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(
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. 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').
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 == '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)
_nac_params = load_helper.get_nac_params(phonon.primitive, _nac_params,
born_filename, is_nac,
units['nac_factor'])
if _dataset is not None:
phonon.dataset = _dataset
if _nac_params is not None:
phonon.nac_params = _nac_params
if _fc is not None:
phonon.force_constants = _fc
else:
_compute_force_constants(
phonon,
dataset=_dataset,
force_constants_filename=force_constants_filename,
force_sets_filename=force_sets_filename,
calculator=calculator,
fc_calculator=fc_calculator)
return phonon