Run sp job after conformer job

Use the `xyzs` from the conformer job to run `sp` jobs. Save the `conformers_after_optimization` using the updated level of theory and energies.
ReactionMechanismGenerator · Sep 15, 2024 · 349e78d · 349e78d
1 parent 352631f
commit 349e78d
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Showing 2 changed files with 29 additions and 1 deletion.
diff --git a/arc/plotter.py b/arc/plotter.py
@@ -901,6 +901,7 @@ def save_conformers_file(project_directory: str,
                          im_freqs: Optional[List[List[float]]] = None,
                          log_content: bool = False,
                          before_optimization: bool = True,
+                         conf_sp: Optional[bool] = False,
                          ):
     """
     Save the conformers before or after optimization.
@@ -936,7 +937,10 @@ def save_conformers_file(project_directory: str,
             content += f'Conformers for {label}, computed using a force field:\n\n'
         else:
             level_of_theory = level_of_theory.simple() if isinstance(level_of_theory, Level) else level_of_theory
-            content += f'Conformers for {label}, optimized at the {level_of_theory} level:\n\n'
+            if not conf_sp:
+                content += f'Conformers for {label}, optimized at the {level_of_theory} level:\n\n'
+            else:
+                content += f'Conformers for {label}, sp at the {level_of_theory} level:\n\n'
         for i, xyz in enumerate(xyzs):
             content += f'conformer {i}:\n'
             if xyz is not None:

diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -555,6 +555,12 @@ def schedule_jobs(self):
                             successful_server_termination = self.end_job(job=job, label=label, job_name=job_name)
                             if successful_server_termination:
                                 troubleshooting_conformer = self.parse_conformer(job=job, label=label, i=i)
+                                if self.conformer_sp_level is not None:
+                                    self.run_job(label=label,
+                                                 xyz=self.species_dict[label].conformers[i],
+                                                 level_of_theory=self.conformer_sp_level,
+                                                 job_type='sp',
+                                                 )
                                 if troubleshooting_conformer:
                                     break
                             # Just terminated a conformer job.
@@ -635,6 +641,17 @@ def schedule_jobs(self):
                             successful_server_termination = self.end_job(job=job, label=label, job_name=job_name)
                             if successful_server_termination:
                                 self.check_sp_job(label=label, job=job)
+                                plotter.save_conformers_file(project_directory=self.project_directory,
+                                                             label=label,
+                                                             xyzs=self.species_dict[label].conformers,
+                                                             level_of_theory=self.conformer_sp_level,
+                                                             multiplicity=self.species_dict[label].multiplicity,
+                                                             charge=self.species_dict[label].charge,
+                                                             is_ts=False,
+                                                             energies=self.species_dict[label].conformer_energies,
+                                                             before_optimization=False,
+                                                             conf_sp=True
+                                                             )  # after optimization
                             self.timer = False
                             break
                     elif 'composite' in job_name:
@@ -2663,6 +2680,13 @@ def check_sp_job(self,
             # This is a CCSD job ran before MRCI. Spawn MRCI
             self.run_sp_job(label)
         elif job.job_status[1]['status'] == 'done':
+            if self.conformer_sp_level is not None:
+                xyz = parser.parse_geometry(path=job.local_path_to_output_file)
+                energy = parser.parse_e_elect(path=job.local_path_to_output_file)
+                for i, conformer in enumerate(self.species_dict[label].conformers):
+                    if conformer == xyz:
+                        self.species_dict[label].conformer_energies[i] = energy
+                        break
             self.post_sp_actions(label,
                                  sp_path=os.path.join(job.local_path_to_output_file),
                                  level=job.level,