def check_symmetry(input_cell,
primitive_axis=None,
symprec=1e-5,
phonopy_version=None):
if primitive_axis is None:
cell = get_primitive(input_cell, np.eye(3), symprec=symprec)
else:
cell = get_primitive(input_cell, primitive_axis, symprec=symprec)
symmetry = Symmetry(cell, symprec)
print get_symmetry_yaml(cell, symmetry, phonopy_version),
if input_cell.get_magnetic_moments() == None:
primitive = find_primitive(cell, symprec)
if not primitive==None:
print "# Primitive cell was found. It is written into PPOSCAR."
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
bravais_lattice, bravais_pos, bravais_numbers = \
spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print "# Bravais lattice is written into BPOSCAR."
write_vasp('BPOSCAR', bravais)
def check_symmetry(input_cell,
primitive_axis=None,
symprec=1e-5,
distance_to_A=1.0,
phonopy_version=None):
if primitive_axis is None:
cell = get_primitive(input_cell, np.eye(3), symprec=symprec)
else:
cell = get_primitive(input_cell, primitive_axis, symprec=symprec)
lattice = cell.get_cell() * distance_to_A
cell.set_cell(lattice)
symmetry = Symmetry(cell, symprec)
print(_get_symmetry_yaml(cell, symmetry, phonopy_version))
if input_cell.get_magnetic_moments() is None:
primitive = find_primitive(cell, symprec)
if primitive is not None:
print("# Primitive cell was found. It is written into PPOSCAR.")
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
(bravais_lattice, bravais_pos,
bravais_numbers) = spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print("# Bravais lattice is written into BPOSCAR.")
write_vasp('BPOSCAR', bravais)
def check_symmetry(input_cell,
primitive_axis=None,
symprec=1e-5,
distance_to_A=1.0,
phonopy_version=None):
if primitive_axis is None:
cell = get_primitive(input_cell, np.eye(3), symprec=symprec)
else:
cell = get_primitive(input_cell, primitive_axis, symprec=symprec)
lattice = cell.get_cell() * distance_to_A
cell.set_cell(lattice)
symmetry = Symmetry(cell, symprec)
print(_get_symmetry_yaml(cell, symmetry, phonopy_version))
if input_cell.get_magnetic_moments() is None:
primitive = find_primitive(cell, symprec)
if primitive is not None:
print("# Primitive cell was found. It is written into PPOSCAR.")
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
(bravais_lattice,
bravais_pos,
bravais_numbers) = spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print("# Bravais lattice is written into BPOSCAR.")
write_vasp('BPOSCAR', bravais)
def check_symmetry(phonon, optional_structure_info):
# Assumed that supercell is unit cell.
print(_get_symmetry_yaml(phonon.supercell, phonon.symmetry,
phonon.version))
if phonon.unitcell.magnetic_moments is None:
base_fname = get_default_cell_filename(phonon.calculator)
symprec = phonon.symmetry.get_symmetry_tolerance()
(bravais_lattice, bravais_pos,
bravais_numbers) = spg.refine_cell(phonon.unitcell, symprec)
bravais = PhonopyAtoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice)
filename = 'B' + base_fname
print("# Symmetrized conventional unit cell is written into %s." %
filename)
trans_mat = guess_primitive_matrix(bravais, symprec=symprec)
primitive = get_primitive(bravais, trans_mat, symprec=symprec)
write_crystal_structure(
filename,
bravais,
interface_mode=phonon.calculator,
optional_structure_info=optional_structure_info)
filename = 'P' + base_fname
print("# Symmetrized primitive is written into %s." % filename)
write_crystal_structure(
filename,
primitive,
interface_mode=phonon.calculator,
optional_structure_info=optional_structure_info)
def check_symmetry(input_cell,
primitive_axis=np.eye(3, dtype=float),
symprec=1e-5,
phonopy_version=None):
cell = Primitive(input_cell, primitive_axis, symprec)
symmetry = Symmetry(cell, symprec)
print get_symmetry_yaml(cell, symmetry, phonopy_version),
if input_cell.get_magnetic_moments() == None:
primitive = find_primitive(cell, symprec)
if not primitive == None:
print "# Primitive cell was found. It is written into PPOSCAR."
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
bravais_lattice, bravais_pos, bravais_numbers = \
spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print "# Bravais lattice is written into BPOSCAR."
write_vasp('BPOSCAR', bravais)