def test_run_jobs(self):
"""Test that run_jobs() works properly."""
qm = QMCalculator(software='mopac',
method='pm3',
fileStore=self.fileStore,
onlyCyclics=True,
maxRadicalNumber=0,
)
output_directory = os.path.join(qm.settings.fileStore, '..', '..')
qm.set_default_output_directory(output_directory)
spc1 = Species().from_smiles('c1ccccc1')
spc2 = Species().from_smiles('CC1C=CC=CC=1')
spc_list = [spc1, spc2]
qm.run_jobs(spc_list, procnum=1)
class TestQMCalculator(unittest.TestCase):
"""
Contains unit tests for the QMSettings class.
"""
mopExecutablePath = Mopac.executablePath
if not os.path.exists(mopExecutablePath):
NO_MOPAC = NO_LICENCE = True
else:
NO_MOPAC = False
process = subprocess.Popen(mopExecutablePath,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdut, stderr = process.communicate(b'\n')
NO_LICENCE = b'To install the MOPAC license' in stderr
gaussExecutablePath = Gaussian.executablePath
NO_GAUSSIAN = not os.path.exists(gaussExecutablePath)
def setUp(self):
"""
A function run before each unit test in this class.
"""
rmg_path = os.path.normpath(os.path.join(get_path(), '..'))
self.fileStore = os.path.join(rmg_path, 'testing', 'qm', 'QMfiles')
self.mop1 = QMCalculator(software='mopac',
method='pm3',
fileStore=self.fileStore)
self.mop2 = QMCalculator(
software='mopac',
method='pm6',
)
self.mop3 = QMCalculator(software='mopac',
method='pm7',
fileStore=self.fileStore)
self.mop4 = QMCalculator(software='mopac',
method='pm8',
fileStore=self.fileStore)
self.gauss1 = QMCalculator(
software='gaussian',
method='pm3',
)
self.gauss2 = QMCalculator(software='gaussian',
method='pm6',
fileStore=self.fileStore)
self.gauss3 = QMCalculator(software='gaussian',
method='pm7',
fileStore=self.fileStore)
self.molpro1 = QMCalculator(software='molpro',
method='mp2',
fileStore=self.fileStore)
self.qmmol1 = QMCalculator(fileStore=self.fileStore)
self.qmmol2 = QMCalculator(fileStore=self.fileStore)
def test_set_default_output_directory(self):
"""
Test that set_default_output_directory() works correctly.
"""
self.assertIsNotNone(self.mop1.settings.fileStore)
self.assertIsNotNone(self.mop3.settings.fileStore)
self.assertIsNotNone(self.gauss2.settings.fileStore)
self.assertIsNone(self.mop2.settings.fileStore)
self.assertIsNone(self.gauss1.settings.fileStore)
self.assertIsNone(self.mop1.settings.scratchDirectory)
self.assertIsNone(self.mop2.settings.scratchDirectory)
self.assertIsNone(self.mop3.settings.scratchDirectory)
self.assertIsNone(self.gauss1.settings.scratchDirectory)
self.assertIsNone(self.gauss2.settings.scratchDirectory)
# Now set the default directories for those not set
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..',
'..')
self.mop1.set_default_output_directory(outputDirectory)
self.mop2.set_default_output_directory(outputDirectory)
self.mop3.set_default_output_directory(outputDirectory)
self.gauss1.set_default_output_directory(outputDirectory)
self.gauss2.set_default_output_directory(outputDirectory)
self.assertIsNotNone(self.mop1.settings.fileStore)
self.assertIsNotNone(self.mop2.settings.fileStore)
self.assertIsNotNone(self.mop3.settings.fileStore)
self.assertIsNotNone(self.gauss1.settings.fileStore)
self.assertIsNotNone(self.gauss2.settings.fileStore)
self.assertIsNotNone(self.mop1.settings.scratchDirectory)
self.assertIsNotNone(self.mop2.settings.scratchDirectory)
self.assertIsNotNone(self.mop3.settings.scratchDirectory)
self.assertIsNotNone(self.gauss1.settings.scratchDirectory)
self.assertIsNotNone(self.gauss2.settings.scratchDirectory)
def test_initialize(self):
"""
Test that initialize() works correctly.
"""
# Now set the default directories for those not set
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..',
'..')
self.mop1.set_default_output_directory(outputDirectory)
self.mop2.set_default_output_directory(outputDirectory)
self.mop3.set_default_output_directory(outputDirectory)
self.gauss1.set_default_output_directory(outputDirectory)
self.gauss2.set_default_output_directory(outputDirectory)
try:
self.mop1.initialize()
self.mop2.initialize()
self.mop3.initialize()
self.gauss1.initialize()
self.gauss2.initialize()
except AssertionError:
self.fail("initialize() raised unexpected AssertionError.")
except Exception:
self.fail(
"initialize() raised Exception. Output file paths not correctly set."
)
def test_get_thermo_data(self):
"""
Test that get_thermo_data() fails when expected.
"""
output_directory = os.path.join(self.mop4.settings.fileStore, '..',
'..')
self.mop4.set_default_output_directory(output_directory)
self.gauss3.set_default_output_directory(output_directory)
self.molpro1.set_default_output_directory(output_directory)
mol = Molecule().from_smiles('C1=CC=C2C=CC=CC2=C1')
with self.assertRaises(Exception):
self.mop4.get_thermo_data(mol)
self.gauss3.get_thermo_data(mol)
self.molpro1.get_thermo_data(mol)
@unittest.skipIf(
NO_MOPAC,
"MOPAC not found. Try resetting your environment variables if you want to use it."
)
@unittest.skipIf(NO_LICENCE,
"MOPAC license not installed. Run mopac for instructions")
def test_get_thermo_data_mopac(self):
"""
Test that Mocpac get_thermo_data() works correctly.
"""
output_directory = os.path.join(self.mop1.settings.fileStore, '..',
'..')
self.mop1.set_default_output_directory(output_directory)
self.mop2.set_default_output_directory(output_directory)
self.mop3.set_default_output_directory(output_directory)
mol = Molecule().from_smiles('C1=CC=C2C=CC=CC2=C1')
for directory in (self.mop1.settings.fileStore,
self.mop1.settings.scratchDirectory):
shutil.rmtree(directory, ignore_errors=True)
for directory in (self.mop2.settings.fileStore,
self.mop2.settings.scratchDirectory):
shutil.rmtree(directory, ignore_errors=True)
for directory in (self.mop3.settings.fileStore,
self.mop3.settings.scratchDirectory):
shutil.rmtree(directory, ignore_errors=True)
thermo1 = self.mop1.get_thermo_data(mol)
thermo2 = self.mop2.get_thermo_data(mol)
thermo3 = self.mop3.get_thermo_data(mol)
self.assertTrue(thermo1.comment.startswith('QM MopacMolPM3'))
self.assertTrue(thermo2.comment.startswith('QM MopacMolPM6'))
self.assertTrue(thermo3.comment.startswith('QM MopacMolPM7'))
self.assertAlmostEqual(thermo1.H298.value_si, 169708.0608,
1) # to 1 decimal place
self.assertAlmostEqual(thermo1.S298.value_si, 334.5007584,
1) # to 1 decimal place
self.assertAlmostEqual(thermo2.H298.value_si, 167704.4270,
1) # to 1 decimal place
self.assertAlmostEqual(thermo2.S298.value_si, 338.0999241,
1) # to 1 decimal place
self.assertAlmostEqual(thermo3.H298.value_si, 166168.8571,
1) # to 1 decimal place
self.assertAlmostEqual(thermo3.S298.value_si, 336.3330406,
1) # to 1 decimal place
@unittest.skipIf(
NO_GAUSSIAN,
"Gaussian not found. Try resetting your environment variables if you want to use it."
)
def test_get_thermo_data_gaussian(self):
"""
Test that Gaussian get_thermo_data() works correctly.
"""
output_directory = os.path.join(self.mop1.settings.fileStore, '..',
'..')
self.gauss1.set_default_output_directory(output_directory)
self.gauss2.set_default_output_directory(output_directory)
mol = Molecule().from_smiles('C1=CC=C2C=CC=CC2=C1')
for directory in (self.gauss1.settings.fileStore,
self.gauss1.settings.scratchDirectory):
shutil.rmtree(directory, ignore_errors=True)
for directory in (self.gauss1.settings.fileStore,
self.gauss2.settings.scratchDirectory):
shutil.rmtree(directory, ignore_errors=True)
thermo1 = self.gauss1.get_thermo_data(mol)
thermo2 = self.gauss2.get_thermo_data(mol)
self.assertTrue(thermo1.comment.startswith('QM GaussianMolPM3'))
self.assertTrue(thermo2.comment.startswith('QM GaussianMolPM6'))
self.assertAlmostEqual(thermo1.H298.value_si, 169908.3376,
0) # to 1 decimal place
self.assertAlmostEqual(thermo1.S298.value_si, 335.5438748,
0) # to 1 decimal place
self.assertAlmostEqual(thermo2.H298.value_si, 169326.2504,
0) # to 1 decimal place
self.assertAlmostEqual(thermo2.S298.value_si, 338.2696063,
0) # to 1 decimal place
@unittest.skipIf(
NO_MOPAC,
"MOPAC not found. Try resetting your environment variables if you want to use it."
)
@unittest.skipIf(NO_LICENCE,
"MOPAC license not installed. Run mopac for instructions")
def test_run_jobs(self):
"""Test that run_jobs() works properly."""
qm = QMCalculator(
software='mopac',
method='pm3',
fileStore=self.fileStore,
onlyCyclics=True,
maxRadicalNumber=0,
)
output_directory = os.path.join(qm.settings.fileStore, '..', '..')
qm.set_default_output_directory(output_directory)
spc1 = Species().from_smiles('c1ccccc1')
spc2 = Species().from_smiles('CC1C=CC=CC=1')
spc_list = [spc1, spc2]
qm.run_jobs(spc_list, procnum=1)
