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Phono3py is going to be modular to be handled from __init__.py.

This commit is contained in:
Atsushi Togo 2014-01-29 16:45:11 +09:00
parent 6754f692f1
commit 4da57f778b
3 changed files with 501 additions and 419 deletions
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83
anharmonic/file_IO.py
View File

@ -357,6 +357,47 @@ def write_supercells_with_three_displacements(supercell,
w3.close()
w4.close()
def write_FORCES_FC3(vaspruns,
disp_dataset,
forces_fc3='FORCES_FC3'):
natom = disp_dataset['natom']
num_disp1 = len(disp_dataset['first_atoms'])
set_of_forces = get_forces_from_vasprun_xmls(vaspruns, natom)
w3 = open(forces_fc3, 'w')
for i, disp1 in enumerate(disp_dataset['first_atoms']):
w3.write("# File: %-5d\n" % (i + 1))
w3.write("# %-5d " % (disp1['number'] + 1))
w3.write("%20.16f %20.16f %20.16f\n" %
tuple(disp1['displacement']))
for forces in set_of_forces[i]:
w3.write("%15.10f %15.10f %15.10f\n" % (tuple(forces)))
count = num_disp1
file_count = num_disp1
for i, disp1 in enumerate(disp_dataset['first_atoms']):
atom1 = disp1['number']
for disp2 in disp1['second_atoms']:
atom2 = disp2['number']
w3.write("# File: %-5d\n" % (count + 1))
w3.write("# %-5d " % (atom1 + 1))
w3.write("%20.16f %20.16f %20.16f\n" % tuple(disp1['displacement']))
w3.write("# %-5d " % (atom2 + 1))
w3.write("%20.16f %20.16f %20.16f\n" % tuple(disp2['displacement']))
# For supercell calculation reduction
if disp2['included']:
for forces in set_of_forces[file_count]:
w3.write("%15.10f %15.10f %15.10f\n" % tuple(forces))
file_count += 1
else:
# for forces in set_of_forces[i]:
# w3.write("%15.10f %15.10f %15.10f\n" % (tuple(forces)))
for j in range(natom):
w3.write("%15.10f %15.10f %15.10f\n" % (0, 0, 0))
count += 1
w3.close()
def write_FORCES_THIRD(vaspruns,
disp_dataset,
forces_third='FORCES_THIRD',
@ -1147,6 +1188,21 @@ def parse_disp_yaml_to_disp_dataset(filename="disp.yaml"):
new_dataset['first_atoms'] = new_first_atoms
return new_dataset
def parse_disp_fc2_yaml(filename="disp_fc2.yaml"):
dataset = parse_yaml(filename)
natom = dataset['natom']
new_dataset = {}
new_dataset['natom'] = natom
new_first_atoms = []
for first_atoms in dataset['first_atoms']:
first_atoms['number'] -= 1
atom1 = first_atoms['number']
disp1 = first_atoms['displacement']
new_first_atoms.append({'number': atom1, 'displacement': disp1})
new_dataset['first_atoms'] = new_first_atoms
return new_dataset
def parse_disp_fc3_yaml(filename="disp_fc3.yaml"):
dataset = parse_yaml(filename)
natom = dataset['natom']
@ -1277,16 +1333,32 @@ def parse_FORCES_THIRD(disp_dataset,
third_forces = parse_force_lines(f3, num_atom)
disp2['forces'] = third_forces
def parse_FORCES_SECOND(disp_dataset,
filename="FORCES_SECOND"):
def parse_FORCES_SECOND(disp_dataset, filename="FORCES_SECOND"):
f2 = open(filename, 'r')
num_atom = disp_dataset['natom']
for disp1 in disp_dataset['first_atoms']:
second_forces = parse_force_lines(f2, num_atom)
disp1['forces'] = second_forces
def parse_FORCE_SETS_with_disp_dataset(disp_dataset,
filename="FORCE_SETS"):
def parse_FORCES_FC2(disp_dataset, filename="FORCES_FC2"):
num_atom = disp_dataset['natom']
num_disp = len(disp_dataset['first_atoms'])
f2 = open(filename, 'r')
forces_fc2 = [parse_force_lines(f2, num_atom) for i in range(num_disp)]
f2.close()
return forces_fc2
def parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3"):
num_atom = disp_dataset['natom']
num_disp = len(disp_dataset['first_atoms'])
for disp1 in disp_dataset['first_atoms']:
num_disp += len(disp1['second_atoms'])
f3 = open(filename, 'r')
forces_fc3 = [parse_force_lines(f3, num_atom) for i in range(num_disp)]
f3.close()
return forces_fc3
def parse_FORCE_SETS_with_disp_dataset(disp_dataset, filename="FORCE_SETS"):
f2 = open(filename, 'r')
num_atom = disp_dataset['natom']
force_sets = parse_FORCE_SETS(num_atom)
@ -1299,8 +1371,7 @@ def parse_DELTA_FC2_SETS(disp_dataset,
delta_fc2s = []
num_atom = disp_dataset['natom']
for first_disp in disp_dataset['first_atoms']:
first_disp['delta_fc2'] = parse_force_constants_lines(fc2_file,
num_atom)
first_disp['delta_fc2'] = parse_force_constants_lines(fc2_file, num_atom)
def parse_DELTA_FC2_FOURTH_SETS(disp_dataset,
filename='DELTA_FC2_FOURTH_SETS'):

145
anharmonic/phonon3/__init__.py
View File

@ -10,6 +10,10 @@ from anharmonic.phonon3.gruneisen import Gruneisen
from anharmonic.phonon3.displacement_fc3 import get_third_order_displacements, direction_to_displacement
from anharmonic.file_IO import write_frequency_shift, write_joint_dos
from anharmonic.other.isotope import Isotope
from phonopy.harmonic.force_constants import get_fc2, set_permutation_symmetry, \
set_translational_invariance
from anharmonic.phonon3.fc3 import get_fc3, set_permutation_symmetry_fc3, \
set_translational_invariance_fc3, cutoff_fc3, cutoff_fc3_by_zero
from phonopy.units import VaspToTHz
class Phono3py:
@ -74,26 +78,28 @@ class Phono3py:
self._frequency_points = None
self._temperatures = None
# Other variables
self._fc2 = None
self._fc3 = None
# Setup interaction
self._interaction = None
self._mesh = None
self._band_indices = None
self._band_indices_flatten = None
if mesh is not None:
self.set_phph_interaction(mesh, band_indices=band_indices)
# Other variables
self._fc2 = None
self._fc3 = None
def set_phph_interaction(self, mesh, band_indices=None):
self._mesh = np.array(mesh, dtype='intc')
self._mesh = np.array(mesh, dtype='intc')
if band_indices is None:
num_band = self._primitive.get_number_of_atoms() * 3
self._band_indices = [np.arange(num_band)]
else:
self._band_indices = band_indices
self._band_indices_flatten = np.hstack(self._band_indices).astype('intc')
def set_phph_interaction(self,
nac_params=None,
nac_q_direction=None,
frequency_scale_factor=None):
self._interaction = Interaction(
self._supercell,
self._primitive,
@ -106,14 +112,6 @@ class Phono3py:
is_nosym=self._is_nosym,
symmetrize_fc3_q=self._symmetrize_fc3_q,
lapack_zheev_uplo=self._lapack_zheev_uplo)
def get_interaction_strength(self):
return self._interaction
def set_dynamical_matrix(self,
nac_params=None,
nac_q_direction=None,
frequency_scale_factor=None):
self._interaction.set_dynamical_matrix(
self._fc2,
self._phonon_supercell,
@ -122,9 +120,103 @@ class Phono3py:
frequency_scale_factor=frequency_scale_factor)
self._interaction.set_nac_q_direction(nac_q_direction=nac_q_direction)
def get_interaction_strength(self):
return self._interaction
def produce_fc2(self,
forces_fc2,
disp_dataset,
is_permutation_symmetry=False,
is_translational_symmetry=False):
for forces, disp1 in zip(forces_fc2, disp_dataset['first_atoms']):
disp1['forces'] = forces
self._fc2 = get_fc2(self._phonon_supercell,
self._phonon_supercell_symmetry,
disp_dataset)
if is_permutation_symmetry:
set_permutation_symmetry(self._fc2)
if is_translational_symmetry:
set_translational_invariance(self._fc2)
def produce_fc3(self,
forces_fc3,
disp_dataset,
cutoff_distance=None, # set fc3 zero
is_translational_symmetry=False,
is_permutation_symmetry=False):
for forces, disp1 in zip(forces_fc3, disp_dataset['first_atoms']):
disp1['forces'] = forces
self._fc2 = get_fc2(self._supercell, self._symmetry, disp_dataset)
if is_permutation_symmetry:
set_permutation_symmetry(self._fc2)
if is_translational_symmetry:
set_translational_invariance(self._fc2)
count = len(disp_dataset['first_atoms'])
for disp1 in disp_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
disp2['delta_forces'] = forces_fc3[count] - disp1['forces']
count += 1
self._fc3 = get_fc3(
self._supercell,
disp_dataset,
self._fc2,
self._symmetry,
is_translational_symmetry=is_translational_symmetry,
is_permutation_symmetry=is_permutation_symmetry,
verbose=self._log_level)
# Reduction of number of supercell-force calculations
if 'cutoff_distance' in disp_dataset:
if self._log_level:
print ("Cutting-off fc3 (cut-off distance: %f)" %
disp_dataset['cutoff_distance'])
cutoff_fc3(self._fc3,
self._supercell,
disp_dataset,
self._symmetry,
verbose=self._log_level)
# Set fc3 elements zero beyond cutoff_distance
if cutoff_distance:
if self._log_level:
print ("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
self.cutoff_fc3_by_zero(cutoff_distance)
# Symmetrize fc3_r
if is_permutation_symmetry:
if self._log_level:
print "Symmetrizing fc3 in real space index exchange..."
set_permutation_symmetry_fc3(self._fc3)
def cutoff_fc3_by_zero(self, cutoff_distance):
cutoff_fc3_by_zero(self._fc3,
self._supercell,
cutoff_distance,
self._symprec)
def set_permutation_symmetry(self):
if self._fc2 is not None:
set_permutation_symmetry(self._fc2)
if self._fc3 is not None:
set_permutation_symmetry_fc3(self._fc3)
def set_translational_invariance(self):
if self._fc2 is not None:
set_translational_invariance(self._fc2)
if self._fc3 is not None:
set_translational_invariance_fc3(self._fc3)
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
@ -178,8 +270,7 @@ class Phono3py:
def run_imag_self_energy(self,
grid_points,
frequency_step=0.1,
temperatures=[0.0, 300.0],
output_filename=None):
temperatures=[0.0, 300.0]):
self._grid_points = grid_points
self._temperatures = temperatures
self._imag_self_energy, self._frequency_points = get_imag_self_energy(
@ -364,16 +455,16 @@ class Phono3py:
self._unitcell, self._phonon_supercell_matrix, self._symprec)
def _build_phonon_primitive_cell(self):
self._phonon_primitive = self._get_primitive_cell(
self._phonon_supercell,
self._phonon_supercell_matrix,
self._primitive_matrix)
if self._phonon_supercell_matrix is None:
self._phonon_primitive = self._primitive
else:
self._phonon_primitive = self._get_primitive_cell(
self._phonon_supercell,
self._phonon_supercell_matrix,
self._primitive_matrix)
def _get_primitive_cell(self, supercell, supercell_matrix, primitive_matrix):
if supercell_matrix is None:
inv_supercell_matrix = np.eye(3)
else:
inv_supercell_matrix = np.linalg.inv(supercell_matrix)
inv_supercell_matrix = np.linalg.inv(supercell_matrix)
if primitive_matrix is None:
t_mat = inv_supercell_matrix
else:

692
scripts/phono3py
View File

@ -40,25 +40,20 @@ import numpy as np
from optparse import OptionParser
from phonopy.interface.vasp import read_vasp
from phonopy.structure.cells import get_supercell, get_primitive, print_cell
from phonopy.structure.symmetry import Symmetry
from phonopy.harmonic.force_constants import get_fc2, get_force_constants, \
set_permutation_symmetry, symmetrize_force_constants, \
set_translational_invariance, show_drift_force_constants
from phonopy.structure.cells import print_cell
from phonopy.harmonic.force_constants import show_drift_force_constants
from phonopy.file_IO import parse_BORN, parse_FORCE_SETS
from phonopy.units import VaspToTHz
from anharmonic.phonon3.fc3 import get_fc3, set_permutation_symmetry_fc3, \
set_translational_invariance_fc3, show_drift_fc3, cutoff_fc3, \
cutoff_fc3_by_zero
from anharmonic.file_IO import write_fc2_dat, write_fc3_dat,\
parse_disp_fc3_yaml, write_FORCES_THIRD, parse_DELTA_FORCES, \
write_DELTA_FC2_SETS, parse_DELTA_FC2_SETS, parse_FORCES_SECOND, \
write_fc3_to_hdf5, write_fc2_to_hdf5, read_fc3_from_hdf5, \
read_fc2_from_hdf5, write_ir_grid_points, write_grid_address, \
write_supercells_with_displacements
from anharmonic.phonon3.fc3 import show_drift_fc3
from anharmonic.file_IO import parse_disp_fc2_yaml, parse_disp_fc3_yaml, \
parse_FORCES_FC2, parse_FORCES_FC3, write_FORCES_FC3, \
write_fc3_to_hdf5, write_fc2_to_hdf5, read_fc3_from_hdf5, \
read_fc2_from_hdf5, write_ir_grid_points, write_grid_address, \
write_supercells_with_displacements
from anharmonic.phonon3.triplets import get_coarse_ir_grid_points
from anharmonic.settings import Phono3pyConfParser
from anharmonic.phonon3 import Phono3py, Phono3pyJointDos, IsotopeScattering, get_gruneisen_parameters
from anharmonic.phonon3 import Phono3py, Phono3pyJointDos, IsotopeScattering, \
get_gruneisen_parameters
phono3py_version = "0.8.2"
@ -413,24 +408,7 @@ if options.forces_third_mode:
if log_level:
print "Displacement dataset is read from %s." % filename
disp_dataset = parse_disp_fc3_yaml()
write_FORCES_THIRD(args, disp_dataset)
print_end()
exit(0)
#########################
# Create DELTA_FC2_SETS #
#########################
# This may not work.
if options.delta_fc2_sets_mode:
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
file_exists(filename, log_level)
if log_level:
print "Displacement dataset is read from %s." % filename
disp_dataset = parse_disp_fc3_yaml()
write_DELTA_FC2_SETS(args, disp_dataset)
write_FORCES_FC3(args, disp_dataset)
print_end()
exit(0)
@ -502,25 +480,88 @@ if options.is_displacement:
##############
# Initialize #
##############
mesh = settings.get_mesh_numbers()
mesh_divs = settings.get_mesh_divisors()
grid_points = settings.get_grid_points()
band_indices = settings.get_band_indices()
cutoff_frequency = settings.get_cutoff_frequency()
if settings.get_multiple_sigmas() is None:
if settings.get_sigma():
sigmas = [settings.get_sigma()]
else:
sigmas = []
else:
sigmas = settings.get_multiple_sigmas()
if settings.get_is_tetrahedron_method():
sigmas = [None] + sigmas
if settings.get_temperatures() is None:
t_max=settings.get_max_temperature()
t_min=settings.get_min_temperature()
t_step=settings.get_temperature_step()
temperature_points = [0.0, 300.0] # For spectra
temperatures = np.arange(t_min, t_max + float(t_step) / 10, t_step)
else:
temperature_points = settings.get_temperatures() # For spectra
temperatures = settings.get_temperatures() # For others
if options.factor is None:
frequency_factor_to_THz = VaspToTHz
else:
frequency_factor_to_THz = options.factor
if settings.get_frequency_pitch() is None:
frequency_step = 0.1
else:
frequency_step = settings.get_frequency_pitch()
if options.freq_scale is None:
frequency_scale_factor = 1.0
else:
frequency_scale_factor = options.freq_scale
phono3py = Phono3py(
unitcell,
settings.get_supercell_matrix(),
primitive_matrix=settings.get_primitive_matrix(),
phonon_supercell_matrix=settings.get_phonon_supercell_matrix(),
symprec=options.symprec)
mesh=mesh,
band_indices=band_indices,
sigmas=sigmas,
cutoff_frequency=cutoff_frequency,
frequency_factor_to_THz=frequency_factor_to_THz,
is_symmetry=True,
is_nosym=options.is_nosym,
symmetrize_fc3_q=options.is_symmetrize_fc3_q,
symprec=options.symprec,
log_level=log_level,
lapack_zheev_uplo=options.uplo)
supercell = phono3py.get_supercell()
primitive = phono3py.get_primitive()
phonon_supercell = phono3py.get_phonon_supercell()
phonon_primitive = phono3py.get_phonon_primitive()
symmetry = phono3py.get_symmetry()
mesh = settings.get_mesh_numbers()
mesh_divs = settings.get_mesh_divisors()
#################
# Show settings #
#################
if log_level:
print "Spacegroup: ", symmetry.get_international_table()
print "---------------------------- primitive cell --------------------------------"
print_cell(primitive)
print "------------------------------- supercell ----------------------------------"
print_cell(supercell, mapping=primitive.get_supercell_to_primitive_map())
print "------------------ ratio (supercell for fc)/(primitive) --------------------"
for vec in np.dot(supercell.get_cell(), np.linalg.inv(primitive.get_cell())):
print "%5.2f"*3 % tuple(vec)
if settings.get_phonon_supercell_matrix() is not None:
print "-------------------- primitive cell for harmonic phonon ---------------------"
print_cell(phonon_primitive)
print "---------------------- supercell for harmonic phonon ------------------------"
print_cell(phonon_supercell, mapping=phonon_primitive.get_supercell_to_primitive_map())
print "--------------- ratio (phonon supercell)/(phonon primitive) -----------------"
for vec in np.dot(phonon_supercell.get_cell(),
np.linalg.inv(phonon_primitive.get_cell())):
print "%5.2f"*3 % tuple(vec)
print "----------------------------------------------------------------------------"
if options.is_translational_symmetry:
print "Translational symmetry:", options.is_translational_symmetry
if options.is_symmetrize_fc2:
@ -538,24 +579,6 @@ if log_level:
print "Supercell for harmonic phonon is introduced."
if settings.get_is_nac():
print "Non-analytical term correction:", settings.get_is_nac()
print "Spacegroup: ", symmetry.get_international_table()
print "---------------------------- primitive cell --------------------------------"
print_cell(primitive)
print "------------------------------- supercell ----------------------------------"
print_cell(supercell, mapping=primitive.get_supercell_to_primitive_map())
print "------------------ ratio (supercell for fc)/(primitive) --------------------"
for vec in np.dot(supercell.get_cell(), np.linalg.inv(primitive.get_cell())):
print "%5.2f"*3 % tuple(vec)
if settings.get_phonon_supercell_matrix() is not None:
print "-------------------- primitive cell for harmonic phonon ---------------------"
print_cell(phonon_primitive)
print "---------------------- supercell for harmonic phonon ------------------------"
print_cell(phonon_supercell, mapping=phonon_primitive.get_supercell_to_primitive_map())
print "--------------- ratio (phonon supercell)/(phonon primitive) -----------------"
for vec in np.dot(phonon_supercell.get_cell(),
np.linalg.inv(phonon_primitive.get_cell())):
print "%5.2f"*3 % tuple(vec)
#####################################################
# Write ir-grid points and grid addresses, and exit #
@ -565,7 +588,7 @@ if options.write_grid_points:
if mesh is None:
print "To write grid points, mesh numbers have to be specified."
else:
(grid_points,
(ir_grid_points,
coarse_grid_weights,
grid_address) = get_coarse_ir_grid_points(
primitive,
@ -576,7 +599,7 @@ if options.write_grid_points:
symprec=options.symprec)
write_ir_grid_points(mesh,
mesh_divs,
grid_points,
ir_grid_points,
coarse_grid_weights,
grid_address,
np.linalg.inv(primitive.get_cell()))
@ -589,102 +612,6 @@ if options.write_grid_points:
print_end()
sys.exit(0)
#######
# fc2 #
#######
if log_level:
print "------------------------------ fc2 ------------------------------"
sys.stdout.flush()
if options.read_fc2 or options.read_delta_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
fc2_with_dim = read_fc2_from_hdf5(filename=filename)
else:
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
file_exists(filename, log_level)
if log_level:
print "Displacement dataset is read from %s." % filename
print "Solving fc2..."
disp_dataset = parse_disp_fc3_yaml(filename=filename)
parse_FORCES_SECOND(disp_dataset)
fc2_with_dim = get_fc2(supercell, symmetry, disp_dataset)
if options.is_symmetrize_fc2:
set_permutation_symmetry(fc2_with_dim)
if options.is_translational_symmetry:
set_translational_invariance(fc2_with_dim)
show_drift_force_constants(fc2_with_dim, name='fc2')
if not options.read_fc2:
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(fc2_with_dim, filename=filename)
if settings.get_phonon_supercell_matrix()==None:
fc2 = fc2_with_dim
else:
if log_level:
print "--------------------------- fc2 extra ---------------------------"
sys.stdout.flush()
# phonon fc2 (FORCE_SETS_EXTRA)
if options.read_fc2_extra:
if input_filename is None:
filename = 'fc2_extra.hdf5'
else:
filename = 'fc2_extra.' + input_filename + '.hdf5'
file_exists(filename, log_level)
if log_level:
print "Reading fc2-extra from %s..." % filename
fc2 = read_fc2_from_hdf5(filename=filename)
else:
if log_level:
print "Solving fc2 extra..."
forces_second_extra = parse_FORCE_SETS(filename="FORCE_SETS_EXTRA")
fc2 = get_fc2(phonon_supercell,
phono3py.get_phonon_supercell_symmetry(),
forces_second_extra)
if options.is_symmetrize_fc2:
set_permutation_symmetry(fc2)
if options.is_translational_symmetry:
set_translational_invariance(fc2)
show_drift_force_constants(fc2, 'fc2-extra')
if not options.read_fc2_extra:
if output_filename is None:
filename = 'fc2_extra.hdf5'
else:
filename = 'fc2_extra.' + output_filename + '.hdf5'
if log_level:
print "Writing fc2-extra to %s..." % filename
write_fc2_to_hdf5(fc2, filename=filename)
if settings.get_is_nac():
file_exists('BORN', log_level)
if settings.get_phonon_supercell_matrix()==None:
nac_params = parse_BORN(primitive)
else:
nac_params = parse_BORN(phonon_primitive)
nac_q_direction = settings.get_nac_q_direction()
else:
nac_params = None
nac_q_direction = None
#######
# fc3 #
#######
@ -692,12 +619,8 @@ if (options.is_joint_dos or
options.is_isotope or
settings.get_read_gamma() or
settings.get_read_amplitude()):
fc3 = None
pass
else:
if log_level:
print "------------------------------ fc3 ------------------------------"
sys.stdout.flush()
if options.read_fc3: # Read fc3.hdf5
if input_filename is None:
filename = 'fc3.hdf5'
@ -707,8 +630,7 @@ else:
if log_level:
print "Reading fc3 from %s..." % filename
fc3 = read_fc3_from_hdf5(filename=filename)
if options.is_translational_symmetry:
set_translational_invariance_fc3(fc3)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_THIRD and FORCES_SECOND
if input_filename is None:
filename = 'disp_fc3.yaml'
@ -719,66 +641,93 @@ else:
print "Displacement dataset is read from %s." % filename
print "Solving fc3:"
disp_dataset = parse_disp_fc3_yaml(filename=filename)
if options.read_delta_fc2:
parse_DELTA_FC2_SETS(disp_dataset)
else:
parse_DELTA_FORCES(disp_dataset)
if 'cutoff_distance' in disp_dataset:
fc3 = get_fc3(
supercell,
disp_dataset,
fc2_with_dim,
symmetry,
verbose=log_level)
if log_level:
print "Cutting-off fc3 (cut-off distance: %f)" % disp_dataset['cutoff_distance']
cutoff_fc3(fc3,
supercell,
disp_dataset,
symmetry,
verbose=log_level)
else:
fc3 = get_fc3(
supercell,
disp_dataset,
fc2_with_dim,
symmetry,
is_translational_symmetry=options.is_translational_symmetry,
is_permutation_symmetry=options.is_symmetrize_fc3_r,
verbose=log_level)
# fc3 is cut-off by the distances among atoms and replaced by zero.
if settings.get_cutoff_fc3_distance() is not None:
cutoff_distance = settings.get_cutoff_fc3_distance()
if log_level:
print "Cutting-off fc3 by zero (cut-off distance: %f)" % cutoff_distance
cutoff_fc3_by_zero(fc3, supercell, cutoff_distance, options.symprec)
# Symmetrize fc3_r
if options.is_symmetrize_fc3_r:
if log_level:
print "Symmetrizing fc3 in real space index exchange..."
set_permutation_symmetry_fc3(fc3)
show_drift_fc3(fc3)
# Write fc3
if not options.read_fc3:
forces_fc3 = parse_FORCES_FC3(disp_dataset)
phono3py.produce_fc3(
forces_fc3,
disp_dataset,
cutoff_distance=settings.get_cutoff_fc3_distance(),
is_translational_symmetry=options.is_translational_symmetry,
is_permutation_symmetry=options.is_symmetrize_fc3_r)
if output_filename is None:
filename = 'fc3.hdf5'
else:
filename = 'fc3.' + output_filename + '.hdf5'
if log_level:
print "Writing fc3 to %s" % filename
write_fc3_to_hdf5(fc3, filename=filename)
write_fc3_to_hdf5(phono3py.get_fc3(), filename=filename)
#============================
# Phonon Gruneisen parameter
#============================
show_drift_fc3(phono3py.get_fc3())
##############
# phonon fc2 #
##############
if options.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
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
phono3py.set_fc2(phonon_fc2)
else:
if settings.get_phonon_supercell_matrix() is None:
if phono3py.get_fc2() is None:
if input_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + input_filename + '.yaml'
if log_level:
print "Displacement dataset is read from %s." % filename
print "Solving fc2:"
file_exists(filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
forces_fc3 = parse_FORCES_FC3(disp_dataset)
phono3py.produce_fc2(forces_fc3, disp_dataset)
else:
if input_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + input_filename + '.yaml'
if log_level:
print "Displacement dataset is read from %s." % filename
print "Solving fc2:"
file_exists(filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=filename)
forces_fc2 = parse_FORCES_FC2(disp_dataset)
phono3py.produce_fc2(forces_fc2, disp_dataset)
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)
show_drift_force_constants(phono3py.get_fc2(), name='fc2')
if settings.get_is_nac():
file_exists('BORN', log_level)
nac_params = parse_BORN(phonon_primitive)
nac_q_direction = settings.get_nac_q_direction()
else:
nac_params = None
nac_q_direction = None
##############################
# Phonon Gruneisen parameter #
##############################
if options.is_gruneisen:
mesh = settings.get_mesh_numbers()
fc2 = phono3py.get_fc2()
fc3 = phono3py.get_fc3()
if len(fc2) != len(fc3):
print_error_message("Supercells used for fc2 and fc3 have to be same.")
if log_level:
print_error()
sys.exit(1)
band_paths = settings.get_bands()
qpoints = settings.get_qpoints()
ion_clamped = settings.get_ion_clamped()
@ -786,10 +735,12 @@ if options.is_gruneisen:
if (mesh is None and
band_paths is None and
qpoints is None):
print_error_message("An option of --mesh, --band, or --qpoints "
"has to be specified.")
if log_level:
print "An option of --mesh, --band, or --qpoints has to be specified."
print_end()
sys.exit(1)
print_error()
sys.exit(1)
if log_level:
print "------ Phonon Gruneisen parameter ------"
@ -828,185 +779,154 @@ if options.is_gruneisen:
filename = 'gruneisen3.' + output_filename + '.yaml'
gr.write_yaml(filename=filename)
#===========================
# phonon-phonon interaction
#===========================
elif settings.get_mesh_numbers() is not None:
mesh = settings.get_mesh_numbers()
grid_points = settings.get_grid_points()
if grid_points is not None:
grid_points = np.array(grid_points)
if options.factor is None:
factor = VaspToTHz
else:
factor = options.factor
if settings.get_sigma() is None:
sigma = None
else:
sigma = settings.get_sigma()
if settings.get_multiple_sigmas() is None:
if sigma:
multiple_sigmas = [sigma]
else:
multiple_sigmas = []
else:
multiple_sigmas = settings.get_multiple_sigmas()
if settings.get_is_tetrahedron_method():
multiple_sigmas = [None] + multiple_sigmas
if settings.get_frequency_pitch() is None:
freq_step = 0.1
else:
freq_step = settings.get_frequency_pitch()
if options.freq_scale is None:
freq_scale = 1.0
else:
freq_scale = options.freq_scale
if settings.get_phonon_supercell_matrix() is None:
supercell_dm = supercell
primitive_dm = primitive
else:
supercell_dm = phonon_supercell
primitive_dm = phonon_primitive
if log_level:
print "--------------------------- Settings ----------------------------"
print "Mesh sampling: [ %d %d %d ]" % tuple(mesh)
if grid_points is not None:
print "Grid points to be calculated:",
if len(grid_points) > 8:
for i, gp in enumerate(grid_points):
if i % 10 == 0:
print
print " ",
print gp,
print
print_end()
if log_level:
print "--------------------------- Settings ----------------------------"
print "Mesh sampling: [ %d %d %d ]" % tuple(mesh)
if mesh_divs is not None and settings.get_is_bterta():
print "Mesh divisors: [ %d %d %d ]" % tuple(mesh_divs)
if band_indices is not None and not settings.get_is_bterta():
print "Band indices:", band_indices
if sigmas:
print "Sigma:",
for sigma in sigmas:
if sigma:
print sigma,
else:
for gp in grid_points:
print gp,
print
sys.stdout.flush()
if options.is_joint_dos:
joint_dos = Phono3pyJointDos(
supercell_dm,
primitive_dm,
mesh,
fc2,
nac_params=nac_params,
sigmas=multiple_sigmas,
frequency_step=freq_step,
frequency_factor_to_THz=factor,
frequency_scale_factor=freq_scale,
is_nosym=options.is_nosym,
symprec=options.symprec,
output_filename=output_filename,
log_level=log_level)
joint_dos.run(grid_points)
elif options.is_isotope:
if log_level:
print "Cutoff frequency:", settings.get_cutoff_frequency()
mass_variances = settings.get_mass_variances()
iso = IsotopeScattering(
mesh,
mass_variances,
frequency_factor_to_THz=factor,
symprec=options.symprec,
cutoff_frequency=settings.get_cutoff_frequency(),
lapack_zheev_uplo=options.uplo)
iso.set_dynamical_matrix(fc2,
supercell_dm,
primitive_dm,
nac_params=nac_params,
frequency_scale_factor=freq_scale)
if settings.get_band_indices() is None:
band_indices = None
print "Tetrahedron-method",
print
if (settings.get_is_linewidth() or
settings.get_is_frequency_shift() or
settings.get_is_bterta()):
print "Temperature:",
if len(temperatures) > 5:
print ((" %.1f " * 5) % tuple(temperatures[:5])), "...",
print " %.1f" % temperatures[-1]
else:
band_indices = np.hstack(self._band_indices).astype('intc')
for sigma in multiple_sigmas:
if log_level:
print "Sigma:", sigma
iso.set_sigma(sigma)
print iso.run(gp, band_indices)
print ("%.1f " * len(temperatures)) % tuple(temperatures)
elif options.is_isotope or options.is_joint_dos:
pass
else:
if log_level:
print "Cutoff frequency:", settings.get_cutoff_frequency()
print "Temperatures:",
print ("%.1f " * len(temperature_points)) % tuple(temperature_points)
if grid_points is not None:
print "Grid point to be calculated:",
if len(grid_points) > 8:
for i, gp in enumerate(grid_points):
if i % 10 == 0:
print
print " ",
print gp,
print
else:
for gp in grid_points:
print gp,
print
if cutoff_frequency:
print "Cutoff frequency:", cutoff_frequency
if log_level > 1:
print "Frequency factor to THz:", frequency_factor_to_THz
print "Frequency step for spectrum:", frequency_step
print "Frequency scale factor:", frequency_scale_factor
sys.stdout.flush()
#############
# Joint DOS #
#############
if options.is_joint_dos:
joint_dos = Phono3pyJointDos(
supercell_dm,
primitive_dm,
mesh,
fc2,
nac_params=nac_params,
sigmas=sigmas,
frequency_step=frequency_step,
frequency_factor_to_THz=frequency_factor_to_THz,
frequency_scale_factor=frequency_scale_factor,
is_nosym=options.is_nosym,
symprec=options.symprec,
output_filename=output_filename,
log_level=log_level)
joint_dos.run(grid_points)
if log_level:
print_end()
######################
# Isotope scattering #
######################
if options.is_isotope:
if log_level:
print "Cutoff frequency:", settings.get_cutoff_frequency()
mass_variances = settings.get_mass_variances()
iso = IsotopeScattering(
mesh,
mass_variances,
frequency_factor_to_THz=frequency_factor_to_THz,
symprec=options.symprec,
cutoff_frequency=settings.get_cutoff_frequency(),
lapack_zheev_uplo=options.uplo)
iso.set_dynamical_matrix(fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor)
if settings.get_band_indices() is None:
band_indices = None
else:
band_indices = np.hstack(self._band_indices).astype('intc')
phono3py = Phono3py(
supercell,
primitive,
mesh,
fc3=fc3,
sigmas=multiple_sigmas,
band_indices=settings.get_band_indices(),
cutoff_frequency=settings.get_cutoff_frequency(),
frequency_factor_to_THz=factor,
is_nosym=options.is_nosym,
symmetrize_fc3_q=options.is_symmetrize_fc3_q,
symprec=options.symprec,
log_level=log_level,
lapack_zheev_uplo=options.uplo)
phono3py.set_dynamical_matrix(fc2,
supercell_dm,
primitive_dm,
nac_params=nac_params,
nac_q_direction=nac_q_direction,
frequency_scale_factor=freq_scale)
if settings.get_temperatures() is None:
t_max=settings.get_max_temperature()
t_min=settings.get_min_temperature()
t_step=settings.get_temperature_step()
temperatures = np.arange(t_min, t_max + float(t_step) / 10,
t_step)
else:
temperatures = settings.get_temperatures()
for sigma in sigmas:
if log_level:
print "Sigma:", sigma
iso.set_sigma(sigma)
print iso.run(gp, band_indices)
if log_level:
print_end()
if settings.get_is_linewidth():
phono3py.run_linewidth(
grid_points,
temperatures=temperatures)
phono3py.write_linewidth(filename=output_filename)
elif settings.get_is_frequency_shift():
phono3py.get_frequency_shift(
grid_points,
epsilon=sigma,
temperatures=temperatures,
output_filename=output_filename)
elif settings.get_is_bterta():
phono3py.run_thermal_conductivity(
temperatures=temperatures,
sigmas=multiple_sigmas,
mass_variances=settings.get_mass_variances(),
grid_points=grid_points,
mesh_divisors=settings.get_mesh_divisors(),
coarse_mesh_shifts=settings.get_coarse_mesh_shifts(),
cutoff_lifetime=settings.get_cutoff_lifetime(),
no_kappa_stars=settings.get_no_kappa_stars(),
gv_delta_q=settings.get_group_velocity_delta_q(),
write_gamma=settings.get_write_gamma(),
read_gamma=settings.get_read_gamma(),
write_amplitude=settings.get_write_amplitude(),
read_amplitude=settings.get_read_amplitude(),
input_filename=input_filename,
output_filename=output_filename)
else:
phono3py.run_imag_self_energy(
grid_points,
frequency_step=freq_step,
temperatures=settings.get_temperatures())
phono3py.write_imag_self_energy(filename=output_filename)
#########
# Ph-ph #
#########
phono3py.set_phph_interaction(nac_params=nac_params,
nac_q_direction=nac_q_direction,
frequency_scale_factor=frequency_scale_factor)
if settings.get_is_linewidth():
phono3py.run_linewidth(
grid_points,
temperatures=temperatures)
phono3py.write_linewidth(filename=output_filename)
elif settings.get_is_frequency_shift():
phono3py.get_frequency_shift(
grid_points,
epsilon=sigma,
temperatures=temperatures,
output_filename=output_filename)
elif settings.get_is_bterta():
phono3py.run_thermal_conductivity(
temperatures=temperatures,
sigmas=sigmas,
mass_variances=settings.get_mass_variances(),
grid_points=grid_points,
mesh_divisors=mesh_divs,
coarse_mesh_shifts=settings.get_coarse_mesh_shifts(),
cutoff_lifetime=settings.get_cutoff_lifetime(),
no_kappa_stars=settings.get_no_kappa_stars(),
gv_delta_q=settings.get_group_velocity_delta_q(),
write_gamma=settings.get_write_gamma(),
read_gamma=settings.get_read_gamma(),
write_amplitude=settings.get_write_amplitude(),
read_amplitude=settings.get_read_amplitude(),
input_filename=input_filename,
output_filename=output_filename)
else:
pass
phono3py.run_imag_self_energy(
grid_points,
frequency_step=frequency_step,
temperatures=temperature_points)
phono3py.write_imag_self_energy(filename=output_filename)
if log_level:
print_end()