def get_lmto_structure(cell):
lattice = cell.get_cell()
(num_atoms,
symbols,
scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
lines = '%% site-data vn=3.0 xpos fast io=62 nbas=%d' % sum(num_atoms)
lines += ' alat=1.0 plat=' + ('%.6f ' * 9 + '\n') % tuple(lattice.ravel())
lines += '# pos '
lines += 'vel eula '
lines += 'vshft PL rlx\n'
atom_species = []
for i, j in zip(symbols, num_atoms):
atom_species.append([i]*j)
for x, y in zip(sum(atom_species, []), scaled_positions):
lines += ' %s' % x
lines += ' %.7f %.7f %.7f' % tuple(y)
lines += ' %.7f %.7f %.7f %.7f %.7f %.7f %.7f' % tuple([0.0] * 7)
lines += ' 0 111\n'
return lines
def get_elk_structure(cell, sp_filenames=None):
"""Return Elk structure in text."""
lattice = cell.get_cell()
(num_atoms, symbols, scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
if sp_filenames is None:
spfnames = [s + ".in" for s in symbols]
else:
spfnames = sp_filenames
lines = ""
lines += "avec\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += "atoms\n"
n_pos = 0
lines += " %d\n" % len(num_atoms)
for i, (n, s) in enumerate(zip(num_atoms, spfnames)):
lines += " '%s'\n" % s
lines += " %d\n" % n
lines += get_scaled_positions_lines(scaled_positions[n_pos:(n_pos +
n)])
if i < len(num_atoms) - 1:
lines += "\n"
n_pos += n
return lines
def get_fleur_structure(cell, speci, N, restlines):
lattice = cell.get_cell()
(num_atoms, symbols, scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
specilong = list(
itertools.chain.from_iterable(itertools.repeat(x, N) for x in speci))
lines = restlines[0] + "\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += '1.0 \n'
lines += '1.0 1.0 1.0 \n \n'
lines += str(sum(num_atoms)) + '\n'
for i in range(sum(num_atoms)):
lines += specilong[i].ljust(6)
currentpos = str(scaled_positions[i]).replace("[", "")
currentpos = currentpos.replace("]", "").split()
for j in range(3):
lines += ' ' + "{:.10f}".format(float(currentpos[j]))
if i < sum(num_atoms) - 1:
lines += "\n"
for x in range(1, len(restlines)):
if len(restlines[x]) == 0:
lines += "\n"
continue
lines += restlines[x]
if x != len(restlines) - 1:
lines += "\n"
return lines
def get_elk_structure(cell, sp_filenames=None):
lattice = cell.get_cell()
(num_atoms,
symbols,
scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
if sp_filenames is None:
spfnames = [s + ".in" for s in symbols]
else:
spfnames = sp_filenames
lines = ""
lines += "avec\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += "atoms\n"
n_pos = 0
lines += " %d\n" % len(num_atoms)
for i, (n, s) in enumerate(zip(num_atoms, spfnames)):
lines += " \'%s\'\n" % s
lines += " %d\n" % n
lines += get_scaled_positions_lines(scaled_positions[n_pos:(n_pos + n)])
if i < len(num_atoms) - 1:
lines += "\n"
n_pos += n
return lines
def write_magnetic_moments(cell, sort_by_elements=False):
magmoms = cell.magnetic_moments
if magmoms is not None:
if sort_by_elements:
(_, _, _,
sort_list) = sort_positions_by_symbols(cell.symbols,
cell.scaled_positions)
else:
sort_list = range(cell.get_number_of_atoms())
with open("MAGMOM", 'w') as w:
w.write(" MAGMOM = ")
for i in sort_list:
w.write("%f " % magmoms[i])
w.write("\n")
w.close()
def get_standardized_cell(self,
to_primitive: bool,
no_idealize: bool,
symprec: float = 1e-5,
no_sort: bool = False,
get_sort_list: list = False):
"""
Get stadandardized cell.
Args:
to_primitive (bool): True => primitive,
False => conventional.
no_idealize (bool): True => not rotate crystal body,
False => rotate crystal body
symprec (float): symmetry tolerance, for more detail
see spglib documentation
no_sort (bool): does not change atoms order
get_sort_list (bool): When no_sort=True, return sort list
Returns:
tuple: If get_sort_list=False, return cell.
If get_sort_list=True, return (cell, sort_list).
"""
spg_cell = spglib.standardize_cell(self._cell_for_spglib,
to_primitive=to_primitive,
no_idealize=no_idealize,
symprec=symprec)
symbols = get_symbols_from_numbers(spg_cell[2])
std_cell = (spg_cell[0], spg_cell[1], symbols)
if no_sort:
return std_cell
num_atoms, unique_symbols, scaled_positions, sort_list = \
sort_positions_by_symbols(
symbols=std_cell[2],
positions=std_cell[1])
symbols = []
for num, symbol in zip(num_atoms, unique_symbols):
symbols.extend([symbol] * num)
sort_std_cell = (std_cell[0], scaled_positions, symbols)
if get_sort_list:
return (sort_std_cell, sort_list)
return sort_std_cell
def get_lmto_structure(cell):
lattice = cell.get_cell()
(num_atoms, symbols, scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
lines = '%% site-data vn=3.0 xpos fast io=62 nbas=%d' % sum(num_atoms)
lines += ' alat=1.0 plat=' + ('%.6f ' * 9 + '\n') % tuple(lattice.ravel())
lines += '# pos '
lines += 'vel eula '
lines += 'vshft PL rlx\n'
atom_species = []
for i, j in zip(symbols, num_atoms):
atom_species.append([i] * j)
for x, y in zip(sum(atom_species, []), scaled_positions):
lines += ' %s' % x
lines += ' %.7f %.7f %.7f' % tuple(y)
lines += ' %.7f %.7f %.7f %.7f %.7f %.7f %.7f' % tuple(
[0.0] * 7)
lines += ' 0 111\n'
return lines
