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 similar_defects(entryset):
"""
Used for grouping similar defects of different charges
Can distinguish identical defects even if they are not in same position
"""
pdc = PointDefectComparator(check_charge=False,
check_primitive_cell=True,
check_lattice_scale=False)
grp_def_sets = []
grp_def_indices = []
for ent_ind, ent in enumerate(entryset):
# TODO: more pythonic way of grouping entry sets with PointDefectComparator.
# this is currently most time intensive part of DefectPhaseDiagram
matched_ind = None
for grp_ind, defgrp in enumerate(grp_def_sets):
if pdc.are_equal(ent.defect, defgrp[0].defect):
matched_ind = grp_ind
break
if matched_ind is not None:
grp_def_sets[matched_ind].append(ent.copy())
grp_def_indices[matched_ind].append(ent_ind)
else:
grp_def_sets.append([ent.copy()])
grp_def_indices.append([ent_ind])
return zip(grp_def_sets, grp_def_indices)
def similar_defects( entryset):
"""
Used for grouping similar defects of different charges
Can distinguish identical defects even if they are not in same position
"""
pdc = PointDefectComparator( check_charge=False, check_primitive_cell=True,
check_lattice_scale=False)
grp_def_sets = []
grp_def_indices = []
for ent_ind, ent in enumerate( entryset):
# TODO: more pythonic way of grouping entry sets with PointDefectComparator.
# this is currently most time intensive part of DefectPhaseDiagram
matched_ind = None
for grp_ind, defgrp in enumerate(grp_def_sets):
if pdc.are_equal( ent.defect, defgrp[0].defect):
matched_ind = grp_ind
break
if matched_ind is not None:
grp_def_sets[matched_ind].append( ent.copy())
grp_def_indices[matched_ind].append( ent_ind)
else:
grp_def_sets.append( [ent.copy()])
grp_def_indices.append( [ent_ind])
return zip(grp_def_sets, grp_def_indices)
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 __init__(self, structure, element):
"""
Initializes an Interstitial generator using Voronoi sites
Args:
structure (Structure): pymatgen structure object
element (str or Element or Species): element for the interstitial
"""
self.structure = structure
self.element = element
framework = list(self.structure.symbol_set)
get_voronoi = TopographyAnalyzer(self.structure,
framework, [],
check_volume=False)
get_voronoi.cluster_nodes()
get_voronoi.remove_collisions()
# trim equivalent nodes with symmetry analysis
struct_to_trim = self.structure.copy()
for poss_inter in get_voronoi.vnodes:
struct_to_trim.append(self.element,
poss_inter.frac_coords,
coords_are_cartesian=False)
symmetry_finder = SpacegroupAnalyzer(struct_to_trim, symprec=1e-1)
equiv_sites_list = symmetry_finder.get_symmetrized_structure(
).equivalent_sites
# do additional screening for sublattice equivalent
# defects which may have slipped through
pdc = PointDefectComparator()
self.unique_defect_seq = []
for poss_site_list in equiv_sites_list:
poss_site = poss_site_list[0]
if poss_site not in self.structure:
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 Voronoi sites
Args:
structure (Structure): pymatgen structure object
element (str or Element or Specie): element for the interstitial
"""
self.structure = structure
self.element = element
framework = list(self.structure.symbol_set)
get_voronoi = TopographyAnalyzer(self.structure, framework, [], check_volume=False)
get_voronoi.cluster_nodes()
get_voronoi.remove_collisions()
# trim equivalent nodes with symmetry analysis
struct_to_trim = self.structure.copy()
for poss_inter in get_voronoi.vnodes:
struct_to_trim.append(self.element, poss_inter.frac_coords, coords_are_cartesian=False)
symmetry_finder = SpacegroupAnalyzer(struct_to_trim, symprec=1e-1)
equiv_sites_list = symmetry_finder.get_symmetrized_structure().equivalent_sites
# do additional screening for sublattice equivalent
# defects which may have slipped through
pdc = PointDefectComparator()
self.unique_defect_seq = []
for poss_site_list in equiv_sites_list:
poss_site = poss_site_list[0]
if poss_site not in self.structure:
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 test_defect_matching(self):
# SETUP DEFECTS FOR TESTING
# symmorphic defect test set
s_struc = Structure.from_file(os.path.join(
test_dir, "CsSnI3.cif")) # tetragonal CsSnI3
identical_Cs_vacs = [
Vacancy(s_struc, s_struc[0]),
Vacancy(s_struc, s_struc[1])
]
identical_I_vacs_sublattice1 = [
Vacancy(s_struc, s_struc[4]),
Vacancy(s_struc, s_struc[5]),
Vacancy(s_struc, s_struc[8]),
Vacancy(s_struc, s_struc[9])
] # in plane halides
identical_I_vacs_sublattice2 = [
Vacancy(s_struc, s_struc[6]),
Vacancy(s_struc, s_struc[7])
] # out of plane halides
pdc = PointDefectComparator()
# NOW TEST DEFECTS
# test vacancy matching
self.assertTrue(
pdc.are_equal(identical_Cs_vacs[0],
identical_Cs_vacs[0])) # trivial vacancy test
self.assertTrue(
pdc.are_equal(
identical_Cs_vacs[0],
identical_Cs_vacs[1])) # vacancies on same sublattice
for i, j in itertools.combinations(range(4), 2):
self.assertTrue(
pdc.are_equal(identical_I_vacs_sublattice1[i],
identical_I_vacs_sublattice1[j]))
self.assertTrue(
pdc.are_equal(identical_I_vacs_sublattice2[0],
identical_I_vacs_sublattice2[1]))
self.assertFalse(
pdc.are_equal(
identical_Cs_vacs[
0], # both vacancies, but different specie types
identical_I_vacs_sublattice1[0]))
self.assertFalse(
pdc.are_equal(
identical_I_vacs_sublattice1[
0], # same specie type, different sublattice
identical_I_vacs_sublattice2[0]))
# test substitutional matching
sub_Cs_on_I_sublattice1_set1 = PeriodicSite(
'Cs', identical_I_vacs_sublattice1[0].site.frac_coords,
s_struc.lattice)
sub_Cs_on_I_sublattice1_set2 = PeriodicSite(
'Cs', identical_I_vacs_sublattice1[1].site.frac_coords,
s_struc.lattice)
sub_Cs_on_I_sublattice2 = PeriodicSite(
'Cs', identical_I_vacs_sublattice2[0].site.frac_coords,
s_struc.lattice)
sub_Rb_on_I_sublattice2 = PeriodicSite(
'Rb', identical_I_vacs_sublattice2[0].site.frac_coords,
s_struc.lattice)
self.assertTrue(
pdc.are_equal( # trivial substitution test
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1),
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1)))
self.assertTrue(
pdc.are_equal( # same sublattice, different coords
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1),
Substitution(s_struc, sub_Cs_on_I_sublattice1_set2)))
self.assertFalse(
pdc.are_equal( # different subs (wrong specie)
Substitution(s_struc, sub_Cs_on_I_sublattice2),
Substitution(s_struc, sub_Rb_on_I_sublattice2)))
self.assertFalse(
pdc.are_equal( # different subs (wrong sublattice)
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1),
Substitution(s_struc, sub_Cs_on_I_sublattice2)))
# test symmorphic interstitial matching
# (using set generated from Voronoi generator, with same sublattice given by saturatated_interstitial_structure function)
inter_H_sublattice1_set1 = PeriodicSite('H', [0., 0.75, 0.25],
s_struc.lattice)
inter_H_sublattice1_set2 = PeriodicSite('H', [0., 0.75, 0.75],
s_struc.lattice)
inter_H_sublattice2 = PeriodicSite(
'H', [0.57796112, 0.06923687, 0.56923687], s_struc.lattice)
inter_H_sublattice3 = PeriodicSite('H', [0.25, 0.25, 0.54018268],
s_struc.lattice)
inter_He_sublattice3 = PeriodicSite('He', [0.25, 0.25, 0.54018268],
s_struc.lattice)
self.assertTrue(
pdc.are_equal( # trivial interstitial test
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice1_set1)))
self.assertTrue(
pdc.are_equal( # same sublattice, different coords
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice1_set2)))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong sublattice)
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice2)))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong sublattice)
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice3)))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong specie)
Interstitial(s_struc, inter_H_sublattice3),
Interstitial(s_struc, inter_He_sublattice3)))
# test non-symmorphic interstitial matching
# (using set generated from Voronoi generator, with same sublattice given by saturatated_interstitial_structure function)
ns_struc = Structure.from_file(os.path.join(test_dir, "CuCl.cif"))
ns_inter_H_sublattice1_set1 = PeriodicSite(
'H', [0.06924513, 0.06308959, 0.86766528], ns_struc.lattice)
ns_inter_H_sublattice1_set2 = PeriodicSite(
'H', [0.43691041, 0.36766528, 0.06924513], ns_struc.lattice)
ns_inter_H_sublattice2 = PeriodicSite(
'H', [0.06022109, 0.60196031, 0.1621814], ns_struc.lattice)
ns_inter_He_sublattice2 = PeriodicSite(
'He', [0.06022109, 0.60196031, 0.1621814], ns_struc.lattice)
self.assertTrue(
pdc.are_equal( # trivial interstitial test
Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
Interstitial(ns_struc, ns_inter_H_sublattice1_set1)))
self.assertTrue(
pdc.are_equal( # same sublattice, different coords
Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
Interstitial(ns_struc, ns_inter_H_sublattice1_set2)))
self.assertFalse(
pdc.are_equal(
Interstitial(ns_struc, ns_inter_H_sublattice1_set1
), # different interstitials (wrong sublattice)
Interstitial(ns_struc, ns_inter_H_sublattice2)))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong specie)
Interstitial(ns_struc, ns_inter_H_sublattice2),
Interstitial(ns_struc, ns_inter_He_sublattice2)))
# test influence of charge on defect matching (default is to be charge agnostic)
vac_diff_chg = identical_Cs_vacs[0].copy()
vac_diff_chg.set_charge(3.)
self.assertTrue(pdc.are_equal(identical_Cs_vacs[0], vac_diff_chg))
chargecheck_pdc = PointDefectComparator(
check_charge=True) # switch to PDC which cares about charge state
self.assertFalse(
chargecheck_pdc.are_equal(identical_Cs_vacs[0], vac_diff_chg))
# test different supercell size
# (comparing same defect but different supercells - default is to not check for this)
sc_agnostic_pdc = PointDefectComparator(check_primitive_cell=True)
sc_scaled_s_struc = s_struc.copy()
sc_scaled_s_struc.make_supercell([2, 2, 3])
sc_scaled_I_vac_sublatt1_ps1 = PeriodicSite(
'I',
identical_I_vacs_sublattice1[0].site.coords,
sc_scaled_s_struc.lattice,
coords_are_cartesian=True)
sc_scaled_I_vac_sublatt1_ps2 = PeriodicSite(
'I',
identical_I_vacs_sublattice1[1].site.coords,
sc_scaled_s_struc.lattice,
coords_are_cartesian=True)
sc_scaled_I_vac_sublatt2_ps = PeriodicSite(
'I',
identical_I_vacs_sublattice2[1].site.coords,
sc_scaled_s_struc.lattice,
coords_are_cartesian=True)
sc_scaled_I_vac_sublatt1_defect1 = Vacancy(
sc_scaled_s_struc, sc_scaled_I_vac_sublatt1_ps1)
sc_scaled_I_vac_sublatt1_defect2 = Vacancy(
sc_scaled_s_struc, sc_scaled_I_vac_sublatt1_ps2)
sc_scaled_I_vac_sublatt2_defect = Vacancy(sc_scaled_s_struc,
sc_scaled_I_vac_sublatt2_ps)
self.assertFalse(
pdc.are_equal(
identical_I_vacs_sublattice1[
0], # trivially same defect site but between different supercells
sc_scaled_I_vac_sublatt1_defect1))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
sc_scaled_I_vac_sublatt1_defect1))
self.assertFalse(
pdc.are_equal(
identical_I_vacs_sublattice1[
1], # same coords, different lattice structure
sc_scaled_I_vac_sublatt1_defect1))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[1],
sc_scaled_I_vac_sublatt1_defect1))
self.assertFalse(
pdc.are_equal(
identical_I_vacs_sublattice1[
0], # same sublattice, different coords
sc_scaled_I_vac_sublatt1_defect2))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
sc_scaled_I_vac_sublatt1_defect2))
self.assertFalse(
sc_agnostic_pdc.are_equal(
identical_I_vacs_sublattice1[
0], # different defects (wrong sublattice)
sc_scaled_I_vac_sublatt2_defect))
# test same structure size, but scaled lattice volume
# (default is to not allow these to be equal, but check_lattice_scale=True allows for this)
vol_agnostic_pdc = PointDefectComparator(check_lattice_scale=True)
vol_scaled_s_struc = s_struc.copy()
vol_scaled_s_struc.scale_lattice(s_struc.volume * 0.95)
vol_scaled_I_vac_sublatt1_defect1 = Vacancy(vol_scaled_s_struc,
vol_scaled_s_struc[4])
vol_scaled_I_vac_sublatt1_defect2 = Vacancy(vol_scaled_s_struc,
vol_scaled_s_struc[5])
vol_scaled_I_vac_sublatt2_defect = Vacancy(vol_scaled_s_struc,
vol_scaled_s_struc[6])
self.assertFalse(
pdc.are_equal(
identical_I_vacs_sublattice1[
0], # trivially same defect (but vol change)
vol_scaled_I_vac_sublatt1_defect1))
self.assertTrue(
vol_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
vol_scaled_I_vac_sublatt1_defect1))
self.assertFalse(
pdc.are_equal(
identical_I_vacs_sublattice1[
0], # same defect, different sublattice point (and vol change)
vol_scaled_I_vac_sublatt1_defect2))
self.assertTrue(
vol_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
vol_scaled_I_vac_sublatt1_defect2))
self.assertFalse(
vol_agnostic_pdc.are_equal(
identical_I_vacs_sublattice1[
0], # different defect (wrong sublattice)
vol_scaled_I_vac_sublatt2_defect))
# test identical defect which has had entire lattice shifted
shift_s_struc = s_struc.copy()
shift_s_struc.translate_sites(range(len(s_struc)), [0.2, 0.3, 0.4],
frac_coords=True,
to_unit_cell=True)
shifted_identical_Cs_vacs = [
Vacancy(shift_s_struc, shift_s_struc[0]),
Vacancy(shift_s_struc, shift_s_struc[1])
]
self.assertTrue(
pdc.are_equal(
identical_Cs_vacs[0], # trivially same defect (but shifted)
shifted_identical_Cs_vacs[0]))
self.assertTrue(
pdc.are_equal(
identical_Cs_vacs[
0], # same defect on different sublattice point (and shifted)
shifted_identical_Cs_vacs[1]))
# test uniform lattice shift within non-symmorphic structure
shift_ns_struc = ns_struc.copy()
shift_ns_struc.translate_sites(range(len(ns_struc)), [0., 0.6, 0.3],
frac_coords=True,
to_unit_cell=True)
shift_ns_inter_H_sublattice1_set1 = PeriodicSite(
'H', ns_inter_H_sublattice1_set1.frac_coords + [0., 0.6, 0.3],
shift_ns_struc.lattice)
shift_ns_inter_H_sublattice1_set2 = PeriodicSite(
'H', ns_inter_H_sublattice1_set2.frac_coords + [0., 0.6, 0.3],
shift_ns_struc.lattice)
self.assertTrue(
pdc.are_equal(
Interstitial(ns_struc, ns_inter_H_sublattice1_set1
), # trivially same defect (but shifted)
Interstitial(shift_ns_struc,
shift_ns_inter_H_sublattice1_set1)))
self.assertTrue(
pdc.are_equal(
Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
# same defect on different sublattice point (and shifted)
Interstitial(shift_ns_struc,
shift_ns_inter_H_sublattice1_set2)))
# test a rotational + supercell type structure transformation (requires check_primitive_cell=True)
rotated_s_struc = s_struc.copy()
rotated_s_struc.make_supercell([[2, 1, 0], [-1, 3, 0], [0, 0, 2]])
rotated_identical_Cs_vacs = [
Vacancy(rotated_s_struc, rotated_s_struc[0]),
Vacancy(rotated_s_struc, rotated_s_struc[1])
]
self.assertFalse(
pdc.are_equal(
identical_Cs_vacs[0], # trivially same defect (but rotated)
rotated_identical_Cs_vacs[0]))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_Cs_vacs[0],
rotated_identical_Cs_vacs[0]))
self.assertFalse(
pdc.are_equal(
identical_Cs_vacs[
0], # same defect on different sublattice (and rotated)
rotated_identical_Cs_vacs[1]))
self.assertTrue(
sc_agnostic_pdc.are_equal(
identical_Cs_vacs[
0], # same defect on different sublattice point (and rotated)
rotated_identical_Cs_vacs[1]))
# test a rotational + supercell + shift type structure transformation for non-symmorphic structure
rotANDshift_ns_struc = ns_struc.copy()
rotANDshift_ns_struc.translate_sites(range(len(ns_struc)),
[0., 0.6, 0.3],
frac_coords=True,
to_unit_cell=True)
rotANDshift_ns_struc.make_supercell([[2, 1, 0], [-1, 3, 0], [0, 0, 2]])
ns_vac_Cs_set1 = Vacancy(ns_struc, ns_struc[0])
rotANDshift_ns_vac_Cs_set1 = Vacancy(rotANDshift_ns_struc,
rotANDshift_ns_struc[0])
rotANDshift_ns_vac_Cs_set2 = Vacancy(rotANDshift_ns_struc,
rotANDshift_ns_struc[1])
self.assertTrue(
sc_agnostic_pdc.are_equal(
ns_vac_Cs_set1, # trivially same defect (but rotated and sublattice shifted)
rotANDshift_ns_vac_Cs_set1))
self.assertTrue(
sc_agnostic_pdc.are_equal(
ns_vac_Cs_set1, # same defect on different sublattice point (shifted and rotated)
rotANDshift_ns_vac_Cs_set2))
def test_defect_matching(self):
# SETUP DEFECTS FOR TESTING
# symmorphic defect test set
s_struc = Structure.from_file(
os.path.join(test_dir, "CsSnI3.cif")) # tetragonal CsSnI3
identical_Cs_vacs = [Vacancy(s_struc, s_struc[0]),
Vacancy(s_struc, s_struc[1])]
identical_I_vacs_sublattice1 = [Vacancy(s_struc, s_struc[4]),
Vacancy(s_struc, s_struc[5]),
Vacancy(s_struc, s_struc[8]),
Vacancy(s_struc,
s_struc[9])] # in plane halides
identical_I_vacs_sublattice2 = [Vacancy(s_struc, s_struc[6]),
Vacancy(s_struc, s_struc[
7])] # out of plane halides
pdc = PointDefectComparator()
# NOW TEST DEFECTS
# test vacancy matching
self.assertTrue(pdc.are_equal(identical_Cs_vacs[0], identical_Cs_vacs[
0])) # trivial vacancy test
self.assertTrue(pdc.are_equal(identical_Cs_vacs[0], identical_Cs_vacs[
1])) # vacancies on same sublattice
for i, j in itertools.combinations(range(4), 2):
self.assertTrue(pdc.are_equal(identical_I_vacs_sublattice1[i],
identical_I_vacs_sublattice1[j]))
self.assertTrue(pdc.are_equal(identical_I_vacs_sublattice2[0],
identical_I_vacs_sublattice2[1]))
self.assertFalse(pdc.are_equal(identical_Cs_vacs[0],
# both vacancies, but different specie types
identical_I_vacs_sublattice1[0]))
self.assertFalse(pdc.are_equal(identical_I_vacs_sublattice1[0],
# same specie type, different sublattice
identical_I_vacs_sublattice2[0]))
# test substitutional matching
sub_Cs_on_I_sublattice1_set1 = PeriodicSite('Cs',
identical_I_vacs_sublattice1[
0].site.frac_coords,
s_struc.lattice)
sub_Cs_on_I_sublattice1_set2 = PeriodicSite('Cs',
identical_I_vacs_sublattice1[
1].site.frac_coords,
s_struc.lattice)
sub_Cs_on_I_sublattice2 = PeriodicSite('Cs',
identical_I_vacs_sublattice2[
0].site.frac_coords,
s_struc.lattice)
sub_Rb_on_I_sublattice2 = PeriodicSite('Rb',
identical_I_vacs_sublattice2[
0].site.frac_coords,
s_struc.lattice)
self.assertTrue(pdc.are_equal( # trivial substitution test
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1),
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1)
))
self.assertTrue(pdc.are_equal( # same sublattice, different coords
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1),
Substitution(s_struc, sub_Cs_on_I_sublattice1_set2)
))
self.assertFalse(pdc.are_equal( # different subs (wrong specie)
Substitution(s_struc, sub_Cs_on_I_sublattice2),
Substitution(s_struc, sub_Rb_on_I_sublattice2)
))
self.assertFalse(pdc.are_equal( # different subs (wrong sublattice)
Substitution(s_struc, sub_Cs_on_I_sublattice1_set1),
Substitution(s_struc, sub_Cs_on_I_sublattice2)
))
# test symmorphic interstitial matching
# (using set generated from Voronoi generator, with same sublattice given by saturatated_interstitial_structure function)
inter_H_sublattice1_set1 = PeriodicSite('H', [0., 0.75, 0.25],
s_struc.lattice)
inter_H_sublattice1_set2 = PeriodicSite('H', [0., 0.75, 0.75],
s_struc.lattice)
inter_H_sublattice2 = PeriodicSite('H',
[0.57796112, 0.06923687, 0.56923687],
s_struc.lattice)
inter_H_sublattice3 = PeriodicSite('H', [0.25, 0.25, 0.54018268],
s_struc.lattice)
inter_He_sublattice3 = PeriodicSite('He', [0.25, 0.25, 0.54018268],
s_struc.lattice)
self.assertTrue(pdc.are_equal( # trivial interstitial test
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice1_set1)
))
self.assertTrue(pdc.are_equal( # same sublattice, different coords
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice1_set2)
))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong sublattice)
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice2)
))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong sublattice)
Interstitial(s_struc, inter_H_sublattice1_set1),
Interstitial(s_struc, inter_H_sublattice3)
))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong specie)
Interstitial(s_struc, inter_H_sublattice3),
Interstitial(s_struc, inter_He_sublattice3)
))
# test non-symmorphic interstitial matching
# (using set generated from Voronoi generator, with same sublattice given by saturatated_interstitial_structure function)
ns_struc = Structure.from_file(os.path.join(test_dir, "CuCl.cif"))
ns_inter_H_sublattice1_set1 = PeriodicSite('H', [0.06924513, 0.06308959,
0.86766528],
ns_struc.lattice)
ns_inter_H_sublattice1_set2 = PeriodicSite('H', [0.43691041, 0.36766528,
0.06924513],
ns_struc.lattice)
ns_inter_H_sublattice2 = PeriodicSite('H', [0.06022109, 0.60196031,
0.1621814],
ns_struc.lattice)
ns_inter_He_sublattice2 = PeriodicSite('He', [0.06022109, 0.60196031,
0.1621814],
ns_struc.lattice)
self.assertTrue(pdc.are_equal( # trivial interstitial test
Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
Interstitial(ns_struc, ns_inter_H_sublattice1_set1)
))
self.assertTrue(pdc.are_equal( # same sublattice, different coords
Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
Interstitial(ns_struc, ns_inter_H_sublattice1_set2)
))
self.assertFalse(pdc.are_equal(
Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
# different interstitials (wrong sublattice)
Interstitial(ns_struc, ns_inter_H_sublattice2)))
self.assertFalse(
pdc.are_equal( # different interstitials (wrong specie)
Interstitial(ns_struc, ns_inter_H_sublattice2),
Interstitial(ns_struc, ns_inter_He_sublattice2)
))
# test influence of charge on defect matching (default is to be charge agnostic)
vac_diff_chg = identical_Cs_vacs[0].copy()
vac_diff_chg.set_charge(3.)
self.assertTrue(pdc.are_equal(identical_Cs_vacs[0], vac_diff_chg))
chargecheck_pdc = PointDefectComparator(
check_charge=True) # switch to PDC which cares about charge state
self.assertFalse(
chargecheck_pdc.are_equal(identical_Cs_vacs[0], vac_diff_chg))
# test different supercell size
# (comparing same defect but different supercells - default is to not check for this)
sc_agnostic_pdc = PointDefectComparator(check_primitive_cell=True)
sc_scaled_s_struc = s_struc.copy()
sc_scaled_s_struc.make_supercell([2, 2, 3])
sc_scaled_I_vac_sublatt1_ps1 = PeriodicSite('I',
identical_I_vacs_sublattice1[
0].site.coords,
sc_scaled_s_struc.lattice,
coords_are_cartesian=True)
sc_scaled_I_vac_sublatt1_ps2 = PeriodicSite('I',
identical_I_vacs_sublattice1[
1].site.coords,
sc_scaled_s_struc.lattice,
coords_are_cartesian=True)
sc_scaled_I_vac_sublatt2_ps = PeriodicSite('I',
identical_I_vacs_sublattice2[
1].site.coords,
sc_scaled_s_struc.lattice,
coords_are_cartesian=True)
sc_scaled_I_vac_sublatt1_defect1 = Vacancy(sc_scaled_s_struc,
sc_scaled_I_vac_sublatt1_ps1)
sc_scaled_I_vac_sublatt1_defect2 = Vacancy(sc_scaled_s_struc,
sc_scaled_I_vac_sublatt1_ps2)
sc_scaled_I_vac_sublatt2_defect = Vacancy(sc_scaled_s_struc,
sc_scaled_I_vac_sublatt2_ps)
self.assertFalse(
pdc.are_equal(identical_I_vacs_sublattice1[0],
# trivially same defect site but between different supercells
sc_scaled_I_vac_sublatt1_defect1))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
sc_scaled_I_vac_sublatt1_defect1))
self.assertFalse(pdc.are_equal(identical_I_vacs_sublattice1[1],
# same coords, different lattice structure
sc_scaled_I_vac_sublatt1_defect1))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[1],
sc_scaled_I_vac_sublatt1_defect1))
self.assertFalse(pdc.are_equal(identical_I_vacs_sublattice1[0],
# same sublattice, different coords
sc_scaled_I_vac_sublatt1_defect2))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
sc_scaled_I_vac_sublatt1_defect2))
self.assertFalse(
sc_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
# different defects (wrong sublattice)
sc_scaled_I_vac_sublatt2_defect))
# test same structure size, but scaled lattice volume
# (default is to not allow these to be equal, but check_lattice_scale=True allows for this)
vol_agnostic_pdc = PointDefectComparator(check_lattice_scale=True)
vol_scaled_s_struc = s_struc.copy()
vol_scaled_s_struc.scale_lattice(s_struc.volume * 0.95)
vol_scaled_I_vac_sublatt1_defect1 = Vacancy(vol_scaled_s_struc,
vol_scaled_s_struc[4])
vol_scaled_I_vac_sublatt1_defect2 = Vacancy(vol_scaled_s_struc,
vol_scaled_s_struc[5])
vol_scaled_I_vac_sublatt2_defect = Vacancy(vol_scaled_s_struc,
vol_scaled_s_struc[6])
self.assertFalse(pdc.are_equal(identical_I_vacs_sublattice1[0],
# trivially same defect (but vol change)
vol_scaled_I_vac_sublatt1_defect1))
self.assertTrue(
vol_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
vol_scaled_I_vac_sublatt1_defect1))
self.assertFalse(
pdc.are_equal(identical_I_vacs_sublattice1[0],
# same defect, different sublattice point (and vol change)
vol_scaled_I_vac_sublatt1_defect2))
self.assertTrue(
vol_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
vol_scaled_I_vac_sublatt1_defect2))
self.assertFalse(
vol_agnostic_pdc.are_equal(identical_I_vacs_sublattice1[0],
# different defect (wrong sublattice)
vol_scaled_I_vac_sublatt2_defect))
# test identical defect which has had entire lattice shifted
shift_s_struc = s_struc.copy()
shift_s_struc.translate_sites(range(len(s_struc)), [0.2, 0.3, 0.4],
frac_coords=True, to_unit_cell=True)
shifted_identical_Cs_vacs = [Vacancy(shift_s_struc, shift_s_struc[0]),
Vacancy(shift_s_struc, shift_s_struc[1])]
self.assertTrue(pdc.are_equal(identical_Cs_vacs[0],
# trivially same defect (but shifted)
shifted_identical_Cs_vacs[0]))
self.assertTrue(pdc.are_equal(identical_Cs_vacs[0],
# same defect on different sublattice point (and shifted)
shifted_identical_Cs_vacs[1]))
# test uniform lattice shift within non-symmorphic structure
shift_ns_struc = ns_struc.copy()
shift_ns_struc.translate_sites(range(len(ns_struc)), [0., 0.6, 0.3],
frac_coords=True, to_unit_cell=True)
shift_ns_inter_H_sublattice1_set1 = PeriodicSite('H',
ns_inter_H_sublattice1_set1.frac_coords + [
0., 0.6, 0.3],
shift_ns_struc.lattice)
shift_ns_inter_H_sublattice1_set2 = PeriodicSite('H',
ns_inter_H_sublattice1_set2.frac_coords + [
0., 0.6, 0.3],
shift_ns_struc.lattice)
self.assertTrue(
pdc.are_equal(Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
# trivially same defect (but shifted)
Interstitial(shift_ns_struc,
shift_ns_inter_H_sublattice1_set1)))
self.assertTrue(
pdc.are_equal(Interstitial(ns_struc, ns_inter_H_sublattice1_set1),
# same defect on different sublattice point (and shifted)
Interstitial(shift_ns_struc,
shift_ns_inter_H_sublattice1_set2)))
# test a rotational + supercell type structure transformation (requires check_primitive_cell=True)
rotated_s_struc = s_struc.copy()
rotated_s_struc.make_supercell([[2, 1, 0], [-1, 3, 0], [0, 0, 2]])
rotated_identical_Cs_vacs = [
Vacancy(rotated_s_struc, rotated_s_struc[0]),
Vacancy(rotated_s_struc, rotated_s_struc[1])]
self.assertFalse(pdc.are_equal(identical_Cs_vacs[0],
# trivially same defect (but rotated)
rotated_identical_Cs_vacs[0]))
self.assertTrue(sc_agnostic_pdc.are_equal(identical_Cs_vacs[0],
rotated_identical_Cs_vacs[0]))
self.assertFalse(pdc.are_equal(identical_Cs_vacs[0],
# same defect on different sublattice (and rotated)
rotated_identical_Cs_vacs[1]))
self.assertTrue(
sc_agnostic_pdc.are_equal(identical_Cs_vacs[0],
# same defect on different sublattice point (and rotated)
rotated_identical_Cs_vacs[1]))
# test a rotational + supercell + shift type structure transformation for non-symmorphic structure
rotANDshift_ns_struc = ns_struc.copy()
rotANDshift_ns_struc.translate_sites(range(len(ns_struc)),
[0., 0.6, 0.3], frac_coords=True,
to_unit_cell=True)
rotANDshift_ns_struc.make_supercell([[2, 1, 0], [-1, 3, 0], [0, 0, 2]])
ns_vac_Cs_set1 = Vacancy(ns_struc, ns_struc[0])
rotANDshift_ns_vac_Cs_set1 = Vacancy(rotANDshift_ns_struc,
rotANDshift_ns_struc[0])
rotANDshift_ns_vac_Cs_set2 = Vacancy(rotANDshift_ns_struc,
rotANDshift_ns_struc[1])
self.assertTrue(sc_agnostic_pdc.are_equal(ns_vac_Cs_set1,
# trivially same defect (but rotated and sublattice shifted)
rotANDshift_ns_vac_Cs_set1))
self.assertTrue(
sc_agnostic_pdc.are_equal(ns_vac_Cs_set1,
# same defect on different sublattice point (shifted and rotated)
rotANDshift_ns_vac_Cs_set2))