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_phonon(structure, NAC=False):
force_atoms_file = structure.get_force_set()['natom']
force_atoms_input = np.product(np.diagonal(structure.get_super_cell_phonon()))*structure.get_number_of_atoms()
if force_atoms_file != force_atoms_input:
print("Error: FORCE_SETS file does not match with SUPERCELL MATRIX")
exit()
#Preparing the bulk type object
bulk = PhonopyAtoms(symbols=structure.get_atomic_types(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell().T)
phonon = Phonopy(bulk, structure.get_super_cell_phonon(),
primitive_matrix=structure.get_primitive_matrix(),
is_auto_displacements=False)
#Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if NAC:
print("Phonopy warning: Using Non Analytical Corrections")
get_is_symmetry = True #from phonopy: settings.get_is_symmetry()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, get_is_symmetry)
phonon.set_nac_params(nac_params=nac_params)
phonon.set_displacement_dataset(structure.get_force_set())
phonon.produce_force_constants(computation_algorithm="svd")
return phonon
def __init__(self, primitive, supercell, folder, vasp=False):
self.atoms = PhonopyAtoms(symbols=primitive.get_chemical_symbols(),
positions=primitive.positions,
masses=primitive.get_masses(),
cell=primitive.cell,
pbc=primitive.pbc)
self.supercell = supercell
self.folder = folder
if not vasp:
self.phonopy = Phonopy(self.atoms, supercell)
self._get_dynmatrix()
self.primitive = self.phonopy._dynamical_matrix.get_primitive()
else:
from matdb.io import vasp_to_xyz
self.phonopy = Phonopy(self.atoms, supercell)
if path.isfile("FORCE_CONSTANTS"):
fc = file_IO.parse_FORCE_CONSTANTS(filename="FORCE_CONSTANTS")
self.phonopy.set_force_constants(fc)
self.phonopy._set_dynamical_matrix()
self.primitive = primitive
vasp_to_xyz(folder)
self.parent = quippy.Atoms(path.join(folder, "output.xyz"))
def BZ_sample(self):
"""Returns a full sampling of the BZ by calculating frequencies at every
unique k-point as sampled on the :attr:`dosmesh` grid.
Returns:
tuple: `(q-points, weights, eigenvalues)` where the `q-points` are
the unique points after symmetry reduction; `weights` are the
corresponding weights for each point; `eigenvalues` is a
:class:`numpy.ndarray` of frequencies (in THz) for each point.
"""
#This is a little convoluted because of how the phonopy API works. We
#want to get a full sampling of the BZ, but with symmetry, and then
#compare the eigenvalues at every point.
if self._bzsample is None:
with chdir(self.phonodir):
atoms = matdb_to_phonopy(self.atoms)
phonpy = Phonopy(atoms, np.array(self.supercell).reshape(3, 3))
phonpy.set_force_constants(roll_fc(self.H))
phonpy._set_dynamical_matrix()
#Phonopy requires full settings to compute the unique grid and
#eigenvalues. We spoof the command-line parser.
parser = get_parser()
(options, args) = parser.parse_args()
option_list = parser.option_list
options.mesh_numbers = ' '.join(map(str, self.dosmesh))
phonopy_conf = PhonopyConfParser(options=options,
option_list=option_list)
settings = phonopy_conf.get_settings()
#Next, set the mesh on the phonopy object and ask it to reduce and
#calculate frequencies.
mesh = settings.get_mesh()
phonpy.set_mesh(*mesh)
self._bzsample = phonpy.get_mesh()[0:3]
return self._bzsample
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 get_phonon(structure,
NAC=False,
setup_forces=True,
super_cell_phonon=np.identity(3),
primitive_matrix=np.identity(3),
symmetrize=True):
"""
Return a phonopy phonon object (instance of the class Phonon)
:param structure: unit cell matrix (lattice vectors in rows)
:param NAC: (Bool) activate/deactivate Non-analytic corrections
:param setup_forces: (Bool) decide if pre-calculate harmonic forces in phonon object
:param super_cell_phonon: 3x3 array containing the supercell to be used to calculate the force constants
:param primitive_matrix: 3x3 array containing the primitive axis (in rows) which define the primitive cell
:param symmetrize: decide if symmetrize the force constants
:return: phonopy phonon object
"""
phonon = Phonopy(structure,
super_cell_phonon,
primitive_matrix=primitive_matrix,
symprec=1e-5,
is_symmetry=symmetrize)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(
structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(
structure.get_force_sets().get_dict())
phonon.produce_force_constants(computation_algorithm="svd")
structure.set_force_constants(
ForceConstants(
phonon.get_force_constants(),
supercell=structure.get_force_sets().get_supercell()))
else:
print('No force sets/constants available!')
exit()
if NAC:
print("Using non-analytical corrections")
primitive = phonon.get_primitive()
try:
nac_params = parse_BORN(primitive, is_symmetry=True)
phonon.set_nac_params(nac_params=nac_params)
except OSError:
print('Required BORN file not found!')
exit()
return phonon
def get_phonon(structure, NAC=False, setup_forces=True, custom_supercell=None):
if custom_supercell is None:
super_cell_phonon = structure.get_supercell_phonon()
else:
super_cell_phonon = custom_supercell
# Preparing the bulk type object
bulk = PhonopyAtoms(symbols=structure.get_atomic_elements(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell().T)
phonon = Phonopy(bulk,
super_cell_phonon,
primitive_matrix=structure.get_primitive_matrix(),
symprec=1e-5)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if NAC:
print("Phonopy warning: Using Non Analytical Corrections")
get_is_symmetry = True # from phonopy: settings.get_is_symmetry()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, get_is_symmetry)
phonon.set_nac_params(nac_params=nac_params)
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(
structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(
structure.get_force_sets().get_dict())
phonon.produce_force_constants(computation_algorithm="svd")
else:
print('No force sets/constants available!')
exit()
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,
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
class HessianSupercell(object):
"""Represents a supercell configuration generator that has a set of eigenvalues
and eigenvectors compatible with Hessian fitting.
Args:
primitive (ase.Atoms): primitive configuration to create the supercell
from.
supercell (np.array): array of `int` supercell matrix.
folder (str): path to the `phonopy` folder where `FORCE_SETS` and
displacements are kept; or where `vasprun.xml` is located when the
full Hessian is calculated using VASP.
Attributes:
phonopy (phonopy.Phonopy): phonopy class for generating dynamical
matrix, eigenvalues and eigenvectors.
"""
def __init__(self, primitive, supercell, folder, vasp=False):
self.atoms = PhonopyAtoms(symbols=primitive.get_chemical_symbols(),
positions=primitive.positions,
masses=primitive.get_masses(),
cell=primitive.cell,
pbc=primitive.pbc)
self.supercell = supercell
self.folder = folder
if not vasp:
self.phonopy = Phonopy(self.atoms, supercell)
self._get_dynmatrix()
self.primitive = self.phonopy._dynamical_matrix.get_primitive()
else:
from matdb.io import vasp_to_xyz
self.phonopy = Phonopy(self.atoms, supercell)
if path.isfile("FORCE_CONSTANTS"):
fc = file_IO.parse_FORCE_CONSTANTS(filename="FORCE_CONSTANTS")
self.phonopy.set_force_constants(fc)
self.phonopy._set_dynamical_matrix()
self.primitive = primitive
vasp_to_xyz(folder)
self.parent = quippy.Atoms(path.join(folder, "output.xyz"))
def diagonalize(self, q):
"""Diagonalizes the dynamical matrix at `q`.
Args:
q (numpy.array): q-point to diagonalize at.
Returns:
tuple: `(eigvals, eigvecs)`, where the eigenvalues are in units of
`THz` and both eigenvalues and eigenvectors are in the *primitive*
cell.
"""
return self.phonopy.get_frequencies_with_eigenvectors(q)
def _get_phase_factor(self, modulation, argument):
"""Returns a phase factor corresponding to the given modulation.
Args:
modulation (numpy.ndarray): list of displacements, one for each
atom.
argument (float): phase angle (in degrees) to manipulate the
displacement by.
"""
u = np.ravel(modulation)
index_max_elem = np.argmax(abs(u))
max_elem = u[index_max_elem]
phase_for_zero = max_elem / abs(max_elem)
phase_factor = np.exp(1j * np.pi * argument / 180) / phase_for_zero
return phase_factor
def _map_eigvec_supercell(self, supercell, eigvec):
"""Maps the specified eigenvector to the target supercell.
Args:
supercell (phonopy.structure.cells.Supercell): the target supercell
that the atoms will be displaced in.
eigvec (numpy.ndarray): target eigenvector from the *primitive* cell.
"""
s2u_map = supercell.get_supercell_to_unitcell_map()
u2u_map = supercell.get_unitcell_to_unitcell_map()
s2uu_map = [u2u_map[x] for x in s2u_map]
result = []
for i in range(supercell.get_number_of_atoms()):
eig_index = s2uu_map[i] * 3
ej = eigvec[eig_index:eig_index + 3]
result.append(ej)
return np.array(result)
def _get_displacements(self, supercell, eigvec, q, amplitude, argument):
"""Returns the vector of displacements for a single eigenvector.
.. warning:: The supercell *must* be comensurate with the selected
q-vector.
Args:
supercell (phonopy.structure.cells.Supercell): the target supercell
that the atoms will be displaced in.
eigvec (numpy.ndarray): target eigenvector from the *primitive* cell.
"""
m = supercell.get_masses()
spos = supercell.get_scaled_positions()
dim = supercell.get_supercell_matrix()
coefs = np.exp(
2j * np.pi * np.dot(np.dot(spos, dim.T), q)) / np.sqrt(m)
meigvec = self._map_eigvec_supercell(supercell, eigvec)
u = (meigvec.T * coefs).T
u = np.array(u) / np.sqrt(len(m))
phase_factor = self._get_phase_factor(u, argument)
u *= phase_factor * amplitude
return u
def iterate(self, method="hessian", supercell=None, q=None, nrattle=0):
"""Returns a list of possible configurations, one for each eigenmode in the
system, that has `supercell` is compatible with the specified `q`
vector.
Args:
method (str): desired method for computing the eigenvalues and
eigenvectors. Possible choices are :meth:`hessian` or
:meth:`dynmat`.
supercell (numpy.ndarray): supercell matrix to use in generating the
configs.
q (numpy.ndarray): q-vector that the resulting supercell should be
compatible with.
nrattle (int): number of additional, empty configs to include via
:meth:`quippy.Atoms.rattle`.
"""
if method == "hessian":
dmd = self.hessian()
elif method == "vasp_hessian":
dmd = self.vasp_hessian()
else:
dmd = self.dynmat(supercell, q)
hname = "hessian1"
seed = quippy.Atoms()
seed.copy_from(dmd["template"])
result = quippy.AtomsList()
result.append(dmd["template"])
#Delete the force, energy and virial information from the copy, so that
#we don't duplicate it all over.
del seed.params["dft_energy"]
del seed.params["dft_virial"]
del seed.properties["dft_force"]
for l, v in zip(dmd["eigvals"], dmd["eigvecs"]):
atc = seed.copy()
#Add this eigenvector to its own configuration.
atc.add_property(hname, 0.0, n_cols=3)
H = np.reshape(v.real, (atc.n, 3)).T
setattr(atc, hname, H)
#Same thing for the eigenvalue. Then save it to the group folder
#structure.
atc.params.set_value(hname, l)
atc.params.set_value("n_hessian", 1)
#atc.add_property("force", 0.0, n_cols=3)
result.append(atc)
for i in range(nrattle):
atRand = seed.copy()
quippy.randomise(atRand.pos, 0.2)
result.append(atRand)
# atz = seed.copy()
# atz.add_property("dft_force", 0.0, n_cols=3)
#atz.params.set_value("dft_energy",
return result
def vasp_hessian(self):
"""Extracts the hessian from `vasprun.xml`.
"""
import xml.etree.ElementTree as ET
tree = ET.parse('vasprun.xml')
root = tree.getroot()
calc = root.getchildren()[-2]
dynm = calc.find("dynmat")
hessian = dynm.getchildren()[0]
H = []
for v in hessian.getchildren():
H.append(map(float, v.text.split()))
H = -np.array(H)
eigvals, eigvecs = np.linalg.eigh(H)
Na = self.primitive.n * int(np.linalg.det(self.supercell))
result = {
"template": self.parent,
"eigvals": [],
"eigvecs": [],
"hessian": H
}
for i, l in enumerate(eigvals):
if np.abs(l) > 1e-3:
result["eigvals"].append(l)
result["eigvecs"].append(eigvecs[:, i].reshape(Na, 3))
return result
def hessian(self):
"""Returns the non-zero eigenvalues and their corresponding eigenvectors.
"""
supercell = self.phonopy.get_supercell()
Na = supercell.get_number_of_atoms()
Nf = Na * 3
H = self.phonopy._dynamical_matrix._force_constants.reshape((Nf, Nf))
eigvals, eigvecs = np.linalg.eigh(H)
result = {
"template": phonopy_to_ase(supercell),
"eigvals": [],
"eigvecs": []
}
for i, l in enumerate(eigvals):
if np.abs(l) > 0.1:
result["eigvals"].append(l)
result["eigvecs"].append(eigvecs[:, i].reshape(Na, 3))
return result
def dynmat(self, supercell, q=None, cutoff=0.1):
"""Returns the non-zero eigenvalues and their corresponding eigenvectors
for the specified supercell.
Args:
supercell (numpy.ndarray): supercell matrix to use in generating the
configs.
q (numpy.ndarray): q-vector that the resulting supercell should be
compatible with.
cutoff (float): minimum value an eigenvalue should have before it is
included in the set.
"""
#We need to determine the supercell matrix that is compatible with the
#given `q` and has `N` atoms.
scell = get_supercell(self.primitive, supercell)
eigvals, eigvecs = self.diagonalize(q)
result = {
"template": phonopy_to_ase(scell),
"eigvals": [],
"eigvecs": []
}
for i, l in enumerate(eigvals):
if np.abs(l) > 0.1:
meigvec = self._map_eigvec_supercell(scell, eigvecs[:, i])
result["eigvals"].append(l)
result["eigvecs"].append(meigvec)
return result
def _get_dynmatrix(self):
"""Extracts the force constants from `FORCE_SETS` and constructs the
dynamical matrix for the calculation.
"""
with chdir(self.folder):
force_sets = file_IO.parse_FORCE_SETS()
self.phonopy.set_displacement_dataset(force_sets)
self.phonopy.produce_force_constants(
calculate_full_force_constants=True,
computation_algorithm="svd")
self.phonopy._set_dynamical_matrix()
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
def get_phonon(structure,
NAC=False,
setup_forces=True,
super_cell_phonon=np.identity(3),
primitive_axis=np.identity(3)):
phonon = Phonopy(structure, super_cell_phonon,
primitive_matrix=primitive_axis,
symprec=1e-5)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(structure.get_force_sets().get_dict())
phonon.produce_force_constants(computation_algorithm="svd")
structure.set_force_constants(ForceConstants(phonon.get_force_constants(),
supercell=structure.get_force_sets().get_supercell()))
else:
print('No force sets/constants available!')
exit()
if NAC:
print("Using non-analytical corrections")
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, is_symmetry=True)
phonon.set_nac_params(nac_params=nac_params)
return phonon
def _get_phonon(self):
cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
phonon = Phonopy(cell,
np.diag([2, 2, 2]),
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0]])
filename = os.path.join(data_dir, "..", "FORCE_SETS_NaCl")
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonon.symmetrize_force_constants()
filename_born = os.path.join(data_dir, "..", "BORN_NaCl")
nac_params = parse_BORN(phonon.get_primitive(), filename=filename_born)
phonon.set_nac_params(nac_params)
return phonon
def get_phonon(structure, NAC=False, setup_forces=True, custom_supercell=None):
if custom_supercell is None:
super_cell_phonon = structure.get_supercell_phonon()
else:
super_cell_phonon = custom_supercell
# Preparing the bulk type object
bulk = PhonopyAtoms(symbols=structure.get_atomic_elements(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell())
phonon = Phonopy(bulk, super_cell_phonon,
primitive_matrix=structure.get_primitive_matrix(),
symprec=1e-5)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(structure.get_force_sets().get_dict())
phonon.produce_force_constants()
structure.set_force_constants(ForceConstants(phonon.get_force_constants(),
supercell=structure.get_force_sets().get_supercell()))
else:
print('No force sets/constants available!')
exit()
if NAC:
print("Warning: Using Non Analytical Corrections")
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, is_symmetry=True)
phonon.set_nac_params(nac_params=nac_params)
return phonon