def test_helium(self):
"""
adjlist: Test that the adjlist reading and writing works with Helium.
"""
smiles = '[He]'
inchi = 'InChI=1S/He'
adjlist = '1 He u0 p1 c0'
adjlist_old = '1 He 0'
adjlist_intermediate = '1 He 0 1'
mol_smiles = Molecule().from_smiles(smiles)
mol_inchi = Molecule().from_inchi(inchi)
mol = Molecule().from_adjacency_list(adjlist)
mol_old = Molecule().from_adjacency_list(adjlist_old)
mol_intermediate = Molecule().from_adjacency_list(adjlist_intermediate)
# Isomorphic check
self.assertTrue(mol_smiles.is_isomorphic(mol))
self.assertTrue(mol_smiles.is_isomorphic(mol_inchi))
self.assertTrue(mol_smiles.is_isomorphic(mol_old))
self.assertTrue(mol_smiles.is_isomorphic(mol_intermediate))
# Adjlist check
self.assertEqual(mol_smiles.to_adjacency_list().strip(), adjlist)
self.assertEqual(mol_inchi.to_adjacency_list().strip(), adjlist)
self.assertEqual(mol.to_adjacency_list().strip(), adjlist)
self.assertEqual(mol_old.to_adjacency_list().strip(), adjlist)
self.assertEqual(mol_intermediate.to_adjacency_list().strip(), adjlist)
self.assertEqual(mol.to_smiles(), smiles)
self.assertEqual(mol.to_inchi(), 'InChI=1S/He')
def test_restart_thermo(self):
"""
Test restarting ARC through the ARC class in main.py via the input_dict argument of the API
Rather than through ARC.py. Check that all files are in place and the log file content.
"""
restart_path = os.path.join(ARC_PATH, 'arc', 'testing', 'restart',
'1_restart_thermo', 'restart.yml')
input_dict = read_yaml_file(path=restart_path)
project = 'arc_project_for_testing_delete_after_usage_restart_thermo'
project_directory = os.path.join(ARC_PATH, 'Projects', project)
input_dict['project'], input_dict[
'project_directory'] = project, project_directory
arc1 = ARC(**input_dict)
arc1.execute()
self.assertEqual(arc1.freq_scale_factor, 0.988)
self.assertTrue(
os.path.isfile(
os.path.join(project_directory, 'output', 'thermo.info')))
with open(os.path.join(project_directory, 'output', 'thermo.info'),
'r') as f:
thermo_dft_ccsdtf12_bac = False
for line in f.readlines():
if 'thermo_DFT_CCSDTF12_BAC' in line:
thermo_dft_ccsdtf12_bac = True
break
self.assertTrue(thermo_dft_ccsdtf12_bac)
with open(
os.path.join(
project_directory,
'arc_project_for_testing_delete_after_usage_restart_thermo.info'
), 'r') as f:
sts, n2h3, oet, lot, ap = False, False, False, False, False
for line in f.readlines():
if 'Considered the following species and TSs:' in line:
sts = True
elif 'Species N2H3' in line:
n2h3 = True
elif 'Overall time since project initiation:' in line:
oet = True
elif 'Levels of theory used:' in line:
lot = True
elif 'ARC project arc_project_for_testing_delete_after_usage_restart_thermo' in line:
ap = True
self.assertTrue(sts)
self.assertTrue(n2h3)
self.assertTrue(oet)
self.assertTrue(lot)
self.assertTrue(ap)
with open(os.path.join(project_directory, 'arc.log'), 'r') as f:
aei, ver, git, spc, rtm, ldb, therm, src, ter =\
False, False, False, False, False, False, False, False, False
for line in f.readlines():
if 'ARC execution initiated on' in line:
aei = True
elif '# Version:' in line:
ver = True
elif 'The current git HEAD for ARC is:' in line:
git = True
elif 'Considering species: CH3CO2_rad' in line:
spc = True
elif 'All jobs for species N2H3 successfully converged. Run time' in line:
rtm = True
elif 'Loading the RMG database...' in line:
ldb = True
elif 'Thermodynamics for H2O2' in line:
therm = True
elif 'Sources of thermoproperties determined by RMG for the parity plots:' in line:
src = True
elif 'ARC execution terminated on' in line:
ter = True
self.assertTrue(aei)
self.assertTrue(ver)
self.assertTrue(git)
self.assertTrue(spc)
self.assertTrue(rtm)
self.assertTrue(ldb)
self.assertTrue(therm)
self.assertTrue(src)
self.assertTrue(ter)
self.assertTrue(
os.path.isfile(
os.path.join(project_directory, 'output',
'thermo_parity_plots.pdf')))
status = read_yaml_file(
os.path.join(project_directory, 'output', 'status.yml'))
self.assertEqual(
status['CH3CO2_rad']['isomorphism'],
'opt passed isomorphism check; '
'Conformers optimized and compared at b3lyp/6-31g(d,p) empiricaldispersion=gd3bj; '
)
self.assertTrue(status['CH3CO2_rad']['job_types']['sp'])
with open(
os.path.join(project_directory, 'output', 'Species', 'H2O2',
'arkane', 'species_dictionary.txt'), 'r') as f:
lines = f.readlines()
adj_list = ''
for line in lines:
if 'H2O2' not in line:
adj_list += line
if line == '\n':
break
mol1 = Molecule().from_adjacency_list(adj_list)
self.assertEqual(mol1.to_smiles(), 'OO')
thermo_library_path = os.path.join(
project_directory, 'output', 'RMG libraries', 'thermo',
'arc_project_for_testing_delete_after_usage_restart_thermo.py')
new_thermo_library_path = os.path.join(
rmg_settings['database.directory'], 'thermo', 'libraries',
'arc_project_for_testing_delete_after_usage_restart_thermo.py')
# copy the generated library to RMG-database
shutil.copyfile(thermo_library_path, new_thermo_library_path)
db = RMGDatabase()
db.load(
path=rmg_settings['database.directory'],
thermo_libraries=[
'arc_project_for_testing_delete_after_usage_restart_thermo'
],
transport_libraries=[],
reaction_libraries=[],
seed_mechanisms=[],
kinetics_families='none',
kinetics_depositories=[],
statmech_libraries=None,
depository=False,
solvation=False,
testing=True,
)
spc2 = Species(smiles='CC([O])=O')
spc2.generate_resonance_structures()
spc2.thermo = db.thermo.get_thermo_data(spc2)
self.assertAlmostEqual(spc2.get_enthalpy(298), -212439.26998495663, 1)
self.assertAlmostEqual(spc2.get_entropy(298), 283.3972662956835, 1)
self.assertAlmostEqual(spc2.get_heat_capacity(1000), 118.751379824224,
1)
self.assertTrue(
'arc_project_for_testing_delete_after_usage_restart_thermo' in
spc2.thermo.comment)
# delete the generated library from RMG-database
os.remove(new_thermo_library_path)
def test_aromatics(self):
"""Test that different aromatics representations returns different SMILES."""
mol1 = Molecule().from_adjacency_list("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,D} {5,S} {11,S}
3 C u0 p0 c0 {2,D} {4,S} {12,S}
4 C u0 p0 c0 {3,S} {6,D} {13,S}
5 C u0 p0 c0 {2,S} {7,D} {10,S}
6 C u0 p0 c0 {1,S} {4,D} {7,S}
7 C u0 p0 c0 {5,D} {6,S} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
mol2 = Molecule().from_adjacency_list("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,S} {5,D} {11,S}
3 C u0 p0 c0 {2,S} {4,D} {12,S}
4 C u0 p0 c0 {3,D} {6,S} {13,S}
5 C u0 p0 c0 {2,D} {7,S} {10,S}
6 C u0 p0 c0 {1,S} {4,S} {7,D}
7 C u0 p0 c0 {5,S} {6,D} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
mol3 = Molecule().from_adjacency_list("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,B} {5,B} {11,S}
3 C u0 p0 c0 {2,B} {4,B} {12,S}
4 C u0 p0 c0 {3,B} {6,B} {13,S}
5 C u0 p0 c0 {2,B} {7,B} {10,S}
6 C u0 p0 c0 {1,S} {4,B} {7,B}
7 C u0 p0 c0 {5,B} {6,B} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
smiles1 = mol1.to_smiles()
smiles2 = mol2.to_smiles()
smiles3 = mol3.to_smiles()
self.assertNotEqual(smiles1, smiles2)
self.assertNotEqual(smiles2, smiles3)
self.assertNotEqual(smiles1, smiles3)
def test_empty_molecule(self):
"""Test that we can safely return a blank identifier for an empty molecule."""
mol = Molecule()
self.assertEqual(mol.to_smiles(), '')
self.assertEqual(mol.to_inchi(), '')
def compare(self, adjlist, smiles):
mol = Molecule().from_adjacency_list(adjlist)
self.assertEquals(smiles, mol.to_smiles())
