Logs

arc/job/adapters/ts/heuristics.py

@@ -455,6 +455,9 @@ def combine_coordinates_with_redundant_atoms(xyz_1: Union[dict, str],
 
     a = mol_1.atoms.index(list(mol_1.atoms[h1].edges.keys())[0])
     b = mol_2.atoms.index(list(mol_2.atoms[h2].edges.keys())[0])
+
+    #log if a and b are different from prev step
+    logger.info(f'Combining coordinates with redundant atoms for atoms A ({a}) and B ({b})')
     if c == a:
         raise ValueError(f'The value for c ({c}) is invalid (it represents atom A, not atom C)')
     if d == b:
@@ -1054,7 +1057,14 @@ def h_abstraction(arc_reaction: 'ARCReaction',
 
         val_inc = - 1 if h2 < b else 0
 
-        b_atom = len(arc_reactant.get_xyz()['symbols']) + b + val_inc
+        b_atom = len(arc_product.get_xyz()['symbols']) + b + val_inc
+
+        # log info a, b, h1, h2, b_atom, a_atom, h_atom, val_inc
+        logger.info(f'a: {a}, b: {b}, h1: {h1}, h2: {h2}, b_atom: {b_atom}, a_atom: {a_atom}, h_atom: {h_atom}, val_inc: {val_inc}')
+        # log len of arc_product.get_xyz()['symbols'] 
+        logger.info(f"len of arc_product.get_xyz()[\'symbols\']: {len(arc_product.get_xyz()['symbols'])}")
+        # log len of arc_reactant.get_xyz()['symbols']
+        logger.info(f"len of arc_reactant.get_xyz()[\'symbols\']: {len(arc_reactant.get_xyz()['symbols'])}")
 
         xyz_guess = crest_ts_conformer_search(xyz_guesses_crest, a_atom, h_atom, b_atom, path=path)
         if xyz_guess is not None:

arc/job/trsh.py

@@ -981,14 +981,15 @@ def trsh_ess_job(label: str,
         elif 'Memory' in job_status['keywords'] and 'too high' in job_status['error'] and server is not None:
             # Reduce memory allocation by 80%, rounded to the nearest 5 GB increment
             couldnt_trsh = False
-            reduced_memory = max(20, round(memory_gb * 0.8 / 5) * 5)  # Ensure reduction, rounded to nearest 5 GB, with 20 GB minimum
+
+            reduced_memory = max(4, round(memory_gb * 0.8 / 5) * 5)  # Ensure reduction, rounded to nearest 5 GB, with 20 GB minimum
             logger.info(f'Troubleshooting {job_type} job in {software} for {label} using less memory: {reduced_memory} GB '
                         f'instead of {memory_gb} GB')
 
             # Check for existing 'waste_memory_' entries and calculate next reduction level
             if f'waste_memory_{reduced_memory}' not in ess_trsh_methods:
                 ess_trsh_methods.append(f'waste_memory_{reduced_memory}')
-                memory_gb = reduced_memory  # Update memory to the reduced value for next iteration
+                memory = reduced_memory  # Update memory to the reduced value for next iteration
             else:
                 couldnt_trsh = True
                 logger.info(f'{logger_phrase} was unsuccessful. No further reductions possible without reaching threshold.')