Conform to new initialization of Species.final_xyz

it is now None instead of ''
ReactionMechanismGenerator · Apr 9, 2019 · 4bed0e4 · 4bed0e4
1 parent 8152037
commit 4bed0e4
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/arc/plotter.py b/arc/plotter.py
@@ -88,7 +88,7 @@ def check_xyz_species_for_drawing(xyz, species):
         xyz = xyz if xyz is not None else species.final_xyz
     if species is not None and not isinstance(species, ARCSpecies):
         raise InputError('Species must be an ARCSpecies instance. Got {0}.'.format(type(species)))
-    if species is not None and not species.final_xyz:
+    if species is not None and species.final_xyz is None:
         raise InputError('Species {0} has an empty final_xyz attribute.'.format(species.label))
     return xyz
 

diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -285,7 +285,8 @@ def __init__(self, project, ess_settings, species_list, composite_method, confor
                             self.run_composite_job(species.label)
                         else:
                             self.run_sp_job(label=species.label)
-                elif self.species_dict[species.label].initial_xyz or self.species_dict[species.label].final_xyz:
+                elif self.species_dict[species.label].initial_xyz is not None\
+                        or self.species_dict[species.label].final_xyz is not None:
                     # For restarting purposes: check before running jobs whether they were already terminated
                     # (check self.output) or whether they are "currently running" (check self.job_dict)
                     # This section takes care of restarting a Species (including a TS), but does not
@@ -331,7 +332,7 @@ def schedule_jobs(self):
         The main job scheduling block
         """
         for species in self.species_dict.values():
-            if not species.initial_xyz and not species.final_xyz and species.conformers\
+            if species.initial_xyz is None and species.final_xyz is None and species.conformers\
                     and any([e is not None for e in species.conformer_energies]):
                 # the species has no xyz, but has conformers and at least one of the conformers has energy
                 self.determine_most_stable_conformer(species.label)
@@ -636,7 +637,7 @@ def run_composite_job(self, label):
         if 'composite' not in self.job_dict[label]:  # Check whether or not composite jobs have been spawned yet
             # we're spawning the first composite job for this species
             self.job_dict[label]['composite'] = dict()
-        if self.species_dict[label].final_xyz != '':
+        if self.species_dict[label].final_xyz is not None:
             xyz = self.species_dict[label].final_xyz
         else:
             xyz = self.species_dict[label].initial_xyz