def testCorrectEntropy(self): """ Tests that correctEntropy effectively makes the isotopomer have the same thermo as isotopeless with the change in entropy corresponding to the symmetry difference. This example compares propane to a asymmetrically labeled propane. """ from rmgpy.thermo.nasa import NASA, NASAPolynomial from copy import deepcopy from rmgpy import constants propanei = Species().fromAdjacencyList( """ 1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} 2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S} 3 C u0 p0 c0 i13 {2,S} {9,S} {10,S} {11,S} 4 H u0 p0 c0 {1,S} 5 H u0 p0 c0 {1,S} 6 H u0 p0 c0 {1,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {2,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {3,S} 11 H u0 p0 c0 {3,S} """) propane = Species().fromAdjacencyList( """ 1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} 2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S} 3 C u0 p0 c0 {2,S} {9,S} {10,S} {11,S} 4 H u0 p0 c0 {1,S} 5 H u0 p0 c0 {1,S} 6 H u0 p0 c0 {1,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {2,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {3,S} 11 H u0 p0 c0 {3,S} """) # get thermo of propane original_thermo = NASA(polynomials=[NASAPolynomial( coeffs=[1.10564,0.0315339,-1.48274e-05,3.39621e-09,-2.97953e-13,-14351.9,18.775], Tmin=(100,'K'), Tmax=(3370.6,'K')), NASAPolynomial( coeffs=[-1.45473,0.0241202,-6.87667e-06,9.03634e-10,-4.48389e-14,-6688.59,43.0459], Tmin=(3370.6,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), comment="""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R)""") propane.thermo = deepcopy(original_thermo) propanei.thermo = deepcopy(original_thermo) correct_entropy(propanei,propane) self.assertAlmostEqual(propane.getEnthalpy(298),propanei.getEnthalpy(298)) self.assertAlmostEqual(propanei.getEntropy(298)-propane.getEntropy(298),constants.R * np.log(2))
def test_thermo(self): """Test that thermodata is loaded correctly from RMG's database""" spc = Species().fromSMILES(str('O=C=O')) spc.thermo = self.rmgdb.thermo.getThermoData(spc) self.assertAlmostEqual(spc.getEnthalpy(298), -393547.040000, 5) self.assertAlmostEqual(spc.getEntropy(298), 213.71872, 5) self.assertAlmostEqual(spc.getHeatCapacity(1000), 54.35016, 5)
def test_restart(self): """ Test restarting ARC through the ARC class in main.py via the input_dict argument of the API Rather than through ARC.py. Check that all files are in place and tst file content. """ restart_path = os.path.join(arc_path, 'arc', 'testing', 'restart(H,H2O2,N2H3,CH3CO2).yml') project = 'arc_project_for_testing_delete_after_usage2' project_directory = os.path.join(arc_path, 'Projects', project) arc1 = ARC(project=project, ess_settings=dict(), input_dict=restart_path, project_directory=project_directory) arc1.execute() with open(os.path.join(project_directory, 'output', 'thermo.info'), 'r') as f: thermo_sft_ccsdtf12_bac = False for line in f.readlines(): if 'thermo_DFT_CCSDTF12_BAC' in line: thermo_sft_ccsdtf12_bac = True break self.assertTrue(thermo_sft_ccsdtf12_bac) with open(os.path.join(project_directory, 'arc_project_for_testing_delete_after_usage2.info'), 'r') as f: sts, n2h3, oet, lot, ap = False, False, False, False, False for line in f.readlines(): if 'Considered the following species and TSs:' in line: sts = True elif 'Species N2H3' in line: n2h3 = True elif 'Overall time since project initiation:' in line: oet = True elif 'Levels of theory used:' in line: lot = True elif 'ARC project arc_project_for_testing_delete_after_usage2' in line: ap = True self.assertTrue(sts) self.assertTrue(n2h3) self.assertTrue(oet) self.assertTrue(lot) self.assertTrue(ap) with open(os.path.join(project_directory, 'arc.log'), 'r') as f: aei, ver, git, spc, rtm, ldb, therm, src, ter = False, False, False, False, False, False, False, False, False for line in f.readlines(): if 'ARC execution initiated on' in line: aei = True elif '# Version:' in line: ver = True elif 'The current git HEAD for ARC is:' in line: git = True elif 'Considering species: CH3CO2_rad' in line: spc = True elif 'All jobs for species N2H3 successfully converged. Run time: 1:16:03' in line: rtm = True elif 'Loading the RMG database...' in line: ldb = True elif 'Thermodynamics for H2O2:' in line: therm = True elif 'Sources of thermoproperties determined by RMG for the parity plots:' in line: src = True elif 'ARC execution terminated on' in line: ter = True self.assertTrue(aei) self.assertTrue(ver) self.assertTrue(git) self.assertTrue(spc) self.assertTrue(rtm) self.assertTrue(ldb) self.assertTrue(therm) self.assertTrue(src) self.assertTrue(ter) self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'thermo_parity_plots.pdf'))) with open(os.path.join(project_directory, 'output', 'Species', 'H2O2', 'species_dictionary.txt'), 'r') as f: lines = f.readlines() adj_list = str(''.join([line for line in lines if (line and 'H2O2' not in line)])) mol1 = Molecule().fromAdjacencyList(adj_list) self.assertEqual(mol1.toSMILES(), str('OO')) thermo_library_path = os.path.join(project_directory, 'output', 'RMG libraries', 'thermo', 'arc_project_for_testing_delete_after_usage2.py') new_thermo_library_path = os.path.join(settings['database.directory'], 'thermo', 'libraries', 'arc_project_for_testing_delete_after_usage2.py') # copy the generated library to RMG-database shutil.copyfile(thermo_library_path, new_thermo_library_path) db = RMGDatabase() db.load( path=settings['database.directory'], thermoLibraries=[str('arc_project_for_testing_delete_after_usage2')], transportLibraries=[], reactionLibraries=[], seedMechanisms=[], kineticsFamilies='none', kineticsDepositories=[], statmechLibraries=None, depository=False, solvation=False, testing=True, ) spc2 = Species().fromSMILES(str('CC([O])=O')) spc2.generate_resonance_structures() spc2.thermo = db.thermo.getThermoData(spc2) self.assertAlmostEqual(spc2.getEnthalpy(298), -178003.44650359568, 1) self.assertAlmostEqual(spc2.getEntropy(298), 283.5983103176096, 1) self.assertAlmostEqual(spc2.getHeatCapacity(1000), 118.99753808225603, 1) self.assertTrue('arc_project_for_testing_delete_after_usage2' in spc2.thermo.comment) # delete the generated library from RMG-database os.remove(new_thermo_library_path)
def testCorrectEntropy(self): """ Tests that correctEntropy effectively makes the isotopomer have the same thermo as isotopeless with the change in entropy corresponding to the symmetry difference. This example compares propane to a asymmetrically labeled propane. """ from rmgpy.thermo.nasa import NASA, NASAPolynomial from copy import deepcopy from rmgpy import constants propanei = Species().fromAdjacencyList(""" 1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} 2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S} 3 C u0 p0 c0 i13 {2,S} {9,S} {10,S} {11,S} 4 H u0 p0 c0 {1,S} 5 H u0 p0 c0 {1,S} 6 H u0 p0 c0 {1,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {2,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {3,S} 11 H u0 p0 c0 {3,S} """) propane = Species().fromAdjacencyList(""" 1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} 2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S} 3 C u0 p0 c0 {2,S} {9,S} {10,S} {11,S} 4 H u0 p0 c0 {1,S} 5 H u0 p0 c0 {1,S} 6 H u0 p0 c0 {1,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {2,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {3,S} 11 H u0 p0 c0 {3,S} """) # get thermo of propane original_thermo = NASA( polynomials=[ NASAPolynomial(coeffs=[ 1.10564, 0.0315339, -1.48274e-05, 3.39621e-09, -2.97953e-13, -14351.9, 18.775 ], Tmin=(100, 'K'), Tmax=(3370.6, 'K')), NASAPolynomial(coeffs=[ -1.45473, 0.0241202, -6.87667e-06, 9.03634e-10, -4.48389e-14, -6688.59, 43.0459 ], Tmin=(3370.6, 'K'), Tmax=(5000, 'K')) ], Tmin=(100, 'K'), Tmax=(5000, 'K'), comment= """Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R)""" ) propane.thermo = deepcopy(original_thermo) propanei.thermo = deepcopy(original_thermo) correct_entropy(propanei, propane) self.assertAlmostEqual(propane.getEnthalpy(298), propanei.getEnthalpy(298)) self.assertAlmostEqual( propanei.getEntropy(298) - propane.getEntropy(298), constants.R * np.log(2))