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