def read_crystal_structure(filename=None,
interface_mode=None,
chemical_symbols=None,
yaml_mode=False):
if filename is None:
unitcell_filename = get_default_cell_filename(interface_mode,
yaml_mode)
else:
unitcell_filename = filename
if not os.path.exists(unitcell_filename):
if filename is None:
return None, (unitcell_filename + " (default file name)", )
else:
return None, (unitcell_filename, )
if yaml_mode:
from phonopy.interface.phonopy_yaml import PhonopyYaml
phpy_yaml = PhonopyYaml()
phpy_yaml.read(unitcell_filename)
unitcell = phpy_yaml.get_unitcell()
return unitcell, (unitcell_filename, )
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(unitcell_filename)
else:
unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
return unitcell, (unitcell_filename, )
if interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(unitcell_filename)
return unitcell, (unitcell_filename, )
if interface_mode == 'pwscf':
from phonopy.interface.pwscf import read_pwscf
unitcell, pp_filenames = read_pwscf(unitcell_filename)
return unitcell, (unitcell_filename, pp_filenames)
if interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
return unitcell, (unitcell_filename, npts, r0s, rmts)
if interface_mode == 'elk':
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(unitcell_filename)
return unitcell, (unitcell_filename, sp_filenames)
if interface_mode == 'siesta':
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(unitcell_filename)
return unitcell, (unitcell_filename, atypes)
if interface_mode == 'crystal':
from phonopy.interface.crystal import read_crystal
unitcell, conv_numbers = read_crystal(unitcell_filename)
return unitcell, (unitcell_filename, conv_numbers)
def read_crystal_structure(filename=None,
interface_mode=None,
chemical_symbols=None,
command_name="phonopy"):
if interface_mode == 'phonopy_yaml':
return _read_phonopy_yaml(filename, command_name)
if filename is None:
cell_filename = get_default_cell_filename(interface_mode)
if not os.path.isfile(cell_filename):
return None, (cell_filename, "(default file name)")
else:
cell_filename = filename
if not os.path.isfile(cell_filename):
return None, (cell_filename, )
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(cell_filename)
else:
unitcell = read_vasp(cell_filename, symbols=chemical_symbols)
return unitcell, (cell_filename, )
elif interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'qe':
from phonopy.interface.qe import read_pwscf
unitcell, pp_filenames = read_pwscf(cell_filename)
return unitcell, (cell_filename, pp_filenames)
elif interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(cell_filename)
return unitcell, (cell_filename, npts, r0s, rmts)
elif interface_mode == 'elk':
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(cell_filename)
return unitcell, (cell_filename, sp_filenames)
elif interface_mode == 'siesta':
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(cell_filename)
return unitcell, (cell_filename, atypes)
elif interface_mode == 'cp2k':
from phonopy.interface.cp2k import read_cp2k
unitcell = read_cp2k(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'crystal':
from phonopy.interface.crystal import read_crystal
unitcell, conv_numbers = read_crystal(cell_filename)
return unitcell, (cell_filename, conv_numbers)
elif interface_mode == 'dftbp':
from phonopy.interface.dftbp import read_dftbp
unitcell = read_dftbp(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'turbomole':
from phonopy.interface.turbomole import read_turbomole
unitcell = read_turbomole(cell_filename)
return unitcell, (cell_filename, )
def read_crystal_structure(filename=None, interface_mode="vasp", chemical_symbols=None, yaml_mode=False):
if filename is None:
unitcell_filename = get_default_cell_filename(interface_mode, yaml_mode)
else:
unitcell_filename = filename
if not os.path.exists(unitcell_filename):
if filename is None:
return None, (unitcell_filename + " (default file name)",)
else:
return None, (unitcell_filename,)
if yaml_mode:
from phonopy.interface.phonopy_yaml import phonopyYaml
unitcell = phonopyYaml(unitcell_filename).get_atoms()
return unitcell, (unitcell_filename,)
if interface_mode == "vasp":
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(unitcell_filename)
else:
unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
return unitcell, (unitcell_filename,)
if interface_mode == "abinit":
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(unitcell_filename)
return unitcell, (unitcell_filename,)
if interface_mode == "pwscf":
from phonopy.interface.pwscf import read_pwscf
unitcell, pp_filenames = read_pwscf(unitcell_filename)
return unitcell, (unitcell_filename, pp_filenames)
if interface_mode == "wien2k":
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
return unitcell, (unitcell_filename, npts, r0s, rmts)
if interface_mode == "elk":
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(unitcell_filename)
return unitcell, (unitcell_filename, sp_filenames)
if interface_mode == "siesta":
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(unitcell_filename)
return unitcell, (unitcell_filename, atypes)
def read_crystal_structure(filename=None,
interface_mode=None,
chemical_symbols=None,
yaml_mode=False):
if filename is None:
unitcell_filename = get_default_cell_filename(interface_mode, yaml_mode)
else:
unitcell_filename = filename
if not os.path.exists(unitcell_filename):
if filename is None:
return None, (unitcell_filename + " (default file name)",)
else:
return None, (unitcell_filename,)
if yaml_mode:
from phonopy.interface.phonopy_yaml import PhonopyYaml
phpy_yaml = PhonopyYaml()
phpy_yaml.read(unitcell_filename)
unitcell = phpy_yaml.get_unitcell()
return unitcell, (unitcell_filename,)
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(unitcell_filename)
else:
unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
return unitcell, (unitcell_filename,)
if interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(unitcell_filename)
return unitcell, (unitcell_filename,)
if interface_mode == 'pwscf':
from phonopy.interface.pwscf import read_pwscf
unitcell, pp_filenames = read_pwscf(unitcell_filename)
return unitcell, (unitcell_filename, pp_filenames)
if interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
return unitcell, (unitcell_filename, npts, r0s, rmts)
if interface_mode == 'elk':
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(unitcell_filename)
return unitcell, (unitcell_filename, sp_filenames)
if interface_mode == 'siesta':
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(unitcell_filename)
return unitcell, (unitcell_filename, atypes)
def test_parse_wien2k_struct():
"""Test structure parsing."""
filename_BaGa2 = os.path.join(data_dir, "BaGa2.struct")
cell, _, _, _ = parse_wien2k_struct(filename_BaGa2)
filename = os.path.join(data_dir, "BaGa2-wien2k.yaml")
cell_ref = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
def test_parse_wien2k_struct(self):
filename_BaGa2 = os.path.join(data_dir,"BaGa2.struct")
cell, npts, r0s, rmts = parse_wien2k_struct(filename_BaGa2)
filename = os.path.join(data_dir,"BaGa2-wien2k.yaml")
cell_ref = get_unitcell_from_phonopy_yaml(filename)
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def test_parse_wien2k_struct(self):
cell, npts, r0s, rmts = parse_wien2k_struct("BaGa2.struct")
lattice = cell.get_cell().T
displacements, supercell = parse_disp_yaml("disp_BaGa2.yaml",
return_cell=True)
symmetry = Symmetry(cell)
print(PhonopyAtoms(atoms=cell))
sym_op = symmetry.get_symmetry_operations()
print(symmetry.get_international_table())
for i, (r, t) in enumerate(
zip(sym_op['rotations'], sym_op['translations'])):
print("--- %d ---" % (i + 1))
print(r)
print(t)
def test_parse_wien2k_struct(self):
filename_BaGa2 = os.path.join(data_dir, "BaGa2.struct")
cell, npts, r0s, rmts = parse_wien2k_struct(filename_BaGa2)
filename = os.path.join(data_dir, "BaGa2-wien2k.yaml")
cell_ref = read_cell_yaml(filename)
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = (cell.get_scaled_positions() -
cell_ref.get_scaled_positions())
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def read_crystal_structure(filename=None,
interface_mode='vasp',
chemical_symbols=None):
if filename is None:
unitcell_filename = get_default_cell_filename(interface_mode)
else:
unitcell_filename = filename
if not os.path.exists(unitcell_filename):
if filename is None:
return None, (unitcell_filename + " (default file name)", )
else:
return None, (unitcell_filename, )
if interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(unitcell_filename)
else:
unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
return unitcell, (unitcell_filename, )
if interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(unitcell_filename)
return unitcell, (unitcell_filename, )
if interface_mode == 'pwscf':
from phonopy.interface.pwscf import read_pwscf
unitcell, pp_filenames = read_pwscf(unitcell_filename)
return unitcell, (unitcell_filename, pp_filenames)
if interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
return unitcell, (unitcell_filename, npts, r0s, rmts)
def read_crystal_structure(filename=None,
interface_mode='vasp',
chemical_symbols=None):
if filename is None:
unitcell_filename = get_default_cell_filename(interface_mode)
else:
unitcell_filename = filename
if not os.path.exists(unitcell_filename):
if filename is None:
return None, (unitcell_filename + " (default file name)",)
else:
return None, (unitcell_filename,)
if interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(unitcell_filename)
else:
unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
return unitcell, (unitcell_filename,)
if interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(unitcell_filename)
return unitcell, (unitcell_filename,)
if interface_mode == 'pwscf':
from phonopy.interface.pwscf import read_pwscf
unitcell, pp_filenames = read_pwscf(unitcell_filename)
return unitcell, (unitcell_filename, pp_filenames)
if interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
return unitcell, (unitcell_filename, npts, r0s, rmts)
def read_crystal_structure(filename=None,
interface_mode=None,
chemical_symbols=None,
command_name="phonopy"):
"""Returns crystal structure information
Returns
-------
tuple
(Unit cell in PhonopyAtoms, optional_structure_info in tuple)
The optional_structure_info is given by a tuple. The first element of
it is the unit cell file name for which the unit cell data are read,
and the rest is dependent on calculator interface.
"""
if interface_mode == 'phonopy_yaml':
return _read_phonopy_yaml(filename, command_name)
if filename is None:
cell_filename = get_default_cell_filename(interface_mode)
if not os.path.isfile(cell_filename):
return None, (cell_filename, "(default file name)")
else:
cell_filename = filename
if not os.path.isfile(cell_filename):
return None, (cell_filename, )
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(cell_filename)
else:
unitcell = read_vasp(cell_filename, symbols=chemical_symbols)
return unitcell, (cell_filename, )
elif interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'qe':
from phonopy.interface.qe import read_pwscf
unitcell, pp_filenames = read_pwscf(cell_filename)
return unitcell, (cell_filename, pp_filenames)
elif interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(cell_filename)
return unitcell, (cell_filename, npts, r0s, rmts)
elif interface_mode == 'elk':
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(cell_filename)
return unitcell, (cell_filename, sp_filenames)
elif interface_mode == 'siesta':
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(cell_filename)
return unitcell, (cell_filename, atypes)
elif interface_mode == 'cp2k':
from phonopy.interface.cp2k import read_cp2k
unitcell, config_tree = read_cp2k(cell_filename)
return unitcell, (cell_filename, config_tree)
elif interface_mode == 'crystal':
from phonopy.interface.crystal import read_crystal
unitcell, conv_numbers = read_crystal(cell_filename)
return unitcell, (cell_filename, conv_numbers)
elif interface_mode == 'dftbp':
from phonopy.interface.dftbp import read_dftbp
unitcell = read_dftbp(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'turbomole':
from phonopy.interface.turbomole import read_turbomole
unitcell = read_turbomole(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'aims':
from phonopy.interface.aims import read_aims
unitcell = read_aims(cell_filename)
return unitcell, (cell_filename, )
else:
raise RuntimeError("No calculator interface was found.")
def read_crystal_structure(filename=None,
interface_mode=None,
chemical_symbols=None,
phonopy_yaml_cls=None):
"""Returns crystal structure information
Parameters
----------
filename : str, optional
Filename that contains cell structure information. Default is None.
The predetermined filename for each interface_mode is used.
interface_mode : str, optional
This is used to recognize the file format. Default is None, which
is equivalent to 'vasp' mode.
chemical_symbols : list of str, optional
This is only used for 'vasp' mode. VASP POSCAR file format can be
written without chemical symbol information. With this option,
chemical symbols can be given.
phonopy_yaml_cls : PhonopyYaml, optional
This brings PhonopyYaml-like class dependent parameters. Here,
currently only the default filenames are provided by this.
Returns
-------
tuple
(Unit cell in PhonopyAtoms, optional_structure_info in tuple)
The optional_structure_info is given by a tuple. The first element of
it is the unit cell file name for which the unit cell data are read,
and the rest is dependent on calculator interface.
"""
if interface_mode == 'phonopy_yaml':
if phonopy_yaml_cls is None:
return _read_phonopy_yaml(filename, PhonopyYaml)
else:
return _read_phonopy_yaml(filename, phonopy_yaml_cls)
if filename is None:
cell_filename = get_default_cell_filename(interface_mode)
if not os.path.isfile(cell_filename):
return None, (cell_filename, "(default file name)")
else:
cell_filename = filename
if not os.path.isfile(cell_filename):
return None, (cell_filename, )
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(cell_filename)
else:
unitcell = read_vasp(cell_filename, symbols=chemical_symbols)
return unitcell, (cell_filename, )
elif interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'qe':
from phonopy.interface.qe import read_pwscf
unitcell, pp_filenames = read_pwscf(cell_filename)
return unitcell, (cell_filename, pp_filenames)
elif interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(cell_filename)
return unitcell, (cell_filename, npts, r0s, rmts)
elif interface_mode == 'elk':
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(cell_filename)
return unitcell, (cell_filename, sp_filenames)
elif interface_mode == 'siesta':
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(cell_filename)
return unitcell, (cell_filename, atypes)
elif interface_mode == 'cp2k':
from phonopy.interface.cp2k import read_cp2k
unitcell, config_tree = read_cp2k(cell_filename)
return unitcell, (cell_filename, config_tree)
elif interface_mode == 'crystal':
from phonopy.interface.crystal import read_crystal
unitcell, conv_numbers = read_crystal(cell_filename)
return unitcell, (cell_filename, conv_numbers)
elif interface_mode == 'dftbp':
from phonopy.interface.dftbp import read_dftbp
unitcell = read_dftbp(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'turbomole':
from phonopy.interface.turbomole import read_turbomole
unitcell = read_turbomole(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'aims':
from phonopy.interface.aims import read_aims
unitcell = read_aims(cell_filename)
return unitcell, (cell_filename, )
elif interface_mode == 'castep':
from phonopy.interface.castep import read_castep
unitcell = read_castep(cell_filename)
return unitcell, (cell_filename, )
else:
raise RuntimeError("No calculator interface was found.")