def log_footer(self):
"""
Output a footer to the log.
"""
execution_time = time_lapse(self.t0)
self.log(f'\n\n\nTotal APIOxy execution time: {execution_time}',
level='always')
self.log(f'APIOxy execution terminated on {time.asctime()}\n',
level='always')
def determine_scaling_factors(
levels: List[Union[Level, dict, str]],
ess_settings: Optional[dict] = None,
init_log: Optional[bool] = True,
) -> list:
"""
Determine the zero-point energy, harmonic frequencies, and fundamental frequencies scaling factors
for a given frequencies level of theory.
Args:
levels (list): A list of frequencies levels of theory for which scaling factors are determined.
Entries are either Level instances, dictionaries, or simple string representations.
If a single entry is given, it will be converted to a list.
ess_settings (dict, optional): A dictionary of available ESS (keys) and a corresponding server list (values).
init_log (bool, optional): Whether to initialize the logger. ``True`` to initialize.
Should be ``True`` when called as a standalone, but ``False`` when called within ARC.
Returns:
list: The determined frequency scaling factors.
"""
if init_log:
initialize_log(log_file='scaling_factor.log',
project='Scaling Factors')
if not isinstance(levels, (list, tuple)):
levels = [levels]
levels = [
Level(repr=level) if not isinstance(level, Level) else level
for level in levels
]
t0 = time.time()
logger.info('\n\n\n')
logger.info(HEADER)
logger.info('\n\nstarting ARC...\n')
# only run opt (fine) and freq
job_types = initialize_job_types(
dict()) # get the defaults, so no job type is missing
job_types = {job_type: False for job_type in job_types.keys()}
job_types['opt'], job_types['fine'], job_types['freq'] = True, True, True
lambda_zpes, zpe_dicts, times = list(), list(), list()
for level in levels:
t1 = time.time()
logger.info(
f'\nComputing scaling factors at the {level} level of theory...\n\n'
)
renamed_level = rename_level(str(level))
project = 'scaling_' + renamed_level
project_directory = os.path.join(arc_path, 'Projects',
'scaling_factors', project)
if os.path.isdir(project_directory):
shutil.rmtree(project_directory)
species_list = get_species_list()
if level.method_type == 'composite':
freq_level = None
composite_method = level
job_types['freq'] = False
else:
freq_level = level
composite_method = None
ess_settings = check_ess_settings(ess_settings or global_ess_settings)
Scheduler(project=project,
project_directory=project_directory,
species_list=species_list,
composite_method=composite_method,
opt_level=freq_level,
freq_level=freq_level,
ess_settings=ess_settings,
job_types=job_types,
allow_nonisomorphic_2d=True)
zpe_dict = dict()
for spc in species_list:
zpe_dict[spc.label] = parse_zpe(
os.path.join(project_directory, 'output', 'Species', spc.label,
'geometry',
'freq.out')) * 1000 # convert to J/mol
zpe_dicts.append(zpe_dict)
lambda_zpes.append(
calculate_truhlar_scaling_factors(zpe_dict=zpe_dict,
level=str(level)))
times.append(time_lapse(t1))
summarize_results(lambda_zpes=lambda_zpes,
levels=[str(level) for level in levels],
zpe_dicts=zpe_dicts,
times=times,
overall_time=time_lapse(t0))
logger.info('\n\n\n')
logger.info(HEADER)
harmonic_freq_scaling_factors = [
lambda_zpe * 1.014 for lambda_zpe in lambda_zpes
]
return harmonic_freq_scaling_factors
def test_time_lapse(self):
"""Test the time_lapse() function"""
t0 = time.time()
time.sleep(2)
lap = common.time_lapse(t0)
self.assertEqual(lap, '00:00:02')
def determine_scaling_factors(levels_of_theory,
ess_settings=None,
init_log=True):
"""
Determine the zero-point energy, harmonic frequencies, and fundamental frequencies scaling factors
for a given frequencies level of theory.
Args:
levels_of_theory (list, str): A list of frequencies levels of theory
for which scaling factors are determined.
A string can also be passed for just one level of theory.
ess_settings (dict, optional): A dictionary of available ESS (keys) and a corresponding server list (values).
init_log (bool, optional): Whether to initialize the logger. True to initialize.
Should be True when called as a stand alone, and False when called within ARC.
Returns:
str: The modified level of theory
"""
if init_log:
initialize_log(log_file='scaling_factor.log',
project='Scaling Factors')
if isinstance(levels_of_theory, (str, unicode)):
levels_of_theory = [levels_of_theory]
if not isinstance(levels_of_theory, list):
raise InputError(
'levels_of_theory must be a list (or a string if only one level is desired). Got: {0}'
.format(type(levels_of_theory)))
t0 = time.time()
logger.info('\n\n\n')
logger.info(HEADER)
logger.info('\n\nstarting ARC...\n')
# only run opt (fine) and freq
job_types = initialize_job_types(
dict()) # get the defaults, so no job type is missing
job_types = {job_type: False for job_type in job_types.keys()}
job_types['opt'], job_types['fine'], job_types['freq'] = True, True, True
lambda_zpes, zpe_dicts, times = list(), list(), list()
for level_of_theory in levels_of_theory:
t1 = time.time()
logger.info(
'\nComputing scaling factors at the {0} level of theory...\n\n'.
format(level_of_theory))
renamed_level = rename_level(level_of_theory)
project = 'scaling_' + renamed_level
project_directory = os.path.join(arc_path, 'Projects',
'scaling_factors', project)
species_list = get_species_list()
if '//' in level_of_theory:
raise InputError(
'Level of theory should either be a composite method or in a method/basis-set format. '
'Got {0}'.format(level_of_theory))
if '/' not in level_of_theory: # assume this is a composite method
freq_level = ''
composite_method = level_of_theory.lower()
job_types['freq'] = False
else:
freq_level = level_of_theory.lower()
composite_method = ''
job_types['freq'] = True
ess_settings = check_ess_settings(ess_settings or global_ess_settings)
Scheduler(project=project,
project_directory=project_directory,
species_list=species_list,
composite_method=composite_method,
opt_level=freq_level,
freq_level=freq_level,
ess_settings=ess_settings,
job_types=job_types,
allow_nonisomorphic_2d=True)
zpe_dict = dict()
for spc in species_list:
try:
zpe = get_zpe(
os.path.join(project_directory, 'output', 'Species',
spc.label, 'geometry', 'freq.out'))
except Exception:
zpe = None
zpe_dict[spc.label] = zpe
zpe_dicts.append(zpe_dict)
lambda_zpes.append(
calculate_truhlar_scaling_factors(zpe_dict, level_of_theory))
times.append(time_lapse(t1))
summarize_results(lambda_zpes, levels_of_theory, zpe_dicts, times,
time_lapse(t0))
logger.info('\n\n\n')
logger.info(HEADER)
harmonic_freq_scaling_factors = [
lambda_zpe * 1.014 for lambda_zpe in lambda_zpes
]
return harmonic_freq_scaling_factors