Added an option to specify the TS adapters in the input file (#657)

Tests added

arc/main.py

@@ -38,6 +38,7 @@
 from arc.exceptions import InputError, SettingsError, SpeciesError
 from arc.imports import settings
 from arc.level import Level
+from arc.job.factory import _registered_job_adapters
 from arc.job.ssh import SSHClient
 from arc.processor import process_arc_project
 from arc.reaction import ARCReaction
@@ -153,6 +154,7 @@ class ARC(object):
         output (dict, optional): Output dictionary with status and final QM file paths for all species.
                                  Only used for restarting.
         running_jobs (dict, optional): A dictionary of jobs submitted in a precious ARC instance, used for restarting.
+        ts_adapters (list, optional): Entries represent different TS adapters.
 
     Attributes:
         project (str): The project's name. Used for naming the working directory.
@@ -218,6 +220,7 @@ 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``.
+        ts_adapters (list): Entries represent different TS adapters.
     """
 
     def __init__(self,
@@ -263,6 +266,7 @@ def __init__(self,
                  thermo_adapter: str = 'Arkane',
                  three_params: bool = True,
                  trsh_ess_jobs: bool = True,
+                 ts_adapters: List[str] = None,
                  ts_guess_level: Optional[Union[str, dict, Level]] = None,
                  verbose=logging.INFO,
                  ):
@@ -315,6 +319,10 @@ def __init__(self,
         self.bac_type = bac_type
         self.arkane_level_of_theory = Level(repr=arkane_level_of_theory) if arkane_level_of_theory is not None else None
         self.freq_scale_factor = freq_scale_factor
+        self.ts_adapters = ts_adapters
+        for ts_adapter in self.ts_adapters or list():
+            if ts_adapter.lower() not in _registered_job_adapters.keys():
+                raise InputError(f'Unknown TS adapter: "{ts_adapter}"')
 
         # attributes related to level of theory specifications
         self.level_of_theory = level_of_theory
@@ -465,6 +473,8 @@ def as_dict(self) -> dict:
             restart_dict['conformer_level'] = self.conformer_level.as_dict()
         if self.dont_gen_confs:
             restart_dict['dont_gen_confs'] = self.dont_gen_confs
+        if self.ts_adapters:
+            restart_dict['ts_adapters'] = self.ts_adapters
         restart_dict['e_confs'] = self.e_confs
         restart_dict['ess_settings'] = self.ess_settings
         if self.freq_level is not None:
@@ -581,6 +591,7 @@ def execute(self) -> dict:
                                    dont_gen_confs=self.dont_gen_confs,
                                    trsh_ess_jobs=self.trsh_ess_jobs,
                                    fine_only=self.fine_only,
+                                   ts_adapters=self.ts_adapters,
                                    )
 
         save_yaml_file(path=os.path.join(self.project_directory, 'output', 'status.yml'), content=self.scheduler.output)

arc/main_test.py

@@ -72,6 +72,7 @@ def test_as_dict(self):
                    species=[spc1],
                    level_of_theory='ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)',
                    three_params=False,
+                   ts_adapters=['heuristics', 'AutoTST', 'GCN', 'xtb_gsm'],
                    )
         arc0.freq_level.args['keyword']['general'] = 'scf=(NDump=30)'
         restart_dict = arc0.as_dict()
@@ -160,7 +161,8 @@ def test_as_dict(self):
                                       'multiplicity': 1,
                                       'number_of_rotors': 0}],
                          'thermo_adapter': 'arkane',
-                         'three_params': False}
+                         'three_params': False,
+                         'ts_adapters': ['heuristics', 'AutoTST', 'GCN', 'xtb_gsm']}
         # import pprint  # left intentionally for debugging
         # print(pprint.pprint(restart_dict))
         self.assertEqual(restart_dict, expected_dict)
@@ -475,6 +477,23 @@ def test_process_level_of_theory(self):
             self.assertIsInstance(arc.opt_level, Level)
             self.assertIsInstance(arc.freq_level, Level)
 
+    def test_unknown_ts_adapter(self):
+        """
+        Tests that ARC raises an error when unknown TS adapters are given.
+        """
+        spc1 = ARCSpecies(label='spc1',
+                          smiles='CC',
+                          compute_thermo=False,
+                          )
+        with self.assertRaises(InputError):
+            arc0 = ARC(project='arc_test',
+                       job_types=self.job_types1,
+                       species=[spc1],
+                       level_of_theory='ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)',
+                       three_params=False,
+                       ts_adapters=['WRONG ADAPTER', 'AutoTST', 'GCN', 'xtb_gsm'],
+                       )
+
     @classmethod
     def tearDownClass(cls):
         """

arc/scheduler.py

@@ -65,12 +65,10 @@
 logger = get_logger()
 
 LOWEST_MAJOR_TS_FREQ, HIGHEST_MAJOR_TS_FREQ, default_job_settings, \
-    default_job_types, rotor_scan_resolution, ts_adapters, max_rotor_trsh = \
+    default_job_types, rotor_scan_resolution, default_ts_adapters, max_rotor_trsh = \
     settings['LOWEST_MAJOR_TS_FREQ'], settings['HIGHEST_MAJOR_TS_FREQ'], settings['default_job_settings'], \
     settings['default_job_types'], settings['rotor_scan_resolution'], settings['ts_adapters'], settings['max_rotor_trsh']
 
-ts_adapters = [ts_adapter.lower() for ts_adapter in ts_adapters]
-
 
 class Scheduler(object):
     """
@@ -161,6 +159,7 @@ 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``.
+        ts_adapters (list, optional): Entries represent different TS adapters.
 
     Attributes:
         project (str): The project's name. Used for naming the working directory.
@@ -214,6 +213,7 @@ 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``.
+        ts_adapters (list): Entries represent different TS adapters.
     """
 
     def __init__(self,
@@ -247,6 +247,7 @@ def __init__(self,
                  trsh_ess_jobs: Optional[bool] = True,
                  kinetics_adapter: str = 'arkane',
                  freq_scale_factor: float = 1.0,
+                 ts_adapters: List[str] = None,
                  ) -> None:
 
         self.project = project
@@ -275,6 +276,8 @@ def __init__(self,
         self.trsh_ess_jobs = trsh_ess_jobs
         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
+        self.ts_adapters = [ts_adapter.lower() for ts_adapter in self.ts_adapters]
         self.output = dict()
 
         self.species_dict, self.rxn_dict = dict(), dict()
@@ -1474,7 +1477,7 @@ def spawn_ts_jobs(self):
                 else:
                     rxn.ts_species.tsg_spawned = True
                     tsg_index = 0
-                    for method in ts_adapters:
+                    for method in self.ts_adapters:
                         if method in all_families_ts_adapters or \
                                 (rxn.family is not None
                                  and rxn.family.label in list(ts_adapters_by_rmg_family.keys())