def setUp(self):
self.silicon = Structure(
Lattice.cubic(5.47),
["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=["tetrahedral", "octahedral"],
op_threshs=[0.3, 0.5],
dl=0.4,
doverlap=1.0,
facmaxdl=1.51)
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 __init__(self, structure, element):
"""
Initializes an Interstitial generator using structure motifs
Args:
structure (Structure): pymatgen structure object
element (str or Element or Species): element for the interstitial
"""
self.structure = structure
self.element = element
interstitial_finder = StructureMotifInterstitial(
self.structure, self.element)
self.unique_defect_seq = []
# eliminate sublattice equivalent defects which may
# have slipped through interstitial finder
pdc = PointDefectComparator()
for poss_site in interstitial_finder.enumerate_defectsites():
now_defect = Interstitial(self.structure, poss_site)
append_defect = True
for unique_defect in self.unique_defect_seq:
if pdc.are_equal(now_defect, unique_defect):
append_defect = False
if append_defect:
self.unique_defect_seq.append(now_defect)
self.count_def = 0 # for counting the index of the generated defect
def __init__(self, structure, element):
"""
Initializes an Interstitial generator using structure motifs
Args:
structure (Structure): pymatgen structure object
element (str or Element or Specie): element for the interstitial
"""
self.structure = structure
self.element = element
interstitial_finder = StructureMotifInterstitial(self.structure, self.element)
self.unique_defect_seq = []
# eliminate sublattice equivalent defects which may
# have slipped through interstitial finder
pdc = PointDefectComparator()
for poss_site in interstitial_finder.enumerate_defectsites():
now_defect = Interstitial( self.structure, poss_site)
append_defect = True
for unique_defect in self.unique_defect_seq:
if pdc.are_equal( now_defect, unique_defect):
append_defect = False
if append_defect:
self.unique_defect_seq.append( now_defect)
self.count_def = 0 # for counting the index of the generated defect
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=["tetrahedral", "octahedral"],
op_threshs=[0.3, 0.5],
dl=0.4,
doverlap=1.0,
facmaxdl=1.51)
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 __init__(self, structure, element):
"""
Initializes an Interstitial generator using structure motifs
Args:
structure (Structure): pymatgen structure object
element (str or Element or Specie): element for the interstitial
"""
self.structure = structure
self.element = element
interstitial_finder = StructureMotifInterstitial(self.structure, self.element)
self.defect_sites = list(interstitial_finder.enumerate_defectsites())
# for multiplicity, neccessary to get prim_structure
spa = SpacegroupAnalyzer(self.structure, symprec=1e-2)
prim_struct = spa.get_primitive_standard_structure()
conv_prim_rat = int(self.structure.num_sites / prim_struct.num_sites)
self.multiplicities = [
int(interstitial_finder.get_defectsite_multiplicity(def_ind) / conv_prim_rat)
for def_ind in range(len(self.defect_sites))
]
self.count_def = 0 # for counting the index of the generated defect
def __init__(self, structure, element):
"""
Initializes an Interstitial generator using structure motifs
Args:
structure (Structure): pymatgen structure object
element (str or Element or Specie): element for the interstitial
"""
self.structure = structure
self.element = element
interstitial_finder = StructureMotifInterstitial(
self.structure, self.element)
self.defect_sites = list(interstitial_finder.enumerate_defectsites())
# for multiplicity, neccessary to get prim_structure
spa = SpacegroupAnalyzer(self.structure, symprec=1e-2)
prim_struct = spa.get_primitive_standard_structure()
conv_prim_rat = int(self.structure.num_sites / prim_struct.num_sites)
self.multiplicities = [
int(
interstitial_finder.get_defectsite_multiplicity(def_ind) /
conv_prim_rat) for def_ind in range(len(self.defect_sites))
]
self.count_def = 0 # for counting the index of the generated defect
def create_interstitial_supercells(structure,element,size=2):
'''
Create interstitial structures with InFiT (Interstitialcy Finding Tool) algorithm with Pymatgen.
Parameters
----------
structure: (Pymatgen Structure)
Bulk structure.
element: (str or Element)
interstitial element.
Returns
-------
interstitials: (dict)
Dictionary with sites (Site object) and supercell structures (Structure object)
'''
int_object = StructureMotifInterstitial(structure,element)
int_sites = int_object.enumerate_defectsites()
int_supercells = int_object.make_supercells_with_defects([[size,0,0],[0,size,0],[0,0,size]])
interstitials = {}
interstitial_sites = {}
interstitial_structures = {}
for i in range(0,len(int_sites)):
int_coord_type = int_object.get_motif_type(i)
interstitial_sites[int_coord_type] = int_sites[i]
struct_int = int_supercells[i+1]
interstitial_structures[int_coord_type] = struct_int
interstitials['sites'] = interstitial_sites
interstitials['structures'] = interstitial_structures
return interstitials
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=["tetrahedral", "octahedral"],
op_threshs=[0.3, 0.5],
dl=0.4,
doverlap=1.0,
facmaxdl=1.51)
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("tetrahedral", 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
del self.diamond
del self.nacl
del self.cscl
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=["tetrahedral", "octahedral"],
op_threshs=[0.3, 0.5],
dl=0.4,
doverlap=1.0,
facmaxdl=1.51)
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("tetrahedral", 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
del self.diamond
del self.nacl
del self.cscl
