def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles([5.47, 5.47, 5.47],
[90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[[0.000000, 0.000000, 0.500000], [0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000], [0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000], [0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000], [0.250000, 0.250000, 0.750000]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.smi = StructureMotifInterstitial(self.silicon,
"Si",
motif_types=["tet", "oct"],
op_threshs=[0.3, 0.5],
dl=0.4,
doverlap=1.0,
facmaxdl=1.01)
self.diamond = Structure(
Lattice([[2.189, 0, 1.264], [0.73, 2.064, 1.264], [0, 0, 2.528]]),
["C0+", "C0+"], [[2.554, 1.806, 4.423], [0.365, 0.258, 0.632]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.nacl = Structure(Lattice([[3.485, 0,
2.012], [1.162, 3.286, 2.012],
[0, 0, 4.025]]), ["Na1+", "Cl1-"],
[[0, 0, 0], [2.324, 1.643, 4.025]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.cscl = Structure(Lattice([[4.209, 0, 0], [0, 4.209, 0],
[0, 0, 4.209]]), ["Cl1-", "Cs1+"],
[[2.105, 2.105, 2.105], [0, 0, 0]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=True,
site_properties=None)
self.square_pyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["C", "C", "C", "C", "C", "C"], [
[0, 0, 0], [1, 0, 0], [-1, 0, 0], [0, 1, 0], [0, -1, 0], \
[0, 0, 1]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_bipyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["P", "Cl", "Cl", "Cl", "Cl", "Cl"], [
[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0], [1.74937, -1.01, 0], \
[-1.74937, -1.01, 0], [0, 0, -2.14]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles([5.47, 5.47, 5.47], [90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[
[0.000000, 0.000000, 0.500000],
[0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000],
[0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000],
[0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000],
[0.250000, 0.250000, 0.750000],
],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None,
)
self.smi = StructureMotifInterstitial(
self.silicon,
"Si",
motif_types=["tet", "oct", "tetoct"],
op_targets=[1.0, 1.0, 1.0],
op_threshs=[0.5, 0.5, 0.5],
dl=0.4,
fac_max_radius=2.5,
drel_overlap=0.5,
write_timings=False,
)
def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles([5.47, 5.47, 5.47],
[90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[[0.000000, 0.000000, 0.500000], [0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000], [0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000], [0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000], [0.250000, 0.250000, 0.750000]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.smi = StructureMotifInterstitial(self.silicon,
"Si",
motif_types=["tet", "oct"],
op_threshs=[0.3, 0.5],
dl=0.4,
doverlap=1.0,
facmaxdl=1.01)
def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles(
[5.47, 5.47, 5.47],
[90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[[0.000000, 0.000000, 0.500000],
[0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000],
[0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000],
[0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000],
[0.250000, 0.250000, 0.750000]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.smi = StructureMotifInterstitial(self.silicon, "Si",
motif_types=["tet", "oct"],
op_threshs=[0.3, 0.5],
dl=0.4, doverlap=1.0, facmaxdl=1.01)
self.diamond = Structure(
Lattice([[2.189, 0, 1.264], [0.73, 2.064, 1.264],
[0, 0, 2.528]]), ["C0+", "C0+"], [[2.554, 1.806, 4.423],
[0.365, 0.258, 0.632]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.nacl = Structure(
Lattice([[3.485, 0, 2.012], [1.162, 3.286, 2.012],
[0, 0, 4.025]]), ["Na1+", "Cl1-"], [[0, 0, 0],
[2.324, 1.643, 4.025]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.cscl = Structure(
Lattice([[4.209, 0, 0], [0, 4.209, 0], [0, 0, 4.209]]),
["Cl1-", "Cs1+"], [[2.105, 2.105, 2.105], [0, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_pyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["C", "C", "C", "C", "C", "C"], [
[0, 0, 0], [1, 0, 0], [-1, 0, 0], [0, 1, 0], [0, -1, 0], \
[0, 0, 1]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_bipyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["P", "Cl", "Cl", "Cl", "Cl", "Cl"], [
[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0], [1.74937, -1.01, 0], \
[-1.74937, -1.01, 0], [0, 0, -2.14]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
class StructureMotifInterstitialTest(PymatgenTest):
def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles([5.47, 5.47, 5.47], [90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[
[0.000000, 0.000000, 0.500000],
[0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000],
[0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000],
[0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000],
[0.250000, 0.250000, 0.750000],
],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None,
)
self.smi = StructureMotifInterstitial(
self.silicon,
"Si",
motif_types=["tet", "oct", "tetoct"],
op_targets=[1.0, 1.0, 1.0],
op_threshs=[0.5, 0.5, 0.5],
dl=0.4,
fac_max_radius=2.5,
drel_overlap=0.5,
write_timings=False,
)
def test_all(self):
self.assertIsInstance(self.smi, StructureMotifInterstitial)
self.assertEqual(len(self.smi.enumerate_defectsites()), 1)
self.assertIsInstance(self.smi.enumerate_defectsites()[0], PeriodicSite)
self.assertEqual("Si", self.smi.enumerate_defectsites()[0].species_string)
self.assertEqual("tet", self.smi.get_motif_type(0))
elem_cn_dict = self.smi.get_coordinating_elements_cns(0)
self.assertEqual(len(list(elem_cn_dict.keys())), 1)
self.assertEqual(list(elem_cn_dict.keys())[0], "Si")
self.assertEqual(elem_cn_dict["Si"], 4)
structs = self.smi.make_supercells_with_defects(np.array([1, 1, 1]))
self.assertEqual(len(structs), 2)
self.assertIsInstance(structs[0], Structure)
def tearDown(self):
del self.smi
del self.silicon
class StructureMotifInterstitialTest(PymatgenTest):
def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles([5.47, 5.47, 5.47],
[90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[[0.000000, 0.000000, 0.500000], [0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000], [0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000], [0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000], [0.250000, 0.250000, 0.750000]],
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=None)
self.smi = StructureMotifInterstitial(
self.silicon,
"Si",
motif_types=["tet", "oct", "tetoct"],
op_targets=[1.0, 1.0, 1.0],
op_threshs=[0.5, 0.5, 0.5],
dl=0.4,
fac_max_radius=2.5,
drel_overlap=0.5,
write_timings=False)
def test_all(self):
self.assertIsInstance(self.smi, StructureMotifInterstitial)
self.assertEqual(len(self.smi.enumerate_defectsites()), 1)
self.assertIsInstance(self.smi.enumerate_defectsites()[0],
PeriodicSite)
self.assertEqual("Si",
self.smi.enumerate_defectsites()[0].species_string)
self.assertEqual("tet", self.smi.get_motif_type(0))
elem_cn_dict = self.smi.get_coordinating_elements_cns(0)
self.assertEqual(len(list(elem_cn_dict.keys())), 1)
self.assertEqual(list(elem_cn_dict.keys())[0], "Si")
self.assertEqual(elem_cn_dict["Si"], 4)
structs = self.smi.make_supercells_with_defects(np.array([1, 1, 1]))
self.assertEqual(len(structs), 2)
self.assertIsInstance(structs[0], Structure)
def tearDown(self):
del self.smi
del self.silicon
class StructureMotifInterstitialTest(PymatgenTest):
def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles(
[5.47, 5.47, 5.47],
[90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[[0.000000, 0.000000, 0.500000],
[0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000],
[0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000],
[0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000],
[0.250000, 0.250000, 0.750000]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.smi = StructureMotifInterstitial(self.silicon, "Si",
motif_types=["tet", "oct"],
op_threshs=[0.3, 0.5],
dl=0.4, doverlap=1.0, facmaxdl=1.01)
self.diamond = Structure(
Lattice([[2.189, 0, 1.264], [0.73, 2.064, 1.264],
[0, 0, 2.528]]), ["C0+", "C0+"], [[2.554, 1.806, 4.423],
[0.365, 0.258, 0.632]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.nacl = Structure(
Lattice([[3.485, 0, 2.012], [1.162, 3.286, 2.012],
[0, 0, 4.025]]), ["Na1+", "Cl1-"], [[0, 0, 0],
[2.324, 1.643, 4.025]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.cscl = Structure(
Lattice([[4.209, 0, 0], [0, 4.209, 0], [0, 0, 4.209]]),
["Cl1-", "Cs1+"], [[2.105, 2.105, 2.105], [0, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_pyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["C", "C", "C", "C", "C", "C"], [
[0, 0, 0], [1, 0, 0], [-1, 0, 0], [0, 1, 0], [0, -1, 0], \
[0, 0, 1]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_bipyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["P", "Cl", "Cl", "Cl", "Cl", "Cl"], [
[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0], [1.74937, -1.01, 0], \
[-1.74937, -1.01, 0], [0, 0, -2.14]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
def test_all(self):
self.assertIsInstance(self.smi, StructureMotifInterstitial)
self.assertEqual(len(self.smi.enumerate_defectsites()), 1)
self.assertIsInstance(self.smi.enumerate_defectsites()[0], PeriodicSite)
self.assertEqual("Si", self.smi.enumerate_defectsites()[0].species_string)
self.assertEqual("tet", self.smi.get_motif_type(0))
elem_cn_dict = self.smi.get_coordinating_elements_cns(0)
self.assertEqual(len(list(elem_cn_dict.keys())), 1)
self.assertEqual(list(elem_cn_dict.keys())[0], "Si")
self.assertEqual(elem_cn_dict["Si"], 4)
structs = self.smi.make_supercells_with_defects(np.array([1, 1, 1]))
self.assertEqual(len(structs), 2)
self.assertIsInstance(structs[0], Structure)
def test_get_neighbors_of_site_with_index(self):
self.assertAlmostEqual(len(get_neighbors_of_site_with_index(
self.diamond, 0)), 4)
self.assertAlmostEqual(len(get_neighbors_of_site_with_index(
self.nacl, 0)), 6)
self.assertAlmostEqual(len(get_neighbors_of_site_with_index(
self.cscl, 0)), 8)
def test_site_is_of_motif_type(self):
for i in range(self.diamond.num_sites):
self.assertEqual(site_is_of_motif_type(
self.diamond, i), "tetrahedral")
for i in range(self.nacl.num_sites):
self.assertEqual(site_is_of_motif_type(
self.nacl, i), "octahedral")
for i in range(self.cscl.num_sites):
self.assertEqual(site_is_of_motif_type(
self.cscl, i), "bcc")
self.assertEqual(site_is_of_motif_type(
self.square_pyramid, 0), "square pyramidal")
for i in range(1, self.square_pyramid.num_sites):
self.assertEqual(site_is_of_motif_type(
self.square_pyramid, i), "unrecognized")
self.assertEqual(site_is_of_motif_type(
self.trigonal_bipyramid, 0), "trigonal bipyramidal")
for i in range(1, self.trigonal_bipyramid.num_sites):
self.assertEqual(site_is_of_motif_type(
self.trigonal_bipyramid, i), "unrecognized")
def tearDown(self):
del self.smi
del self.silicon
del self.diamond
del self.nacl
del self.cscl