Use output consistently throughout main (#760)

Solves a KeyError issue with an empty output dict in main, especially
after ARC cannot find a TS for a reaction.

arc/main.py

@@ -634,9 +634,11 @@ def execute(self) -> dict:
                                    ts_adapters=self.ts_adapters,
                                    report_e_elect=self.report_e_elect,
                                    skip_nmd=self.skip_nmd,
+                                   output=self.output,
                                    )
 
-        save_yaml_file(path=os.path.join(self.project_directory, 'output', 'status.yml'), content=self.scheduler.output)
+        self.output = self.scheduler.output
+        save_yaml_file(path=os.path.join(self.project_directory, 'output', 'status.yml'), content=self.output)
 
         if not self.keep_checks:
             delete_check_files(self.project_directory)
@@ -650,7 +652,7 @@ def execute(self) -> dict:
                             project_directory=self.project_directory,
                             species_dict=self.scheduler.species_dict,
                             reactions=self.scheduler.rxn_list,
-                            output_dict=self.scheduler.output,
+                            output_dict=self.output,
                             bac_type=self.bac_type,
                             freq_scale_factor=self.freq_scale_factor,
                             compute_thermo=self.compute_thermo,
@@ -708,7 +710,7 @@ def save_project_info_file(self):
         txt += '\nConsidered the following species and TSs:\n'
         for species in self.species:
             descriptor = 'TS' if species.is_ts else 'Species'
-            failed = '' if self.scheduler.output[species.label]['convergence'] else ' (Failed!)'
+            failed = '' if self.output[species.label]['convergence'] else ' (Failed!)'
             txt += f'{descriptor} {species.label}{failed} (run time: {species.run_time})\n'
         if self.reactions:
             for rxn in self.reactions:
@@ -730,14 +732,14 @@ def save_project_info_file(self):
             if not species.is_ts:
                 spc_dict = dict()
                 spc_dict['label'] = species.label
-                spc_dict['success'] = self.scheduler.output[species.label]['convergence']
+                spc_dict['success'] = self.output[species.label]['convergence']
                 spc_dict['smiles'] = species.mol.copy(deep=True).to_smiles() if species.mol is not None else None
                 spc_dict['adj'] = species.mol.copy(deep=True).to_adjacency_list() if species.mol is not None else None
                 content['species'].append(spc_dict)
         for reaction in self.reactions:
             rxn_dict = dict()
             rxn_dict['label'] = reaction.label
-            rxn_dict['success'] = self.scheduler.output[reaction.ts_species.label]['convergence']
+            rxn_dict['success'] = self.output[reaction.ts_species.label]['convergence']
             content['reactions'].append(rxn_dict)
         save_yaml_file(path=path, content=content)
 
@@ -750,7 +752,7 @@ def summary(self) -> dict:
         """
         status_dict = {}
         logger.info(f'\n\n\nAll jobs terminated. Summary for project {self.project}:\n')
-        for label, output in self.scheduler.output.items():
+        for label, output in self.output.items():
             if output['convergence']:
                 status_dict[label] = True
                 logger.info(f'Species {label} converged successfully\n')

arc/scheduler.py

@@ -164,6 +164,7 @@ class Scheduler(object):
         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``.
+        output (dict, optional): Output dictionary with status per job type and final QM file paths for all species.
 
     Attributes:
         project (str): The project's name. Used for naming the working directory.
@@ -257,6 +258,7 @@ def __init__(self,
                  ts_adapters: List[str] = None,
                  report_e_elect: Optional[bool] = False,
                  skip_nmd: Optional[bool] = False,
+                 output: Optional[dict] = None,
                  ) -> None:
 
         self.project = project
@@ -287,7 +289,7 @@ def __init__(self,
         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.output = output or dict()
         self.output_multi_spc = dict()
         self.report_e_elect = report_e_elect
         self.skip_nmd = skip_nmd