Merge pull request #415 from ReactionMechanismGenerator/loop

Delete a non-converged species from the running_jobs dict

arc/job/trsh.py

@@ -447,13 +447,14 @@ def trsh_negative_freq(label: str,
     neg_freqs_trshed = neg_freqs_trshed if neg_freqs_trshed is not None else list()
     job_types = job_types if job_types is not None else ['rotors']
     output_errors, output_warnings, conformers, current_neg_freqs_trshed = list(), list(), list(), list()
-    factor = 1.1
+    factor, factor_increase = 1.1, 0.2
+    max_times_to_trsh_neg_freq = 5
     try:
         freqs, normal_disp_modes = parse_normal_displacement_modes(path=log_file)
     except NotImplementedError as e:
         logger.error(f'Could not troubleshoot negative frequency for species {label}, got:\n{e}')
         return [], [], output_errors, []
-    if len(neg_freqs_trshed) > 10:
+    if len(neg_freqs_trshed) > max_times_to_trsh_neg_freq:
         logger.error(f'Species {label} was troubleshooted for negative frequencies too many times.')
         if 'rotors' not in job_types:
             logger.error('The rotor scans feature is turned off, '
@@ -483,7 +484,7 @@ def trsh_negative_freq(label: str,
         elif len(neg_freqs_idx) == 1 and any([np.allclose(freqs[0], vf, rtol=1e-04, atol=1e-02)
                                               for vf in neg_freqs_trshed]):
             # species has one negative frequency, and has been troubleshooted for it before
-            factor = 1 + 0.1 * (len(neg_freqs_trshed) + 1)
+            factor = 1 + factor_increase * (len(neg_freqs_trshed) + 1)
             logger.info(f'Species {label} has a negative frequency ({freqs[largest_neg_freq_idx]}) for the '
                         f'{len(neg_freqs_trshed)} time. Perturbing its geometry using the respective vibrational '
                         f'displacements, this time using a larger factor (x {factor})')
@@ -1317,6 +1318,7 @@ def scan_quality_check(label: str,
                 broken_bond_label = bond_change.sort_values().index[-1]  # the largest change
                 # Freeze the bonds, no further freezing other ics to prevent over-constraining
                 broken_bonds = [scan_conformers['atoms'][broken_bond_label]]
+                invalidate = True
                 invalidation_reason = f'Bond ({broken_bonds}) broke during the scan.'
                 message = f'Rotor scan of {label} between pivots {pivots} has broken bonds: ' \
                           f'{broken_bonds}. ARC will attempt to troubleshoot this rotor scan.'
@@ -1345,16 +1347,18 @@ def scan_quality_check(label: str,
         # 1.3 Check consistency
         if 0 in changed_ic_dict.keys() and len(changed_ic_dict) == 1:
             # Smooth scan with different initial and final conformer
+            invalidate = True
             invalidation_reason = 'Inconsistent initial and final conformers'
             message = f'Rotor scan of {label} between pivots {pivots} has inconsistent initial ' \
-                      f'and final conformers. Internal coordinates {changed_ic_dict[0]} are different. ' \
+                      f'and final conformers.\nInternal coordinates {changed_ic_dict[0]} are different. ' \
                       f'ARC will attempt to troubleshoot this rotor scan.'
             logger.error(message)
             actions = {'freeze': [scan_conformers['atoms'][ic_label]
                                   for ic_label in changed_ic_dict[0]]}
             return invalidate, invalidation_reason, message, actions
         elif len(changed_ic_dict) > 0:
             # Not smooth scan
+            invalidate = True
             invalidation_reason = 'Significant difference observed between consecutive conformers'
             message = f'Rotor scan of {label} between pivots {pivots} is inconsistent between ' \
                       f'two consecutive conformers.\nInconsistent consecutive conformers and problematic ' \

arc/plotter.py

@@ -985,8 +985,16 @@ def plot_torsion_angles(torsion_angles, torsions_sampling_points=None, wells_dic
     return num_comb
 
 
-def plot_1d_rotor_scan(angles=None, energies=None, results=None, path=None, scan=None, comment='', units='degrees',
-                       original_dihedral=None, label=None):
+def plot_1d_rotor_scan(angles=None,
+                       energies=None,
+                       results=None,
+                       path=None,
+                       scan=None,
+                       comment='',
+                       units='degrees',
+                       original_dihedral=None,
+                       label=None,
+                       ):
     """
     Plots a 1D rotor PES for energy vs. angles. Either ``angles`` and ``energies`` or ``results`` must be given.
 

arc/scheduler.py

@@ -471,6 +471,8 @@ def schedule_jobs(self):
             for label in self.unique_species_labels:
                 if self.output[label]['convergence'] is False:
                     # skip unconverged species
+                    if label in self.running_jobs:
+                        del self.running_jobs[label]
                     continue
                 # look for completed jobs and decide what jobs to run next
                 self.get_servers_jobs_ids()  # updates `self.servers_jobs_ids`
@@ -1618,7 +1620,7 @@ def process_directed_scans(self, label, pivots):
                               'top': ``list``,
                               'scan': ``list``,
                               'number_of_running_jobs': ``int``,
-                              'success': ``bool``,
+                              'success': ``Optional[bool]``,
                               'invalidation_reason': ``str``,
                               'times_dihedral_set': ``int``,
                               'scan_path': <path to scan output file>,
@@ -2345,7 +2347,7 @@ def check_scan_job(self, label: str, job: Job) -> None:
                               'top': ``list``,
                               'scan': ``list``,
                               'number_of_running_jobs': ``int``,
-                              'success': ``bool``,
+                              'success': ``Optional[bool]``,
                               'invalidation_reason': ``str``,
                               'times_dihedral_set': ``int``,
                               'scan_path': <path to scan output file>,
@@ -2436,14 +2438,14 @@ def check_scan_job(self, label: str, job: Job) -> None:
         else:
             raise SchedulerError(f'Could not match rotor with pivots {job.pivots} in species {label}')
 
-        # This is a bad rotor scan, and we can do nothing about it at this moment.
-        if invalidate and not actions:
-            self.species_dict[label].rotors_dict[i]['success'] = False
+        # This is a bad rotor scan
+        if invalidate:
+            self.species_dict[label].rotors_dict[i]['success'] = None if len(actions) else False
 
-        # Better to save the path and invalidation reason for debugging and tracing the file
-        # if ``success`` is null, it means that the job is being troubleshot
+        # Better to save the path and invalidation reason for debugging and tracking the file
+        # if ``success`` is None, it means that the job is being troubleshooted
         self.species_dict[label].rotors_dict[i]['scan_path'] = job.local_path_to_output_file
-        self.species_dict[label].rotors_dict[i]['invalidation_reason'] = invalidation_reason
+        self.species_dict[label].rotors_dict[i]['invalidation_reason'] += invalidation_reason
 
         # If energies were obtained, draw the scan curve
         if energies is not None and len(energies):
@@ -2479,7 +2481,8 @@ def check_directed_scan(self, label, pivots, scan, energies):
             - adjust to ND, merge with check_directed_scan_job (this one isn't being called)
         """
         # If the job has not converged, troubleshoot
-        invalidate, invalidation_reason, message, actions = scan_quality_check(label=label, pivots=pivots,
+        invalidate, invalidation_reason, message, actions = scan_quality_check(label=label,
+                                                                               pivots=pivots,
                                                                                energies=energies)
         if actions:
             # the rotor scan is problematic, troubleshooting is required