Added a feature that allows not to trsh rotors (#786)

1D rotor scans for large systems fail too often. In some applications
we'd like to compute rotors, but if they fail that means that more
sophisticated methods should be applied. Currently ARC tries to
troubleshoot the rotor runs, taking too long, and not always succeeding.
This PR keeps the above default behavior, but adds an option to avoid
trshing rotor runs

Author: alongd

arc/main.py

@@ -152,6 +152,7 @@ class ARC(object):
                                        format (``True``, default) or classical two-parameter Arrhenius equation format
                                        (``False``).
         trsh_ess_jobs (bool, optional): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
+        trsh_rotors (bool, optional): Whether to attempt troubleshooting failed rotor scan jobs. Default is ``True``.
         output (dict, optional): Output dictionary with status and final QM file paths for all species.
                                  Only used for restarting.
         output_multi_spc (dict, optional): Output dictionary with status and final QM file paths for the multi species. 
@@ -227,6 +228,7 @@ class ARC(object):
         three_params (bool): Compute rate coefficients using the modified three-parameter Arrhenius equation
                              format (``True``) or classical two-parameter Arrhenius equation format (``False``).
         trsh_ess_jobs (bool): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
+        trsh_rotors (bool): Whether to attempt troubleshooting failed rotor scan jobs. Default is ``True``.
         ts_adapters (list): Entries represent different TS adapters.
         report_e_elect (bool): Whether to report electronic energy.
         skip_nmd (bool): Whether to skip normal mode displacement check.
@@ -279,6 +281,7 @@ def __init__(self,
                  thermo_adapter: str = 'Arkane',
                  three_params: bool = True,
                  trsh_ess_jobs: bool = True,
+                 trsh_rotors: bool = True,
                  ts_adapters: List[str] = None,
                  ts_guess_level: Optional[Union[str, dict, Level]] = None,
                  verbose=logging.INFO,
@@ -317,6 +320,7 @@ def __init__(self,
         self.compute_rates = compute_rates
         self.three_params = three_params
         self.trsh_ess_jobs = trsh_ess_jobs
+        self.trsh_rotors = trsh_rotors
         self.compute_transport = compute_transport
         self.thermo_adapter = StatmechEnum(thermo_adapter.lower()).value
         self.kinetics_adapter = StatmechEnum(kinetics_adapter.lower()).value
@@ -440,6 +444,10 @@ def __init__(self,
             logger.info('\n')
             logger.warning('Not troubleshooting ESS jobs!')
             logger.info('\n')
+        elif not self.trsh_rotors:
+            logger.info('\n')
+            logger.warning('Not troubleshooting rotor scan jobs!')
+            logger.info('\n')
 
         self.scheduler = None
         self.restart_dict = self.as_dict()
@@ -544,6 +552,8 @@ def as_dict(self) -> dict:
             restart_dict['three_params'] = self.three_params
         if not self.trsh_ess_jobs:
             restart_dict['trsh_ess_jobs'] = self.trsh_ess_jobs
+        if not self.trsh_rotors:
+            restart_dict['trsh_rotors'] = self.trsh_rotors
         if self.ts_guess_level is not None and str(self.ts_guess_level).split()[0] != default_levels_of_theory['ts_guesses']:
             restart_dict['ts_guess_level'] = self.ts_guess_level.as_dict() \
                 if not isinstance(self.ts_guess_level, (dict, str)) else self.ts_guess_level
@@ -617,6 +627,7 @@ def execute(self) -> dict:
                                    e_confs=self.e_confs,
                                    dont_gen_confs=self.dont_gen_confs,
                                    trsh_ess_jobs=self.trsh_ess_jobs,
+                                   trsh_rotors=self.trsh_rotors,
                                    fine_only=self.fine_only,
                                    ts_adapters=self.ts_adapters,
                                    report_e_elect=self.report_e_elect,

arc/scheduler.py

@@ -162,6 +162,7 @@ class Scheduler(object):
         kinetics_adapter (str, optional): The statmech software to use for kinetic rate coefficient calculations.
         freq_scale_factor (float, optional): The harmonic frequencies scaling factor.
         trsh_ess_jobs (bool, optional): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
+        trsh_rotors (bool, optional): Whether to attempt troubleshooting failed rotor scan jobs. Default is ``True``.
         ts_adapters (list, optional): Entries represent different TS adapters.
         report_e_elect (bool, optional): Whether to report electronic energy. Default is ``False``.
         skip_nmd (bool, optional): Whether to skip normal mode displacement check. Default is ``False``.
@@ -219,6 +220,7 @@ class Scheduler(object):
         kinetics_adapter (str): The statmech software to use for kinetic rate coefficient calculations.
         freq_scale_factor (float): The harmonic frequencies scaling factor.
         trsh_ess_jobs (bool): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
+        trsh_rotors (bool): Whether to attempt troubleshooting failed rotor scan jobs. Default is ``True``.
         ts_adapters (list): Entries represent different TS adapters.
         report_e_elect (bool): Whether to report electronic energy.
         skip_nmd (bool): Whether to skip normal mode displacement check.
@@ -253,6 +255,7 @@ def __init__(self,
                  e_confs: Optional[float] = 5,
                  fine_only: Optional[bool] = False,
                  trsh_ess_jobs: Optional[bool] = True,
+                 trsh_rotors: Optional[bool] = True,
                  kinetics_adapter: str = 'arkane',
                  freq_scale_factor: float = 1.0,
                  ts_adapters: List[str] = None,
@@ -284,6 +287,7 @@ def __init__(self,
         self.job_types = job_types if job_types is not None else default_job_types
         self.fine_only = fine_only
         self.trsh_ess_jobs = trsh_ess_jobs
+        self.trsh_rotors = trsh_rotors
         self.kinetics_adapter = kinetics_adapter
         self.freq_scale_factor = freq_scale_factor
         self.ts_adapters = ts_adapters if ts_adapters is not None else default_ts_adapters
@@ -2888,7 +2892,7 @@ def check_scan_job(self,
 
                 if len(list(actions.keys())) \
                         and 'pivTS' not in self.species_dict[label].rotors_dict[job.rotor_index]['invalidation_reason'] \
-                        and self.trsh_ess_jobs:
+                        and self.trsh_ess_jobs and self.trsh_rotors:
                     # The rotor scan is problematic (and does not block a TS reaction zone), troubleshooting is required.
                     logger.info(f'Trying to troubleshoot rotor '
                                 f'{self.species_dict[label].rotors_dict[job.rotor_index]["pivots"]} '
@@ -3219,9 +3223,9 @@ def troubleshoot_scan_job(self,
             - ``True`` if the troubleshooting is valid.
             - The actions are applied in the troubleshooting.
         """
-        if not self.trsh_ess_jobs:
+        if not self.trsh_ess_jobs or not self.trsh_rotors:
             logger.warning(f'Not troubleshooting failed scan job {job.job_name}. To enable troubleshooting, '
-                           f'set the "trsh_ess_jobs" to "True".')
+                           f'set the "trsh_ess_jobs" and the "trsh_rotors" arguments to "True".')
             return False, dict()
 
         label = job.species_label
@@ -3413,7 +3417,7 @@ def troubleshoot_ess(self,
             level_of_theory (Level, dict, str): The level of theory to use.
             conformer (int, optional): The conformer index.
         """
-        if not self.trsh_ess_jobs:
+        if not self.trsh_ess_jobs or not self.trsh_rotors and job.job_type == 'scan':
             logger.warning(f'Not troubleshooting failed {label} job {job.job_name}. '
                            f'To enable troubleshooting, set the "trsh_ess_jobs" argument to "True".')
             return None