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Cleaning phono4py code

This commit is contained in:
Atsushi Togo 2015-01-20 17:05:59 +09:00
parent fd1cf13bfb
commit 52f87342a5
4 changed files with 137 additions and 149 deletions
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13
anharmonic/file_IO.py
View File

@ -1395,19 +1395,6 @@ def parse_disp_fc4_yaml(filename="disp_fc4.yaml"):
return new_dataset
def parse_DELTA_FORCES(disp_dataset,
filethird='FORCES_THIRD',
filesecond='FORCES_SECOND'):
forces_third = open(filethird, 'r')
forces_second = open(filesecond, 'r')
num_atom = disp_dataset['natom']
for disp1 in disp_dataset['first_atoms']:
second_forces = parse_force_lines(forces_second, num_atom)
for disp2 in disp1['second_atoms']:
third_forces = parse_force_lines(forces_third, num_atom)
disp2['delta_forces'] = third_forces - second_forces
def parse_DELTA_FORCES_FOURTH(disp_dataset,
file4='FORCES_FOURTH',
file3='FORCES_THIRD',

95
anharmonic/phonon4/__init__.py
View File

@ -1,15 +1,18 @@
import numpy as np
from anharmonic.phonon4.frequency_shift import FrequencyShift
from phonopy.units import VaspToTHz
from phonopy.harmonic.force_constants import set_translational_invariance, set_permutation_symmetry, get_fc2
from phonopy.structure.symmetry import Symmetry
class Phono4py:
def __init__(self,
fc4,
supercell,
primitive,
mesh,
mesh=None,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_symmetry=True,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
@ -18,24 +21,106 @@ class Phono4py:
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._mesh = np.intc(mesh)
self._mesh = None
if mesh is not None:
self._mesh = np.array(mesh, dtype='intc')
if band_indices is None:
self._band_indices = [
np.arange(primitive.get_number_of_atoms() * 3)]
np.arange(primitive.get_number_of_atoms() * 3,
dtype='intc')]
else:
self._band_indices = band_indices
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._band_indices_flatten = np.intc(
[x for bi in self._band_indices for x in bi])
self._band_indices_flatten = np.array(
[x for bi in self._band_indices for x in bi],
dtype='intc')
self._frequency_shifts = None
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
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_symmetry(self):
return self._symmetry
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):
file_count = 0
for forces, disp1 in zip(forces_fc2, disp_dataset['first_atoms']):
disp1['forces'] = forces
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,
displacement_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 disp1['third_atoms']:
disp3['delta_forces'] = (forces_fc4[file_count] -
disp2['forces'])
file_count += 1
self._fc4 = get_fc4(
self._supercell,
displacement_dataset,
self._fc3,
self._symmetry,
is_translational_symmetry=(translational_symmetry_type > 0),
is_permutation_symmetry=is_permutation_symmetry,
verbose=self._log_level)
def set_frequency_shift(self, temperatures=None):
self._interaction = FrequencyShift(
self._fc4,

3
anharmonic/phonon4/fc4.py
View File

@ -51,6 +51,9 @@ def get_fc4(supercell,
if is_translational_symmetry:
set_translational_invariance_fc4_per_index(fc4)
if is_permutation_symmetry:
set_permutation_symmetry_fc4(fc4)
return fc4
def set_translational_invariance_fc4(fc4):

175
scripts/phono4py
View File

@ -48,9 +48,6 @@ from phonopy.units import VaspToTHz
from anharmonic.phonon3.fc3 import set_permutation_symmetry_fc3, set_translational_invariance_fc3, show_drift_fc3, get_fc3
from anharmonic.file_IO import \
parse_disp_fc3_yaml, parse_disp_fc4_yaml,\
parse_DELTA_FORCES, parse_DELTA_FORCES_FOURTH,\
write_DELTA_FC2_SETS, parse_DELTA_FC2_SETS, \
write_DELTA_FC2_FOURTH_SETS, parse_DELTA_FC2_FOURTH_SETS,\
write_FORCES_FOURTH, parse_FORCES_SECOND, \
read_fc4_from_hdf5, read_fc3_from_hdf5, read_fc2_from_hdf5, \
write_fc4_to_hdf5, write_fc3_to_hdf5, write_fc2_to_hdf5, \
@ -89,7 +86,6 @@ parser.set_defaults(amplitude=None,
band_indices=None,
cell_poscar=None,
factor=None,
fc2_fourth_sets_mode=False,
forces_fourth_mode=False,
grid_points=None,
is_nodiag=False,
@ -103,7 +99,6 @@ parser.set_defaults(amplitude=None,
log_level=None,
mesh_numbers=None,
primitive_axis=None,
read_fc2_fourth=False,
read_fc2=False,
read_fc3=False,
read_fc4=False,
@ -120,10 +115,6 @@ parser.add_option("--bi", "--band_indices", dest="band_indices",
parser.add_option("-c", "--cell", dest="cell_poscar",
action="store", type="string",
help="Read unit cell", metavar="FILE")
parser.add_option("--create_fc2_fourth",
dest="fc2_fourth_sets_mode",
action="store_true",
help="Create DELTA_FC2_FOURTH_SETS, DELTA_FC2_SETS, and fc2.hdf")
parser.add_option("--cf4", "--create_f4",
dest="forces_fourth_mode",
action="store_true",
@ -141,10 +132,6 @@ parser.add_option("--fc2",
dest="read_fc2",
action="store_true",
help="Read second order force constants")
parser.add_option("--fc2_fourth",
dest="read_fc2_fourth",
action="store_true",
help="Read DELTA_FC2_FOURTH_SETS, DELTA_FC2_SETS, and fc2.hdf")
parser.add_option("--fc3",
dest="read_fc3",
action="store_true",
@ -206,13 +193,6 @@ if options.log_level is None:
else:
log_level = options.log_level
# Create FC2_FOURTH_SETS
if options.fc2_fourth_sets_mode:
displacements = parse_disp_fc3_yaml()
write_DELTA_FC2_FOURTH_SETS(args, displacements)
print_end()
exit(0)
# Create FC2_FOURTH_SETS
if options.forces_fourth_mode:
displacements = parse_disp_fc4_yaml()
@ -258,11 +238,6 @@ unitcell = read_vasp(unitcell_filename,
# Supercell and Symmetry
supercell = get_supercell(unitcell, settings.get_supercell_matrix())
symmetry = Symmetry(supercell, options.symprec)
# Log
if log_level:
print "Spacegroup: ", symmetry.get_international_table()
###############################################################
# Create supercells with displacements and exit (pre-process) #
@ -299,116 +274,69 @@ else:
for vec in np.dot(supercell.get_cell(), np.linalg.inv(primitive.get_cell())):
print "%5.2f"*3 % tuple(vec)
# fc2
if options.factor is None:
factor = VaspToTHz
else:
factor = options.factor
mesh = settings.get_mesh_numbers()
phono4py = Phono4py(fc4,
supercell,
primitive,
mesh,
band_indices=settings.get_band_indices(),
frequency_factor_to_THz=factor,
cutoff_frequency=1e-2,
is_nosym=options.is_nosym,
symprec=options.symprec,
log_level=log_level)
if not options.read_fc4: # Read fc4.hdf
displacements = parse_disp_fc4_yaml()
forces_fc4 = parse_FORCES_FC4(displacements)
translational_symmetry_type = is_translational_symmetry * 1
phono4py.produce_fc4(
forces_fc4,
displacements,
translational_symmetry_type=translational_symmetry_type,
is_permutation_symmetry=is_symmetrize_fc4_r,
is_permutation_symmetry_fc3=is_symmetrize_fc3_r,
is_permutation_symmetry_fc2=is_symmetrize_fc2)
if options.read_fc2:
if log_level:
print "----- Read fc2 -----"
sys.stdout.flush()
if os.path.exists('fc2.hdf5'):
fc2 = read_fc2_from_hdf5()
else:
print "fc2.hdf5 not found"
if log_level:
print_end()
sys.exit(0)
phono4py.set_fc2(read_fc2_from_hdf5())
else:
if log_level:
print "----- Solve fc2 -----"
sys.stdout.flush()
disp_dataset = parse_disp_fc4_yaml()
parse_FORCES_SECOND(disp_dataset)
fc2 = get_fc2(supercell, symmetry, disp_dataset)
if options.is_symmetrize_fc2:
set_permutation_symmetry(fc2)
if options.is_translational_symmetry:
set_translational_invariance(fc2)
if not options.read_fc2:
if log_level:
print "----- Write fc2.hdf5 -----"
write_fc2_to_hdf5(fc2)
# fc3
if options.read_fc3: # Read fc3.hdf5
write_fc2_to_hdf5(phono4py.get_fc2())
show_drift_force_constants(phono4py.get_fc2(), name='fc2')
if options.read_fc3:
if log_level:
print "----- Read fc3 -----"
sys.stdout.flush()
fc3 = read_fc3_from_hdf5()
if options.is_translational_symmetry:
set_translational_invariance_fc3(fc3)
phono4py.set_fc3(read_fc3_from_hdf5())
else:
if log_level:
print "----- Solve fc3 -----"
sys.stdout.flush()
if options.read_fc2_fourth: # fc3 from DELTA_FC2_SETS
displacements = parse_disp_fc3_yaml()
parse_DELTA_FC2_SETS(displacements)
else: # fc3 from DELTA_FORCES
displacements = parse_disp_fc3_yaml()
parse_DELTA_FORCES(displacements)
if options.is_translational_symmetry:
translational_symmetry_type = 1
else:
translational_symmetry_type = 0
fc3 = get_fc3(
supercell,
displacements,
fc2,
symmetry,
translational_symmetry_type=translational_symmetry_type,
is_permutation_symmetry=options.is_symmetrize_fc3_r,
verbose=log_level)
if options.is_symmetrize_fc3_r:
if log_level:
print "----- Symmetrize fc3 by index exchange in real space -----"
set_permutation_symmetry_fc3(fc3)
show_drift_fc3(fc3)
if not options.read_fc3:
if log_level:
print "----- Write fc3.hdf5 -----"
write_fc3_to_hdf5(fc3)
write_fc3_to_hdf5(phono4py.get_fc3())
show_drift_fc3(phono4py.get_fc3())
# fc4
if options.read_fc4: # Read fc4.hdf
if options.read_fc4:
if log_level:
print "----- Read fc4 -----"
sys.stdout.flush()
fc4 = read_fc4_from_hdf5()
if options.is_translational_symmetry:
if log_level:
print "----- Impose translational invariance "
print "condition to fc4 -----"
set_translational_invariance_fc4(fc4)
phono4py.set_fc4(read_fc4_from_hdf5())
else:
if options.read_fc2_fourth:
displacements = parse_disp_fc4_yaml()
parse_DELTA_FC2_FOURTH_SETS(displacements)
else: # fc4 from FORCES_FOURTH, FORCES_THIRD and FORCES_SECOND
displacements = parse_disp_fc4_yaml()
parse_DELTA_FORCES_FOURTH(displacements)
fc4 = get_fc4(
supercell,
displacements,
fc3,
symmetry,
is_translational_symmetry=options.is_translational_symmetry,
is_permutation_symmetry=options.is_symmetrize_fc4_r,
verbose=log_level)
write_fc4_to_hdf5(phono4py.get_fc4())
show_drift_fc4(phono4py.get_fc4())
if options.is_symmetrize_fc4_r:
if log_level:
print "----- Symmetrize fc4 by index exchange in real space -----"
set_permutation_symmetry_fc4(fc4)
if log_level:
print "(Calculating fc4 drift...)"
show_drift_fc4(fc4)
@ -418,24 +346,9 @@ else:
print "----- Write fc4.hdf5 -----"
write_fc4_to_hdf5(fc4)
if options.factor is None:
factor = VaspToTHz
else:
factor = options.factor
mesh = settings.get_mesh_numbers()
# Frequency shift
if mesh is not None:
phono4py = Phono4py(fc4,
supercell,
primitive,
mesh,
band_indices=settings.get_band_indices(),
frequency_factor_to_THz=factor,
cutoff_frequency=1e-2,
is_nosym=options.is_nosym,
symprec=options.symprec,
log_level=log_level)
phono4py.set_frequency_shift(temperatures=settings.get_temperatures())
phono4py.set_dynamical_matrix(fc2,
supercell,