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.rmgdb = rmgdb.make_rmg_database_object()
rmgdb.load_families_only(cls.rmgdb)
cls.rxn1 = ARCReaction(reactants=['CH4', 'OH'],
products=['CH3', 'H2O'])
cls.rxn1.rmg_reaction = Reaction(reactants=[
Species().fromSMILES(str('C')),
Species().fromSMILES(str('[OH]'))
],
products=[
Species().fromSMILES(
str('[CH3]')),
Species().fromSMILES(str('O'))
])
cls.rxn2 = ARCReaction(reactants=['C2H5', 'OH'],
products=['C2H4', 'H2O'])
cls.rxn2.rmg_reaction = Reaction(reactants=[
Species().fromSMILES(str('C[CH2]')),
Species().fromSMILES(str('[OH]'))
],
products=[
Species().fromSMILES(str('C=C')),
Species().fromSMILES(str('O'))
])
cls.rxn3 = ARCReaction(reactants=['CH3CH2NH'], products=['CH2CH2NH2'])
cls.rxn3.rmg_reaction = Reaction(
reactants=[Species().fromSMILES(str('CC[NH]'))],
products=[Species().fromSMILES(str('[CH2]CN'))])
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.rmgdb = rmgdb.make_rmg_database_object()
rmgdb.load_rmg_database(rmgdb=cls.rmgdb)
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,
)
def test_append_conformers(self):
"""Test that ARC correctly parses its own conformer files"""
ess_settings = {'gaussian': 'server1', 'molpro': 'server2', 'qchem': 'server1'}
project_directory = os.path.join(arc_path, 'Projects', 'arc_project_for_testing_delete_after_usage4')
spc1 = ARCSpecies(label=str('vinoxy'), smiles=str('C=C[O]'))
rmgdb = make_rmg_database_object()
job_types1 = {'conformers': True,
'opt': True,
'fine_grid': False,
'freq': True,
'sp': True,
'1d_rotors': False,
'orbitals': False,
'lennard_jones': False,
}
sched1 = Scheduler(project='project_test', ess_settings=ess_settings, species_list=[spc1],
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=rmgdb,
project_directory=project_directory, testing=True, job_types=job_types1,
orbitals_level=default_levels_of_theory['orbitals'], adaptive_levels=None)
xyzs = ["""O 1.09068700 0.26516800 -0.16706300
C 2.92204100 -1.18335700 -0.38884900
C 2.27655500 -0.00373900 0.08543500
H 2.36544800 -1.88781000 -0.99914600
H 3.96112000 -1.38854500 -0.14958800
H 2.87813500 0.68828400 0.70399400
""",
"""O 1.19396100 -0.06003700 0.03890100
C 3.18797000 0.77061300 -0.87352700
C 2.43591200 -0.04439300 0.02171600
H 4.27370000 0.76090200 -0.86286100
H 2.66641700 1.41155700 -1.57757300
H 3.00398000 -0.68336800 0.72359800
""",
"""O 1.35241100 -1.02956000 -0.24056200
C -0.72084300 0.01308200 0.09573000
C 0.69217700 0.01185100 -0.09044300
H -1.25803800 -0.93018100 0.10926800
H -1.26861200 0.94177100 0.22420100
H 1.20290400 0.99303700 -0.09819400
""",
"""O -1.40102900 -0.98575100 -0.11588500
C 0.72457000 -0.01076700 0.06448800
C -0.69494600 0.03450000 -0.06206300
H 1.22539000 -0.97248000 0.11741200
H 1.31277400 0.90087100 0.10878400
H -1.16675800 1.03362600 -0.11273700
"""]
energies = [0, 5, 5, 5] # J/mol
save_conformers_file(project_directory=project_directory, label='vinoxy', xyzs=xyzs, level_of_theory='level1',
multiplicity=2, charge=0)
self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'Species', 'vinoxy', 'geometry',
'conformers', 'conformers_before_optimization.txt')))
save_conformers_file(project_directory=project_directory, label='vinoxy', xyzs=xyzs, level_of_theory='level1',
multiplicity=2, charge=0, energies=energies)
self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'Species', 'vinoxy', 'geometry',
'conformers', 'conformers_after_optimization.txt')))
spc2 = ARCSpecies(label=str('vinoxy'), smiles=str('C=C[O]'), xyz=os.path.join(
project_directory, 'output', 'Species', 'vinoxy', 'geometry', 'conformers',
'conformers_before_optimization.txt'))
spc3 = ARCSpecies(label=str('vinoxy'), smiles=str('C=C[O]'), xyz=os.path.join(
project_directory, 'output', 'Species', 'vinoxy', 'geometry', 'conformers',
'conformers_after_optimization.txt'))
self.assertEqual(spc2.conformers[2], xyzs[2])
self.assertEqual(spc3.conformers[2], xyzs[2])
self.assertEqual(spc3.conformer_energies[2], energies[2])
