def find_primitive(atoms, symprec=1e-4):
"""
find the primitive cell withh regard to the magnetic structure. a atoms object is returned.
"""
#atoms_mag,sym_dict=ref_atoms_mag(atoms)
cell, scaled_pos, chem_nums = spglib.find_primitive(atoms, symprec=symprec)
print(chem_nums)
chem_sym = 'H%d' % (len(chem_nums))
new_atoms = Atoms(chem_sym)
new_atoms.set_atomic_numbers(chem_nums)
new_atoms.set_cell(cell)
new_atoms.set_scaled_positions(scaled_pos)
#new_atoms=rev_ref_atoms(new_atoms,sym_dict)
return new_atoms
def get_prim_atoms(atoms, symprec=1e-4):
return spglib.find_primitive(atoms, symprec=symprec)
def get_primitive(input_file='POSCAR',
input_format=None,
output_file=None,
output_format=None,
threshold=1e-5,
angle_tolerance=-1.,
verbose=False):
if output_file is None:
verbose = True
if verbose:
def vprint(*args):
for arg in args:
print(arg,)
print("")
else:
def vprint(*args):
pass
try:
if input_format is None:
A = ase.io.read(input_file)
else:
A = ase.io.read(input_file, format=input_format)
except IOError as e:
raise Exception("I/O error({0}): {1}".format(e.errno, e.strerror))
vprint(
"# Space group: ",
str(
spglib.get_spacegroup(
A, symprec=threshold, angle_tolerance=angle_tolerance)),
'\n')
cell, positions, atomic_numbers = spglib.find_primitive(
A, symprec=threshold, angle_tolerance=angle_tolerance)
if positions is None:
print("This space group doesn't have a more primitive unit cell.")
else:
vprint("Primitive cell vectors:")
vprint(cell, '\n')
vprint("Atomic positions and proton numbers:")
for position, number in zip(positions, atomic_numbers):
vprint(position, '\t', number)
if output_file is None:
pass
else:
atoms = ase.Atoms(
scaled_positions=positions,
cell=cell,
numbers=atomic_numbers,
pbc=True)
if output_format is None:
try:
atoms.write(output_file, vasp5=True)
except TypeError:
atoms.write(output_file)
elif output_format is "vasp":
atoms.write(output_file, format="vasp", vasp5=True)
else:
atoms.write(output_file, format=output_format)
def get_primitive(input_file='POSCAR',
input_format=None,
output_file=None,
output_format=None,
threshold=1e-5,
angle_tolerance=-1.,
verbose=False):
if output_file is None:
verbose = True
if verbose:
def vprint(*args):
for arg in args:
print(arg, )
print("")
else:
def vprint(*args):
pass
try:
if input_format is None:
A = ase.io.read(input_file)
else:
A = ase.io.read(input_file, format=input_format)
except IOError as e:
raise Exception("I/O error({0}): {1}".format(e.errno, e.strerror))
vprint(
"# Space group: ",
str(
spglib.get_spacegroup(A,
symprec=threshold,
angle_tolerance=angle_tolerance)), '\n')
cell, positions, atomic_numbers = spglib.find_primitive(
A, symprec=threshold, angle_tolerance=angle_tolerance)
if positions is None:
print("This space group doesn't have a more primitive unit cell.")
else:
vprint("Primitive cell vectors:")
vprint(cell, '\n')
vprint("Atomic positions and proton numbers:")
for position, number in zip(positions, atomic_numbers):
vprint(position, '\t', number)
if output_file is None:
pass
else:
atoms = ase.Atoms(scaled_positions=positions,
cell=cell,
numbers=atomic_numbers,
pbc=True)
if output_format is None:
try:
atoms.write(output_file, vasp5=True)
except TypeError:
atoms.write(output_file)
elif output_format is "vasp":
atoms.write(output_file, format="vasp", vasp5=True)
else:
atoms.write(output_file, format=output_format)