def __init__(self,
force_constants_filename=None,
poscar=None,
poscar_ideal=None,
phonopy_conf=None,
is_symmetrized=True):
if poscar_ideal is None:
poscar_ideal = poscar
force_constants = parse_FORCE_CONSTANTS(force_constants_filename)
atoms = read_vasp(poscar)
atoms_ideal = read_vasp(poscar_ideal)
supercell_matrix = read_supercell_matrix(phonopy_conf)
# force_constants_analyzer.generate_symmetrized_force_constants(
# atoms_symmetry)
# force_constants_analyzer.write_force_constants_pair()
super(VaspFCAnalyzer, self).__init__(force_constants=force_constants,
atoms=atoms,
atoms_ideal=atoms_ideal,
supercell_matrix=supercell_matrix,
is_symmetrized=True)
# force_constants_analyzer.check_translational_invariance()
self.generate_symmetrized_force_constants()
self.write_force_constants_symmetrized()
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 __init__(self,
force_constants_filename=None,
poscar=None,
poscar_ideal=None,
phonopy_conf=None,
is_symmetrized=True):
if poscar_ideal is None:
poscar_ideal = poscar
force_constants = parse_FORCE_CONSTANTS(force_constants_filename)
atoms = read_vasp(poscar)
atoms_ideal = read_vasp(poscar_ideal)
supercell_matrix = read_supercell_matrix(phonopy_conf)
# force_constants_analyzer.generate_symmetrized_force_constants(
# atoms_symmetry)
# force_constants_analyzer.write_force_constants_pair()
super(VaspFCAnalyzer, self).__init__(
force_constants=force_constants,
atoms=atoms,
atoms_ideal=atoms_ideal,
supercell_matrix=supercell_matrix,
is_symmetrized=True)
# force_constants_analyzer.check_translational_invariance()
self.generate_symmetrized_force_constants()
self.write_force_constants_symmetrized()
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 prepare_L1_2(self):
unitcell = read_vasp("poscars/POSCAR_L1_2")
primitive_matrix = [
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
]
unitcell_ideal = read_vasp("poscars/POSCAR_fcc")
return unitcell, unitcell_ideal, primitive_matrix
def prepare_L1_2(self):
unitcell = read_vasp(os.path.join(POSCAR_DIR, "POSCAR_L1_2"))
primitive_matrix = [
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
]
unitcell_ideal = read_vasp(os.path.join(POSCAR_DIR, "POSCAR_fcc"))
return unitcell, unitcell_ideal, primitive_matrix
def prepare_L1_2(self):
unitcell = read_vasp("poscars/POSCAR_L1_2")
primitive_matrix = [
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
]
unitcell_ideal = read_vasp("poscars/POSCAR_fcc")
return unitcell, unitcell_ideal, primitive_matrix
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 _get_phonon(self):
cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
phonon = Phonopy(cell,
np.diag([2, 2, 2]),
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
filename = os.path.join(data_dir, "FORCE_SETS_NaCl")
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
born_elems = {'Na': [[1.08703, 0, 0],
[0, 1.08703, 0],
[0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0],
[0, -1.08672, 0],
[0, 0, -1.08672]]}
born = [born_elems[s] for s in ['Na', 'Cl']]
epsilon = [[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({'born': born,
'factor': factors,
'dielectric': epsilon})
return phonon
def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp("POSCAR_%s" % spgtype)
phonon = Phonopy(cell, np.diag(dim), primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(filename="FORCE_SETS_%s" % spgtype)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def setUp(self):
self._atoms = read_vasp('poscars/POSCAR_fcc_2x2x2')
self._primitive_matrix = np.array([
[0.00, 0.25, 0.25],
[0.25, 0.00, 0.25],
[0.25, 0.25, 0.00],
])
def setUp(self):
self._atoms = read_vasp(os.path.join(POSCAR_DIR, 'POSCAR_fcc_2x2x2'))
self._primitive_matrix = np.array([
[0.00, 0.25, 0.25],
[0.25, 0.00, 0.25],
[0.25, 0.25, 0.00],
])
def test_a3(self):
filename = "../poscars/POSCAR_A3"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms)
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '6/mmm')
p = [0.0, 0.0, 0.5] # A (6/mmm)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '6/mmm')
p = [1.0 / 3.0, 1.0 / 3.0, 0.0] # K (-6m2)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '-6m2')
p = [0.5, 0.0, 0.0] # M (mmm)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, 'mmm')
p = [0.5, 0.0, 0.5] # L (mmm)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, 'mmm')
p = [0.0, 0.0, 0.25] # DT (6mm)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '6mm')
def create_supercells_with_displacements():
"""Create supercells with displacements."""
cell = read_vasp("POSCAR-unitcell")
ph3 = Phono3py(cell, np.diag([2, 2, 2]), primitive_matrix="F")
ph3.generate_displacements(distance=0.03)
print(ph3.supercells_with_displacements) # List of PhonopyAtoms
print(ph3.displacements.shape) # (supercells, atoms, xyz)
def test_cl12pd6(self):
filename = "../poscars/POSCAR_Cl12Pd6"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms) # 148
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '-3')
def test_thcl4(self):
filename = "../poscars/POSCAR_ThCl4"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms) # 88
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '4/m')
def input_files(self, path_POSCAR, path_FORCECONSTANT):
bulk = read_vasp(path_POSCAR)
self.phonon = Phonopy(bulk,
self.super_cell,
primitive_matrix=self.primitive_cell)
force_constants = file_IO.parse_FORCE_CONSTANTS(path_FORCECONSTANT)
self.phonon.set_force_constants(force_constants)
return self.phonon
def main():
import argparse
from phonopy.interface.vasp import read_vasp
parser = argparse.ArgumentParser()
parser.add_argument('atoms', type=str, help="POSCAR")
args = parser.parse_args()
atoms = read_vasp(args.atoms)
VolumeVoronoi(atoms).run()
def test_97(self):
filename = "../poscars/POSCAR_NaGdCu2F8"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms)
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '422')
def _compare(cell):
cell_ref = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
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_b_h(self):
filename = "tests/poscars/POSCAR_WC"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms)
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '-6m2')
def _compare(self, cell):
cell_ref = read_vasp(os.path.join(data_dir, "../POSCAR_NaCl"))
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 _get_phonon(spgtype, dim, pmat):
cell = read_vasp(os.path.join(data_dir, "POSCAR_%s" % spgtype))
phonon = Phonopy(cell, np.diag(dim), primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(
filename=os.path.join(data_dir, "FORCE_SETS_%s" % spgtype))
phonon.dataset = force_sets
phonon.produce_force_constants()
return phonon
def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp(os.path.join(data_dir, "POSCAR_%s" % spgtype))
phonon = Phonopy(cell, np.diag(dim), primitive_matrix=pmat)
filename = os.path.join(data_dir, "FORCE_SETS_%s" % spgtype)
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
print(phonon.get_symmetry().get_pointgroup())
return phonon
def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp(os.path.join(data_dir,"POSCAR_%s" % spgtype))
phonon = Phonopy(cell,
np.diag(dim),
primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(filename=os.path.join(data_dir,"FORCE_SETS_%s" % spgtype))
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def get_frequency(poscar_filename, force_sets_filename):
bulk = read_vasp(poscar_filename)
volume = bulk.get_volume()
phonon = Phonopy(bulk, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_force_sets(force_sets)
phonon.set_post_process([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def get_frequency(poscar_filename, force_sets_filename):
bulk = read_vasp(poscar_filename)
volume = bulk.get_volume()
phonon = Phonopy(bulk, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_force_sets(force_sets)
phonon.set_post_process([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def test_B3(self):
unitcell = read_vasp("poscars/POSCAR_B3_conv")
primitive_matrix = [
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
]
primitive = get_primitive(unitcell, primitive_matrix)
self.check(unitcell, primitive)
def test_B3(self):
unitcell = read_vasp("poscars/POSCAR_B3_conv")
primitive_matrix = [
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
]
primitive = get_primitive(unitcell, primitive_matrix)
self.check(unitcell, primitive)
def test_B3(self):
unitcell = read_vasp(os.path.join(POSCAR_DIR, "POSCAR_B3_conv"))
primitive_matrix = [
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
]
primitive = get_primitive(unitcell, primitive_matrix)
self.check(unitcell, primitive)
def get_frequency(poscar_filename, force_sets_filename):
unitcell = read_vasp(poscar_filename)
volume = unitcell.get_volume()
phonon = Phonopy(unitcell, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0]])
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def create_primitive(self, filename="POSCAR", conf_file=None):
from phonopy.structure.cells import get_primitive
from phonopy.interface.vasp import read_vasp
if conf_file is None:
self._check_conf_files()
else:
self.set_conf_file(conf_file)
primitive_matrix = self._read_primitive_matrix()
atoms = read_vasp(filename)
return get_primitive(atoms, primitive_matrix)
def create_primitive(self, filename="POSCAR", conf_file=None):
from phonopy.structure.cells import get_primitive
from phonopy.interface.vasp import read_vasp
if conf_file is None:
self._check_conf_files()
else:
self.set_conf_file(conf_file)
primitive_matrix = self._read_primitive_matrix()
atoms = read_vasp(filename)
return get_primitive(atoms, primitive_matrix)
def test_read_vasp():
"""Test read_vasp."""
cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
filename = os.path.join(data_dir, "NaCl-vasp.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 _compare(self, cell):
cell_ref = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
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 _poscar_failed(cell_filename):
"""Determine if fall back happens
1) read_vasp (parsing POSCAR-style file) is failed. --> fallback
ValueError is raised by read_vasp when the POSCAR-style format
is broken. By this way, we assume the input crystal structure
is not in the POSCAR-style format and is in the phonopy.yaml
type.
2) The file given by get_default_cell_filename('vasp') is not
found at the current directory. --> fallback
This is the trigger to look for the phonopy.yaml type file.
3) The given file with cell_filename is not found. --> not fallback
This case will not invoke phonopy.yaml mode and here nothing
is done, i.e., fallback_reason = None.
This error will be caught in the following part again be
handled properly (read_crystal_structure).
"""
fallback_reason = None
try:
if cell_filename is None:
read_vasp(get_default_cell_filename('vasp'))
else:
read_vasp(cell_filename)
except ValueError:
# (1) see above
fallback_reason = "read_vasp parsing failed"
except FileNotFoundError:
if cell_filename is None:
# (2) see above
fallback_reason = "default file not found"
else:
# (3) see above
pass
return fallback_reason
def test_sc(self):
filename = "../poscars/POSCAR_Sc"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms) # 178
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '622')
p = [1.0 / 3.0, 1.0 / 3.0, 0.0] # K (32)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '32')
def test_a13(self):
filename = "../poscars/POSCAR_A13"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms) # 213
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '432')
p = [0.0, 0.5, 0.5] # X (422)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '422')
def test_b3(self):
filename = "../poscars/POSCAR_B3_conv"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms) # 216
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '-43m')
p = [0.0, 0.5, 0.5] # X (-42m)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '-42m')
def test_read_vasp(self):
cell = read_vasp(os.path.join(data_dir, "../POSCAR_NaCl"))
filename = os.path.join(data_dir, "NaCl-vasp.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 create_list_element_indices(self):
from phonopy.interface.vasp import read_vasp
filename = self._variables["poscar"]
atoms = read_vasp(filename)
symbols = atoms.get_chemical_symbols()
reduced_symbols = sorted(set(symbols), key=symbols.index)
list_element_indices = []
for s in reduced_symbols:
indices = [i for i, x in enumerate(symbols) if x == s]
list_element_indices.append((s, indices))
self._natoms = atoms.get_number_of_atoms()
self._list_element_indices = list_element_indices
def _get_phonon_NaCl(self):
cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
phonon = Phonopy(cell,
np.diag([2, 2, 2]),
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
filename = os.path.join(data_dir, "..", "FORCE_SETS_NaCl")
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
filename_born = os.path.join(data_dir, "..", "BORN_NaCl")
nac_params = parse_BORN(phonon.get_primitive(), filename=filename_born)
phonon.set_nac_params(nac_params)
return phonon
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 _get_phonon(self):
cell = read_vasp(os.path.join(data_dir, "../POSCAR_NaCl"))
phonon = Phonopy(cell, np.diag([2, 2, 2]), primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
filename = os.path.join(data_dir, "FORCE_SETS_NaCl")
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
supercell = phonon.get_supercell()
born_elems = {
"Na": [[1.08703, 0, 0], [0, 1.08703, 0], [0, 0, 1.08703]],
"Cl": [[-1.08672, 0, 0], [0, -1.08672, 0], [0, 0, -1.08672]],
}
born = [born_elems[s] for s in ["Na", "Cl"]]
epsilon = [[2.43533967, 0, 0], [0, 2.43533967, 0], [0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({"born": born, "factor": factors, "dielectric": epsilon})
return phonon
def test_fcc_conv(self):
filename = "../poscars/POSCAR_fcc"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms)
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, 'm-3m')
rotations = symmetry.get_group_of_wave_vector([0.00, 0.25, 0.25])[0]
self.check_irreps(rotations, 'mm2')
rotations = symmetry.get_group_of_wave_vector([0.25, 0.00, 0.25])[0]
self.check_irreps(rotations, 'mm2')
rotations = symmetry.get_group_of_wave_vector([0.25, 0.25, 0.00])[0]
self.check_irreps(rotations, 'mm2')
def test_properties(self):
cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
phonon = Phonopy(cell,
np.diag([2, 2, 2]),
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
filename = os.path.join(data_dir, "..", "FORCE_SETS_NaCl")
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
dynmat = phonon.dynamical_matrix
dynmat.set_dynamical_matrix([0, 0, 0])
self.assertTrue(id(dynmat.primitive)
== id(dynmat.get_primitive()))
self.assertTrue(id(dynmat.supercell)
== id(dynmat.get_supercell()))
np.testing.assert_allclose(dynmat.dynamical_matrix,
dynmat.get_dynamical_matrix())
def test_mgnh(self):
filename = "../poscars/POSCAR_MgNH"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms) # 216
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, '6/m')
p = [1.0 / 3.0, 1.0 / 3.0, 0.0] # K (-6)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '-6')
p = [0.0, 0.0, 0.25] # DT (6)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '6')
p = [1.0 / 3.0, 1.0 / 3.0, 0.25] # P (3)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '3')
def test_reduce_vectors_to_primitive_for_multidimensional_vectors(self):
vectors_adjuster = self._vectors_adjuster
atoms = read_vasp("poscars/POSCAR_fcc")
primitive_matrix = [
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
]
primitive = get_primitive(atoms, primitive_matrix)
vectors = self.get_eigvec_0()[None, :, None]
reduced_vectors = vectors_adjuster.reduce_vectors_to_primitive(
vectors, primitive)
nexpansion = 4
exp = np.array([
0.5,
0.0,
0.0,
])[None, :, None]
exp *= np.sqrt(nexpansion)
self.assertTrue(np.all(np.abs(reduced_vectors - exp) < 1e-6))
def test_fcc_prim(self):
filename = "../poscars/POSCAR_fcc_prim"
atoms = read_vasp(filename)
symmetry = UnfolderSymmetry(atoms)
rotations = symmetry.get_pointgroup_operations()
self.check_irreps(rotations, 'm-3m')
rotations = symmetry.get_group_of_wave_vector([0.00, 0.25, -0.25])[0]
self.check_irreps(rotations, 'mm2')
p = [0.50, 0.25, 0.75] # W (-42m)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '-42m')
rotations = symmetry.get_group_of_wave_vector([0.50, 0.25, 0.25])[0]
self.check_irreps(rotations, 'mm2')
rotations = symmetry.get_group_of_wave_vector([0.25, 0.50, 0.25])[0]
self.check_irreps(rotations, 'mm2')
rotations = symmetry.get_group_of_wave_vector([0.25, 0.25, 0.50])[0]
self.check_irreps(rotations, 'mm2')
p = [0.5, 0.3, 0.7] # Q (2)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '2')
p = [0.4, 0.4, 0.1] # C (m)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, 'm')
p = [0.4, 0.2, 0.1] # GP (1)
rotations = symmetry.get_group_of_wave_vector(p)[0]
self.check_irreps(rotations, '1')
def setUp(self):
atoms = read_vasp("POSCAR_sc")
self._symmetry = UnfolderSymmetry(atoms)
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS
from phonopy.file_IO import parse_FORCE_CONSTANTS, write_FORCE_CONSTANTS
cell = read_vasp("POSCAR")
phonon = Phonopy(cell, [[2, 0, 0], [0, 2, 0], [0, 0, 2]])
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
write_FORCE_CONSTANTS(phonon.get_force_constants(), filename="FORCE_CONSTANTS")
force_constants = parse_FORCE_CONSTANTS()
phonon.set_force_constants(force_constants)
phonon.symmetrize_force_constants(iteration=1)
write_FORCE_CONSTANTS(phonon.get_force_constants(), filename="FORCE_CONSTANTS_NEW")
parser = OptionParser()
parser.set_defaults( w2v = False,
v2w = False)
parser.add_option("-w", dest="w2v",
action="store_true",
help="Convert WIEN2k to VASP")
parser.add_option("-v", dest="v2w",
action="store_true",
help="Convert VASP to WIEN2k")
(options, args) = parser.parse_args()
from phonopy.units import Bohr
if options.v2w:
cell = read_vasp(args[0])
lattice = cell.get_cell() / Bohr
cell.set_cell( lattice )
npts, r0s, rmts = parse_core_param(open(args[1]))
text = get_wien2k_struct(cell, npts, r0s, rmts)
print text
elif options.w2v:
cell, npts, r0s, rmts = parse_wien2k_struct(args[0])
positions = cell.get_scaled_positions()
lattice = cell.get_cell() * Bohr
cell.set_cell( lattice )
cell.set_scaled_positions( positions )
clean_scaled_positions( cell )
write_vasp("POSCAR.wien2k", cell, direct=True)
w = open("wien2k_core.dat", 'w')