Merge pull request #139 from ReactionMechanismGenerator/fix_job_types

Fix job types
ReactionMechanismGenerator · Jun 18, 2019 · b3b0cf8 · b3b0cf8
2 parents 515462f + 0b5840c
commit b3b0cf8
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Showing 3 changed files with 28 additions and 7 deletions.
diff --git a/arc/job/job.py b/arc/job/job.py
@@ -190,7 +190,7 @@ def __init__(self, project, ess_settings, species_name, xyz, job_type, level_of_
                             raise JobError('Could not find the Gaussian software to run the double-hybrid method {0}.\n'
                                            'ess_settings is:\n{1}'.format(self.method, self.ess_settings))
                         self.software = 'gaussian'
-                    if 'ccs' in self.method or 'cis' in self.method or 'pv' in self.basis_set:
+                    if 'ccs' in self.method or 'cis' in self.method:
                         if 'molpro' in self.ess_settings.keys():
                             self.software = 'molpro'
                         elif 'gaussian' in self.ess_settings.keys():
@@ -260,6 +260,13 @@ def __init__(self, project, ess_settings, species_name, xyz, job_type, level_of_
                             raise JobError('Could not find the Gaussian software to run {0}/{1}'.format(
                                 self.method, self.basis_set))
                         self.software = 'gaussian'
+                    if 'pv' in self.basis_set:
+                        if 'molpro' in self.ess_settings.keys():
+                            self.software = 'molpro'
+                        elif 'gaussian' in self.ess_settings.keys():
+                            self.software = 'gaussian'
+                        elif 'qchem' in self.ess_settings.keys():
+                            self.software = 'qchem'
                     else:
                         if 'gaussian' in self.ess_settings.keys():
                             self.software = 'gaussian'

diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -318,7 +318,7 @@ def __init__(self, project, ess_settings, species_list, composite_method, confor
                             and 'opt' not in self.job_dict[species.label] and not self.composite_method \
                             and 'geo' not in self.output[species.label]:
                         self.run_opt_job(species.label)
-                    elif 'opt converged' in self.output[species.label]['status']:
+                    elif 'opt converged' in self.output[species.label]['status'] and not self.composite_method:
                         # opt is done
                         if 'freq' not in self.output[species.label] and 'freq' not in self.job_dict[species.label]:
                             if self.species_dict[species.label].is_ts\
@@ -632,10 +632,22 @@ def run_conformer_jobs(self):
                                          job_type='conformer', conformer=i)
                     elif len(self.species_dict[label].conformers) == 1:
                         logging.info('Only one conformer is available for species {0}, '
-                                     'using it for geometry optimization'.format(label))
+                                     'using it as initial xyz'.format(label))
                         self.species_dict[label].initial_xyz = self.species_dict[label].conformers[0]
                         if not self.composite_method:
-                            self.run_opt_job(label)
+                            if self.job_types['opt']:
+                                self.run_opt_job(label)
+                            else:
+                                if self.job_types['freq']:
+                                    self.run_freq_job(label)
+                                if self.job_types['sp']:
+                                    self.run_sp_job(label)
+                                if self.job_types['1d_rotors']:
+                                    self.run_scan_jobs(label)
+                                if self.job_types['onedmin']:
+                                    self.run_onedmin_job(label)
+                                if self.job_types['orbitals']:
+                                    self.run_orbitals_job(label)
                         else:
                             self.run_composite_job(label)
 
@@ -746,8 +758,10 @@ def run_sp_job(self, label):
                 self.run_job(label=label, xyz=self.species_dict[label].final_xyz, level_of_theory='ccsd/vdz',
                              job_type='sp')
         if self.job_types['sp']:
-            self.run_job(label=label, xyz=self.species_dict[label].final_xyz,
-                         level_of_theory=self.sp_level, job_type='sp')
+            xyz = self.species_dict[label].final_xyz or self.species_dict[label].initial_xyz
+            if xyz is None:
+                xyz = self.species_dict[label].conformers[0]
+            self.run_job(label=label, xyz=xyz, level_of_theory=self.sp_level, job_type='sp')
 
     def run_scan_jobs(self, label):
         """

diff --git a/arc/species/species.py b/arc/species/species.py
@@ -750,7 +750,7 @@ def determine_multiplicity(self, smiles, adjlist, mol):
             if xyz is None and len(self.conformers):
                 xyz = self.conformers[0]
             if xyz:
-                _, atoms, _, _, _ = get_xyz_matrix(xyz)
+                atoms = get_xyz_matrix(xyz)[1]
                 electrons = 0
                 for atom in atoms:
                     for number, symbol in symbol_by_number.items():