class TestReaction(unittest.TestCase):
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_label(self):
self.assertEqual(self.reaction.label, "CC+[O]O_[CH2]C+OO")
self.assertEqual(self.reaction2.get_label(), "CC+[O]O_C[CH2]+OO")
def test_rmg_reaction(self):
test_reaction = RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")])
self.assertTrue(
test_reaction.is_isomorphic(self.reaction.get_rmg_reaction()))
self.assertTrue(
test_reaction.is_isomorphic(self.reaction2.get_rmg_reaction()))
def test_databases(self):
rmg_database, ts_databases = self.reaction.load_databases()
self.assertIsInstance(rmg_database, RMGDatabase)
self.assertIsInstance(ts_databases, dict)
self.assertIsInstance(ts_databases["H_Abstraction"], TransitionStates)
rmg_database, ts_databases = self.reaction2.load_databases()
self.assertIsInstance(rmg_database, RMGDatabase)
self.assertIsInstance(ts_databases, dict)
self.assertIsInstance(ts_databases["H_Abstraction"], TransitionStates)
def test_disance_data(self):
d12 = 1.38
d13 = 2.43
# 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,
self.reaction.distance_data.distances["d12"],
places=1)
self.assertAlmostEquals(d13,
self.reaction.distance_data.distances["d13"],
places=1)
self.assertAlmostEquals(d23,
self.reaction.distance_data.distances["d23"],
places=1)
self.assertAlmostEquals(d12,
self.reaction2.distance_data.distances["d12"],
places=1)
self.assertAlmostEquals(d13,
self.reaction2.distance_data.distances["d13"],
places=1)
self.assertAlmostEquals(d23,
self.reaction2.distance_data.distances["d23"],
places=1)
def test_generate_reactants_and_products(self):
reactants, products = self.reaction.generate_reactants_and_products()
self.assertIsInstance(reactants, list)
self.assertIsInstance(products, list)
self.assertEquals(len(reactants), 2)
self.assertAlmostEquals(len(products), 2)
reactants, products = self.reaction2.generate_reactants_and_products()
self.assertIsInstance(reactants, list)
self.assertIsInstance(products, list)
self.assertEquals(len(reactants), 2)
self.assertAlmostEquals(len(products), 2)
def test_labeled_reaction(self):
test_reaction = RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")])
labeled_reaction, reaction_family = self.reaction.get_labeled_reaction(
)
self.assertEquals(reaction_family.lower(), "h_abstraction")
self.assertTrue(test_reaction.is_isomorphic(labeled_reaction))
merged = labeled_reaction.reactants[0].merge(
labeled_reaction.reactants[1])
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_oxygen)
merged = labeled_reaction.products[0].merge(
labeled_reaction.products[1])
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_oxygen)
labeled_reaction, reaction_family = self.reaction2.get_labeled_reaction(
)
self.assertEquals(reaction_family.lower(), "h_abstraction")
self.assertTrue(test_reaction.is_isomorphic(labeled_reaction))
merged = labeled_reaction.reactants[0].merge(
labeled_reaction.reactants[1])
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_oxygen)
merged = labeled_reaction.products[0].merge(
labeled_reaction.products[1])
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_oxygen)
def test_rmg_complexes(self):
self.reaction.get_labeled_reaction()
self.reaction.get_rmg_complexes()
self.assertEquals(len(self.reaction.complexes), 2)
self.assertEquals(
len(self.reaction.complexes["forward"].get_all_labeled_atoms()), 3)
self.assertEquals(
len(self.reaction.complexes["reverse"].get_all_labeled_atoms()), 3)
self.reaction2.get_labeled_reaction()
self.reaction2.get_rmg_complexes()
self.assertEquals(len(self.reaction2.complexes), 2)
self.assertEquals(
len(self.reaction2.complexes["forward"].get_all_labeled_atoms()),
3)
self.assertEquals(
len(self.reaction2.complexes["reverse"].get_all_labeled_atoms()),
3)
def test_ts(self):
self.assertEquals(len(self.reaction.ts), 2)
self.assertEquals(len(self.reaction.ts["forward"]), 1)
self.assertEquals(len(self.reaction.ts["reverse"]), 1)
self.assertIsInstance(self.reaction.ts["forward"][0], TS)
self.assertIsInstance(self.reaction.ts["reverse"][0], TS)
self.assertEquals(len(self.reaction2.ts), 2)
self.assertEquals(len(self.reaction2.ts["forward"]), 1)
self.assertEquals(len(self.reaction2.ts["reverse"]), 1)
self.assertIsInstance(self.reaction2.ts["forward"][0], TS)
self.assertIsInstance(self.reaction2.ts["reverse"][0], TS)
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())
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)
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"))
class TestStatMech(unittest.TestCase):
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("$AUTOTST/test")
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label)):
os.makedirs(os.path.join(directory, "ts", self.reaction.label))
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
self.reaction.label + ".log")):
shutil.copy(
os.path.join(directory, "bin", "log-files",
self.reaction.label + "_forward_0.log"),
os.path.join(directory, "ts", self.reaction.label,
self.reaction.label + ".log"))
for sp in self.reaction.reactants + self.reaction.products:
for smiles in sp.conformers.keys():
if not os.path.exists(
os.path.join(directory, "species", smiles)):
os.makedirs(os.path.join(directory, "species", smiles))
if not os.path.exists(
os.path.join(directory, "species", smiles,
smiles + ".log")):
shutil.copy(
os.path.join(directory, "bin", "log-files",
smiles + "_0.log"),
os.path.join(directory, "species", smiles,
smiles + ".log"))
self.statmech = StatMech(reaction=self.reaction, directory=directory)
def tearDown(self):
directory = os.path.expandvars("$AUTOTST/test")
if os.path.exists(os.path.join(directory, "ts")):
shutil.rmtree(os.path.join(directory, "ts"))
if os.path.exists(os.path.join(directory, "species")):
shutil.rmtree(os.path.join(directory, "species"))
for head, _, files in os.walk(os.path.expandvars("$AUTOTST")):
for fi in files:
if fi.endswith(".symm"):
os.remove(os.path.join(head, fi))
def test_get_atoms(self):
ts = self.reaction.ts["forward"][0]
atom_dict = self.statmech.get_atoms(ts)
self.assertEqual(atom_dict["H"], 7)
self.assertEqual(atom_dict["C"], 2)
self.assertEqual(atom_dict["O"], 2)
#def test_get_bonds(self):
### For somereason, this test doesn't work on travis...
# ts = self.reaction.ts["forward"][0]
# bond_dict = self.statmech.get_bonds(ts)
# self.assertEqual(bond_dict["O-O"], 1)
# self.assertEqual(bond_dict["O-H"], 1)
# self.assertEqual(bond_dict["C-C"], 1)
# self.assertEqual(bond_dict["C-H"], 6)
def test_write_conformer_file(self):
species = self.reaction.reactants[0]
conformer = species.conformers.values()[0][0]
self.assertTrue(self.statmech.write_conformer_file(conformer))
self.assertTrue(
os.path.exists(
os.path.join(self.statmech.directory, "species",
conformer.smiles, conformer.smiles + ".py")))
# Running it again to see if it recognizes that a .py file was already written
self.assertTrue(self.statmech.write_conformer_file(conformer))
def test_write_species_file(self):
species = self.reaction.reactants[0]
self.statmech.write_species_files(species)
for smiles in species.conformers.keys():
self.assertTrue(
os.path.exists(
os.path.join(self.statmech.directory, "species", smiles,
smiles + ".py")))
def test_write_ts_input(self):
ts = self.reaction.ts["forward"][0]
self.assertTrue(self.statmech.write_ts_input(ts))
self.assertTrue(
os.path.exists(
os.path.join(self.statmech.directory, "ts",
self.reaction.label,
self.reaction.label + ".py")))
self.assertTrue(self.statmech.write_ts_input(ts))
def test_write_kinetics_input(self):
self.statmech.write_kinetics_input()
self.assertTrue(
os.path.exists(
os.path.join(self.statmech.directory, "ts",
self.reaction.label,
self.reaction.label + ".kinetics.py")))
def test_write_files(self):
self.statmech.write_files()
for mol in self.reaction.reactants + self.reaction.products:
for confs in mol.conformers.values():
conf = confs[0]
self.assertTrue(
os.path.exists(
os.path.join(self.statmech.directory, "species",
conf.smiles, conf.smiles + ".py")))
self.assertTrue(
os.path.exists(
os.path.join(self.statmech.directory, "ts",
self.reaction.label,
self.reaction.label + ".py")))
self.assertTrue(
os.path.exists(
os.path.join(self.statmech.directory, "ts",
self.reaction.label,
self.reaction.label + ".kinetics.py")))
def test_run(self):
self.statmech.write_files()
self.statmech.run()
self.assertIsInstance(self.statmech.kinetics_job.reaction, RMGReaction)
self.assertIsInstance(self.statmech.kinetics_job.reaction.kinetics,
Arrhenius)
def test_set_results(self):
self.test_run()
self.statmech.set_results()
self.assertTrue(
self.reaction.rmg_reaction.isIsomorphic(
self.statmech.kinetics_job.reaction))
self.assertTrue(
self.statmech.reaction.rmg_reaction.isIsomorphic(
self.statmech.kinetics_job.reaction))