(self):
self.cscl = Structure.from_spacegroup("Pm-3m", Lattice.cubic(4.2),
["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
self.lifepo4 = self.get_structure("LiFePO4")
self.tei = Structure.from_file(get_path("icsd_TeI.cif"),
primitive=False)
self.LiCoO2 = Structure.from_file(get_path("icsd_LiCoO2.cif"),
primitive=False)
self.p1 = Structure(Lattice.from_parameters(3, 4, 5, 31, 43, 50),
["H", "He"], [[0, 0, 0], [0.1, 0.2, 0.3]])
self.graphite = self.get_structure("Graphite")
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.cubic = self.lattice
self.tetragonal = Lattice.tetragonal(10, 20)
self.orthorhombic = Lattice.orthorhombic(10, 20, 30)
self.monoclinic = Lattice.monoclinic(10, 20, 30, 66)
self.hexagonal = Lattice.hexagonal(10, 20)
self.rhombohedral = Lattice.rhombohedral(10, 77)
self.cubic_partial_pbc = Lattice.cubic(10.0, pbc=(True, True, False))
family_names = [
"cubic",
"tetragonal",
"orthorhombic",
"monoclinic",
"hexagonal",
"rhombohedral",
]
self.families = {}
for name in family_names:
self.families[name] = getattr(self, name)
def test_selling_dist(self):
# verification process described here: https://github.com/materialsproject/pymatgen/pull/1888#issuecomment-818072164
np.testing.assert_(
Lattice.selling_dist(Lattice.cubic(5), Lattice.cubic(5)) == 0)
hex_lattice = Lattice.hexagonal(5, 8)
triclinic_lattice = Lattice.from_parameters(4, 10, 11, 100, 110, 80)
np.testing.assert_allclose(Lattice.selling_dist(
hex_lattice, triclinic_lattice),
76,
rtol=0.1)
np.testing.assert_allclose(
Lattice.selling_dist(Lattice.tetragonal(10, 12),
Lattice.tetragonal(10.1, 11.9)),
3.7,
rtol=0.1,
)
np.testing.assert_allclose(
Lattice.selling_dist(
Lattice.cubic(5),
Lattice.from_parameters(8, 10, 12, 80, 90, 95)),
115.6,
rtol=0.1,
)
def test_cell_intensity(self):
# Test that bcc structure gives lower intensity for h + k + l != even.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(2, 1, 0)]
point2 = [(2, 2, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
spacings2 = c.get_interplanar_spacings(cubic, point2)
angles = c.bragg_angles(spacings)
angles2 = c.bragg_angles(spacings2)
cellint = c.cell_intensity(cubic, angles)
cellint2 = c.cell_intensity(cubic, angles2)
self.assertGreater(cellint2[(2, 2, 0)], cellint[(2, 1, 0)])
def setUp(self):
lattice = Lattice.cubic(3.010)
frac_coords = [[0.00000, 0.00000,
0.00000], [0.00000, 0.50000, 0.50000],
[0.50000, 0.00000,
0.50000], [0.50000, 0.50000, 0.00000],
[0.50000, 0.00000,
0.00000], [0.50000, 0.50000, 0.50000],
[0.00000, 0.00000, 0.50000],
[0.00000, 0.50000, 0.00000]]
species = ['Mg', 'Mg', 'Mg', 'Mg', 'O', 'O', 'O', 'O']
MgO = Structure(lattice, species, frac_coords)
self.MgO = MgO.add_oxidation_state_by_element({"Mg": 2, "O": -6})
def test_merge_sites(self):
species = [{
'Ag': 0.5
}, {
'Cl': 0.25
}, {
'Cl': 0.1
}, {
'Ag': 0.5
}, {
'F': 0.15
}, {
'F': 0.1
}]
coords = [[0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0.5, 0.5], [0, 0, 0],
[0.5, 0.5, 1.501], [0.5, 0.5, 1.501]]
s = Structure(Lattice.cubic(1), species, coords)
s.merge_sites(mode="s")
self.assertEqual(s[0].specie.symbol, 'Ag')
self.assertEqual(s[1].species_and_occu,
Composition({
'Cl': 0.35,
'F': 0.25
}))
self.assertArrayAlmostEqual(s[1].frac_coords, [.5, .5, .5005])
# Test for TaS2 with spacegroup 166 in 160 setting.
l = Lattice.from_lengths_and_angles([3.374351, 3.374351, 20.308941],
[90.000000, 90.000000, 120.000000])
species = ["Ta", "S", "S"]
coords = [[0.000000, 0.000000,
0.944333], [0.333333, 0.666667, 0.353424],
[0.666667, 0.333333, 0.535243]]
tas2 = Structure.from_spacegroup(160, l, species, coords)
assert len(tas2) == 13
tas2.merge_sites(mode="d")
assert len(tas2) == 9
l = Lattice.from_lengths_and_angles([3.587776, 3.587776, 19.622793],
[90.000000, 90.000000, 120.000000])
species = ["Na", "V", "S", "S"]
coords = [[0.333333, 0.666667,
0.165000], [0.000000, 0.000000, 0.998333],
[0.333333, 0.666667, 0.399394],
[0.666667, 0.333333, 0.597273]]
navs2 = Structure.from_spacegroup(160, l, species, coords)
assert len(navs2) == 18
navs2.merge_sites(mode="d")
assert len(navs2) == 12
def test_interplanar_angle(self):
# test interplanar angles. Reference values from KW Andrews,
# Interpretation of Electron Diffraction pp70-90.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
phi = c.get_interplanar_angle(cubic, (0, 0, -1), (0, -1, 0))
self.assertAlmostEqual(90, phi, places=1)
tet = self.get_structure("Li10GeP2S12")
phi = c.get_interplanar_angle(tet, (0, 0, 1), (1, 0, 3))
self.assertAlmostEqual(25.796, phi, places=1)
latt = Lattice.hexagonal(2, 4)
hex = Structure(latt, ["Ab"], [[0, 0, 0]])
phi = c.get_interplanar_angle(hex, (0, 0, 1), (1, 0, 6))
self.assertAlmostEqual(21.052, phi, places=1)
def setUp(self):
zno1 = Structure.from_file(get_path("ZnO-wz.cif"), primitive=False)
zno55 = SlabGenerator(zno1, [1, 0, 0], 5, 5, lll_reduce=False,
center_slab=False).get_slab()
Ti = Structure(Lattice.hexagonal(4.6, 2.82), ["Ti", "Ti", "Ti"],
[[0.000000, 0.000000, 0.000000],
[0.333333, 0.666667, 0.500000],
[0.666667, 0.333333, 0.500000]])
Ag_fcc = Structure(Lattice.cubic(4.06), ["Ag", "Ag", "Ag", "Ag"],
[[0.000000, 0.000000, 0.000000],
[0.000000, 0.500000, 0.500000],
[0.500000, 0.000000, 0.500000],
[0.500000, 0.500000, 0.000000]])
self.ti = Ti
self.agfcc = Ag_fcc
self.zno1 = zno1
self.zno55 = zno55
self.h = Structure(Lattice.cubic(3), ["H"],
[[0, 0, 0]])
self.libcc = Structure(Lattice.cubic(3.51004), ["Li", "Li"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", [0.25, 0.35, 0.45], self.lattice)
self.site2 = PeriodicSite({"Si": 0.5}, [0, 0, 0], self.lattice)
self.assertEqual(self.site2.species, Composition({Element('Si'): 0.5}),
"Inconsistent site created!")
self.propertied_site = PeriodicSite(Specie("Fe", 2),
[0.25, 0.35, 0.45],
self.lattice,
properties={
'magmom': 5.1,
'charge': 4.2
})
self.dummy_site = PeriodicSite("X", [0, 0, 0], self.lattice)
def test_get_slabs(self):
gen = SlabGenerator(self.get_structure("CsCl"), [0, 0, 1], 10, 10)
#Test orthogonality of some internal variables.
a, b, c = gen.oriented_unit_cell.lattice.matrix
self.assertAlmostEqual(np.dot(a, gen._normal), 0)
self.assertAlmostEqual(np.dot(b, gen._normal), 0)
self.assertEqual(len(gen.get_slabs()), 1)
s = self.get_structure("LiFePO4")
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
self.assertEqual(len(gen.get_slabs()), 5)
self.assertEqual(len(gen.get_slabs(bonds={("P", "O"): 3})), 2)
# There are no slabs in LFP that does not break either P-O or Fe-O
# bonds for a miller index of [0, 0, 1].
self.assertEqual(len(gen.get_slabs(
bonds={("P", "O"): 3, ("Fe", "O"): 3})), 0)
#If we allow some broken bonds, there are a few slabs.
self.assertEqual(len(gen.get_slabs(
bonds={("P", "O"): 3, ("Fe", "O"): 3},
max_broken_bonds=2)), 2)
# At this threshold, only the origin and center Li results in
# clustering. All other sites are non-clustered. So the of
# slabs is of sites in LiFePO4 unit cell - 2 + 1.
self.assertEqual(len(gen.get_slabs(tol=1e-4)), 15)
LiCoO2=Structure.from_file(get_path("icsd_LiCoO2.cif"),
primitive=False)
gen = SlabGenerator(LiCoO2, [0, 0, 1], 10, 10)
lco = gen.get_slabs(bonds={("Co", "O"): 3})
self.assertEqual(len(lco), 1)
a, b, c = gen.oriented_unit_cell.lattice.matrix
self.assertAlmostEqual(np.dot(a, gen._normal), 0)
self.assertAlmostEqual(np.dot(b, gen._normal), 0)
scc = Structure.from_spacegroup("Pm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
gen = SlabGenerator(scc, [0, 0, 1], 10, 10)
slabs = gen.get_slabs()
self.assertEqual(len(slabs), 1)
gen = SlabGenerator(scc, [1, 1, 1], 10, 10, max_normal_search=1)
slabs = gen.get_slabs()
self.assertEqual(len(slabs), 1)
def test_selling_vector(self):
a1 = 10
np.testing.assert_array_almost_equal(
Lattice.cubic(a1).selling_vector.round(4),
np.array([0, 0, 0, -(a1**2), -(a1**2), -(a1**2)]),
)
a2, c2 = 5, 8
np.testing.assert_array_almost_equal(
Lattice.tetragonal(a2, c2).selling_vector.round(4),
np.array([0, 0, 0, -(a2**2), -(a2**2), -(c2**2)]),
)
a3, b3, c3 = 4, 6, 7
np.testing.assert_array_almost_equal(
Lattice.orthorhombic(a3, b3, c3).selling_vector.round(4),
np.array([0, 0, 0, -(a3**2), -(b3**2), -(c3**2)]),
)
def test_apply_transformation(self):
s = self.get_structure("LiFePO4")
trans = SlabTransformation([0, 0, 1], 10, 10, shift=0.25)
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
slab_from_gen = gen.get_slab(0.25)
slab_from_trans = trans.apply_transformation(s)
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix, slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords, slab_from_trans.cart_coords)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"], [[0, 0, 0]])
trans = SlabTransformation([1, 1, 1], 10, 10)
slab_from_trans = trans.apply_transformation(fcc)
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10)
slab_from_gen = gen.get_slab()
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix, slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords, slab_from_trans.cart_coords)
