def setUp(self):
os.environ["PATH"] = os.path.expandvars(
"$AUTOTST/test/bin:") + os.environ["PATH"]
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.calculator = Gaussian(
directory=os.path.expandvars("$AUTOTST/test"))
self.job = Job(reaction=self.reaction,
calculator=self.calculator,
partition="test")
def setUp(self):
os.environ["PATH"] = os.path.expandvars(
"$AUTOTST/test/bin:") + os.environ["PATH"]
os.environ["TEST_STATUS"] = "None"
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.calculator = Gaussian(
directory=os.path.expandvars("$AUTOTST/test"))
self.job = Job(reaction=self.reaction,
calculator=self.calculator,
partition="test",
username="******",
exclude="test",
account="test")
self.job2 = Job(reaction=self.reaction,
calculator=self.calculator,
partition="test",
username="******",
exclude="test",
account=["test"])
def get_rotor_info(self, conformer, torsion):
"""
Formats and returns info about torsion as it should appear in an Arkane species.py
The following are needed for an Arkane input file:
- scanLog :: Gaussian output log of freq calculation on optimized geometry
- pivots :: torsion center: j,k of i,j,k,l (Note Arkane begins indexing with 1)
- top :: ID of all atoms in one top (Note Arkane begins indexing with 1)
Parameters:
- conformer (Conformer): autotst conformer object
- torsion (Torsion): autotst torsion object
Returns:
- info (str): a string containing all of the relevant information for a hindered rotor scan
"""
#torsion = conformer.torsions[torsion_index]
_, j, k, _ = torsion.atom_indices
# Adjusted since mol's IDs start from 0 while Arkane's start from 1
tor_center_adj = [j+1, k+1]
if isinstance(conformer, TS):
tor_log = os.path.join(
self.directory,
"ts",
conformer.reaction_label,
"rotors",
comformer.reaction_label + f"_36by10_{j}_{k}.log"
)
label = comformer.reaction_label + f"_36by10_{j}_{k}"
elif isinstance(conformer, Conformer):
tor_log = os.path.join(
self.directory,
"species",
conformer.smiles,
"rotors",
conformer.smiles + f'_36by10_{j}_{k}.log'
)
label = conformer.smiles + f'_36by10_{j}_{k}'
if not os.path.exists(tor_log):
logging.info(
f"Torsion log file does not exist for {torsion}")
return ""
try:
validated = all(Job(directory=self.directory).verify_rotor(conformer=conformer, label=label))
except AttributeError:
validated = False
if not validated:
logging.error(f'Rotor {label} could not be verified, using RRHO approximation instead.')
return ''
top_IDs = []
for num, tf in enumerate(torsion.mask):
if tf:
top_IDs.append(num)
# Adjusted to start from 1 instead of 0
top_IDs_adj = [ID+1 for ID in top_IDs]
info = f" HinderedRotor(scanLog=Log('{tor_log}'), pivots={tor_center_adj}, top={top_IDs_adj}, fit='fourier'),"
return info
class JobTest(unittest.TestCase):
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.calculator = Gaussian(
directory=os.path.expandvars("$AUTOTST/test"))
self.job = Job(reaction=self.reaction,
calculator=self.calculator,
partition="test")
os.environ["PATH"] = os.path.expandvars(
"$AUTOTST/test/bin:") + os.environ["PATH"]
def test_read_log(self):
path = os.path.expandvars("$AUTOTST/test/bin/log-files/CC_0.log")
atoms = self.job.read_log(path)
self.assertEqual(len(atoms), 8)
carbon_count = 0
hydrogen_count = 0
for atom in atoms:
if atom.symbol == "H":
hydrogen_count += 1
elif atom.symbol == "C":
carbon_count += 1
self.assertEqual(hydrogen_count, 6)
self.assertEqual(carbon_count, 2)
def test_write_input(self):
self.assert_(True)
def test_check_complete(self):
### I don't know how to create alaises in a python script
self.assertFalse(self.job.check_complete("test1"))
self.assertTrue(self.job.check_complete("test2"))
### For conformers
def test_submit_conformer(self):
if os.path.exists(os.path.expandvars("$AUTOTST/test/species")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/species"))
self.reaction.generate_reactants_and_products()
conformer = self.reaction.reactants[0].conformers.values()[0][0]
label = self.job.submit_conformer(conformer)
self.assertEquals(label, "{}_{}".format(conformer.smiles,
conformer.index))
def test_calculate_conformer(self):
if os.path.exists(os.path.expandvars("$AUTOTST/test/species")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/species"))
conformer = Conformer(smiles='CC', index=0)
result = self.job.calculate_conformer(conformer=conformer)
self.assertTrue(result)
conformer = Conformer(smiles='CC(Cl)(Cl)Cl', index=0)
result = self.job.calculate_conformer(conformer=conformer)
self.assertFalse(result)
def test_calculate_species(self):
if os.path.exists(os.path.expandvars("$AUTOTST/test/species")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/species"))
self.reaction.generate_reactants_and_products()
for species in self.reaction.reactants + self.reaction.products:
self.job.calculate_species(species)
for smiles in species.conformers.keys():
self.assertTrue(
os.path.exists(
os.path.join(
os.path.expandvars("$AUTOTST/test/species/"),
smiles, smiles + ".log")))
def test_submit_transitionstate(self):
if os.path.exists(os.path.expandvars("$AUTOTST/test/ts")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/ts"))
ts = self.reaction.ts["forward"][0]
ts.get_molecules()
for opt_type in ["shell", "center", "overall"]:
label = self.job.submit_transitionstate(ts, opt_type=opt_type)
if opt_type == "overall":
self.assertEqual(
label, "{}_{}_{}".format(ts.reaction_label, ts.direction,
ts.index))
else:
self.assertEqual(
label,
"{}_{}_{}_{}".format(ts.reaction_label, ts.direction,
opt_type, ts.index))
def test_calculate_transitionstate(self):
if os.path.exists(os.path.expandvars("$AUTOTST/test/ts")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/ts"))
ts = self.reaction.ts["forward"][0]
ts.get_molecules()
result = self.job.calculate_transitionstate(ts)
self.assertTrue(result)
def test_calculate_reaction(self):
del self.reaction.ts["reverse"]
result = self.job.calculate_reaction()
self.assertTrue(result)
def tearDown(self):
if os.path.exists(os.path.expandvars("$AUTOTST/test/species")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/species"))
if os.path.exists(os.path.expandvars("$AUTOTST/test/ts")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/ts"))
def test_setup2(self):
job = Job(directory=".")
self.assertEqual(job.directory, ".")
self.assertEqual(job.scratch, ".")
class JobTest(unittest.TestCase):
def setUp(self):
os.environ["PATH"] = os.path.expandvars(
"$AUTOTST/test/bin:") + os.environ["PATH"]
os.environ["TEST_STATUS"] = "None"
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.calculator = Gaussian(
directory=os.path.expandvars("$AUTOTST/test"))
self.job = Job(reaction=self.reaction,
calculator=self.calculator,
partition="test",
username="******",
exclude="test",
account="test")
self.job2 = Job(reaction=self.reaction,
calculator=self.calculator,
partition="test",
username="******",
exclude="test",
account=["test"])
def test_setup(self):
self.assertEqual(self.job.username, "test")
self.assertEqual(self.job.exclude, "test")
self.assertEqual(self.job.partition, "test")
self.assertEqual(self.job.account, "test")
self.assertEqual(self.job.label, self.reaction.label)
def test_setup2(self):
job = Job(directory=".")
self.assertEqual(job.directory, ".")
self.assertEqual(job.scratch, ".")
def test_read_log(self):
path = os.path.expandvars("$AUTOTST/test/bin/log-files/CC_0.log")
atoms = self.job.read_log(path)
self.assertEqual(len(atoms), 8)
carbon_count = 0
hydrogen_count = 0
for atom in atoms:
if atom.symbol == "H":
hydrogen_count += 1
elif atom.symbol == "C":
carbon_count += 1
self.assertEqual(hydrogen_count, 6)
self.assertEqual(carbon_count, 2)
def test_write_input(self):
self.assertTrue(True)
def test_check_complete(self):
### I don't know how to create alaises in a python script
os.environ["TEST_STATUS"] = "None"
self.assertFalse(self.job.check_complete("test1"))
self.assertTrue(self.job.check_complete("test2"))
def test_submit(self):
result = self.job.submit("echo testing")
self.assertTrue(result)
### For conformers
def test_submit_conformer(self):
self.reaction.generate_reactants_and_products()
conformer = list(self.reaction.reactants[0].conformers.values())[0][0]
label = self.job.submit_conformer(conformer)
self.assertEqual(label, f"{conformer.smiles}_{conformer.index}")
def test_submit_conformer2(self):
self.reaction.generate_reactants_and_products()
conformer = list(self.reaction.reactants[0].conformers.values())[0][0]
label = self.job2.submit_conformer(conformer)
self.assertEqual(label, f"{conformer.smiles}_{conformer.index}")
def test_calculate_conformer(self):
conformer = Conformer(smiles='CC', index=0)
result = self.job.calculate_conformer(conformer=conformer)
self.assertTrue(result)
def test_calculate_species(self):
self.reaction.generate_reactants_and_products()
for species in self.reaction.reactants + self.reaction.products:
self.job.calculate_species(species)
for smiles in species.conformers.keys():
self.assertTrue(
os.path.exists(
os.path.join(
os.path.expandvars("$AUTOTST/test/species/"),
smiles, smiles + ".log")))
def test_submit_transitionstate(self):
ts = self.reaction.ts["forward"][0]
ts.get_molecules()
for opt_type in ["shell", "center", "overall"]:
label = self.job.submit_transitionstate(ts, opt_type=opt_type)
if opt_type == "overall":
self.assertEqual(
label, f"{ts.reaction_label}_{ts.direction}_{ts.index}")
else:
self.assertEqual(
label,
f"{ts.reaction_label}_{ts.direction}_{opt_type}_{ts.index}"
)
def test_submit_transitionstate2(self):
ts = self.reaction.ts["forward"][0]
ts.get_molecules()
for opt_type in ["shell", "center", "overall"]:
label = self.job2.submit_transitionstate(ts, opt_type=opt_type)
if opt_type == "overall":
self.assertEqual(
label, f"{ts.reaction_label}_{ts.direction}_{ts.index}")
else:
self.assertEqual(
label,
f"{ts.reaction_label}_{ts.direction}_{opt_type}_{ts.index}"
)
def test_calculate_transitionstate(self):
ts = self.reaction.ts["forward"][0]
ts.get_molecules()
result = self.job.calculate_transitionstate(ts)
self.assertTrue(result)
def test_calculate_reaction(self):
del self.reaction.ts["reverse"]
result = self.job.calculate_reaction()
self.assertTrue(result)