Merge pull request #424 from ReactionMechanismGenerator/scan_fixes

Scan fixes

arc/job/job.py

@@ -242,6 +242,13 @@ def __init__(self,
         self.xyz = check_xyz_dict(xyz)
         self.radius = radius
         self.directed_scan_type = directed_scan_type
+        self.directed_dihedrals = None
+        if directed_dihedrals is not None:
+            if isinstance(directed_dihedrals[0], list):
+                self.directed_dihedrals = [[float(d) for d in dd] for dd in directed_dihedrals]
+            else:
+                self.directed_dihedrals = [float(d) for d in directed_dihedrals]  # it's a string in the restart dict
+
         self.rotor_index = rotor_index
         self.directed_scans = directed_scans
         self.directed_dihedrals = [float(d) for d in directed_dihedrals] if directed_dihedrals is not None \
@@ -394,7 +401,9 @@ def as_dict(self) -> dict:
         if self.occ is not None:
             job_dict['occ'] = self.occ
         if self.directed_dihedrals is not None:
-            job_dict['directed_dihedrals'] = ['{0:.2f}'.format(dihedral) for dihedral in self.directed_dihedrals]
+            job_dict['directed_dihedrals'] = ['{0:.2f}'.format(dihedral) if not isinstance(dihedral, list)
+                                              else ['{0:.2f}'.format(d) for d in dihedral]
+                                              for dihedral in self.directed_dihedrals]
         if self.directed_scans is not None:
             job_dict['directed_scans'] = self.directed_scans
         if self.directed_scan_type is not None:
@@ -1290,7 +1299,8 @@ def run(self):
         if self.fine:
             logger.info(f'Running job {self.job_name} for {self.species_name} (fine opt)')
         elif self.directed_dihedrals is not None and self.directed_scans is not None:
-            dihedrals = ['{0:.2f}'.format(dihedral) for dihedral in self.directed_dihedrals]
+            dihedrals = ['{0:.2f}'.format(dihedral) if not isinstance(dihedral, list)
+                         else ['{0:.2f}'.format(d) for d in dihedral] for dihedral in self.directed_dihedrals]
             logger.info(f'Running job {self.job_name} for {self.species_name} (pivots: {self.directed_scans}, '
                         f'dihedrals: {dihedrals})')
         elif self.pivots:

arc/plotter.py

@@ -1140,11 +1140,14 @@ def plot_2d_rotor_scan(results, path=None, label='', cmap='Blues', resolution=90
     zero_phi0, zero_phi1 = list(), list()
     energies = np.zeros(shape=(phis0.size, phis1.size), dtype=np.float64)
     keys_list = list(results['directed_scan'].keys())
+    e_min = None
     for i, phi0 in enumerate(phis0):
         for j, phi1 in enumerate(phis1):
             key = tuple(f'{dihedral:.2f}' for dihedral in [phi0, phi1])
             if key in keys_list:
                 energies[i, j] = results['directed_scan'][key]['energy']
+                if e_min is None or energies[i, j] < e_min:
+                    e_min = energies[i, j]
             else:
                 keys = list()
                 keys.append(tuple(f'{dihedral:.2f}' for dihedral in [360.0 - phi0, phi1]))
@@ -1159,6 +1162,8 @@ def plot_2d_rotor_scan(results, path=None, label='', cmap='Blues', resolution=90
                 keys.append(tuple(f'{dihedral:.2f}' for dihedral in [phi0 - 360.0, phi1]))
                 keys.append(tuple(f'{dihedral:.2f}' for dihedral in [phi0, phi1 - 360.0]))
                 keys.append(tuple(f'{dihedral:.2f}' for dihedral in [phi0 - 360.0, phi1 - 360.0]))
+                keys.append(tuple(f'{dihedral:.2f}' for dihedral in [phi0 - 360.0, phi1 + 360.0]))
+                keys.append(tuple(f'{dihedral:.2f}' for dihedral in [phi0 + 360.0, phi1 - 360.0]))
                 for key_ in keys:
                     if key_ in keys_list:
                         energies[i, j] = results['directed_scan'][key_]['energy']
@@ -1170,6 +1175,10 @@ def plot_2d_rotor_scan(results, path=None, label='', cmap='Blues', resolution=90
                 zero_phi0.append(phi0)
                 zero_phi1.append(phi1)
 
+    for i, phi0 in enumerate(phis0):
+        for j, phi1 in enumerate(phis1):
+            energies[i, j] -= e_min
+
     fig = plt.figure(num=None, figsize=(12, 8), dpi=resolution, facecolor='w', edgecolor='k')
 
     plt.contourf(phis0, phis1, energies, 20, cmap=cmap)

arc/scheduler.py

@@ -583,7 +583,7 @@ def schedule_jobs(self):
                             and self.job_dict[label]['scan'][job_name].job_id not in self.servers_jobs_ids:
                         job = self.job_dict[label]['scan'][job_name]
                         successful_server_termination = self.end_job(job=job, label=label, job_name=job_name)
-                        if successful_server_termination:
+                        if successful_server_termination and job.directed_scans is None:
                             self.check_scan_job(label=label, job=job)
                         self.timer = False
                         break
@@ -3008,6 +3008,8 @@ def troubleshoot_ess(self,
                          shift=shift,
                          directed_dihedrals=job.directed_dihedrals,
                          directed_scans=job.directed_scans,
+                         directed_scan_type=job.directed_scan_type,
+                         rotor_index = job.rotor_index,
                          cpu_cores=cpu_cores,
                          )
         self.save_restart_dict()

arc/species/vectors.py

@@ -209,6 +209,8 @@ def calculate_dihedral_angle(coords: Union[list, tuple, dict],
         raise TypeError(f'coords must be a list or a tuple, got\n{coords}\nwhich is a {type(coords)}')
     if index not in [0, 1]:
         raise VectorsError(f'index must be either 0 or 1, got {index}')
+    if torsion is None:
+        raise VectorsError(f'torsion cannot be None')
     if len(torsion) != 4:
         raise VectorsError(f'torsion atom list must be of length four, got {len(torsion)}')
     if len(set(torsion)) < 4: