def generateKineticsModel(reaction, tunneling='', plot=False):
logging.info('Calculating rate coefficient for {0}...'.format(reaction))
if len(reaction.reactants) == 1:
kunits = 's^-1'
elif len(reaction.reactants) == 2:
kunits = 'm^3/(mol*s)'
elif len(reaction.reactants) == 3:
kunits = 'm^6/(mol^2*s)'
else:
kunits = ''
Tlist = 1000.0/numpy.arange(0.4, 3.35, 0.05)
klist = reaction.calculateTSTRateCoefficients(Tlist, tunneling)
arrhenius = Arrhenius().fitToData(Tlist, klist, kunits)
klist2 = arrhenius.getRateCoefficients(Tlist)
reaction.kinetics = arrhenius
if plot:
logging.info('Plotting kinetics model for {0}...'.format(reaction))
import pylab
pylab.semilogy(1000.0 / Tlist, klist * reaction.degeneracy, 'ok')
pylab.semilogy(1000.0 / Tlist, klist2 * reaction.degeneracy, '-k')
pylab.xlabel('1000 / Temperature (1000/K)')
pylab.ylabel('Rate coefficient (SI units)')
pylab.show()
def testTSTCalculation(self):
"""
A test of the transition state theory k(T) calculation function,
using the reaction H + C2H4 -> C2H5.
"""
Tlist = 1000.0/numpy.arange(0.4, 3.35, 0.05)
klist = self.reaction.calculateTSTRateCoefficients(Tlist, tunneling='')
arrhenius = Arrhenius().fitToData(Tlist, klist, kunits='')
klist2 = arrhenius.getRateCoefficients(Tlist)
# Check that the correct Arrhenius parameters are returned
self.assertAlmostEqual(arrhenius.A.value/1.07506e+07, 1.0, 3)
self.assertAlmostEqual(arrhenius.n.value/1.47803, 1.0, 3)
self.assertAlmostEqual(arrhenius.Ea.value/10194., 1.0, 3)
# Check that the fit is satisfactory
for i in range(len(Tlist)):
self.assertTrue(abs(1 - klist2[i] / klist[i]) < 0.01)
