Merge pull request #150 from ReactionMechanismGenerator/fixes

Minor conformers/xyz files fixes
ReactionMechanismGenerator · Jul 30, 2019 · 7cac46e · 7cac46e
2 parents 686c2dd + 5de663a
commit 7cac46e
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Showing 5 changed files with 11 additions and 9 deletions.
diff --git a/arc/plotter.py b/arc/plotter.py
@@ -714,7 +714,7 @@ def save_conformers_file(project_directory, label, xyzs, level_of_theory, multip
         ts_methods (list, optional): Entries are method names used to generate the TS guess.
     """
     spc_dir = 'rxns' if is_ts else 'Species'
-    geo_dir = os.path.join(project_directory, 'output', spc_dir, label, 'geometry')
+    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):

diff --git a/arc/plotterTest.py b/arc/plotterTest.py
@@ -80,7 +80,7 @@ def test_save_conformers_file(self):
                                      xyzs=spc1.conformers, level_of_theory='APFD/def2tzvp',
                                      multiplicity=spc1.multiplicity, charge=spc1.charge, is_ts=False,
                                      energies=spc1.conformer_energies)
-        conf_file_path = os.path.join(project_directory, 'output', 'Species', label, 'geometry',
+        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))
 

diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -1251,6 +1251,7 @@ def parse_opt_geo(self, label, job):
                     self.check_freq_job(label, job)
                 self.output[label]['status'] += 'opt converged; '
                 self.species_dict[label].opt_level = self.opt_level
+                plotter.save_geo(species=self.species_dict[label], project_directory=self.project_directory)
                 if self.species_dict[label].is_ts:
                     rxn_str = ' of reaction {0}'.format(self.species_dict[label].rxn_label)
                 else:
@@ -1603,7 +1604,6 @@ def check_all_done(self, label):
                 (self.species_dict[label].is_ts or self.species_dict[label].number_of_atoms == 1 or
                 ('freq converged' in status and 'opt converged' in status)))):
             self.output[label]['status'] += 'ALL converged'
-            plotter.save_geo(species=self.species_dict[label], project_directory=self.project_directory)
             if self.species_dict[label].is_ts:
                 self.species_dict[label].make_ts_report()
                 logger.info(self.species_dict[label].ts_report + '\n')

diff --git a/arc/schedulerTest.py b/arc/schedulerTest.py
@@ -93,7 +93,7 @@ def test_conformers(self):
 H      -1.16566701    0.32023496   -0.81630508"""
         self.assertEqual(self.sched1.species_dict[label].initial_xyz, expecting)
         methylamine_conf_path = os.path.join(self.sched1.project_directory, 'output', 'Species', 'methylamine',
-                                             'geometry', 'conformers_after_optimization.txt')
+                                             'geometry', 'conformers', 'conformers_after_optimization.txt')
         self.assertTrue(os.path.isfile(methylamine_conf_path))
         with open(methylamine_conf_path, 'r') as f:
             lines = f.readlines()
@@ -109,7 +109,7 @@ def test_conformers(self):
                              xyzs=self.sched1.species_dict['C2H6'].conformers, level_of_theory='level1',
                              multiplicity=1, charge=0)
         c2h6_conf_path = os.path.join(self.sched1.project_directory, 'output', 'Species', 'C2H6', 'geometry',
-                                      'conformers_before_optimization.txt')
+                                      'conformers', 'conformers_before_optimization.txt')
         self.assertTrue(os.path.isfile(c2h6_conf_path))
         with open(c2h6_conf_path, 'r') as f:
             lines = f.readlines()

diff --git a/arc/species/speciesTest.py b/arc/species/speciesTest.py
@@ -641,18 +641,20 @@ def test_append_conformers(self):
         save_conformers_file(project_directory=project_directory, label='vinoxy', xyzs=xyzs, level_of_theory='level1',
                              multiplicity=2, charge=0)
         self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'Species', 'vinoxy', 'geometry',
-                                                    'conformers_before_optimization.txt')))
+                                                    'conformers', 'conformers_before_optimization.txt')))
 
         save_conformers_file(project_directory=project_directory, label='vinoxy', xyzs=xyzs, level_of_theory='level1',
                              multiplicity=2, charge=0, energies=energies)
         self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'Species', 'vinoxy', 'geometry',
-                                                    'conformers_after_optimization.txt')))
+                                                    'conformers', 'conformers_after_optimization.txt')))
 
         spc2 = ARCSpecies(label=str('vinoxy'), smiles=str('C=C[O]'), xyz=os.path.join(
-            project_directory, 'output', 'Species', 'vinoxy', 'geometry', 'conformers_before_optimization.txt'))
+            project_directory, 'output', 'Species', 'vinoxy', 'geometry', 'conformers',
+            'conformers_before_optimization.txt'))
 
         spc3 = ARCSpecies(label=str('vinoxy'), smiles=str('C=C[O]'), xyz=os.path.join(
-            project_directory, 'output', 'Species', 'vinoxy', 'geometry', 'conformers_after_optimization.txt'))
+            project_directory, 'output', 'Species', 'vinoxy', 'geometry', 'conformers',
+            'conformers_after_optimization.txt'))
 
         self.assertEqual(spc2.conformers[2], xyzs[2])
         self.assertEqual(spc3.conformers[2], xyzs[2])