Merge pull request #111 from goldmanm/auto_optical_isomers_and_log_re…

…factor_pair_pr Update determine_qm_software to new Arkane
ReactionMechanismGenerator · Apr 25, 2019 · d40572b · d40572b
2 parents 0510966 + 2f19efe
commit d40572b
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Showing 3 changed files with 19 additions and 27 deletions.
diff --git a/arc/parser.py b/arc/parser.py
@@ -6,7 +6,7 @@
 import numpy as np
 import os
 
-from arkane.statmech import Log
+from arkane.statmech import determine_qm_software
 
 from arc.species.converter import get_xyz_string, standardize_xyz_string
 from arc.arc_exceptions import InputError
@@ -97,9 +97,8 @@ def parse_xyz_from_file(path):
             else:
                 break
     elif 'out' in file_extension or 'log' in file_extension:
-        log = Log(path='')
-        log.determine_qm_software(fullpath=path)
-        coord, number, _ = log.software_log.loadGeometry()
+        log = determine_qm_software(fullpath=path)
+        coord, number, _ = log.loadGeometry()
         xyz = get_xyz_string(coord=coord, number=number)
     else:
         record = False

diff --git a/arc/scheduler.py b/arc/scheduler.py
@@ -14,7 +14,7 @@
 
 import cclib
 
-from arkane.statmech import Log
+from arkane.statmech import determine_qm_software
 from rmgpy.reaction import Reaction
 from rmgpy.exceptions import InputError as RMGInputError
 
@@ -742,9 +742,8 @@ def parse_conformer_energy(self, job, label, i):
         Parse E0 (J/mol) from the conformer opt output file, and save it in the 'conformer_energies' attribute.
         """
         if job.job_status[1] == 'done':
-            log = Log(path='')
-            log.determine_qm_software(fullpath=job.local_path_to_output_file)
-            self.species_dict[label].conformer_energies[i] = log.software_log.loadEnergy()  # in J/mol
+            log = determine_qm_software(fullpath=job.local_path_to_output_file)
+            self.species_dict[label].conformer_energies[i] = log.loadEnergy()  # in J/mol
             logging.debug('energy for {0} is {1}'.format(i, self.species_dict[label].conformer_energies[i]))
         else:
             logging.warn('Conformer {i} for {label} did not converge!'.format(i=i, label=label))
@@ -767,14 +766,13 @@ def determine_most_stable_conformer(self, label):
         else:
             conformer_xyz = None
             xyzs = list()
-            log = Log(path='')
             if self.species_dict[label].conformer_energies:
                 xyzs = self.species_dict[label].conformers
             else:
                 for job in self.job_dict[label]['conformers'].values():
-                    log.determine_qm_software(fullpath=job.local_path_to_output_file)
+                    log = determine_qm_software(fullpath=job.local_path_to_output_file)
                     try:
-                        coord, number, _ = log.software_log.loadGeometry()
+                        coord, number, _ = log.loadGeometry()
                     except RMGInputError:
                         xyzs.append(None)
                     else:
@@ -903,9 +901,8 @@ def parse_composite_geo(self, label, job):
         logging.debug('parsing composite geo for {0}'.format(job.job_name))
         freq_ok = False
         if job.job_status[1] == 'done':
-            log = Log(path='')
-            log.determine_qm_software(fullpath=job.local_path_to_output_file)
-            coord, number, _ = log.software_log.loadGeometry()
+            log = determine_qm_software(fullpath=job.local_path_to_output_file)
+            coord, number, _ = log.loadGeometry()
             self.species_dict[label].final_xyz = get_xyz_string(coord=coord, number=number)
             self.output[label]['status'] += 'composite converged; '
             self.output[label]['composite'] = os.path.join(job.local_path, 'output.out')
@@ -944,9 +941,8 @@ def parse_opt_geo(self, label, job):
         """
         logging.debug('parsing opt geo for {0}'.format(job.job_name))
         if job.job_status[1] == 'done':
-            log = Log(path='')
-            log.determine_qm_software(fullpath=job.local_path_to_output_file)
-            coord, number, _ = log.software_log.loadGeometry()
+            log = determine_qm_software(fullpath=job.local_path_to_output_file)
+            coord, number, _ = log.loadGeometry()
             self.species_dict[label].final_xyz = get_xyz_string(coord=coord, number=number)
             if not job.fine and self.fine:
                 # Run opt again using a finer grid.
@@ -1110,10 +1106,9 @@ def check_scan_job(self, label, job):
                 invalidate = False
                 if job.job_status[1] == 'done':
                     # ESS converged. Get PES scan using Arkane:
-                    log = Log(path='')
-                    log.determine_qm_software(fullpath=job.local_path_to_output_file)
+                    log = determine_qm_software(fullpath=job.local_path_to_output_file)
                     try:
-                        v_list, angle = log.software_log.loadScanEnergies()
+                        v_list, angle = log.loadScanEnergies()
                     except ZeroDivisionError:
                         logging.error('Energies from rotor scan of {label} between pivots {pivots} could not'
                                       'be read. Invalidating rotor.'.format(label=label, pivots=job.pivots))

diff --git a/arc/species/species.py b/arc/species/species.py
@@ -14,7 +14,7 @@
 import pybel as pyb
 
 from arkane.common import ArkaneSpecies, symbol_by_number
-from arkane.statmech import Log
+from arkane.statmech import determine_qm_software
 from rmgpy.molecule.converter import toOBMol
 from rmgpy.molecule.element import getElement
 from rmgpy.molecule.molecule import Atom, Molecule
@@ -1374,9 +1374,8 @@ def determine_rotor_symmetry(rotor_path, label, pivots):
     A second criterion for a symmetric rotor is that the highest and lowest peaks must be within 10% of
     the highest peak value. This is only applied if the highest peak is above 2 kJ/mol.
     """
-    log = Log(path='')
-    log.determine_qm_software(fullpath=rotor_path)
-    energies, _ = log.software_log.loadScanEnergies()
+    log = determine_qm_software(fullpath=rotor_path)
+    energies, _ = log.loadScanEnergies()
 
     symmetry = None
     max_e = max(energies)
@@ -1460,9 +1459,8 @@ def determine_rotor_type(rotor_path):
     Determine whether this rotor should be treated as a HinderedRotor of a FreeRotor
     according to it's maximum peak
     """
-    log = Log(path='')
-    log.determine_qm_software(fullpath=rotor_path)
-    energies, _ = log.software_log.loadScanEnergies()
+    log = determine_qm_software(fullpath=rotor_path)
+    energies, _ = log.loadScanEnergies()
     max_val = max(energies) * 0.001  # convert to kJ/mol (Arkane used SI)
     return 'FreeRotor' if max_val < minimum_barrier else 'HinderedRotor'