def desired_pressure_status(self) -> None:
d = self.settings
if d['high_verbosity']:
save_to_output(
d['qha_output'],
"The pressure range can be dealt with: [{0:6.2f} to {1:6.2f}] GPa"
.format(self.p_tv_gpa[:, 0].max(), self.p_tv_gpa[:, -1].min()))
if self.p_tv_gpa[:, -1].min() < self.desired_pressures_gpa.max():
ntv_max = int(
(self.p_tv_gpa[:, -1].min() - self.desired_pressures_gpa.min())
/ d['DELTA_P'])
save_to_output(
d['qha_output'],
textwrap.dedent("""\
!!!ATTENTION!!!
DESIRED PRESSURE is too high (NTV is too large)!
QHA results might not be right!
Please reduce the NTV accordingly, for example, try to set NTV < {:4d}.
""".format(ntv_max)))
raise ValueError(
"DESIRED PRESSURE is too high (NTV is too large), qha results might not be right!"
)
def read_input(self):
self._degeneracies = tuple(self.settings['input'].values())
input_data_files = tuple(self.settings['input'].keys())
formula_unit_numbers = []
volumes = []
static_energies = []
frequencies = []
q_weights = []
for inp in input_data_files:
nm_tmp, volumes_tmp, static_energies_tmp, freq_tmp, weights_tmp = read_input(
inp)
if not qha.tools.is_monotonic_decreasing(volumes_tmp):
# TODO: Clean this sentence
save_to_output(
self.settings['qha_output'],
"Check the input file to make sure the volume decreases")
raise ValueError(
"Check the input file to make sure the volumes are monotonic decreasing!"
)
formula_unit_numbers.append(nm_tmp)
volumes.append(volumes_tmp)
static_energies.append(static_energies_tmp)
frequencies.append(freq_tmp)
q_weights.append(weights_tmp)
formula_unit_numbers = np.array(formula_unit_numbers)
volumes = np.array(volumes)
static_energies = np.array(static_energies)
frequencies = np.array(frequencies)
q_weights = np.array(q_weights)
if not len(set(formula_unit_numbers)) == 1:
raise RuntimeError(
"All the formula unit number in all inputs should be the same!"
)
if len(volumes.shape) == 1:
raise RuntimeError(
"All configurations should have same number of volumes!")
# Choose any of them since they are all the same
self._formula_unit_number = formula_unit_numbers[0]
self._volumes = volumes
self._static_energies = static_energies
self._frequencies = frequencies
self._q_weights = q_weights
def run(self, namespace):
start_time_total = time.time()
user_settings = {}
file_settings = namespace.settings
settings = from_yaml(file_settings)
for key in ('input', 'calculation', 'thermodynamic_properties',
'static_only', 'energy_unit', 'T_MIN', 'NT', 'DT',
'DT_SAMPLE', 'P_MIN', 'NTV', 'DELTA_P', 'DELTA_P_SAMPLE',
'volume_ratio', 'order', 'p_min_modifier', 'T4FV',
'output_directory', 'high_verbosity'):
try:
user_settings.update({key: settings[key]})
except KeyError:
continue
if not os.path.exists(user_settings['output_directory']):
os.makedirs(user_settings['output_directory'])
user_settings.update({
'qha_output':
os.path.join(user_settings['output_directory'], 'output.txt')
})
try:
os.remove(user_settings['qha_output'])
except OSError:
pass
save_to_output(user_settings['qha_output'], make_starting_string())
calculation_type = user_settings['calculation'].lower()
if calculation_type == 'single':
calc = Calculator(user_settings)
print("You have single-configuration calculation assumed.")
elif calculation_type == 'same phonon dos':
calc = SamePhDOSCalculator(user_settings)
print(
"You have multi-configuration calculation with the same phonon DOS assumed."
)
elif calculation_type == 'different phonon dos':
calc = DifferentPhDOSCalculator(user_settings)
print(
"You have multi-configuration calculation with different phonon DOS assumed."
)
else:
raise ValueError(
"The 'calculation' in your settings in not recognized! It must be one of:"
"'single', 'same phonon dos', 'different phonon dos'!")
save_to_output(
user_settings['qha_output'],
make_tp_info(calc.temperature_array[0],
calc.temperature_array[-1 - 4],
calc.desired_pressures_gpa[0],
calc.desired_pressures_gpa[-1]))
calc.read_input()
print(
"Caution: If negative frequencies found, they are currently treated as 0!"
)
tmp = calc.where_negative_frequencies
# Don't delete this parenthesis!
if tmp is not None and not (tmp.T[-1].max() <= 2):
if calc.frequencies.ndim == 4: # Multiple configuration
for indices in tmp:
print(
"Found negative frequency in {0}th configuration {1}th volume {2}th q-point {3}th band"
.format(*tuple(indices + 1)))
elif calc.frequencies.ndim == 3: # Single configuration
for indices in tmp:
print(
"Found negative frequency in {0}th volume {1}th q-point {2}th band"
.format(*tuple(indices + 1)))
calc.refine_grid()
if user_settings['high_verbosity']:
save_to_output(
user_settings['qha_output'],
'The volume range used in this calculation expanded x {0:6.4f}'
.format(calc.v_ratio))
calc.desired_pressure_status()
temperature_array = calc.temperature_array
desired_pressures_gpa = calc.desired_pressures_gpa
temperature_sample = calc.temperature_sample_array
p_sample_gpa = calc.pressure_sample_array
results_folder = pathlib.Path(user_settings['output_directory'])
calculation_option = {
'F': 'f_tp',
'G': 'g_tp',
'H': 'h_tp',
'U': 'u_tp',
'V': 'v_tp',
'Cv': 'cv_tp_jmolk',
'Cp': 'cp_tp_jmolk',
'Bt': 'bt_tp_gpa',
'Btp': 'btp_tp',
'Bs': 'bs_tp_gpa',
'alpha': 'alpha_tp',
'gamma': 'gamma_tp',
}
file_ftv_fitted = results_folder / 'f_tv_fitted_ev_ang3.txt'
save_x_tv(calc.f_tv_ev, temperature_array, calc.finer_volumes_ang3,
temperature_sample, file_ftv_fitted)
file_ftv_non_fitted = results_folder / 'f_tv_nonfitted_ev_ang3.txt'
save_x_tv(calc.vib_ev, temperature_array, calc.volumes_ang3,
temperature_sample, file_ftv_non_fitted)
file_ptv_gpa = results_folder / 'p_tv_gpa.txt'
save_x_tv(calc.p_tv_gpa, temperature_array, calc.finer_volumes_ang3,
temperature_sample, file_ptv_gpa)
file_stv_j = results_folder / 's_tv_j.txt'
save_x_tv(calc.s_tv_j, temperature_array, calc.finer_volumes_ang3,
temperature_sample, file_stv_j)
for idx in calc.settings['thermodynamic_properties']:
if idx in ['F', 'G', 'H', 'U']:
attr_name = calculation_option[idx] + \
'_' + calc.settings['energy_unit']
file_name = attr_name + '.txt'
file_dir = results_folder / file_name
save_x_tp(getattr(calc, attr_name), temperature_array,
desired_pressures_gpa, p_sample_gpa, file_dir)
if idx == 'V':
v_bohr3 = calculation_option[idx] + '_' + 'bohr3'
file_name_bohr3 = v_bohr3 + '.txt'
file_dir_au = results_folder / file_name_bohr3
v_ang3 = calculation_option[idx] + '_' + 'ang3'
file_name_ang3 = v_ang3 + '.txt'
file_dir_ang3 = results_folder / file_name_ang3
save_x_tp(getattr(calc, v_bohr3), temperature_array,
desired_pressures_gpa, p_sample_gpa, file_dir_au)
save_x_tp(getattr(calc, v_ang3), temperature_array,
desired_pressures_gpa, p_sample_gpa, file_dir_ang3)
if idx in ['Cv', 'Cp', 'Bt', 'Btp', 'Bs', 'alpha', 'gamma']:
attr_name = calculation_option[idx]
file_name = attr_name + '.txt'
file_dir = results_folder / file_name
save_x_tp(getattr(calc, attr_name), temperature_array,
desired_pressures_gpa, p_sample_gpa, file_dir)
end_time_total = time.time()
time_elapsed = end_time_total - start_time_total
save_to_output(user_settings['qha_output'],
make_ending_string(time_elapsed))