Don't continue to process conformers if one is being troubleshooted (#…

…637) Fixes #636 Also added CH2's geometry
ReactionMechanismGenerator · Apr 16, 2023 · 8b1a8ee · 8b1a8ee
2 parents 8b01a7b + 4bee0f4
commit 8b1a8ee
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Showing 2 changed files with 17 additions and 2 deletions.
diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -523,7 +523,9 @@ def schedule_jobs(self):
                             # this is a completed conformer job
                             successful_server_termination = self.end_job(job=job, label=label, job_name=job_name)
                             if successful_server_termination:
-                                self.parse_conformer(job=job, label=label, i=i)
+                                troubleshooting_conformer = self.parse_conformer(job=job, label=label, i=i)
+                                if troubleshooting_conformer:
+                                    break
                             # Just terminated a conformer job.
                             # Are there additional conformer jobs currently running for this species?
                             for spec_jobs in job_list:
@@ -1845,6 +1847,9 @@ def parse_conformer(self,
             job (JobAdapter): The conformer job object.
             label (str): The TS species label.
             i (int): The conformer index.
+
+        Returns:
+            bool: Whether the conformer job is being troubleshooted by running a new job.
         """
         if job.job_status[1]['status'] == 'done':
             xyz = parser.parse_geometry(path=job.local_path_to_output_file)
@@ -1868,6 +1873,8 @@ def parse_conformer(self,
             logger.warning(f'Conformer {i} for {label} did not converge.')
             if job.times_rerun == 0 and self.trsh_ess_jobs:
                 self._run_a_job(job=job, label=label, rerun=True)
+                return True
+        return False
 
     def determine_most_stable_conformer(self, label):
         """

diff --git a/arc/species/conformers.py b/arc/species/conformers.py
@@ -107,7 +107,15 @@
                           'index': 0,
                           'FF energy': 0,
                           'source': 'CHEAT_SHEET',
-                          'torsion_dihedrals': {}}}
+                          'torsion_dihedrals': {}},
+               '[CH2]': {'xyz': converter.str_to_xyz("""C  0.0	0.000000  0.1051320
+                                                        H  0.0  0.988263 -0.3153960
+                                                        H  0.0 -0.988263 -0.3153960"""),
+                          'index': 0,  # Singlet CH2 forms the same H-C-H angle as triplet CH2
+                          'FF energy': 0,
+                          'source': 'CHEAT_SHEET',
+                          'torsion_dihedrals': {}},
+               }
 
 
 def generate_conformers(mol_list: Union[List[Molecule], Molecule],