class Phono4py:
def __init__(
self,
unitcell,
supercell_matrix,
primitive_matrix=None,
mesh=None,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_symmetry=True,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo="L",
):
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
if mesh is None:
self._mesh = None
else:
self._mesh = np.array(mesh, dtype="intc")
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_symmetry = is_symmetry
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
self._supercells_with_displacements = None
self._displacement_dataset = None
if band_indices is None:
num_band = self._primitive.get_number_of_atoms() * 3
self._band_indices = [np.arange(num_band, dtype="intc")]
else:
self._band_indices = band_indices
self._band_indices_flatten = np.array([x for bi in self._band_indices for x in bi], dtype="intc")
self._symmetry = Symmetry(self._supercell, self._symprec, self._is_symmetry)
self._frequency_shifts = None
def get_fc2(self):
return self._fc2
def set_fc2(self, fc2):
self._fc2 = fc2
def get_fc3(self):
return self._fc3
def set_fc3(self, fc3):
self._fc3 = fc3
def get_fc4(self):
return self._fc4
def set_fc4(self, fc4):
self._fc4 = fc4
def get_primitive(self):
return self._primitive
def get_unitcell(self):
return self._unitcell
def get_supercell(self):
return self._supercell
def get_symmetry(self):
return self._symmetry
def get_displacement_dataset(self):
return self._displacement_dataset
def get_supercells_with_displacements(self):
if self._supercells_with_displacements is None:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def generate_displacements(self, distance=0.03, is_plusminus="auto", is_diagonal=True):
direction_dataset = get_fourth_order_displacements(
self._supercell, self._symmetry, is_plusminus=is_plusminus, is_diagonal=is_diagonal
)
self._displacement_dataset = direction_to_displacement(direction_dataset, distance, self._supercell)
def produce_fc4(
self,
forces_fc4,
displacement_dataset,
translational_symmetry_type=0,
is_permutation_symmetry=False,
is_permutation_symmetry_fc3=False,
is_permutation_symmetry_fc2=False,
):
disp_dataset = displacement_dataset
file_count = 0
for disp1 in disp_dataset["first_atoms"]:
disp1["forces"] = forces_fc4[file_count]
file_count += 1
self._fc2 = get_fc2(self._supercell, self._symmetry, disp_dataset)
if is_permutation_symmetry_fc2:
set_permutation_symmetry(self._fc2)
if translational_symmetry_type:
set_translational_invariance(self._fc2, translational_symmetry_type=translational_symmetry_type)
for disp1 in disp_dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
disp2["forces"] = forces_fc4[file_count]
disp2["delta_forces"] = disp2["forces"] - disp1["forces"]
file_count += 1
self._fc3 = get_fc3(
self._supercell,
disp_dataset,
self._fc2,
self._symmetry,
translational_symmetry_type=translational_symmetry_type,
is_permutation_symmetry=is_permutation_symmetry_fc3,
verbose=self._log_level,
)
for disp1 in disp_dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
for disp3 in disp2["third_atoms"]:
disp3["delta_forces"] = forces_fc4[file_count] - disp2["forces"]
file_count += 1
self._fc4 = get_fc4(
self._supercell,
disp_dataset,
self._fc3,
self._symmetry,
translational_symmetry_type=translational_symmetry_type,
is_permutation_symmetry=is_permutation_symmetry,
verbose=self._log_level,
)
def set_frequency_shift(self, temperatures=None):
self._interaction = FrequencyShift(
self._fc4,
self._supercell,
self._primitive,
self._mesh,
temperatures=temperatures,
band_indices=self._band_indices_flatten,
frequency_factor_to_THz=self._frequency_factor_to_THz,
is_nosym=self._is_nosym,
symprec=self._symprec,
cutoff_frequency=self._cutoff_frequency,
log_level=self._log_level,
lapack_zheev_uplo=self._lapack_zheev_uplo,
)
self._grid_address = self._interaction.get_grid_address()
self._frequencies = self._interaction.get_phonons()[0]
self._temperatures = temperatures
def set_dynamical_matrix(
self, fc2, supercell, primitive, nac_params=None, nac_q_direction=None, frequency_scale_factor=None
):
self._interaction.set_dynamical_matrix(
fc2, supercell, primitive, nac_params=nac_params, frequency_scale_factor=frequency_scale_factor
)
self._interaction.set_nac_q_direction(nac_q_direction=nac_q_direction)
def run_frequency_shift(self, grid_points):
if self._log_level:
print "------------------------",
print "Frequency shifts of fc4 ",
print "------------------------"
freq_shifts = []
num_band = len(self._band_indices_flatten)
for i, gp in enumerate(grid_points):
qpoint = self._grid_address[gp].astype(float) / self._mesh
if self._log_level:
print "=========================",
print "Grid point %d (%d/%d)" % (gp, i + 1, len(grid_points)),
print "========================="
print "q-point:", qpoint
self._interaction.set_grid_point(gp)
self._interaction.run()
f_shifts_at_temps = self._interaction.get_frequency_shifts()
if self._log_level:
print "Harmonic phonon frequencies:"
freqs = self._frequencies[gp][self._band_indices_flatten]
print "%7s " % "",
print ("%8.4f " * num_band) % tuple(freqs)
print "Frequency shifts:"
for t, f_shift in zip(self._temperatures, f_shifts_at_temps):
print "%7.1f " % t,
print ("%8.4f " * num_band) % tuple(f_shift)
freq_shifts.append(f_shifts_at_temps)
self._frequency_shifts = np.array(freq_shifts, dtype="double")
for i, gp in enumerate(grid_points):
for j, bi in enumerate(self._band_indices):
pos = 0
for k in range(j):
pos += len(self._band_indices[k])
write_frequency_shift(gp, bi, self._temperatures, freq_shifts[i][:, pos : (pos + len(bi))], self._mesh)
def get_frequency_shift(self):
return self._frequency_shifts
def _build_supercells_with_displacements(self):
supercells = []
magmoms = self._supercell.get_magnetic_moments()
masses = self._supercell.get_masses()
numbers = self._supercell.get_atomic_numbers()
lattice = self._supercell.get_cell()
for disp1 in self._displacement_dataset["first_atoms"]:
disp_cart1 = disp1["displacement"]
positions = self._supercell.get_positions()
positions[disp1["number"]] += disp_cart1
supercells.append(
Atoms(numbers=numbers, masses=masses, magmoms=magmoms, positions=positions, cell=lattice, pbc=True)
)
for disp1 in self._displacement_dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
positions = self._supercell.get_positions()
positions[disp1["number"]] += disp_cart1
positions[disp2["number"]] += disp2["displacement"]
supercells.append(
Atoms(numbers=numbers, masses=masses, magmoms=magmoms, positions=positions, cell=lattice, pbc=True)
)
for disp1 in self._displacement_dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
for disp3 in disp2["third_atoms"]:
positions = self._supercell.get_positions()
positions[disp1["number"]] += disp_cart1
positions[disp2["number"]] += disp2["displacement"]
positions[disp3["number"]] += disp3["displacement"]
supercells.append(
Atoms(
numbers=numbers, masses=masses, magmoms=magmoms, positions=positions, cell=lattice, pbc=True
)
)
self._supercells_with_displacements = supercells
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell, self._supercell_matrix, self._symprec)
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
self._primitive = self._get_primitive_cell(self._supercell, self._supercell_matrix, self._primitive_matrix)
def _get_primitive_cell(self, supercell, supercell_matrix, primitive_matrix):
inv_supercell_matrix = np.linalg.inv(supercell_matrix)
if primitive_matrix is None:
t_mat = inv_supercell_matrix
else:
t_mat = np.dot(inv_supercell_matrix, primitive_matrix)
return get_primitive(supercell, t_mat, self._symprec)
class Phono4py:
def __init__(self,
unitcell,
supercell_matrix,
primitive_matrix=None,
mesh=None,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_symmetry=True,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo='L'):
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
if mesh is None:
self._mesh = None
else:
self._mesh = np.array(mesh, dtype='intc')
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_symmetry = is_symmetry
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
self._supercells_with_displacements = None
self._displacement_dataset = None
if band_indices is None:
num_band = self._primitive.get_number_of_atoms() * 3
self._band_indices = [np.arange(num_band, dtype='intc')]
else:
self._band_indices = band_indices
self._band_indices_flatten = np.array(
[x for bi in self._band_indices for x in bi], dtype='intc')
self._symmetry = Symmetry(self._supercell, self._symprec,
self._is_symmetry)
self._frequency_shifts = None
def get_fc2(self):
return self._fc2
def set_fc2(self, fc2):
self._fc2 = fc2
def get_fc3(self):
return self._fc3
def set_fc3(self, fc3):
self._fc3 = fc3
def get_fc4(self):
return self._fc4
def set_fc4(self, fc4):
self._fc4 = fc4
def get_primitive(self):
return self._primitive
def get_unitcell(self):
return self._unitcell
def get_supercell(self):
return self._supercell
def get_symmetry(self):
return self._symmetry
def get_displacement_dataset(self):
return self._displacement_dataset
def get_supercells_with_displacements(self):
if self._supercells_with_displacements is None:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def generate_displacements(self,
distance=0.03,
is_plusminus='auto',
is_diagonal=True):
direction_dataset = get_fourth_order_displacements(
self._supercell,
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal)
self._displacement_dataset = direction_to_displacement(
direction_dataset, distance, self._supercell)
def produce_fc4(self,
forces_fc4,
displacement_dataset,
translational_symmetry_type=0,
is_permutation_symmetry=False,
is_permutation_symmetry_fc3=False,
is_permutation_symmetry_fc2=False):
disp_dataset = displacement_dataset
file_count = 0
for disp1 in disp_dataset['first_atoms']:
disp1['forces'] = forces_fc4[file_count]
file_count += 1
self._fc2 = get_fc2(self._supercell, self._symmetry, disp_dataset)
if is_permutation_symmetry_fc2:
set_permutation_symmetry(self._fc2)
if translational_symmetry_type:
set_translational_invariance(
self._fc2,
translational_symmetry_type=translational_symmetry_type)
for disp1 in disp_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
disp2['forces'] = forces_fc4[file_count]
disp2['delta_forces'] = disp2['forces'] - disp1['forces']
file_count += 1
self._fc3 = get_fc3(
self._supercell,
disp_dataset,
self._fc2,
self._symmetry,
translational_symmetry_type=translational_symmetry_type,
is_permutation_symmetry=is_permutation_symmetry_fc3,
verbose=self._log_level)
for disp1 in disp_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
for disp3 in disp2['third_atoms']:
disp3['delta_forces'] = (forces_fc4[file_count] -
disp2['forces'])
file_count += 1
self._fc4 = get_fc4(
self._supercell,
disp_dataset,
self._fc3,
self._symmetry,
translational_symmetry_type=translational_symmetry_type,
is_permutation_symmetry=is_permutation_symmetry,
verbose=self._log_level)
def set_frequency_shift(self, temperatures=None):
self._interaction = FrequencyShift(
self._fc4,
self._supercell,
self._primitive,
self._mesh,
temperatures=temperatures,
band_indices=self._band_indices_flatten,
frequency_factor_to_THz=self._frequency_factor_to_THz,
is_nosym=self._is_nosym,
symprec=self._symprec,
cutoff_frequency=self._cutoff_frequency,
log_level=self._log_level,
lapack_zheev_uplo=self._lapack_zheev_uplo)
self._grid_address = self._interaction.get_grid_address()
self._frequencies = self._interaction.get_phonons()[0]
self._temperatures = temperatures
def set_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
nac_q_direction=None,
frequency_scale_factor=None):
self._interaction.set_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor)
self._interaction.set_nac_q_direction(nac_q_direction=nac_q_direction)
def run_frequency_shift(self, grid_points):
if self._log_level:
print "------------------------",
print "Frequency shifts of fc4 ",
print "------------------------"
freq_shifts = []
num_band = len(self._band_indices_flatten)
for i, gp in enumerate(grid_points):
qpoint = self._grid_address[gp].astype(float) / self._mesh
if self._log_level:
print "=========================",
print "Grid point %d (%d/%d)" % (gp, i + 1, len(grid_points)),
print "========================="
print "q-point:", qpoint
self._interaction.set_grid_point(gp)
self._interaction.run()
f_shifts_at_temps = self._interaction.get_frequency_shifts()
if self._log_level:
print "Harmonic phonon frequencies:"
freqs = self._frequencies[gp][self._band_indices_flatten]
print "%7s " % "",
print("%8.4f " * num_band) % tuple(freqs)
print "Frequency shifts:"
for t, f_shift in zip(self._temperatures, f_shifts_at_temps):
print "%7.1f " % t,
print("%8.4f " * num_band) % tuple(f_shift)
freq_shifts.append(f_shifts_at_temps)
self._frequency_shifts = np.array(freq_shifts, dtype='double')
for i, gp in enumerate(grid_points):
for j, bi in enumerate(self._band_indices):
pos = 0
for k in range(j):
pos += len(self._band_indices[k])
write_frequency_shift(gp, bi, self._temperatures,
freq_shifts[i][:, pos:(pos + len(bi))],
self._mesh)
def get_frequency_shift(self):
return self._frequency_shifts
def _build_supercells_with_displacements(self):
supercells = []
magmoms = self._supercell.get_magnetic_moments()
masses = self._supercell.get_masses()
numbers = self._supercell.get_atomic_numbers()
lattice = self._supercell.get_cell()
for disp1 in self._displacement_dataset['first_atoms']:
disp_cart1 = disp1['displacement']
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
supercells.append(
Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
for disp1 in self._displacement_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
positions[disp2['number']] += disp2['displacement']
supercells.append(
Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
for disp1 in self._displacement_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
for disp3 in disp2['third_atoms']:
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
positions[disp2['number']] += disp2['displacement']
positions[disp3['number']] += disp3['displacement']
supercells.append(
Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
self._supercells_with_displacements = supercells
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell, self._supercell_matrix,
self._symprec)
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
self._primitive = self._get_primitive_cell(self._supercell,
self._supercell_matrix,
self._primitive_matrix)
def _get_primitive_cell(self, supercell, supercell_matrix,
primitive_matrix):
inv_supercell_matrix = np.linalg.inv(supercell_matrix)
if primitive_matrix is None:
t_mat = inv_supercell_matrix
else:
t_mat = np.dot(inv_supercell_matrix, primitive_matrix)
return get_primitive(supercell, t_mat, self._symprec)
class Phono4py:
def __init__(self,
fc4,
supercell,
primitive,
mesh,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo='L'):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._mesh = np.intc(mesh)
if band_indices is None:
self._band_indices = [
np.arange(primitive.get_number_of_atoms() * 3)
]
else:
self._band_indices = band_indices
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
self._band_indices_flatten = np.intc(
[x for bi in self._band_indices for x in bi])
self._frequency_shifts = None
def set_frequency_shift(self, temperatures=None):
self._interaction = FrequencyShift(
self._fc4,
self._supercell,
self._primitive,
self._mesh,
temperatures=temperatures,
band_indices=self._band_indices_flatten,
frequency_factor_to_THz=self._frequency_factor_to_THz,
is_nosym=self._is_nosym,
symprec=self._symprec,
cutoff_frequency=self._cutoff_frequency,
log_level=self._log_level,
lapack_zheev_uplo=self._lapack_zheev_uplo)
def set_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
nac_q_direction=None,
frequency_scale_factor=None):
self._interaction.set_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor)
self._interaction.set_nac_q_direction(nac_q_direction=nac_q_direction)
def run_frequency_shift(self, grid_points):
if self._log_level:
print "----- Frequency shifts of fc4 -----"
freq_shifts = []
for i, gp in enumerate(grid_points):
if self._log_level:
print "=====================",
print "Grid point %d (%d/%d)" % (gp, i + 1, len(grid_points)),
print "====================="
self._interaction.set_grid_point(gp)
self._interaction.run()
freq_shifts.append(self._interaction.get_frequency_shifts())
self._frequency_shifts = np.double(freq_shifts)
print self._frequency_shifts
def get_frequency_shift(self):
return self._frequency_shifts
class Phono4py:
def __init__(self,
fc4,
supercell,
primitive,
mesh,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo='L'):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._mesh = np.intc(mesh)
if band_indices is None:
self._band_indices = [
np.arange(primitive.get_number_of_atoms() * 3)]
else:
self._band_indices = band_indices
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
self._band_indices_flatten = np.intc(
[x for bi in self._band_indices for x in bi])
self._frequency_shifts = None
def set_frequency_shift(self, temperatures=None):
self._interaction = FrequencyShift(
self._fc4,
self._supercell,
self._primitive,
self._mesh,
temperatures=temperatures,
band_indices=self._band_indices_flatten,
frequency_factor_to_THz=self._frequency_factor_to_THz,
is_nosym=self._is_nosym,
symprec=self._symprec,
cutoff_frequency=self._cutoff_frequency,
log_level=self._log_level,
lapack_zheev_uplo=self._lapack_zheev_uplo)
def set_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
nac_q_direction=None,
frequency_scale_factor=None):
self._interaction.set_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor)
self._interaction.set_nac_q_direction(nac_q_direction=nac_q_direction)
def run_frequency_shift(self, grid_points):
if self._log_level:
print "----- Frequency shifts of fc4 -----"
freq_shifts = []
for i, gp in enumerate(grid_points):
if self._log_level:
print "=====================",
print "Grid point %d (%d/%d)" % (gp, i + 1, len(grid_points)),
print "====================="
self._interaction.set_grid_point(gp)
self._interaction.run()
freq_shifts.append(self._interaction.get_frequency_shifts())
self._frequency_shifts = np.double(freq_shifts)
print self._frequency_shifts
def get_frequency_shift(self):
return self._frequency_shifts