Merge pull request #124 from ReactionMechanismGenerator/tsg

 Allow defining a TS species simply with .xyz guesses

arc/scheduler.py

@@ -642,10 +642,9 @@ def run_ts_conformer_jobs(self, label):
         elif len(self.species_dict[label].conformers) == 1:
             if 'opt' not in self.job_dict[label] and 'composite' not in self.job_dict[label]:
                 # proceed only if opt (/composite) not already spawned
-                if self.species_dict[label].rxn_label is None:
-                    raise SchedulerError('TS {0} is missing a reaction label'.format(label))
-                rxn = ' ' if not self.species_dict[label].is_ts else\
-                    ' of reaction ' + self.species_dict[label].rxn_label
+                rxn = ''
+                if self.species_dict[label].rxn_label is not None:
+                    rxn = ' of reaction ' + self.species_dict[label].rxn_label
                 logging.info('Only one TS guess is available for species {0}{1},'
                              ' using it for geometry optimization'.format(label, rxn))
                 self.species_dict[label].initial_xyz = self.species_dict[label].conformers[0]

arc/species/species.py

@@ -552,6 +552,16 @@ def generate_conformers(self):
             tsg_index = 0
             self.successful_methods = list()
             self.unsuccessful_methods = list()
+            for i, xyz in enumerate(self.conformers):
+                # when defining a TS species with xyz, it is saved in self.conformers via self.process_xyz()
+                # make TSGuess objects out of them if don't already exist
+                for tsg in self.ts_guesses:
+                    if xyz == tsg.xyz:
+                        break
+                else:
+                    self.ts_guesses.append(TSGuess(method='user guess {0}'.format(i), xyz=xyz))
+                    self.ts_guesses[-1].success = True
+            self.conformers = list()
             for tsg in self.ts_guesses:
                 if tsg.success:
                     self.conformers.append(tsg.xyz)