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_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_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)