def test_xyz_from_dict(self):
"""Test correctly assigning xyz from dictionary"""
species_dict1 = {'label': 'tst_spc_1', 'xyz': 'C 0.1 0.5 0.0'}
species_dict2 = {'label': 'tst_spc_2', 'initial_xyz': 'C 0.2 0.5 0.0'}
species_dict3 = {'label': 'tst_spc_3', 'final_xyz': 'C 0.3 0.5 0.0'}
species_dict4 = {'label': 'tst_spc_4', 'xyz': ['C 0.4 0.5 0.0', 'C 0.5 0.5 0.0']}
spc1 = ARCSpecies(species_dict=species_dict1)
spc2 = ARCSpecies(species_dict=species_dict2)
spc3 = ARCSpecies(species_dict=species_dict3)
spc4 = ARCSpecies(species_dict=species_dict4)
self.assertIsNone(spc1.initial_xyz)
self.assertIsNone(spc1.final_xyz)
self.assertEqual(spc1.conformers, ['C 0.1 0.5 0.0'])
self.assertEqual(spc1.conformer_energies, [None])
self.assertEqual(spc2.initial_xyz, 'C 0.2 0.5 0.0')
self.assertIsNone(spc2.final_xyz)
self.assertEqual(spc2.conformers, [])
self.assertEqual(spc2.conformer_energies, [])
self.assertIsNone(spc3.initial_xyz)
self.assertEqual(spc3.final_xyz, 'C 0.3 0.5 0.0')
self.assertEqual(spc3.conformers, [])
self.assertEqual(spc3.conformer_energies, [])
self.assertIsNone(spc4.initial_xyz)
self.assertIsNone(spc4.final_xyz)
self.assertEqual(spc4.conformers, ['C 0.4 0.5 0.0', 'C 0.5 0.5 0.0'])
self.assertEqual(spc4.conformer_energies, [None, None])
def arc_species_from_rmg_reaction(self):
"""
A helper function for generating the ARC Species (.r_species and .p_species) from the RMG Reaction object
"""
if self.rmg_reaction is not None and not len(self.r_species) and not len(self.p_species):
self.r_species = [ARCSpecies(label=spc.label, mol=spc.molecule[0]) for spc in self.rmg_reaction.reactants]
self.p_species = [ARCSpecies(label=spc.label, mol=spc.molecule[0]) for spc in self.rmg_reaction.products]
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 get_rotors_dict(self):
"""
Determine possible unique rotors in the species to be treated as hindered rotors,
taking into account all localized structures.
The resulting rotors are saved in {'pivots': [1, 3], 'top': [3, 7], 'scan': [2, 1, 3, 7]} format.
"""
rotors_dict = {}
logging.disable(50)
species = ARCSpecies(label=self.label,
xyz=self.xyz,
charge=self.charge,
multiplicity=self.spin_multiplicity)
if species is None:
return rotors_dict
species.determine_rotors()
logging.disable(logging.NOTSET)
for i in species.rotors_dict:
rotors_dict[i + 1] = {}
pivots = species.rotors_dict[i]['pivots']
top = species.rotors_dict[i]['top']
scan = species.rotors_dict[i]['scan']
rotors_dict[i + 1]['pivots'] = pivots
rotors_dict[i + 1]['top'] = top
rotors_dict[i + 1]['scan'] = scan
return rotors_dict
def test_get_radius(self):
"""Test determining the species radius"""
spc1 = ARCSpecies(label='r1', smiles='O=C=O')
self.assertAlmostEqual(spc1.radius, 2.065000, 5)
spc2 = ARCSpecies(label='r1', smiles='CCCCC')
self.assertAlmostEqual(spc2.radius, 3.734040, 5)
spc3 = ARCSpecies(label='r1', smiles='CCO')
self.assertAlmostEqual(spc3.radius, 2.495184, 5)
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.maxDiff = None
cls.ch4 = ARCSpecies(label='CH4', smiles='C')
cls.nh3 = ARCSpecies(label='NH3', smiles='N')
cls.h = ARCSpecies(label='H', smiles='[H]')
cls.ch4_bde_1_2_a = ARCSpecies(label='CH4_BDE_1_2_A', smiles='[CH3]')
cls.ch4.e0, cls.h.e0, cls.ch4_bde_1_2_a.e0 = 10, 25, 35
cls.ch4.bdes = [(1, 2)]
def test_save_geo(self):
"""Test saving the geometry files for a species"""
spc = ARCSpecies(label='methylamine',
smiles='CN',
multiplicity=1,
charge=0)
spc.final_xyz = str_to_xyz(
"""N -0.74566988 -0.11773792 0.00000000
C 0.70395487 0.03951260 0.00000000
H 1.12173564 -0.45689176 -0.87930074
H 1.06080468 1.07995075 0.00000000
H 1.12173564 -0.45689176 0.87930074
H -1.16115119 0.31478894 0.81506145
H -1.16115119 0.31478894 -0.81506145""")
spc.opt_level = 'opt/level'
project = 'arc_project_for_testing_delete_after_usage'
project_directory = os.path.join(arc_path, 'Projects', project)
xyz_path = os.path.join(project_directory, 'output', 'Species',
spc.label, 'geometry', 'methylamine.xyz')
gjf_path = os.path.join(project_directory, 'output', 'Species',
spc.label, 'geometry', 'methylamine.gjf')
plotter.save_geo(species=spc, project_directory=project_directory)
xyz_data = """7
methylamine optimized at opt/level
N -0.74566988 -0.11773792 0.00000000
C 0.70395487 0.03951260 0.00000000
H 1.12173564 -0.45689176 -0.87930074
H 1.06080468 1.07995075 0.00000000
H 1.12173564 -0.45689176 0.87930074
H -1.16115119 0.31478894 0.81506145
H -1.16115119 0.31478894 -0.81506145
"""
gjf_data = """# hf/3-21g
methylamine optimized at opt/level
0 1
N -0.74566988 -0.11773792 0.00000000
C 0.70395487 0.03951260 0.00000000
H 1.12173564 -0.45689176 -0.87930074
H 1.06080468 1.07995075 0.00000000
H 1.12173564 -0.45689176 0.87930074
H -1.16115119 0.31478894 0.81506145
H -1.16115119 0.31478894 -0.81506145
"""
with open(xyz_path, 'r') as f:
data = f.read()
self.assertEqual(data, xyz_data)
with open(gjf_path, 'r') as f:
data = f.read()
self.assertEqual(data, gjf_data)
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.maxDiff = None
# Method 1: RMG Species object (here by SMILES)
cls.spc1_rmg = Species(molecule=[Molecule().fromSMILES(str('C=C[O]'))]) # delocalized radical + amine
cls.spc1_rmg.label = str('vinoxy')
cls.spc1 = ARCSpecies(rmg_species=cls.spc1_rmg)
# Method 2: ARCSpecies object by XYZ (also give SMILES for thermo BAC)
oh_xyz = str("""O 0.00000000 0.00000000 -0.12002167
H 0.00000000 0.00000000 0.85098324""")
cls.spc2 = ARCSpecies(label=str('OH'), xyz=oh_xyz, smiles=str('[OH]'), multiplicity=2, charge=0)
# Method 3: ARCSpecies object by SMILES
cls.spc3 = ARCSpecies(label=str('methylamine'), smiles=str('CN'), multiplicity=1, charge=0)
# Method 4: ARCSpecies object by RMG Molecule object
mol4 = Molecule().fromSMILES(str('C=CC'))
cls.spc4 = ARCSpecies(label=str('propene'), mol=mol4, multiplicity=1, charge=0)
# Method 5: ARCSpecies by AdjacencyList (to generate AdjLists, see https://rmg.mit.edu/molecule_search)
n2h4_adj = str("""1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 N u0 p1 c0 {1,S} {5,S} {6,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}""")
cls.spc5 = ARCSpecies(label=str('N2H4'), adjlist=n2h4_adj, multiplicity=1, charge=0)
n3_xyz = str("""N -1.1997440839 -0.1610052059 0.0274738287
H -1.4016624407 -0.6229695533 -0.8487034080
H -0.0000018759 1.2861082773 0.5926077870
N 0.0000008520 0.5651072858 -0.1124621525
H -1.1294692206 -0.8709078271 0.7537518889
N 1.1997613019 -0.1609980472 0.0274604887
H 1.1294795781 -0.8708998550 0.7537444446
H 1.4015274689 -0.6230592706 -0.8487058662""")
cls.spc6 = ARCSpecies(label=str('N3'), xyz=n3_xyz, multiplicity=1, smiles=str('NNN'))
xyz1 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'AIBN.gjf')
cls.spc7 = ARCSpecies(label='AIBN', smiles=str('N#CC(C)(C)N=NC(C)(C)C#N'), xyz=xyz1)
hso3_xyz = str("""S -0.12383700 0.10918200 -0.21334200
O 0.97332200 -0.98800100 0.31790100
O -1.41608500 -0.43976300 0.14487300
O 0.32370100 1.42850400 0.21585900
H 1.84477700 -0.57224200 0.35517700""")
cls.spc8 = ARCSpecies(label=str('HSO3'), xyz=hso3_xyz, multiplicity=2, charge=0, smiles=str('O[S](=O)=O'))
nh_s_adj = str("""1 N u0 p2 c0 {2,S}
2 H u0 p0 c0 {1,S}""")
nh_s_xyz = str("""N 0.50949998 0.00000000 0.00000000
H -0.50949998 0.00000000 0.00000000""")
cls.spc9 = ARCSpecies(label=str('NH2(S)'), adjlist=nh_s_adj, xyz=nh_s_xyz, multiplicity=1, charge=0)
def test_save_conformers_file(self):
"""test the save_conformers_file function"""
project = 'arc_project_for_testing_delete_after_usage'
project_directory = os.path.join(arc_path, 'Projects', project)
label = 'butanol'
spc1 = ARCSpecies(label=label, smiles='CCCCO')
spc1.generate_conformers(n_confs=3)
self.assertIn(len(spc1.conformers), [2, 3])
plotter.save_conformers_file(project_directory=project_directory, label=spc1.label,
xyzs=spc1.conformers, level_of_theory='APFD/def2tzvp',
multiplicity=spc1.multiplicity, charge=spc1.charge, is_ts=False,
energies=spc1.conformer_energies)
conf_file_path = os.path.join(project_directory, 'output', 'Species', label, 'geometry', 'conformers',
'conformers_before_optimization.txt')
self.assertTrue(os.path.isfile(conf_file_path))
def test_determine_unique_species_labels(self):
"""Test the determine_unique_species_labels method"""
spc0 = ARCSpecies(label='spc0', smiles='CC', compute_thermo=False)
spc1 = ARCSpecies(label='spc1', smiles='CC', compute_thermo=False)
spc2 = ARCSpecies(label='spc2', smiles='CC', compute_thermo=False)
arc0 = ARC(
project='arc_test',
job_types=self.job_types1,
species=[spc0, spc1, spc2],
level_of_theory='ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)')
self.assertEqual(arc0.unique_species_labels, ['spc0', 'spc1', 'spc2'])
spc3 = ARCSpecies(label='spc0', smiles='CC', compute_thermo=False)
arc0.species.append(spc3)
with self.assertRaises(ValueError):
arc0.determine_unique_species_labels()
def test_set_vector_length(self):
"""Test changing a vector's length"""
v1 = [1, 0, 0]
self.assertEqual(vectors.get_vector_length(v1), 1)
v1_transformed = vectors.set_vector_length(v1, 5)
self.assertAlmostEqual(vectors.get_vector_length(v1_transformed), 5)
v1 = [1, 1, 1]
self.assertEqual(vectors.get_vector_length(v1), 3 ** 0.5)
v1_transformed = vectors.set_vector_length(v1, 5)
self.assertAlmostEqual(vectors.get_vector_length(v1_transformed), 5)
label = 'CNCC'
pivot = 0
xyz = {'symbols': ('N', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'),
'isotopes': (14, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1),
'coords': ((0.7419854952964929, -0.18588322859265055, -0.8060295165375653),
(-0.38476668007897186, -0.8774643553523614, -0.1815530887172187),
(-1.4977348513273125, 0.05995564693605262, 0.26652181022311233),
(1.5633235727172392, 0.5360966415350092, 0.15477859056711452),
(-0.04458112063725271, -1.4936027355391557, 0.6589418973690523),
(-0.7986335015469359, -1.5715787743431335, -0.9219907626214912),
(-2.348455608682208, -0.5210498432021002, 0.6375394558854425),
(-1.8523669868240424, 0.6790455638159553, -0.5642494434208211),
(-1.170505453235269, 0.7210016856743618, 1.0746899133307615),
(2.4283037770451084, 0.9651590522064675, -0.36083882142892065),
(1.945994527876002, -0.1322800197070601, 0.9328203647772167),
(1.0178974719106297, 1.3595978302624294, 0.6250164549219148),
(0.39953935748654607, 0.4610025363062083, -1.5156468543485933))}
mol = ARCSpecies(label='CNCC', xyz=xyz).mol
v1 = vectors.get_lp_vector(label, mol, xyz, pivot)
self.assertAlmostEqual(vectors.get_vector_length(v1), 1) # should return a unit vector
v1_transformed = vectors.set_vector_length(v1, 5)
self.assertAlmostEqual(vectors.get_vector_length(v1_transformed), 5)
def get_mapped_product_xyz(self):
"""
Uses the mapping from product onto reactant to create a new ARC Species for the mapped product.
For now, only functional for A <=> B reactions.
Returns:
Tuple[dict, ARCSpecies]:
dict: Mapped product atoms in ARC dictionary format.
ARCSpecies: ARCSpecies object created from mapped coordinates.
"""
product = self.p_species[0]
mapping = self.atom_map
original_xyz_str = xyz_to_str(product.get_xyz())
original_xyz = np.array(original_xyz_str.split('\n'))
mapped_xyz = '\n'.join(original_xyz[mapping].tolist())
# create another product with the mapped atoms since ARCSpecies objects preserve this ordering
# in RDKit objects and in RMG-Py Molecule objects
mapped_product = ARCSpecies(
label=product.label,
smiles=product.mol.smiles,
multiplicity=product.multiplicity,
charge=product.charge,
xyz=mapped_xyz,
)
mapped_xyz = str_to_xyz(mapped_xyz)
return mapped_xyz, mapped_product
def test_rmg_species_conversion_into_arc_species(self):
"""Test the conversion of an RMG species into an ARCSpecies"""
self.spc1_rmg.label = None
self.spc = ARCSpecies(rmg_species=self.spc1_rmg, label=str('vinoxy'))
self.assertEqual(self.spc.label, str('vinoxy'))
self.assertEqual(self.spc.multiplicity, 2)
self.assertEqual(self.spc.charge, 0)
def test_as_dict(self):
"""Test the as_dict() method of ARC"""
spc1 = ARCSpecies(label='spc1', smiles=str('CC'), generate_thermo=False)
arc0 = ARC(project='arc_test', job_types=self.job_types1, initial_trsh='scf=(NDump=30)',
arc_species_list=[spc1], level_of_theory='ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)')
restart_dict = arc0.as_dict()
expected_dict = {'composite_method': '',
'conformer_level': 'b3lyp/6-31g(d,p) empiricaldispersion=gd3bj',
'ts_guess_level': 'b3lyp/6-31g(d,p) empiricaldispersion=gd3bj',
'opt_level': 'b3lyp/6-311+g(3df,2p)',
'freq_level': 'b3lyp/6-311+g(3df,2p)',
'freq_scale_factor': 0.967,
'initial_trsh': 'scf=(NDump=30)',
'max_job_time': 120,
'model_chemistry': 'ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)',
'output': {},
'project': 'arc_test',
'running_jobs': {},
'reactions': [],
'scan_level': '',
'sp_level': 'ccsd(t)-f12/cc-pvdz-f12',
'job_memory': 14,
'job_types': {'1d_rotors': False,
'conformers': True,
'fine': False,
'freq': True,
'onedmin': False,
'opt': True,
'orbitals': False,
'sp': True},
't_min': None,
't_max': None,
't_count': None,
'use_bac': True,
'confs_to_dft': 5,
'allow_nonisomorphic_2d': False,
'calc_freq_factor': True,
'ess_settings': {'gaussian': ['local', 'server2'], 'onedmin': ['server1'],
'molpro': ['server2'], 'qchem': ['server1']},
'species': [{'bond_corrections': {'C-C': 1, 'C-H': 6},
'arkane_file': None,
'E0': None,
'charge': 0,
'external_symmetry': None,
'optical_isomers': None,
'generate_thermo': False,
'is_ts': False,
'label': 'spc1',
'long_thermo_description': "Bond corrections: {'C-C': 1, 'C-H': 6}\n",
'mol': '1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}\n2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}\n3 H u0 p0 c0 {1,S}\n4 H u0 p0 c0 {1,S}\n5 H u0 p0 c0 {1,S}\n6 H u0 p0 c0 {2,S}\n7 H u0 p0 c0 {2,S}\n8 H u0 p0 c0 {2,S}\n',
'multiplicity': 1,
'neg_freqs_trshed': [],
'number_of_rotors': 0,
'rotors_dict': {},
'force_field': 'MMFF94',
't1': None}],
}
self.assertEqual(restart_dict, expected_dict)
def test_consistent_atom_order(self):
"""Test that the atom order is preserved whether starting from SMILES or from xyz"""
spc1 = ARCSpecies(label='spc1', smiles='CCCO')
xyz1 = spc1.get_xyz()
for adj, coord in zip(spc1.mol.toAdjacencyList().splitlines(), xyz1.splitlines()):
if adj and coord:
self.assertEqual(adj.split()[1], coord.split()[0])
xyz2 = """C -0.37147383 -0.54225753 0.07779977
C 0.99011397 0.11006088 -0.10715587
H -0.33990169 -1.22256017 0.93731544
H -0.60100180 -1.16814809 -0.79292035
H 1.26213386 0.70273091 0.77209458
O 1.96607463 -0.90691160 -0.28642183
H 0.99631715 0.75813344 -0.98936747
H -1.27803075 1.09840370 1.16400304
C -1.46891192 0.48768649 0.27579733
H -2.43580767 -0.00829320 0.40610628
H -1.54270451 1.15356356 -0.58992943
H 2.82319256 -0.46240839 -0.40178723"""
spc2 = ARCSpecies(label='spc2', xyz=xyz2)
for adj, coord in zip(spc2.mol.toAdjacencyList().splitlines(), xyz2.splitlines()):
if adj and coord:
self.assertEqual(adj.split()[1], coord.split()[0])
n3_xyz = str("""N -1.1997440839 -0.1610052059 0.0274738287
H -1.4016624407 -0.6229695533 -0.8487034080
H -0.0000018759 1.2861082773 0.5926077870
N 0.0000008520 0.5651072858 -0.1124621525
H -1.1294692206 -0.8709078271 0.7537518889
N 1.1997613019 -0.1609980472 0.0274604887
H 1.1294795781 -0.8708998550 0.7537444446
H 1.4015274689 -0.6230592706 -0.8487058662""")
spc3 = ARCSpecies(label=str('N3'), xyz=n3_xyz, multiplicity=1, smiles=str('NNN'))
self.assertEqual(spc3.mol.atoms[1].symbol, 'H')
spc3.generate_conformers()
self.assertEqual(len(spc3.conformers), 5)
xyz4 = """O -1.48027320 0.36597456 0.41386552
C -0.49770656 -0.40253648 -0.26500019
C 0.86215119 0.24734211 -0.11510338
H -0.77970114 -0.46128090 -1.32025907
H -0.49643724 -1.41548311 0.14879346
H 0.84619526 1.26924854 -0.50799415
H 1.14377239 0.31659216 0.94076336
H 1.62810781 -0.32407050 -0.64676910
H -1.22610851 0.40421362 1.35170355"""
spc4 = ARCSpecies(label='CCO', smiles='CCO', xyz=xyz4) # define from xyz for consistent atom order
for atom1, atom2 in zip(spc4.mol.atoms, spc4.mol_list[0].atoms):
self.assertEqual(atom1.symbol, atom2.symbol)
def test_get_lp_vector(self):
"""Test the lone pair vector"""
xyz1 = converter.str_to_xyz(
"""O 1.13971727 -0.35763357 -0.91809799
N -0.16022228 -0.63832421 -0.32863338
C -0.42909096 0.49864538 0.54457751
H -1.36471297 0.33135829 1.08632108
H 0.37059419 0.63632068 1.27966893
H -0.53867601 1.41749835 -0.03987146
H 0.03832076 -1.45968957 0.24914206
H 0.94407000 -0.42817536 -1.87310674""")
spc1 = ARCSpecies(label='tst1', smiles='CN(O)', xyz=xyz1)
vector = vectors.get_lp_vector(label='tst1',
mol=spc1.mol,
xyz=xyz1,
pivot=1)
self.assertAlmostEqual(vector[0], -0.7582151013592212, 5)
self.assertAlmostEqual(vector[1], -0.14276808320949216, 5)
self.assertAlmostEqual(vector[2], -0.6361816835523585, 5)
self.assertAlmostEqual((sum([vi**2 for vi in vector]))**0.5, 1)
# puts the following dummy atom in xyz1: 'Cl -0.91844 -0.78109 -0.96482'
xyz2 = converter.str_to_xyz(
"""N -0.70735114 0.81971647 0.24999886
C 0.58016992 0.65919122 -0.42405305
C 1.44721132 -0.43727777 0.17945348
C -1.63900905 -0.25796649 -0.04936095
H 1.11974047 1.60931343 -0.33768790
H 0.43764604 0.48458543 -1.49689220
H 1.00255021 -1.42757899 0.04242741
H 2.42947502 -0.44523307 -0.30432399
H 1.60341053 -0.27376799 1.25093890
H -1.81252045 -0.34624671 -1.12667881
H -2.60396918 -0.04100469 0.41960198
H -1.29274859 -1.22036999 0.33877281
H -0.56460509 0.87663914 1.25780346""")
spc2 = ARCSpecies(label='tst2', smiles='CNCC', xyz=xyz2)
vector = vectors.get_lp_vector(label='tst2',
mol=spc2.mol,
xyz=xyz2,
pivot=0)
self.assertAlmostEqual(vector[0], -0.40585301456248446, 5)
self.assertAlmostEqual(vector[1], 0.8470158636326891, 5)
self.assertAlmostEqual(vector[2], -0.34328917449449764, 5)
self.assertAlmostEqual((sum([vi**2 for vi in vector]))**0.5, 1)
def test_from_dict(self):
"""Test Species.from_dict()"""
species_dict = self.spc2.as_dict()
spc = ARCSpecies(species_dict=species_dict)
self.assertEqual(spc.multiplicity, 2)
self.assertEqual(spc.charge, 0)
self.assertEqual(spc.label, 'OH')
self.assertEqual(spc.mol.toSMILES(), '[OH]')
self.assertFalse(spc.is_ts)
def parse_species_in_arc_input(input_path: str) -> dict:
"""
A function used to get species scope from the ARC input file.
"""
spc_info = {}
try:
input_file = read_yaml_file(input_path)
except:
# Bad input path
return spc_info
if not 'species' in input_file:
# An input file without species information, weird!
return spc_info
for spc in input_file['species']:
label = spc['label']
if 'smiles' in spc:
try:
spc_info[label] = {
'label': label,
'species': ARCSpecies(label=label, smiles=spc['smiles']),
'smiles': spc['smiles'],
'ts': False
}
except:
pass
elif 'xyz' in spc:
try:
mol = xyz_to_mol(spc['xyz'])
except:
pass
else:
smiles = mol.to_smiles()
spc_info[label] = {
'label': label,
'species': ARCSpecies(label=label, smiles=smiles),
'smiles': smiles,
'ts': False
}
if label not in spc_info:
# Cannot get smiles or xyz
spc_info[label] = {'label': label, 'ts': False}
return spc_info
def test_log_bde_report(self):
"""Test the log_bde_report() function"""
path = os.path.join(arc_path, 'arc', 'testing', 'bde_report_test.txt')
bde_report = {
'aniline': {
(1, 2): 431.43,
(5, 8): 465.36,
(6, 9): 458.70,
(3, 10): 463.16,
(4, 11): 463.16,
(7, 12): 458.70,
(1, 13): 372.31,
(1, 14): 372.31,
(5, 6): 'N/A'
}
}
xyz = """N 2.28116100 -0.20275000 -0.29653100
C 0.90749600 -0.08067400 -0.11852200
C 0.09862900 -1.21367300 -0.02143500
C 0.30223500 1.17638000 -0.08930600
C -1.87236600 0.16329100 0.13332800
C -1.27400900 -1.08769400 0.10342700
C -1.07133200 1.29144700 0.03586700
H -2.94554700 0.25749800 0.23136900
H -1.88237600 -1.98069300 0.17844600
H 0.55264300 -2.19782900 -0.04842100
H 0.91592000 2.06653500 -0.16951700
H -1.51965000 2.27721000 0.05753400
H 2.68270800 -1.06667200 0.02551200
H 2.82448700 0.59762700 -0.02174900"""
aniline = ARCSpecies(label='aniline',
xyz=xyz,
smiles='c1ccc(cc1)N',
bdes=['all_h', (1, 2), (5, 6)])
spc_dict = {'aniline': aniline}
plotter.log_bde_report(path, bde_report, spc_dict)
with open(path, 'r') as f:
content = f.read()
expected_content = """ BDE report for aniline:
Pivots Atoms BDE (kJ/mol)
-------- ----- ------------
(1, 13) N - H 372.31
(1, 14) N - H 372.31
(1, 2) N - C 431.43
(6, 9) C - H 458.70
(7, 12) C - H 458.70
(3, 10) C - H 463.16
(4, 11) C - H 463.16
(5, 8) C - H 465.36
(5, 6) C - C N/A
"""
self.assertEqual(content, expected_content)
def test_charge_and_multiplicity(self):
"""Test determination of molecule charge and multiplicity"""
spc1 = ARCSpecies(label='spc1', mol=Molecule(SMILES=str('C[CH]C')), generate_thermo=False)
spc2 = ARCSpecies(label='spc2', mol=Molecule(SMILES=str('CCC')), generate_thermo=False)
spc3 = ARCSpecies(label='spc3', smiles=str('N[NH]'), generate_thermo=False)
spc4 = ARCSpecies(label='spc4', smiles=str('NNN'), generate_thermo=False)
adj1 = """multiplicity 2
1 O u1 p2 c0 {2,S}
2 H u0 p0 c0 {1,S}
"""
adj2 = """1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 N u0 p1 c0 {1,S} {3,S} {7,S}
3 O u0 p2 c0 {2,S} {8,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
"""
spc5 = ARCSpecies(label='spc5', adjlist=str(adj1), generate_thermo=False)
spc6 = ARCSpecies(label='spc6', adjlist=str(adj2), generate_thermo=False)
xyz1 = """O 0.00000000 0.00000000 -0.10796235
H 0.00000000 0.00000000 0.86318839"""
xyz2 = """N -0.74678912 -0.11808620 0.00000000
C 0.70509190 0.01713703 0.00000000
H 1.11547042 -0.48545356 0.87928385
H 1.11547042 -0.48545356 -0.87928385
H 1.07725194 1.05216961 0.00000000
H -1.15564250 0.32084669 0.81500594
H -1.15564250 0.32084669 -0.81500594"""
spc7 = ARCSpecies(label='spc7', xyz=xyz1, generate_thermo=False)
spc8 = ARCSpecies(label='spc8', xyz=xyz2, generate_thermo=False)
self.assertEqual(spc1.charge, 0)
self.assertEqual(spc2.charge, 0)
self.assertEqual(spc3.charge, 0)
self.assertEqual(spc4.charge, 0)
self.assertEqual(spc5.charge, 0)
self.assertEqual(spc6.charge, 0)
self.assertEqual(spc7.charge, 0)
self.assertEqual(spc8.charge, 0)
self.assertEqual(spc1.multiplicity, 2)
self.assertEqual(spc2.multiplicity, 1)
self.assertEqual(spc3.multiplicity, 2)
self.assertEqual(spc4.multiplicity, 1)
self.assertEqual(spc5.multiplicity, 2)
self.assertEqual(spc6.multiplicity, 1)
self.assertEqual(spc7.multiplicity, 2)
self.assertEqual(spc8.multiplicity, 1)
def test_as_dict(self):
"""Test the as_dict() method of ARC"""
self.maxDiff = None
ess_settings = {}
spc1 = ARCSpecies(label='spc1', smiles=str('CC'), generate_thermo=False)
arc0 = ARC(project='arc_test', ess_settings=ess_settings, scan_rotors=False, initial_trsh='scf=(NDump=30)',
arc_species_list=[spc1])
restart_dict = arc0.as_dict()
expected_dict = {'composite_method': '',
'conformer_level': 'b97-d3/6-311+g(d,p)',
'ts_guess_level': 'b3lyp/6-31+g(d,p)',
'ess_settings': {'ssh': True},
'fine': True,
'opt_level': 'wb97xd/6-311++g(d,p)',
'freq_level': 'wb97xd/6-311++g(d,p)',
'generate_conformers': True,
'initial_trsh': 'scf=(NDump=30)',
'max_job_time': 120,
'model_chemistry': 'ccsd(t)-f12/cc-pvtz-f12',
'output': {},
'project': 'arc_test',
'running_jobs': {},
'reactions': [],
'scan_level': '',
'scan_rotors': False,
'sp_level': 'ccsd(t)-f12/cc-pvtz-f12',
't_min': None,
't_max': None,
't_count': None,
'use_bac': True,
'visualize_orbitals': True,
'allow_nonisomorphic_2d': False,
'species': [{'bond_corrections': {'C-C': 1, 'C-H': 6},
'arkane_file': None,
'E0': None,
'charge': 0,
'external_symmetry': None,
'optical_isomers': None,
'final_xyz': '',
'generate_thermo': False,
'is_ts': False,
'label': u'spc1',
'long_thermo_description': "Bond corrections: {'C-C': 1, 'C-H': 6}\n",
'mol': '1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}\n2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}\n3 H u0 p0 c0 {1,S}\n4 H u0 p0 c0 {1,S}\n5 H u0 p0 c0 {1,S}\n6 H u0 p0 c0 {2,S}\n7 H u0 p0 c0 {2,S}\n8 H u0 p0 c0 {2,S}\n',
'multiplicity': 1,
'neg_freqs_trshed': [],
'number_of_rotors': 0,
'rotors_dict': {},
't1': None}],
}
self.assertEqual(restart_dict, expected_dict)
def test_add_hydrogen_for_bde(self):
"""Test the add_hydrogen_for_bde method"""
spc0 = ARCSpecies(label='spc0', smiles='CC', compute_thermo=False)
arc0 = ARC(
project='arc_test',
job_types=self.job_types1,
species=[spc0],
level_of_theory='ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)')
arc0.add_hydrogen_for_bde()
self.assertEqual(len(arc0.species), 1)
spc1 = ARCSpecies(label='spc1',
smiles='CC',
compute_thermo=False,
bdes=['all_h'])
arc1 = ARC(
project='arc_test',
job_types=self.job_types1,
species=[spc1],
level_of_theory='ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)')
arc1.add_hydrogen_for_bde()
self.assertEqual(len(arc1.species), 2)
self.assertIn('H', [spc.label for spc in arc1.species])
def test_unsorted_xyz_mol_from_xyz(self):
"""Test atom order conservation when xyz isn't sorted with heavy atoms first"""
n3h5 = ARCSpecies(label=str('N3H5'), xyz=self.xyz6, smiles=str('NNN'))
expected_adjlist = """1 N u0 p1 c0 {2,S} {4,S} {5,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {4,S}
4 N u0 p1 c0 {1,S} {3,S} {6,S}
5 H u0 p0 c0 {1,S}
6 N u0 p1 c0 {4,S} {7,S} {8,S}
7 H u0 p0 c0 {6,S}
8 H u0 p0 c0 {6,S}
"""
self.assertEqual(n3h5.mol.toAdjacencyList(), expected_adjlist)
self.assertEqual(n3h5.initial_xyz, self.xyz6)
def test_get_vector_length(self):
"""Test getting a vector's length"""
# unit vector
v1 = [1, 0, 0]
self.assertEqual(vectors.get_vector_length(v1), 1)
# a vector with 0 entries
v1 = [0, 0, 0]
self.assertEqual(vectors.get_vector_length(v1), 0)
# 10D vector
v1 = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
self.assertAlmostEqual(vectors.get_vector_length(v1), 19.6214169) # default: places=7
# 1D vector
v1 = [2]
self.assertEqual(vectors.get_vector_length(v1), 2)
# a vector with small entries
v1 = [0.0000001, 0.0000002, 0.0000003]
self.assertAlmostEqual(vectors.get_vector_length(v1), 0.000000374165739, places=15)
# a vector with large entries
v1 = [100, 200, 300]
self.assertAlmostEqual(vectors.get_vector_length(v1), 374.165738677394000) # default: places=7
# a real example borrowed from test_set_vector_length
label = 'CNCC'
pivot = 0
xyz = {'symbols': ('N', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'),
'isotopes': (14, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1),
'coords': ((0.7419854952964929, -0.18588322859265055, -0.8060295165375653),
(-0.38476668007897186, -0.8774643553523614, -0.1815530887172187),
(-1.4977348513273125, 0.05995564693605262, 0.26652181022311233),
(1.5633235727172392, 0.5360966415350092, 0.15477859056711452),
(-0.04458112063725271, -1.4936027355391557, 0.6589418973690523),
(-0.7986335015469359, -1.5715787743431335, -0.9219907626214912),
(-2.348455608682208, -0.5210498432021002, 0.6375394558854425),
(-1.8523669868240424, 0.6790455638159553, -0.5642494434208211),
(-1.170505453235269, 0.7210016856743618, 1.0746899133307615),
(2.4283037770451084, 0.9651590522064675, -0.36083882142892065),
(1.945994527876002, -0.1322800197070601, 0.9328203647772167),
(1.0178974719106297, 1.3595978302624294, 0.6250164549219148),
(0.39953935748654607, 0.4610025363062083, -1.5156468543485933))}
mol = ARCSpecies(label='CNCC', xyz=xyz).mol
v1 = vectors.get_lp_vector(label, mol, xyz, pivot)
# --> Returns a unit vector pointing from the pivotal (nitrogen) atom towards its lone electron pairs orbital.
self.assertAlmostEqual(vectors.get_vector_length(v1), 1)
def test_number_of_heavy_atoms_property(self):
"""Test that the number_of_heavy_atoms property functions correctly"""
self.assertEqual(self.spc1.number_of_heavy_atoms, 3)
self.assertEqual(self.spc2.number_of_heavy_atoms, 1)
self.assertEqual(self.spc3.number_of_heavy_atoms, 2)
self.assertEqual(self.spc4.number_of_heavy_atoms, 3)
self.assertEqual(self.spc5.number_of_heavy_atoms, 2)
self.assertEqual(self.spc6.number_of_heavy_atoms, 3)
self.assertEqual(self.spc7.number_of_heavy_atoms, 12)
self.assertEqual(self.spc8.number_of_heavy_atoms, 4)
self.assertEqual(self.spc9.number_of_heavy_atoms, 1)
xyz10 = """N 0.82269400 0.19834500 -0.33588000
C -0.57469800 -0.02442800 0.04618900
H -1.08412400 -0.56416500 -0.75831900
H -0.72300600 -0.58965300 0.98098100
H -1.07482500 0.94314300 0.15455500
H 1.31266200 -0.68161600 -0.46770200
H 1.32129900 0.71837500 0.38017700
"""
spc10 = ARCSpecies(label='spc10', xyz=xyz10)
self.assertEqual(spc10.number_of_heavy_atoms, 2)
def test_as_dict(self):
"""Test the as_dict() method of ARC"""
spc1 = ARCSpecies(
label='spc1',
smiles='CC',
compute_thermo=False,
)
arc0 = ARC(
project='arc_test',
job_types=self.job_types1,
species=[spc1],
level_of_theory='ccsd(t)-f12/cc-pvdz-f12//b3lyp/6-311+g(3df,2p)',
three_params=False,
)
arc0.freq_level.args['keyword']['general'] = 'scf=(NDump=30)'
restart_dict = arc0.as_dict()
long_thermo_description = restart_dict['species'][0][
'long_thermo_description']
self.assertIn('Bond corrections:', long_thermo_description)
self.assertIn("'C-C': 1", long_thermo_description)
self.assertIn("'C-H': 6", long_thermo_description)
expected_dict = {
'T_count':
50,
'T_max':
None,
'T_min':
None,
'allow_nonisomorphic_2d':
False,
'arkane_level_of_theory': {
'basis': 'cc-pvdz-f12',
'method': 'ccsd(t)-f12',
'method_type': 'wavefunction',
'software': 'molpro'
},
'calc_freq_factor':
True,
'compute_transport':
False,
'conformer_level': {
'basis': 'def2svp',
'compatible_ess': ['gaussian', 'terachem'],
'method': 'wb97xd',
'method_type': 'dft',
'software': 'gaussian'
},
'e_confs':
5.0,
'ess_settings': {
'gaussian': ['local', 'server2'],
'molpro': ['server2'],
'onedmin': ['server1'],
'orca': ['local'],
'qchem': ['server1'],
'terachem': ['server1']
},
'freq_level': {
'basis': '6-311+g(3df,2p)',
'method': 'b3lyp',
'method_type': 'dft',
'software': 'gaussian'
},
'freq_scale_factor':
0.967,
'irc_level': {
'basis': 'def2tzvp',
'compatible_ess': ['gaussian', 'terachem'],
'method': 'wb97xd',
'method_type': 'dft',
'software': 'gaussian'
},
'job_memory':
14,
'job_types': {
'bde': True,
'conformers': True,
'fine': False,
'freq': True,
'irc': True,
'onedmin': False,
'opt': True,
'orbitals': False,
'rotors': False,
'sp': True
},
'kinetics_adapter':
'Arkane',
'max_job_time':
120,
'n_confs':
10,
'opt_level': {
'basis': '6-311+g(3df,2p)',
'method': 'b3lyp',
'method_type': 'dft',
'software': 'gaussian'
},
'output': {},
'project':
'arc_test',
'reactions': [],
'running_jobs': {},
'sp_level': {
'basis': 'cc-pvdz-f12',
'method': 'ccsd(t)-f12',
'method_type': 'wavefunction',
'software': 'molpro'
},
'species': [{
'arkane_file':
None,
'bond_corrections': {
'C-C': 1,
'C-H': 6
},
'charge':
0,
'compute_thermo':
False,
'consider_all_diastereomers':
True,
'force_field':
'MMFF94s',
'is_ts':
False,
'label':
'spc1',
'long_thermo_description':
long_thermo_description,
'mol':
'1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}\n'
'2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}\n'
'3 H u0 p0 c0 {1,S}\n'
'4 H u0 p0 c0 {1,S}\n'
'5 H u0 p0 c0 {1,S}\n'
'6 H u0 p0 c0 {2,S}\n'
'7 H u0 p0 c0 {2,S}\n'
'8 H u0 p0 c0 {2,S}\n',
'multiplicity':
1,
'number_of_rotors':
0
}],
'thermo_adapter':
'Arkane',
'three_params':
False
}
# import pprint # left intentionally for debugging
# print(pprint.pprint(restart_dict))
self.assertEqual(restart_dict, expected_dict)
def get_species_list() -> list:
"""
Generates the standardized species list.
Returns:
list: The standardized species list initialized with xyz.
"""
c2h2_xyz = {
'symbols': ('C', 'C', 'H', 'H'),
'isotopes': (12, 12, 1, 1),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.203142),
(0.0, -0.0, 2.265747), (-0.0, -0.0, -1.062605))
}
ch4_xyz = {
'symbols': ('C', 'H', 'H', 'H', 'H'),
'isotopes': (12, 1, 1, 1, 1),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.08744517), (1.02525314, 0.0,
-0.36248173),
(-0.51262658, 0.88789525,
-0.36248173), (-0.51262658, -0.88789525, -0.36248173))
}
co2_xyz = {
'symbols': ('C', 'O', 'O'),
'isotopes': (12, 16, 16),
'coords':
((0.0, 0.0, 0.0), (0.0, 0.0, 1.1594846), (0.0, 0.0, -1.1594846))
}
co_xyz = {
'symbols': ('O', 'C'),
'isotopes': (16, 12),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.12960815))
}
f2_xyz = {
'symbols': ('F', 'F'),
'isotopes': (19, 19),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.3952041))
}
ch2o_xyz = {
'symbols': ('O', 'C', 'H', 'H'),
'isotopes': (16, 12, 1, 1),
'coords': ((0.0, 0.0, 0.674622), (0.0, 0.0, -0.529707),
(0.0, 0.935488, -1.109367), (0.0, -0.935488, -1.109367))
}
h2o_xyz = {
'symbols': ('O', 'H', 'H'),
'isotopes': (16, 1, 1),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.95691441), (0.92636305, 0.0,
-0.23986808))
}
h2_xyz = {
'symbols': ('H', 'H'),
'isotopes': (1, 1),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.74187646))
}
hcn_xyz = {
'symbols': ('C', 'N', 'H'),
'isotopes': (12, 14, 1),
'coords':
((0.0, 0.0, -0.500365), (0.0, 0.0, 0.65264), (0.0, 0.0, -1.566291))
}
hf_xyz = {
'symbols': ('F', 'H'),
'isotopes': (19, 1),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.91538107))
}
n2o_xyz = {
'symbols': ('N', 'N', 'O'),
'isotopes': (14, 14, 16),
'coords':
((0.0, 0.0, 0.0), (0.0, 0.0, 1.12056262), (0.0, 0.0, 2.30761092))
}
n2_xyz = {
'symbols': ('N', 'N'),
'isotopes': (14, 14),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.09710935))
}
nh3_xyz = {
'symbols': ('N', 'H', 'H', 'H'),
'isotopes': (14, 1, 1, 1),
'coords':
((0.0, 0.0, 0.11289), (0.0, 0.938024, -0.263409),
(0.812353, -0.469012, -0.263409), (-0.812353, -0.469012, -0.263409))
}
oh_xyz = {
'symbols': ('O', 'H'),
'isotopes': (16, 1),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.967))
}
cl2_xyz = {
'symbols': ('Cl', 'Cl'),
'isotopes': (35, 35),
'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.1))
}
c2h2 = ARCSpecies(label='C2H2', smiles='C#C', multiplicity=1, charge=0)
c2h2.initial_xyz = c2h2_xyz
ch4 = ARCSpecies(label='CH4', smiles='C', multiplicity=1, charge=0)
ch4.initial_xyz = ch4_xyz
co2 = ARCSpecies(label='CO2', smiles='O=C=O', multiplicity=1, charge=0)
co2.initial_xyz = co2_xyz
co = ARCSpecies(label='CO', smiles='[C-]#[O+]', multiplicity=1, charge=0)
co.initial_xyz = co_xyz
f2 = ARCSpecies(label='F2', smiles='[F][F]', multiplicity=1, charge=0)
f2.initial_xyz = f2_xyz
ch2o = ARCSpecies(label='CH2O', smiles='C=O', multiplicity=1, charge=0)
ch2o.initial_xyz = ch2o_xyz
h2o = ARCSpecies(label='H2O', smiles='O', multiplicity=1, charge=0)
h2o.initial_xyz = h2o_xyz
h2 = ARCSpecies(label='H2', smiles='[H][H]', multiplicity=1, charge=0)
h2.initial_xyz = h2_xyz
hcn = ARCSpecies(label='HCN', smiles='C#N', multiplicity=1, charge=0)
hcn.initial_xyz = hcn_xyz
hf = ARCSpecies(label='HF', smiles='F', multiplicity=1, charge=0)
hf.initial_xyz = hf_xyz
n2o = ARCSpecies(label='N2O',
smiles='[N-]=[N+]=O',
multiplicity=1,
charge=0)
n2o.initial_xyz = n2o_xyz
n2 = ARCSpecies(label='N2', smiles='N#N', multiplicity=1, charge=0)
n2.initial_xyz = n2_xyz
nh3 = ARCSpecies(label='NH3', smiles='N', multiplicity=1, charge=0)
nh3.initial_xyz = nh3_xyz
oh = ARCSpecies(label='OH', smiles='[OH]', multiplicity=2, charge=0)
oh.initial_xyz = oh_xyz
cl2 = ARCSpecies(label='Cl2', smiles='[Cl][Cl]', multiplicity=1, charge=0)
cl2.initial_xyz = cl2_xyz
species_list = [
c2h2, ch4, co2, co, f2, ch2o, h2o, h2, hcn, hf, n2o, n2, nh3, oh, cl2
]
return species_list
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.maxDiff = None
cls.xyz1 = """C 0.00000000 0.00000000 0.00000000
H 0.63003260 0.63003260 0.63003260
H -0.63003260 -0.63003260 0.63003260
H -0.63003260 0.63003260 -0.63003260
H 0.63003260 -0.63003260 -0.63003260"""
cls.xyz2 = """O 1.17464110 -0.15309781 0.00000000
N 0.06304988 0.35149648 0.00000000
C -1.12708952 -0.11333971 0.00000000
H -1.93800144 0.60171738 0.00000000
H -1.29769464 -1.18742971 0.00000000"""
cls.xyz3 = """S 1.02558264 -0.04344404 -0.07343859
O -0.25448248 1.10710477 0.18359696
N -1.30762173 0.15796567 -0.10489290
C -0.49011438 -1.03704380 0.15365747
H -0.64869950 -1.85796321 -0.54773423
H -0.60359153 -1.37304859 1.18613964
H -1.43009127 0.23517346 -1.11797908
"""
cls.xyz4 = """S -0.06618943 -0.12360663 -0.07631983
O -0.79539707 0.86755487 1.02675668
O -0.68919931 0.25421823 -1.34830853
N 0.01546439 -1.54297548 0.44580391
C 1.59721519 0.47861334 0.00711000
H 1.94428095 0.40772394 1.03719428
H 2.20318015 -0.14715186 -0.64755729
H 1.59252246 1.51178950 -0.33908352
H -0.87856890 -2.02453514 0.38494433
H -1.34135876 1.49608206 0.53295071"""
cls.xyz5 = """O 2.64631000 -0.59546000 0.29327900
O 2.64275300 2.05718500 -0.72942300
C 1.71639100 1.97990400 0.33793200
C -3.48200000 1.50082200 0.03091100
C -3.85550400 -1.05695100 -0.03598300
C 3.23017500 -1.88003900 0.34527100
C -2.91846400 0.11144600 0.02829400
C 0.76935400 0.80820200 0.23396500
C -1.51123800 -0.09830700 0.09199100
C 1.28495500 -0.50051800 0.22531700
C -0.59550400 0.98573400 0.16444900
C -0.94480400 -1.39242500 0.08331900
C 0.42608700 -1.59172200 0.14650400
H 2.24536500 1.93452800 1.29979800
H 1.14735500 2.91082400 0.31665700
H -3.24115200 2.03800800 0.95768700
H -3.08546100 2.10616100 -0.79369800
H -4.56858900 1.48636200 -0.06630800
H -4.89652000 -0.73067200 -0.04282300
H -3.69325500 -1.65970000 -0.93924100
H -3.72742500 -1.73294900 0.81894100
H 3.02442400 -2.44854700 -0.56812500
H 4.30341500 -1.72127600 0.43646000
H 2.87318600 -2.44236600 1.21464900
H -0.97434200 2.00182800 0.16800300
H -1.58581300 -2.26344700 0.02264400
H 0.81122400 -2.60336100 0.13267800
H 3.16280800 1.25020800 -0.70346900
"""
cls.xyz6 = """N -1.1997440839 -0.1610052059 0.0274738287
H -1.4016624407 -0.6229695533 -0.8487034080
H -0.0000018759 1.2861082773 0.5926077870
N 0.0000008520 0.5651072858 -0.1124621525
H -1.1294692206 -0.8709078271 0.7537518889
N 1.1997613019 -0.1609980472 0.0274604887
H 1.1294795781 -0.8708998550 0.7537444446
H 1.4015274689 -0.6230592706 -0.8487058662"""
nh_s_adj = str("""1 N u0 p2 c0 {2,S}
2 H u0 p0 c0 {1,S}""")
nh_s_xyz = str("""N 0.50949998 0.00000000 0.00000000
H -0.50949998 0.00000000 0.00000000""")
cls.spc1 = ARCSpecies(label=str('NH2(S)'),
adjlist=nh_s_adj,
xyz=nh_s_xyz,
multiplicity=1,
charge=0)
spc = Species().fromAdjacencyList(nh_s_adj)
cls.spc2 = ARCSpecies(label=str('NH2(S)'),
rmg_species=spc,
xyz=nh_s_xyz)
cls.spc3 = ARCSpecies(label=str('NCN(S)'),
smiles=str('[N]=C=[N]'),
multiplicity=1,
charge=0)
cls.spc4 = ARCSpecies(label=str('NCN(T)'),
smiles=str('[N]=C=[N]'),
multiplicity=3,
charge=0)
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.maxDiff = None
project = 'processor_test'
project_directory = os.path.join(arc_path, 'Projects', project)
ch4 = ARCSpecies(label='CH4', smiles='C')
nh3 = ARCSpecies(label='NH3', smiles='N')
h = ARCSpecies(label='H', smiles='[H]')
ch4_BDE_1_2_A = ARCSpecies(label='CH4_BDE_1_2_A', smiles='[CH3]')
ch4.e0, h.e0, ch4_BDE_1_2_A.e0 = 10, 25, 35
ch4.bdes = [(1, 2)]
species_dict = {
'CH4': ch4,
'NH3': nh3,
'H': h,
'CH4_BDE_1_2_A': ch4_BDE_1_2_A
}
output_dict = {
'CH4': {
'conformers': '',
'convergence': True,
'errors': '',
'info': '',
'isomorphism': '',
'job_types': {
'1d_rotors': True,
'composite': False,
'conformers': True,
'fine_grid': False,
'freq': True,
'lennard_jones': False,
'onedmin': False,
'opt': True,
'orbitals': False,
'bde': True,
'sp': True
},
'paths': {
'composite': '',
'freq': '',
'geo': '',
'sp': ''
},
'restart': '',
'warnings': ''
},
'NH3': {
'conformers': '',
'convergence': True,
'errors': '',
'info': '',
'isomorphism': '',
'job_types': {
'1d_rotors': True,
'composite': False,
'conformers': True,
'fine_grid': False,
'freq': True,
'lennard_jones': False,
'onedmin': False,
'opt': True,
'orbitals': False,
'bde': True,
'sp': True
},
'paths': {
'composite': '',
'freq': '',
'geo': '',
'sp': ''
},
'restart': '',
'warnings': ''
},
'H': {
'conformers': '',
'convergence': True,
'errors': '',
'info': '',
'isomorphism': '',
'job_types': {
'1d_rotors': True,
'composite': False,
'conformers': True,
'fine_grid': False,
'freq': False,
'lennard_jones': False,
'onedmin': False,
'opt': False,
'orbitals': False,
'bde': True,
'sp': True
},
'paths': {
'composite': '',
'freq': '',
'geo': '',
'sp': ''
},
'restart': '',
'warnings': ''
},
'CH4_BDE_1_2_A': {
'conformers': '',
'convergence': True,
'errors': '',
'info': '',
'isomorphism': '',
'job_types': {
'1d_rotors': True,
'composite': False,
'conformers': True,
'fine_grid': False,
'freq': True,
'lennard_jones': False,
'onedmin': False,
'opt': True,
'orbitals': False,
'bde': True,
'sp': True
},
'paths': {
'composite': '',
'freq': '',
'geo': '',
'sp': ''
},
'restart': '',
'warnings': ''
},
}
cls.processor0 = Processor(project=project,
project_directory=project_directory,
species_dict=species_dict,
rxn_list=list(),
output=output_dict,
use_bac=True,
model_chemistry='b3lyp/6-311+g(3df,2p)',
lib_long_desc='',
rmgdatabase=None)
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,
)
