def load(supercell_matrix,
primitive_matrix=None,
nac_params=None,
unitcell=None,
calculator="vasp",
unitcell_filename=None,
born_filename=None,
force_sets_filename=None,
force_constants_filename=None,
factor=VaspToTHz,
frequency_scale_factor=None,
symprec=1e-5,
is_symmetry=True,
log_level=0):
if unitcell is None:
_unitcell, _ = read_crystal_structure(filename=unitcell_filename,
interface_mode=calculator)
else:
_unitcell = unitcell
# units keywords: factor, nac_factor, distance_to_A
units = get_default_physical_units(calculator)
phonon = Phonopy(_unitcell,
supercell_matrix,
primitive_matrix=primitive_matrix,
factor=units['factor'])
if nac_params is None:
if born_filename is None:
_nac_params = None
else:
_nac_params = parse_BORN(phonon.primitive, filename=born_filename)
else:
_nac_params = nac_params
if _nac_params is not None:
if _nac_params['factor'] is None:
_nac_params['factor'] = units['nac_factor']
phonon.set_nac_params(_nac_params)
if force_constants_filename is not None:
dot_split = force_constants_filename.split('.')
p2s_map = phonon.primitive.get_primitive_to_supercell_map()
if len(dot_split) > 1 and dot_split[-1] == 'hdf5':
fc = read_force_constants_hdf5(filename=force_constants_filename,
p2s_map=p2s_map)
else:
fc = parse_FORCE_CONSTANTS(filename=force_constants_filename,
p2s_map=p2s_map)
phonon.set_force_constants(fc)
elif force_sets_filename is not None:
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def get_BORN_txt(structure, parameters, nac_data, symprec=1.e-5):
from phonopy.structure.cells import get_primitive, get_supercell
from phonopy.structure.symmetry import Symmetry
from phonopy.interface import get_default_physical_units
from phonopy.structure.atoms import Atoms as PhonopyAtoms
born_charges = nac_data.get_array('born_charges')
epsilon = nac_data.get_array('epsilon')
print ('inside born parameters')
pmat = parameters['primitive']
smat = parameters['supercell']
ucell = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
num_atom = len(born_charges)
assert num_atom == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(born_charges))
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=True, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = born_charges[u_indep_atoms].copy()
factor = get_default_physical_units('vasp')['nac_factor'] # born charges in VASP units
born_txt = ('{}\n'.format(factor))
for num in epsilon.flatten():
born_txt += ('{0:4.8f}'.format(num))
born_txt += ('\n')
for atom in reduced_borns:
for num in atom:
born_txt += ('{0:4.8f}'.format(num))
born_txt += ('\n')
born_txt += ('{}\n'.format(factor))
return born_txt
def get_phonopy_instance(structure, phonon_settings_dict, params):
from phonopy import Phonopy
phonon = Phonopy(phonopy_atoms_from_structure(structure),
phonon_settings_dict['supercell_matrix'],
primitive_matrix='auto',
symprec=phonon_settings_dict['symmetry_tolerance'])
if 'nac_params' in params:
from phonopy.interface 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.set_nac_params(nac_params)
return phonon
def get_born_parameters(phonon, born_charges, epsilon, symprec=1e-5):
from phonopy.structure.cells import get_primitive, get_supercell
from phonopy.structure.symmetry import Symmetry
from phonopy.interface import get_default_physical_units
print('inside born parameters')
pmat = phonon.get_primitive_matrix()
smat = phonon.get_supercell_matrix()
ucell = phonon.get_unitcell()
print pmat
print smat
print ucell
num_atom = len(born_charges)
assert num_atom == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(born_charges))
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=True, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = born_charges[u_indep_atoms].copy()
factor = get_default_physical_units('vasp')[
'nac_factor'] # born charges in VASP units
born_dict = {
'born': reduced_borns,
'dielectric': epsilon,
'factor': factor
}
print('final born dict', born_dict)
return born_dict
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(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