def interstitial_tetrahedral(lattice, species, interstitial_species=None,
min_atoms=0, supercell=None, index=-1):
"""
Create a crystal structure with a tetrahedral interstitial atom between
four atoms.
Parameters
----------
lattice : str
Lattice to use for the base crystal structure. Valid choices are 'bcc'
and 'fcc'.
species : int or str
Identity of species used to construct the lattice.
interstitial_species : int or str, optional
Identity of the interstitial species; if not specified, creates a
self-interstitial.
min_atoms : int, optional
Construct a supercell to include at least this many atoms.
supercell : (int, int, int), optional
Request a specific supercell of bulk material. If not given,
max_atoms will be used instead to create a cubic cell.
index : int, optional
Index of nearest lattice atom to the interstitial. Additional atom is
placed along the <210> direction in bcc and <221> in fcc.
Returns
-------
ase.Atoms
Lattice with a tetrahedral interstitial atom.
"""
species = Element(species)
if interstitial_species is None:
interstitial_species = species
else:
interstitial_species = Element(interstitial_species)
ibulk = bulk(species, lattice, min_atoms, supercell)
lattice_constant = ibulk.info['lattice_constant']
if lattice.lower() == 'bcc':
displacement = [lattice_constant/4.0, lattice_constant/2.0, 0]
elif lattice.lower() == 'fcc':
displacement = [lattice_constant/4.0,
lattice_constant/4.0,
lattice_constant/2.0]
else:
raise NotImplementedError("Tetrahedral defects not implemented in "
"{0}".format(lattice))
if index < 0:
index += len(ibulk)
# Move into tetrahedral position
ibulk.append(Atom(interstitial_species,
position=ibulk[index].position + displacement))
return ibulk
def interstitial_dumbbell(lattice, species, direction='111',
interstitial_species=None, min_atoms=0,
supercell=None, index=-1):
"""
Create a crystal structure, such as bcc or fcc, with a dumbbell
interstitial atom along the given lattice direction.
Parameters
----------
lattice : str
Lattice type to generate, valid values are 'bcc' and 'fcc' or anything
accepted by sats bulk.
species : int or str
Identity of species used to construct the lattice.
direction : str
Lattice direction along which to create the dumbbell.
interstitial_species : int or str, optional
Identity of the interstitial species; if not specified, creates a
self-interstitial.
min_atoms : int, optional
Construct a supercell to include at least this many atoms.
supercell : (int, int, int), optional
Request a specific supercell of bulk material. If not given,
max_atoms will be used instead to create a cubic cell.
index : int, optional
Index of atom with which to create the dumbbell. Added atom is always
at the end.
Returns
-------
ase.Atoms
Lattice with a dumbbell interstitial atom.
"""
species = Element(species)
if interstitial_species is None:
interstitial_species = species
else:
interstitial_species = Element(interstitial_species)
ibulk = bulk(species, lattice, min_atoms, supercell)
lattice_constant = ibulk.info['lattice_constant']
if index < 0:
index += len(ibulk)
# parses the digits from any string, ignoring brackets etc.
direction = [int(x) for x in re.findall('[+-]*[0-9]', direction)]
displacement = [1.0/x if x else 0.0 for x in direction]
# Move 1/3 of the <111> atom separation in each direction
magnitude = lattice_constant/(12*sum(x**2 for x in displacement))**0.5
displacement = [x*magnitude for x in displacement]
ibulk.append(Atom(interstitial_species,
position=ibulk[index].position + displacement))
ibulk[index].position -= displacement
return ibulk
def vacancy(lattice, species, n_vacancies=1, min_atoms=0, direction=None):
"""
Helper function to create a vacancy in a lattice. Multiple vacancies are
created in a line along close packed directions.
Parameters
----------
lattice : str
Lattice type for the bulk structure. Generated as a sats bulk.
species : int or str
Identity of species used to construct the lattice.
n_vacancies : int, optional
Number of vacancies to create in a row.
min_atoms : int, optional
Construct a supercell to include at least this many atoms.
direction : tuple of int, optional
Create vacancy row along this direction. If none is specified then
the close packed direction is used.
Returns
-------
vacancy : ase.Atoms
Lattice with the requested defect.
"""
species = Element(species)
vbulk = bulk(species, lattice, min_atoms)
if direction is None:
direction = {
'bcc': (1, 1, 1),
'hcp': (1 / 3.0**0.5, 1, 0),
'fcc': (1, 1, 0)
}[lattice]
# order from lowest x, y and z to get an origin
sites = [
atom.index for atom in sorted(vbulk, key=lambda a: (a.c, a.a, a.b))
]
origin = vbulk[sites[0]]
line_atoms = []
# index all the atoms along the line from origin
for atom in vbulk:
separation = atom.position - origin.position
if norm(cross(separation, direction)) < 1.0e-5:
line_atoms.append((norm(separation), atom.index))
if n_vacancies >= 1:
for atom in sorted(line_atoms, reverse=True)[-n_vacancies:]:
del vbulk[atom[1]]
return vbulk