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Scan l103 (#687)
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Invalidate scan jobs that failed with internal coordinate error (L103)
A test was added
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@kfir4444
kfir4444 authored Oct 5, 2023
2 parents 6e84f83 + 611df4e commit 067e76c
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Showing 4 changed files with 46,884 additions and 19 deletions.
2 changes: 1 addition & 1 deletion arc/job/adapters/gaussian.py
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ def __init__(self,
xyz=xyz,
)
if isinstance(self.level, Level) and self.level.basis is not None:
self.level.basis = re.sub('def2-', 'def2', self.level.basis.lower())
self.level.basis = re.sub('def2-', 'def2', self.level.basis.lower())

if self.checkfile is None:
if os.path.isfile(os.path.join(self.local_path, 'check.chk')):
Expand Down
26 changes: 13 additions & 13 deletions arc/scheduler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2643,25 +2643,26 @@ def check_scan_job(self,
label (str): The species label.
job (JobAdapter): The rotor scan job object.
"""
# If the job has not converged, troubleshoot ESS.
# Besides, according to the experience, 'Internal coordinate error' cannot be handled by
# troubleshoot_ess() for scan jobs. It is usually related to bond or angle changes which
# messes up the internal coordinates during the scan. It can be resolved
# by conformer-based scan troubleshooting method, yet its energies are readable.
if job.job_status[1]['status'] != 'done' and job.job_status[1]['error'] != 'Internal coordinate error':
self.troubleshoot_ess(label=label,
job=job,
level_of_theory=job.level)
return None
# Otherwise, check the scan job quality.
# An 'Internal coordinate error' cannot be handled by troubleshooting, so we don't even try.
# It is usually related to bond or angle changes which mess up the internal coordinates during the scan.
invalidate, actions, energies, angles = False, list(), list(), list()
invalidation_reason, message = '', ''
if job.job_status[1]['status'] != 'done':
if job.job_status[1]['error'] == 'Internal coordinate error':
invalidate = True
invalidation_reason = 'Internal coordinate error; '
else:
self.troubleshoot_ess(label=label,
job=job,
level_of_theory=job.level)
return None

if job.rotor_index not in self.species_dict[label].rotors_dict.keys():
raise SchedulerError(f'Could not match rotor {job.rotor_index} of species {label} '
f'with pivots {self.species_dict[label].rotors_dict[job.rotor_index]["pivots"]} '
f'to any of the existing rotors in the species.\n'
f'The rotors dict of {label} is:\n{pprint.pformat(self.species_dict[label].rotors_dict)}')

invalidation_reason, message = '', ''
if self.species_dict[label].rotors_dict[job.rotor_index]['dimensions'] == 1:
# This is a 1D scan.
# Read energy profile (in kJ/mol), it may be used in the troubleshooting.
Expand Down Expand Up @@ -2752,7 +2753,6 @@ def check_scan_job(self,
'original_dihedrals'],
)

# Save the restart dictionary
self.save_restart_dict()

def check_directed_scan(self, label, pivots, scan, energies):
Expand Down
55 changes: 50 additions & 5 deletions arc/scheduler_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
from arc.scheduler import Scheduler, species_has_freq, species_has_geo, species_has_sp, species_has_sp_and_freq
from arc.imports import settings
from arc.reaction import ARCReaction
from arc.species.converter import str_to_xyz
from arc.species.species import ARCSpecies


Expand All @@ -37,27 +38,37 @@ def setUpClass(cls):
cls.maxDiff = None
cls.ess_settings = {'gaussian': ['server1'], 'molpro': ['server2', 'server1'], 'qchem': ['server1']}
cls.project_directory = os.path.join(ARC_PATH, 'Projects', 'arc_project_for_testing_delete_after_usage3')
cls.spc1 = ARCSpecies(label='methylamine', smiles='CN')
xyz1 = str_to_xyz("""C -0.57422867 -0.01669771 0.01229213
N 0.82084044 0.08279104 -0.37769346
H -1.05737005 -0.84067772 -0.52007494
H -1.10211468 0.90879867 -0.23383011
H -0.66133128 -0.19490562 1.08785111
H 0.88047852 0.26966160 -1.37780789
H 1.27889520 -0.81548721 -0.22940984""")
cls.spc1 = ARCSpecies(label='methylamine', smiles='CN', xyz=xyz1)
cls.spc2 = ARCSpecies(label='C2H6', smiles='CC')
xyz3 = """C 1.11424367 -0.01231165 -0.11493630
C -0.07257945 -0.17830906 -0.16010022
O -1.38500471 -0.36381519 -0.20928090
H 2.16904830 0.12689206 -0.07152274
H -1.82570782 0.42754384 -0.56130718"""
cls.spc3 = ARCSpecies(label='CtripCO', smiles='C#CO', xyz=xyz3)
xyz2 = {'symbols': ('C',), 'isotopes': (12,), 'coords': ((0.0, 0.0, 0.0),)}
cls.job1 = job_factory(job_adapter='gaussian', project='project_test', ess_settings=cls.ess_settings,
species=[cls.spc1], xyz=xyz2, job_type='conformers',
species=[cls.spc1], xyz=xyz1, job_type='conformers',
conformer=0, level=Level(repr={'method': 'b97-d3', 'basis': '6-311+g(d,p)'}),
project_directory=cls.project_directory, job_num=101)
cls.job2 = job_factory(job_adapter='gaussian', project='project_test', ess_settings=cls.ess_settings,
species=[cls.spc1], xyz=xyz2, job_type='conformers',
species=[cls.spc1], xyz=xyz1, job_type='conformers',
conformer=1, level=Level(repr={'method': 'b97-d3', 'basis': '6-311+g(d,p)'}),
project_directory=cls.project_directory, job_num=102)
cls.job3 = job_factory(job_adapter='qchem', project='project_test', ess_settings=cls.ess_settings,
species=[cls.spc2], job_type='freq',
level=Level(repr={'method': 'wb97x-d3', 'basis': '6-311+g(d,p)'}),
project_directory=cls.project_directory, job_num=103)
cls.job4 = job_factory(job_adapter='gaussian', project='project_test_4', ess_settings=cls.ess_settings,
species=[cls.spc1], xyz=xyz1, job_type='scan', torsions=[[3, 1, 2, 6]], rotor_index=0,
level=Level(repr={'method': 'b3lyp', 'basis': 'cbsb7'}),
project_directory=cls.project_directory, job_num=104)
cls.rmg_database = rmgdb.make_rmg_database_object()
cls.job_types1 = {'conformers': True,
'opt': True,
Expand All @@ -68,6 +79,13 @@ def setUpClass(cls):
'orbitals': False,
'lennard_jones': False,
}
cls.job_types2 = {'conformers': True,
'opt': True,
'fine': False,
'freq': True,
'sp': True,
'rotors': True,
}
cls.sched1 = Scheduler(project='project_test_1', ess_settings=cls.ess_settings,
species_list=[cls.spc1, cls.spc2, cls.spc3],
composite_method=None,
Expand Down Expand Up @@ -100,6 +118,19 @@ def setUpClass(cls):
orbitals_level=default_levels_of_theory['orbitals'],
adaptive_levels=None,
)
cls.sched3 = Scheduler(project='project_test_4', ess_settings=cls.ess_settings,
species_list=[cls.spc1],
composite_method=Level(repr='CBS-QB3'),
conformer_level=Level(repr=default_levels_of_theory['conformer']),
opt_level=Level(repr=default_levels_of_theory['freq_for_composite']),
freq_level=Level(repr=default_levels_of_theory['freq_for_composite']),
scan_level=Level(repr=default_levels_of_theory['scan_for_composite']),
ts_guess_level=Level(repr=default_levels_of_theory['ts_guesses']),
rmg_database=cls.rmg_database,
project_directory=cls.project_directory,
testing=True,
job_types=cls.job_types2,
)

def test_conformers(self):
"""Test the parse_conformer_energy() and determine_most_stable_conformer() methods"""
Expand Down Expand Up @@ -311,6 +342,20 @@ def test_deduce_job_adapter(self):
job_adapter_5 = self.sched1.deduce_job_adapter(level=level_5, job_type=job_type_5)
self.assertEqual(job_adapter_5, 'terachem')

def test_check_scan_job(self):
"""Test the check_scan_job() method."""
self.job4.job_status[1]['status'] = 'done'
self.job4.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'rotor_scans', 'N2O3.out')
self.sched3.check_scan_job(label='methylamine', job=self.job4)
self.assertTrue(self.sched3.species_dict['methylamine'].rotors_dict[self.job4.rotor_index]['success'])

self.job4.local_path_to_output_file = os.path.join(ARC_PATH, 'arc', 'testing', 'rotor_scans', 'l103_err.out')
self.job4.job_status[1]['status'] = 'errored'
self.job4.job_status[1]['error'] = 'Internal coordinate error'
self.sched3.check_scan_job(label='methylamine', job=self.job4)
self.assertFalse(self.sched3.species_dict['methylamine'].rotors_dict[self.job4.rotor_index]['success'])
self.assertIn('Internal coordinate error', self.sched3.species_dict['methylamine'].rotors_dict[self.job4.rotor_index]['invalidation_reason'])

def test_check_rxn_e0_by_spc(self):
"""Test the check_rxn_e0_by_spc() method."""
rxn_dict = \
Expand Down Expand Up @@ -586,7 +631,7 @@ def test_check_rxn_e0_by_spc(self):
{'element': {'number': 1, 'isotope': -1}, 'radical_electrons': 0, 'charge': 0, 'label': '',
'lone_pairs': 0, 'id': -26573, 'props': {'inRing': False}, 'atomtype': 'H',
'edges': {-26580: 1.0}}], 'multiplicity': 2, 'props': {},
'atom_order': [-26582, -26581, -26580, -26579, -26578, -26577, -26576, -26575, -26574, -26573]},
'atom_order': [-26582, -26581, -26580, -26579, -26578, -26577, -26576, -26575, -26574, -26573]},
'initial_xyz': 'C -0.94073000 -1.08641400 -0.13521400\nC -0.33120900 0.27400500 -0.10738200\nC 1.03297600 0.48550500 0.47374300\nH -0.34195200 -1.93903700 0.19367700\nH -2.02636000 -1.19201700 -0.17452300\nH -0.43853800 -0.46541200 -1.16876000\nH -1.02644700 1.11801000 -0.14324700\nH 1.47599100 1.43717700 0.14587900\nH 1.72184900 -0.32388500 0.18160800\nH 1.00079200 0.49179200 1.58006000',
'final_xyz': 'C -0.94403900 -1.08919600 -0.13528100\nC -0.33161500 0.27504900 -0.10775400\nC 1.03465100 0.48772700 0.47568400\nH -0.35007600 -1.93768200 0.18473700\nH -2.02160800 -1.19512500 -0.17500700\nH -0.44246400 -0.46665500 -1.16369500\nH -1.02252600 1.11305500 -0.14369600\nH 1.47717100 1.43311000 0.14664900\nH 1.72023500 -0.31816900 0.18700200\nH 1.00664300 0.49760900 1.57720100',
'checkfile': '/storage/ce_dana/alongd/runs/ARC/debug13/calcs/TSs/TS0/opt_a24061/check.chk'},
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