def generate_defect_structure(self, supercell=(1, 1, 1)):
"""
Returns Defective Substitution structure, decorated with charge.
If bulk structure had any site properties, all of these properties are
removed in the resulting defect structure.
Args:
supercell (int, [3x1], or [[]] (3x3)): supercell integer, vector, or scaling matrix
"""
defect_structure = Structure( self.bulk_structure.copy().lattice,
[site.specie for site in self.bulk_structure],
[site.frac_coords for site in self.bulk_structure],
to_unit_cell=True, coords_are_cartesian = False,
site_properties = None) #remove all site_properties
defect_structure.make_supercell(supercell)
#create a trivial defect structure to find where supercell transformation moves the defect
struct_for_defect_site = Structure( self.bulk_structure.copy().lattice,
[self.site.specie],
[self.site.frac_coords],
to_unit_cell=True, coords_are_cartesian = False)
struct_for_defect_site.make_supercell(supercell)
defect_site = struct_for_defect_site[0]
poss_deflist = sorted(
defect_structure.get_sites_in_sphere(defect_site.coords, 0.1, include_index=True), key=lambda x: x[1])
defindex = poss_deflist[0][2]
subsite = defect_structure.pop(defindex)
defect_structure.append(self.site.specie.symbol, subsite.coords, coords_are_cartesian=True,
properties = None)
defect_structure.set_charge(self.charge)
return defect_structure
def generate_defect_structure(self, supercell=(1, 1, 1)):
"""
Returns Defective Substitution structure, decorated with charge.
If bulk structure had any site properties, all of these properties are
removed in the resulting defect structure.
Args:
supercell (int, [3x1], or [[]] (3x3)): supercell integer, vector, or scaling matrix
"""
defect_structure = Structure(
self.bulk_structure.copy().lattice,
[site.specie for site in self.bulk_structure],
[site.frac_coords for site in self.bulk_structure],
to_unit_cell=True,
coords_are_cartesian=False,
site_properties=None,
) # remove all site_properties
defect_structure.make_supercell(supercell)
# create a trivial defect structure to find where supercell transformation moves the defect
struct_for_defect_site = Structure(
self.bulk_structure.copy().lattice,
[self.site.specie],
[self.site.frac_coords],
to_unit_cell=True,
coords_are_cartesian=False,
)
struct_for_defect_site.make_supercell(supercell)
defect_site = struct_for_defect_site[0]
poss_deflist = sorted(
defect_structure.get_sites_in_sphere(defect_site.coords,
0.1,
include_index=True),
key=lambda x: x[1],
)
defindex = poss_deflist[0][2]
subsite = defect_structure.pop(defindex)
defect_structure.append(
self.site.specie.symbol,
subsite.coords,
coords_are_cartesian=True,
properties=None,
)
defect_structure.set_charge(self.charge)
return defect_structure
