Only add a species to the thermo library if requested (#612)

Here we add a new attribute to ARCSpecies, `include_in_thermo_lib`
We already have an attribute called `compute_thermo`, which will cause
ARC not to process the species via statmech. The new attribute will make
ARC compute thermo data, but it won't be included in the final RMG
thermo library output.
The rational is to facilitate a new T3 feature where species that
participate in reactions we compute will not end up in the thermo
library if their thermo data is already known to a satisfactory
precision. However, for post-analysis purposes, it could still be
beneficial to have the thermo data already process by ARC/Arkane.

arc/plotter.py

@@ -765,7 +765,7 @@ def save_thermo_lib(species_list: list,
         lib_path = os.path.join(path, 'thermo', f'{name}.py')
         thermo_library = ThermoLibrary(name=name, long_desc=lib_long_desc)
         for i, spc in enumerate(species_list):
-            if spc.thermo is not None:
+            if spc.thermo is not None and spc.include_in_thermo_lib:
                 spc.long_thermo_description += f'\nExternal symmetry: {spc.external_symmetry}, ' \
                                                f'optical isomers: {spc.optical_isomers}\n'
                 spc.long_thermo_description += f'\nGeometry:\n{xyz_to_str(spc.final_xyz)}'

arc/species/species.py

@@ -116,6 +116,7 @@ class ARCSpecies(object):
         bond_corrections (dict, optional): The bond additivity corrections (BAC) to be used. Determined from the
                                            structure if not directly given.
         compute_thermo (bool, optional): Whether to calculate thermodynamic properties for this species.
+        include_in_thermo_lib (bool, optional): Whether to include in the output RMG library.
         e0_only (bool, optional): Whether to only run statmech (w/o thermo) to compute E0.
         species_dict (dict, optional): A dictionary to create this object from (used when restarting ARC).
         yml_path (str, optional): Path to an Arkane YAML file representing a species (for loading the object).
@@ -225,6 +226,7 @@ class ARCSpecies(object):
         t1 (float): The T1 diagnostic parameter from Molpro.
         neg_freqs_trshed (list): A list of negative frequencies this species was troubleshooted for.
         compute_thermo (bool): Whether to calculate thermodynamic properties for this species.
+        include_in_thermo_lib (bool): Whether to include in the output RMG library.
         e0_only (bool): Whether to only run statmech (w/o thermo) to compute E0.
         thermo (HeatCapacityModel): The thermodata calculated by ARC.
         rmg_thermo (HeatCapacityModel): The thermodata generated by RMG for comparison.
@@ -294,6 +296,7 @@ def __init__(self,
                  charge: Optional[int] = None,
                  checkfile: Optional[str] = None,
                  compute_thermo: Optional[bool] = None,
+                 include_in_thermo_lib: Optional[bool] = True,
                  consider_all_diastereomers: bool = True,
                  directed_rotors: Optional[dict] = None,
                  e0_only: bool = False,
@@ -388,6 +391,7 @@ def __init__(self,
             self.chosen_ts_method = None
             self.chosen_ts_list = list()
             self.compute_thermo = compute_thermo if compute_thermo is not None else not self.is_ts
+            self.include_in_thermo_lib = include_in_thermo_lib
             self.e0_only = e0_only
             self.long_thermo_description = ''
             self.opt_level = None
@@ -620,6 +624,8 @@ def as_dict(self,
         species_dict['multiplicity'] = self.multiplicity
         species_dict['charge'] = self.charge
         species_dict['compute_thermo'] = self.compute_thermo
+        if not self.include_in_thermo_lib:
+            species_dict['include_in_thermo_lib'] = self.include_in_thermo_lib
         species_dict['number_of_rotors'] = self.number_of_rotors
         if self.external_symmetry is not None:
             species_dict['external_symmetry'] = self.external_symmetry
@@ -786,6 +792,7 @@ def from_dict(self, species_dict):
         self.multiplicity = species_dict['multiplicity'] if 'multiplicity' in species_dict else None
         self.charge = species_dict['charge'] if 'charge' in species_dict else 0
         self.compute_thermo = species_dict['compute_thermo'] if 'compute_thermo' in species_dict else not self.is_ts
+        self.include_in_thermo_lib = species_dict['include_in_thermo_lib'] if 'include_in_thermo_lib' in species_dict else True
         self.e0_only = species_dict['e0_only'] if 'e0_only' in species_dict else False
         self.number_of_radicals = species_dict['number_of_radicals'] if 'number_of_radicals' in species_dict else None
         self.opt_level = species_dict['opt_level'] if 'opt_level' in species_dict else None