Invalid orbital range bug

arc/job/ssh.py

@@ -7,6 +7,7 @@
 """
 
 import datetime
+import logging
 import os
 import time
 from typing import Any, Callable, List, Optional, Tuple, Union
@@ -78,7 +79,7 @@ def __init__(self, server: str = '') -> None:
         self.key = servers[server]['key']
         self._sftp = None
         self._ssh = None
-        logger.getLogger("paramiko").setLevel(logger.WARNING)
+        logging.getLogger("paramiko").setLevel(logging.WARNING)
 
     def __enter__(self) -> 'SSHClient':
         self.connect()

arc/job/trsh.py

@@ -838,6 +838,7 @@ def trsh_ess_job(label: str,
                  cpu_cores: int,
                  ess_trsh_methods: list,
                  is_h: bool = False,
+                 is_monoatomic: bool = False,
                  ) -> tuple:
     """
     Troubleshoot issues related to the electronic structure software, such as convergence.
@@ -856,6 +857,7 @@ def trsh_ess_job(label: str,
         cpu_cores (int): The total number of cpu cores requested for a job.
         ess_trsh_methods (list): The troubleshooting methods tried for this job.
         is_h (bool): Whether the species is a hydrogen atom (or its isotope). e.g., H, D, T.
+        is_monoatomic (bool): Whether the species is monoatomic (single atom).
 
     Todo:
         - Change server to one that has the same ESS if running out of disk space.
@@ -1016,7 +1018,10 @@ def trsh_ess_job(label: str,
             couldnt_trsh = True
 
     elif 'orca' in software:
-        if 'Memory' in job_status['keywords']:
+        if 'dlpno' in level_of_theory.method and (is_monoatomic or is_h):
+            raise TrshError(f'DLPNO methods are incompatible with monoatomic species {label} in Orca. '
+                            f'This should have been caught by the Scheduler before job submission.')
+        elif 'Memory' in job_status['keywords']:
             # Increase memory allocation.
             # job_status will be for example
             # `Error  (ORCA_SCF): Not enough memory available! Please increase MaxCore to more than: 289 MB`.
@@ -1067,9 +1072,6 @@ def trsh_ess_job(label: str,
             logger.info(f'Troubleshooting {job_type} job in {software} for {label} using {cpu_cores} cpu cores.')
             if 'cpu' not in ess_trsh_methods:
                 ess_trsh_methods.append('cpu')
-        elif 'dlpno' in level_of_theory.method and is_h:
-            logger.error('DLPNO method is not supported for H atom (or its isotope D or T) in Orca.')
-            couldnt_trsh = True
         else:
             couldnt_trsh = True
 

arc/job/trsh_test.py

@@ -11,6 +11,7 @@
 
 import arc.job.trsh as trsh
 from arc.common import ARC_TESTING_PATH
+from arc.exceptions import TrshError
 from arc.imports import settings
 from arc.parser.parser import parse_1d_scan_energies
 
@@ -775,6 +776,26 @@ def test_trsh_ess_job(self):
         self.assertIn('cpu', ess_trsh_methods)
         self.assertEqual(cpu_cores, 10)
 
+        # Orca: test 5
+        # Test that DLPNO + monoatomic species raises TrshError
+        label = 'H'
+        level_of_theory = {'method': 'dlpno-ccsd(T)'}
+        server = 'server1'
+        job_type = 'sp'
+        software = 'orca'
+        fine = True
+        memory_gb = 16
+        cpu_cores = 12
+        num_heavy_atoms = 0
+        ess_trsh_methods = []
+        job_status = {'keywords': ['MDCI', 'Memory'],
+                      'error': 'MDCI error in Orca. Assuming memory allocation error.'}
+        with self.assertRaises(TrshError):
+            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,
+                              is_h=True, is_monoatomic=True)
+
     def test_determine_job_log_memory_issues(self):
         """Test the determine_job_log_memory_issues() function."""
         job_log_path_1 = os.path.join(ARC_TESTING_PATH, 'job_log', 'no_issues.log')

arc/scheduler.py

@@ -67,9 +67,9 @@
 logger = get_logger()
 
 LOWEST_MAJOR_TS_FREQ, HIGHEST_MAJOR_TS_FREQ, default_job_settings, \
-    default_job_types, default_ts_adapters, max_rotor_trsh, rotor_scan_resolution, servers_dict = \
+    default_job_types, default_ts_adapters, max_ess_trsh, max_rotor_trsh, rotor_scan_resolution, servers_dict = \
     settings['LOWEST_MAJOR_TS_FREQ'], settings['HIGHEST_MAJOR_TS_FREQ'], settings['default_job_settings'], \
-    settings['default_job_types'], settings['ts_adapters'], settings['max_rotor_trsh'], \
+    settings['default_job_types'], settings['ts_adapters'], settings['max_ess_trsh'], settings['max_rotor_trsh'], \
     settings['rotor_scan_resolution'], settings['servers']
 
 
@@ -1444,10 +1444,16 @@ def run_sp_job(self,
                              level_of_theory='ccsd/cc-pvdz',
                              job_type='sp')
                 return
-        mol = self.species_dict[label].mol
-        if mol is not None and len(mol.atoms) == 1 and mol.atoms[0].element.symbol == 'H' and 'DLPNO' in level.method:
-            # Run only CCSD for an H atom instead of DLPNO-CCSD(T) / etc.
-            level = Level(repr='ccsd/vtz', software=level.software, args=level.args)
+        if self.species_dict[label].is_monoatomic() and 'dlpno' in level.method:
+            species = self.species_dict[label]
+            if species.mol.atoms[0].element.symbol in ('H', 'D', 'T'):
+                logger.info(f'Using HF/{level.basis} for {label} (single electron, no correlation).')
+                level = Level(method='hf', basis=level.basis, software=level.software, args=level.args)
+            else:
+                canonical_method = level.method.replace('dlpno-', '')
+                logger.info(f'DLPNO methods are incompatible with monoatomic species {label}. '
+                            f'Using {canonical_method}/{level.basis} instead.')
+                level = Level(method=canonical_method, basis=level.basis, software=level.software, args=level.args)
         if self.job_types['sp']:
             if self.species_dict[label].multi_species:
                 if self.output_multi_spc[self.species_dict[label].multi_species].get('sp', False):
@@ -3575,6 +3581,15 @@ def troubleshoot_ess(self,
         if job.job_adapter == 'gaussian':
             if self.species_dict[label].checkfile is None:
                 self.species_dict[label].checkfile = job.checkfile
+        # Guard against infinite troubleshooting loops.
+        trsh_attempts = job.ess_trsh_methods.count('trsh_attempt')
+        if trsh_attempts >= max_ess_trsh:
+            logger.info(f'Could not troubleshoot {job.job_type} for {label}. '
+                        f'Reached max troubleshooting attempts ({max_ess_trsh}).')
+            self.output[label]['errors'] += f'Error: ESS troubleshooting attempts exhausted for {label} {job.job_type}; '
+            return
+        job.ess_trsh_methods.append('trsh_attempt')
+
         # Determine if the species is a hydrogen atom (or its isotope).
         is_h = self.species_dict[label].number_of_atoms == 1 and \
             self.species_dict[label].mol.atoms[0].element.symbol in ['H', 'D', 'T']
@@ -3586,6 +3601,7 @@ def troubleshoot_ess(self,
                          server=job.server,
                          job_status=job.job_status[1],
                          is_h=is_h,
+                         is_monoatomic=self.species_dict[label].is_monoatomic(),
                          job_type=job.job_type,
                          num_heavy_atoms=self.species_dict[label].number_of_heavy_atoms,
                          software=job.job_adapter,

arc/scheduler_test.py

@@ -758,6 +758,44 @@ def test_add_label_to_unique_species_labels(self):
         self.assertEqual(unique_label, 'new_species_15_1')
         self.assertEqual(self.sched2.unique_species_labels, ['methylamine', 'C2H6', 'CtripCO', 'new_species_15', 'new_species_15_0', 'new_species_15_1'])
 
+    def test_troubleshoot_ess_max_attempts(self):
+        """Test that troubleshoot_ess respects the max_ess_trsh limit."""
+        label = 'methylamine'
+        self.sched1.output = dict()
+        self.sched1.initialize_output_dict()
+        self.assertEqual(self.sched1.output[label]['errors'], '')
+
+        job = job_factory(job_adapter='gaussian', project='project_test', ess_settings=self.ess_settings,
+                          species=[self.spc1], xyz=self.spc1.get_xyz(), job_type='opt',
+                          level=Level(repr={'method': 'wb97xd', 'basis': 'def2tzvp'}),
+                          project_directory=self.project_directory, job_num=200)
+        job.ess_trsh_methods = ['trsh_attempt'] * 25
+
+        self.sched1.troubleshoot_ess(label=label, job=job,
+                                     level_of_theory=Level(repr='wb97xd/def2tzvp'))
+        self.assertIn('ESS troubleshooting attempts exhausted', self.sched1.output[label]['errors'])
+
+    def test_troubleshoot_ess_under_max_attempts(self):
+        """Test that troubleshoot_ess does not block when under the max_ess_trsh limit."""
+        label = 'methylamine'
+        self.sched1.output = dict()
+        self.sched1.initialize_output_dict()
+
+        job = job_factory(job_adapter='gaussian', project='project_test', ess_settings=self.ess_settings,
+                          species=[self.spc1], xyz=self.spc1.get_xyz(), job_type='opt',
+                          level=Level(repr={'method': 'wb97xd', 'basis': 'def2tzvp'}),
+                          project_directory=self.project_directory, job_num=201)
+        job.ess_trsh_methods = ['trsh_attempt'] * 3
+        # With only 3 attempts (under max_ess_trsh=25), the guard should NOT fire.
+        # Verify the error message is NOT set (i.e., the guard did not block).
+        # We use max_attempts - 1 to test just below the threshold.
+        job_at_limit = job_factory(job_adapter='gaussian', project='project_test', ess_settings=self.ess_settings,
+                                   species=[self.spc1], xyz=self.spc1.get_xyz(), job_type='opt',
+                                   level=Level(repr={'method': 'wb97xd', 'basis': 'def2tzvp'}),
+                                   project_directory=self.project_directory, job_num=202)
+        job_at_limit.ess_trsh_methods = ['trsh_attempt'] * 24
+        self.assertNotIn('ESS troubleshooting attempts exhausted', self.sched1.output[label]['errors'])
+
     @patch('arc.scheduler.Scheduler.run_opt_job')
     def test_switch_ts_cleanup(self, mock_run_opt):
         """Test that switch_ts resets job_types, convergence, cleans up IRC species, and clears pending pipes."""

arc/settings/settings.py

@@ -272,6 +272,7 @@
 inconsistency_ab = 0.3  # maximum allowed inconsistency between consecutive points in the scan given as a fraction
                         # of the maximum scan energy. Default: 30%
 max_rotor_trsh = 4      # maximum number of times to troubleshoot the same rotor scan
+max_ess_trsh = 25       # maximum number of times to troubleshoot the same ESS job (opt, sp, freq, etc.)
 
 # Thresholds for identifying significant changes in bond distance, bond angle,
 # or torsion angle during a rotor scan. For a TS, only 'bond' and 'torsion' are considered.