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Give each TestScheduler test its own scheduler and project directory #1009

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216 changes: 111 additions & 105 deletions arc/scheduler_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
from unittest.mock import MagicMock, patch
import os
import shutil
import tempfile
from types import SimpleNamespace


Expand Down Expand Up @@ -75,105 +76,125 @@ class TestScheduler(unittest.TestCase):
"""
Contains unit tests for the Scheduler class
"""
@classmethod
def setUpClass(cls):
def make_project_directory(self, name):
"""
A method that is run before all unit tests in this class.
Create a unique project directory for the running test and schedule its removal.

Args:
name (str): A descriptive name, used as the directory name prefix.

Returns:
str: The path of the created directory.
"""
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')
projects_path = os.path.join(ARC_PATH, 'Projects')
os.makedirs(projects_path, exist_ok=True)
project_directory = tempfile.mkdtemp(prefix=f'{name}_', dir=projects_path)
self.addCleanup(shutil.rmtree, project_directory, ignore_errors=True)
return project_directory

def setUp(self):
"""
A method that is run before each unit test in this class.

The fixtures below are rebuilt per test: many of these tests mutate the schedulers,
the species and the jobs they are handed, so a fixture shared across tests (or across
xdist workers, each of which runs its own class-level setup) would make the outcome of
one test depend on which other tests ran before it.
"""
self.maxDiff = None
self.ess_settings = {'gaussian': ['server1'], 'molpro': ['server2', 'server1'], 'qchem': ['server1']}
self.project_directory = self.make_project_directory('arc_project_for_testing_delete_after_usage3')
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')
self.spc1 = ARCSpecies(label='methylamine', smiles='CN', xyz=xyz1)
self.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)
cls.job1 = job_factory(job_adapter='gaussian', project='project_test', ess_settings=cls.ess_settings,
species=[cls.spc1], xyz=xyz1, job_type='conf_opt',
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=xyz1, job_type='conf_opt',
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.job_types1 = {'conf_opt': True,
'conf_sp': False,
'opt': True,
'fine': False,
'freq': True,
'sp': True,
'rotors': False,
'orbitals': False,
'lennard_jones': False,
}
cls.job_types2 = {'conf_opt': True,
'conf_sp': False,
'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,
conformer_opt_level=Level(repr=default_levels_of_theory['conformer']),
opt_level=Level(repr=default_levels_of_theory['opt']),
freq_level=Level(repr=default_levels_of_theory['freq']),
sp_level=Level(repr=default_levels_of_theory['sp']),
scan_level=Level(repr=default_levels_of_theory['scan']),
ts_guess_level=Level(repr=default_levels_of_theory['ts_guesses']),
project_directory=cls.project_directory,
testing=True,
job_types=cls.job_types1,
orbitals_level=default_levels_of_theory['orbitals'],
adaptive_levels=None,
)
cls.sched2 = Scheduler(project='project_test_2', ess_settings=cls.ess_settings,
species_list=[cls.spc1, cls.spc2, cls.spc3],
composite_method=None,
conformer_opt_level=Level(repr=default_levels_of_theory['conformer']),
opt_level=Level(repr=default_levels_of_theory['opt']),
freq_level=Level(repr=default_levels_of_theory['freq']),
sp_level=Level(repr=default_levels_of_theory['sp']),
scan_level=Level(repr=default_levels_of_theory['scan']),
ts_guess_level=Level(repr=default_levels_of_theory['ts_guesses']),
project_directory=cls.project_directory,
testing=True,
job_types=cls.job_types1,
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_opt_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']),
project_directory=cls.project_directory,
testing=True,
job_types=cls.job_types2,
)
self.spc3 = ARCSpecies(label='CtripCO', smiles='C#CO', xyz=xyz3)
self.job1 = job_factory(job_adapter='gaussian', project='project_test', ess_settings=self.ess_settings,
species=[self.spc1], xyz=xyz1, job_type='conf_opt',
conformer=0, level=Level(repr={'method': 'b97-d3', 'basis': '6-311+g(d,p)'}),
project_directory=self.project_directory, job_num=101)
self.job2 = job_factory(job_adapter='gaussian', project='project_test', ess_settings=self.ess_settings,
species=[self.spc1], xyz=xyz1, job_type='conf_opt',
conformer=1, level=Level(repr={'method': 'b97-d3', 'basis': '6-311+g(d,p)'}),
project_directory=self.project_directory, job_num=102)
self.job3 = job_factory(job_adapter='qchem', project='project_test', ess_settings=self.ess_settings,
species=[self.spc2], job_type='freq',
level=Level(repr={'method': 'wb97x-d3', 'basis': '6-311+g(d,p)'}),
project_directory=self.project_directory, job_num=103)
self.job4 = job_factory(job_adapter='gaussian', project='project_test_4', ess_settings=self.ess_settings,
species=[self.spc1], xyz=xyz1, job_type='scan', torsions=[[3, 1, 2, 6]], rotor_index=0,
level=Level(repr={'method': 'b3lyp', 'basis': 'cbsb7'}),
project_directory=self.project_directory, job_num=104)
self.job_types1 = {'conf_opt': True,
'conf_sp': False,
'opt': True,
'fine': False,
'freq': True,
'sp': True,
'rotors': False,
'orbitals': False,
'lennard_jones': False,
}
self.job_types2 = {'conf_opt': True,
'conf_sp': False,
'opt': True,
'fine': False,
'freq': True,
'sp': True,
'rotors': True,
}
self.sched1 = Scheduler(project='project_test_1', ess_settings=self.ess_settings,
species_list=[self.spc1, self.spc2, self.spc3],
composite_method=None,
conformer_opt_level=Level(repr=default_levels_of_theory['conformer']),
opt_level=Level(repr=default_levels_of_theory['opt']),
freq_level=Level(repr=default_levels_of_theory['freq']),
sp_level=Level(repr=default_levels_of_theory['sp']),
scan_level=Level(repr=default_levels_of_theory['scan']),
ts_guess_level=Level(repr=default_levels_of_theory['ts_guesses']),
project_directory=self.project_directory,
testing=True,
job_types=self.job_types1,
orbitals_level=default_levels_of_theory['orbitals'],
adaptive_levels=None,
)
self.sched2 = Scheduler(project='project_test_2', ess_settings=self.ess_settings,
species_list=[self.spc1, self.spc2, self.spc3],
composite_method=None,
conformer_opt_level=Level(repr=default_levels_of_theory['conformer']),
opt_level=Level(repr=default_levels_of_theory['opt']),
freq_level=Level(repr=default_levels_of_theory['freq']),
sp_level=Level(repr=default_levels_of_theory['sp']),
scan_level=Level(repr=default_levels_of_theory['scan']),
ts_guess_level=Level(repr=default_levels_of_theory['ts_guesses']),
project_directory=self.project_directory,
testing=True,
job_types=self.job_types1,
orbitals_level=default_levels_of_theory['orbitals'],
adaptive_levels=None,
)
self.sched3 = Scheduler(project='project_test_4', ess_settings=self.ess_settings,
species_list=[self.spc1],
composite_method=Level(repr='CBS-QB3'),
conformer_opt_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']),
project_directory=self.project_directory,
testing=True,
job_types=self.job_types2,
)

def test_conformers(self):
"""Test the parse_conformer_energy() and determine_most_stable_conformer() methods"""
Expand Down Expand Up @@ -347,6 +368,7 @@ def test_determine_adaptive_level(self):

def test_initialize_output_dict(self):
"""Test Scheduler.initialize_output_dict"""
self.sched1.output['C2H6']['info'] = 'some text'
self.assertTrue(self.sched1._does_output_dict_contain_info())
self.sched1.output = dict()
self.assertEqual(self.sched1.output, dict())
Expand Down Expand Up @@ -745,7 +767,7 @@ def test_check_rxn_e0_by_spc(self):
'job_types': {'conf_opt': True, 'conf_sp': False, 'opt': True, 'freq': True, 'sp': True, 'rotors': True, 'irc': True, 'fine': True},
},
}
project_directory = os.path.join(ARC_PATH, 'Projects', 'arc_project_for_testing_delete_after_usage6')
project_directory = self.make_project_directory('arc_project_for_testing_delete_after_usage6')
os.makedirs(os.path.join(project_directory, 'output', 'Species', 'nC3H7', 'geometry'), exist_ok=True)
os.makedirs(os.path.join(project_directory, 'output', 'Species', 'iC3H7', 'geometry'), exist_ok=True)
os.makedirs(os.path.join(project_directory, 'output', 'rxns', 'TS0', 'geometry'), exist_ok=True)
Expand All @@ -757,7 +779,7 @@ def test_check_rxn_e0_by_spc(self):
dst=os.path.join(project_directory, 'output', 'rxns', 'TS0', 'geometry', 'freq.out'))
sched = Scheduler(project='test_rxn_e0_check',
ess_settings=self.ess_settings,
project_directory=os.path.join(ARC_PATH, 'Projects', 'arc_project_for_testing_delete_after_usage6'),
project_directory=project_directory,
rxn_list=[rxn],
species_list=rxn.r_species + rxn.p_species + [rxn.ts_species],
kinetics_adapter='arkane',
Expand All @@ -774,20 +796,16 @@ def test_check_rxn_e0_by_spc(self):
job_type='freq',
level=Level(repr='B3LYP/6-31G(d,p)'),
project='test_project',
project_directory=os.path.join(ARC_PATH,
'Projects',
'arc_project_for_testing_delete_after_usage6'),
project_directory=project_directory,
)
job_1.local_path_to_output_file = os.path.join(ARC_TESTING_PATH, 'freq', 'TS_nC3H7-iC3H7.out')
check_ts(reaction=rxn, verbose=True, job=job_1, checks=['NMD'])
self.assertEqual(rxn.ts_species.ts_checks, {'E0': None, 'e_elect': True, 'IRC': None, 'freq': True, 'NMD': True, 'warnings': ''})

def test_save_e_elect(self):
"""Test the save_e_elect() method."""
project_directory = os.path.join(ARC_PATH, 'Projects', 'save_e_elect')
project_directory = self.make_project_directory('save_e_elect')
e_elect_summary_path = os.path.join(project_directory, 'output', 'e_elect_summary.yml')
if os.path.isfile(os.path.join(project_directory, 'output', 'e_elect_summary.yml')):
os.remove(os.path.join(project_directory, 'output', 'e_elect_summary.yml'))
sched = Scheduler(project='test_save_e_elect',
ess_settings=self.ess_settings,
project_directory=project_directory,
Expand All @@ -811,7 +829,6 @@ def test_save_e_elect(self):
sp_path=os.path.join(ARC_TESTING_PATH, 'sp', 'mehylamine_CCSD(T).out'))
content = read_yaml_file(e_elect_summary_path)
self.assertEqual(content, {'formaldehyde': -300621.95378630824, 'mehylamine': -251360.00924747565})
shutil.rmtree(project_directory, ignore_errors=True)

def test_species_has_geo_sp_freq(self):
"""Test the species_has_geo() / species_has_sp() / species_has_freq() functions."""
Expand Down Expand Up @@ -1954,17 +1971,6 @@ def test_run_job_does_not_alias_level_args(self, mock_job_factory):
args['keyword']['dft_grid'] = 'defgrid2'
self.assertEqual(level.args, {'keyword': {'opt': 'opt=(verytight)'}, 'block': dict()})

@classmethod
def tearDownClass(cls):
"""
A function that is run ONCE after all unit tests in this class.
Delete all project directories created during these unit tests
"""
projects = ['arc_project_for_testing_delete_after_usage3', 'arc_project_for_testing_delete_after_usage6']
for project in projects:
project_directory = os.path.join(ARC_PATH, 'Projects', project)
shutil.rmtree(project_directory, ignore_errors=True)


class TestSpawnTsJobsAdmission(unittest.TestCase):
"""
Expand Down
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