Report energy in conformers_before_optimization.txt (#743)

The previous `conformers_before_optimization.txt` doesn't include energy
information for the conformer before the optimization, so the updated
one will include this.

arc/common.py

@@ -756,9 +756,7 @@ def extremum_list(lst: list,
     Returns: Optional[Union[int, None]]
         The entry with the minimal/maximal value.
     """
-    if len(lst) == 0:
-        return None
-    elif all([entry is None for entry in lst]):
+    if lst is None or len(lst) == 0 or all([entry is None for entry in lst]):
         return None
     elif len(lst) == 1:
         return lst[0]

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_optimization: bool = True,
                          ):
     """
     Save the conformers before or after optimization.
@@ -918,21 +919,22 @@ def save_conformers_file(project_directory: str,
         ts_methods (list, optional): Entries are method names used to generate the TS guess.
         im_freqs (list, optional): Entries lists of imaginary frequencies.
         log_content (bool): Whether to log the content of the conformers file. ``True`` to log, default is ``False``.
+        before_optimization (bool): Whether the conformers are before DFT optimization. ``True`` for before, default is ``True``.
     """
     spc_dir = 'rxns' if is_ts else 'Species'
     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):
-        optimized = True
-        min_e = extremum_list(energies, return_min=True)
-        conf_path = os.path.join(geo_dir, 'conformers_after_optimization.txt')
-    else:
-        optimized = False
+    if before_optimization:
         conf_path = os.path.join(geo_dir, 'conformers_before_optimization.txt')
+    else:
+        conf_path = os.path.join(geo_dir, 'conformers_after_optimization.txt')
+    min_e = extremum_list(energies, return_min=True)
     with open(conf_path, 'w') as f:
         content = ''
-        if optimized:
+        if before_optimization:
+            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'
         for i, xyz in enumerate(xyzs):
@@ -950,7 +952,7 @@ 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 min_e is not None:
                     if energies[i] == min_e:
                         content += 'Relative Energy: 0 kJ/mol (lowest)'
                     elif energies[i] is not None:

arc/plotter_test.py

@@ -92,7 +92,8 @@ def test_save_conformers_file(self):
         plotter.save_conformers_file(project_directory=project_directory, label=spc1.label,
                                      xyzs=spc1.conformers, level_of_theory='APFD/def2tzvp',
                                      multiplicity=spc1.multiplicity, charge=spc1.charge, is_ts=False,
-                                     energies=spc1.conformer_energies)
+                                     energies=spc1.conformer_energies,
+                                     before_optimization=True,)
         conf_file_path = os.path.join(project_directory, 'output', 'Species', label, 'geometry', 'conformers',
                                       'conformers_before_optimization.txt')
         self.assertTrue(os.path.isfile(conf_file_path))

arc/scheduler.py

@@ -1145,6 +1145,7 @@ def run_ts_conformer_jobs(self, label: str):
                         f'{tsg.method_direction if tsg.method_direction is not None else ""} '
                         f'{tsg.method_index if tsg.method_index is not None else ""} '
                         for tsg in self.species_dict[label].ts_guesses],
+            before_optimization=True,
         )
         successful_tsgs = [tsg for tsg in self.species_dict[label].ts_guesses if tsg.success]
         if len(successful_tsgs) > 1:
@@ -1852,6 +1853,8 @@ 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_optimization=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 \
@@ -2028,8 +2031,9 @@ def determine_most_stable_conformer(self, label):
                                          multiplicity=self.species_dict[label].multiplicity,
                                          charge=self.species_dict[label].charge,
                                          is_ts=False,
-                                         energies=self.species_dict[label].conformer_energies,  # after optimization
-                                         )
+                                         energies=self.species_dict[label].conformer_energies,
+                                         before_optimization=False,
+                                         )  # after optimization
             # Run isomorphism checks if a 2D representation is available
             if self.species_dict[label].mol is not None:
                 for i, xyz in enumerate(xyzs):
@@ -2244,6 +2248,7 @@ def determine_most_likely_ts_conformer(self, label: str):
                             for tsg in self.species_dict[label].ts_guesses],
                 im_freqs=[tsg.imaginary_freqs for tsg in self.species_dict[label].ts_guesses]
                     if any(tsg.imaginary_freqs is not None for tsg in self.species_dict[label].ts_guesses) else None,
+                before_optimization=False,
             )
 
     def parse_composite_geo(self,
@@ -2579,6 +2584,7 @@ def check_negative_freq(self,
                                 for tsg in self.species_dict[label].ts_guesses],
                     im_freqs=[tsg.imaginary_freqs for tsg in self.species_dict[label].ts_guesses]
                         if any(tsg.imaginary_freqs is not None for tsg in self.species_dict[label].ts_guesses) else None,
+                    before_optimization=False,
                 )
                 if not self.testing:
                     # Update restart dictionary and save the yaml restart file:

arc/scheduler_test.py

@@ -184,16 +184,18 @@ def test_conformers(self):
                              xyzs=self.sched1.species_dict['C2H6'].conformers,
                              level_of_theory=Level(method='CBS-QB3'),
                              multiplicity=1,
-                             charge=0)
+                             charge=0,
+                             before_optimization=True,)
         c2h6_conf_path = os.path.join(self.sched1.project_directory, 'output', 'Species', 'C2H6', 'geometry',
                                       'conformers', 'conformers_before_optimization.txt')
         self.assertTrue(os.path.isfile(c2h6_conf_path))
         with open(c2h6_conf_path, 'r') as f:
             lines = f.readlines()
-        self.assertEqual(lines[0], 'conformer 0:\n')
-        self.assertEqual(lines[1][0], 'C')
-        self.assertEqual(lines[9], '\n')
-        self.assertEqual(lines[10], 'SMILES: CC\n')
+        self.assertEqual(lines[0], 'Conformers for C2H6, computed using a force field:\n')
+        self.assertEqual(lines[2], 'conformer 0:\n')
+        self.assertEqual(lines[3][0], 'C')
+        self.assertEqual(lines[11], '\n')
+        self.assertEqual(lines[12], 'SMILES: CC\n')
 
     def test_check_negative_freq(self):
         """Test the check_negative_freq() method"""

arc/species/species.py

@@ -1119,7 +1119,7 @@ def generate_conformers(self,
                                                       )
         if len(lowest_confs):
             self.conformers.extend([conf['xyz'] for conf in lowest_confs])
-            self.conformer_energies.extend([None] * len(lowest_confs))
+            self.conformer_energies.extend([conf['FF energy'] for conf in lowest_confs])
         else:
             xyz = self.get_xyz(generate=False)
             if xyz is None or not xyz:

arc/species/species_test.py

@@ -1538,13 +1538,15 @@ def test_append_conformers(self):
 
         # test w/o energies
         save_conformers_file(project_directory=project_directory, label='vinoxy', xyzs=xyzs,
-                             level_of_theory=Level(repr='level1'), multiplicity=2, charge=0)
+                             level_of_theory=Level(repr='level1'), multiplicity=2, charge=0,
+                             before_optimization=True,)
         self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'Species', 'vinoxy', 'geometry',
                                                     'conformers', 'conformers_before_optimization.txt')))
 
         # test with energies
         save_conformers_file(project_directory=project_directory, label='vinoxy', xyzs=xyzs,
-                             level_of_theory=Level(repr='level1'), multiplicity=2, charge=0, energies=energies)
+                             level_of_theory=Level(repr='level1'), multiplicity=2, charge=0, 
+                             energies=energies, before_optimization=False,)
         self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'Species', 'vinoxy', 'geometry',
                                                     'conformers', 'conformers_after_optimization.txt')))