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Still continue refactoring of main phonopy script

This commit is contained in:
Atsushi Togo 2020-05-11 10:11:32 +09:00
parent 0c6b6cd4c7
commit 54c351d016
5 changed files with 262 additions and 228 deletions
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82
phonopy/cui/load.py
View File

@ -32,10 +32,8 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import os
import numpy as np
from phonopy.api_phonopy import Phonopy
from phonopy.file_IO import parse_FORCE_SETS, parse_FORCE_CONSTANTS
from phonopy.interface.phonopy_yaml import PhonopyYaml
from phonopy.interface.calculator import get_default_physical_units
import phonopy.cui.load_helper as load_helper
@ -267,13 +265,12 @@ def load(phonopy_yaml=None, # phonopy.yaml-like must be the first argument.
phonon.nac_params = ret_nac_params
# Displacements, forces, and force constants
_set_dataset_and_force_constants(
load_helper.set_dataset_and_force_constants(
phonon,
_dataset,
_fc,
force_constants_filename=force_constants_filename,
force_sets_filename=force_sets_filename,
calculator=_calculator,
fc_calculator=fc_calculator,
produce_fc=produce_fc,
symmetrize_fc=symmetrize_fc,
@ -281,80 +278,3 @@ def load(phonopy_yaml=None, # phonopy.yaml-like must be the first argument.
log_level=log_level)
return phonon
def _set_dataset_and_force_constants(
phonon,
dataset,
fc, # From phonopy_yaml
force_constants_filename=None,
force_sets_filename=None,
calculator=None,
fc_calculator=None,
produce_fc=True,
symmetrize_fc=True,
is_compact_fc=True,
log_level=0):
natom = phonon.supercell.get_number_of_atoms()
# dataset and fc are those obtained from phonopy_yaml unless None.
if dataset is not None:
phonon.dataset = dataset
if fc is not None:
phonon.force_constants = fc
_dataset = None
if force_constants_filename is not None:
dot_split = force_constants_filename.split('.')
p2s_map = phonon.primitive.p2s_map
if len(dot_split) > 1 and dot_split[-1] == 'hdf5':
_fc = load_helper.read_force_constants_from_hdf5(
filename=force_constants_filename,
p2s_map=p2s_map,
calculator=calculator)
else:
_fc = parse_FORCE_CONSTANTS(filename=force_constants_filename,
p2s_map=p2s_map)
phonon.force_constants = _fc
if log_level:
print("Force constants were read from \"%s\"."
% force_constants_filename)
elif force_sets_filename is not None:
_dataset = parse_FORCE_SETS(natom=natom, filename=force_sets_filename)
if log_level:
print("Force sets were read from \"%s\"." % force_sets_filename)
elif phonon.forces is None and phonon.force_constants is None:
# unless provided these from phonopy_yaml.
if os.path.isfile("FORCE_SETS"):
_dataset = parse_FORCE_SETS(natom=natom)
if log_level:
print("Force sets were read from \"FORCE_SETS\".")
if phonon.force_constants is None:
# Overwrite dataset
if _dataset is not None:
phonon.dataset = _dataset
if produce_fc:
_produce_force_constants(phonon,
fc_calculator,
symmetrize_fc,
is_compact_fc,
log_level)
def _produce_force_constants(phonon,
fc_calculator,
symmetrize_fc,
is_compact_fc,
log_level):
try:
phonon.produce_force_constants(
calculate_full_force_constants=(not is_compact_fc),
fc_calculator=fc_calculator)
except RuntimeError:
pass
if symmetrize_fc:
phonon.symmetrize_force_constants(show_drift=(log_level > 0))
if log_level:
print("Force constants were symmetrized.")

83
phonopy/cui/load_helper.py
View File

@ -38,7 +38,8 @@ from phonopy.interface.calculator import read_crystal_structure
from phonopy.structure.cells import get_primitive_matrix_by_centring
from phonopy.file_IO import (
parse_BORN, read_force_constants_hdf5,
read_physical_unit_in_force_constants_hdf5)
read_physical_unit_in_force_constants_hdf5,
parse_FORCE_SETS, parse_FORCE_CONSTANTS)
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.interface.calculator import get_force_constant_conversion_factor
@ -144,6 +145,66 @@ def read_force_constants_from_hdf5(filename='force_constants.hdf5',
return fc * factor
def set_dataset_and_force_constants(
phonon,
dataset,
fc, # From phonopy_yaml
force_constants_filename=None,
force_sets_filename=None,
fc_calculator=None,
fc_calculator_options=None,
produce_fc=True,
symmetrize_fc=True,
is_compact_fc=True,
log_level=0):
natom = phonon.supercell.get_number_of_atoms()
# dataset and fc are those obtained from phonopy_yaml unless None.
if dataset is not None:
phonon.dataset = dataset
if fc is not None:
phonon.force_constants = fc
_dataset = None
if force_constants_filename is not None:
dot_split = force_constants_filename.split('.')
p2s_map = phonon.primitive.p2s_map
if len(dot_split) > 1 and dot_split[-1] == 'hdf5':
_fc = read_force_constants_from_hdf5(
filename=force_constants_filename,
p2s_map=p2s_map,
calculator=phonon.calculator)
else:
_fc = parse_FORCE_CONSTANTS(filename=force_constants_filename,
p2s_map=p2s_map)
phonon.force_constants = _fc
if log_level:
print("Force constants were read from \"%s\"."
% force_constants_filename)
elif force_sets_filename is not None:
_dataset = parse_FORCE_SETS(natom=natom, filename=force_sets_filename)
if log_level:
print("Force sets were read from \"%s\"." % force_sets_filename)
elif phonon.forces is None and phonon.force_constants is None:
# unless provided these from phonopy_yaml.
if os.path.isfile("FORCE_SETS"):
_dataset = parse_FORCE_SETS(natom=natom)
if log_level:
print("Force sets were read from \"FORCE_SETS\".")
if phonon.force_constants is None:
# Overwrite dataset
if _dataset is not None:
phonon.dataset = _dataset
if produce_fc:
_produce_force_constants(phonon,
fc_calculator,
fc_calculator_options,
symmetrize_fc,
is_compact_fc,
log_level)
def _get_primitive_matrix(pmat, unitcell, symprec):
if type(pmat) is str and pmat in ('F', 'I', 'A', 'C', 'R', 'auto'):
if pmat == 'auto':
@ -168,3 +229,23 @@ def _get_primitive_matrix(pmat, unitcell, symprec):
raise RuntimeError(msg)
return _pmat
def _produce_force_constants(phonon,
fc_calculator,
fc_calculator_options,
symmetrize_fc,
is_compact_fc,
log_level):
try:
phonon.produce_force_constants(
calculate_full_force_constants=(not is_compact_fc),
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
except RuntimeError:
pass
if symmetrize_fc:
phonon.symmetrize_force_constants(show_drift=(log_level > 0))
if log_level:
print("Force constants were symmetrized.")

4
phonopy/cui/phonopy_argparse.py
View File

@ -212,8 +212,8 @@ def get_parser(symmetrize_fc=False,
"--hdf5", dest="is_hdf5", action="store_true", default=False,
help="Use hdf5 for force constants")
parser.add_argument(
"--hdf5-compression", dest="hdf5_compression", default="gzip",
help="hdf5 compression filter")
"--hdf5-compression", dest="hdf5_compression", default=None,
help="hdf5 compression filter (default: gzip)")
parser.add_argument(
"--hiphive", dest="use_hiphive", action="store_true", default=False,
help="Use hiPhive for generating force constants")

293
phonopy/cui/phonopy_script.py
View File

@ -39,6 +39,7 @@ from phonopy import Phonopy, __version__
from phonopy.structure.cells import print_cell
from phonopy.structure.atoms import atom_data, symbol_map
from phonopy.interface.phonopy_yaml import PhonopyYaml
from phonopy.interface.fc_calculator import fc_calculator_names
from phonopy.interface.calculator import (
get_interface_mode, write_supercells_with_displacements,
get_default_physical_units, get_default_displacement_distance)
@ -52,7 +53,8 @@ from phonopy.file_IO import (
get_born_parameters, parse_QPOINTS)
from phonopy.cui.create_force_sets import create_FORCE_SETS
from phonopy.cui.load_helper import (
read_force_constants_from_hdf5, get_nac_params)
read_force_constants_from_hdf5, get_nac_params,
set_dataset_and_force_constants)
from phonopy.cui.show_symmetry import check_symmetry
from phonopy.cui.settings import PhonopyConfParser
from phonopy.cui.collect_cell_info import collect_cell_info
@ -210,12 +212,13 @@ def print_cells(phonon, unitcell_filename):
def print_settings(settings,
phonon,
is_primitive_axes_auto,
primitive_matrix,
supercell_matrix,
unitcell_filename,
load_phonopy_yaml,
interface_mode):
load_phonopy_yaml):
primitive_matrix = phonon.primitive_matrix
supercell_matrix = phonon.supercell_matrix
interface_mode = phonon.calculator
run_mode = settings.get_run_mode()
if interface_mode:
print("Calculator interface: %s" % interface_mode)
@ -425,16 +428,13 @@ def create_FORCE_SETS_from_args(args, log_level):
sys.exit(error_num)
def store_force_constants(phonon,
settings,
phpy_yaml,
unitcell_filename,
compression,
log_level):
def produce_force_constants(phonon,
settings,
phpy_yaml,
unitcell_filename,
log_level):
num_satom = phonon.supercell.get_number_of_atoms()
p2s_map = phonon.primitive.p2s_map
interface_mode = phonon.calculator
physical_units = get_default_physical_units(interface_mode)
if settings.get_read_force_constants():
if settings.get_is_hdf5() or settings.get_readfc_format() == 'hdf5':
@ -450,7 +450,7 @@ def store_force_constants(phonon,
fc = read_force_constants_from_hdf5(
filename="force_constants.hdf5",
p2s_map=p2s_map,
calculator=interface_mode)
calculator=phonon.calculator)
fc_filename = "force_constants.hdf5"
else:
file_exists("FORCE_CONSTANTS", log_level)
@ -527,15 +527,8 @@ def store_force_constants(phonon,
print_error()
sys.exit(1)
fc_calculator = None
if settings.get_fc_calculator() is not None:
from phonopy.interface.fc_calculator import fc_calculator_names
if settings.get_fc_calculator().lower() in fc_calculator_names:
fc_calculator = settings.get_fc_calculator().lower()
fc_calculator_options = None
if settings.get_fc_calculator_options() is not None:
fc_calculator_options = settings.get_fc_calculator_options()
(fc_calculator,
fc_calculator_options) = get_fc_calculator_params(settings)
phonon.dataset = force_sets
if log_level:
@ -550,12 +543,45 @@ def store_force_constants(phonon,
phonon.produce_force_constants(
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
else: # Only force constants between atoms in primitive cell and supercell
else:
# Only force constants between atoms in primitive cell and
# supercell
phonon.produce_force_constants(
calculate_full_force_constants=False,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
def store_force_constants(phonon,
settings,
phpy_yaml,
unitcell_filename,
load_phonopy_yaml,
log_level):
physical_units = get_default_physical_units(phonon.calculator)
p2s_map = phonon.primitive.p2s_map
if load_phonopy_yaml:
(fc_calculator,
fc_calculator_options) = get_fc_calculator_params(settings)
is_full_fc = (settings.get_fc_spg_symmetry() or
settings.get_is_full_fc())
set_dataset_and_force_constants(
phonon,
phpy_yaml.dataset,
phpy_yaml.force_constants,
fc_calculator=fc_calculator,
produce_fc=True,
symmetrize_fc=False,
is_compact_fc=(not is_full_fc),
log_level=log_level)
else:
produce_force_constants(phonon,
settings,
phpy_yaml,
unitcell_filename,
log_level)
# Impose cutoff radius on force constants
cutoff_radius = settings.get_cutoff_radius()
if cutoff_radius:
@ -583,10 +609,11 @@ def store_force_constants(phonon,
if settings.get_write_force_constants():
if settings.get_is_hdf5() or settings.get_writefc_format() == 'hdf5':
fc_unit = physical_units['force_constants_unit']
write_force_constants_to_hdf5(phonon.get_force_constants(),
p2s_map=p2s_map,
physical_unit=fc_unit,
compression=compression)
write_force_constants_to_hdf5(
phonon.get_force_constants(),
p2s_map=p2s_map,
physical_unit=fc_unit,
compression=settings.get_hdf5_compression())
if log_level:
print("Force constants are written into "
"\"force_constants.hdf5\".")
@ -641,7 +668,7 @@ def store_nac_params(phonon,
print("NAC parameters were read from \"%s\"."
% unitcell_filename)
if file_exists("BORN", log_level):
if nac_params is None and file_exists("BORN", log_level):
nac_params = read_BORN(phonon)
if nac_params is not None and log_level:
print("NAC parameters were read from \"%s\"." % "BORN")
@ -843,55 +870,57 @@ def run(phonon, settings, plot_conf, log_level):
else:
phonon.write_yaml_mesh()
# Thermal property
if settings.get_is_thermal_properties():
#
# Thermal property
#
if settings.get_is_thermal_properties():
if log_level:
if settings.get_is_projected_thermal_properties():
print("Calculating projected thermal properties...")
else:
print("Calculating thermal properties...")
tprop_range = settings.get_thermal_property_range()
tstep = tprop_range['step']
tmax = tprop_range['max']
tmin = tprop_range['min']
phonon.run_thermal_properties(
t_min=tmin,
t_max=tmax,
t_step=tstep,
is_projection=settings.get_is_projected_thermal_properties(),
band_indices=settings.get_band_indices(),
cutoff_frequency=settings.get_cutoff_frequency(),
pretend_real=settings.get_pretend_real())
phonon.write_yaml_thermal_properties()
if log_level:
if settings.get_is_projected_thermal_properties():
print("Calculating projected thermal properties...")
else:
print("Calculating thermal properties...")
tprop_range = settings.get_thermal_property_range()
tstep = tprop_range['step']
tmax = tprop_range['max']
tmin = tprop_range['min']
phonon.run_thermal_properties(
t_min=tmin,
t_max=tmax,
t_step=tstep,
is_projection=settings.get_is_projected_thermal_properties(),
band_indices=settings.get_band_indices(),
cutoff_frequency=settings.get_cutoff_frequency(),
pretend_real=settings.get_pretend_real())
phonon.write_yaml_thermal_properties()
if log_level:
print("#%11s %15s%15s%15s%15s" % ('T [K]',
'F [kJ/mol]',
'S [J/K/mol]',
'C_v [J/K/mol]',
'E [kJ/mol]'))
tp = phonon.get_thermal_properties_dict()
temps = tp['temperatures']
fe = tp['free_energy']
entropy = tp['entropy']
heat_capacity = tp['heat_capacity']
for T, F, S, CV in zip(temps, fe, entropy, heat_capacity):
print(("%12.3f " + "%15.7f" * 4) %
(T, F, S, CV, F + T * S / 1000))
if log_level:
print("#%11s %15s%15s%15s%15s" % ('T [K]',
'F [kJ/mol]',
'S [J/K/mol]',
'C_v [J/K/mol]',
'E [kJ/mol]'))
tp = phonon.get_thermal_properties_dict()
temps = tp['temperatures']
fe = tp['free_energy']
entropy = tp['entropy']
heat_capacity = tp['heat_capacity']
for T, F, S, CV in zip(temps, fe, entropy, heat_capacity):
print(("%12.3f " + "%15.7f" * 4) %
(T, F, S, CV, F + T * S / 1000))
if plot_conf['plot_graph']:
plot = phonon.plot_thermal_properties()
if plot_conf['save_graph']:
plot.savefig('thermal_properties.pdf')
else:
plot.show()
if plot_conf['plot_graph']:
plot = phonon.plot_thermal_properties()
if plot_conf['save_graph']:
plot.savefig('thermal_properties.pdf')
else:
plot.show()
#
# Thermal displacements
#
if (settings.get_is_thermal_displacements() and
run_mode in ('mesh', 'band_mesh')):
elif (settings.get_is_thermal_displacements() and
run_mode in ('mesh', 'band_mesh')):
p_direction = settings.get_projection_direction()
if log_level and p_direction is not None:
c_direction = np.dot(p_direction, phonon.primitive.cell)
@ -926,8 +955,8 @@ def run(phonon, settings, plot_conf, log_level):
#
# Thermal displacement matrices
#
if (settings.get_is_thermal_displacement_matrices() and
run_mode in ('mesh', 'band_mesh')):
elif (settings.get_is_thermal_displacement_matrices() and
run_mode in ('mesh', 'band_mesh')):
if log_level:
print("Calculating thermal displacement matrices...")
tprop_range = settings.get_thermal_property_range()
@ -953,8 +982,8 @@ def run(phonon, settings, plot_conf, log_level):
#
# Projected DOS
#
if (settings.get_pdos_indices() is not None and
run_mode in ('mesh', 'band_mesh')):
elif (settings.get_pdos_indices() is not None and
run_mode in ('mesh', 'band_mesh')):
p_direction = settings.get_projection_direction()
if (log_level and
p_direction is not None and
@ -999,9 +1028,9 @@ def run(phonon, settings, plot_conf, log_level):
#
# Total DOS
#
if ((plot_conf['plot_graph'] or settings.get_is_dos_mode()) and
not is_pdos_auto(settings) and
run_mode in ('mesh', 'band_mesh')):
elif ((plot_conf['plot_graph'] or settings.get_is_dos_mode()) and
not is_pdos_auto(settings) and
run_mode in ('mesh', 'band_mesh')):
phonon.run_total_dos(
sigma=settings.get_sigma(),
freq_min=settings.get_min_frequency(),
@ -1029,7 +1058,7 @@ def run(phonon, settings, plot_conf, log_level):
#
# Momemt
#
if (settings.get_is_moment() and
elif (settings.get_is_moment() and
run_mode in ('mesh', 'band_mesh')):
freq_min = settings.get_min_frequency()
freq_max = settings.get_max_frequency()
@ -1100,7 +1129,7 @@ def run(phonon, settings, plot_conf, log_level):
#
# Animation
#
if run_mode == 'anime':
elif run_mode == 'anime':
anime_type = settings.get_anime_type()
if anime_type == "v_sim":
q_point = settings.get_anime_qpoint()
@ -1132,7 +1161,7 @@ def run(phonon, settings, plot_conf, log_level):
#
# Modulation
#
if run_mode == 'modulation':
elif run_mode == 'modulation':
mod_setting = settings.get_modulation()
phonon_modes = mod_setting['modulations']
dimension = mod_setting['dimension']
@ -1181,7 +1210,7 @@ def run(phonon, settings, plot_conf, log_level):
#
# Ir-representation
#
if run_mode == 'irreps':
elif run_mode == 'irreps':
if phonon.set_irreps(
settings.get_irreps_q_point(),
is_little_cogroup=settings.get_is_little_cogroup(),
@ -1207,16 +1236,6 @@ def start_phonopy(**argparse_control):
if args.loglevel is not None:
log_level = args.loglevel
# HDF5 compression filter
try:
compression = int(args.hdf5_compression)
except ValueError: # str
compression = args.hdf5_compression
if compression.lower() == "none":
compression = None
except TypeError: # None
compression = args.hdf5_compression
if args.is_graph_save:
import matplotlib
matplotlib.use('Agg')
@ -1233,9 +1252,7 @@ def start_phonopy(**argparse_control):
if deprecated:
show_deprecated_option_warnings(deprecated)
return (args,
log_level,
compression,
return (args, log_level,
{'plot_graph': args.is_graph_plot,
'save_graph': args.is_graph_save,
'with_legend': args.is_legend})
@ -1295,6 +1312,19 @@ def auto_primitive_axes(primitive_matrix):
return (type(primitive_matrix) is str and primitive_matrix == 'auto')
def get_fc_calculator_params(settings):
fc_calculator = None
if settings.get_fc_calculator() is not None:
if settings.get_fc_calculator().lower() in fc_calculator_names:
fc_calculator = settings.get_fc_calculator().lower()
fc_calculator_options = None
if settings.get_fc_calculator_options() is not None:
fc_calculator_options = settings.get_fc_calculator_options()
return fc_calculator, fc_calculator_options
def get_cell_info(settings, cell_filename, symprec, log_level):
"""calculator interface and crystal structure information"""
@ -1321,9 +1351,9 @@ def get_cell_info(settings, cell_filename, symprec, log_level):
# Set magnetic moments
magmoms = settings.get_magnetic_moments()
if magmoms is not None:
unitcell = cell_info[0]
unitcell = cell_info['unitcell']
if len(magmoms) == unitcell.get_number_of_atoms():
unitcell.set_magnetic_moments(magmoms)
unitcell.magnetic_moments = magmoms
else:
error_text = "Invalid MAGMOM setting"
print_error_message(error_text)
@ -1331,8 +1361,7 @@ def get_cell_info(settings, cell_filename, symprec, log_level):
print_error()
sys.exit(1)
primitive_matrix = cell_info[2]
if primitive_matrix == 'auto':
if auto_primitive_axes(cell_info['primitive_matrix']):
error_text = ("'PRIMITIVE_AXES = auto', 'BAND = auto', or no DIM "
"setting is not allowed with MAGMOM.")
print_error_message(error_text)
@ -1357,9 +1386,10 @@ def show_symmetry_info_then_exit(cell_info, symprec):
sys.exit(0)
def init_phonopy(settings, cell_info, symprec, run_mode, log_level):
def init_phonopy(settings, cell_info, symprec, log_level):
# Prepare phonopy object
if run_mode == 'displacements' and settings.get_temperatures() is None:
if (settings.get_run_mode() == 'displacements' and
settings.get_temperatures() is None):
phonon = Phonopy(cell_info['unitcell'],
cell_info['supercell_matrix'],
primitive_matrix=cell_info['primitive_matrix'],
@ -1395,6 +1425,23 @@ def init_phonopy(settings, cell_info, symprec, run_mode, log_level):
if settings.get_masses() is not None:
phonon.masses = settings.get_masses()
# Atomic species without mass case
symbols_with_no_mass = []
if phonon.primitive.masses is None:
for s in phonon.primitive.symbols:
if (atom_data[symbol_map[s]][3] is None and
s not in symbols_with_no_mass):
symbols_with_no_mass.append(s)
print_error_message(
"Atomic mass of \'%s\' is not implemented in phonopy." % s)
print_error_message(
"MASS tag can be used to set atomic masses.")
if len(symbols_with_no_mass) > 0:
if log_level:
print_end()
sys.exit(1)
return phonon
@ -1404,7 +1451,7 @@ def main(**argparse_control):
############################################
load_phonopy_yaml = argparse_control.get('load_phonopy_yaml', False)
args, log_level, compression, plot_conf = start_phonopy(**argparse_control)
args, log_level, plot_conf = start_phonopy(**argparse_control)
# Phonopy utils to create FORCE_SETS and FORCE_CONSTANTS
create_phonopy_files_then_exit(args, log_level)
@ -1437,20 +1484,17 @@ def main(**argparse_control):
######################
# Initialize phonopy #
######################
run_mode = settings.get_run_mode()
phonon = init_phonopy(settings, cell_info, symprec, run_mode, log_level)
phonon = init_phonopy(settings, cell_info, symprec, log_level)
################################################
# Show phonopy settings and crystal structures #
################################################
if log_level:
print_settings(settings,
phonon,
auto_primitive_axes(cell_info['primitive_matrix']),
phonon.primitive_matrix,
phonon.supercell_matrix,
unitcell_filename,
load_phonopy_yaml,
phonon.calculator)
load_phonopy_yaml)
if cell_info['magmoms'] is None:
print("Spacegroup: %s" %
phonon.get_symmetry().get_international_table())
@ -1465,7 +1509,8 @@ def main(**argparse_control):
#########################################################
# Create constant amplitude displacements and then exit #
#########################################################
if run_mode == 'displacements' and settings.get_temperatures() is None:
if (settings.get_run_mode() == 'displacements' and
settings.get_temperatures() is None):
if settings.get_displacement_distance() is None:
displacement_distance = get_default_displacement_distance(
phonon.calculator)
@ -1492,7 +1537,7 @@ def main(**argparse_control):
settings,
cell_info['phonopy_yaml'],
unitcell_filename,
compression,
load_phonopy_yaml,
log_level)
##################################
@ -1505,31 +1550,11 @@ def main(**argparse_control):
load_phonopy_yaml,
log_level)
########
# Misc #
########
# Atomic species without mass case
symbols_with_no_mass = []
if phonon.primitive.masses is None:
for s in phonon.primitive.symbols:
if (atom_data[symbol_map[s]][3] is None and
s not in symbols_with_no_mass):
symbols_with_no_mass.append(s)
print_error_message(
"Atomic mass of \'%s\' is not implemented in phonopy." % s)
print_error_message(
"MASS tag can be used to set atomic masses.")
if len(symbols_with_no_mass) > 0:
if log_level:
print_end()
sys.exit(1)
###################################################################
# Create random displacements at finite temperature and then exit #
###################################################################
if (run_mode == 'displacements' and
settings.get_random_displacements() is not None):
if (settings.get_run_mode() == 'displacements' and
settings.get_temperatures() is not None):
phonon.generate_displacements(
number_of_snapshots=settings.get_random_displacements(),
random_seed=settings.get_random_seed(),
@ -1544,8 +1569,8 @@ def main(**argparse_control):
#######################
# Phonon calculations #
#######################
if run_mode not in ('band', 'mesh', 'band_mesh', 'anime', 'modulation',
'irreps', 'qpoints'):
if settings.get_run_mode() not in ('band', 'mesh', 'band_mesh', 'anime',
'modulation', 'irreps', 'qpoints'):
print("-" * 76)
print(" One of the following run modes may be specified for phonon "
"calculations.")

28
phonopy/cui/settings.py
View File

@ -928,12 +928,16 @@ class ConfParser(object):
# Compression option for writing int hdf5
if conf_key == 'hdf5_compression':
if (type(confs['hdf5_compression']) is str and
confs['hdf5_compression'].lower() == 'none'):
self.set_parameter('hdf5_compression', None)
else:
self.set_parameter('hdf5_compression',
confs['hdf5_compression'])
hdf5_compression = confs['hdf5_compression']
try:
compression = int(hdf5_compression)
except ValueError: # str
compression = hdf5_compression
if compression.lower() == "none":
compression = None
except TypeError: # None (this will not happen)
compression = hdf5_compression
self.set_parameter('hdf5_compression', compression)
def set_parameter(self, key, val):
self._parameters[key] = val
@ -2421,10 +2425,14 @@ class PhonopyConfParser(ConfParser):
if 'include_all' in params:
self._settings.set_include_all(params['include_all'])
# ***********************************************************
# This has to come last in this method to overwrite run_mode.
# ***********************************************************
if 'pdos' in params and params['pdos'] == 'auto':
if 'band_paths' in params:
self._settings.set_run_mode('band_mesh')
else:
self._settings.set_run_mode('mesh')
if 'mesh_numbers' in params and 'band_paths' in params:
self._settings.set_run_mode('band_mesh')
elif ('pdos' in params and
params['pdos'] == 'auto' and
'band_paths' in params):
self._settings.set_run_mode('band_mesh')