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Merge branch 'pr/287' to get Enoch's CanTherm fixes, examples, and tests.
This closes #287. 1) It now alerts the user if they are not using the lowest energy conformer (based on the hindered rotor scans). 2) There is an example for methoxy decomposition. 3) There are some unit tests.
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‎examples/cantherm/reactions/methoxy/README‎

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to run, execute 'run-cantherm'
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(if not executable and if you are using linux, use the command: chmod +x run-cantherm)

‎examples/cantherm/reactions/methoxy/input.py‎

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title = 'methoxy decomposition to H + CH2O'
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description = \
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"""
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This example illustrates how to manually set up a CanTherm input file for a small P-dep reaction system [using only the
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RRHO assumption, and without tunneling, although this can be easily implemented]. Such a calculation is desireable if the user
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wishes to supply experimentally determined freqeuncies, for example. Althgou some coommented notes below may be useful,
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see http://greengroup.github.io/RMG-Py/users/cantherm/index.html for more documented information about CanTherm and
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creating input files. (information pertaining this file is adopted by Dames and Golden, 2013, JPCA 117 (33) 7686-96.)
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"""
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transitionState(
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label = 'TS3',
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E0 = (34.1,'kcal/mol'), # this INCLUDES the ZPE. Note that other energy units are also possible (e.g., kJ/mol)
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spinMultiplicity = 2,
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opticalIsomers = 1,
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frequency = (-967,'cm^-1'),
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modes = [ # these modes are used to compute the partition functions
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HarmonicOscillator(frequencies=([466,581,1169,1242,1499,1659,2933,3000],'cm^-1')),
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NonlinearRotor(rotationalConstant=([0.970, 1.029, 3.717],"cm^-1"),symmetry=1, quantum=False),
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IdealGasTranslation(mass=(31.01843,"g/mol")) #this must be included for every species/ts
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],
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)
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transitionState(
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label = 'TS2',
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E0 = (38.9,'kcal/mol'),
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spinMultiplicity = 2,
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opticalIsomers = 1,
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frequency = (-1934,'cm^-1'),
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modes = [
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HarmonicOscillator(frequencies=([792, 987 ,1136, 1142, 1482 ,2441 ,3096, 3183],'cm^-1')),
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NonlinearRotor(rotationalConstant=([0.928,0.962,5.807],"cm^-1"),symmetry=1, quantum=False),
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IdealGasTranslation(mass=(31.01843,"g/mol"))
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],
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)
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transitionState(
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label = 'TS1',
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E0 = (39.95,'kcal/mol'),
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spinMultiplicity = 2,
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opticalIsomers = 1,
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frequency = (-1756,'cm^-1'),
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modes = [
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HarmonicOscillator(frequencies=([186 ,626 ,1068, 1234, 1474, 1617, 2994 ,3087],'cm^-1')),
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NonlinearRotor(rotationalConstant=([0.966,0.986,5.253],"cm^-1"),symmetry=1, quantum=False),
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IdealGasTranslation(mass=(31.01843,"g/mol"))
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],
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)
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species(
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label = 'methoxy',
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structure = SMILES('C[O]'),
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E0 = (9.44,'kcal/mol'),
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modes = [
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HarmonicOscillator(frequencies=([758,960,1106 ,1393,1403,1518,2940,3019,3065],'cm^-1')),
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NonlinearRotor(rotationalConstant=([0.916, 0.921, 5.251],"cm^-1"),symmetry=3, quantum=False),
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IdealGasTranslation(mass=(31.01843,"g/mol")),
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],
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spinMultiplicity = 3.88, # 3+exp(-89/T)
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opticalIsomers = 1,
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molecularWeight = (31.01843,'amu'),
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collisionModel = TransportData(sigma=(3.69e-10,'m'), epsilon=(4.0,'kJ/mol')),
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energyTransferModel = SingleExponentialDown(alpha0=(0.956,'kJ/mol'), T0=(300,'K'), n=0.95),
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)
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species(
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label = 'CH2O',
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E0 = (28.69,'kcal/mol'),
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molecularWeight = (30.0106,"g/mol"),
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collisionModel = TransportData(sigma=(3.69e-10,'m'), epsilon=(4.0,'kJ/mol')),
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energyTransferModel = SingleExponentialDown(alpha0=(0.956,'kJ/mol'), T0=(300,'K'), n=0.95),
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spinMultiplicity = 1,
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opticalIsomers = 1,
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modes = [
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HarmonicOscillator(frequencies=([1180,1261,1529,1764,2931,2999],'cm^-1')),
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NonlinearRotor(rotationalConstant=([1.15498821005263, 1.3156969584727, 9.45570474524524],"cm^-1"),symmetry=2, quantum=False),
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IdealGasTranslation(mass=(30.0106,"g/mol")),
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],
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)
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species(
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label = 'H',
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E0 = (0.000,'kcal/mol'),
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molecularWeight = (1.00783,"g/mol"),
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collisionModel = TransportData(sigma=(3.69e-10,'m'), epsilon=(4.0,'kJ/mol')),
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energyTransferModel = SingleExponentialDown(alpha0=(0.956,'kJ/mol'), T0=(300,'K'), n=0.95),
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modes = [
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IdealGasTranslation(mass=(1.00783,"g/mol")),
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],
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spinMultiplicity = 2,
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opticalIsomers = 1,
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)
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species(
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label = 'CH2Ob', #this is a special system with two chemically equivalent product channels. Thus, different labels are used.
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E0 = (28.69,'kcal/mol'),
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molecularWeight = (30.0106,"g/mol"),
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collisionModel = TransportData(sigma=(3.69e-10,'m'), epsilon=(4.0,'kJ/mol')),
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energyTransferModel = SingleExponentialDown(alpha0=(0.956,'kJ/mol'), T0=(300,'K'), n=0.95),
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spinMultiplicity = 1,
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opticalIsomers = 1,
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modes = [
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HarmonicOscillator(frequencies=([1180,1261,1529,1764,2931,2999],'cm^-1')),
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NonlinearRotor(rotationalConstant=([1.15498821005263, 1.3156969584727, 9.45570474524524],"cm^-1"),symmetry=2, quantum=False),
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IdealGasTranslation(mass=(30.0106,"g/mol")),
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],
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)
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species(
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label = 'Hb',
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E0 = (0.0001,'kcal/mol'),
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molecularWeight = (1.00783,"g/mol"),
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collisionModel = TransportData(sigma=(3.69e-10,'m'), epsilon=(4.0,'kJ/mol')),
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energyTransferModel = SingleExponentialDown(alpha0=(0.956,'kJ/mol'), T0=(300,'K'), n=0.95),
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modes = [
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IdealGasTranslation(mass=(1.00783,"g/mol")),
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],
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spinMultiplicity = 2,
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opticalIsomers = 1,
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)
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species(
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label = 'CH2OH',
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E0 = (0.00,'kcal/mol'),
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molecularWeight = (31.01843,"g/mol"),
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modes = [
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HarmonicOscillator(frequencies=([418,595, 1055, 1198, 1368, 1488, 3138, 3279, 3840],'cm^-1')),
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# below is an example of how to include hindered rotors
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#HinderedRotor(inertia=(5.75522e-47,'kg*m^2'), symmetry=1, barrier=(22427.8,'J/mol'), semiclassical=False),
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NonlinearRotor(rotationalConstant=([0.868,0.993,6.419],"cm^-1"),symmetry=1, quantum=False),
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IdealGasTranslation(mass=(31.01843,"g/mol")),
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],
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spinMultiplicity = 2,
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opticalIsomers = 2,
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collisionModel = TransportData(sigma=(3.69e-10,'m'), epsilon=(4.0,'kJ/mol')),
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energyTransferModel = SingleExponentialDown(alpha0=(0.956,'kJ/mol'), T0=(300,'K'), n=0.95),
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)
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species(
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label = 'He',
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# freqScaleFactor = 1, # TypeError: species() got an unexpected keyword argument 'freqScaleFactor'.
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structure = SMILES('[He]'),
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molecularWeight = (4.003,'amu'),
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collisionModel = TransportData(sigma=(2.55e-10,'m'), epsilon=(0.0831,'kJ/mol')),
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energyTransferModel = SingleExponentialDown(alpha0=(0.956,'kJ/mol'), T0=(300,'K'), n=0.95),
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)
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reaction(
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label = 'CH2O+H=Methoxy',
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# label = 'Methoxy = CH2O+H',
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reactants = ['CH2O','H'],
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products = ['methoxy'],
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# reactants = ['methoxy'],
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# products = ['CH2O', 'H'],
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transitionState = 'TS3',
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#tunneling='Eckart',
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)
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reaction(
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# label = 'CH2Ob+Hb=CH2OH',
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label = 'CH2OH = CH2Ob+Hb',
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# products = ['CH2OH'],
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reactants = ['CH2OH'],
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# reactants = ['CH2Ob','Hb'],
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products = ['CH2Ob', 'Hb'],
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transitionState = 'TS1',
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#tunneling='Eckart',
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)
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reaction(
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label = 'CH2OH = Methoxy',
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# reactants = ['methoxy'],
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# products = ['CH2OH'],
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# label = 'Methoxy = CH2OH',
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products = ['methoxy'],
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reactants = ['CH2OH'],
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transitionState = 'TS2',
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#tunneling='Eckart',
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)
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kinetics('CH2O+H=Methoxy')
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#kinetics('Methoxy = CH2O+H' )
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#kinetics('Methoxy = CH2OH' )
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kinetics('CH2OH = Methoxy')
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kinetics('CH2OH = CH2Ob+Hb' )
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#kinetics('CH2Ob+Hb=CH2OH')
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network(
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label = 'methoxy',
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isomers = [
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'methoxy',
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'CH2OH',
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],
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reactants = [
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('CH2O','H'),
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# ('CH2Ob','Hb'),
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],
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bathGas = {
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'He': 1,
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},
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)
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pressureDependence(
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label = 'methoxy',
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Tmin = (450,'K'), Tmax = (1200,'K'), Tcount = 4,
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Tlist = ([450,500,678,700],'K'),
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Pmin = (0.01,'atm'), Pmax = (1000,'atm'), Pcount = 7,
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Plist = ([0.01,0.1,1,3,10,100,1000],'atm'),
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maximumGrainSize = (0.5,'kcal/mol'),
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minimumGrainCount = 500,
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method = 'modified strong collision',
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#Other methods include: 'reservoir state', 'chemically-significant eigenvalues',
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interpolationModel = ('pdeparrhenius'),
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activeKRotor = True,
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# activeJRotor = False, #causes cantherm to crash
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rmgmode = False,
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)

‎examples/cantherm/reactions/methoxy/run-cantherm‎

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#!/bin/bash
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python ../../../../cantherm.py input.py

‎rmgpy/cantherm/common.py‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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################################################################################
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#
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# RMG - Reaction Mechanism Generator
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#
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# Copyright (c) 2002-2009 Prof. William H. Green (whgreen@mit.edu) and the
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# RMG Team (rmg_dev@mit.edu)
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#
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# Permission is hereby granted, free of charge, to any person obtaining a
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# copy of this software and associated documentation files (the "Software"),
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# to deal in the Software without restriction, including without limitation
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# the rights to use, copy, modify, merge, publish, distribute, sublicense,
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# and/or sell copies of the Software, and to permit persons to whom the
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# Software is furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included in
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# all copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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#
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################################################################################
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import numpy
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import os.path
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import logging
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import rmgpy.constants as constants
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################################################################################
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def checkConformerEnergy(Vlist,path):
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"""
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Check to see that the starting energy of the species in the potential energy scan calculation
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is not 0.5 kcal/mol (or more) higher than any other energies in the scan. If so, print and
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log a warning message.
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"""
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Vlist = numpy.array(Vlist, numpy.float64)
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Vdiff = (Vlist[0] - numpy.min(Vlist))*constants.E_h*constants.Na/1000
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if Vdiff >= 2: #we choose 2 kJ/mol to be the critical energy
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logging.warning('the species corresponding to ' + str(os.path.basename(path)) + ' is different in energy from the lowest energy conformer by ' + "%0.2f" % Vdiff + ' kJ/mol. This can cause significant errors in your computed rate constants. ')
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