def testThermoRestart(self):
"""
Restart tests for the :class:`rmg.thermo.ThermoGAData`,
:class:`rmg.thermo.ThermoWilhoitData`, and
:class:`rmg.thermo.ThermoNASAData` classes.
"""
import rmg.thermo as thermo
# Create
thermoGAData0 = thermo.ThermoGAData(H298=-3.08, S298=64.27,
Cp=[12.28, 14.34, 16.30, 18.05, 20.92, 23.08, 26.39], comment='acetyl')
thermoWilhoitData0 = thermo.convertGAtoWilhoit(thermoGAData0, 6, 1, False)
thermoNASAData0 = thermo.convertWilhoitToNASA(thermoWilhoitData0)
# Pickle
f = open('test.pkl', 'wb');
cPickle.dump(thermoGAData0, f)
cPickle.dump(thermoWilhoitData0, f)
cPickle.dump(thermoNASAData0, f)
f.close()
# Unpickle
f = open('test.pkl', 'rb')
thermoGAData = cPickle.load(f)
thermoWilhoitData = cPickle.load(f)
thermoNASAData = cPickle.load(f)
f.close()
# Compare
self.assertTrue(thermoGAData0.equals(thermoGAData))
self.assertTrue(thermoWilhoitData0.equals(thermoWilhoitData))
self.assertTrue(thermoNASAData0.equals(thermoNASAData))
def testOxygenFromGA(self): """Check conversion of GA values for molecular oxygen to NASA form """ oxygen = structure.Structure(SMILES='O=O') oxygen.updateAtomTypes() GAthermoData = species.getThermoData(oxygen,thermoClass=thermo.ThermoGAData) WilhoitData = thermo.convertGAtoWilhoit(GAthermoData, atoms=2, rotors=0, linear=True) print WilhoitData NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData)
def testEnthalpy(self): """Check the NASA H matches the GA H for propane. Uses Propane as a test-case. atoms=11, rotors=2, linear=False """ propane = structure.Structure(SMILES='CCC') propane.updateAtomTypes() GAthermoData = species.getThermoData(propane,thermoClass=thermo.ThermoGAData) WilhoitData = thermo.convertGAtoWilhoit(GAthermoData, atoms=11, rotors=2, linear=False) NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData) Tlist = thermo.ThermoGAData.CpTlist # just check at defined data points for T in Tlist: ga = GAthermoData.getEnthalpy(T) nasa = NASAthermoData.getEnthalpy(T) err = abs(ga-nasa) limit = 2000.0 # J/mol # the wilhoit should be more accurate then trapezoid integration of GA, so wouldn't want them to be exactly the same self.assertTrue(err<limit,"GA (%.1f) and NASA (%.1f) differ by more than %s J/mol at %dK"%(ga,nasa,limit,T))
def testEntropy(self): """Check the NASA S matches the GA S for propane. Uses Propane as a test-case. atoms=11, rotors=2, linear=False """ propane = structure.Structure(SMILES='CCC') propane.updateAtomTypes() GAthermoData = species.getThermoData(propane,thermoClass=thermo.ThermoGAData) WilhoitData = thermo.convertGAtoWilhoit(GAthermoData, atoms=11, rotors=2, linear=False) NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData) Tlist = thermo.ThermoGAData.CpTlist # just check at defined data points for T in Tlist: ga = GAthermoData.getEntropy(T) nasa = NASAthermoData.getEntropy(T) err = abs(ga-nasa) limit = 4.0 # J/mol/K self.assertTrue(err<limit,"GA (%.1f) and NASA (%.1f) differ by more than %s J/mol/K at %dK"%(ga,nasa,limit,T))
def testHeatCapacity(self): """Check the NASA Cp matches the GA Cp for propane. Uses Propane as a test-case. atoms=11, rotors=2, linear=False """ hexadiene = species.Species(SMILES='CCC') hexadiene.getResonanceIsomers() GAthermoData = hexadiene.getThermoData() WilhoitData = thermo.convertGAtoWilhoit(GAthermoData, atoms=11, rotors=2, linear=False) NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData) Tlist = thermo.ThermoGAData.CpTlist # just check at defined data points for T in Tlist: ga = GAthermoData.getHeatCapacity(T) nasa = NASAthermoData.getHeatCapacity(T) err = abs(ga-nasa) limit = 10.0 # J/mol/K self.assertTrue(err<limit,"GA (%.1f) and NASA (%.1f) differ by more than %s J/mol/K at %dK"%(ga,nasa,limit,T))
def testNASAcreated(self): """Can we make NASA polynomial data""" cp0, cpInf, a0, a1, a2, a3, I, J = (1.0,1.0,1.0,1.0,1.0,1.0, 1.0, 1.0) comment = "Stupid thermo." WilhoitData = thermo.ThermoWilhoitData( cp0, cpInf, a0, a1, a2, a3, I, J, comment=comment) NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData)