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="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_read_pwscf(self):
cell, pp_filenames = read_pwscf("NaCl-pwscf.in")
cell_ref = get_unitcell_from_phonopy_yaml("NaCl-pwscf.yaml")
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_read_pwscf(self):
cell, pp_filenames = read_pwscf(os.path.join(data_dir,"NaCl-pwscf.in"))
filename = os.path.join(data_dir,"NaCl-abinit-pwscf.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 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)
