def setUp(self):
"""
A function run before each unit test in this class.
"""
self.frequency = -2017.96
self.E0_reac = -295.563
self.E0_TS = -12.7411
self.E0_prod = (-10.2664) + (-253.48)
self.tunneling = Eckart(
frequency=(self.frequency, "cm^-1"),
E0_reac=(self.E0_reac, "kJ/mol"),
E0_TS=(self.E0_TS, "kJ/mol"),
E0_prod=(self.E0_prod, "kJ/mol"),
)
def reaction(label, reactants, products, transitionState=None, kinetics=None, tunneling=''):
"""Load a reaction from an input file"""
global reaction_dict, species_dict, transition_state_dict
if label in reaction_dict:
label = label + transitionState
if label in reaction_dict:
raise ValueError('Multiple occurrences of reaction with label {0!r}.'.format(label))
logging.info('Loading reaction {0}...'.format(label))
reactants = sorted([species_dict[spec] for spec in reactants])
products = sorted([species_dict[spec] for spec in products])
if transitionState:
transitionState = transition_state_dict[transitionState]
if transitionState and (tunneling == '' or tunneling is None):
transitionState.tunneling = None
elif tunneling.lower() == 'wigner':
transitionState.tunneling = Wigner(frequency=None)
elif tunneling.lower() == 'eckart':
transitionState.tunneling = Eckart(frequency=None, E0_reac=None, E0_TS=None, E0_prod=None)
elif transitionState and not isinstance(tunneling, TunnelingModel):
raise ValueError('Unknown tunneling model {0!r}.'.format(tunneling))
rxn = Reaction(label=label, reactants=reactants, products=products, transition_state=transitionState,
kinetics=kinetics)
if rxn.transition_state is None and rxn.kinetics is None:
logging.info('estimating rate of reaction {0} using RMG-database')
if not all([m.molecule != [] for m in rxn.reactants + rxn.products]):
raise ValueError('chemical structures of reactants and products not available for RMG estimation of '
'reaction {0}'.format(label))
db = get_db('kinetics')
rxns = db.generate_reactions_from_libraries(reactants=rxn.reactants, products=rxn.products)
rxns = [r for r in rxns if r.elementary_high_p]
if rxns:
for r in rxns:
if isinstance(rxn.kinetics, PDepKineticsModel):
boo = rxn.generate_high_p_limit_kinetics()
if boo:
rxn = r
break
if rxns == [] or not boo:
logging.info('No library reactions tagged with elementary_high_p found for reaction {0}, generating '
'reactions from RMG families'.format(label))
rxn = list(db.generate_reactions_from_families(reactants=rxn.reactants, products=rxn.products))
model = CoreEdgeReactionModel()
model.verbose_comments = True
for r in rxn:
model.apply_kinetics_to_reaction(r)
if isinstance(rxn, Reaction):
reaction_dict[label] = rxn
else:
for i in range(len(rxn)):
reaction_dict[label + str(i)] = rxn[i]
return rxn
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.frequency = -2017.96
self.E0_reac = -295.563
self.E0_TS = -12.7411
self.E0_prod = (-10.2664) + (-253.48)
self.tunneling = Eckart(
frequency = (self.frequency,"cm^-1"),
E0_reac = (self.E0_reac,"kJ/mol"),
E0_TS = (self.E0_TS,"kJ/mol"),
E0_prod = (self.E0_prod,"kJ/mol"),
)
def reaction(label,
reactants,
products,
transitionState,
kinetics=None,
tunneling=''):
global reactionDict, speciesDict, transitionStateDict
#label = 'reaction'+transitionState
if label in reactionDict:
label = label + transitionState
if label in reactionDict:
raise ValueError(
'Multiple occurrences of reaction with label {0!r}.'.format(
label))
logging.info('Loading reaction {0}...'.format(label))
reactants = sorted([speciesDict[spec] for spec in reactants])
products = sorted([speciesDict[spec] for spec in products])
transitionState = transitionStateDict[transitionState]
if tunneling.lower() == 'wigner':
transitionState.tunneling = Wigner(frequency=None)
elif tunneling.lower() == 'eckart':
transitionState.tunneling = Eckart(frequency=None,
E0_reac=None,
E0_TS=None,
E0_prod=None)
elif tunneling == '' or tunneling is None:
transitionState.tunneling = None
elif not isinstance(tunneling, TunnelingModel):
raise ValueError('Unknown tunneling model {0!r}.'.format(tunneling))
rxn = Reaction(label=label,
reactants=reactants,
products=products,
transitionState=transitionState,
kinetics=kinetics)
reactionDict[label] = rxn
return rxn
def reaction(label, reactants, products, transitionState=None, tunneling=''):
"""Load a reaction from an input file"""
global reaction_dict, species_dict, transition_state_dict
if label in reaction_dict:
label = label + transitionState
if label in reaction_dict:
raise ValueError(
'Multiple occurrences of reaction with label {0!r}.'.format(
label))
logging.info('Loading reaction {0}...'.format(label))
reactants = sorted([species_dict[spec] for spec in reactants])
products = sorted([species_dict[spec] for spec in products])
if transitionState:
transitionState = transition_state_dict[transitionState]
if transitionState and (tunneling == '' or tunneling is None):
transitionState.tunneling = None
elif tunneling.lower() == 'wigner':
transitionState.tunneling = Wigner(frequency=None)
elif tunneling.lower() == 'eckart':
transitionState.tunneling = Eckart(frequency=None,
E0_reac=None,
E0_TS=None,
E0_prod=None)
elif transitionState and not isinstance(tunneling, TunnelingModel):
raise ValueError('Unknown tunneling model {0!r}.'.format(tunneling))
rxn = Reaction(label=label,
reactants=reactants,
products=products,
transition_state=transitionState,
output_directory=output_directory)
if isinstance(rxn, Reaction):
reaction_dict[label] = rxn
return rxn
class TestEckart(unittest.TestCase):
"""
Contains unit tests of the :class:`Eckart` class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.frequency = -2017.96
self.E0_reac = -295.563
self.E0_TS = -12.7411
self.E0_prod = (-10.2664) + (-253.48)
self.tunneling = Eckart(
frequency=(self.frequency, "cm^-1"),
E0_reac=(self.E0_reac, "kJ/mol"),
E0_TS=(self.E0_TS, "kJ/mol"),
E0_prod=(self.E0_prod, "kJ/mol"),
)
def test_frequency(self):
"""
Test that the Eckart frequency property was properly set.
"""
self.assertAlmostEqual(self.tunneling.frequency.value_si,
self.frequency, 4)
def test_E0_reac(self):
"""
Test that the Eckart E0_reac property was properly set.
"""
self.assertAlmostEqual(self.tunneling.E0_reac.value_si * 0.001,
self.E0_reac, 4)
def test_E0_TS(self):
"""
Test that the Eckart E0_TS property was properly set.
"""
self.assertAlmostEqual(self.tunneling.E0_TS.value_si * 0.001,
self.E0_TS, 4)
def test_E0_prod(self):
"""
Test that the Eckart E0_prod property was properly set.
"""
self.assertAlmostEqual(self.tunneling.E0_prod.value_si * 0.001,
self.E0_prod, 4)
def test_calculateTunnelingFactor(self):
"""
Test the Eckart.calculateTunnelingFactor() method.
"""
Tlist = numpy.array([300, 500, 1000, 1500, 2000])
kexplist = numpy.array([1623051., 7.69349, 1.46551, 1.18111, 1.09858])
for T, kexp in zip(Tlist, kexplist):
kact = self.tunneling.calculateTunnelingFactor(T)
self.assertAlmostEqual(kexp, kact, delta=1e-3 * kexp)
def test_pickle(self):
"""
Test that an Eckart object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
tunneling = cPickle.loads(cPickle.dumps(self.tunneling, -1))
self.assertAlmostEqual(self.tunneling.frequency.value,
tunneling.frequency.value, 2)
self.assertEqual(self.tunneling.frequency.units,
tunneling.frequency.units)
self.assertAlmostEqual(self.tunneling.E0_reac.value,
tunneling.E0_reac.value, 3)
self.assertEqual(self.tunneling.E0_reac.units, tunneling.E0_reac.units)
self.assertAlmostEqual(self.tunneling.E0_TS.value,
tunneling.E0_TS.value, 3)
self.assertEqual(self.tunneling.E0_TS.units, tunneling.E0_TS.units)
self.assertAlmostEqual(self.tunneling.E0_prod.value,
tunneling.E0_prod.value, 3)
self.assertEqual(self.tunneling.E0_prod.units, tunneling.E0_prod.units)
def test_repr(self):
"""
Test that an Eckart object can be successfully reconstructed
from its repr() output with no loss of information.
"""
tunneling = None
exec('tunneling = {0!r}'.format(self.tunneling))
self.assertAlmostEqual(self.tunneling.frequency.value,
tunneling.frequency.value, 2)
self.assertEqual(self.tunneling.frequency.units,
tunneling.frequency.units)
self.assertAlmostEqual(self.tunneling.E0_reac.value,
tunneling.E0_reac.value, 3)
self.assertEqual(self.tunneling.E0_reac.units, tunneling.E0_reac.units)
self.assertAlmostEqual(self.tunneling.E0_TS.value,
tunneling.E0_TS.value, 3)
self.assertEqual(self.tunneling.E0_TS.units, tunneling.E0_TS.units)
self.assertAlmostEqual(self.tunneling.E0_prod.value,
tunneling.E0_prod.value, 3)
self.assertEqual(self.tunneling.E0_prod.units, tunneling.E0_prod.units)
class TestEckart(unittest.TestCase):
"""
Contains unit tests of the :class:`Eckart` class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.frequency = -2017.96
self.E0_reac = -295.563
self.E0_TS = -12.7411
self.E0_prod = (-10.2664) + (-253.48)
self.tunneling = Eckart(
frequency = (self.frequency,"cm^-1"),
E0_reac = (self.E0_reac,"kJ/mol"),
E0_TS = (self.E0_TS,"kJ/mol"),
E0_prod = (self.E0_prod,"kJ/mol"),
)
def test_frequency(self):
"""
Test that the Eckart frequency property was properly set.
"""
self.assertAlmostEqual(self.tunneling.frequency.value_si, self.frequency, 4)
def test_E0_reac(self):
"""
Test that the Eckart E0_reac property was properly set.
"""
self.assertAlmostEqual(self.tunneling.E0_reac.value_si*0.001, self.E0_reac, 4)
def test_E0_TS(self):
"""
Test that the Eckart E0_TS property was properly set.
"""
self.assertAlmostEqual(self.tunneling.E0_TS.value_si*0.001, self.E0_TS, 4)
def test_E0_prod(self):
"""
Test that the Eckart E0_prod property was properly set.
"""
self.assertAlmostEqual(self.tunneling.E0_prod.value_si*0.001, self.E0_prod, 4)
def test_calculateTunnelingFactor(self):
"""
Test the Eckart.calculateTunnelingFactor() method.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
kexplist = numpy.array([1623051., 7.69349, 1.46551, 1.18111, 1.09858])
for T, kexp in zip(Tlist, kexplist):
kact = self.tunneling.calculateTunnelingFactor(T)
self.assertAlmostEqual(kexp, kact, delta=1e-3*kexp)
def test_pickle(self):
"""
Test that an Eckart object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
tunneling = cPickle.loads(cPickle.dumps(self.tunneling,-1))
self.assertAlmostEqual(self.tunneling.frequency.value, tunneling.frequency.value, 2)
self.assertEqual(self.tunneling.frequency.units, tunneling.frequency.units)
self.assertAlmostEqual(self.tunneling.E0_reac.value, tunneling.E0_reac.value, 3)
self.assertEqual(self.tunneling.E0_reac.units, tunneling.E0_reac.units)
self.assertAlmostEqual(self.tunneling.E0_TS.value, tunneling.E0_TS.value, 3)
self.assertEqual(self.tunneling.E0_TS.units, tunneling.E0_TS.units)
self.assertAlmostEqual(self.tunneling.E0_prod.value, tunneling.E0_prod.value, 3)
self.assertEqual(self.tunneling.E0_prod.units, tunneling.E0_prod.units)
def test_repr(self):
"""
Test that an Eckart object can be successfully reconstructed
from its repr() output with no loss of information.
"""
tunneling = None
exec('tunneling = {0!r}'.format(self.tunneling))
self.assertAlmostEqual(self.tunneling.frequency.value, tunneling.frequency.value, 2)
self.assertEqual(self.tunneling.frequency.units, tunneling.frequency.units)
self.assertAlmostEqual(self.tunneling.E0_reac.value, tunneling.E0_reac.value, 3)
self.assertEqual(self.tunneling.E0_reac.units, tunneling.E0_reac.units)
self.assertAlmostEqual(self.tunneling.E0_TS.value, tunneling.E0_TS.value, 3)
self.assertEqual(self.tunneling.E0_TS.units, tunneling.E0_TS.units)
self.assertAlmostEqual(self.tunneling.E0_prod.value, tunneling.E0_prod.value, 3)
self.assertEqual(self.tunneling.E0_prod.units, tunneling.E0_prod.units)
