def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction2 = Reaction(rmg_reaction=RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")]))
def test_reaction_families(self):
# R_Addition_MultipleBond
reaction = Reaction("C#C+[OH]_[CH]=CO")
_, family = reaction.get_labeled_reaction()
self.assertEqual(family.lower(), "R_Addition_MultipleBond".lower())
# intra_H_migration
reaction = Reaction("C[CH]O_CC[O]")
_, family = reaction.get_labeled_reaction()
self.assertEqual(family.lower(), "intra_H_migration".lower())
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction2 = Reaction(rmg_reaction=RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")]))
self.ts = self.reaction.ts["forward"][0]
self.ts2 = self.reaction.ts["forward"][0]
self.ts.get_molecules()
self.ts2.get_molecules()
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.io = InputOutput(
reaction=self.reaction,
directory=os.path.expandvars("$AUTOTST/test/")
)
try:
os.makedirs(os.path.join(
os.path.expandvars("$AUTOTST/test/"),
"ts",
self.reaction.label
))
except OSError:
try:
shutil.copy(
os.path.join(
os.path.expandvars("$AUTOTST/test/bin/log-files"),
self.reaction.label + "_forward_0.log"
),
os.path.join(
os.path.expandvars("$AUTOTST/test/"),
"ts",
self.reaction.label,
self.reaction.label + ".log"
)
)
except:
pass
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction.get_labeled_reaction()
self.reaction.generate_reactants_and_products()
directory = os.path.expandvars("$AUTOTST/test")
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label)):
os.makedirs(os.path.join(directory, "ts", self.reaction.label))
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
self.reaction.label + ".log")):
shutil.copy(
os.path.join(directory, "bin", "log-files",
self.reaction.label + "_forward_0.log"),
os.path.join(directory, "ts", self.reaction.label,
self.reaction.label + ".log"))
for sp in self.reaction.reactants + self.reaction.products:
for smiles in sp.conformers.keys():
if not os.path.exists(
os.path.join(directory, "species", smiles)):
os.makedirs(os.path.join(directory, "species", smiles))
if not os.path.exists(
os.path.join(directory, "species", smiles,
smiles + ".log")):
shutil.copy(
os.path.join(directory, "bin", "log-files",
smiles + "_0.log"),
os.path.join(directory, "species", smiles,
smiles + ".log"))
self.statmech = StatMech(reaction=self.reaction, directory=directory)
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction.get_labeled_reaction()
self.ts = self.reaction.ts["forward"][0]
self.ts.get_molecules()
directory = os.path.expandvars("$AUTOTST/test")
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
"conformers")):
os.makedirs(
os.path.join(directory, "ts", self.reaction.label,
"conformers"))
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
self.reaction.label + ".log")):
shutil.copy(
os.path.join(directory, "bin", "log-files",
self.reaction.label + "_forward_0.log"),
os.path.join(directory, "ts", self.reaction.label,
"conformers",
self.reaction.label + "_forward_0.log"))
self.directory = directory
self.vibrational_analysis = VibrationalAnalysis(
transitionstate=self.ts, directory=self.directory)
def setUp(self):
os.environ["PATH"] = os.path.expandvars(
"$AUTOTST/test/bin:") + os.environ["PATH"]
rxn = Reaction(label='C+[O]O_[CH3]+OO')
ts = rxn.ts["forward"][0]
ts.get_molecules()
self.gaussian = Gaussian(conformer=ts)
def setUp(self):
os.environ["PATH"] = os.path.expandvars(
"$AUTOTST/test/bin:") + os.environ["PATH"]
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.calculator = Gaussian(
directory=os.path.expandvars("$AUTOTST/test"))
self.job = Job(reaction=self.reaction,
calculator=self.calculator,
partition="test")
def test_symmetry_number(self):
self.assertEquals(self.ts.symmetry_number, 1)
self.assertEquals(self.ts2.symmetry_number, 1)
reactions_to_test = {
"[CH3]+[OH]_C+[O]": 3,
# TODO add other reactions here
}
for reaction_string, expected_symmetry in reactions_to_test.items():
rxn = Reaction(reaction_string)
rxn.get_labeled_reaction()
ts = rxn.ts["forward"][0]
self.assertEquals(ts.symmetry_number, expected_symmetry)
def test_estimate_distances(self):
reaction = Reaction("CC+[O]O_[CH2]C+OO")
labeled_reaction, _ = reaction.get_labeled_reaction()
distance_data = self.ts_database.estimate_distances(labeled_reaction)
d12 = 1.38
d13 = 2.53
# d13 in reactionTest is smaller than the distance in baseTest.py because
# d13 is edited to be smaller in reaction.py. The value returned from the database
# is ~2.53 but is reduced to ~2.43 when called from the reaction object itself
d23 = 1.16
self.assertAlmostEquals(d12, distance_data.distances["d12"], places=1)
self.assertAlmostEquals(d13, distance_data.distances["d13"], places=1)
self.assertAlmostEquals(d23, distance_data.distances["d23"], places=1)
def setUp(self):
os.environ["PATH"] = os.path.expandvars(
"$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 setUp(self):
rxn = Reaction(label='C+[O]O_[CH3]+OO')
ts = rxn.ts["forward"][0]
ts.get_molecules()
self.gaussian = Gaussian(conformer=ts)
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.family = "H_Abstraction"
self.method = "m062x/cc-pVTZ"
self.short_description = "test case"