Merge pull request #414 from ReactionMechanismGenerator/unconverged_s…

…pecies

If a species gets invalidated, delete its jobs and don't spawn new ones

arc/job/job.py

@@ -1167,7 +1167,10 @@ def write_input_file(self):
                     if up_file['source'] == 'path':
                         source_path = up_file['local']
                         destination_path = os.path.join(self.local_path, up_file['name'])
-                        shutil.copyfile(source_path, destination_path)
+                        try:
+                            shutil.copyfile(source_path, destination_path)
+                        except shutil.SameFileError:
+                            pass
                     elif up_file['source'] == 'input_files':
                         with open(os.path.join(self.local_path, up_file['name']), 'w') as f:
                             f.write(input_files[up_file['local']])
@@ -1211,7 +1214,10 @@ def _upload_check_file(self, local_check_file_path=None):
         else:
             # running locally, just copy the check file to the job folder
             new_check_file_path = os.path.join(self.local_path, 'check.chk')
-            shutil.copyfile(local_check_file_path, new_check_file_path)
+            try:
+                shutil.copyfile(local_check_file_path, new_check_file_path)
+            except shutil.SameFileError:
+                pass
 
     def _download_output_file(self):
         """

arc/job/trsh.py

@@ -460,7 +460,7 @@ def trsh_negative_freq(label: str,
                          'cannot troubleshoot geometry using dihedral modifications.')
             output_warnings.append('rotors = False; ')
         logger.error('Invalidating species.')
-        output_errors.append('Error: Encountered negative frequencies too many times; ')
+        output_errors.append('Error: Encountered negative frequencies too many times; Invalidating species; ')
     else:
         neg_freqs_idx = list()  # store indices w.r.t. vibfreqs
         largest_neg_freq_idx = 0  # index in vibfreqs

arc/scheduler.py

@@ -89,7 +89,7 @@ class Scheduler(object):
                                      },
                             'conformers': <comments>,
                             'isomorphism': <comments>,
-                            'convergence': <status>,  # boolean
+                            'convergence': <status>,  # Optional[bool]
                             'restart': <comments>,
                             'info': <comments>,
                             'warnings': <comments>,
@@ -469,6 +469,9 @@ def schedule_jobs(self):
             self.timer = True
             job_list = list()
             for label in self.unique_species_labels:
+                if self.output[label]['convergence'] is False:
+                    # skip unconverged species
+                    continue
                 # look for completed jobs and decide what jobs to run next
                 self.get_servers_jobs_ids()  # updates `self.servers_jobs_ids`
                 try:
@@ -2720,6 +2723,10 @@ def troubleshoot_negative_freq(self, label, job):
         self.species_dict[label].neg_freqs_trshed.extend(current_neg_freqs_trshed)
         for output_error in output_errors:
             self.output[label]['errors'] += output_error
+            if 'Invalidating species' in output_error:
+                logger.info(f'Deleting all currently running jobs for species {label}...')
+                self.delete_all_species_jobs(label)
+                self.output[label]['convergence'] = False
         for output_warning in output_warnings:
             self.output[label]['warnings'] += output_warning
         if len(confs):
@@ -3196,7 +3203,7 @@ def initialize_output_dict(self, label: Optional[str] = None):
                     for key in keys:
                         if key not in self.output[species.label]:
                             if key == 'convergence':
-                                self.output[species.label][key] = False
+                                self.output[species.label][key] = None
                             else:
                                 self.output[species.label][key] = ''
 

arc/schedulerTest.py

@@ -215,7 +215,7 @@ def test_initialize_output_dict(self):
         self.sched1.initialize_output_dict()
         self.assertFalse(self.sched1._does_output_dict_contain_info())
         empty_species_dict = {'conformers': '',
-                              'convergence': False,
+                              'convergence': None,
                               'errors': '',
                               'info': '',
                               'isomorphism': '',
@@ -235,7 +235,7 @@ def test_initialize_output_dict(self):
                                         'sp': ''},
                               'restart': '',
                               'warnings': ''}
-        initialized_output_dict = {'C2H6':empty_species_dict,
+        initialized_output_dict = {'C2H6': empty_species_dict,
                                    'CtripCO': empty_species_dict,
                                    'methylamine': empty_species_dict,
                                    }