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Allow user to input paths to previous jobs #393

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Allow user to input paths to previous jobs #393

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8 changes: 6 additions & 2 deletions arc/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,7 @@ class ARC(object):
compute_rates (bool, optional): Whether to compute rate coefficients for converged reactions.
compute_transport (bool, optional): Whether to compute transport properties for converged species.
statmech_adapter (str, optional): The statmech software to use.
previous_job_paths (dict, optional): A dictionary for paths to previously run files needed for this job

Attributes:
project (str): The project's name. Used for naming the working directory.
Expand Down Expand Up @@ -182,6 +183,7 @@ class ARC(object):
statmech_adapter (str): The statmech software to use.
fine_only (bool): If ``self.job_types['fine'] and not self.job_types['opt']`` ARC will not run optimization
jobs without fine=True
previous_job_paths (dict, optional): A dictionary for paths to previously run files needed for this job
"""

def __init__(self, input_dict=None, project=None, arc_species_list=None, arc_rxn_list=None, level_of_theory='',
Expand All @@ -192,7 +194,7 @@ def __init__(self, input_dict=None, project=None, arc_species_list=None, arc_rxn
job_memory=None, ess_settings=None, bath_gas=None, adaptive_levels=None, freq_scale_factor=None,
calc_freq_factor=True, n_confs=10, e_confs=5, dont_gen_confs=None, keep_checks=False,
solvation=None, compare_to_rmg=True, compute_thermo=True, compute_rates=True, compute_transport=True,
specific_job_type='', statmech_adapter='Arkane'):
specific_job_type='', statmech_adapter='Arkane', previous_job_paths=None):
self.__version__ = VERSION
self.verbose = verbose
self.output = dict()
Expand All @@ -207,6 +209,7 @@ def __init__(self, input_dict=None, project=None, arc_species_list=None, arc_rxn
self.calc_freq_factor = calc_freq_factor
self.keep_checks = keep_checks
self.compare_to_rmg = compare_to_rmg
self.previous_job_paths = previous_job_paths

if input_dict is None:
if project is None:
Expand Down Expand Up @@ -618,7 +621,8 @@ def execute(self) -> dict:
T_count=self.T_count or 50,
lib_long_desc=self.lib_long_desc,
rmg_database=self.rmg_database,
compare_to_rmg=self.compare_to_rmg)
compare_to_rmg=self.compare_to_rmg,
previous_job_paths=self.previous_job_paths)

status_dict = self.summary()
log_footer(execution_time=self.execution_time)
Expand Down
16 changes: 16 additions & 0 deletions arc/processor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ def process_arc_project(statmech_adapter: str,
lib_long_desc: str = '',
rmg_database: Type[RMGDatabase] = None,
compare_to_rmg: bool = True,
previous_job_paths: dict = None,
) -> None:
"""
Process an RMG project, generate thermo and rate coefficients using statistical mechanics (statmech).
Expand All @@ -75,7 +76,22 @@ def process_arc_project(statmech_adapter: str,
rmg_database (RMGDatabase, optional): The RMG database object.
compare_to_rmg (bool, optional): If ``True``, ARC's calculations will be compared against estimations
from RMG's database.
previous_job_paths (dict, optional): A dictionary for paths to previously run files needed for this job
"""
# First, add previous paths to the output dictionary
if previous_job_paths is not None:
print('Checking to see if previous job paths need to be appended')
for spcs_label in species_dict.keys():
if spcs_label in previous_job_paths.keys():
if 'geo' in previous_job_paths[spcs_label].keys():
geo_path = previous_job_paths[spcs_label]['geo']
output_dict[spcs_label]['paths']['geo'] = geo_path
print(f'Geometry path {geo_path} added for species {spcs_label}')
if 'freq' in previous_job_paths[spcs_label].keys():
freq_path = previous_job_paths[spcs_label]['freq']
output_dict[spcs_label]['paths']['freq'] = freq_path
print(f'Frequency path {freq_path} added for species {spcs_label}')

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Just curious, when shall we use different logs for geo and freq? I used to thought we can use results from freq for both freq and geo.

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I think we use freq only for both geo and freqs, but that's done at the adapter level, processor stores all our paths and passes them along.

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So, it seems like, we don't have to assign geo and freq separately here?

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I can just pass freq if you want as long as there is no reason why the user we need to specify a separate geo file (I can't think of any reason) and as long as ARC won't freak out about not having a file for geo

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let's accept both, but if geo isn't given, override it with freq. Does that sound reasonable?

T_min = T_min or (300, 'K')
T_max = T_max or (3000, 'K')
if isinstance(T_min, (int, float)):
Expand Down