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 init_phono3py(settings, cell_info, interface_mode, output_filename,
symprec, log_level):
physical_units = get_default_physical_units(interface_mode)
distance_to_A = physical_units['distance_to_A']
# Change unit of lattice parameters to angstrom
unitcell = cell_info['unitcell'].copy()
if distance_to_A is not None:
lattice = unitcell.cell
lattice *= distance_to_A
unitcell.cell = lattice
# updated_settings keys
# ('grid_points', 'sigmas', 'temperature_points', 'temperatures',
# 'frequency_factor_to_THz', 'num_frequency_points',
# 'frequency_step', 'frequency_scale_factor',
# 'cutoff_frequency')
updated_settings = get_default_values(settings)
phono3py = Phono3py(
unitcell,
cell_info['supercell_matrix'],
primitive_matrix=cell_info['primitive_matrix'],
phonon_supercell_matrix=cell_info['phonon_supercell_matrix'],
masses=settings.masses,
mesh=settings.mesh_numbers,
band_indices=settings.band_indices,
sigmas=updated_settings['sigmas'],
sigma_cutoff=settings.sigma_cutoff_width,
cutoff_frequency=updated_settings['cutoff_frequency'],
frequency_factor_to_THz=updated_settings['frequency_factor_to_THz'],
is_symmetry=settings.is_symmetry,
is_mesh_symmetry=settings.is_mesh_symmetry,
symmetrize_fc3q=settings.is_symmetrize_fc3_q,
symprec=symprec,
calculator=interface_mode,
log_level=log_level,
lapack_zheev_uplo=settings.lapack_zheev_uplo)
check_supercell_in_yaml(cell_info, phono3py, log_level)
if cell_info['phonopy_yaml'] is not None:
if (cell_info['phonopy_yaml'].phonon_supercell is not None
and phono3py.phonon_supercell is not None):
if not cells_isclose(cell_info['phonopy_yaml'].phonon_supercell,
phono3py.phonon_supercell):
if log_level:
print("Generated phonon supercell is inconsistent with "
"that in \"%s\"." %
cell_info['optional_structure_info'][0])
print_error()
sys.exit(1)
return phono3py, updated_settings
def _get_phono3pyobject_phono3py(self, structure, potential,
kpoint_density,
displacementdistancephono3py,
max_distance_third_order):
cell = get_phonopy_structure(structure)
kpoint = Kpoints.automatic_density(structure=structure,
kppa=kpoint_density,
force_gamma=True)
mesh = kpoint.kpts[0]
phono3py = Phono3py(cell,
self.smat,
primitive_matrix=[[1, 0., 0.], [0., 1, 0.],
[0., 0., 1]],
mesh=mesh,
log_level=1)
phono3py.generate_displacements(
distance=displacementdistancephono3py,
cutoff_pair_distance=max_distance_third_order)
scells_with_disps = phono3py.get_supercells_with_displacements()
disp_dataset = phono3py.get_displacement_dataset()
numatoms = len(scells_with_disps[0].get_scaled_positions())
dummy_force = np.zeros((numatoms, 3))
set_of_forces = []
for scell in scells_with_disps:
if scell is not None:
# this part is adapted from: https://web.archive.org/web/20200610084959/https://github.com/phonopy/phonopy/blob/develop/example/ase/8Si-phonon.py
# Copyright by Atsushi Togo
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(potential)
forces = cell.get_forces()
drift_force = forces.sum(axis=0)
print(("[Phonopy] Drift force:" + "%11.5f" * 3) %
tuple(drift_force))
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
else:
set_of_forces.append(dummy_force)
phono3py.produce_fc3(set_of_forces,
displacement_dataset=disp_dataset,
symmetrize_fc3r=True)
fc3 = phono3py.get_fc3()
show_drift_fc3(fc3)
return phono3py
def init_phono3py(settings, cell_info, interface_mode, symprec, log_level):
"""Initialize phono3py and update settings by default values."""
physical_units = get_default_physical_units(interface_mode)
distance_to_A = physical_units["distance_to_A"]
# Change unit of lattice parameters to angstrom
unitcell = cell_info["unitcell"].copy()
if distance_to_A is not None:
lattice = unitcell.cell
lattice *= distance_to_A
unitcell.cell = lattice
# updated_settings keys
# ('sigmas', 'temperature_points', 'temperatures',
# 'frequency_factor_to_THz', 'num_frequency_points',
# 'frequency_step', 'frequency_scale_factor',
# 'cutoff_frequency')
updated_settings = get_default_values(settings)
phono3py = Phono3py(
unitcell,
cell_info["supercell_matrix"],
primitive_matrix=cell_info["primitive_matrix"],
phonon_supercell_matrix=cell_info["phonon_supercell_matrix"],
cutoff_frequency=updated_settings["cutoff_frequency"],
frequency_factor_to_THz=updated_settings["frequency_factor_to_THz"],
is_symmetry=settings.is_symmetry,
is_mesh_symmetry=settings.is_mesh_symmetry,
use_grg=settings.use_grg,
store_dense_gp_map=(not settings.emulate_v1),
store_dense_svecs=(not settings.emulate_v1),
symprec=symprec,
calculator=interface_mode,
log_level=log_level,
)
phono3py.masses = settings.masses
phono3py.band_indices = settings.band_indices
phono3py.sigmas = updated_settings["sigmas"]
phono3py.sigma_cutoff = settings.sigma_cutoff_width
check_supercell_in_yaml(cell_info, phono3py, distance_to_A, log_level)
return phono3py, updated_settings
def get_phono3py_instance(structure, phonon_settings_dict, params):
from phono3py import Phono3py
if 'phonon_supercell_matrix' in phonon_settings_dict:
ph_smat = phonon_settings_dict['phonon_supercell_matrix']
else:
ph_smat = None
ph3py = Phono3py(phonopy_atoms_from_structure(structure),
supercell_matrix=phonon_settings_dict['supercell_matrix'],
primitive_matrix='auto',
phonon_supercell_matrix=ph_smat,
symprec=phonon_settings_dict['symmetry_tolerance'])
if 'nac_params' in params:
from phonopy.interface.calculator import get_default_physical_units
units = get_default_physical_units('vasp')
factor = units['nac_factor']
nac_params = {
'born': params['nac_params'].get_array('born_charges'),
'dielectric': params['nac_params'].get_array('epsilon'),
'factor': factor
}
ph3py.nac_params = nac_params
return ph3py
if __name__ == '__main__':
infile = 'geometry.unitcell.in'
supercell_matrix = np.diag([4, 4, 1])
mesh = [21, 21, 1]
temperatures = [80]
symprec = 1e-5
cutoff_pair_distance = 6.0
print("cutoff_pair_distance: %.2f" % cutoff_pair_distance)
atoms = read(infile, format='aims')
print("Cell:")
print(atoms.get_cell()[:])
cell = to_phonopy_atoms(atoms, wrap=False)
phono3py = Phono3py(unitcell=cell,
supercell_matrix=supercell_matrix,
mesh=mesh,
symprec=symprec,
log_level=2) # log_level=0 make phono3py quiet
print("Cell symmetry by international table: %s" %
phono3py._symmetry._international_table)
print("Supercell symmetry by international table: %s" %
phono3py._phonon_supercell_symmetry._international_table)
print("Symmetry precision %g" % symprec)
print("Primitive cell:")
print(phono3py._primitive)
# sys.exit(0)
create_supercells_with_displacements(
phono3py, cutoff_pair_distance=cutoff_pair_distance)
from os import environ
environ['CUDA_VISIBLE_DEVICES'] = ''
from phonopy.interface import vasp
atoms = vasp.read_vasp(unitcell_f)
from phono3py import Phono3py
pho = Phono3py(
unitcell=atoms,
supercell_matrix=NNN3,
primitive_matrix=prim_mat,
phonon_supercell_matrix=NNN2,
# masses = None,
# mesh = None,
# band_indices = None,
# sigmas = None,
# sigma_cutoff = None,
# cutoff_frequency = 1e-4,
# frequency_factor_to_THz = VaspToTHz,
# is_symmetry = True,
# is_mesh_symmetry = True,
symmetrize_fc3q=sym_fc,
# symprec = 1e-5,
# calculator = None,
# log_level = 0,
# lapack_zheev_uplo = 'L',
)
if nac:
pho.set_nac_params(nac_params)
from ase.dft.kpoints import ibz_points
points = ibz_points['hexagonal']
def create_phono3py_supercells(unitcell,
supercell_matrix,
phonon_supercell_matrix,
displacement_distance,
is_plusminus,
is_diagonal,
cutoff_pair_distance,
optional_structure_info,
is_symmetry,
symprec,
interface_mode='vasp',
output_filename=None,
log_level=1):
if displacement_distance is None:
distance = get_default_displacement_distance(interface_mode)
else:
distance = displacement_distance
phono3py = Phono3py(unitcell,
supercell_matrix,
phonon_supercell_matrix=phonon_supercell_matrix,
is_symmetry=is_symmetry,
symprec=symprec)
supercell = phono3py.get_supercell()
phono3py.generate_displacements(distance=distance,
cutoff_pair_distance=cutoff_pair_distance,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal)
dds = phono3py.get_displacement_dataset()
if log_level:
print('')
print("Displacement distance: %s" % distance)
if output_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + output_filename + '.yaml'
num_disps, num_disp_files = write_disp_fc3_yaml(dds,
supercell,
filename=filename)
cells_with_disps = phono3py.supercells_with_displacements
ids = []
disp_cells = []
for i, cell in enumerate(cells_with_disps):
if cell is not None:
ids.append(i + 1)
disp_cells.append(cell)
additional_info = get_additional_info_to_write_supercells(
interface_mode, phono3py)
write_supercells_with_displacements(interface_mode,
supercell,
disp_cells,
optional_structure_info,
displacement_ids=ids,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements: %d" % num_disps)
if cutoff_pair_distance is not None:
print("Cutoff distance for displacements: %s" %
cutoff_pair_distance)
print("Number of displacement supercell files created: %d" %
num_disp_files)
if phonon_supercell_matrix is not None:
phonon_dds = phono3py.phonon_dataset
phonon_supercell = phono3py.phonon_supercell
phonon_supercell_matrix = phono3py.phonon_supercell_matrix
if output_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + output_filename + '.yaml'
num_disps = write_disp_fc2_yaml(phonon_dds,
phonon_supercell,
filename=filename)
cells_with_disps = phono3py.phonon_supercells_with_displacements
additional_info = get_additional_info_to_write_fc2_supercells(
interface_mode, phono3py)
write_supercells_with_displacements(interface_mode,
supercell,
cells_with_disps,
optional_structure_info,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py
def load(
phono3py_yaml=None, # phono3py.yaml-like must be the first argument.
supercell_matrix=None,
primitive_matrix=None,
phonon_supercell_matrix=None,
mesh=None,
is_nac=True,
calculator=None,
unitcell=None,
supercell=None,
nac_params=None,
unitcell_filename=None,
supercell_filename=None,
born_filename=None,
forces_fc3_filename=None,
forces_fc2_filename=None,
fc3_filename=None,
fc2_filename=None,
fc_calculator=None,
factor=None,
frequency_scale_factor=None,
is_symmetry=True,
is_mesh_symmetry=True,
symprec=1e-5,
log_level=0):
"""Create Phono3py instance from parameters and/or input files.
When unitcell and unitcell_filename are not given, file name that is
default for the chosen calculator is looked for in the current directory
as the default behaviour.
When force_sets_filename and force_constants_filename are not given,
'FORCES_FC3' and 'FORCES_FC2' are looked for in the current directory
as the default behaviour.
Parameters
----------
phono3py_yaml : str, optional
Filename of "phono3py.yaml"-like file. If this is given, the data
in the file are parsed. Default is None.
supercell_matrix : array_like, optional
Supercell matrix multiplied to input cell basis vectors.
shape=(3, ) or (3, 3), where the former is considered a diagonal
matrix. Default is the unit matrix.
dtype=int
primitive_matrix : array_like or str, optional
Primitive matrix multiplied to input cell basis vectors. Default is
the identity matrix. Default is None, which is equivalent to 'auto'.
shape=(3, 3), dtype=float.
When 'F', 'I', 'A', 'C', or 'R' is given instead of a 3x3 matrix,
the primitive matrix defined at
https://atztogo.github.io/spglib/definition.html
is used.
phonon_supercell_matrix : array_like, optional
Supercell matrix used for fc2. In phono3py, supercell matrix for fc3
and fc2 can be different to support longer range interaction of fc2
than that of fc3. Unless setting this, supercell_matrix is used.
This is only valide when unitcell or unitcell_filename is given.
Default is None.
mesh : array_like, optional
Grid mesh numbers in reciprocal cell.
shape=(3,), dtype='intc'
is_nac : bool, optional
If True, look for 'BORN' file. If False, NAS is turned off.
The priority for NAC is nac_params > born_filename > is_nac ('BORN').
Default is True.
calculator : str, optional.
Calculator used for computing forces. This is used to switch the set
of physical units. Default is None, which is equivalent to "vasp".
unitcell : PhonopyAtoms, optional
Input unit cell. Default is None. The priority for cell is
unitcell_filename > supercell_filename > unitcell > supercell.
supercell : PhonopyAtoms, optional
Input supercell. Default value of primitive_matrix is set to
'auto' (can be overwitten). supercell_matrix is ignored. Default is
None. The priority for cell is
unitcell_filename > supercell_filename > unitcell > supercell.
nac_params : dict, optional
Parameters required for non-analytical term correction. Default is
None. The priority for NAC is nac_params > born_filename > is_nac.
{'born': Born effective charges
(array_like, shape=(primitive cell atoms, 3, 3), dtype=float),
'dielectric': Dielectric constant matrix
(array_like, shape=(3, 3), dtype=float),
'factor': unit conversion facotr (float)}
unitcell_filename : str, optional
Input unit cell filename. Default is None. The priority for cell is
unitcell_filename > supercell_filename > unitcell > supercell.
supercell_filename : str, optional
Input supercell filename. When this is specified, supercell_matrix is
ignored. Default is None. The priority for cell is
1. unitcell_filename (with supercell_matrix)
2. supercell_filename
3. unitcell (with supercell_matrix)
4. supercell.
born_filename : str, optional
Filename corresponding to 'BORN', a file contains non-analytical term
correction parameters.
The priority for NAC is nac_params > born_filename > is_nac ('BORN').
forces_fc3_filename : str, optional
Filename of a file corresponding to 'FORCES_FC3', a file contains sets
of forces or optionally displacements (type-2). Default is None.
The priority for force constants is
fc3_filename > forces_fc3_filename > 'fc3.hdf5' > 'FORCES_FC3'.
forces_fc2_filename : str, optional
Filename of a file corresponding to 'FORCES_FC2', a file contains sets
of forces or optionally displacements (type-2). Default is None.
The priority for force constants is
fc2_filename > forces_fc2_filename > 'fc2.hdf5' > 'FORCES_FC2'.
fc3_filename : str, optional
Filename of a file corresponding to 'fc3.hdf5', a file contains
third-order force constants. Default is None.
The priority for force constants is
fc3_filename > forces_fc3_filename > 'fc3.hdf5' > 'FORCES_FC3'.
fc2_filename : str, optional
Filename of a file corresponding to 'fc2.hdf5', a file contains
second-order force constants. Default is None.
The priority for force constants is
fc2_filename > forces_fc2_filename > 'fc2.hdf5' > 'FORCES_FC2'.
fc_calculator : str, optional
Force constants calculator. Currently only 'alm'. Default is None.
factor : float, optional
Phonon frequency unit conversion factor. Unless specified, default
unit conversion factor for each calculator is used.
frequency_scale_factor : float, optional
Factor multiplied to calculated phonon frequency. Default is None,
i.e., effectively 1.
is_symmetry : bool, optional
Setting False, crystal symmetry except for lattice translation is not
considered. Default is True.
is_mesh_symmetry : bool, optional
Setting False, reciprocal mesh symmetry is not considered.
Default is True.
symprec : float, optional
Tolerance used to find crystal symmetry. Default is 1e-5.
log_level : int, optional
Verbosity control. Default is 0.
"""
if phono3py_yaml is None:
cell, smat, pmat = load_helper.get_cell_settings(
supercell_matrix=supercell_matrix,
primitive_matrix=primitive_matrix,
unitcell=unitcell,
supercell=supercell,
unitcell_filename=unitcell_filename,
supercell_filename=supercell_filename,
calculator=calculator,
symprec=symprec)
if phonon_supercell_matrix is not None:
if unitcell is None and unitcell_filename is None:
msg = ("phonon_supercell_matrix can be used only when "
"unitcell or unitcell_filename is given.")
raise RuntimeError(msg)
ph_smat = load_helper.get_supercell_matrix(phonon_supercell_matrix)
else:
ph_smat = None
_nac_params = nac_params
else:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(phono3py_yaml)
cell = ph3py_yaml.unitcell
smat = ph3py_yaml.supercell_matrix
ph_smat = ph3py_yaml.phonon_supercell_matrix
if smat is None:
smat = np.eye(3, dtype='intc', order='C')
if primitive_matrix == 'auto':
pmat = 'auto'
else:
pmat = ph3py_yaml.primitive_matrix
if is_nac:
_nac_params = ph3py_yaml.nac_params
else:
_nac_params = None
# units keywords: factor, nac_factor, distance_to_A
units = get_default_physical_units(calculator)
if factor is None:
_factor = units['factor']
else:
_factor = factor
ph3py = Phono3py(cell,
smat,
primitive_matrix=pmat,
phonon_supercell_matrix=ph_smat,
mesh=mesh,
frequency_factor_to_THz=_factor,
symprec=symprec,
is_symmetry=is_symmetry,
is_mesh_symmetry=is_mesh_symmetry,
calculator=calculator,
log_level=log_level)
_nac_params = load_helper.get_nac_params(ph3py.primitive, _nac_params,
born_filename, is_nac,
units['nac_factor'])
_set_force_constants(ph3py,
dataset=None,
fc3_filename=fc3_filename,
fc2_filename=fc2_filename,
forces_fc3_filename=forces_fc3_filename,
forces_fc2_filename=forces_fc2_filename,
fc_calculator=fc_calculator)
if mesh is not None:
ph3py.set_phph_interaction(
nac_params=_nac_params,
frequency_scale_factor=frequency_scale_factor)
return ph3py
def create_phono3py_supercells(cell_info,
settings,
symprec,
output_filename=None,
interface_mode='vasp',
log_level=1):
"""create displacements and supercells
Distance unit used is that for the calculator interface.
The default unit is Angstron.
"""
optional_structure_info = cell_info['optional_structure_info']
if settings.displacement_distance is None:
distance = get_default_displacement_distance(interface_mode)
else:
distance = settings.displacement_distance
phono3py = Phono3py(
cell_info['unitcell'],
cell_info['supercell_matrix'],
primitive_matrix=cell_info['primitive_matrix'],
phonon_supercell_matrix=cell_info['phonon_supercell_matrix'],
is_symmetry=settings.is_symmetry,
symprec=symprec,
calculator=interface_mode)
phono3py.generate_displacements(
distance=distance,
cutoff_pair_distance=settings.cutoff_pair_distance,
is_plusminus=settings.is_plusminus_displacement,
is_diagonal=settings.is_diagonal_displacement)
if log_level:
print('')
print("Unit cell was read from \"%s\"." %
optional_structure_info[0])
print("Displacement distance: %s" % distance)
if output_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + output_filename + '.yaml'
num_disps, num_disp_files = write_disp_fc3_yaml(phono3py.dataset,
phono3py.supercell,
filename=filename)
ids = []
disp_cells = []
for i, cell in enumerate(phono3py.supercells_with_displacements):
if cell is not None:
ids.append(i + 1)
disp_cells.append(cell)
additional_info = get_additional_info_to_write_supercells(
interface_mode, phono3py.supercell_matrix)
write_supercells_with_displacements(interface_mode,
phono3py.supercell,
disp_cells,
optional_structure_info,
displacement_ids=ids,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements: %d" % num_disps)
if settings.cutoff_pair_distance is not None:
print("Cutoff distance for displacements: %s" %
settings.cutoff_pair_distance)
print("Number of displacement supercell files created: %d" %
num_disp_files)
if phono3py.phonon_supercell_matrix is not None:
if output_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + output_filename + '.yaml'
num_disps = write_disp_fc2_yaml(phono3py.phonon_dataset,
phono3py.phonon_supercell,
filename=filename)
additional_info = get_additional_info_to_write_fc2_supercells(
interface_mode, phono3py.phonon_supercell_matrix)
write_supercells_with_displacements(
interface_mode,
phono3py.supercell,
phono3py.phonon_supercells_with_displacements,
optional_structure_info,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py
def create_phono3py_supercells(
cell_info,
settings,
symprec,
output_filename=None,
interface_mode="vasp",
log_level=1,
write_disp_yaml=False,
):
"""Create displacements and supercells.
Distance unit used is that for the calculator interface.
The default unit is Angstron.
Parameters
----------
write_disp_yaml : bool
Write old-style files of disp_fc3.yaml and disp_fc2.yaml. Default is False.
"""
optional_structure_info = cell_info["optional_structure_info"]
if settings.displacement_distance is None:
distance = get_default_displacement_distance(interface_mode)
else:
distance = settings.displacement_distance
phono3py = Phono3py(
cell_info["unitcell"],
cell_info["supercell_matrix"],
primitive_matrix=cell_info["primitive_matrix"],
phonon_supercell_matrix=cell_info["phonon_supercell_matrix"],
is_symmetry=settings.is_symmetry,
symprec=symprec,
calculator=interface_mode,
)
phono3py.generate_displacements(
distance=distance,
cutoff_pair_distance=settings.cutoff_pair_distance,
is_plusminus=settings.is_plusminus_displacement,
is_diagonal=settings.is_diagonal_displacement,
)
if log_level:
print("")
print('Unit cell was read from "%s".' % optional_structure_info[0])
print("Displacement distance: %s" % distance)
if write_disp_yaml:
if output_filename is None:
filename = "disp_fc3.yaml"
else:
filename = "disp_fc3." + output_filename + ".yaml"
num_disps, num_disp_files = write_disp_fc3_yaml(
phono3py.dataset, phono3py.supercell, filename=filename
)
ids = []
disp_cells = []
for i, cell in enumerate(phono3py.supercells_with_displacements):
if cell is not None:
ids.append(i + 1)
disp_cells.append(cell)
additional_info = get_additional_info_to_write_supercells(
interface_mode, phono3py.supercell_matrix
)
write_supercells_with_displacements(
interface_mode,
phono3py.supercell,
disp_cells,
optional_structure_info,
displacement_ids=ids,
zfill_width=5,
additional_info=additional_info,
)
if log_level:
num_disps = len(phono3py.supercells_with_displacements)
num_disp_files = len(disp_cells)
print("Number of displacements: %d" % num_disps)
if settings.cutoff_pair_distance is not None:
print(
"Cutoff distance for displacements: %s" % settings.cutoff_pair_distance
)
print("Number of displacement supercell files created: %d" % num_disp_files)
if phono3py.phonon_supercell_matrix is not None:
if write_disp_yaml:
if output_filename is None:
filename = "disp_fc2.yaml"
else:
filename = "disp_fc2." + output_filename + ".yaml"
num_disps = write_disp_fc2_yaml(
phono3py.phonon_dataset, phono3py.phonon_supercell, filename=filename
)
additional_info = get_additional_info_to_write_fc2_supercells(
interface_mode, phono3py.phonon_supercell_matrix
)
write_supercells_with_displacements(
interface_mode,
phono3py.supercell,
phono3py.phonon_supercells_with_displacements,
optional_structure_info,
zfill_width=5,
additional_info=additional_info,
)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py
def load(
phono3py_yaml=None, # phono3py.yaml-like must be the first argument.
supercell_matrix=None,
primitive_matrix=None,
phonon_supercell_matrix=None,
mesh=None,
is_nac=True,
calculator=None,
unitcell=None,
supercell=None,
nac_params=None,
unitcell_filename=None,
supercell_filename=None,
born_filename=None,
forces_fc3_filename=None,
forces_fc2_filename=None,
fc3_filename=None,
fc2_filename=None,
fc_calculator=None,
fc_calculator_options=None,
factor=None,
frequency_scale_factor=None,
produce_fc=True,
is_symmetry=True,
symmetrize_fc=True,
is_mesh_symmetry=True,
is_compact_fc=False,
symprec=1e-5,
log_level=0):
"""Create Phono3py instance from parameters and/or input files.
"phono3py_yaml"-like file is parsed unless crystal structure information
is given by unitcell_filename, supercell_filename, unitcell
(PhonopyAtoms-like), or supercell (PhonopyAtoms-like).
Even when "phono3py_yaml"-like file is parse, parameters except for
crystal structure can be overwritten.
'fc3.hdf5' is read if found in current directory.
Unless 'fc3.hdf5' is found and if 'FORCES_FC3' and 'disp_fc3.yaml" are
found, these are read and fc3 and fc2 are produced.
if 'fc2.hdf5' is found, this is read.
Unless 'fc2.hdf5' is found and if 'FORCES_FC2' and 'disp_fc2.yaml" are
found, these are read and fc2 is produced.
When force_sets_filename and force_constants_filename are not given,
'FORCES_FC3' and 'FORCES_FC2' are looked for in the current directory
as the default behaviour. When 'FORCES_FC3' ('FORCES_FC2') is given in
the type-1 format, 'disp_fc3.yaml' ('disp_fc2.yaml') is also necessary
and read.
Crystal structure
-----------------
Means to provide crystal structure(s) and their priority:
1. unitcell_filename (with supercell_matrix)
2. supercell_filename
3. unitcell (with supercell_matrix)
4. supercell.
5. phono3py_yaml-like
Force sets or force constants
-----------------------------
Optional. Means to provide information to generate force constants
and their priority:
1. fc3_filename (fc2_filename)
2. forces_fc3_filename (forces_fc2_filename). Do not forget that
for type-1 format, disp_fc3.yaml (disp_fc2.yaml) has to be given,
too.
3. 'fc3.hdf5' and 'fc2.hdf5' are searched in current directory.
4. 'FORCES_FC3' and 'FORCES_FC2' are searched in current directory.
'FORCES_FC2' is optional. For type-1 format, 'disp_fc3.yaml' and
optionally 'disp_fc2.yaml' are also searched in current
directory. When 'FORCES_FC2' is not found, 'FORCES_FC3' is used
to create fc2.
Parameters for non-analytical term correctiion (NAC)
----------------------------------------------------
Optional. Means to provide NAC parameters and their priority:
1. born_filename
2. nac_params
3. phono3py_yaml_like.nac_params if existed and is_nac=True.
4. 'BORN' is searched in current directory when is_nac=True.
Parameters
----------
phono3py_yaml : str, optional
Filename of "phono3py.yaml"-like file. If this is given, the data
in the file are parsed. Default is None.
supercell_matrix : array_like, optional
Supercell matrix multiplied to input cell basis vectors.
shape=(3, ) or (3, 3), where the former is considered a diagonal
matrix. Default is the unit matrix.
dtype=int
primitive_matrix : array_like or str, optional
Primitive matrix multiplied to input cell basis vectors. Default is
the identity matrix. Default is None, which is equivalent to 'auto'.
shape=(3, 3), dtype=float.
When 'F', 'I', 'A', 'C', or 'R' is given instead of a 3x3 matrix,
the primitive matrix defined at
https://spglib.github.io/spglib/definition.html
is used.
phonon_supercell_matrix : array_like, optional
Supercell matrix used for fc2. In phono3py, supercell matrix for fc3
and fc2 can be different to support longer range interaction of fc2
than that of fc3. Unless setting this, supercell_matrix is used.
This is only valide when unitcell or unitcell_filename is given.
Default is None.
mesh : array_like, optional
Grid mesh numbers in reciprocal cell.
shape=(3,), dtype='intc'
is_nac : bool, optional
If True, look for 'BORN' file. If False, NAS is turned off.
Default is True.
calculator : str, optional.
Calculator used for computing forces. This is used to switch the set
of physical units. Default is None, which is equivalent to "vasp".
unitcell : PhonopyAtoms, optional
Input unit cell. Default is None.
supercell : PhonopyAtoms, optional
Input supercell. With given, default value of primitive_matrix is set
to 'auto' (can be overwitten). supercell_matrix is ignored. Default is
None.
nac_params : dict, optional
Parameters required for non-analytical term correction. Default is
None.
{'born': Born effective charges
(array_like, shape=(primitive cell atoms, 3, 3), dtype=float),
'dielectric': Dielectric constant matrix
(array_like, shape=(3, 3), dtype=float),
'factor': unit conversion facotr (float)}
unitcell_filename : str, optional
Input unit cell filename. Default is None.
supercell_filename : str, optional
Input supercell filename. When this is specified, supercell_matrix is
ignored. Default is None.
born_filename : str, optional
Filename corresponding to 'BORN', a file contains non-analytical term
correction parameters.
forces_fc3_filename : sequence or str, optional
A two-elemental sequence of filenames corresponding to
('FORCES_FC3', 'disp_fc3.yaml') in the type-1 format or a filename
(str) corresponding to 'FORCES_FC3' in the type-2 format.
Default is None.
forces_fc2_filename : str or tuple, optional
A two-elemental sequence of filenames corresponding to
('FORCES_FC2', 'disp_fc2.yaml') in the type-1 format or a filename
(str) corresponding to 'FORCES_FC2' in the type-2 format.
Default is None.
fc3_filename : str, optional
Filename of a file corresponding to 'fc3.hdf5', a file contains
third-order force constants. Default is None.
fc2_filename : str, optional
Filename of a file corresponding to 'fc2.hdf5', a file contains
second-order force constants. Default is None.
fc_calculator : str, optional
Force constants calculator. Currently only 'alm'. Default is None.
fc_calculator_options : str, optional
Optional parameters that are passed to the external fc-calculator.
This is given as one text string. How to parse this depends on the
fc-calculator. For alm, each parameter is splitted by comma ',',
and each set of key and value pair is written in 'key = value'.
factor : float, optional
Phonon frequency unit conversion factor. Unless specified, default
unit conversion factor for each calculator is used.
frequency_scale_factor : float, optional
Factor multiplied to calculated phonon frequency. Default is None,
i.e., effectively 1.
produce_fc : bool, optional
Setting False, force constants are not calculated from displacements
and forces. Default is True.
is_symmetry : bool, optional
Setting False, crystal symmetry except for lattice translation is not
considered. Default is True.
symmetrize_fc : bool, optional
Setting False, force constants are not symmetrized when creating
force constants from displacements and forces. Default is True.
is_mesh_symmetry : bool, optional
Setting False, reciprocal mesh symmetry is not considered.
Default is True.
is_compact_fc : bool
fc3 are created in the array whose shape is
True: (primitive, supercell, supecell, 3, 3, 3)
False: (supercell, supercell, supecell, 3, 3, 3)
and for fc2
True: (primitive, supecell, 3, 3)
False: (supercell, supecell, 3, 3)
where 'supercell' and 'primitive' indicate number of atoms in these
cells. Default is False.
symprec : float, optional
Tolerance used to find crystal symmetry. Default is 1e-5.
log_level : int, optional
Verbosity control. Default is 0.
"""
if (supercell is not None or supercell_filename is not None
or unitcell is not None or unitcell_filename is not None):
cell, smat, pmat = load_helper.get_cell_settings(
supercell_matrix=supercell_matrix,
primitive_matrix=primitive_matrix,
unitcell=unitcell,
supercell=supercell,
unitcell_filename=unitcell_filename,
supercell_filename=supercell_filename,
calculator=calculator,
symprec=symprec)
if phonon_supercell_matrix is not None:
if unitcell is None and unitcell_filename is None:
msg = ("phonon_supercell_matrix can be used only when "
"unitcell or unitcell_filename is given.")
raise RuntimeError(msg)
ph_smat = phonon_supercell_matrix
else:
ph_smat = None
_nac_params = nac_params
ph3py_yaml = None
elif phono3py_yaml is not None:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(phono3py_yaml)
cell = ph3py_yaml.unitcell
smat = ph3py_yaml.supercell_matrix
ph_smat = ph3py_yaml.phonon_supercell_matrix
if smat is None:
smat = np.eye(3, dtype='intc', order='C')
if primitive_matrix == 'auto':
pmat = 'auto'
else:
pmat = ph3py_yaml.primitive_matrix
if nac_params is not None:
_nac_params = nac_params
elif is_nac:
_nac_params = ph3py_yaml.nac_params
else:
_nac_params = None
# units keywords: factor, nac_factor, distance_to_A
physical_units = get_default_physical_units(calculator)
if factor is None:
_factor = physical_units['factor']
else:
_factor = factor
ph3py = Phono3py(cell,
smat,
primitive_matrix=pmat,
phonon_supercell_matrix=ph_smat,
frequency_factor_to_THz=_factor,
symprec=symprec,
is_symmetry=is_symmetry,
is_mesh_symmetry=is_mesh_symmetry,
calculator=calculator,
log_level=log_level)
ph3py.mesh_number = mesh
# NAC params
if (born_filename is not None or nac_params is not None
or is_nac and os.path.isfile("BORN")):
ph3py.nac_params = load_helper.get_nac_params(
ph3py.primitive,
_nac_params,
born_filename,
is_nac,
physical_units['nac_factor'],
log_level=log_level)
set_dataset_and_force_constants(
ph3py,
ph3py_yaml=ph3py_yaml,
fc3_filename=fc3_filename,
fc2_filename=fc2_filename,
forces_fc3_filename=forces_fc3_filename,
forces_fc2_filename=forces_fc2_filename,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
produce_fc=produce_fc,
symmetrize_fc=symmetrize_fc,
is_compact_fc=is_compact_fc,
log_level=log_level)
if mesh is not None:
ph3py.init_phph_interaction(
frequency_scale_factor=frequency_scale_factor)
return ph3py
def create_phono3py_supercells(unitcell,
supercell_matrix,
phonon_supercell_matrix,
displacement_distance,
is_plusminus,
is_diagonal,
cutoff_pair_distance,
write_supercells_with_displacements,
optional_structure_file_information,
is_symmetry,
symprec,
interface_mode='vasp',
output_filename=None,
log_level=1):
if displacement_distance is None:
if interface_mode in ('qe', 'abinit', 'turbomole'):
distance = 0.06
elif interface_mode == 'crystal':
distance = 0.03
else:
distance = 0.03
else:
distance = displacement_distance
phono3py = Phono3py(
unitcell,
supercell_matrix,
phonon_supercell_matrix=phonon_supercell_matrix,
is_symmetry=is_symmetry,
symprec=symprec)
supercell = phono3py.get_supercell()
phono3py.generate_displacements(
distance=distance,
cutoff_pair_distance=cutoff_pair_distance,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal)
dds = phono3py.get_displacement_dataset()
if log_level:
print('')
print("Displacement distance: %s" % distance)
if output_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + output_filename + '.yaml'
num_disps, num_disp_files = write_disp_fc3_yaml(dds,
supercell,
filename=filename)
cells_with_disps = phono3py.get_supercells_with_displacements()
if interface_mode == 'qe':
pp_filenames = optional_structure_file_information[1]
write_supercells_with_displacements(supercell,
cells_with_disps,
pp_filenames,
width=5)
elif interface_mode == 'crystal':
conv_numbers = optional_structure_file_information[1]
# N_FC3 = num_unitcells_in_supercell (here for FC3 supercell)
N_FC3 = abs(determinant(supercell_matrix))
write_supercells_with_displacements(supercell,
cells_with_disps,
conv_numbers,
N_FC3,
width=5,
template_file="TEMPLATE3")
elif interface_mode == 'abinit':
write_supercells_with_displacements(supercell,
cells_with_disps,
width=5)
elif interface_mode == 'turbomole':
write_supercells_with_displacements(supercell,
cells_with_disps,
width=5)
else: # VASP
write_supercells_with_displacements(supercell,
cells_with_disps,
width=5)
if log_level:
print("Number of displacements: %d" % num_disps)
if cutoff_pair_distance is not None:
print("Cutoff distance for displacements: %s" %
cutoff_pair_distance)
print("Number of displacement supercell files created: %d" %
num_disp_files)
if phonon_supercell_matrix is not None:
phonon_dds = phono3py.get_phonon_displacement_dataset()
phonon_supercell = phono3py.get_phonon_supercell()
if output_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + output_filename + '.yaml'
num_disps = write_disp_fc2_yaml(phonon_dds,
phonon_supercell,
filename=filename)
cells_with_disps = phono3py.get_phonon_supercells_with_displacements()
if interface_mode == 'qe':
pp_filenames = optional_structure_file_information[1]
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
pp_filenames,
pre_filename="supercell_fc2",
width=5)
elif interface_mode == 'crystal':
conv_numbers = optional_structure_file_information[1]
# N = num_unitcells_in_supercell (here for FC2 supercell)
N_FC2 = abs(determinant(phonon_supercell_matrix))
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
conv_numbers,
N_FC2,
pre_filename="supercell_fc2",
width=5,
template_file="TEMPLATE")
elif interface_mode == 'abinit':
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
pre_filename="supercell_fc2",
width=5)
elif interface_mode == 'turbomole':
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
pre_filename="supercell_fc2",
width=5)
else:
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
pre_filename="POSCAR_FC2",
width=5)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py