def get_point_defect(self,
symprec=1e-3,
doped_out='all',
doped_in=['Vac'],
num=[1]):
cell = self.no_defect_cell
cg = ConfigurationGenerator(cell, symprec)
sites = _get_sites(list(cell.atoms),
doped_out=doped_out,
doped_in=doped_in)
if num == None:
confs = cg.cons_specific_cell(sites, e_num=None, symprec=symprec)
comment = ["-".join(doped_in) + "-all_concentration"]
else:
purity_atom_num = sum(
[1 if len(site) > 1 else 0 for site in sites])
confs = cg.cons_specific_cell(sites,
e_num=[purity_atom_num - sum(num)] +
num,
symprec=symprec)
comment = list(chain(*zip(doped_in, [str(i) for i in num])))
comment = '-'.join(doped_out) + '-' + '-'.join(comment) + '-defect'
folder = comment
if not os.path.isdir(folder):
os.makedirs(folder)
deg = []
idx = 0
for c, _deg in confs:
write_poscar(c, folder, idx)
deg.append(_deg)
idx += 1
np.savetxt(os.path.join(folder, "deg.txt"), deg, fmt='%d')
def get_point_defect(self,
symprec=1e-3,
doped_out='all',
doped_in=['Vac'],
num=[1]):
cg = ConfigurationGenerator(self.no_defect_cell, symprec)
sites = _get_sites(list(self.atoms),
doped_out=doped_out,
doped_in=doped_in)
if doped_out == 'all':
if len(np.unique(self.atoms)) > 1 and len(doped_in) > 1:
raise ValueError(
"Multiple species elements doped in and multiple elements doped out is ambiguous"
)
confs = cg.cons_specific_cell(sites,
e_num=[len(self.atoms) - sum(num)] +
num,
symprec=symprec)
else:
purity_atom_num = np.where(self.atoms == s2n(doped_out))[0].size
confs = cg.cons_specific_cell(sites,
e_num=[purity_atom_num - sum(num)] +
num,
symprec=symprec)
comment = list(chain(*zip(doped_in, [str(i) for i in num])))
folder = doped_out + '-' + '-'.join(comment) + '-defect'
if not os.path.exists('./' + folder):
os.mkdir('./' + folder)
else:
rmtree('./' + folder)
os.mkdir('./' + folder)
idx = 0
for c, _ in confs:
write_poscar(c, folder, idx)
idx += 1
def get_mole_point_defect(self,
symprec=1e-3,
doped_out='all',
doped_in=['Vac'],
num=[1]):
pos, lat, atoms = self.positions, self.lattice, self.atoms
mole = Molecule(np.dot(pos, lat), atoms)
cg = mole_CG(mole, symprec)
sites = _get_sites(list(mole.atoms),
doped_out=doped_out,
doped_in=doped_in)
if num == None:
confs = cg.get_configurations(sites, e_num=None)
comment = ["-".join(doped_in) + "-all_concentration"]
else:
purity_atom_num = sum(
[1 if len(site) > 1 else 0 for site in sites])
confs = cg.get_configurations(sites,
e_num=[purity_atom_num - sum(num)] +
num)
comment = list(chain(*zip(doped_in, [str(i) for i in num])))
folder = '-'.join(doped_out) + '-' + '-'.join(comment) + '-defect'
if not os.path.exists('./' + folder):
os.mkdir('./' + folder)
else:
rmtree('./' + folder)
os.mkdir('./' + folder)
deg = []
idx = 0
for c, _deg in confs:
c.lattice = lat
c._positions = np.dot(c.positions, np.linalg.inv(lat))
write_poscar(c, folder, idx)
deg.append(_deg)
idx += 1
np.savetxt(os.path.join(folder, "deg.txt"), deg, fmt='%d')
def get_tetrahedral_defect(self,
isunique=False,
doped_in='H',
min_d=1.5,
folder='tetrahedral-defect'):
all_basis = generate_all_basis(1, 1, 1)
direct_lattice = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
extend_S = np.zeros((0, 3))
for basis in all_basis:
new_basis = np.sum([(direct_lattice[ii] * basis[ii]).tolist()
for ii in range(3)],
axis=0)
extend_S = np.vstack(
(extend_S,
self.positions + np.tile(new_basis, len(self.atoms)).reshape(
(-1, 3))))
idx = np.sum((extend_S <= 1.2) & (extend_S >= -0.2), axis=1)
idx = np.where(idx == 3)[0]
extend_S = np.dot(extend_S[idx], self.lattice)
n = extend_S.shape[0]
d = np.zeros((n, n))
for ii in range(n):
d[ii, ii + 1:] = np.linalg.norm(extend_S[ii] - extend_S[ii + 1:],
axis=1)
d = d + d.T
first_tetra, sec_tetra, third_tetra = [], [], []
for ii in range(n):
temp_d = sorted(d[ii])
idx = np.where(abs(d[ii] - temp_d[1]) < min_d)[0]
if len(idx) < 3:
continue
for comb in combinations(idx, 3):
comb_list = list(comb)
tmp = d[comb_list][:, comb_list]
comb_list.append(ii)
if np.std(tmp[tmp > 0]) < 0.01:
if abs(tmp[0, 1] - temp_d[1]) < 0.1:
first_tetra.append(comb_list)
else:
sec_tetra.append(comb_list)
else:
tmp = d[comb_list][:, comb_list]
tmp = np.triu(tmp)
tmp = sorted(tmp[tmp > 0])
if (np.std(tmp[0:4]) < 0.1 or np.std(tmp[1:5]) < 0.1
or np.std(tmp[2:]) < 0.1) and np.std(tmp) < 0.5:
third_tetra.append(comb_list)
all_tetra = []
if len(first_tetra) != 0:
first_tetra = np.unique(np.sort(first_tetra, axis=1), axis=0)
first_tetra = refine_points(first_tetra,
extend_S,
self.lattice,
min_d=min_d)
all_tetra.append(first_tetra)
if len(sec_tetra) != 0:
sec_tetra = np.unique(np.sort(sec_tetra, axis=1), axis=0)
sec_tetra = refine_points(sec_tetra,
extend_S,
self.lattice,
min_d=min_d)
all_tetra.append(sec_tetra)
if len(third_tetra) != 0:
third_tetra = np.unique(np.sort(third_tetra, axis=1), axis=0)
third_tetra = refine_points(third_tetra,
extend_S,
self.lattice,
min_d=min_d)
all_tetra.append(third_tetra)
if isunique:
if not os.path.exists(folder):
os.mkdir(folder)
else:
rmtree(folder)
os.mkdir(folder)
idx = 0
# deg = []
for tetra in all_tetra:
if len(tetra) == 0:
continue
new_pos = np.vstack((self.positions, tetra))
new_atoms = np.hstack((self.atoms, s2n(doped_in) * np.ones(
(tetra.shape[0], ))))
new_cell = Cell(self.lattice, new_pos, new_atoms)
equi_atoms = new_cell.get_symmetry()['equivalent_atoms']
purity_atom_type = np.unique(equi_atoms[-tetra.shape[0]:])
for atom_type in purity_atom_type:
new_uniq_pos = np.vstack(
(self.positions, new_pos[atom_type]))
new_uniq_atoms = np.hstack(
(self.atoms, s2n(doped_in) * np.ones((1, ))))
new_uniq_cell = Cell(self.lattice, new_uniq_pos,
new_uniq_atoms)
# deg.append(len(np.where(equi_atoms == atom_type)[0]))
write_poscar(new_uniq_cell, folder, idx)
idx += 1
# np.savetxt(folder+'/deg.txt',deg,fmt='%d')
else:
if not os.path.exists(folder):
os.mkdir(folder)
else:
rmtree(folder)
os.mkdir(folder)
idx = 0
for tetra in all_tetra:
if len(tetra) == 0:
continue
new_pos = np.vstack((self.positions, tetra))
new_atoms = np.hstack((self.atoms, s2n(doped_in) * np.ones(
(tetra.shape[0], ))))
new_cell = Cell(self.lattice, new_pos, new_atoms)
write_poscar(new_cell, folder, idx)
idx += 1