def get_phonon(structure, NAC=False, setup_forces=True, custom_supercell=None):
super_cell_phonon = structure.get_supercell_phonon()
if not(isinstance(custom_supercell, type(None))):
super_cell_phonon = custom_supercell
#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, super_cell_phonon,
primitive_matrix=structure.get_primitive_matrix())
# 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 not structure.forces_available():
# if not np.array(structure.get_force_constants()).any() and not np.array(structure.get_force_sets()).any():
print('No force sets/constants available!')
exit()
if np.array(structure.get_force_constants()).any():
phonon.set_force_constants(structure.get_force_constants())
else:
phonon.set_displacement_dataset(structure.get_force_sets())
phonon.produce_force_constants(computation_algorithm="svd")
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 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,
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,
symprec=1e-5):
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=symprec)
# 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
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 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
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()