mirror of https://github.com/phonopy/phonopy.git
Since file became small, the contents are returned to phono3py script.
This commit is contained in:
Atsushi Togo
parent
f3e7dc2bc5
commit
1c979ec3fb
557
scripts/phono3py
557
scripts/phono3py
|
|
@ -34,4 +34,559 @@
|
|||
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
# POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
import anharmonic.cui.phono3py
|
||||
import sys
|
||||
import numpy as np
|
||||
from phonopy.interface.vasp import read_vasp
|
||||
from phonopy.file_IO import parse_BORN, write_FORCE_SETS, parse_FORCE_SETS
|
||||
from phonopy.units import VaspToTHz
|
||||
from anharmonic.file_IO import (parse_disp_fc2_yaml, parse_disp_fc3_yaml,
|
||||
parse_FORCES_FC2, parse_FORCES_FC3,
|
||||
write_FORCES_FC3_vasp, write_FORCES_FC2_vasp,
|
||||
write_FORCES_FC2)
|
||||
from anharmonic.cui.settings import Phono3pyConfParser
|
||||
from anharmonic.phonon3 import (Phono3py, Phono3pyJointDos, Phono3pyIsotope)
|
||||
from anharmonic.other.gruneisen import get_gruneisen_parameters
|
||||
from anharmonic.cui.phono3py_argparse import get_parser
|
||||
from anharmonic.cui.show_log import (print_phono3py, print_version, print_end,
|
||||
print_error,
|
||||
show_phono3py_settings,
|
||||
show_phono3py_cells, file_exists)
|
||||
from anharmonic.cui.triplets_info import write_grid_points, show_num_triplets
|
||||
from anharmonic.cui.translate_settings import get_phono3py_configurations
|
||||
from anharmonic.cui.create_supercells import create_phono3py_supercells
|
||||
from anharmonic.cui.create_force_constants import create_phono3py_force_constants
|
||||
|
||||
phono3py_version = "0.9.14"
|
||||
|
||||
# Parse arguments
|
||||
parser = get_parser()
|
||||
(options, args) = parser.parse_args()
|
||||
option_list = parser.option_list
|
||||
|
||||
# Log level
|
||||
log_level = 1
|
||||
if options.verbose:
|
||||
log_level = 2
|
||||
if options.quiet:
|
||||
log_level = 0
|
||||
if options.log_level is not None:
|
||||
log_level=options.log_level
|
||||
|
||||
# Input and output filename extension
|
||||
input_filename = options.input_filename
|
||||
output_filename = options.output_filename
|
||||
if options.input_output_filename is not None:
|
||||
input_filename = options.input_output_filename
|
||||
output_filename = options.input_output_filename
|
||||
|
||||
# Title
|
||||
if log_level:
|
||||
print_phono3py()
|
||||
print_version(phono3py_version)
|
||||
|
||||
#####################
|
||||
# Create FORCES_FC3 #
|
||||
#####################
|
||||
if options.forces_fc3_mode or options.forces_fc3_file_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()
|
||||
|
||||
if options.forces_fc3_file_mode:
|
||||
file_exists(args[0], log_level)
|
||||
filenames = [x.strip() for x in open(args[0])]
|
||||
else:
|
||||
filenames = args
|
||||
write_FORCES_FC3_vasp(filenames, disp_dataset)
|
||||
|
||||
if log_level:
|
||||
print("FORCES_FC3 has been created.")
|
||||
print_end()
|
||||
exit(0)
|
||||
|
||||
#####################
|
||||
# Create FORCES_FC2 #
|
||||
#####################
|
||||
if options.forces_fc2_mode:
|
||||
if input_filename is None:
|
||||
filename = 'disp_fc2.yaml'
|
||||
else:
|
||||
filename = 'disp_fc2.' + input_filename + '.yaml'
|
||||
file_exists(filename, log_level)
|
||||
if log_level:
|
||||
print("Displacement dataset is read from %s." % filename)
|
||||
disp_dataset = parse_disp_fc2_yaml()
|
||||
write_FORCES_FC2_vasp(args, disp_dataset)
|
||||
|
||||
if log_level:
|
||||
print("FORCES_FC2 has been created.")
|
||||
print_end()
|
||||
exit(0)
|
||||
|
||||
if options.force_sets_to_forces_fc2_mode:
|
||||
filename = 'FORCE_SETS'
|
||||
file_exists(filename, log_level)
|
||||
disp_dataset = parse_FORCE_SETS(filename=filename)
|
||||
write_FORCES_FC2(disp_dataset)
|
||||
|
||||
if log_level:
|
||||
print("FORCES_FC2 has been created from FORCE_SETS.")
|
||||
print_end()
|
||||
exit(0)
|
||||
|
||||
#####################################
|
||||
# Create FORCE_SETS from FORCES_FC* #
|
||||
#####################################
|
||||
if options.force_sets_mode:
|
||||
if options.phonon_supercell_dimension is not None:
|
||||
if input_filename is None:
|
||||
filename = 'disp_fc2.yaml'
|
||||
else:
|
||||
filename = 'disp_fc2.' + input_filename + '.yaml'
|
||||
file_exists(filename, log_level)
|
||||
disp_dataset = parse_disp_fc2_yaml()
|
||||
forces = parse_FORCES_FC2(disp_dataset)
|
||||
else:
|
||||
if input_filename is None:
|
||||
filename = 'disp_fc3.yaml'
|
||||
else:
|
||||
filename = 'disp_fc3.' + input_filename + '.yaml'
|
||||
file_exists(filename, log_level)
|
||||
disp_dataset = parse_disp_fc3_yaml()
|
||||
forces = parse_FORCES_FC3(disp_dataset)
|
||||
|
||||
if log_level:
|
||||
print("Displacement dataset is read from %s." % filename)
|
||||
|
||||
for force_set, disp1 in zip(forces, disp_dataset['first_atoms']):
|
||||
disp1['forces'] = force_set
|
||||
write_FORCE_SETS(disp_dataset)
|
||||
|
||||
if log_level:
|
||||
print("FORCE_SETS has been created.")
|
||||
print_end()
|
||||
exit(0)
|
||||
|
||||
##################
|
||||
# Parse settings #
|
||||
##################
|
||||
if len(args) > 0:
|
||||
settings = Phono3pyConfParser(filename=args[0],
|
||||
options=options,
|
||||
option_list=option_list).get_settings()
|
||||
else:
|
||||
settings = Phono3pyConfParser(options=options,
|
||||
option_list=option_list).get_settings()
|
||||
|
||||
#############
|
||||
# Run modes #
|
||||
#############
|
||||
run_mode = None
|
||||
if settings.get_is_gruneisen():
|
||||
run_mode = "gruneisen"
|
||||
elif settings.get_is_joint_dos():
|
||||
run_mode = "jdos"
|
||||
elif (settings.get_is_isotope() and
|
||||
not (settings.get_is_bterta() or settings.get_is_lbte())):
|
||||
run_mode = "isotope"
|
||||
elif settings.get_is_linewidth():
|
||||
run_mode = "linewidth"
|
||||
elif settings.get_is_imag_self_energy():
|
||||
run_mode = "imag_self_energy"
|
||||
elif settings.get_is_frequency_shift():
|
||||
run_mode = "frequency_shift"
|
||||
elif settings.get_is_bterta():
|
||||
run_mode = "conductivity-RTA"
|
||||
elif settings.get_is_lbte():
|
||||
run_mode = "conductivity-LBTE"
|
||||
|
||||
if log_level:
|
||||
print("Run mode: %s" % run_mode)
|
||||
|
||||
##########################
|
||||
# Read crystal structure #
|
||||
##########################
|
||||
if options.cell_poscar is None:
|
||||
file_exists('POSCAR', log_level)
|
||||
unitcell_filename = 'POSCAR'
|
||||
else:
|
||||
file_exists(options.cell_poscar, log_level)
|
||||
unitcell_filename = options.cell_poscar
|
||||
unitcell = read_vasp(unitcell_filename, settings.get_chemical_symbols())
|
||||
|
||||
######################
|
||||
# Translate settings #
|
||||
######################
|
||||
conf = get_phono3py_configurations(settings, options)
|
||||
primitive_matrix = conf['primitive_matrix']
|
||||
supercell_matrix = conf['supercell_matrix']
|
||||
phonon_supercell_matrix = conf['phonon_supercell_matrix']
|
||||
masses = conf['masses']
|
||||
mesh = conf['mesh']
|
||||
mesh_divs = conf['mesh_divs']
|
||||
coarse_mesh_shifts = conf['coarse_mesh_shifts']
|
||||
grid_points = conf['grid_points']
|
||||
band_indices = conf['band_indices']
|
||||
sigmas = conf['sigmas']
|
||||
temperature_points = conf['temperature_points']
|
||||
temperatures = conf['temperatures']
|
||||
frequency_factor_to_THz = conf['frequency_factor_to_THz']
|
||||
num_frequency_points = conf['num_frequency_points']
|
||||
frequency_step = conf['frequency_step']
|
||||
frequency_scale_factor = conf['frequency_scale_factor']
|
||||
cutoff_frequency = conf['cutoff_frequency']
|
||||
tsym_type = conf['tsym_type']
|
||||
|
||||
symprec = options.symprec
|
||||
|
||||
#################################################
|
||||
# Create supercells with displacements and exit #
|
||||
#################################################
|
||||
if settings.get_create_displacements():
|
||||
create_phono3py_supercells(unitcell,
|
||||
supercell_matrix,
|
||||
phonon_supercell_matrix,
|
||||
output_filename,
|
||||
symprec,
|
||||
settings,
|
||||
log_level)
|
||||
if log_level:
|
||||
print_end()
|
||||
sys.exit(0)
|
||||
|
||||
#####################
|
||||
# Initiate phono3py #
|
||||
#####################
|
||||
phono3py = Phono3py(
|
||||
unitcell,
|
||||
supercell_matrix,
|
||||
primitive_matrix=primitive_matrix,
|
||||
phonon_supercell_matrix=phonon_supercell_matrix,
|
||||
masses=masses,
|
||||
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=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()
|
||||
|
||||
if log_level:
|
||||
show_phono3py_cells(symmetry,
|
||||
primitive,
|
||||
supercell,
|
||||
phonon_primitive,
|
||||
phonon_supercell,
|
||||
settings)
|
||||
|
||||
#####################################################
|
||||
# Write ir-grid points and grid addresses, and exit #
|
||||
#####################################################
|
||||
if options.write_grid_points:
|
||||
write_grid_points(primitive,
|
||||
mesh,
|
||||
mesh_divs,
|
||||
coarse_mesh_shifts,
|
||||
options,
|
||||
log_level)
|
||||
|
||||
if log_level:
|
||||
print_end()
|
||||
sys.exit(0)
|
||||
|
||||
##################################################
|
||||
# Show reduced number of triplets at grid points #
|
||||
##################################################
|
||||
if options.show_num_triplets:
|
||||
show_num_triplets(primitive,
|
||||
mesh,
|
||||
mesh_divs,
|
||||
grid_points,
|
||||
coarse_mesh_shifts,
|
||||
options,
|
||||
log_level)
|
||||
|
||||
if log_level:
|
||||
print_end()
|
||||
sys.exit(0)
|
||||
|
||||
###################
|
||||
# Force constants #
|
||||
###################
|
||||
create_phono3py_force_constants(phono3py,
|
||||
settings,
|
||||
options.read_fc3,
|
||||
options.read_fc2,
|
||||
tsym_type,
|
||||
options.is_symmetrize_fc3_r,
|
||||
options.is_symmetrize_fc3_q,
|
||||
options.is_symmetrize_fc2,
|
||||
input_filename,
|
||||
output_filename,
|
||||
log_level)
|
||||
|
||||
##################################
|
||||
# Non-analytical term correction #
|
||||
##################################
|
||||
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 settings.get_is_gruneisen():
|
||||
fc2 = phono3py.get_fc2()
|
||||
fc3 = phono3py.get_fc3()
|
||||
if len(fc2) != len(fc3):
|
||||
print("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()
|
||||
|
||||
if (mesh is None and
|
||||
band_paths is None and
|
||||
qpoints is None):
|
||||
|
||||
print("An option of --mesh, --band, or --qpoints has to be specified.")
|
||||
if log_level:
|
||||
print_error()
|
||||
sys.exit(1)
|
||||
|
||||
if log_level:
|
||||
print("-" * 23 + " Phonon Gruneisen parameter " + "-" * 23)
|
||||
if mesh is not None:
|
||||
print("Mesh sampling: [ %d %d %d ]" % tuple(mesh))
|
||||
elif band_paths is not None:
|
||||
print("Paths in reciprocal reduced coordinates:")
|
||||
for path in band_paths:
|
||||
print("[%5.2f %5.2f %5.2f] --> [%5.2f %5.2f %5.2f]" %
|
||||
(tuple(path[0]) + tuple(path[-1])))
|
||||
if ion_clamped:
|
||||
print("To be calculated with ion clamped.")
|
||||
|
||||
sys.stdout.flush()
|
||||
|
||||
gr = get_gruneisen_parameters(fc2,
|
||||
fc3,
|
||||
supercell,
|
||||
primitive,
|
||||
nac_params=nac_params,
|
||||
nac_q_direction=nac_q_direction,
|
||||
ion_clamped=ion_clamped,
|
||||
factor=VaspToTHz,
|
||||
symprec=symprec)
|
||||
if mesh is not None:
|
||||
gr.set_sampling_mesh(mesh, is_gamma_center=True)
|
||||
elif band_paths is not None:
|
||||
gr.set_band_structure(band_paths)
|
||||
elif qpoints is not None:
|
||||
gr.set_qpoints(qpoints)
|
||||
gr.run()
|
||||
|
||||
if output_filename is None:
|
||||
filename = 'gruneisen3.yaml'
|
||||
else:
|
||||
filename = 'gruneisen3.' + output_filename + '.yaml'
|
||||
gr.write_yaml(filename=filename)
|
||||
|
||||
if log_level:
|
||||
print_end()
|
||||
sys.exit(0)
|
||||
|
||||
#################
|
||||
# Show settings #
|
||||
#################
|
||||
if mesh is None:
|
||||
print("Mesh is not specified.")
|
||||
if log_level:
|
||||
print_error()
|
||||
sys.exit(0)
|
||||
|
||||
if log_level:
|
||||
show_phono3py_settings(settings,
|
||||
mesh,
|
||||
mesh_divs,
|
||||
band_indices,
|
||||
sigmas,
|
||||
temperatures,
|
||||
temperature_points,
|
||||
grid_points,
|
||||
cutoff_frequency,
|
||||
frequency_factor_to_THz,
|
||||
frequency_step,
|
||||
num_frequency_points,
|
||||
log_level)
|
||||
|
||||
#############
|
||||
# Joint DOS #
|
||||
#############
|
||||
if run_mode == "jdos":
|
||||
joint_dos = Phono3pyJointDos(
|
||||
phonon_supercell,
|
||||
phonon_primitive,
|
||||
mesh,
|
||||
phono3py.get_fc2(),
|
||||
nac_params=nac_params,
|
||||
nac_q_direction=nac_q_direction,
|
||||
sigmas=sigmas,
|
||||
cutoff_frequency=cutoff_frequency,
|
||||
frequency_step=frequency_step,
|
||||
num_frequency_points=num_frequency_points,
|
||||
temperatures=temperature_points,
|
||||
frequency_factor_to_THz=frequency_factor_to_THz,
|
||||
frequency_scale_factor=frequency_scale_factor,
|
||||
is_nosym=options.is_nosym,
|
||||
symprec=symprec,
|
||||
output_filename=output_filename,
|
||||
log_level=log_level)
|
||||
joint_dos.run(grid_points)
|
||||
if log_level:
|
||||
print_end()
|
||||
sys.exit(0)
|
||||
|
||||
######################
|
||||
# Isotope scattering #
|
||||
######################
|
||||
if settings.get_is_isotope() and settings.get_mass_variances() is None:
|
||||
from phonopy.structure.atoms import isotope_data
|
||||
symbols = phonon_primitive.get_chemical_symbols()
|
||||
in_database = True
|
||||
for s in set(symbols):
|
||||
if not s in isotope_data:
|
||||
print("%s is not in the list of isotope databese" % s)
|
||||
print("(not implemented).")
|
||||
print("Use --mass_variances option.")
|
||||
in_database = False
|
||||
if not in_database:
|
||||
if log_level:
|
||||
print_end()
|
||||
sys.exit(0)
|
||||
|
||||
if run_mode == "isotope":
|
||||
mass_variances = settings.get_mass_variances()
|
||||
if band_indices is not None:
|
||||
band_indices = np.hstack(band_indices).astype('intc')
|
||||
iso = Phono3pyIsotope(
|
||||
mesh,
|
||||
phonon_primitive,
|
||||
mass_variances=mass_variances,
|
||||
band_indices=band_indices,
|
||||
sigmas=sigmas,
|
||||
frequency_factor_to_THz=frequency_factor_to_THz,
|
||||
symprec=symprec,
|
||||
cutoff_frequency=settings.get_cutoff_frequency(),
|
||||
lapack_zheev_uplo=options.uplo)
|
||||
iso.set_dynamical_matrix(phono3py.get_fc2(),
|
||||
phonon_supercell,
|
||||
phonon_primitive,
|
||||
nac_params=nac_params,
|
||||
frequency_scale_factor=frequency_scale_factor)
|
||||
iso.run(grid_points)
|
||||
if log_level:
|
||||
print_end()
|
||||
sys.exit(0)
|
||||
|
||||
#########
|
||||
# Ph-ph #
|
||||
#########
|
||||
ave_pp = settings.get_constant_averaged_pp_interaction()
|
||||
phono3py.set_phph_interaction(
|
||||
nac_params=nac_params,
|
||||
nac_q_direction=nac_q_direction,
|
||||
constant_averaged_interaction=ave_pp,
|
||||
frequency_scale_factor=frequency_scale_factor,
|
||||
unit_conversion=options.pp_unit_conversion)
|
||||
|
||||
if run_mode == "linewidth":
|
||||
if grid_points is None:
|
||||
print("Grid point(s) has to be specified with --gp or --ga option.")
|
||||
if log_level:
|
||||
print_error()
|
||||
sys.exit(1)
|
||||
phono3py.run_linewidth(
|
||||
grid_points,
|
||||
temperatures=temperatures,
|
||||
run_with_g=settings.get_run_with_g(),
|
||||
write_details=settings.get_write_detailed_gamma())
|
||||
phono3py.write_linewidth(filename=output_filename)
|
||||
elif run_mode == "imag_self_energy":
|
||||
if not settings.get_run_with_g() and settings.get_scattering_event_class():
|
||||
print("--run_without_g and --scattering_event_class can not used "
|
||||
"together.")
|
||||
if log_level:
|
||||
print_error()
|
||||
sys.exit(1)
|
||||
if grid_points is None:
|
||||
print("Grid point(s) has to be specified with --gp or --ga option.")
|
||||
if log_level:
|
||||
print_error()
|
||||
sys.exit(1)
|
||||
phono3py.run_imag_self_energy(
|
||||
grid_points,
|
||||
frequency_step=frequency_step,
|
||||
num_frequency_points=num_frequency_points,
|
||||
temperatures=temperature_points,
|
||||
scattering_event_class=settings.get_scattering_event_class(),
|
||||
run_with_g=settings.get_run_with_g(),
|
||||
write_details=settings.get_write_detailed_gamma())
|
||||
phono3py.write_imag_self_energy(filename=output_filename)
|
||||
elif run_mode == "frequency_shift":
|
||||
phono3py.get_frequency_shift(
|
||||
grid_points,
|
||||
epsilons=sigmas,
|
||||
temperatures=temperatures,
|
||||
output_filename=output_filename)
|
||||
elif run_mode == "conductivity-RTA" or run_mode == "conductivity-LBTE":
|
||||
phono3py.run_thermal_conductivity(
|
||||
is_LBTE=settings.get_is_lbte(),
|
||||
temperatures=temperatures,
|
||||
sigmas=sigmas,
|
||||
is_isotope=settings.get_is_isotope(),
|
||||
mass_variances=settings.get_mass_variances(),
|
||||
grid_points=grid_points,
|
||||
boundary_mfp=settings.get_boundary_mfp(),
|
||||
use_averaged_pp_interaction=settings.get_average_pp_interaction(),
|
||||
gamma_unit_conversion=options.gamma_unit_conversion,
|
||||
mesh_divisors=mesh_divs,
|
||||
coarse_mesh_shifts=settings.get_coarse_mesh_shifts(),
|
||||
is_reducible_collision_matrix=options.is_reducible_collision_matrix,
|
||||
no_kappa_stars=settings.get_no_kappa_stars(),
|
||||
gv_delta_q=settings.get_group_velocity_delta_q(),
|
||||
run_with_g=settings.get_run_with_g(),
|
||||
pinv_cutoff=settings.get_pinv_cutoff(),
|
||||
write_gamma=settings.get_write_gamma(),
|
||||
read_gamma=settings.get_read_gamma(),
|
||||
write_collision=settings.get_write_collision(),
|
||||
read_collision=settings.get_read_collision(),
|
||||
input_filename=input_filename,
|
||||
output_filename=output_filename)
|
||||
else:
|
||||
if log_level:
|
||||
print("** None of anharmonic properties were calculated. **")
|
||||
|
||||
if log_level:
|
||||
print_end()
|
||||
|
|
|
|||
Loading…
Reference in New Issue