def _get_sites(atoms, doped_out, doped_in):
doped_in = [s2n(i) for i in doped_in]
if doped_out == 'all':
return [tuple([atom] + doped_in) for atom in atoms]
else:
doped_out = s2n(doped_out)
_ins = tuple([doped_out] + doped_in)
return [_ins if atom == doped_out else (atom, ) for atom in atoms]
def get_magnetic_config(self,
magnetic_atom,
magmon=1,
magmon_identity=False,
symprec=1e-3):
cell = self.no_defect_cell
cg = ConfigurationGenerator(cell, symprec)
doped_in = get_symbol(
np.setdiff1d(range(1, 56), np.unique(cell.atoms))[0])
sites = _get_sites(list(cell.atoms),
doped_out=magnetic_atom,
doped_in=[doped_in])
n = len(cell.atoms)
magmom = []
magnetic_atom_idx = np.where(
cell.atoms == s2n(magnetic_atom[0]))[0].astype("int")
atoms_type = get_identity_atoms(cell, symprec)
unique_atoms_type = np.unique(atoms_type)
for num in range(len(magnetic_atom_idx) // 2 + 1):
confs = cg.cons_specific_cell(
sites,
e_num=[len(magnetic_atom_idx) - num, num],
symprec=symprec)
for c, _def in confs:
tmp_magmom = np.zeros((n, ))
tmp_magmom[magnetic_atom_idx] = magmon
mag_idx = [np.where(np.linalg.norm(cell.positions-c.positions[_idx],axis=1)<0.01)[0][0] \
for _idx in np.where(c.atoms==s2n(doped_in[0]))[0]]
tmp_magmom[mag_idx] = -magmon
if magmon_identity:
flag = True
for i in unique_atoms_type:
if len(
np.unique(tmp_magmom[np.where(
atoms_type == i)[0]])) != 1:
flag = False
break
if flag:
magmom.append(tmp_magmom.tolist())
else:
magmom.append(tmp_magmom.tolist())
# remove the equivalent AFM -1 1/1 -1
final_magmom = set()
final_magmom.add(tuple(magmom[0]))
for idx in range(1, len(magmom)):
mag = np.array(magmom[idx]).astype("int")
if tuple(mag) in final_magmom:
continue
idx_up = np.where(mag == magmon)[0].astype("int")
idx_down = np.where(mag == -magmon)[0].astype("int")
mag[idx_up] = -magmon
mag[idx_down] = magmon
if tuple(mag) in final_magmom:
continue
final_magmom.add(tuple(mag))
final_magmom = np.array([list(i) for i in final_magmom])
np.savetxt("INCAR-magmon", final_magmom, fmt='%2d')
def _get_sites(l_atoms, ele, l_sub):
ele_n = s2n(ele)
l_sub_n = [s2n(sub_n) for sub_n in l_sub]
sites = []
for a in l_atoms:
if a == ele_n:
sites.append(tuple([a] + l_sub_n))
else:
sites.append(tuple([a]))
return sites
def _get_sites(atoms, doped_out, doped_in):
doped_in = [s2n(i) for i in doped_in]
if doped_out == ['all']:
return [tuple([atom] + doped_in) for atom in atoms]
elif len(doped_out) > 1:
doped_out = [s2n(i) for i in doped_out]
return [
tuple([atom] + doped_in) if atom in doped_out else (atom, )
for atom in atoms
]
else:
doped_out = [s2n(i) for i in doped_out]
_ins = tuple(doped_out + doped_in)
return [_ins if atom == doped_out else (atom, ) for atom in atoms]
def get_purity_defect(self,
symprec=1e-3,
purity_out='all',
purity_in='Vacc',
num=1):
cg = ConfigurationGenerator(self.no_defect_cell, symprec)
sites = _get_sites(list(self.atoms),
purity_out=purity_out,
purity_in=purity_in)
if purity_out == 'all':
confs = cg.cons_specific_cell(sites,
e_num=(len(self.atoms) - num, num),
symprec=symprec)
else:
purity_atom_num = np.where(self.atoms == s2n(purity_out))[0].size
confs = cg.cons_specific_cell(sites,
e_num=(purity_atom_num - num, num),
symprec=symprec)
folder = purity_out + '-' + purity_in + '-defect'
if not os.path.exists('./' + folder):
os.mkdir('./' + folder)
else:
rmtree('./' + folder)
os.mkdir('./' + folder)
idx = 0
for c, _ in confs:
wirite_poscar(c, purity_out + '-' + purity_in, folder, idx)
idx += 1
def get_purity_defect(self,
symprec=1e-3,
isunique=True,
purity_atom='all',
style='Vacc'):
cg = ConfigurationGenerator(self.no_defect_cell, symprec)
sites = _get_sites(list(self.atoms),
l_sub=purity_atom,
purity_atom=style)
if purity_atom == 'all':
confs = cg.cons_specific_cell(sites,
e_num=(len(self.atoms) - 1, 1),
symprec=symprec)
else:
purity_atom_num = np.where(self.atoms == s2n(purity_atom))[0].size
confs = cg.cons_specific_cell(sites,
e_num=(purity_atom_num - 1, 1),
symprec=symprec)
folder = style + 'defect'
if not os.path.exists('./' + folder):
os.mkdir('./' + folder)
else:
rmtree('./' + folder)
os.mkdir('./' + folder)
idx = 0
for c, _ in confs:
wirite_poscar(c, purity_atom, folder, idx)
idx += 1
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_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
def conf(cell_filename, comment, pmode, cmode, dimension, volume, element,
substitutes, number, symprec, comprec, verbose):
"""
<parent_cell_file> is the parent cell to generating configurations by sites disorder.\n
The non-primitive cell can only used as argument when '--pmode=sc'.\n
Command line tool only provide configurations generator for elements disorder, for more flexible usage such as specific site disorder, please see document http:// , or use python library directly.
"""
cell = read_vasp(cell_filename)
cg = ConfigurationGenerator(cell, symprec)
if pmode == 'varv' and cmode == 'vc':
click.secho("Expanding and generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
(min_v, max_v) = volume
if min_v == -1:
min_v = 1
sites = _get_sites(list(cell.atoms), element, substitutes)
confs = cg.cons_max_volume(sites,
max_v,
min_volume=min_v,
dimension=dimension,
symprec=symprec)
for idx, c in enumerate(confs):
c = c.get_primitive_cell()
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'svc' and cmode == 'vc':
click.secho("Expanding and generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
(min_v, max_v) = volume
sites = _get_sites(list(cell.atoms), element, substitutes)
confs = cg.cons_specific_volume(sites,
volume=max_v,
e_num=None,
dimension=dimension,
symprec=symprec)
f_deg = open('deg.txt', 'a')
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'svc' and cmode == 'cc':
click.secho("Expanding and generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
(min_v, max_v) = volume
l_atoms = cell.atoms.tolist()
sites = _get_sites(l_atoms, element, substitutes)
# number to enum
ele_n = s2n(element)
e_total = l_atoms.count(ele_n) * max_v
e_n = e_total - sum(number) # 第一个元素的数量
e_num = [e_n] + list(number) # 各个元素的数量
confs = cg.cons_specific_volume(sites,
volume=max_v,
e_num=e_num,
dimension=dimension,
symprec=symprec)
f_deg = open('deg.txt', 'a')
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'sc' and cmode == 'vc':
click.secho("Generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
l_atoms = cell.atoms.tolist()
sites = _get_sites(l_atoms, element, substitutes)
confs = cg.cons_specific_cell(sites, None, symprec=symprec)
f_deg = open('deg.txt', 'a')
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
# import pdb; pdb.set_trace()
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'sc' and cmode == 'cc':
click.secho("Generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
l_atoms = cell.atoms.tolist()
sites = _get_sites(l_atoms, element, substitutes)
# number to enum
ele_n = s2n(element)
e_total = l_atoms.count(ele_n)
e_n = e_total - sum(number) # 第一个元素的数量
e_num = [e_n] + list(number) # 各个元素的数量
confs = cg.cons_specific_cell(sites, e_num, symprec=symprec)
f_deg = open('deg.txt', 'a')
# TODO f.close()
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
else:
click.secho("ERROR: --pmode={:s} --cmode={:s} not supported.".format(
pmode, cmode),
bold=True,
bg='red',
fg='white')
def _get_sites(atoms, purity_out='all', purity_in='Vacc'):
if purity_out == 'all':
return [(i, s2n(purity_in)) for i in atoms]
else:
return [(i, s2n(purity_in)) if i == s2n(purity_out) else (i, )
for i in atoms]
def _get_sites(atoms, l_sub='all', purity_atom='Vacc'):
if l_sub == 'all':
return [(i, s2n(purity_atom)) for i in atoms]
else:
return [(i, s2n(purity_atom)) if i == s2n(l_sub) else (i, )
for i in atoms]
