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,
use_alm=False,
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'.
use_alm : bool, optional
Default is False.
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,
use_alm=use_alm)
else:
phonon.force_constants = _fc
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,
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(
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 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,
use_alm=False,
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'.
use_alm : bool, optional
Default is False.
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:
raise RuntimeError("%s could not be parsed.")
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,
use_alm=use_alm)
else:
phonon.force_constants = _fc
return phonon