def test_bath_gas(self):
"""Test correctly assigning the bath_gas attribute"""
self.assertIsNone(self.job1.bath_gas)
job2 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='onedmin',
level_of_theory='b3lyp/6-31+g(d)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job2.bath_gas, 'N2')
job2 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='onedmin',
level_of_theory='b3lyp/6-31+g(d)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100,
bath_gas='Ar')
self.assertEqual(job2.bath_gas, 'Ar')
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
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=str('methylamine'), smiles=str('CN'))
cls.spc2 = ARCSpecies(label=str('C2H6'), smiles=str('CC'))
cls.job1 = Job(project='project_test', ess_settings=cls.ess_settings, species_name='methylamine',
xyz='C 0.0 0.0 0.0', job_type='conformer', conformer=0, level_of_theory='b97-d3/6-311+g(d,p)',
multiplicity=1, project_directory=cls.project_directory, job_num=101)
cls.job2 = Job(project='project_test', ess_settings=cls.ess_settings, species_name='methylamine',
xyz='C 0.0 0.0 0.0', job_type='conformer', conformer=1, level_of_theory='b97-d3/6-311+g(d,p)',
multiplicity=1, project_directory=cls.project_directory, job_num=102)
cls.job3 = Job(project='project_test', ess_settings=cls.ess_settings, species_name='C2H6', xyz='C 0.0 0.0 0.0',
job_type='freq', level_of_theory='wb97x-d3/6-311+g(d,p)', multiplicity=1,
project_directory=cls.project_directory, software='qchem', job_num=103)
cls.rmgdb = rmgdb.make_rmg_database_object()
cls.job_types1 = {'conformers': True,
'opt': True,
'fine_grid': False,
'freq': True,
'sp': True,
'1d_rotors': False,
'orbitals': False,
'lennard_jones': False,
}
cls.sched1 = Scheduler(project='project_test', ess_settings=cls.ess_settings, species_list=[cls.spc1, cls.spc2],
composite_method='', conformer_level=default_levels_of_theory['conformer'],
opt_level=default_levels_of_theory['opt'], freq_level=default_levels_of_theory['freq'],
sp_level=default_levels_of_theory['sp'], scan_level=default_levels_of_theory['scan'],
ts_guess_level=default_levels_of_theory['ts_guesses'], rmgdatabase=cls.rmgdb,
project_directory=cls.project_directory, testing=True, job_types=cls.job_types1,
orbitals_level=default_levels_of_theory['orbitals'], adaptive_levels=None)
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.maxDiff = None
cls.ess_settings = {
'gaussian': ['server1', 'server2'],
'molpro': ['server2'],
'qchem': ['server1'],
'onedmin': ['server1']
}
cls.job1 = Job(project='project_test',
ess_settings=cls.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='b3lyp/6-31+g(d)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
cls.job1.initial_time = datetime.datetime(2019, 3, 15, 19, 53, 7, 0)
cls.job1.final_time = datetime.datetime(2019, 3, 15, 19, 53, 8, 0)
cls.job1.determine_run_time()
def test_from_dict(self):
"""Test Job.from_dict()"""
job_dict = self.job1.as_dict()
job = Job(**job_dict)
self.assertEqual(job.multiplicity, 1)
self.assertEqual(job.charge, 0)
self.assertEqual(job.species_name, 'tst_spc')
self.assertEqual(job.server, 'server1')
self.assertEqual(job.level.as_dict(), {'method': 'b3lyp', 'basis': '6-31+g(d)',
'method_type': 'dft', 'software': 'gaussian'})
self.assertEqual(job.job_type, 'scan')
self.assertEqual(job.project_directory.split('/')[-1], 'project_test')
self.assertFalse(job.is_ts)
def test_bath_gas(self):
"""Test correctly assigning the bath_gas attribute"""
self.assertIsNone(self.job1.bath_gas)
job2 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz=self.xyz_c,
job_type='onedmin',
level={
'method': 'b3lyp',
'basis': '6-31+g(d)'
},
multiplicity=1,
testing=True,
project_directory=os.path.join(ARC_PATH, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job2.bath_gas, 'N2')
job2 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz=self.xyz_c,
job_type='onedmin',
level={
'method': 'b3lyp',
'basis': '6-31+g(d)'
},
multiplicity=1,
testing=True,
project_directory=os.path.join(ARC_PATH, 'Projects',
'project_test'),
fine=True,
job_num=100,
bath_gas='Ar')
self.assertEqual(job2.bath_gas, 'Ar')
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.maxDiff = None
cls.ess_settings = {
'gaussian': ['server1', 'server2'],
'molpro': ['server2'],
'qchem': ['server1'],
'onedmin': ['server1'],
'orca': ['server1'],
'terachem': ['server1']
}
cls.xyz_c = {
'symbols': ('C', ),
'isotopes': (12, ),
'coords': ((0.0, 0.0, 0.0), )
}
cls.job1 = Job(
project='arc_project_for_testing_delete_after_usage3',
ess_settings=cls.ess_settings,
species_name='tst_spc',
xyz=cls.xyz_c,
job_type='opt',
level=Level(repr={
'method': 'b3lyp',
'basis': '6-31+g(d)'
}),
multiplicity=1,
fine=True,
job_num=100,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
initial_time=datetime.datetime(2019, 3, 15, 19, 53, 7, 0),
final_time='2019-3-15 19:53:08',
)
cls.job1.determine_run_time()
def test_automatic_ess_assignment(self):
"""Test that the Job module correctly assigns a software for specific methods and basis sets"""
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='b3lyp/6-311++G(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='ccsd(t)/avtz',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'molpro')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='wb97xd/6-311++g(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='wb97x-d3/6-311++g(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'qchem')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='b97/6-311++g(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='m062x/6-311++g(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='opt',
level_of_theory='m06-2x/6-311++g(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'qchem')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='scan',
level_of_theory='m062x/6-311++g(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test',
ess_settings=self.ess_settings,
species_name='tst_spc',
xyz='C 0.0 0.0 0.0',
job_type='scan',
level_of_theory='m06-2x/6-311++g(d,p)',
multiplicity=1,
testing=True,
project_directory=os.path.join(arc_path, 'Projects',
'project_test'),
fine=True,
job_num=100)
self.assertEqual(job0.software, 'qchem')
self.assertEqual(job0.memory, 15000)
self.assertEqual(job0.max_job_time, 120)
def test_format_max_job_time(self):
"""Test that the maximum job time can be formatted properly, including days, minutes, and seconds"""
test_job = Job.__new__(Job)
test_job.max_job_time = 59.888
self.assertEqual(test_job.format_max_job_time('days'), '2-11:53:16')
self.assertEqual(test_job.format_max_job_time('hours'), '59:53:16')
def test_automatic_ess_assignment(self):
"""Test that the Job module correctly assigns a software for specific methods and basis sets"""
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='opt', level={'method': 'b3lyp', 'basis': '6-311++G(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='opt', level={'method': 'ccsd(t)', 'basis': 'avtz'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'molpro')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='opt', level={'method': 'wb97xd2', 'basis': '6-311++g(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'terachem')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='opt', level={'method': 'wb97x-d3', 'basis': '6-311++g(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'qchem')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='opt', level={'method': 'b97', 'basis': '6-311++g(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='opt', level={'method': 'm062x', 'basis': '6-311++g(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='opt', level={'method': 'm06-2x', 'basis': '6-311++g(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'qchem')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='scan', level={'method': 'm062x', 'basis': '6-311++g(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'gaussian')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='scan', level={'method': 'm06-2x', 'basis': '6-311++g(d,p)'},
multiplicity=1, testing=True,
project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True, job_num=100)
self.assertEqual(job0.software, 'qchem')
job0 = Job(project='project_test', ess_settings=self.ess_settings, species_name='tst_spc', xyz=self.xyz_c,
job_type='sp', level={'method': 'dlpno-ccsd(t)', 'basis': 'aug-cc-pvtz',
'auxiliary_basis': 'aug-cc-pvtz/c'}, multiplicity=1,
testing=True, project_directory=os.path.join(arc_path, 'Projects', 'project_test'), fine=True,
job_num=100)
self.assertEqual(job0.software, 'orca')
self.assertEqual(job0.total_job_memory_gb, 14)
self.assertEqual(job0.max_job_time, 120)
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
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')
cls.spc2 = ARCSpecies(label='C2H6', smiles='CC')
xyz1 = """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=xyz1)
xyz2 = {
'symbols': ('C', ),
'isotopes': (12, ),
'coords': ((0.0, 0.0, 0.0), )
}
cls.job1 = Job(project='project_test',
ess_settings=cls.ess_settings,
species_name='methylamine',
xyz=xyz2,
job_type='conformer',
conformer=0,
level={
'method': 'b97-d3',
'basis': '6-311+g(d,p)'
},
multiplicity=1,
project_directory=cls.project_directory,
job_num=101)
cls.job2 = Job(project='project_test',
ess_settings=cls.ess_settings,
species_name='methylamine',
xyz=xyz2,
job_type='conformer',
conformer=1,
level={
'method': 'b97-d3',
'basis': '6-311+g(d,p)'
},
multiplicity=1,
project_directory=cls.project_directory,
job_num=102)
cls.job3 = Job(project='project_test',
ess_settings=cls.ess_settings,
species_name='C2H6',
xyz=xyz2,
job_type='freq',
level={
'method': 'wb97x-d3',
'basis': '6-311+g(d,p)'
},
multiplicity=1,
project_directory=cls.project_directory,
software='qchem',
job_num=103)
cls.rmg_database = rmgdb.make_rmg_database_object()
cls.job_types1 = {
'conformers': True,
'opt': True,
'fine_grid': False,
'freq': True,
'sp': True,
'rotors': False,
'orbitals': False,
'lennard_jones': False,
}
cls.sched1 = Scheduler(
project='project_test',
ess_settings=cls.ess_settings,
species_list=[cls.spc1, cls.spc2, cls.spc3],
composite_method=None,
conformer_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']),
rmg_database=cls.rmg_database,
project_directory=cls.project_directory,
testing=True,
job_types=cls.job_types1,
orbitals_level=default_levels_of_theory['orbitals'],
adaptive_levels=None,
)