def testRunJobs(self):
"""Test that runJobs() works properly."""
qm = QMCalculator(
software='mopac',
method='pm3',
fileStore=self.fileStore,
onlyCyclics=True,
maxRadicalNumber=0,
)
outputDirectory = os.path.join(qm.settings.fileStore, '..', '..')
qm.setDefaultOutputDirectory(outputDirectory)
spc1 = Species().fromSMILES('c1ccccc1')
spc2 = Species().fromSMILES('CC1C=CC=CC=1')
spcList = [spc1, spc2]
qm.runJobs(spcList, 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("\n")
NO_LICENCE = '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.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(), '..'))
fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles')
self.mop1 = QMCalculator(software='mopac',
method='pm3',
fileStore=fileStore)
self.mop2 = QMCalculator(
software='mopac',
method='pm6',
)
self.mop3 = QMCalculator(software='mopac',
method='pm7',
fileStore=fileStore)
self.mop4 = QMCalculator(software='mopac',
method='pm8',
fileStore=fileStore)
self.gauss1 = QMCalculator(
software='gaussian',
method='pm3',
)
self.gauss2 = QMCalculator(software='gaussian',
method='pm6',
fileStore=fileStore)
self.gauss3 = QMCalculator(software='gaussian',
method='pm7',
fileStore=fileStore)
self.molpro1 = QMCalculator(software='molpro',
method='mp2',
fileStore=fileStore)
self.qmmol1 = QMCalculator(fileStore=fileStore)
self.qmmol2 = QMCalculator(fileStore=fileStore)
def testSetDefaultOutputDirectory(self):
"""
Test that setDefaultOutputDirectory() 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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(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 testInitialize(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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(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 testGetThermoData(self):
"""
Test that getThermoData() fails when expected.
"""
outputDirectory = os.path.join(self.mop4.settings.fileStore, '..',
'..')
self.mop4.setDefaultOutputDirectory(outputDirectory)
self.gauss3.setDefaultOutputDirectory(outputDirectory)
self.molpro1.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
with self.assertRaises(Exception):
self.mop4.getThermoData(mol)
self.gauss3.getThermoData(mol)
self.molpro1.getThermoData(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 testGetThermoDataMopac(self):
"""
Test that Mocpac getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..',
'..')
self.mop1.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('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.getThermoData(mol)
thermo2 = self.mop2.getThermoData(mol)
thermo3 = self.mop3.getThermoData(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 testGetThermoDataGaussian(self):
"""
Test that Gaussian getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..',
'..')
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('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.getThermoData(mol)
thermo2 = self.gauss2.getThermoData(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
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("\n")
NO_LICENCE = '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.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(),'..'))
fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles')
self.mop1 = QMCalculator(software = 'mopac',
method = 'pm3',
fileStore = fileStore
)
self.mop2 = QMCalculator(software = 'mopac',
method = 'pm6',
)
self.mop3 = QMCalculator(software = 'mopac',
method = 'pm7',
fileStore = fileStore
)
self.mop4 = QMCalculator(software = 'mopac',
method = 'pm8',
fileStore = fileStore
)
self.gauss1 = QMCalculator(software = 'gaussian',
method = 'pm3',
)
self.gauss2 = QMCalculator(software = 'gaussian',
method = 'pm6',
fileStore = fileStore
)
self.gauss3 = QMCalculator(software = 'gaussian',
method = 'pm7',
fileStore = fileStore
)
self.molpro1 = QMCalculator(software = 'molpro',
method = 'mp2',
fileStore = fileStore
)
self.qmmol1 = QMCalculator(fileStore=fileStore)
self.qmmol2 = QMCalculator(fileStore=fileStore)
def testSetDefaultOutputDirectory(self):
"""
Test that setDefaultOutputDirectory() 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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(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 testInitialize(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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(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 testGetThermoData(self):
"""
Test that getThermoData() fails when expected.
"""
outputDirectory = os.path.join(self.mop4.settings.fileStore, '..', '..')
self.mop4.setDefaultOutputDirectory(outputDirectory)
self.gauss3.setDefaultOutputDirectory(outputDirectory)
self.molpro1.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
with self.assertRaises(Exception):
self.mop4.getThermoData(mol)
self.gauss3.getThermoData(mol)
self.molpro1.getThermoData(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 testGetThermoDataMopac(self):
"""
Test that Mocpac getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..', '..')
self.mop1.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('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.getThermoData(mol)
thermo2 = self.mop2.getThermoData(mol)
thermo3 = self.mop3.getThermoData(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 testGetThermoDataGaussian(self):
"""
Test that Gaussian getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..', '..')
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('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.getThermoData(mol)
thermo2 = self.gauss2.getThermoData(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
class TestQMCalculator(unittest.TestCase):
"""
Contains unit tests for the QMSettings class.
"""
mopacEnv = os.getenv('MOPAC_DIR', default="/opt/mopac")
if os.path.exists(os.path.join(mopacEnv , 'MOPAC2012.exe')):
mopExecutablePath = os.path.join(mopacEnv , 'MOPAC2012.exe')
elif os.path.exists(os.path.join(mopacEnv , 'MOPAC2009.exe')):
mopExecutablePath = os.path.join(mopacEnv , 'MOPAC2009.exe')
else:
mopExecutablePath = os.path.join(mopacEnv , '(MOPAC 2009 or 2012)')
gaussEnv = os.getenv('GAUSS_EXEDIR') or os.getenv('g09root') or os.getenv('g03root') or ""
# GAUSS_EXEDIR may be a list like "path1:path2:path3"
for possibleDir in gaussEnv.split(':'):
if os.path.exists(os.path.join(possibleDir , 'g09')):
gaussExecutablePath = os.path.join(possibleDir , 'g09')
break
elif os.path.exists(os.path.join(possibleDir , 'g03')):
gaussExecutablePath = os.path.join(possibleDir , 'g03')
break
else:
gaussExecutablePath = os.path.join(gaussEnv , '(g03 or g09)')
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(),'..'))
fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles')
self.mop1 = QMCalculator(software = 'mopac',
method = 'pm3',
fileStore = fileStore
)
self.mop2 = QMCalculator(software = 'mopac',
method = 'pm6',
)
self.mop3 = QMCalculator(software = 'mopac',
method = 'pm7',
fileStore = fileStore
)
self.mop4 = QMCalculator(software = 'mopac',
method = 'pm8',
fileStore = fileStore
)
self.gauss1 = QMCalculator(software = 'gaussian',
method = 'pm3',
)
self.gauss2 = QMCalculator(software = 'gaussian',
method = 'pm6',
fileStore = fileStore
)
self.gauss3 = QMCalculator(software = 'gaussian',
method = 'pm7',
fileStore = fileStore
)
self.molpro1 = QMCalculator(software = 'molpro',
method = 'mp2',
fileStore = fileStore
)
self.qmmol1 = QMCalculator(fileStore=fileStore)
self.qmmol2 = QMCalculator(fileStore=fileStore)
def testSetDefaultOutputDirectory(self):
"""
Test that setDefaultOutputDirectory() 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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(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 testInitialize(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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(outputDirectory)
try:
self.mop1.initialize()
self.mop2.initialize()
self.mop3.initialize()
self.gauss1.initialize()
self.gauss2.initialize()
except AssertionError:
self.fail("checkAllSet() raised unexpected AssertionError.")
except Exception:
self.fail("initialize() raised Exception. Output file paths not correctly set.")
def testGetThermoData(self):
"""
Test that getThermoData() fails when expected.
"""
outputDirectory = os.path.join(self.mop4.settings.fileStore, '..', '..')
self.mop4.setDefaultOutputDirectory(outputDirectory)
self.gauss3.setDefaultOutputDirectory(outputDirectory)
self.molpro1.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
with self.assertRaises(Exception):
self.mop4.getThermoData(mol)
self.gauss3.getThermoData(mol)
self.molpro1.getThermoData(mol)
@unittest.skipIf(os.path.exists(mopExecutablePath)==False, "If MOPAC installed, try checking your environment variables.")
def testGetThermoDataMopac(self):
"""
Test that getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..', '..')
self.mop1.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
try:
fileList = os.listdir(self.mop1.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.mop1.settings.fileStore, fileName))
except OSError:
pass
try:
fileList = os.listdir(self.mop2.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.mop2.settings.fileStore, fileName))
except OSError:
pass
try:
fileList = os.listdir(self.mop3.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.mop3.settings.fileStore, fileName))
except OSError:
pass
thermo1 = self.mop1.getThermoData(mol)
thermo2 = self.mop2.getThermoData(mol)
thermo3 = self.mop3.getThermoData(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(os.path.exists(gaussExecutablePath)==False, "If GAUSSIAN installed, try checking your environment variables.")
def testGetThermoDataGaussian(self):
"""
Test that getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..', '..')
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
try:
fileList = os.listdir(self.gauss1.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.gauss1.settings.fileStore, fileName))
except OSError:
pass
try:
fileList = os.listdir(self.gauss2.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.gauss2.settings.fileStore, fileName))
except OSError:
pass
thermo1 = self.gauss1.getThermoData(mol)
thermo2 = self.gauss2.getThermoData(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
class TestQMCalculator(unittest.TestCase):
"""
Contains unit tests for the QMSettings class.
"""
mopacEnv = os.getenv('MOPAC_DIR', default="/opt/mopac")
if os.path.exists(os.path.join(mopacEnv , 'MOPAC2012.exe')):
mopExecutablePath = os.path.join(mopacEnv , 'MOPAC2012.exe')
elif os.path.exists(os.path.join(mopacEnv , 'MOPAC2009.exe')):
mopExecutablePath = os.path.join(mopacEnv , 'MOPAC2009.exe')
else:
mopExecutablePath = os.path.join(mopacEnv , '(MOPAC 2009 or 2012)')
gaussEnv = os.getenv('GAUSS_EXEDIR') or os.getenv('g09root') or os.getenv('g03root') or ""
# GAUSS_EXEDIR may be a list like "path1:path2:path3"
for possibleDir in gaussEnv.split(':'):
if os.path.exists(os.path.join(possibleDir , 'g09')):
gaussExecutablePath = os.path.join(possibleDir , 'g09')
break
elif os.path.exists(os.path.join(possibleDir , 'g03')):
gaussExecutablePath = os.path.join(possibleDir , 'g03')
break
else:
gaussExecutablePath = os.path.join(gaussEnv , '(g03 or g09)')
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(),'..'))
fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles')
self.mop1 = QMCalculator(software = 'mopac',
method = 'pm3',
fileStore = fileStore
)
self.mop2 = QMCalculator(software = 'mopac',
method = 'pm6',
)
self.mop3 = QMCalculator(software = 'mopac',
method = 'pm7',
fileStore = fileStore
)
self.mop4 = QMCalculator(software = 'mopac',
method = 'pm8',
fileStore = fileStore
)
self.gauss1 = QMCalculator(software = 'gaussian',
method = 'pm3',
)
self.gauss2 = QMCalculator(software = 'gaussian',
method = 'pm6',
fileStore = fileStore
)
self.gauss3 = QMCalculator(software = 'gaussian',
method = 'pm7',
fileStore = fileStore
)
self.molpro1 = QMCalculator(software = 'molpro',
method = 'mp2',
fileStore = fileStore
)
self.qmmol1 = QMCalculator(fileStore=fileStore)
self.qmmol1.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'qm', 'bin')
self.qmmol2 = QMCalculator(fileStore=fileStore)
self.qmmol2.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'hexadiene', 'input.py')
def testSetDefaultOutputDirectory(self):
"""
Test that setDefaultOutputDirectory() 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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(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 testCheckPaths(self):
"""
Test that checkPaths() works correctly.
"""
with self.assertRaises(Exception):
self.qmmol1.checkPaths()
self.qmmol2.checkPaths()
def testInitialize(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.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(outputDirectory)
try:
self.mop1.initialize()
self.mop2.initialize()
self.mop3.initialize()
self.gauss1.initialize()
self.gauss2.initialize()
except AssertionError:
self.fail("checkAllSet() raised unexpected AssertionError.")
except Exception:
self.fail("initialize() raised Exception. Output file paths not correctly set.")
def testGetThermoData(self):
"""
Test that getThermoData() fails when expected.
"""
outputDirectory = os.path.join(self.mop4.settings.fileStore, '..', '..')
self.mop4.setDefaultOutputDirectory(outputDirectory)
self.gauss3.setDefaultOutputDirectory(outputDirectory)
self.molpro1.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
with self.assertRaises(Exception):
self.mop4.getThermoData(mol)
self.gauss3.getThermoData(mol)
self.molpro1.getThermoData(mol)
@unittest.skipIf(os.path.exists(mopExecutablePath)==False, "If MOPAC installed, try checking your environment variables.")
def testGetThermoDataMopac(self):
"""
Test that getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..', '..')
self.mop1.setDefaultOutputDirectory(outputDirectory)
self.mop2.setDefaultOutputDirectory(outputDirectory)
self.mop3.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
try:
fileList = os.listdir(self.mop1.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.mop1.settings.fileStore, fileName))
except OSError:
pass
try:
fileList = os.listdir(self.mop2.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.mop2.settings.fileStore, fileName))
except OSError:
pass
try:
fileList = os.listdir(self.mop3.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.mop3.settings.fileStore, fileName))
except OSError:
pass
thermo1 = self.mop1.getThermoData(mol)
thermo2 = self.mop2.getThermoData(mol)
thermo3 = self.mop3.getThermoData(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(os.path.exists(gaussExecutablePath)==False, "If GAUSSIAN installed, try checking your environment variables.")
def testGetThermoDataGaussian(self):
"""
Test that getThermoData() works correctly.
"""
outputDirectory = os.path.join(self.mop1.settings.fileStore, '..', '..')
self.gauss1.setDefaultOutputDirectory(outputDirectory)
self.gauss2.setDefaultOutputDirectory(outputDirectory)
mol = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
try:
fileList = os.listdir(self.gauss1.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.gauss1.settings.fileStore, fileName))
except OSError:
pass
try:
fileList = os.listdir(self.gauss2.settings.fileStore)
for fileName in fileList:
os.remove(os.path.join(self.gauss2.settings.fileStore, fileName))
except OSError:
pass
thermo1 = self.gauss1.getThermoData(mol)
thermo2 = self.gauss2.getThermoData(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