def _convert_unit_in_dataset(dataset, calculator):
physical_units = get_default_physical_units(calculator)
force_to_eVperA = physical_units['force_to_eVperA']
distance_to_A = physical_units['distance_to_A']
if 'first_atoms' in dataset:
for d1 in dataset['first_atoms']:
if distance_to_A is not None:
disp = _to_ndarray(d1['displacement'])
d1['displacement'] = disp * distance_to_A
if force_to_eVperA is not None and 'forces' in d1:
forces = _to_ndarray(d1['forces'])
d1['forces'] = forces * force_to_eVperA
if 'second_atoms' in d1:
for d2 in d1['second_atoms']:
if distance_to_A is not None:
disp = _to_ndarray(d2['displacement'])
d2['displacement'] = disp * distance_to_A
if force_to_eVperA is not None and 'forces' in d2:
forces = _to_ndarray(d2['forces'])
d2['forces'] = forces * force_to_eVperA
else:
if distance_to_A is not None and 'displacements' in dataset:
disp = _to_ndarray(dataset['displacements'])
dataset['displacements'] = disp * distance_to_A
if force_to_eVperA is not None and 'forces' in dataset:
forces = _to_ndarray(dataset['forces'])
dataset['forces'] = forces * force_to_eVperA
def _convert_unit_in_dataset(dataset, calculator):
physical_units = get_default_physical_units(calculator)
force_to_eVperA = physical_units["force_to_eVperA"]
distance_to_A = physical_units["distance_to_A"]
if "first_atoms" in dataset:
for d1 in dataset["first_atoms"]:
if distance_to_A is not None:
disp = _to_ndarray(d1["displacement"])
d1["displacement"] = disp * distance_to_A
if force_to_eVperA is not None and "forces" in d1:
forces = _to_ndarray(d1["forces"])
d1["forces"] = forces * force_to_eVperA
if "second_atoms" in d1:
for d2 in d1["second_atoms"]:
if distance_to_A is not None:
disp = _to_ndarray(d2["displacement"])
d2["displacement"] = disp * distance_to_A
if force_to_eVperA is not None and "forces" in d2:
forces = _to_ndarray(d2["forces"])
d2["forces"] = forces * force_to_eVperA
else:
if distance_to_A is not None and "displacements" in dataset:
disp = _to_ndarray(dataset["displacements"])
dataset["displacements"] = disp * distance_to_A
if force_to_eVperA is not None and "forces" in dataset:
forces = _to_ndarray(dataset["forces"])
dataset["forces"] = forces * force_to_eVperA
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 finalize_phono3py(
phono3py: Phono3py,
confs_dict,
log_level,
displacements_mode=False,
filename=None,
):
"""Write phono3py.yaml and then exit.
Parameters
----------
phono3py : Phono3py
Phono3py instance.
confs_dict : dict
This contains the settings and command options that the user set.
log_level : int
Log level. 0 means quiet.
displacements_mode : Bool
When True, crystal structure is written in the length unit of
calculator interface in phono3py_disp.yaml. Otherwise, the
default unit (angstrom) is used.
filename : str, optional
phono3py.yaml is written in this filename.
"""
if filename is None:
yaml_filename = "phono3py.yaml"
else:
yaml_filename = filename
if displacements_mode:
_calculator = phono3py.calculator
else:
_calculator = None
_physical_units = get_default_physical_units(_calculator)
yaml_settings = {"force_sets": False, "displacements": displacements_mode}
ph3py_yaml = Phono3pyYaml(configuration=confs_dict,
physical_units=_physical_units,
settings=yaml_settings)
ph3py_yaml.set_phonon_info(phono3py)
ph3py_yaml.calculator = _calculator
with open(yaml_filename, "w") as w:
w.write(str(ph3py_yaml))
if log_level > 0:
print("")
if displacements_mode:
print(f'Displacement dataset was written in "{yaml_filename}".')
else:
print(f'Summary of calculation was written in "{yaml_filename}".')
print_end()
sys.exit(0)
def get_phonopy_instance(structure, phonon_settings_dict, params):
from phonopy import Phonopy
phonon = Phonopy(phonopy_atoms_from_structure(structure),
supercell_matrix=phonon_settings_dict['supercell_matrix'],
primitive_matrix='auto',
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
}
phonon.nac_params = nac_params
return phonon
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 run_task(self, fw_spec):
unitcell = read_vasp("POSCAR-unitcell")
phonon = phonopy.Phonopy(unitcell, self.get("supercell"))
supercell = phonon.get_supercell()
phonon.generate_displacements()
supercells = phonon.supercells_with_displacements
ids = np.arange(len(supercells)) + 1
write_supercells_with_displacements(supercell, supercells, ids)
units = get_default_physical_units("vasp")
phpy_yaml = PhonopyYaml(physical_units=units,
settings={
'force_sets': False,
'born_effective_charge': False,
'dielectric_constant': False,
'displacements': True
})
phpy_yaml.set_phonon_info(phonon)
with open("phonopy_disp.yaml", 'w') as w:
w.write(str(phpy_yaml))
# g_min = -12.4
g_max = None
g_min = None
# f_max = 5.5
# f_min = -0.25
f_max = None
f_min = None
if nac:
from phonopy.interface.vasp import get_born_vasprunxml
born_chg, eps, _ = get_born_vasprunxml(
is_symmetry=False,
symmetrize_tensors=True,
)
from phonopy.interface.calculator import get_default_physical_units
nac_factor = get_default_physical_units('vasp')['nac_factor']
nac_params = {
'born': born_chg,
'dielectric': eps,
'factor': nac_factor,
# 'method':'wang',
}
else:
nac_params = None
from os import environ
environ['CUDA_VISIBLE_DEVICES'] = ''
from phonopy.interface import vasp
atoms = vasp.read_vasp(unitcell_f)
from phono3py import Phono3py
def phonopy_to_abinit(unit_cell,
supercell_matrix,
out_ddb_path,
ngqpt=None,
qpt_list=None,
force_constants=None,
force_sets=None,
born=None,
primitive_matrix="auto",
symprec=1e-5,
tolsym=None,
supercell=None,
calculator=None,
manager=None,
workdir=None,
pseudos=None,
verbose=False):
"""
Converts the data from phonopy to an abinit DDB file. The data can be provided
in form of arrays or paths to the phonopy files that should be parsed.
The minimal input should contains the FORCE_CONSTANTS or FORCE_SETS.
If BORN is present the Born effective charges (BEC) and dielectric
tensor will also be added to the DDB.
The best agreement is obtained with supercell_matrix and ngqpt being
equivalent (i.e. supercell_matrix a diagonal matrix with ngqpt as diagonal
elements). Non diagonal supercell_matrix are allowed as well, but the information
encoded in the DDB will be the result of an interpolation done through phonopy.
Phonopy is used to convert the IFC to the dynamical matrix. However, in order to
determine the list of q-points in the irreducible Brillouin zone and to prepare the
base for the final DDB file, abinit will be called for a very short and inexpensive run.
Performs a check to verify if the two codes identify the same symmetries and it gives a
warning in case of failure. Mismatching symmetries may lead to incorrect conversions.
Args:
unit_cell: a |Structure| object that identifies the unit cell used for the phonopy
calculation.
supercell_matrix: a 3x3 array representing the supercell matrix used to generated the
forces with phonopy.
out_ddb_path: a full path to the file where the new DDB will be written
ngqpt: a list of 3 elements indicating the grid of q points that will be used in the DDB.
qpt_list: alternatively to ngqpt an explicit list of q-points can be provided here.
At least one among ngqpt and qpt_list should be defined.
force_constants: an array with shape (num atoms unit cell, num atoms supercell, 3, 3)
containing the force constants. Alternatively a string with the path to the
FORCE_CONSTANTS file. This or force_set should be defined. If both given this
has precedence.
force_sets: a dictionary obtained from the force sets generated with phonopy.
Alternatively a string with the path to the FORCE_SETS file. This or force_constants
should be defined.
born: a dictionary with "dielectric" and "born" keywords as obtained from the nac_params
in phonopy. Alternatively a string with the path to the BORN file. Notice that
the "factor" attribute is not taken into account, so the values should be in
default phonopy units.
primitive_matrix: a 3x3 array with the primitive matrix passed to Phonopy. "auto" will
use spglib to try to determine it automatically. If the DDB file should contain the
actual unit cell this should be the identity matrix.
symprec: distance tolerance in Cartesian coordinates to find crystal symmetry in phonopy.
It might be that the value should be tuned so that it leads to the the same symmetries
as in the abinit calculation.
tolsym: Gives the tolerance to identify symmetries in abinit. See abinit documentation for
more details.
supercell: if given it should represent the supercell used to get the force constants,
without any perturbation. It will be used to match it to the phonopy supercell
and sort the IFC in the correct order.
calculator: a string with the name of the calculator. Will be used to set the conversion
factor for the force constants coming from phonopy.
manager: |TaskManager| object. If None, the object is initialized from the configuration file
pseudos: List of filenames or list of |Pseudo| objects or |PseudoTable| object. It will be
used by abinit to generate the base DDB file. If None the abipy.data.hgh_pseudos.HGH_TABLE
table will be used.
verbose: verbosity level. Set it to a value > 0 to get more information
workdir: path to the directory where the abinit calculation will be executed.
Returns:
a DdbFile instance of the file written in out_ddb_path.
"""
if ngqpt is None and qpt_list is None:
raise ValueError(
"at least one among nqgpt and qpt_list should be defined")
if force_sets is None and force_constants is None:
raise ValueError(
"at least one of force_sets and force_constants should be provided"
)
phon_at = get_phonopy_structure(unit_cell)
if isinstance(force_constants, str):
force_constants = parse_FORCE_CONSTANTS(filename=force_constants)
elif force_constants is not None:
force_constants = np.array(force_constants)
force_sets = None
if isinstance(force_sets, str):
force_sets = parse_FORCE_SETS(filename=force_sets)
# no nac_params here, otherwise they will be used for the interpolation
phonon = Phonopy(phon_at,
supercell_matrix,
primitive_matrix=primitive_matrix,
nac_params=None,
symprec=symprec,
calculator=calculator)
primitive = get_pmg_structure(phonon.primitive)
if isinstance(born, str):
born = parse_BORN(phonon.primitive, filename=born)
if supercell is not None:
ph_supercell = get_pmg_structure(phonon.supercell)
if not np.allclose(supercell.lattice.matrix,
ph_supercell.lattice.matrix):
raise RuntimeError("The lattice of the supercells do not match")
sc_mapping = []
for i, site_orig in enumerate(supercell):
for j, site_ph in enumerate(ph_supercell):
d = supercell.lattice.get_distance_and_image(
site_orig.frac_coords, site_ph.frac_coords)[0]
if d < 1e-5:
sc_mapping.append(j)
break
else:
raise RuntimeError(
f"Could not find a match for site {i} with coords "
f"{site_orig.cart_coords} in the supercell.")
# cross check that the same atom was not matched twice
n_matches = len(set(sc_mapping))
if n_matches < len(supercell):
raise RuntimeError(
f"Found matches for {n_matches} different atoms in the supercell: {sc_mapping}"
)
force_constants = force_constants[:, sc_mapping]
if force_constants is not None:
phonon.set_force_constants(force_constants)
else:
phonon.dataset = force_sets
phonon.produce_force_constants()
if calculator:
units = get_default_physical_units(calculator)
fc_factor = get_force_constant_conversion_factor(
units["force_constants_unit"], None)
phonon.set_force_constants(phonon.force_constants * fc_factor)
if pseudos is None:
from abipy.data.hgh_pseudos import HGH_TABLE
pseudos = HGH_TABLE
inp = minimal_scf_input(primitive, pseudos)
# get the qpoints list if not defined
if qpt_list is None:
inp["ngkpt"] = ngqpt
qpt_list = inp.abiget_ibz(verbose=verbose)[0]
dm_list = get_dm(phonon, qpt_list, primitive)
if born is not None:
# for the conversion of the BEC the zion (i.e. the ionic charge of the pseudo)
# it is an additive factor and should be the same that goes in the header of the DDB,
# so take it from the pseudos used to generate it.
zion = inp.valence_electrons_per_atom
born_data = generate_born_deriv(born, zion, primitive)
else:
born_data = None
inp = minimal_scf_input(primitive, pseudos)
if tolsym is not None:
inp["tolsym"] = tolsym
task = inp.run_in_shell(workdir=workdir, manager=manager, verbose=verbose)
# use the output of abinit to check that the spacegroup identified by
# phonopy and abinit are the same.
with GsrFile(task.opath_from_ext("GSR.nc")) as gsr:
abi_spg = gsr.structure.abi_spacegroup.spgid
spglib_spg = phonon.symmetry.dataset["number"]
if abi_spg != spglib_spg:
warnings.warn(
"The space group number obtained based on the DDB symmetries differs "
f"from the one calculated with spglib: {abi_spg} versus "
f"{spglib_spg}. The convertion may be incorrect. Try changing symprec or tolsym."
)
tmp_ddb_path = task.opath_from_ext("DDB")
ddb = DdbFile(tmp_ddb_path)
# remove the blocks generated by the calculation and that are meaningless
ddb.remove_block(dord=0)
ddb.remove_block(dord=1)
add_data_ddb(ddb, dm_list, qpt_list, born_data)
ddb.write(out_ddb_path)
new_ddb = DdbFile(out_ddb_path)
return new_ddb
def load(
phonopy_yaml=None, # phonopy.yaml-like must be the first argument.
supercell_matrix=None,
primitive_matrix=None,
is_nac=True,
calculator=None,
unitcell=None,
supercell=None,
nac_params=None,
unitcell_filename=None,
supercell_filename=None,
born_filename=None,
force_sets_filename=None,
force_constants_filename=None,
fc_calculator=None,
factor=None,
frequency_scale_factor=None,
symprec=1e-5,
is_symmetry=True,
log_level=0):
"""Create Phonopy 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,
'FORCE_SETS' is looked for in the current directory as the default
behaviour.
Parameters
----------
phonopy_yaml : str, optional
Filename of "phonopy.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.
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.
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 cell. 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. 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.
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').
force_sets_filename : str, optional
Filename of a file corresponding to 'FORCE_SETS', a file contains sets
of forces and displacements. Default is None.
The priority for force constants is
force_constants_filename > force_sets_filename > 'FORCE_SETS'.
force_constants_filename : str, optional
Filename of a file corresponding to 'FORCE_CONSTANTS' or
'force_constants.hdf5', a file contains force constants.
Default is None.
The priority for force constants is
force_constants_filename > force_sets_filename > 'FORCE_SETS'.
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.
symprec : float, optional
Tolerance used to find crystal symmetry. Default is 1e-5.
is_symmetry : bool, optional
Setting False, crystal symmetry except for lattice translation is not
considered. Default is True.
log_level : int, optional
Verbosity control. Default is 0.
"""
if phonopy_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)
_nac_params = nac_params
_dataset = None
_fc = None
else:
phpy_yaml = PhonopyYaml()
phpy_yaml.read(phonopy_yaml)
cell = phpy_yaml.unitcell
smat = phpy_yaml.supercell_matrix
if smat is None:
smat = np.eye(3, dtype='intc', order='C')
if primitive_matrix is 'auto':
pmat = 'auto'
else:
pmat = phpy_yaml.primitive_matrix
if is_nac:
_nac_params = phpy_yaml.nac_params
else:
_nac_params = None
_dataset = phpy_yaml.dataset
_fc = phpy_yaml.force_constants
# units keywords: factor, nac_factor, distance_to_A
units = get_default_physical_units(calculator)
if factor is None:
_factor = units['factor']
else:
_factor = factor
phonon = Phonopy(cell,
smat,
primitive_matrix=pmat,
factor=_factor,
frequency_scale_factor=frequency_scale_factor,
symprec=symprec,
is_symmetry=is_symmetry,
calculator=calculator,
log_level=log_level)
load_helper.set_nac_params(phonon, _nac_params, born_filename, is_nac,
units['nac_factor'])
if _fc is None:
load_helper.set_force_constants(
phonon,
dataset=_dataset,
force_constants_filename=force_constants_filename,
force_sets_filename=force_sets_filename,
calculator=calculator,
fc_calculator=fc_calculator)
else:
phonon.force_constants = _fc
return phonon
force_gap_scells = api_q.calc_force_sets_GAP(gp_xml_file, Scells_quippy)
#parse force set and calc force constants
phonon_scell.set_forces(force_gap_scells)
PhonIO.write_FORCE_SETS(phonon_scell.get_displacement_dataset()
) # write forces & displacements to FORCE_SET
force_set = PhonIO.parse_FORCE_SETS() # parse force_sets
phonon_scell.set_displacement_dataset(
force_set) # force_set is a list of forces and displacements
if NAC == True:
nac_params = PhonIO.get_born_parameters(
open("BORN"), phonon_scell.get_primitive(),
phonon_scell.get_primitive_symmetry())
if nac_params['factor'] == None:
physical_units = get_default_physical_units(interface_mode)
nac_params['factor'] = physical_units['nac_factor']
phonon_scell._nac_params = nac_params
phonon_scell.produce_force_constants()
phonon_scell.symmetrize_force_constants()
api_ph.write_ShengBTE_FC2(phonon_scell.get_force_constants(),
filename='FORCE_CONSTANTS_2ND')
# phonopy 2.7 changed format, ShengBTE won't read, use the file in api_qpv to write.
# calc and plot bandstructure
bands = api_ph.qpoints_Band_paths(Qpoints, Band_points)
phonon_scell.set_band_structure(bands,
is_eigenvectors=True,
labels=band_labels)
phonon_scell.write_yaml_band_structure()
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 load(phonopy_yaml=None, # phonopy.yaml-like must be the first argument.
supercell_matrix=None,
primitive_matrix=None,
is_nac=True,
calculator=None,
unitcell=None,
supercell=None,
nac_params=None,
unitcell_filename=None,
supercell_filename=None,
born_filename=None,
force_sets_filename=None,
force_constants_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_compact_fc=True,
symprec=1e-5,
log_level=0):
"""Create Phonopy instance from parameters and/or input files.
"phonopy_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 "phonopy_yaml"-like file is parse, parameters except for
crystal structure can be overwritten.
Phonopy default files of 'FORCE_SETS' and 'BORN' are parsed when they
are found in current directory and those data are not yet provided by
other means.
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. phonopy_yaml
Force sets or force constants
-----------------------------
Optional. Means to provide information to generate force constants
and their priority:
1. force_constants_filename
2. force_sets_filename
3. phonopy_yaml if force constants are found in phonoy_yaml.
4. phonopy_yaml if forces are found in phonoy_yaml.dataset.
5. 'FORCE_CONSTANTS' is searched in current directory.
6. 'force_constants.hdf5' is searched in current directory.
7. 'FORCE_SETS' is searched in current directory.
When both of 3 and 4 are satisfied but not others, force constants and
dataset are stored in Phonopy instance, but force constants are not
produced from dataset.
Parameters for non-analytical term correctiion (NAC)
----------------------------------------------------
Optional. Means to provide NAC parameters and their priority:
1. born_filename
2. nac_params
3. phonopy_yaml.nac_params if existed and is_nac=True.
4. 'BORN' is searched in current directory when is_nac=True.
Parameters
----------
phonopy_yaml : str, optional
Filename of "phonopy.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
None, which is equivalent to 'auto'.
For array_like, shape=(3, 3), dtype=float.
When 'F', 'I', 'A', 'C', or 'R' is given instead of a 3x3 matrix,
the primitive matrix for the character found at
https://spglib.github.io/spglib/definition.html
is used.
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.
force_sets_filename : str, optional
Filename of a file corresponding to 'FORCE_SETS', a file contains sets
of forces and displacements. Default is None.
force_constants_filename : str, optional
Filename of a file corresponding to 'FORCE_CONSTANTS' or
'force_constants.hdf5', a file contains 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_compact_fc : bool
Force constants are produced in the array whose shape is
True: (primitive, supecell, 3, 3)
False: (supercell, supecell, 3, 3)
where 'supercell' and 'primitive' indicate number of atoms in these
cells. 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 (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,
log_level=log_level)
_calculator = calculator
_nac_params = nac_params
_dataset = None
_fc = None
elif phonopy_yaml is not None:
phpy_yaml = PhonopyYaml()
phpy_yaml.read(phonopy_yaml)
cell = phpy_yaml.unitcell
smat = phpy_yaml.supercell_matrix
if smat is None:
smat = np.eye(3, dtype='intc', order='C')
if primitive_matrix is not None:
pmat = get_primitive_matrix(primitive_matrix, symprec=symprec)
else:
pmat = phpy_yaml.primitive_matrix
if nac_params is not None:
_nac_params = nac_params
elif is_nac:
_nac_params = phpy_yaml.nac_params
else:
_nac_params = None
_dataset = phpy_yaml.dataset
_fc = phpy_yaml.force_constants
if calculator is None:
_calculator = phpy_yaml.calculator
else:
_calculator = calculator
else:
msg = ("Cell information could not found. "
"Phonopy instance loading failed.")
raise RuntimeError(msg)
if log_level and _calculator is not None:
print("Set \"%s\" mode." % _calculator)
# units keywords: factor, nac_factor, distance_to_A
units = get_default_physical_units(_calculator)
if factor is None:
_factor = units['factor']
else:
_factor = factor
phonon = Phonopy(cell,
smat,
primitive_matrix=pmat,
factor=_factor,
frequency_scale_factor=frequency_scale_factor,
symprec=symprec,
is_symmetry=is_symmetry,
calculator=_calculator,
log_level=log_level)
# NAC params
if born_filename is not None or _nac_params is not None or is_nac:
ret_nac_params = load_helper.get_nac_params(
primitive=phonon.primitive,
nac_params=_nac_params,
born_filename=born_filename,
is_nac=is_nac,
nac_factor=units['nac_factor'],
log_level=log_level)
if ret_nac_params is not None:
phonon.nac_params = ret_nac_params
# Displacements, forces, and force constants
load_helper.set_dataset_and_force_constants(
phonon,
_dataset,
_fc,
force_constants_filename=force_constants_filename,
force_sets_filename=force_sets_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)
return phonon
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 main(**argparse_control):
load_phono3py_yaml = argparse_control.get('load_phono3py_yaml', False)
args, log_level = start_phono3py(**argparse_control)
physical_units = get_default_physical_units(get_interface_mode(vars(args)))
if load_phono3py_yaml:
input_filename = None
output_filename = None
else:
(input_filename,
output_filename) = get_input_output_filenames_from_args(args)
settings, confs, cell_filename = read_phono3py_settings(
args, argparse_control, log_level)
if args.force_sets_to_forces_fc2_mode:
create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level)
if args.force_sets_mode:
create_FORCE_SETS_from_FORCES_FCx_then_exit(
settings.phonon_supercell_matrix, input_filename, log_level)
if args.write_grid_points:
run_mode = "write_grid_info"
elif args.show_num_triplets:
run_mode = "show_triplets_info"
else:
run_mode = None
# -----------------------------------------------------------------------
# ----------------- 'args' should not be used below. --------------------
# -----------------------------------------------------------------------
####################################
# Create FORCES_FC3 and FORCES_FC2 #
####################################
create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
output_filename, log_level)
###########################################################
# Symmetry tolerance. Distance unit depends on interface. #
###########################################################
if settings.symmetry_tolerance is None:
symprec = 1e-5
else:
symprec = settings.symmetry_tolerance
cell_info = get_cell_info(settings, cell_filename, symprec, log_level)
unitcell_filename = cell_info['optional_structure_info'][0]
interface_mode = cell_info['interface_mode']
# ph3py_yaml = cell_info['phonopy_yaml']
if run_mode is None:
run_mode = get_run_mode(settings)
######################################################
# Create supercells with displacements and then exit #
######################################################
if settings.create_displacements:
phono3py = create_phono3py_supercells(cell_info,
settings,
symprec,
output_filename=output_filename,
interface_mode=interface_mode,
log_level=log_level)
finalize_phono3py(phono3py,
confs,
log_level,
displacements_mode=True,
filename="phono3py_disp.yaml")
#######################
# Initialize phono3py #
#######################
# updated_settings keys
# ('grid_points', 'sigmas', 'temperature_points', 'temperatures',
# 'frequency_factor_to_THz', 'num_frequency_points',
# 'frequency_step', 'frequency_scale_factor',
# 'cutoff_frequency')
phono3py, updated_settings = init_phono3py(settings, cell_info,
interface_mode, output_filename,
symprec, log_level)
#################################################
# Show phono3py settings and crystal structures #
#################################################
if log_level:
show_general_settings(settings, run_mode, phono3py, unitcell_filename,
input_filename, output_filename)
if log_level > 1:
show_phono3py_cells(phono3py, settings)
else:
print("Spacegroup: %s" % phono3py.symmetry.get_international_table())
print("Use -v option to watch primitive cell, unit cell, "
"and supercell structures.")
##################
# Check settings #
##################
run_modes_with_mesh = ("conductivity-RTA", "conductivity-LBTE",
"imag_self_energy", "jdos", "isotope",
"write_grid_info", "show_triplets_info")
run_modes_with_gp = ("imag_self_energy", "jdos", "isotope")
if phono3py.mesh_numbers is None and run_mode in run_modes_with_mesh:
print("")
print("Mesh numbers have to be specified.")
print("")
if log_level:
print_error()
sys.exit(1)
if (run_mode in run_modes_with_gp
and updated_settings['grid_points'] is None):
print("")
print("Grid point(s) has to be specified.")
print("")
if log_level:
print_error()
sys.exit(1)
#########################################################
# Write ir-grid points and grid addresses and then exit #
#########################################################
if run_mode == "write_grid_info":
write_grid_points(phono3py.primitive,
phono3py.mesh_numbers,
mesh_divs=settings.mesh_divisors,
band_indices=settings.band_indices,
sigmas=updated_settings['sigmas'],
temperatures=updated_settings['temperatures'],
coarse_mesh_shifts=settings.coarse_mesh_shifts,
is_kappa_star=settings.is_kappa_star,
is_lbte=(settings.write_collision
or settings.is_lbte),
compression=settings.hdf5_compression,
symprec=symprec)
if log_level:
print_end()
sys.exit(0)
################################################################
# Show reduced number of triplets at grid points and then exit #
################################################################
if run_mode == "show_triplets_info":
show_num_triplets(phono3py.primitive,
phono3py.mesh_numbers,
mesh_divs=settings.mesh_divisors,
band_indices=settings.band_indices,
grid_points=updated_settings['grid_points'],
coarse_mesh_shifts=settings.coarse_mesh_shifts,
is_kappa_star=settings.is_kappa_star,
symprec=symprec)
if log_level:
print_end()
sys.exit(0)
##################################
# Non-analytical term correction #
##################################
store_nac_params(phono3py,
settings,
cell_info['phonopy_yaml'],
unitcell_filename,
log_level,
nac_factor=Hartree * Bohr,
load_phonopy_yaml=load_phono3py_yaml)
###################
# Force constants #
###################
store_force_constants(phono3py, settings, cell_info['phonopy_yaml'],
physical_units, input_filename, output_filename,
load_phono3py_yaml, log_level)
############################################
# Phonon Gruneisen parameter and then exit #
############################################
if settings.is_gruneisen:
run_gruneisen_then_exit(phono3py, settings, output_filename, log_level)
#################
# Show settings #
#################
if log_level and run_mode is not None:
show_phono3py_settings(phono3py, settings, updated_settings, log_level)
###########################
# Joint DOS and then exit #
###########################
if run_mode == "jdos":
run_jdos_then_exit(phono3py, settings, updated_settings,
output_filename, log_level)
################################################
# Mass variances for phonon-isotope scattering #
################################################
if settings.is_isotope and settings.mass_variances is None:
from phonopy.structure.atoms import isotope_data
symbols = phono3py.phonon_primitive.symbols
in_database = True
for s in set(symbols):
if s not in isotope_data:
print("%s is not in the list of isotope databese" % s)
print("(not implemented).")
print("Use --mass_variances option.")
in_database = False
if not in_database:
if log_level:
print_end()
sys.exit(0)
#########################################
# Phonon-isotope lifetime and then exit #
#########################################
if run_mode == "isotope":
run_isotope_then_exit(phono3py, settings, updated_settings, log_level)
########################################
# Initialize phonon-phonon interaction #
########################################
if run_mode is not None:
init_phph_interaction(phono3py, settings, updated_settings,
input_filename, output_filename, log_level)
#######################################################
# Run imaginary part of self energy of bubble diagram #
#######################################################
if run_mode == "imag_self_energy":
phono3py.run_imag_self_energy(
updated_settings['grid_points'],
updated_settings['temperature_points'],
frequency_step=updated_settings['frequency_step'],
num_frequency_points=updated_settings['num_frequency_points'],
scattering_event_class=settings.scattering_event_class,
write_txt=True,
write_gamma_detail=settings.write_gamma_detail,
output_filename=output_filename)
#####################################################
# Run frequency shift calculation of bubble diagram #
#####################################################
elif run_mode == "real_self_energy":
phono3py.run_real_self_energy(
updated_settings['grid_points'],
updated_settings['temperature_points'],
frequency_step=updated_settings['frequency_step'],
num_frequency_points=updated_settings['num_frequency_points'],
write_txt=True,
output_filename=output_filename)
#######################################################
# Run spectral function calculation of bubble diagram #
#######################################################
elif run_mode == "spectral_function":
phono3py.run_spectral_function(
updated_settings['grid_points'],
updated_settings['temperature_points'],
frequency_step=updated_settings['frequency_step'],
num_frequency_points=updated_settings['num_frequency_points'],
num_points_in_batch=updated_settings['num_points_in_batch'],
write_txt=True,
write_hdf5=True,
output_filename=output_filename)
####################################
# Run lattice thermal conductivity #
####################################
elif run_mode == "conductivity-RTA" or run_mode == "conductivity-LBTE":
phono3py.run_thermal_conductivity(
is_LBTE=settings.is_lbte,
temperatures=updated_settings['temperatures'],
is_isotope=settings.is_isotope,
mass_variances=settings.mass_variances,
grid_points=updated_settings['grid_points'],
boundary_mfp=settings.boundary_mfp,
solve_collective_phonon=settings.solve_collective_phonon,
use_ave_pp=settings.use_ave_pp,
gamma_unit_conversion=settings.gamma_conversion_factor,
mesh_divisors=settings.mesh_divisors,
coarse_mesh_shifts=settings.coarse_mesh_shifts,
is_reducible_collision_matrix=settings.
is_reducible_collision_matrix,
is_kappa_star=settings.is_kappa_star,
gv_delta_q=settings.group_velocity_delta_q,
is_full_pp=settings.is_full_pp,
pinv_cutoff=settings.pinv_cutoff,
pinv_solver=settings.pinv_solver,
write_gamma=settings.write_gamma,
read_gamma=settings.read_gamma,
write_kappa=True,
is_N_U=settings.is_N_U,
write_gamma_detail=settings.write_gamma_detail,
write_collision=settings.write_collision,
read_collision=settings.read_collision,
write_pp=settings.write_pp,
read_pp=settings.read_pp,
write_LBTE_solution=settings.write_LBTE_solution,
compression=settings.hdf5_compression,
input_filename=input_filename,
output_filename=output_filename)
else:
if log_level:
print("-" * 11 +
" None of ph-ph interaction calculation was performed. " +
"-" * 11)
finalize_phono3py(phono3py, confs, log_level)
