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 get_string(self, radius=10.):
"""
Returns a string representation of atomic shell coordinates to be used
in the feff.inp file.
Args:
radius:
Maximum atomic shell radius to include in atoms list
Returns:
String representation of Atomic Coordinate Shells.
"""
nopts = len(self.struct.species)
ptatoms = []
for i in range(0, nopts):
ptatoms.append(self.struct.species[i].symbol)
index = ptatoms.index(self.central_atom)
pt = self.struct.cart_coords[index]
sphere = Structure.get_sites_in_sphere(self.struct, pt, radius)
xshift = pt[0]
yshift = pt[1]
zshift = pt[2]
end = len(sphere)
row = []
for i in range(end):
atom = sphere[i][0]
atm = re.sub(r"[^aA-zZ]+", "", atom.species_string)
ipot = self.pot_dict[atm]
x = atom.coords[0] - xshift
y = atom.coords[1] - yshift
z = atom.coords[2] - zshift
distance = sphere[i][1]
row.append(["{:f}".format(x), "{:f}".format(y), "{:f}".format(z),
ipot, atm, "{:f}".format(distance), i])
row_sorted = sorted(row, key=itemgetter(5))
row_sorted[0][3] = 0
for i in range(end):
row_sorted[i][6] = i
row_sorted = str_aligned(row_sorted, ["* x", "y", "z", "ipot",
"Atom", "Distance", "Number"])
atom_list = row_sorted.replace("--", "**")
return ''.join(["ATOMS\n", atom_list, "\nEND\n"])
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 perturb_neighboring_atoms(structure: Structure,
center: List[float],
cutoff: float,
distance: float,
inserted_atom_indices: List[int]
) -> Tuple[Structure, list]:
""" Return the structure with randomly perturbed atoms near the center
Args:
structure (Structure):
pmg Structure class object
center (list):
Fractional coordinates of a central position.
cutoff (float):
Radius of a sphere in which atoms are perturbed.
distance (float):
Max displacement distance for the perturbation.
inserted_atom_indices (list):
Inserted atom indices, which will not be perturbed.
Return:
Tuple of perturbed Structure and list of perturbed atom indices.
"""
perturbed_structure = structure.copy()
cartesian_coords = structure.lattice.get_cartesian_coords(center)
# neighbor is (PeriodicSite, distance, index)
neighbors = structure.get_sites_in_sphere(
pt=cartesian_coords, r=cutoff, include_index=True)
if not neighbors:
logger.warning(f"No neighbors withing the cutoff {cutoff}.")
sites = []
for i in neighbors:
# not perturb inserted atoms
if i[2] in inserted_atom_indices:
continue
# Since translate_sites accepts only one vector, iterate this.
vector = normalized_random_3d_vector() * distance * np.random.random()
site_index = i[2]
sites.append(site_index)
perturbed_structure.translate_sites(
indices=site_index, vector=vector, frac_coords=False)
return perturbed_structure, sites
def get_string(self, radius=10.):
"""
Returns a string representation of atomic shell coordinates to be used
in the feff.inp file.
Args:
radius: Maximum atomic shell radius to include in atoms list
Returns:
String representation of Atomic Coordinate Shells.
"""
#Internal variables:
#
#nopts = number of potentials in unit cell used
#ptatoms = list of atom potential atom symbols in unit cell
#index = index number of absorbing atom in list
#pt = coordinates of absorbing atom
#sphere = sites around absorbing atom within radius
#x,y,zshift = coordinate shift to place absorbing atom at (0,0,0)
#atom = site in sphere
#atm = atomic symbol string for atom at atom site
#ipot = index for that atom symbol in potential dictionary
#distance = distance of that atom site from absorbing atom
nopts = len(self.struct.species)
ptatoms = [self.struct.species[i].symbol for i in range(nopts)]
index = ptatoms.index(self.central_atom)
pt = self.struct.cart_coords[index]
sphere = Structure.get_sites_in_sphere(self.struct, pt, radius)
xshift = pt[0]
yshift = pt[1]
zshift = pt[2]
end = len(sphere)
row = []
for i in range(end):
atom = sphere[i][0]
atm = re.sub(r"[^aA-zZ]+", "", atom.species_string)
ipot = self.pot_dict[atm]
x = atom.coords[0] - xshift
y = atom.coords[1] - yshift
z = atom.coords[2] - zshift
distance = sphere[i][1]
row.append(["{:f}".format(x), "{:f}".format(y), "{:f}".format(z),
ipot, atm, "{:f}".format(distance), i])
#after this point table is built
row_sorted = sorted(row, key=itemgetter(5))
row_sorted[0][3] = 0
for i in range(end):
row_sorted[i][6] = i
row_sorted = str_aligned(row_sorted, ["* x", "y", "z", "ipot",
"Atom", "Distance", "Number"])
atom_list = row_sorted.replace("--", "**")
return ''.join(["ATOMS\n", atom_list, "\nEND\n"])
def get_string(self, radius=10.):
"""
Returns a string representation of atomic shell coordinates to be used
in the feff.inp file.
Args:
radius: Maximum atomic shell radius to include in atoms list
Returns:
String representation of Atomic Coordinate Shells.
"""
#Internal variables:
#
#nopts = number of potentials in unit cell used
#ptatoms = list of atom potential atom symbols in unit cell
#index = index number of absorbing atom in list
#pt = coordinates of absorbing atom
#sphere = sites around absorbing atom within radius
#x,y,zshift = coordinate shift to place absorbing atom at (0,0,0)
#atom = site in sphere
#atm = atomic symbol string for atom at atom site
#ipot = index for that atom symbol in potential dictionary
#distance = distance of that atom site from absorbing atom
nopts = len(self.struct.species)
ptatoms = [self.struct.species[i].symbol for i in range(nopts)]
index = ptatoms.index(self.central_atom)
pt = self.struct.cart_coords[index]
sphere = Structure.get_sites_in_sphere(self.struct, pt, radius)
xshift = pt[0]
yshift = pt[1]
zshift = pt[2]
end = len(sphere)
row = []
for i in range(end):
atom = sphere[i][0]
atm = re.sub(r"[^aA-zZ]+", "", atom.species_string)
ipot = self.pot_dict[atm]
x = atom.coords[0] - xshift
y = atom.coords[1] - yshift
z = atom.coords[2] - zshift
distance = sphere[i][1]
row.append([
"{:f}".format(x), "{:f}".format(y), "{:f}".format(z), ipot,
atm, "{:f}".format(distance), i
])
#after this point table is built
row_sorted = sorted(row, key=itemgetter(5))
row_sorted[0][3] = 0
for i in range(end):
row_sorted[i][6] = i
row_sorted = str_aligned(
row_sorted,
["* x", "y", "z", "ipot", "Atom", "Distance", "Number"])
atom_list = row_sorted.replace("--", "**")
return ''.join(["ATOMS\n", atom_list, "\nEND\n"])
