Updates

arc/job/adapters/gaussian.py

@@ -267,17 +267,25 @@ def write_input_file(self) -> None:
             self.level.method = 'cbs-qb3'
 
         # Job type specific options
-        max_c = self.args['trsh'].split()[1] if 'max_cycles' in self.args['trsh'] else 100
+        max_c = 100
+        if 'trsh' in self.args and 'trsh' in self.args['trsh']:
+            for item in self.args['trsh']['trsh']:
+                match = re.search(r'maxcycle=(\d+)', item)
+                if match:
+                    max_c = int(match.group(1))
+                    break
+
+
         if self.job_type in ['opt', 'conformers', 'optfreq', 'composite']:
-            keywords = ['ts', 'calcfc', 'noeigentest', f'maxcycles={max_c}'] if self.is_ts else ['calcfc']
+            keywords = ['ts', 'calcfc', 'noeigentest', f'maxcycle={max_c}'] if self.is_ts else ['calcfc']
             if self.level.method in ['rocbs-qb3']:
                 # There are no analytical 2nd derivatives (FC) for this method.
-                keywords = ['ts', 'noeigentest', 'maxcycles=100'] if self.is_ts else []
+                keywords = ['ts', 'noeigentest', f'maxcycle={max_c}'] if self.is_ts else []
             if self.fine:
                 if self.level.method_type in ['dft', 'composite']:
                     # Note that the Acc2E argument is not available in Gaussian03
                     input_dict['fine'] = f'integral=(grid=ultrafine, {integral_algorithm})'
-                    # input_dict['trsh'] may have scf=(...) in it, so we need to  add the tight and direct keywords to it
+                    # input_dict['trsh'] may have scf=(...) in it, so we need to add the tight and direct keywords to it
                     scf_start = input_dict['trsh'].find('scf=(')
                     scf_end = input_dict['trsh'].find(')', scf_start)
                     scf_fine_content = 'tight,direct'
@@ -295,7 +303,7 @@ def write_input_file(self) -> None:
                 if self.is_ts:
                     keywords.extend(['tight', 'maxstep=5'])
                 else:
-                    keywords.extend(['tight', 'maxstep=5'])
+                    keywords.extend(['tight', 'maxstep=5', f'maxcycle={max_c}'])
             input_dict['job_type_1'] = "opt" if self.level.method_type not in ['dft', 'composite', 'wavefunction']\
                 else f"opt=({', '.join(key for key in keywords)})"
 

arc/job/adapters/gaussian_test.py

@@ -789,7 +789,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  uwb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    scf=(direct,tight)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  uwb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    scf=(direct,tight)
 
 anion
 
@@ -807,7 +807,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    scf=(direct,tight)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    scf=(direct,tight)
 
 ethanol
 
@@ -833,7 +833,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(direct,tight,xqc)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(direct,tight,xqc)
 
 ethanol
 
@@ -859,7 +859,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(NDamp=30,direct,tight,xqc)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(NDamp=30,direct,tight,xqc)
 
 ethanol
 
@@ -885,7 +885,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
 
 ethanol
 
@@ -911,7 +911,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,cartesian,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)       nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
+#P opt=(calcfc,cartesian,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)       nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
 
 ethanol
 
@@ -991,7 +991,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    int=grid=300590  scf=(direct,tight)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    int=grid=300590  scf=(direct,tight)
 
 ethanol
 
@@ -1017,7 +1017,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(Fermi,NDamp=30,NoDIIS,NoVarAcc,Noincfock,direct,tight,xqc)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(Fermi,NDamp=30,NoDIIS,NoVarAcc,Noincfock,direct,tight,xqc)
 
 ethanol
 
@@ -1043,7 +1043,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      scf=(NDamp=30,NoDIIS,NoVarAcc,direct,tight,xqc)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      scf=(NDamp=30,NoDIIS,NoVarAcc,direct,tight,xqc)
 
 ethanol
 
@@ -1070,7 +1070,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight) guess=INDO wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     int=grid=300590   scf=(NDamp=30,NoDIIS,NoVarAcc,direct,tight,xqc)
+#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=INDO wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     int=grid=300590   scf=(NDamp=30,NoDIIS,NoVarAcc,direct,tight,xqc)
 
 ethanol
 

arc/job/trsh.py

@@ -4,11 +4,11 @@
 
 import math
 import os
-import re
 from typing import List, Optional, Tuple, Union
 
 import numpy as np
 import pandas as pd
+import re
 
 from arc.common import (check_torsion_change,
                         convert_to_hours,
@@ -18,26 +18,26 @@
                         get_number_with_ordinal_indicator,
                         is_same_pivot,
                         is_same_sequence_sublist,
-                        is_str_float,
+                        is_str_float
                         )
 from arc.exceptions import InputError, SpeciesError, TrshError
 from arc.imports import settings
+from arc.level import Level
 from arc.job.local import execute_command
 from arc.job.ssh import SSHClient
-from arc.level import Level
 from arc.species import ARCSpecies
 from arc.species.conformers import determine_smallest_atom_index_in_scan
-from arc.species.converter import displace_xyz, ics_to_scan_constraints
+from arc.species.converter import (displace_xyz, ics_to_scan_constraints)
 from arc.species.species import determine_rotor_symmetry
 from arc.species.vectors import calculate_dihedral_angle, calculate_distance
-
 from arc.parser import (parse_1d_scan_coords,
                         parse_normal_mode_displacement,
                         parse_scan_args,
                         parse_scan_conformers,
                         parse_xyz_from_file,
                         )
 
+
 logger = get_logger()
 
 
@@ -947,6 +947,7 @@ def trsh_ess_job(label: str,
         if attempted_ess_trsh_methods:
             if attempted_ess_trsh_methods == ess_trsh_methods:
                 logger.info(f'{logger_phrase} was not successful. Already attempted all possible troubleshooting methods. Will not troubleshoot again.')
+                ess_trsh_methods.append("all_attempted")
                 couldnt_trsh = True
             else:
                 if logger_info:
@@ -1543,9 +1544,8 @@ def scan_quality_check(label: str,
             # Find the dihedrals in degrees of the lowest conformer:
             min_index = np.argmin(energies)
             conf_xyzs = parse_1d_scan_coords(log_file)
-            if len(conf_xyzs) > min_index:
-                actions = {'change conformer': conf_xyzs[min_index]}
-                return invalidate, invalidation_reason, message, actions
+            actions = {'change conformer': conf_xyzs[min_index]}
+            return invalidate, invalidation_reason, message, actions
 
         # 1.3 Check consistency
         if 0 in changed_ic_dict.keys() and len(changed_ic_dict) == 1:

arc/job/trsh_test.py

@@ -423,7 +423,7 @@ def test_trsh_ess_job(self):
                                                                     num_heavy_atoms, cpu_cores, ess_trsh_methods)
         self.assertTrue(couldnt_trsh)
         self.assertIn(
-            "Error: Could not troubleshoot opt for ethanol! Tried troubleshooting with the following methods: ['scf=(NoDIIS)', 'int=(Acc2E=14)', 'checkfile=None', 'scf=(qc)', 'NoSymm', 'scf=(NDamp=30)', 'guess=INDO', 'scf=(Fermi)', 'scf=(Noincfock)', 'scf=(NoVarAcc)']; ",
+            "Error: Could not troubleshoot opt for ethanol! Tried troubleshooting with the following methods: ['scf=(NoDIIS)', 'int=(Acc2E=14)', 'checkfile=None', 'scf=(qc)', 'NoSymm', 'scf=(NDamp=30)', 'guess=INDO', 'scf=(Fermi)', 'scf=(Noincfock)', 'scf=(NoVarAcc)', 'all_attempted']; ",
             output_errors,
         )
 
@@ -545,6 +545,7 @@ def test_trsh_ess_job(self):
             memory, shift, cpu_cores, couldnt_trsh = trsh.trsh_ess_job(label, level_of_theory, server, job_status,
                                                                     job_type, software, fine, memory_gb,
                                                                     num_heavy_atoms, cpu_cores, ess_trsh_methods)
+        self.assertIn('all_attempted', ess_trsh_methods)
         self.assertTrue(couldnt_trsh)
 
         # Test Q-Chem

arc/scheduler.py

@@ -3355,12 +3355,13 @@ def troubleshoot_opt_jobs(self, label):
                 if previous_job_num >= 0 and job.fine:
                     previous_job = self.job_dict[label]['opt']['opt_a' + str(previous_job_num)]
                     if not previous_job.fine and previous_job.job_status[0] == 'done' \
-                            and previous_job.job_status[1]['status'] == 'done':
+                            and previous_job.job_status[1]['status'] == 'done' \
+                                and 'all_attempted' not in job.ess_trsh_methods:
                         # The present job with a fine grid failed in the ESS calculation.
                         # A *previous* job without a fine grid terminated successfully on the server and ESS.
                         # So use the xyz determined w/o the fine grid, and output an error message to alert users.
                         logger.error(f'Optimization job for {label} with a fine grid terminated successfully '
-                                     f'on the server, but crashed during calculation. NOT running with fine '
+                                     f'on the server, but crashed during calculation after troubleshooting. NOT running with fine '
                                      f'grid again.')
                         self.parse_opt_geo(label=label, job=previous_job)
                         trsh_opt = False