def testSpg(self):
doc, s = castep2dict(REAL_PATH +
"data/Na3Zn4-swap-ReOs-OQMD_759599.castep")
crystal = Crystal(doc)
print(crystal.get_space_group(symprec=0.01))
print(crystal.get_space_group(symprec=0.001))
self.assertEqual(crystal.get_space_group(symprec=0.0000001), "Pm")
def test_getters_setters(self):
doc, s = castep2dict(REAL_PATH +
"data/Na3Zn4-swap-ReOs-OQMD_759599.castep")
crystal = Crystal(doc)
self.assertEqual(list(crystal.lattice_cart[0]),
[9.0397727, 0.0081202, 0.0000000])
self.assertEqual(crystal.num_atoms, 14)
with self.assertRaises(AttributeError):
crystal["positions_frac"] = [[0, 1, 2]]
# check we can set fields to the same value
crystal["new_field"] = [1, 2, 3]
crystal["new_field"] = [1, 2, 3]
crystal["new_field_2"] = np.nan
crystal["new_field_2"] = np.nan
crystal["new_field_3"] = [1, 2, 4]
with self.assertRaises(AttributeError):
crystal["new_field_3"] = [1, 2, 5]
crystal["new_field_4"] = [1, 2, np.nan]
crystal["new_field_4"] = [1, 2, np.nan]
crystal["new_field_5"] = [1, np.nan, 2]
with self.assertRaises(AttributeError):
crystal["new_field_5"] = [1, 2, np.nan]
crystal["new_field_6"] = np.linspace(0, 1, 1000).tolist()
crystal["new_field_6"] = np.array(crystal["new_field_6"],
copy=True).tolist()
def testCoordination(self):
doc, s = magres2dict(REAL_PATH + "data/magres_files/NaP_QE6.magres")
crystal = Crystal(doc, voronoi=True)
for atom in crystal:
print(atom, atom.coordination)
print(crystal.coordination_lists)
print(crystal.coordination_stats)
def test_minimal_init(self):
doc = Crystal(
dict(
lattice_abc=np.asarray([[3, 3, 3], [90, 90, 90]]),
atom_types=["Na", "Cl"],
positions_frac=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
)
self.assertEqual(doc.stoichiometry, [["Cl", 1.0], ["Na", 1.0]])
self.assertEqual(doc.lattice_abc, ((3.0, 3.0, 3.0), (90.0, 90.0, 90.0)))
self.assertEqual(
doc.lattice_cart, ((3.0, 0.0, 0.0), (0.0, 3.0, 0.0), (0.0, 0.0, 3.0))
)
self.assertEqual(len(doc.sites), 2)
self.assertEqual(doc.num_atoms, 2)
self.assertEqual(doc.concentration, [0.5, 0.5])
self.assertEqual(doc.positions_abs, [[0, 0, 0], [1.5, 1.5, 1.5]])
self.assertEqual(doc.positions_frac, [[0, 0, 0], [0.5, 0.5, 0.5]])
self.assertEqual(doc.formula, "ClNa")
self.assertEqual(doc.cell_volume, 27.0)
self.assertEqual(doc.space_group, "Pm-3m")
doc = Crystal(
dict(
lattice_cart=((3.0, 0.0, 0.0), (0.0, 3.0, 0.0), (0.0, 0.0, 3.0)),
atom_types=["Na", "Cl"],
positions_abs=[[0, 0, 0], [1.5, 1.5, 1.5]],
)
)
self.assertEqual(doc.lattice_abc, ((3.0, 3.0, 3.0), (90.0, 90.0, 90.0)))
self.assertEqual(
doc.lattice_cart, ((3.0, 0.0, 0.0), (0.0, 3.0, 0.0), (0.0, 0.0, 3.0))
)
self.assertEqual(doc.stoichiometry, [["Cl", 1.0], ["Na", 1.0]])
self.assertEqual(len(doc.sites), 2)
self.assertEqual(doc.num_atoms, 2)
self.assertEqual(doc.concentration, [0.5, 0.5])
self.assertEqual(doc.positions_abs, [[0.0, 0.0, 0.0], [1.5, 1.5, 1.5]])
self.assertEqual(doc.positions_frac, [[0, 0, 0], [0.5, 0.5, 0.5]])
self.assertEqual(doc.formula, "ClNa")
self.assertEqual(doc.cell_volume, 27.0)
self.assertEqual(doc.space_group, "Pm-3m")
def test_set_positions(self):
doc, s = castep2dict(REAL_PATH +
"data/Na3Zn4-swap-ReOs-OQMD_759599.castep")
doc = Crystal(doc)
copydoc = copy.deepcopy(doc)
old_pos = np.asarray(doc.positions_frac)
copydoc.set_positions(np.zeros_like(old_pos), fractional=True)
np.testing.assert_array_almost_equal(
np.asarray(copydoc.positions_frac), np.zeros_like(old_pos))
np.testing.assert_array_almost_equal(np.asarray(copydoc.positions_abs),
np.zeros_like(old_pos))
self.assertNotAlmostEqual(doc.positions_frac[-1][0], 0.0)
def testSites(self):
doc, s = castep2dict(REAL_PATH +
"data/Na3Zn4-swap-ReOs-OQMD_759599.castep")
del doc["lattice_cart"]
crystal = Crystal(doc)
np.testing.assert_array_almost_equal(crystal[0].coords,
[0.776467, 0.466319, 0.0])
with self.assertRaises(RuntimeError):
crystal[0].set_position([0.5, 0.6, 0.7, 0.8], "fractional")
with self.assertRaises(RuntimeError):
crystal[0].set_position([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
"fractional")
self.assertEqual([atom for atom in crystal],
[atom[1] for atom in enumerate(crystal)])
atom = Site(
species="Cl",
position=[0.2, 0.5, 0.2],
lattice=[[10, 0, 0], [0, 10, 0], [0, 0, 10]],
)
atom2 = copy.deepcopy(atom)
atom2.species = "Br"
self.assertEqual(atom.species, "Cl")
self.assertEqual(atom2.species, "Br")
atom2.set_position([1.2, -0.5, 0.2], "fractional")
np.testing.assert_array_almost_equal(
atom2.displacement_between_sites(atom), [0.0, 0.0, 0.0],
decimal=10)
self.assertAlmostEqual(atom2.distance_between_sites(atom),
0.0,
places=10)
atom2.set_position([1.3, -0.5, 0.2], "fractional")
np.testing.assert_array_almost_equal(
atom2.displacement_between_sites(atom), [1.0, 0.0, 0.0],
decimal=10)
self.assertAlmostEqual(atom2.distance_between_sites(atom),
1.0,
places=10)
atom2.set_position([1.3, -0.5, 0.3], "fractional")
np.testing.assert_array_almost_equal(
atom2.displacement_between_sites(atom), [1.0, 0.0, 1.0],
decimal=10)
self.assertAlmostEqual(atom2.distance_between_sites(atom),
np.sqrt(2),
places=10)
def testBondStats(self):
doc, s = magres2dict(REAL_PATH + "data/magres_files/NaP_QE6.magres")
crystal = Crystal(doc)
print(crystal.bonding_stats)
def testBondLengths(self):
doc, s = magres2dict(REAL_PATH + "data/magres_files/NaP_QE6.magres")
crystal = Crystal(doc)
print(crystal.bond_lengths)
def testVoronoi(self):
doc, s = magres2dict(REAL_PATH + "data/magres_files/NaP_QE6.magres")
crystal = Crystal(doc)
print(crystal.unique_sites)
def testFromMagres(self):
doc, s = magres2dict(REAL_PATH + "data/magres_files/NaP_QE6.magres")
crystal = Crystal(doc)
for atom in crystal:
print(atom, atom["chemical_shielding_iso"],
atom["chemical_shift_asymmetry"])
