Merge pull request #78 from ReactionMechanismGenerator/incons_az

Changed rotor inconsistency_ab
ReactionMechanismGenerator · Mar 5, 2019 · 4c0d38b · 4c0d38b
2 parents ca0a264 + ac05f5c
commit 4c0d38b
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Showing 2 changed files with 10 additions and 9 deletions.
diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -953,9 +953,9 @@ def check_scan_job(self, label, job):
                             # initial and final points differ by more than `inconsistency_az` kJ/mol.
                             # seems like this rotor broke the conformer. Invalidate
                             error_message = 'Rotor scan of {label} between pivots {pivots} is inconsistent by more' \
-                                            ' than {inconsistency} kJ/mol between initial and final positions.' \
+                                            ' than {incons_az} kJ/mol between initial and final positions.' \
                                             ' Invalidating rotor.\nv_list[0] = {v0}, v_list[-1] = {vneg1}'.format(
-                                             label=label, pivots=job.pivots, inconsistency=inconsistency_az,
+                                             label=label, pivots=job.pivots, incons_az=inconsistency_az,
                                              v0=v_list[0], vneg1=v_list[-1])
                             logging.error(error_message)
                             message += error_message + '; '
@@ -965,13 +965,13 @@ def check_scan_job(self, label, job):
                         if not invalidate:
                             v_last = v_list[-1]
                             for v in v_list:
-                                if abs(v - v_last) > inconsistency_ab:
+                                if abs(v - v_last) > inconsistency_ab * max(v_list):
                                     # Two consecutive points on the scan differ by more than `inconsistency_ab` kJ/mol.
                                     # This is a serious inconsistency. Invalidate
                                     error_message = 'Rotor scan of {label} between pivots {pivots} is inconsistent by' \
-                                                    'more than {inconsistency} kJ/mol between two consecutive points.' \
+                                                    'more than {incons_ab} kJ/mol between two consecutive points.' \
                                                     ' Invalidating rotor.'.format(label=label, pivots=job.pivots,
-                                                                                  inconsistency=inconsistency_ab)
+                                                                                  incons_ab=inconsistency_ab * max(v_list))
                                     logging.error(error_message)
                                     message += error_message + '; '
                                     invalidate = True

diff --git a/arc/settings.py b/arc/settings.py
@@ -92,7 +92,8 @@
 rotor_scan_resolution = 8.0  # degrees. Default: 8.0
 
 # rotor validation parameters
-inconsistency_az = 5   # maximum allowed inconsistency (kJ/mol) between initial and final rotor scan points. Default: 5
-inconsistency_ab = 10  # maximum allowed inconsistency (kJ/mol) between consecutive points in the scan. Default: 10
-maximum_barrier = 40   # a rotor threshold (kJ/mol) above which the rotor is not considered. Default: 40 (~10 kcal/mol)
-minimum_barrier = 0.5  # a rotor threshold (kJ/mol) below which it is considered a FreeRotor. Default: 0.5 kJ/mol
+inconsistency_az = 5    # maximum allowed inconsistency (kJ/mol) between initial and final rotor scan points. Default: 5
+inconsistency_ab = 0.5  # maximum allowed inconsistency between consecutive points in the scan given as a fraction
+#  of the maximum scan energy. Default: 50%
+maximum_barrier = 40    # a rotor threshold (kJ/mol) above which the rotor is not considered. Default: 40 (~10 kcal/mol)
+minimum_barrier = 0.5   # a rotor threshold (kJ/mol) below which it is considered a FreeRotor. Default: 0.5 kJ/mol