def parse_QPOINTS(filename="QPOINTS"):
with open(filename, 'r') as f:
num_qpoints = int(f.readline().strip())
qpoints = []
for i in range(num_qpoints):
qpoints.append([fracval(x) for x in f.readline().strip().split()])
return np.array(qpoints)
def parse_QPOINTS(filename="QPOINTS"):
f = open(filename, 'r')
num_qpoints = int(f.readline().strip())
qpoints = []
for i in range(num_qpoints):
qpoints.append([fracval(x) for x in f.readline().strip().split()])
return np.array(qpoints)
def parse_QPOINTS(filename="QPOINTS"):
from phonopy.cui.settings import fracval
with open(filename, 'r') as f:
num_qpoints = int(f.readline().strip())
qpoints = []
for i in range(num_qpoints):
qpoints.append([fracval(x) for x in f.readline().strip().split()])
return np.array(qpoints)
def parse_QPOINTS(filename="QPOINTS"):
from phonopy.cui.settings import fracval
f = open(filename, 'r')
num_qpoints = int(f.readline().strip())
qpoints = []
for i in range(num_qpoints):
qpoints.append([fracval(x) for x in f.readline().strip().split()])
return np.array(qpoints)
def _get_numerical_values(self, char_string, num_type='float'):
m = 1
if '*' in char_string:
m = int(char_string.split('*')[0])
str_val = char_string.split('*')[1]
else:
m = 1
str_val = char_string
if num_type == 'float':
a = fracval(str_val)
else:
a = int(str_val)
return [a] * m
def _get_numerical_values(self, char_string, num_type='float'):
m = 1
if '*' in char_string:
m = int(char_string.split('*')[0])
str_val = char_string.split('*')[1]
else:
m = 1
str_val = char_string
if num_type == 'float':
a = fracval(str_val)
else:
a = int(str_val)
return [a] * m
def _get_numerical_values(self, char_string, num_type="float"):
m = 1
if "*" in char_string:
m = int(char_string.split("*")[0])
str_val = char_string.split("*")[1]
else:
m = 1
str_val = char_string
if num_type == "float":
a = fracval(str_val)
else:
a = int(str_val)
return [a] * m
def _get_numerical_values(self, char_string, num_type="float"):
vals = []
m = 1
if "*" in char_string:
m = int(char_string.split("*")[0])
str_val = char_string.split("*")[1]
else:
m = 1
str_val = char_string
if num_type == "float":
a = fracval(str_val)
else:
a = int(str_val)
return [a] * m
def _parse_conf(self):
confs = self._confs
for conf_key in confs.keys():
if conf_key == 'dim_fc2':
matrix = [int(x) for x in confs['dim_fc2'].split()]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error(
"Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error(
"Determinant of supercell matrix has " +
"to be positive.")
else:
self.set_parameter('dim_fc2', matrix)
if conf_key == 'boundary_mfp':
self.set_parameter('boundary_mfp',
float(confs['boundary_mfp']))
if conf_key == 'constant_averaged_pp_interaction':
self.set_parameter(
'constant_averaged_pp_interaction',
float(confs['constant_averaged_pp_interaction']))
if conf_key == 'cutoff_fc3_distance':
self.set_parameter('cutoff_fc3_distance',
float(confs['cutoff_fc3_distance']))
if conf_key == 'cutoff_pair_distance':
self.set_parameter('cutoff_pair_distance',
float(confs['cutoff_pair_distance']))
if conf_key == 'grid_addresses':
vals = [
int(x)
for x in confs['grid_addresses'].replace(',', ' ').split()
]
if len(vals) % 3 == 0 and len(vals) > 0:
self.set_parameter('grid_addresses',
np.reshape(vals, (-1, 3)))
else:
self.setting_error("Grid addresses are incorrectly set.")
if conf_key == 'grid_points':
vals = [
int(x)
for x in confs['grid_points'].replace(',', ' ').split()
]
self.set_parameter('grid_points', vals)
if conf_key == 'ion_clamped':
if confs['ion_clamped'] == '.true.':
self.set_parameter('ion_clamped', True)
if conf_key == 'bterta':
if confs['bterta'] == '.true.':
self.set_parameter('is_bterta', True)
if conf_key == 'imag_self_energy':
if confs['imag_self_energy'] == '.true.':
self.set_parameter('is_imag_self_energy', True)
if conf_key == 'isotope':
if confs['isotope'] == '.true.':
self.set_parameter('is_isotope', True)
if conf_key == 'lbte':
if confs['lbte'] == '.true.':
self.set_parameter('is_lbte', True)
if conf_key == 'linewidth':
if confs['linewidth'] == '.true.':
self.set_parameter('is_linewidth', True)
if conf_key == 'frequency_shift':
if confs['frequency_shift'] == '.true.':
self.set_parameter('is_frequency_shift', True)
if conf_key == 'mass_variances':
vals = [fracval(x) for x in confs['mass_variances'].split()]
if len(vals) < 1:
self.setting_error(
"Mass variance parameters are incorrectly set.")
else:
self.set_parameter('mass_variances', vals)
if conf_key == 'max_freepath':
self.set_parameter('max_freepath',
float(confs['max_freepath']))
if conf_key == 'mesh_divisors':
vals = [x for x in confs['mesh_divisors'].split()]
if len(vals) == 3:
self.set_parameter('mesh_divisors', [int(x) for x in vals])
elif len(vals) == 6:
divs = [int(x) for x in vals[:3]]
is_shift = [x.lower() == 't' for x in vals[3:]]
for i in range(3):
if is_shift[i] and (divs[i] % 2 != 0):
is_shift[i] = False
self.setting_error(
"Coarse grid shift along the " +
["first", "second", "third"][i] +
" axis is not allowed.")
self.set_parameter('mesh_divisors', divs + is_shift)
else:
self.setting_error("Mesh divisors are incorrectly set.")
if conf_key == 'no_kappa_stars':
if confs['no_kappa_stars'] == '.true.':
self.set_parameter('no_kappa_stars', True)
if conf_key == 'pinv_cutoff':
self.set_parameter('pinv_cutoff', float(confs['pinv_cutoff']))
if conf_key == 'read_amplitude':
if confs['read_amplitude'] == '.true.':
self.set_parameter('read_amplitude', True)
if conf_key == 'read_collision':
if confs['read_collision'] == 'all':
self.set_parameter('read_collision', 'all')
else:
vals = [int(x) for x in confs['read_collision'].split()]
self.set_parameter('read_collision', vals)
if conf_key == 'read_gamma':
if confs['read_gamma'] == '.true.':
self.set_parameter('read_gamma', True)
if conf_key == 'run_with_g':
if confs['run_with_g'] == '.false.':
self.set_parameter('run_with_g', False)
if conf_key == 'scattering_event_class':
self.set_parameter('scattering_event_class',
confs['scattering_event_class'])
if conf_key == 'temperatures':
vals = [fracval(x) for x in confs['temperatures'].split()]
if len(vals) < 1:
self.setting_error("Temperatures are incorrectly set.")
else:
self.set_parameter('temperatures', vals)
if conf_key == 'average_pp_interaction':
if confs['average_pp_interaction'] == '.true.':
self.set_parameter('average_pp_interaction', True)
if conf_key == 'write_amplitude':
if confs['write_amplitude'] == '.true.':
self.set_parameter('write_amplitude', True)
if conf_key == 'write_detailed_gamma':
if confs['write_detailed_gamma'] == '.true.':
self.set_parameter('write_detailed_gamma', True)
if conf_key == 'write_gamma':
if confs['write_gamma'] == '.true.':
self.set_parameter('write_gamma', True)
if conf_key == 'write_collision':
if confs['write_collision'] == '.true.':
self.set_parameter('write_collision', True)
def _parse_conf(self):
confs = self._confs
for conf_key in confs.keys():
if conf_key == 'dim_extra':
matrix = [ int(x) for x in confs['dim_extra'].replace(",", " ").split() ]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error("Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error('Determinant of supercell matrix has to be positive.')
else:
self.set_parameter('dim_extra', matrix)
if conf_key == "mesh_shift":
vals = [fracval(x) for x in confs['mesh_shift'].replace(",", " ").split()]
for i in range(3-len(vals)):
vals += [0.0] # Correction for incomplete shift set
self.set_parameter('mesh_shift', vals[:3])
if conf_key == 'band_indices':
vals = []
for sum_set in confs['band_indices'].replace(",", " ").split(','):
vals.append([int(x) - 1 for x in sum_set.replace(",", " ").split()])
self.set_parameter('band_indices', vals)
if conf_key == 'grid_points':
vals = [int(x) for x in confs['grid_points'].replace(",", " ").split()]
self.set_parameter('grid_points', vals)
if conf_key == 'bterta':
if confs['bterta'] == '.true.':
self.set_parameter('is_bterta', True)
if conf_key == 'linewidth':
if confs['linewidth'] == '.true.':
self.set_parameter('is_linewidth', True)
if conf_key == 'read_fc2':
if confs['read_fc2']== '.true.':
self.set_parameter('read_fc2',True)
if conf_key == 'read_fc2_extra':
if confs['read_fc2_extra']== '.true.':
self.set_parameter('read_fc2_extra',True)
if conf_key == 'max_freepath':
self.set_parameter('max_freepath', float(confs['max_freepath']))
if conf_key == 'no_kappa_stars':
if confs['no_kappa_stars'] == '.true.':
self.set_parameter('no_kappa_stars', True)
if conf_key == 'read_gamma':
if confs['read_gamma'] == '.true.':
self.set_parameter('read_gamma', True)
if conf_key == 'temperature':
vals = confs['temperature']
self.set_parameter('temperature', vals)
if conf_key == 'write_gamma':
if confs['write_gamma'] == '.true.':
self.set_parameter('write_gamma', True)
def _parse_conf(self):
confs = self._confs
for conf_key in confs.keys():
if conf_key == 'dim_extra':
matrix = [ int(x) for x in confs['dim_extra'].replace(",", " ").split() ]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error("Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error('Determinant of supercell matrix has to be positive.')
else:
self.set_parameter('dim_extra', matrix)
if conf_key == 'band_indices':
vals = []
for sum_set in confs['band_indices'].split(','):
vals.append([int(x) - 1 for x in sum_set.split()])
self.set_parameter('band_indices', vals)
if conf_key == 'cutoff_pair':
cutpair=[ float(x) for x in confs['cutoff_pair'].replace(","," ").split()]
self.set_parameter('cutoff_pair',cutpair)
if conf_key == 'cutoff_triplet':
cutfc3 = [ float(x) for x in confs['cutoff_triplet'].replace(","," ").split()]
self.set_parameter('cutoff_triplet',cutfc3)
if conf_key == 'cutoff_radius':
cutfc3q = [ float(x) for x in confs['cutoff_radius'].replace(","," ").split()]
self.set_parameter('cutoff_radius',cutfc3q)
if conf_key == "cutoff_delta":
self.set_parameter("cutoff_delta", float(confs["cutoff_delta"]))
if conf_key == 'cutoff_frequency':
self.set_parameter('cutoff_frequency', confs['cutoff_frequency'])
if conf_key == 'cutoff_hfrequency':
self.set_parameter('cutoff_hfrequency', confs['cutoff_hfrequency'])
if conf_key == 'cutoff_lifetime':
self.set_parameter('cutoff_lifetime', confs['cutoff_lifetime'])
if conf_key == "diff_kappa":
self.set_parameter("diff_kappa", confs['diff_kappa'])
if conf_key == "diff_gamma":
self.set_parameter("diff_gamma", confs['diff_gamma'])
if conf_key == 'grid_points':
vals = [int(x) for x in confs['grid_points'].replace(",", " ").split()]
self.set_parameter('grid_points', vals)
if conf_key == 'ion_clamped':
if confs['ion_clamped'] == '.true.':
self.set_parameter('ion_clamped', True)
if conf_key == "ite":
if confs['ite'] == ".true.":
self.set_parameter('is_ite',True)
if conf_key == "ite_cg":
if confs['ite_cg'] == ".true.":
self.set_parameter('is_ite_cg',True)
if conf_key == "length":
self.set_parameter('length', confs['length'])
if conf_key == "ise":
if confs['ise'] == ".true.":
self.set_parameter('is_ise',True)
if conf_key == 'bterta':
if confs['bterta'] == '.true.':
self.set_parameter('is_bterta', True)
if conf_key == 'linewidth':
if confs['linewidth'] == '.true.':
self.set_parameter('is_linewidth', True)
if conf_key == 'nu':
if confs['nu'] is not None:
nu = confs['nu'].strip().upper()[0]
if nu == "N" or nu == "U":
self.set_parameter('nu',nu)
if conf_key == 'read_fc2':
if confs['read_fc2']== '.true.':
self.set_parameter('read_fc2',True)
if conf_key == 'read_fc2_extra':
if confs['read_fc2_extra']== '.true.':
self.set_parameter('read_fc2_extra',True)
if conf_key == 'read_fc3':
if confs['read_fc3']== '.true.':
self.set_parameter('read_fc3',True)
if conf_key == 'frequency_shift':
if confs['frequency_shift'] == '.true.':
self.set_parameter('is_frequency_shift', True)
if conf_key == 'mass_variances':
vals = [fracval(x) for x in confs['mass_variances'].split()]
if len(vals) < 1:
self.setting_error("Mass variance parameters are incorrectly set.")
else:
self.set_parameter('mass_variances', vals)
if conf_key == "max_ite":
self.set_parameter("max_ite", int(confs['max_ite']))
if conf_key == 'max_freepath':
self.set_parameter('max_freepath', float(confs['max_freepath']))
if conf_key == 'mesh_divisors':
vals = [x for x in confs['mesh_divisors'].split()]
if len(vals) == 3:
self.set_parameter('mesh_divisors', [int(x) for x in vals])
elif len(vals) == 6:
divs = [int(x) for x in vals[:3]]
is_shift = [x.lower() == 't' for x in vals[3:]]
for i in range(3):
if is_shift[i] and (divs[i] % 2 != 0):
is_shift[i] = False
self.setting_error("Coarse grid shift along the " +
["first", "second", "third"][i] +
" axis is not allowed.")
self.set_parameter('mesh_divisors', divs + is_shift)
else:
self.setting_error("Mesh divisors are incorrectly set.")
if conf_key == 'multiple_sigmas':
vals = [fracval(x) for x in confs['multiple_sigmas'].replace(",", " ").split()]
if len(vals) < 1:
self.setting_error("Mutiple sigmas are incorrectly set.")
else:
self.set_parameter('multiple_sigmas', vals)
if conf_key == "adaptive_sigma_step":
self.set_parameter("adaptive_sigma_step", int(confs['adaptive_sigma_step']))
if conf_key == 'kappa_write_step':
self.set_parameter('kappa_write_step', int(confs['kappa_write_step']))
if conf_key == 'no_kappa_stars':
if confs['no_kappa_stars'] == '.true.':
self.set_parameter('no_kappa_stars', True)
if conf_key == 'read_amplitude':
if confs['read_amplitude'] == '.true.':
self.set_parameter('read_amplitude', True)
if conf_key == 'read_gamma':
if confs['read_gamma'] == '.true.':
self.set_parameter('read_gamma', True)
if conf_key == 'temperatures':
vals = [fracval(x) for x in confs['temperatures'].replace(",", " ").split()]
if len(vals) < 1:
self.setting_error("Temperatures are incorrectly set.")
else:
self.set_parameter('temperatures', vals)
if conf_key == 'write_amplitude':
if confs['write_amplitude'] == '.true.':
self.set_parameter('write_amplitude', True)
if conf_key == 'write_gamma':
if confs['write_gamma'] == '.true.':
self.set_parameter('write_gamma', True)
if conf_key == "write_triplet":
if confs['write_triplet'] == '.true.':
self.set_parameter('write_triplet', True)
def _parse_conf(self):
confs = self._confs
for conf_key in confs.keys():
if conf_key == 'create_displacements':
if confs['create_displacements'] == '.true.':
self.set_parameter('create_displacements', True)
if conf_key == 'dim_fc2':
matrix = [ int(x) for x in confs['dim_fc2'].split() ]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error(
"Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error(
"Determinant of supercell matrix has " +
"to be positive.")
else:
self.set_parameter('dim_fc2', matrix)
if conf_key == 'boundary_mfp':
self.set_parameter('boundary_mfp',
float(confs['boundary_mfp']))
if conf_key == 'constant_averaged_pp_interaction':
self.set_parameter(
'constant_averaged_pp_interaction',
float(confs['constant_averaged_pp_interaction']))
if conf_key == 'cutoff_fc3_distance':
self.set_parameter('cutoff_fc3_distance',
float(confs['cutoff_fc3_distance']))
if conf_key == 'cutoff_pair_distance':
self.set_parameter('cutoff_pair_distance',
float(confs['cutoff_pair_distance']))
if conf_key == 'frequency_scale_factor':
self.set_parameter('frequency_scale_factor',
float(confs['frequency_scale_factor']))
if conf_key == 'full_pp':
if confs['full_pp'] == '.true.':
self.set_parameter('is_full_pp', True)
if conf_key == 'gamma_conversion_factor':
self.set_parameter('gamma_conversion_factor',
float(confs['gamma_conversion_factor']))
if conf_key == 'grid_addresses':
vals = [int(x) for x in
confs['grid_addresses'].replace(',', ' ').split()]
if len(vals) % 3 == 0 and len(vals) > 0:
self.set_parameter('grid_addresses',
np.reshape(vals, (-1, 3)))
else:
self.setting_error("Grid addresses are incorrectly set.")
if conf_key == 'grid_points':
vals = [int(x) for x in
confs['grid_points'].replace(',', ' ').split()]
self.set_parameter('grid_points', vals)
if conf_key == 'ion_clamped':
if confs['ion_clamped'] == '.true.':
self.set_parameter('ion_clamped', True)
if conf_key == 'bterta':
if confs['bterta'] == '.true.':
self.set_parameter('is_bterta', True)
if conf_key == 'frequency_shift':
if confs['frequency_shift'] == '.true.':
self.set_parameter('is_frequency_shift', True)
if conf_key == 'gruneisen':
if confs['gruneisen'] == '.true.':
self.set_parameter('is_gruneisen', True)
if conf_key == 'imag_self_energy':
if confs['imag_self_energy'] == '.true.':
self.set_parameter('is_imag_self_energy', True)
if conf_key == 'isotope':
if confs['isotope'] == '.true.':
self.set_parameter('is_isotope', True)
if conf_key == 'joint_dos':
if confs['joint_dos'] == '.true.':
self.set_parameter('is_joint_dos', True)
if conf_key == 'lbte':
if confs['lbte'] == '.true.':
self.set_parameter('is_lbte', True)
if conf_key == 'linewidth':
if confs['linewidth'] == '.true.':
self.set_parameter('is_linewidth', True)
if conf_key == 'reducible_collision_matrix':
if confs['reducible_collision_matrix'] == '.true.':
self.set_parameter('is_reducible_collision_matrix', True)
if conf_key == 'symmetrize_fc2':
if confs['symmetrize_fc2'] == '.true.':
self.set_parameter('is_symmetrize_fc2', True)
if conf_key == 'symmetrize_fc3_q':
if confs['symmetrize_fc3_q'] == '.true.':
self.set_parameter('is_symmetrize_fc3_q', True)
if conf_key == 'symmetrize_fc3_r':
if confs['symmetrize_fc3_r'] == '.true.':
self.set_parameter('is_symmetrize_fc3_r', True)
if conf_key == 'mass_variances':
vals = [fracval(x) for x in confs['mass_variances'].split()]
if len(vals) < 1:
self.setting_error("Mass variance parameters are incorrectly set.")
else:
self.set_parameter('mass_variances', vals)
if conf_key == 'max_freepath':
self.set_parameter('max_freepath', float(confs['max_freepath']))
if conf_key == 'mesh_divisors':
vals = [x for x in confs['mesh_divisors'].split()]
if len(vals) == 3:
self.set_parameter('mesh_divisors', [int(x) for x in vals])
elif len(vals) == 6:
divs = [int(x) for x in vals[:3]]
is_shift = [x.lower() == 't' for x in vals[3:]]
for i in range(3):
if is_shift[i] and (divs[i] % 2 != 0):
is_shift[i] = False
self.setting_error("Coarse grid shift along the " +
["first", "second", "third"][i] +
" axis is not allowed.")
self.set_parameter('mesh_divisors', divs + is_shift)
else:
self.setting_error("Mesh divisors are incorrectly set.")
if conf_key == 'kappa_star':
if confs['kappa_star'] == '.false.':
self.set_parameter('is_kappa_star', False)
if conf_key == 'pinv_cutoff':
self.set_parameter('pinv_cutoff', float(confs['pinv_cutoff']))
if conf_key == 'pp_conversion_factor':
self.set_parameter('pp_conversion_factor',
float(confs['pp_conversion_factor']))
if conf_key == 'read_amplitude':
if confs['read_amplitude'] == '.true.':
self.set_parameter('read_amplitude', True)
if conf_key == 'read_collision':
if confs['read_collision'] == 'all':
self.set_parameter('read_collision', 'all')
else:
vals = [int(x) for x in confs['read_collision'].split()]
self.set_parameter('read_collision', vals)
if conf_key == 'read_fc2':
if confs['read_fc2'] == '.true.':
self.set_parameter('read_fc2', True)
if conf_key == 'read_fc3':
if confs['read_fc3'] == '.true.':
self.set_parameter('read_fc3', True)
if conf_key == 'read_gamma':
if confs['read_gamma'] == '.true.':
self.set_parameter('read_gamma', True)
if conf_key == 'read_phonon':
if confs['read_phonon'] == '.true.':
self.set_parameter('read_phonon', True)
if conf_key == 'run_with_g':
if confs['run_with_g'] == '.false.':
self.set_parameter('run_with_g', False)
if conf_key == 'scattering_event_class':
self.set_parameter('scattering_event_class',
confs['scattering_event_class'])
if conf_key == 'temperatures':
vals = [fracval(x) for x in confs['temperatures'].split()]
if len(vals) < 1:
self.setting_error("Temperatures are incorrectly set.")
else:
self.set_parameter('temperatures', vals)
if conf_key == 'use_ave_pp':
if confs['use_ave_pp'] == '.true.':
self.set_parameter('use_ave_pp', True)
if conf_key == 'write_amplitude':
if confs['write_amplitude'] == '.true.':
self.set_parameter('write_amplitude', True)
if conf_key == 'write_detailed_gamma':
if confs['write_detailed_gamma'] == '.true.':
self.set_parameter('write_detailed_gamma', True)
if conf_key == 'write_gamma':
if confs['write_gamma'] == '.true.':
self.set_parameter('write_gamma', True)
if conf_key == 'write_collision':
if confs['write_collision'] == '.true.':
self.set_parameter('write_collision', True)
if conf_key == 'write_phonon':
if confs['write_phonon'] == '.true.':
self.set_parameter('write_phonon', True)
def _parse_conf(self):
confs = self._confs
for conf_key in confs.keys():
if conf_key == 'dim_extra':
matrix = [
int(x)
for x in confs['dim_extra'].replace(",", " ").split()
]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error(
"Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error(
'Determinant of supercell matrix has to be positive.'
)
else:
self.set_parameter('dim_extra', matrix)
if conf_key == "mesh_shift":
vals = [
fracval(x)
for x in confs['mesh_shift'].replace(",", " ").split()
]
for i in range(3 - len(vals)):
vals += [0.0] # Correction for incomplete shift set
self.set_parameter('mesh_shift', vals[:3])
if conf_key == 'band_indices':
vals = []
for sum_set in confs['band_indices'].replace(",",
" ").split(','):
vals.append([
int(x) - 1 for x in sum_set.replace(",", " ").split()
])
self.set_parameter('band_indices', vals)
if conf_key == 'grid_points':
vals = [
int(x)
for x in confs['grid_points'].replace(",", " ").split()
]
self.set_parameter('grid_points', vals)
if conf_key == 'bterta':
if confs['bterta'] == '.true.':
self.set_parameter('is_bterta', True)
if conf_key == 'linewidth':
if confs['linewidth'] == '.true.':
self.set_parameter('is_linewidth', True)
if conf_key == 'read_fc2':
if confs['read_fc2'] == '.true.':
self.set_parameter('read_fc2', True)
if conf_key == 'read_fc2_extra':
if confs['read_fc2_extra'] == '.true.':
self.set_parameter('read_fc2_extra', True)
if conf_key == 'max_freepath':
self.set_parameter('max_freepath',
float(confs['max_freepath']))
if conf_key == 'no_kappa_stars':
if confs['no_kappa_stars'] == '.true.':
self.set_parameter('no_kappa_stars', True)
if conf_key == 'read_gamma':
if confs['read_gamma'] == '.true.':
self.set_parameter('read_gamma', True)
if conf_key == 'temperature':
vals = confs['temperature']
self.set_parameter('temperature', vals)
if conf_key == 'write_gamma':
if confs['write_gamma'] == '.true.':
self.set_parameter('write_gamma', True)
def _parse_conf(self):
confs = self._confs
for conf_key in confs.keys():
if conf_key == 'dim_extra':
matrix = [
int(x)
for x in confs['dim_extra'].replace(",", " ").split()
]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error(
"Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error(
'Determinant of supercell matrix has to be positive.'
)
else:
self.set_parameter('dim_extra', matrix)
if conf_key == 'band_indices':
vals = []
for sum_set in confs['band_indices'].split(','):
vals.append([int(x) - 1 for x in sum_set.split()])
self.set_parameter('band_indices', vals)
if conf_key == 'cutoff_pair':
cutpair = [
float(x)
for x in confs['cutoff_pair'].replace(",", " ").split()
]
self.set_parameter('cutoff_pair', cutpair)
if conf_key == 'cutoff_triplet':
cutfc3 = [
float(x)
for x in confs['cutoff_triplet'].replace(",", " ").split()
]
self.set_parameter('cutoff_triplet', cutfc3)
if conf_key == 'cutoff_radius':
cutfc3q = [
float(x)
for x in confs['cutoff_radius'].replace(",", " ").split()
]
self.set_parameter('cutoff_radius', cutfc3q)
if conf_key == "cutoff_delta":
self.set_parameter("cutoff_delta",
float(confs["cutoff_delta"]))
if conf_key == 'cutoff_frequency':
self.set_parameter('cutoff_frequency',
confs['cutoff_frequency'])
if conf_key == 'cutoff_hfrequency':
self.set_parameter('cutoff_hfrequency',
confs['cutoff_hfrequency'])
if conf_key == 'cutoff_lifetime':
self.set_parameter('cutoff_lifetime', confs['cutoff_lifetime'])
if conf_key == "diff_kappa":
self.set_parameter("diff_kappa", confs['diff_kappa'])
if conf_key == "diff_gamma":
self.set_parameter("diff_gamma", confs['diff_gamma'])
if conf_key == 'grid_points':
vals = [
int(x)
for x in confs['grid_points'].replace(",", " ").split()
]
self.set_parameter('grid_points', vals)
if conf_key == 'ion_clamped':
if confs['ion_clamped'] == '.true.':
self.set_parameter('ion_clamped', True)
if conf_key == "ite":
if confs['ite'] == ".true.":
self.set_parameter('is_ite', True)
if conf_key == "ite_cg":
if confs['ite_cg'] == ".true.":
self.set_parameter('is_ite_cg', True)
if conf_key == "length":
self.set_parameter('length', confs['length'])
if conf_key == "ise":
if confs['ise'] == ".true.":
self.set_parameter('is_ise', True)
if conf_key == 'bterta':
if confs['bterta'] == '.true.':
self.set_parameter('is_bterta', True)
if conf_key == 'linewidth':
if confs['linewidth'] == '.true.':
self.set_parameter('is_linewidth', True)
if conf_key == 'nu':
if confs['nu'] is not None:
nu = confs['nu'].strip().upper()[0]
if nu == "N" or nu == "U":
self.set_parameter('nu', nu)
if conf_key == 'read_fc2':
if confs['read_fc2'] == '.true.':
self.set_parameter('read_fc2', True)
if conf_key == 'read_fc2_extra':
if confs['read_fc2_extra'] == '.true.':
self.set_parameter('read_fc2_extra', True)
if conf_key == 'read_fc3':
if confs['read_fc3'] == '.true.':
self.set_parameter('read_fc3', True)
if conf_key == 'frequency_shift':
if confs['frequency_shift'] == '.true.':
self.set_parameter('is_frequency_shift', True)
if conf_key == 'mass_variances':
vals = [fracval(x) for x in confs['mass_variances'].split()]
if len(vals) < 1:
self.setting_error(
"Mass variance parameters are incorrectly set.")
else:
self.set_parameter('mass_variances', vals)
if conf_key == "max_ite":
self.set_parameter("max_ite", int(confs['max_ite']))
if conf_key == 'max_freepath':
self.set_parameter('max_freepath',
float(confs['max_freepath']))
if conf_key == 'mesh_divisors':
vals = [x for x in confs['mesh_divisors'].split()]
if len(vals) == 3:
self.set_parameter('mesh_divisors', [int(x) for x in vals])
elif len(vals) == 6:
divs = [int(x) for x in vals[:3]]
is_shift = [x.lower() == 't' for x in vals[3:]]
for i in range(3):
if is_shift[i] and (divs[i] % 2 != 0):
is_shift[i] = False
self.setting_error(
"Coarse grid shift along the " +
["first", "second", "third"][i] +
" axis is not allowed.")
self.set_parameter('mesh_divisors', divs + is_shift)
else:
self.setting_error("Mesh divisors are incorrectly set.")
if conf_key == 'multiple_sigmas':
vals = [
fracval(x) for x in confs['multiple_sigmas'].replace(
",", " ").split()
]
if len(vals) < 1:
self.setting_error("Mutiple sigmas are incorrectly set.")
else:
self.set_parameter('multiple_sigmas', vals)
if conf_key == "adaptive_sigma_step":
self.set_parameter("adaptive_sigma_step",
int(confs['adaptive_sigma_step']))
if conf_key == 'kappa_write_step':
self.set_parameter('kappa_write_step',
int(confs['kappa_write_step']))
if conf_key == 'no_kappa_stars':
if confs['no_kappa_stars'] == '.true.':
self.set_parameter('no_kappa_stars', True)
if conf_key == 'read_amplitude':
if confs['read_amplitude'] == '.true.':
self.set_parameter('read_amplitude', True)
if conf_key == 'read_gamma':
if confs['read_gamma'] == '.true.':
self.set_parameter('read_gamma', True)
if conf_key == 'temperatures':
vals = [
fracval(x)
for x in confs['temperatures'].replace(",", " ").split()
]
if len(vals) < 1:
self.setting_error("Temperatures are incorrectly set.")
else:
self.set_parameter('temperatures', vals)
if conf_key == 'write_amplitude':
if confs['write_amplitude'] == '.true.':
self.set_parameter('write_amplitude', True)
if conf_key == 'write_gamma':
if confs['write_gamma'] == '.true.':
self.set_parameter('write_gamma', True)
if conf_key == "write_triplet":
if confs['write_triplet'] == '.true.':
self.set_parameter('write_triplet', True)
def _parse_conf(self):
ConfParser.parse_conf(self)
confs = self._confs
for conf_key in confs.keys():
# Boolean
if conf_key in ('read_fc2', 'read_fc3', 'read_gamma',
'read_phonon', 'read_pp', 'use_ave_pp',
'collective_phonon', 'write_gamma_detail',
'write_gamma', 'write_collision', 'write_phonon',
'write_pp', 'write_LBTE_solution', 'full_pp',
'ion_clamped', 'bterta', 'compact_fc',
'real_self_energy', 'gruneisen',
'imag_self_energy', 'isotope', 'joint_dos', 'lbte',
'N_U', 'spectral_function',
'reducible_collision_matrix', 'symmetrize_fc2',
'symmetrize_fc3_q', 'symmetrize_fc3_r',
'kappa_star'):
if confs[conf_key].lower() == '.true.':
self.set_parameter(conf_key, True)
elif confs[conf_key].lower() == '.false.':
self.set_parameter(conf_key, False)
# float
if conf_key in ('boundary_mfp', 'cutoff_fc3_distance',
'cutoff_pair_distance', 'gamma_conversion_factor',
'max_freepath', 'pinv_cutoff',
'pp_conversion_factor', 'sigma_cutoff_width'):
self.set_parameter(conf_key, float(confs[conf_key]))
# int
if conf_key in ('pinv_solver', 'num_points_in_batch'):
self.set_parameter(conf_key, int(confs[conf_key]))
# specials
if conf_key in ('create_forces_fc2', 'create_forces_fc3'):
if type(confs[conf_key]) is str:
fnames = confs[conf_key].split()
else:
fnames = confs[conf_key]
self.set_parameter(conf_key, fnames)
if conf_key == 'dim_fc2':
matrix = [int(x) for x in confs['dim_fc2'].split()]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error(
"Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error(
"Determinant of supercell matrix has " +
"to be positive.")
else:
self.set_parameter('dim_fc2', matrix)
if conf_key in ('constant_averaged_pp_interaction' 'const_ave_pp'):
self.set_parameter('const_ave_pp',
float(confs['const_ave_pp']))
if conf_key == 'grid_addresses':
vals = [
int(x)
for x in confs['grid_addresses'].replace(',', ' ').split()
]
if len(vals) % 3 == 0 and len(vals) > 0:
self.set_parameter('grid_addresses',
np.reshape(vals, (-1, 3)))
else:
self.setting_error("Grid addresses are incorrectly set.")
if conf_key == 'grid_points':
vals = [
int(x)
for x in confs['grid_points'].replace(',', ' ').split()
]
self.set_parameter('grid_points', vals)
if conf_key == 'lapack_zheev_uplo':
self.set_parameter('lapack_zheev_uplo',
confs['lapack_zheev_uplo'].upper())
if conf_key == 'mass_variances':
vals = [fracval(x) for x in confs['mass_variances'].split()]
if len(vals) < 1:
self.setting_error(
"Mass variance parameters are incorrectly set.")
else:
self.set_parameter('mass_variances', vals)
if conf_key == 'mesh_divisors':
vals = [x for x in confs['mesh_divisors'].split()]
if len(vals) == 3:
self.set_parameter('mesh_divisors', [int(x) for x in vals])
elif len(vals) == 6:
divs = [int(x) for x in vals[:3]]
is_shift = [x.lower() == 't' for x in vals[3:]]
for i in range(3):
if is_shift[i] and (divs[i] % 2 != 0):
is_shift[i] = False
self.setting_error(
"Coarse grid shift along the " +
["first", "second", "third"][i] +
" axis is not allowed.")
self.set_parameter('mesh_divisors', divs + is_shift)
else:
self.setting_error("Mesh divisors are incorrectly set.")
if conf_key == 'read_collision':
if confs['read_collision'] == 'all':
self.set_parameter('read_collision', 'all')
else:
vals = [int(x) for x in confs['read_collision'].split()]
self.set_parameter('read_collision', vals)
if conf_key == 'scattering_event_class':
self.set_parameter('scattering_event_class',
int(confs['scattering_event_class']))
def _parse_conf(self):
confs = self._confs
for conf_key in confs.keys():
if conf_key == 'dim_extra':
matrix = [ int(x) for x in confs['dim_extra'].split() ]
if len(matrix) == 9:
matrix = np.array(matrix).reshape(3, 3)
elif len(matrix) == 3:
matrix = np.diag(matrix)
else:
self.setting_error(
"Number of elements of dim2 has to be 3 or 9.")
if matrix.shape == (3, 3):
if np.linalg.det(matrix) < 1:
self.setting_error(
"Determinant of supercell matrix has " +
"to be positive.")
else:
self.set_parameter('dim_extra', matrix)
if conf_key == 'cutoff_fc3_distance':
self.set_parameter('cutoff_fc3_distance',
float(confs['cutoff_fc3_distance']))
if conf_key == 'cutoff_pair_distance':
self.set_parameter('cutoff_pair_distance',
float(confs['cutoff_pair_distance']))
if conf_key == 'cutoff_frequency':
self.set_parameter('cutoff_frequency',
float(confs['cutoff_frequency']))
if conf_key == 'cutoff_lifetime':
self.set_parameter('cutoff_lifetime',
float(confs['cutoff_lifetime']))
if conf_key == 'grid_points':
vals = [int(x) for x in
confs['grid_points'].replace(',', ' ').split()]
self.set_parameter('grid_points', vals)
if conf_key == 'ion_clamped':
if confs['ion_clamped'] == '.true.':
self.set_parameter('ion_clamped', True)
if conf_key == 'bterta':
if confs['bterta'] == '.true.':
self.set_parameter('is_bterta', True)
if conf_key == 'lbte':
if confs['lbte'] == '.true.':
self.set_parameter('is_lbte', True)
if conf_key == 'linewidth':
if confs['linewidth'] == '.true.':
self.set_parameter('is_linewidth', True)
if conf_key == 'frequency_shift':
if confs['frequency_shift'] == '.true.':
self.set_parameter('is_frequency_shift', True)
if conf_key == 'mass_variances':
vals = [fracval(x) for x in confs['mass_variances'].split()]
if len(vals) < 1:
self.setting_error("Mass variance parameters are incorrectly set.")
else:
self.set_parameter('mass_variances', vals)
if conf_key == 'max_freepath':
self.set_parameter('max_freepath', float(confs['max_freepath']))
if conf_key == 'mesh_divisors':
vals = [x for x in confs['mesh_divisors'].split()]
if len(vals) == 3:
self.set_parameter('mesh_divisors', [int(x) for x in vals])
elif len(vals) == 6:
divs = [int(x) for x in vals[:3]]
is_shift = [x.lower() == 't' for x in vals[3:]]
for i in range(3):
if is_shift[i] and (divs[i] % 2 != 0):
is_shift[i] = False
self.setting_error("Coarse grid shift along the " +
["first", "second", "third"][i] +
" axis is not allowed.")
self.set_parameter('mesh_divisors', divs + is_shift)
else:
self.setting_error("Mesh divisors are incorrectly set.")
if conf_key == 'no_kappa_stars':
if confs['no_kappa_stars'] == '.true.':
self.set_parameter('no_kappa_stars', True)
if conf_key == 'read_amplitude':
if confs['read_amplitude'] == '.true.':
self.set_parameter('read_amplitude', True)
if conf_key == 'read_gamma':
if confs['read_gamma'] == '.true.':
self.set_parameter('read_gamma', True)
if conf_key == 'read_collision':
if confs['read_collision'] == 'all':
self.set_parameter('read_collision', 'all')
else:
vals = [int(x) for x in confs['read_collision'].split()]
self.set_parameter('read_collision', vals)
if conf_key == 'temperatures':
vals = [fracval(x) for x in confs['temperatures'].split()]
if len(vals) < 1:
self.setting_error("Temperatures are incorrectly set.")
else:
self.set_parameter('temperatures', vals)
if conf_key == 'write_amplitude':
if confs['write_amplitude'] == '.true.':
self.set_parameter('write_amplitude', True)
if conf_key == 'write_gamma':
if confs['write_gamma'] == '.true.':
self.set_parameter('write_gamma', True)
if conf_key == 'write_collision':
if confs['write_collision'] == '.true.':
self.set_parameter('write_collision', True)