report energy in conformers_before_optimization.txt

ReactionMechanismGenerator · May 22, 2024 · 9591699 · 9591699
1 parent 3631196
commit 9591699
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Showing 2 changed files with 12 additions and 5 deletions.
diff --git a/arc/plotter.py b/arc/plotter.py
@@ -900,6 +900,7 @@ def save_conformers_file(project_directory: str,
                          ts_methods: Optional[List[str]] = None,
                          im_freqs: Optional[List[List[float]]] = None,
                          log_content: bool = False,
+                         before_optimized: Optional[bool] = None,
                          ):
     """
     Save the conformers before or after optimization.
@@ -923,18 +924,22 @@ def save_conformers_file(project_directory: str,
     geo_dir = os.path.join(project_directory, 'output', spc_dir, label, 'geometry', 'conformers')
     if not os.path.exists(geo_dir):
         os.makedirs(geo_dir)
-    if energies is not None and any(e is not None for e in energies):
+    if before_optimized or energies is None or not any(e is not None for e in energies):
+        optimized = False
+        conf_path = os.path.join(geo_dir, 'conformers_before_optimization.txt')
+        min_e = extremum_list(energies, return_min=True) if before_optimized else None
+    else:
         optimized = True
         min_e = extremum_list(energies, return_min=True)
         conf_path = os.path.join(geo_dir, 'conformers_after_optimization.txt')
-    else:
-        optimized = False
-        conf_path = os.path.join(geo_dir, 'conformers_before_optimization.txt')
     with open(conf_path, 'w') as f:
         content = ''
         if optimized:
             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 before_optimized:
+            level_of_theory = level_of_theory.simple() if isinstance(level_of_theory, Level) else level_of_theory
+            content += f'Conformers for {label}, generated at the {level_of_theory} level:\n\n'
         for i, xyz in enumerate(xyzs):
             content += f'conformer {i}:\n'
             if xyz is not None:
@@ -950,7 +955,7 @@ def save_conformers_file(project_directory: str,
                     content += f'TS guess method: {ts_methods[i]}\n'
                 if im_freqs is not None and im_freqs[i] is not None:
                     content += f'Imaginary frequencies: {im_freqs[i]}\n'
-                if optimized:
+                if optimized or before_optimized:
                     if energies[i] == min_e:
                         content += 'Relative Energy: 0 kJ/mol (lowest)'
                     elif energies[i] is not None:

diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -1845,6 +1845,8 @@ def process_conformers(self, label):
                                      multiplicity=self.species_dict[label].multiplicity,
                                      charge=self.species_dict[label].charge,
                                      is_ts=False,
+                                     energies=self.species_dict[label].conformer_energies,
+                                     before_optimized=True,
                                      )  # before optimization
         self.species_dict[label].conformers_before_opt = tuple(self.species_dict[label].conformers)
         if self.species_dict[label].initial_xyz is None and self.species_dict[label].final_xyz is None \