Change conformer_level to conformer_opt_level

arc/main.py

@@ -80,6 +80,7 @@ class ARC(object):
                                          instead (e.g., ``opt_level``).
         composite_method (str, dict, Level, optional): Composite method.
         conformer_level (str, dict, Level, optional): Level of theory for conformer searches.
+        conformer_opt_level (str, dict, Level, optional): Level of theory for conformer searches, interchangable with `conformer_level`.
         opt_level (str, dict, Level, optional): Level of theory for geometry optimization.
         freq_level (str, dict, Level, optional): Level of theory for frequency calculations.
         sp_level (str, dict, Level, optional): Level of theory for single point calculations.
@@ -167,7 +168,7 @@ class ARC(object):
         reactions (list): A list of :ref:`ARCReaction <reaction>` objects.
         level_of_theory (str): A shortcut representing either sp//geometry levels or a composite method.
         composite_method (Level): Composite method.
-        conformer_level (Level): Level of theory for conformer searches.
+        conformer_opt_level (Level): Level of theory for conformer searches.
         opt_level (Level): Level of theory for geometry optimization.
         freq_level (Level): Level of theory for frequency calculations.
         sp_level (Level): Level of theory for single point calculations.
@@ -245,6 +246,7 @@ def __init__(self,
                  compute_thermo: bool = True,
                  compute_transport: bool = False,
                  conformer_level: Optional[Union[str, dict, Level]] = None,
+                 conformer_opt_level: Optional[Union[str, dict, Level]] = None,
                  dont_gen_confs: List[str] = None,
                  e_confs: float = 5.0,
                  ess_settings: Dict[str, Union[str, List[str]]] = None,
@@ -346,7 +348,7 @@ def __init__(self,
         # attributes related to level of theory specifications
         self.level_of_theory = level_of_theory
         self.composite_method = composite_method or None
-        self.conformer_level = conformer_level or None
+        self.conformer_opt_level = conformer_level or conformer_opt_level or None
         self.opt_level = opt_level or None
         self.freq_level = freq_level or None
         self.sp_level = sp_level or None
@@ -489,8 +491,8 @@ def as_dict(self) -> dict:
             restart_dict['compute_thermo'] = self.compute_thermo
         if self.compute_transport:
             restart_dict['compute_transport'] = self.compute_transport
-        if self.conformer_level is not None and str(self.conformer_level).split()[0] != default_levels_of_theory['conformer']:
-            restart_dict['conformer_level'] = self.conformer_level.as_dict()
+        if self.conformer_opt_level is not None:
+            restart_dict['conformer_opt_level'] = self.conformer_opt_level.as_dict()
         if self.dont_gen_confs:
             restart_dict['dont_gen_confs'] = self.dont_gen_confs
         if self.ts_adapters is not None:
@@ -608,7 +610,7 @@ def execute(self) -> dict:
                                    species_list=self.species,
                                    rxn_list=self.reactions,
                                    composite_method=self.composite_method,
-                                   conformer_level=self.conformer_level,
+                                   conformer_opt_level=self.conformer_opt_level,
                                    opt_level=self.opt_level,
                                    freq_level=self.freq_level,
                                    sp_level=self.sp_level,
@@ -689,7 +691,7 @@ def save_project_info_file(self):
         txt = ''
         txt += f'ARC v{self.__version__}\n'
         txt += f'ARC project {self.project}\n\nLevels of theory used:\n\n'
-        txt += f'Conformers:       {self.conformer_level}\n'
+        txt += f'Conformers:       {self.conformer_opt_level}\n'
         txt += f'TS guesses:       {self.ts_guess_level}\n'
         if self.composite_method is not None:
             txt += f'Composite method: {self.composite_method} {fine_txt}\n'
@@ -975,13 +977,13 @@ def set_levels_of_theory(self):
 
         logger.info('\n\nUsing the following levels of theory:\n')
 
-        if self.conformer_level is None:
-            self.conformer_level = default_levels_of_theory['conformer']
+        if self.conformer_opt_level is None:
+            self.conformer_opt_level = default_levels_of_theory['conformer']
             default_flag = ' (default)'
         else:
             default_flag = ''
-        self.conformer_level = Level(repr=self.conformer_level)
-        logger.info(f'Conformers:{default_flag} {self.conformer_level}')
+        self.conformer_opt_level = Level(repr=self.conformer_opt_level)
+        logger.info(f'Conformers opt:{default_flag} {self.conformer_opt_level}')
 
         if self.reactions or any([spc.is_ts for spc in self.species]):
             if not self.ts_guess_level:

arc/main_test.py

@@ -84,7 +84,7 @@ def test_as_dict(self):
                                                     'method': 'ccsd(t)-f12',
                                                     'method_type': 'wavefunction',
                                                     'software': 'molpro'},
-                         'conformer_level': {'basis': 'def2svp',
+                         'conformer_opt_level': {'basis': 'def2svp',
                                              'compatible_ess': ['gaussian', 'terachem'],
                                              'method': 'wb97xd',
                                              'method_type': 'dft',
@@ -152,7 +152,7 @@ def test_as_dict(self):
     def test_from_dict(self):
         """Test the from_dict() method of ARC"""
         restart_dict = {'composite_method': '',
-                        'conformer_level': 'b97-d3/6-311+g(d,p)',
+                        'conformer_opt_level': 'b97-d3/6-311+g(d,p)',
                         'freq_level': 'wb97x-d3/6-311+g(d,p)',
                         'freq_scale_factor': 0.96,
                         'opt_level': 'wb97x-d3/6-311+g(d,p)',

arc/reaction_test.py

@@ -1928,7 +1928,7 @@ def test_load_ts_xyz_user_guess_from_files(self):
         Scheduler(project=arc_object.project,
                   species_list=arc_object.species,
                   rxn_list=arc_object.reactions,
-                  conformer_level=arc_object.conformer_level,
+                  conformer_opt_level=arc_object.conformer_opt_level,
                   opt_level=arc_object.opt_level,
                   freq_level=arc_object.freq_level,
                   sp_level=arc_object.sp_level,
@@ -1950,7 +1950,7 @@ def test_load_ts_xyz_user_guess_from_files(self):
         Scheduler(project=arc_object.project,
                   species_list=arc_object.species,
                   rxn_list=arc_object.reactions,
-                  conformer_level=arc_object.conformer_level,
+                  conformer_opt_level=arc_object.conformer_opt_level,
                   opt_level=arc_object.opt_level,
                   freq_level=arc_object.freq_level,
                   sp_level=arc_object.sp_level,

arc/scheduler.py

@@ -130,7 +130,7 @@ class Scheduler(object):
         rxn_list (list): Contains input :ref:`ARCReaction <reaction>` objects.
         project_directory (str): Folder path for the project: the input file path or ARC/Projects/project-name.
         composite_method (str, optional): A composite method to use.
-        conformer_level (Union[str, dict], optional): The level of theory to use for conformer comparisons.
+        conformer_opt_level (Union[str, dict], optional): The level of theory to use for conformer comparisons.
         opt_level (Union[str, dict], optional): The level of theory to use for geometry optimizations.
         freq_level (Union[str, dict], optional): The level of theory to use for frequency calculations.
         sp_level (Union[str, dict], optional): The level of theory to use for single point energy calculations.
@@ -202,7 +202,7 @@ class Scheduler(object):
         bath_gas (str): A bath gas. Currently used in OneDMin to calc L-J parameters.
                         Allowed values are He, Ne, Ar, Kr, H2, N2, O2.
         composite_method (str): A composite method to use.
-        conformer_level (dict): The level of theory to use for conformer comparisons.
+        conformer_opt_level (dict): The level of theory to use for conformer comparisons.
         opt_level (dict): The level of theory to use for geometry optimizations.
         freq_level (dict): The level of theory to use for frequency calculations.
         sp_level (dict): The level of theory to use for single point energy calculations.
@@ -230,7 +230,7 @@ def __init__(self,
                  species_list: list,
                  project_directory: str,
                  composite_method: Optional[Level] = None,
-                 conformer_level: Optional[Level] = None,
+                 conformer_opt_level: Optional[Level] = None,
                  opt_level: Optional[Level] = None,
                  freq_level: Optional[Level] = None,
                  sp_level: Optional[Level] = None,
@@ -310,7 +310,7 @@ def __init__(self,
         self.report_time = time.time()  # init time for reporting status every 1 hr
         self.servers = list()
         self.composite_method = composite_method
-        self.conformer_level = conformer_level
+        self.conformer_opt_level = conformer_opt_level
         self.ts_guess_level = ts_guess_level
         self.opt_level = opt_level
         self.freq_level = freq_level
@@ -1840,16 +1840,16 @@ def process_directed_scans(self, label: str, pivots: Union[List[int], List[List[
 
     def process_conformers(self, label):
         """
-        Process the generated conformers and spawn DFT jobs at the conformer_level.
-        If more than one conformer is available, they will be optimized at the DFT conformer_level.
+        Process the generated conformers and spawn DFT jobs at the conformer_opt_level.
+        If more than one conformer is available, they will be optimized at the DFT conformer_opt_level.
 
         Args:
             label (str): The species label.
         """
         plotter.save_conformers_file(project_directory=self.project_directory,
                                      label=label,
                                      xyzs=self.species_dict[label].conformers,
-                                     level_of_theory=self.conformer_level,
+                                     level_of_theory=self.conformer_opt_level,
                                      multiplicity=self.species_dict[label].multiplicity,
                                      charge=self.species_dict[label].charge,
                                      is_ts=False,
@@ -1864,7 +1864,7 @@ def process_conformers(self, label):
                 for i, xyz in enumerate(self.species_dict[label].conformers):
                     self.run_job(label=label,
                                  xyz=xyz,
-                                 level_of_theory=self.conformer_level,
+                                 level_of_theory=self.conformer_opt_level,
                                  job_type='conformers',
                                  conformer=i,
                                  )
@@ -2027,7 +2027,7 @@ def determine_most_stable_conformer(self, label):
             plotter.save_conformers_file(project_directory=self.project_directory,
                                          label=label,
                                          xyzs=self.species_dict[label].conformers,
-                                         level_of_theory=self.conformer_level,
+                                         level_of_theory=self.conformer_opt_level,
                                          multiplicity=self.species_dict[label].multiplicity,
                                          charge=self.species_dict[label].charge,
                                          is_ts=False,
@@ -2088,7 +2088,7 @@ def determine_most_stable_conformer(self, label):
                                 conformer_xyz = xyz
                             if 'Conformers optimized and compared' not in self.output[label]['conformers']:
                                 self.output[label]['conformers'] += \
-                                    f'Conformers optimized and compared at {self.conformer_level.simple()}; '
+                                    f'Conformers optimized and compared at {self.conformer_opt_level.simple()}; '
                             break
                         else:
                             if i == 0:
@@ -2127,11 +2127,11 @@ def determine_most_stable_conformer(self, label):
                     else:
                         # troubleshoot when all conformers of a species failed isomorphic test
                         logger.warning(f'Isomorphism check for all conformers of species {label} failed at '
-                                       f'{self.conformer_level.simple()}. '
+                                       f'{self.conformer_opt_level.simple()}. '
                                        f'Attempting to troubleshoot using a different level.')
                         self.output[label]['conformers'] += \
                             f'Error: No conformer was found to be isomorphic with the 2D graph representation at ' \
-                            f'{self.conformer_level.simple()}; '
+                            f'{self.conformer_opt_level.simple()}; '
                         self.troubleshoot_conformer_isomorphism(label=label)
             else:
                 logger.warning(f'Could not run isomorphism check for species {label} due to missing 2D graph '
@@ -3171,7 +3171,7 @@ def troubleshoot_negative_freq(self,
             for i, xyz in enumerate(self.species_dict[label].conformers):
                 self.run_job(label=label,
                              xyz=xyz,
-                             level_of_theory=self.conformer_level,
+                             level_of_theory=self.conformer_opt_level,
                              job_type='conformers',
                              conformer=i,
                              )

arc/scheduler_test.py

@@ -89,7 +89,7 @@ def setUpClass(cls):
         cls.sched1 = Scheduler(project='project_test_1', ess_settings=cls.ess_settings,
                                species_list=[cls.spc1, cls.spc2, cls.spc3],
                                composite_method=None,
-                               conformer_level=Level(repr=default_levels_of_theory['conformer']),
+                               conformer_opt_level=Level(repr=default_levels_of_theory['conformer']),
                                opt_level=Level(repr=default_levels_of_theory['opt']),
                                freq_level=Level(repr=default_levels_of_theory['freq']),
                                sp_level=Level(repr=default_levels_of_theory['sp']),
@@ -105,7 +105,7 @@ def setUpClass(cls):
         cls.sched2 = Scheduler(project='project_test_2', ess_settings=cls.ess_settings,
                                species_list=[cls.spc1, cls.spc2, cls.spc3],
                                composite_method=None,
-                               conformer_level=Level(repr=default_levels_of_theory['conformer']),
+                               conformer_opt_level=Level(repr=default_levels_of_theory['conformer']),
                                opt_level=Level(repr=default_levels_of_theory['opt']),
                                freq_level=Level(repr=default_levels_of_theory['freq']),
                                sp_level=Level(repr=default_levels_of_theory['sp']),
@@ -121,7 +121,7 @@ def setUpClass(cls):
         cls.sched3 = Scheduler(project='project_test_4', ess_settings=cls.ess_settings,
                                species_list=[cls.spc1],
                                composite_method=Level(repr='CBS-QB3'),
-                               conformer_level=Level(repr=default_levels_of_theory['conformer']),
+                               conformer_opt_level=Level(repr=default_levels_of_theory['conformer']),
                                opt_level=Level(repr=default_levels_of_theory['freq_for_composite']),
                                freq_level=Level(repr=default_levels_of_theory['freq_for_composite']),
                                scan_level=Level(repr=default_levels_of_theory['scan_for_composite']),
@@ -221,7 +221,7 @@ def test_determine_adaptive_level(self):
                            ess_settings=self.ess_settings,
                            species_list=[self.spc1, self.spc2],
                            composite_method=None,
-                           conformer_level=default_levels_of_theory['conformer'],
+                           conformer_opt_level=default_levels_of_theory['conformer'],
                            opt_level=default_levels_of_theory['opt'],
                            freq_level=default_levels_of_theory['freq'],
                            sp_level=default_levels_of_theory['sp'],

arc/testing/restart/1_restart_thermo/restart.yml

@@ -9,7 +9,7 @@ arkane_level_of_theory:
   software: gaussian
 calc_freq_factor: true
 compute_transport: false
-conformer_level:
+conformer_opt_level:
   basis: 6-31g(d,p)
   dispersion: empiricaldispersion=gd3bj
   method: b3lyp

arc/testing/restart/2_restart_rate/restart.yml

@@ -3,7 +3,7 @@ calc_freq_factor: false
 compare_to_rmg: false
 composite_method: ''
 bac_type: null
-conformer_level:
+conformer_opt_level:
   auxiliary_basis: ''
   basis: def2svp
   dispersion: ''

arc/testing/restart/3_restart_bde/restart.yml

@@ -9,7 +9,7 @@ arkane_level_of_theory:
   software: gaussian
 compare_to_rmg: false
 compute_transport: false
-conformer_level:
+conformer_opt_level:
   basis: def2svp
   compatible_ess:
   - gaussian

arc/testing/restart/5_TS1/restart.yml

@@ -4,7 +4,7 @@ arkane_level_of_theory:
   method: ccsd(t)-f12
   method_type: wavefunction
   software: molpro
-conformer_level:
+conformer_opt_level:
   basis: def2tzvp
   compatible_ess:
   - gaussian