def produce_fc2(self,
forces_fc2,
displacement_dataset=None,
symmetrize_fc2=False,
is_compact_fc=False,
use_alm=False):
if displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = displacement_dataset
if use_alm:
from phono3py.other.alm_wrapper import get_fc2 as get_fc2_alm
self._fc2 = get_fc2_alm(self._phonon_supercell, forces_fc2,
disp_dataset,
self._phonon_supercell_symmetry)
else:
for forces, disp1 in zip(forces_fc2, disp_dataset['first_atoms']):
disp1['forces'] = forces
if is_compact_fc:
p2s_map = self._phonon_primitive.get_primitive_to_supercell_map(
)
else:
p2s_map = None
self._fc2 = get_fc2(self._phonon_supercell,
self._phonon_supercell_symmetry,
disp_dataset,
atom_list=p2s_map)
if symmetrize_fc2:
if is_compact_fc:
symmetrize_compact_force_constants(self._fc2,
self._phonon_primitive)
else:
symmetrize_force_constants(self._fc2)
def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
if input_filename is None:
filename = "fc2.hdf5"
else:
filename = "fc2." + input_filename + ".hdf5"
file_exists(filename, log_level)
if log_level:
print('Reading fc2 from "%s".' % filename)
num_atom = phono3py.phonon_supercell.get_number_of_atoms()
p2s_map = phono3py.phonon_primitive.p2s_map
try:
phonon_fc2 = read_fc2_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
if phonon_fc2.shape[1] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc2:
if phonon_fc2.shape[0] == phonon_fc2.shape[1]:
symmetrize_force_constants(phonon_fc2)
else:
symmetrize_compact_force_constants(phonon_fc2,
phono3py.phonon_primitive)
phono3py.fc2 = phonon_fc2
def _extract_fc_list(self):
fc_list = []
for fc_filename in self._fc_filenames:
force_constants = parse_FORCE_CONSTANTS(fc_filename)
symmetrize_force_constants(force_constants)
fc_list.append(force_constants)
return fc_list
def produce_fc3(
self,
forces_fc3,
displacement_dataset=None,
cutoff_distance=None, # set fc3 zero
symmetrize_fc3r=False,
is_compact_fc=False,
use_alm=False,
alm_options=None):
if displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = displacement_dataset
if use_alm:
from phono3py.other.alm_wrapper import get_fc3 as get_fc3_alm
fc2, fc3 = get_fc3_alm(self._supercell,
self._primitive,
forces_fc3,
disp_dataset,
self._symmetry,
alm_options=alm_options,
is_compact_fc=is_compact_fc,
log_level=self._log_level)
else:
fc2, fc3 = self._get_fc3(forces_fc3,
disp_dataset,
is_compact_fc=is_compact_fc)
if symmetrize_fc3r:
if is_compact_fc:
set_translational_invariance_compact_fc3(
fc3, self._primitive)
set_permutation_symmetry_compact_fc3(fc3, self._primitive)
if self._fc2 is None:
symmetrize_compact_force_constants(
fc2, self._primitive)
else:
set_translational_invariance_fc3(fc3)
set_permutation_symmetry_fc3(fc3)
if self._fc2 is None:
symmetrize_force_constants(fc2)
# Set fc2 and fc3
self._fc3 = fc3
# Normally self._fc2 is overwritten in produce_fc2
if self._fc2 is None:
self._fc2 = fc2
def produce_fc2(self,
forces_fc2,
displacement_dataset=None,
symmetrize_fc2=False,
is_compact_fc=False,
use_alm=False,
alm_options=None):
if displacement_dataset is None:
if self._phonon_displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = self._phonon_displacement_dataset
else:
disp_dataset = displacement_dataset
for forces, disp1 in zip(forces_fc2, disp_dataset['first_atoms']):
disp1['forces'] = forces
if is_compact_fc:
p2s_map = self._phonon_primitive.p2s_map
else:
p2s_map = None
if use_alm:
from phonopy.interface.alm import get_fc2 as get_fc2_alm
self._fc2 = get_fc2_alm(self._phonon_supercell,
self._phonon_primitive,
disp_dataset,
atom_list=p2s_map,
alm_options=alm_options,
log_level=self._log_level)
else:
self._fc2 = get_fc2(self._phonon_supercell,
self._phonon_supercell_symmetry,
disp_dataset,
atom_list=p2s_map)
if symmetrize_fc2:
if is_compact_fc:
symmetrize_compact_force_constants(
self._fc2, self._phonon_primitive)
else:
symmetrize_force_constants(self._fc2)
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
return self
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
self._set_dynamical_matrix()
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
return self
def produce_fc3(
self,
forces_fc3=None,
displacement_dataset=None,
cutoff_distance=None, # set fc3 zero
symmetrize_fc3r=False,
is_compact_fc=False,
fc_calculator=None,
fc_calculator_options=None):
"""Calculate fc3 from displacements and forces
Parameters
----------
forces_fc3 :
Dummy argument
displacement_dataset : dict
Displacements in supercells. There are two types of formats.
Type 1. Two atomic displacement in each supercell:
{'natom': number of atoms in supercell,
'first_atoms': [
{'number': atom index of first displaced atom,
'displacement': displacement in Cartesian coordinates,
'forces': forces on atoms in supercell,
'second_atoms': [
{'number': atom index of second displaced atom,
'displacement': displacement in Cartesian coordinates},
'forces': forces on atoms in supercell,
... ] }, ... ] }
Type 2. All atomic displacements in each supercell:
{'displacements': ndarray, dtype='double', order='C',
shape=(supercells, atoms in supercell, 3)
'forces': ndarray, dtype='double',, order='C',
shape=(supercells, atoms in supercell, 3)}
In type 2, displacements and forces can be given by numpy array
with different shape but that can be reshaped to
(supercells, natom, 3).
cutoff_distance : float
After creating force constants, fc elements where any pair
distance in atom triplets larger than cutoff_distance are set zero.
symmetrize_fc3r : bool
Only for type 1 displacement_dataset, translational and
permutation symmetries are applied after creating fc3. This
symmetrization is not very sophisticated and can break space
group symmetry, but often useful. If better symmetrization is
expected, it is recommended to use external force constants
calculator such as ALM. Default is False.
is_compact_fc : bool
fc3 shape is
False: (supercell, supercell, supecell, 3, 3, 3)
True: (primitive, supercell, supecell, 3, 3, 3)
where 'supercell' and 'primitive' indicate number of atoms in these
cells. Default is False.
fc_calculator : str or None
Force constants calculator given by str.
fc_calculator_options : dict
Options for external force constants calculator.
"""
if displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = displacement_dataset
if forces_fc3 is not None:
self.forces = forces_fc3
msg = ("Forces have to be stored in disp_dataset as written in "
"this method's docstring for the type1 dataset.")
warnings.warn(msg, DeprecationWarning)
if fc_calculator is not None:
from phono3py.other.fc_calculator import (
get_fc3, get_displacements_and_forces_fc3)
disps, forces = get_displacements_and_forces_fc3(disp_dataset)
fc2, fc3 = get_fc3(self._supercell,
self._primitive,
disps,
forces,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
is_compact_fc=is_compact_fc,
log_level=self._log_level)
else:
fc2, fc3 = get_phono3py_fc3(self._supercell,
self._primitive,
disp_dataset,
self._symmetry,
is_compact_fc=is_compact_fc,
verbose=self._log_level)
if symmetrize_fc3r:
if is_compact_fc:
set_translational_invariance_compact_fc3(
fc3, self._primitive)
set_permutation_symmetry_compact_fc3(fc3, self._primitive)
if self._fc2 is None:
symmetrize_compact_force_constants(
fc2, self._primitive)
else:
set_translational_invariance_fc3(fc3)
set_permutation_symmetry_fc3(fc3)
if self._fc2 is None:
symmetrize_force_constants(fc2)
# Set fc2 and fc3
self._fc3 = fc3
# Normally self._fc2 is overwritten in produce_fc2
if self._fc2 is None:
self._fc2 = fc2
def produce_fc2(self,
forces_fc2=None,
displacement_dataset=None,
symmetrize_fc2=False,
is_compact_fc=False,
fc_calculator=None,
fc_calculator_options=None):
"""Calculate fc2 from displacements and forces
Parameters
----------
forces_fc2 :
Dummy argument
displacement_dataset : dict
Displacements in supercells. There are two types of formats.
Type 1. Two atomic displacement in each supercell:
{'natom': number of atoms in supercell,
'first_atoms': [
{'number': atom index of first displaced atom,
'displacement': displacement in Cartesian coordinates,
'forces': forces on atoms in supercell,
'second_atoms': [
{'number': atom index of second displaced atom,
'displacement': displacement in Cartesian coordinates},
'forces': forces on atoms in supercell,
... ] }, ... ] }
Type 2. All atomic displacements in each supercell:
{'displacements': ndarray, dtype='double', order='C',
shape=(supercells, atoms in supercell, 3)
'forces': ndarray, dtype='double',, order='C',
shape=(supercells, atoms in supercell, 3)}
In type 2, displacements and forces can be given by numpy array
with different shape but that can be reshaped to
(supercells, natom, 3).
symmetrize_fc2 : bool
Only for type 1 displacement_dataset, translational and
permutation symmetries are applied after creating fc3. This
symmetrization is not very sophisticated and can break space
group symmetry, but often useful. If better symmetrization is
expected, it is recommended to use external force constants
calculator such as ALM. Default is False.
is_compact_fc : bool
fc2 shape is
False: (supercell, supecell, 3, 3)
True: (primitive, supecell, 3, 3)
where 'supercell' and 'primitive' indicate number of atoms in these
cells. Default is False.
fc_calculator : str or None
Force constants calculator given by str.
fc_calculator_options : dict
Options for external force constants calculator.
"""
if displacement_dataset is None:
if self._phonon_displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = self._phonon_displacement_dataset
else:
disp_dataset = displacement_dataset
if forces_fc2 is not None:
self.phonon_forces = forces_fc2
msg = ("Forces have to be stored in disp_dataset as written in "
"this method's docstring for the type1 dataset.")
warnings.warn(msg, DeprecationWarning)
if is_compact_fc:
p2s_map = self._phonon_primitive.p2s_map
else:
p2s_map = None
if fc_calculator is not None:
disps, forces = get_displacements_and_forces(disp_dataset)
self._fc2 = get_fc2(self._phonon_supercell,
self._phonon_primitive,
disps,
forces,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
atom_list=p2s_map,
log_level=self._log_level)
else:
self._fc2 = get_phonopy_fc2(self._phonon_supercell,
self._phonon_supercell_symmetry,
disp_dataset,
atom_list=p2s_map)
if symmetrize_fc2:
if is_compact_fc:
symmetrize_compact_force_constants(self._fc2,
self._phonon_primitive)
else:
symmetrize_force_constants(self._fc2)
def symmetrize_force_constants(self):
symmetrize_force_constants(self._force_constants)
self._set_dynamical_matrix()
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
force_to_eVperA=None,
distance_to_A=None,
compression=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3r = (settings.get_is_symmetrize_fc3_r() or
settings.get_fc_symmetry())
symmetrize_fc3q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = (settings.get_is_symmetrize_fc2() or
settings.get_fc_symmetry())
if settings.get_use_alm_fc2():
symmetrize_fc2 = False
if settings.get_use_alm_fc3():
symmetrize_fc3r = False
alm_options = None
if settings.get_use_alm_fc3() or settings.get_use_alm_fc2():
if settings.get_alm_options() is not None:
alm_option_types = {'solver': str,
'cutoff_distance': float}
alm_options = {}
for option_str in settings.get_alm_options().split(","):
key, val = [x.strip() for x in option_str.split('=')[:2]]
if key.lower() in alm_option_types:
option_value = alm_option_types[key.lower()](val)
alm_options[key.lower()] = option_value
if log_level:
show_phono3py_force_constants_settings(read_fc3,
read_fc2,
symmetrize_fc3r,
symmetrize_fc3q,
symmetrize_fc2,
settings)
# fc3
if (settings.get_is_joint_dos() or
(settings.get_is_isotope() and
not (settings.get_is_bterta() or settings.get_is_lbte())) or
settings.get_read_gamma() or
settings.get_read_pp() or
settings.get_write_phonon() or
settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
if input_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc3 from %s" % filename)
p2s_map = phono3py.get_primitive().get_primitive_to_supercell_map()
try:
fc3 = read_fc3_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[1] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc3r:
set_translational_invariance_fc3(fc3)
set_permutation_symmetry_fc3(fc3)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc3r,
symmetrize_fc2,
input_filename,
output_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc3(),
alm_options,
compression,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
cutoff_distance = settings.get_cutoff_fc3_distance()
if cutoff_distance is not None and cutoff_distance > 0:
if log_level:
print("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
phono3py.cutoff_fc3_by_zero(cutoff_distance)
if log_level:
show_drift_fc3(phono3py.get_fc3(),
primitive=phono3py.get_primitive())
# fc2
phonon_primitive = phono3py.get_phonon_primitive()
phonon_supercell = phono3py.get_phonon_supercell()
p2s_map = phonon_primitive.get_primitive_to_supercell_map()
if read_fc2:
if input_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print("Reading fc2 from %s" % filename)
num_atom = phonon_supercell.get_number_of_atoms()
try:
phonon_fc2 = read_fc2_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
if phonon_fc2.shape[1] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc2:
if phonon_fc2.shape[0] == phonon_fc2.shape[1]:
symmetrize_force_constants(phonon_fc2)
else:
symmetrize_compact_force_constants(phonon_fc2,
phonon_primitive)
phono3py.set_fc2(phonon_fc2)
else:
if phonon_supercell_matrix is None:
if not _create_phono3py_fc2(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc2,
input_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc2(),
alm_options,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc2,
input_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc2(),
alm_options,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(),
filename=filename,
p2s_map=p2s_map,
compression=compression)
if log_level:
show_drift_force_constants(phono3py.get_fc2(),
primitive=phonon_primitive,
name='fc2')
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
self._set_dynamical_matrix()