def testAcetyl(self):
"""
Tests the acetyl radical.
"""
struct = structure.Structure(SMILES="C[C]=O")
thermoData = rmg.thermo.model.ThermoData(
H298=-3.08 * 4184,
S298=64.27 * 4.184,
Cp=[
12.28 * 4.184,
14.34 * 4.184,
16.30 * 4.184,
18.05 * 4.184,
20.92 * 4.184,
23.08 * 4.184,
26.39 * 4.184,
],
)
spectralData = data.generateSpectralData(struct, thermoData)
frequencies0 = [mode.frequency for mode in spectralData.modes if isinstance(mode, modes.HarmonicOscillator)]
frequencies0.sort()
frequencies = [2750.0, 2800.0, 2850.0, 1350.0, 1500.0, 750.0, 1050.0, 1375.0, 1855.0, 455.0, 2761.6297]
frequencies.sort()
self.assertTrue(len(frequencies0) == len(frequencies))
for freq1, freq2 in zip(frequencies0, frequencies):
self.assertAlmostEqual(
freq1 / freq2, 1.0, 1, "Harmonic oscillator frequencies %s and %s do not match." % (freq1, freq2)
)
frequencies0 = [mode.frequency for mode in spectralData.modes if isinstance(mode, modes.HinderedRotor)]
frequencies0.sort()
frequencies = [448.9323]
frequencies.sort()
barriers0 = [mode.barrier for mode in spectralData.modes if isinstance(mode, modes.HinderedRotor)]
barriers0.sort()
barriers = [1941.5089]
barriers.sort()
self.assertTrue(len(frequencies0) == len(frequencies))
self.assertTrue(len(barriers0) == len(barriers))
for freq1, freq2 in zip(frequencies0, frequencies):
self.assertAlmostEqual(
freq1 / freq2, 1.0, 1, "Hindered rotor frequencies %s and %s do not match." % (freq1, freq2)
)
for barr1, barr2 in zip(barriers0, barriers):
self.assertAlmostEqual(
barr1 / barr2, 1.0, 1, "Hindered rotor barriers %s and %s do not match." % (barr1, barr2)
)
def testOxygen(self):
"""
Tests the oxygen molecule.
"""
struct = structure.Structure(SMILES="O=O")
thermoData = rmg.thermo.model.ThermoData(
H298=0.0 * 4184,
S298=49.00 * 4.184,
Cp=[7.00 * 4.184, 7.22 * 4.184, 7.44 * 4.184, 7.65 * 4.184, 8.07 * 4.184, 8.35 * 4.184, 8.72 * 4.184],
)
spectralData = data.generateSpectralData(struct, thermoData)
frequencies0 = [mode.frequency for mode in spectralData.modes if isinstance(mode, modes.HarmonicOscillator)]
frequencies = [1482.2752]
self.assertTrue(len(frequencies0) == len(frequencies))
for freq1, freq2 in zip(frequencies0, frequencies):
self.assertAlmostEqual(
freq1 / freq2, 1.0, 1, "Harmonic oscillator frequencies %s and %s do not match." % (freq1, freq2)
)
def testAcetylperoxy(self):
"""
Tests the acetylperoxy radical.
"""
struct = structure.Structure(SMILES="CC(=O)O[O]")
thermoData = rmg.thermo.model.ThermoData(
H298=-38.57 * 4184,
S298=75.56 * 4.184,
Cp=[
19.48 * 4.184,
23.22 * 4.184,
26.33 * 4.184,
28.81 * 4.184,
32.39 * 4.184,
34.76 * 4.184,
37.99 * 4.184,
],
)
spectralData = data.generateSpectralData(struct, thermoData)
frequencies0 = [mode.frequency for mode in spectralData.modes if isinstance(mode, modes.HarmonicOscillator)]
frequencies0.sort()
frequencies = [
2750.0,
2800.0,
2850.0,
1350.0,
1500.0,
750.0,
1050.0,
1375.0,
492.5,
1135.0,
586.74145,
586.74145,
586.74145,
586.74145,
1444.6377,
1444.6377,
]
frequencies.sort()
self.assertTrue(len(frequencies0) == len(frequencies))
for freq1, freq2 in zip(frequencies0, frequencies):
self.assertAlmostEqual(
freq1 / freq2, 1.0, 1, "Harmonic oscillator frequencies %s and %s do not match." % (freq1, freq2)
)
frequencies0 = [mode.frequency for mode in spectralData.modes if isinstance(mode, modes.HinderedRotor)]
frequencies0.sort()
frequencies = [40.0, 150.0]
frequencies.sort()
barriers0 = [mode.barrier for mode in spectralData.modes if isinstance(mode, modes.HinderedRotor)]
barriers0.sort()
barriers = [1120.2859, 2173.5399]
barriers.sort()
self.assertTrue(len(frequencies0) == len(frequencies))
self.assertTrue(len(barriers0) == len(barriers))
for freq1, freq2 in zip(frequencies0, frequencies):
self.assertAlmostEqual(
freq1 / freq2, 1.0, 1, "Hindered rotor frequencies %s and %s do not match." % (freq1, freq2)
)
for barr1, barr2 in zip(barriers0, barriers):
self.assertAlmostEqual(
barr1 / barr2, 1.0, 1, "Hindered rotor barriers %s and %s do not match." % (barr1, barr2)
)
def testHydroperoxylvinoxy(self):
"""
Tests the hydroperoxylvinoxy radical.
"""
struct = structure.Structure(SMILES="[CH2]C(=O)OO")
thermoData = rmg.thermo.model.ThermoData(
H298=-32.95 * 4184,
S298=79.25 * 4.184,
Cp=[
21.79 * 4.184,
25.53 * 4.184,
28.35 * 4.184,
30.47 * 4.184,
33.34 * 4.184,
35.12 * 4.184,
37.57 * 4.184,
],
)
spectralData = data.generateSpectralData(struct, thermoData)
frequencies0 = [mode.frequency for mode in spectralData.modes if isinstance(mode, modes.HarmonicOscillator)]
frequencies0.sort()
frequencies = [
3000.0,
3100.0,
440.0,
815.0,
1455.0,
3615.0,
1310.0,
387.5,
850.0,
660.71709,
660.71709,
660.71709,
1167.9948,
1167.9948,
1167.9948,
]
frequencies.sort()
self.assertTrue(len(frequencies0) == len(frequencies))
for freq1, freq2 in zip(frequencies0, frequencies):
self.assertAlmostEqual(
freq1 / freq2, 1.0, 1, "Harmonic oscillator frequencies %s and %s do not match." % (freq1, freq2)
)
frequencies0 = [mode.frequency for mode in spectralData.modes if isinstance(mode, modes.HinderedRotor)]
frequencies0.sort()
frequencies = [100.0, 300.0, 300.0]
frequencies.sort()
barriers0 = [mode.barrier for mode in spectralData.modes if isinstance(mode, modes.HinderedRotor)]
barriers0.sort()
barriers = [779.05087, 2311.3714, 2311.3714]
barriers.sort()
self.assertTrue(len(frequencies0) == len(frequencies))
self.assertTrue(len(barriers0) == len(barriers))
for freq1, freq2 in zip(frequencies0, frequencies):
self.assertAlmostEqual(
freq1 / freq2, 1.0, 1, "Hindered rotor frequencies %s and %s do not match." % (freq1, freq2)
)
for barr1, barr2 in zip(barriers0, barriers):
self.assertAlmostEqual(
barr1 / barr2, 1.0, 1, "Hindered rotor barriers %s and %s do not match." % (barr1, barr2)
)