def test_threebody(self):
r = ct.ThreeBodyReaction()
r.reactants = {'O':1, 'H':1}
r.products = {'OH':1}
r.rate = ct.Arrhenius(5e11, -1.0, 0.0)
r.efficiencies = {'AR':0.7, 'H2':2.0, 'H2O':6.0}
gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
species=self.species, reactions=[r])
gas2.TPX = self.gas.TPX
self.assertNear(gas2.forward_rate_constants[0],
self.gas.forward_rate_constants[1])
self.assertNear(gas2.net_rates_of_progress[0],
self.gas.net_rates_of_progress[1])
def remove(seed, num, exclude):
np.random.seed(seed)
reactions = gas.reactions()
removed = []
rcandidates = range(0, len(reactions))
rcandidates = [item for item in rcandidates if item not in exclude]
removed = np.random.choice(rcandidates, size=num, replace=False)
for ind in removed:
if (gas.reaction_type(ind) == 1):
newreac = ct.ElementaryReaction(reactants=reactions[ind].reactants,
products=reactions[ind].products)
gas.modify_reaction(ind, newreac)
if (gas.reaction_type(ind) == 2):
newreac = ct.ThreeBodyReaction(reactants=reactions[ind].reactants,
products=reactions[ind].products)
gas.modify_reaction(ind, newreac)
if (gas.reaction_type(ind) == 4):
newreac = ct.FalloffReaction(reactants=reactions[ind].reactants,
products=reactions[ind].products)
gas.modify_reaction(ind, newreac)
return removed
def perturb_parameter_thisisthecomplicatedonethatdoesntwork(
self, parameter, new_value):
param_info = self.model_parameter_info[parameter]
reaction_number = param_info['reaction_number']
parameter_type = param_info['parameter_type']
print(parameter)
print(param_info)
reaction = self.gas.reaction(reaction_number)
print(reaction.rate)
rate = None
efficiencies = None
reactants = reaction.reactant_string
products = reaction.product_string
rtype = reaction.reaction_type
pressurestring = 'pressure'
HasFalloff = False
if pressurestring in parameter_type:
HasFalloff = True
if HasFalloff:
highrate = reaction.high_rate
lowrate = reaction.low_rate
if rtype == 4:
newreaction = ct.FalloffReaction(reactants=reactants,
products=products)
if rtype == 8:
newreaction = ct.ChemicallyActivatedReaction(
reactants=reactants, products=products)
else:
rate = reaction.rate
if rtype == 2:
newreaction = ct.ThreeBodyReaction(reactants=reactants,
products=products)
else:
newreaction = ct.ElementaryReaction(reactants=reactants,
products=products)
if parameter_type == 'A_factor':
old_A = rate.pre_exponential_factor
old_b = rate.temperature_exponent
old_E = rate.activation_energy
new_A = new_value
newreaction.rate = ct.Arrhenius(A=new_A, b=old_b, E=old_E)
if parameter_type == 'Energy':
old_A = rate.pre_exponential_factor
old_b = rate.temperature_exponent
old_E = rate.activation_energy
new_E = new_value
newreaction.rate = ct.Arrhenius(A=old_A, b=old_b, E=new_E)
if parameter_type == 'High_pressure_A':
rate = highrate
old_A = rate.pre_exponential_factor
old_b = rate.temperature_exponent
old_E = rate.activation_energy
new_A = new_value
newreaction.high_rate = ct.Arrhenius(A=new_A, b=old_b, E=old_E)
if parameter_type == 'High_pressure_E':
rate = highrate
old_A = rate.pre_exponential_factor
old_b = rate.temperature_exponent
old_E = rate.activation_energy
new_E = new_value
newreaction.high_rate = ct.Arrhenius(A=old_A, b=old_b, E=new_E)
if parameter_type == 'Low_pressure_A':
rate = lowrate
old_A = rate.pre_exponential_factor
old_b = rate.temperature_exponent
old_E = rate.activation_energy
new_A = new_value
newreaction.low_rate = ct.Arrhenius(A=new_A, b=old_b, E=old_E)
if parameter_type == 'Low_pressure_E':
rate = lowrate
old_A = rate.pre_exponential_factor
old_b = rate.temperature_exponent
old_E = rate.activation_energy
new_E = new_value
newreaction.low_rate = ct.Arrhenius(A=old_A, b=old_b, E=new_E)
self.gas.modify_reaction(reaction_number, newreaction)
if parameter_type == 'Efficiency':
efficiencies = copy.deepcopy(reaction.efficiencies)
species = param_info['species']
efficiencies[species] = new_value
reaction.efficiencies = efficiencies
return
def residual(eta, k0, observations, measure_ind, tmaxes, temperatures,
pressures, initials, maxes, yields):
rstart = timeit.default_timer()
ret = 0
reactions = gas.reaction_equations()
k = k0 * 10**eta
if (gas.reaction_type(measure_ind) == 1):
newrate = ct.ElementaryReaction(gas.reactions()[measure_ind].reactants,
gas.reactions()[measure_ind].products)
newrate.rate = ct.Arrhenius(
k,
gas.reactions()[measure_ind].rate.temperature_exponent,
gas.reactions()[measure_ind].rate.activation_energy)
gas.modify_reaction(measure_ind, newrate)
if (gas.reaction_type(measure_ind) == 2):
newrate = ct.ThreeBodyReaction(
reactants=gas.reactions()[measure_ind].reactants,
products=gas.reactions()[measure_ind].products)
newrate.efficiencies = gas.reactions()[measure_ind].efficiencies
newrate.rate = ct.Arrhenius(
k,
gas.reactions()[measure_ind].rate.temperature_exponent,
gas.reactions()[measure_ind].rate.activation_energy)
gas.modify_reaction(measure_ind, newrate)
if (gas.reaction_type(measure_ind) == 4):
newrate = ct.FalloffReaction(
reactants=gas.reactions()[measure_ind].reactants,
products=gas.reactions()[measure_ind].products)
newrate.efficiencies = gas.reactions()[measure_ind].efficiencies
newrate.falloff = gas.reactions()[measure_ind].falloff
newrate.low_rate = ct.Arrhenius(
k,
gas.reactions()[measure_ind].low_rate.temperature_exponent,
gas.reactions()[measure_ind].low_rate.temperature_exponent,
gas.reactions()[measure_ind].low_rate.activation_energy)
newrate.high_rate = gas.reactions()[measure_ind].high_rate
gas.modify_reaction(measure_ind, newrate)
sys.stdout.flush()
for i in range(0, nmeasure):
states = runsim_nosense(tmaxes[i], temperatures[i], pressures[i],
initials[i])
for n in maxes:
lst1 = observations[i].X[:, n]
lst2 = states.X[:, n]
ind1 = np.array(np.where(np.sign(np.diff(lst1)) == -1))[0, 0]
if np.any(np.sign(np.diff(lst2)) == -1):
ind2 = np.array(np.where(np.sign(np.diff(lst2)) == -1))[0, 0]
else:
ind2 = len(lst2) - 1
ret += ((1.0 * ind2 / ind1 - 1)**2 +
(lst2[ind2] / lst1[ind1] - 1)**2) / nmeasure
if (outflag == 1):
print(temperatures[i], tmaxes[i], pressures[i] / ct.one_atm,
(1.0 * ind2 / ind1 - 1), (lst2[ind2] / lst1[ind1] - 1))
sys.stdout.flush()
for n in yields:
lst1 = observations[i].X[:, n]
lst2 = states.X[:, n]
ret += ((lst2[-1] / lst1[-1] - 1)**2) / nmeasure
if (outflag == 1):
print(temperatures[i], tmaxes[i], pressures[i] / ct.one_atm,
(lst2[-1] / lst1[-1] - 1))
sys.stdout.flush()
if (outflag == 1):
rstop = timeit.default_timer()
print('iter time: %f' % (rstop - rstart))
print('residual: ', ret)
print('x: ', eta)
sys.stdout.flush()
return np.sqrt(ret)
if (outflag == 1):
print(result)
sys.stdout.flush()
reactions = gas.reaction_equations()
if (gas.reaction_type(measure_ind) == 1):
newrate = ct.ElementaryReaction(
gas.reactions()[measure_ind].reactants,
gas.reactions()[measure_ind].products)
newrate.rate = ct.Arrhenius(
k,
gas.reactions()[measure_ind].rate.temperature_exponent,
gas.reactions()[measure_ind].rate.activation_energy)
gas.modify_reaction(measure_ind, newrate)
if (gas.reaction_type(measure_ind) == 2):
newrate = ct.ThreeBodyReaction(
reactants=gas.reactions()[measure_ind].reactants,
products=gas.reactions()[measure_ind].products)
newrate.efficiencies = gas.reactions()[measure_ind].efficiencies
newrate.rate = ct.Arrhenius(
k,
gas.reactions()[measure_ind].rate.temperature_exponent,
gas.reactions()[measure_ind].rate.activation_energy)
gas.modify_reaction(measure_ind, newrate)
if (gas.reaction_type(measure_ind) == 4):
newrate = ct.FalloffReaction(
reactants=gas.reactions()[measure_ind].reactants,
products=gas.reactions()[measure_ind].products)
newrate.efficiencies = gas.reactions()[measure_ind].efficiencies
newrate.falloff = gas.reactions()[measure_ind].falloff
newrate.low_rate = ct.Arrhenius(
k,
def _build_cantera_solution(cls, gdata):
p_ref = gdata['ref_pressure']
species_list = list()
for s in gdata['species']:
spec = gdata['species'][s]
ctspec = ct.Species(
s, ','.join(
[f'{k}:{spec["atom_map"][k]}' for k in spec['atom_map']]))
if spec['cp'][0] == 'constant':
Tmin, Tmax, T0, h0, s0, cp = spec['cp'][1:]
ctspec.thermo = ct.ConstantCp(Tmin, Tmax, p_ref,
list([T0, h0, s0, cp]))
elif spec['cp'][0] == 'NASA7':
Tmin, Tmid, Tmax, low_coeffs, high_coeffs = spec['cp'][1:]
coeffs = [Tmid] + high_coeffs + low_coeffs
ctspec.thermo = ct.NasaPoly2(Tmin, Tmax, p_ref, coeffs)
species_list.append(ctspec)
reaction_list = list()
for rxn in gdata['reactions']:
type, reactants_stoich, products_stoich, reversible = rxn[:4]
fwd_pre_exp_value, fwd_temp_exponent, fwd_act_energy = rxn[4:7]
fwd_rate = ct.Arrhenius(fwd_pre_exp_value, fwd_temp_exponent,
fwd_act_energy)
if type == 'simple' or type == 'simple-special':
ctrxn = ct.ElementaryReaction(reactants_stoich,
products_stoich)
ctrxn.rate = fwd_rate
elif type == 'three-body' or type == 'three-body-special':
ctrxn = ct.ThreeBodyReaction(reactants_stoich, products_stoich)
ctrxn.rate = fwd_rate
ctrxn.efficiencies = rxn[7]
ctrxn.default_efficiency = rxn[8]
elif type == 'Lindemann' or type == 'Lindemann-special':
ctrxn = ct.FalloffReaction(reactants_stoich, products_stoich)
ctrxn.efficiencies = rxn[7]
ctrxn.default_efficiency = rxn[8]
flf_pre_exp_value, flf_temp_exponent, flf_act_energy = rxn[
9:12]
ctrxn.high_rate = fwd_rate
ctrxn.low_rate = ct.Arrhenius(flf_pre_exp_value,
flf_temp_exponent,
flf_act_energy)
ctrxn.falloff = ct.Falloff()
elif type == 'Troe' or type == 'Troe-special':
ctrxn = ct.FalloffReaction(reactants_stoich, products_stoich)
ctrxn.efficiencies = rxn[7]
ctrxn.default_efficiency = rxn[8]
flf_pre_exp_value, flf_temp_exponent, flf_act_energy = rxn[
9:12]
troe_params = rxn[12]
ctrxn.high_rate = fwd_rate
ctrxn.low_rate = ct.Arrhenius(flf_pre_exp_value,
flf_temp_exponent,
flf_act_energy)
if len(troe_params) == 4 and abs(troe_params[3]) < 1e-300:
ctrxn.falloff = ct.TroeFalloff(troe_params[:3])
else:
ctrxn.falloff = ct.TroeFalloff(troe_params)
if 'special' in type:
ctrxn.orders = rxn[-1]
ctrxn.reversible = reversible
reaction_list.append(ctrxn)
return ct.Solution(thermo='IdealGas',
kinetics='GasKinetics',
species=species_list,
reactions=reaction_list)
def set_mechanism(self, mech_dict, species_dict={}, bnds=[]):
def get_Arrhenius_parameters(entry):
A = entry['pre_exponential_factor']
b = entry['temperature_exponent']
Ea = entry['activation_energy']
return A, b, Ea
if len(species_dict) == 0:
species = self.gas.species()
else:
species = []
for n in range(len(species_dict)):
s_dict = species_dict[n]
s = ct.Species(name=s_dict['name'],
composition=s_dict['composition'],
charge=s_dict['charge'],
size=s_dict['size'])
thermo = s_dict['type'](s_dict['T_low'], s_dict['T_high'],
s_dict['P_ref'], s_dict['coeffs'])
s.thermo = thermo
species.append(s)
# Set kinetics data
rxns = []
for rxnIdx in range(len(mech_dict)):
if 'ElementaryReaction' == mech_dict[rxnIdx]['rxnType']:
rxn = ct.ElementaryReaction(mech_dict[rxnIdx]['reactants'],
mech_dict[rxnIdx]['products'])
rxn.allow_negative_pre_exponential_factor = True
A, b, Ea = get_Arrhenius_parameters(
mech_dict[rxnIdx]['rxnCoeffs'][0])
rxn.rate = ct.Arrhenius(A, b, Ea)
elif 'ThreeBodyReaction' == mech_dict[rxnIdx]['rxnType']:
rxn = ct.ThreeBodyReaction(mech_dict[rxnIdx]['reactants'],
mech_dict[rxnIdx]['products'])
A, b, Ea = get_Arrhenius_parameters(
mech_dict[rxnIdx]['rxnCoeffs'][0])
rxn.rate = ct.Arrhenius(A, b, Ea)
rxn.efficiencies = mech_dict[rxnIdx]['rxnCoeffs'][0][
'efficiencies']
elif 'PlogReaction' == mech_dict[rxnIdx]['rxnType']:
rxn = ct.PlogReaction(mech_dict[rxnIdx]['reactants'],
mech_dict[rxnIdx]['products'])
rates = []
for plog in mech_dict[rxnIdx]['rxnCoeffs']:
pressure = plog['Pressure']
A, b, Ea = get_Arrhenius_parameters(plog)
rates.append((pressure, ct.Arrhenius(A, b, Ea)))
rxn.rates = rates
elif 'FalloffReaction' == mech_dict[rxnIdx]['rxnType']:
rxn = ct.FalloffReaction(mech_dict[rxnIdx]['reactants'],
mech_dict[rxnIdx]['products'])
# high pressure limit
A, b, Ea = get_Arrhenius_parameters(
mech_dict[rxnIdx]['rxnCoeffs']['high_rate'])
rxn.high_rate = ct.Arrhenius(A, b, Ea)
# low pressure limit
A, b, Ea = get_Arrhenius_parameters(
mech_dict[rxnIdx]['rxnCoeffs']['low_rate'])
rxn.low_rate = ct.Arrhenius(A, b, Ea)
# falloff parameters
if mech_dict[rxnIdx]['rxnCoeffs']['falloff_type'] == 'Troe':
falloff_param = mech_dict[rxnIdx]['rxnCoeffs'][
'falloff_parameters']
if falloff_param[-1] == 0.0:
falloff_param = falloff_param[0:-1]
rxn.falloff = ct.TroeFalloff(falloff_param)
else:
rxn.falloff = ct.SriFalloff(
mech_dict[rxnIdx]['rxnCoeffs']['falloff_parameters'])
rxn.efficiencies = mech_dict[rxnIdx]['rxnCoeffs'][
'efficiencies']
elif 'ChebyshevReaction' == mech_dict[rxnIdx]['rxnType']:
rxn = ct.ChebyshevReaction(mech_dict[rxnIdx]['reactants'],
mech_dict[rxnIdx]['products'])
rxn.set_parameters(Tmin=mech_dict['Tmin'],
Tmax=mech_dict['Tmax'],
Pmin=mech_dict['Pmin'],
Pmax=mech_dict['Pmax'],
coeffs=mech_dict['coeffs'])
rxn.duplicate = mech_dict[rxnIdx]['duplicate']
rxn.reversible = mech_dict[rxnIdx]['reversible']
rxn.allow_negative_orders = True
rxn.allow_nonreactant_orders = True
rxns.append(rxn)
self.gas = ct.Solution(thermo='IdealGas',
kinetics='GasKinetics',
species=species,
reactions=rxns)
self.set_rate_expression_coeffs(bnds) # set copy of coeffs
self.set_thermo_expression_coeffs() # set copy of thermo coeffs
def toCantera(self, speciesList=None, useChemkinIdentifier = False):
"""
Converts the RMG Reaction object to a Cantera Reaction object
with the appropriate reaction class.
If useChemkinIdentifier is set to False, the species label is used
instead. Be sure that species' labels are unique when setting it False.
"""
from rmgpy.kinetics import Arrhenius, ArrheniusEP, MultiArrhenius, PDepArrhenius, MultiPDepArrhenius, Chebyshev, ThirdBody, Lindemann, Troe
import cantera as ct
if speciesList is None:
speciesList = []
# Create the dictionaries containing species strings and their stoichiometries
# for initializing the cantera reaction object
ctReactants = {}
for reactant in self.reactants:
if useChemkinIdentifier:
reactantName = reactant.toChemkin()
else:
reactantName = reactant.label
if reactantName in ctReactants:
ctReactants[reactantName] += 1
else:
ctReactants[reactantName] = 1
ctProducts = {}
for product in self.products:
if useChemkinIdentifier:
productName = product.toChemkin()
else:
productName = product.label
if productName in ctProducts:
ctProducts[productName] += 1
else:
ctProducts[productName] = 1
if self.kinetics:
if isinstance(self.kinetics, Arrhenius):
# Create an Elementary Reaction
ctReaction = ct.ElementaryReaction(reactants=ctReactants, products=ctProducts)
elif isinstance(self.kinetics, MultiArrhenius):
# Return a list of elementary reactions which are duplicates
ctReaction = [ct.ElementaryReaction(reactants=ctReactants, products=ctProducts) for arr in self.kinetics.arrhenius]
elif isinstance(self.kinetics, PDepArrhenius):
ctReaction = ct.PlogReaction(reactants=ctReactants, products=ctProducts)
elif isinstance(self.kinetics, MultiPDepArrhenius):
ctReaction = [ct.PlogReaction(reactants=ctReactants, products=ctProducts) for arr in self.kinetics.arrhenius]
elif isinstance(self.kinetics, Chebyshev):
ctReaction = ct.ChebyshevReaction(reactants=ctReactants, products=ctProducts)
elif isinstance(self.kinetics, ThirdBody):
ctReaction = ct.ThreeBodyReaction(reactants=ctReactants, products=ctProducts)
elif isinstance(self.kinetics, Lindemann) or isinstance(self.kinetics, Troe):
ctReaction = ct.FalloffReaction(reactants=ctReactants, products=ctProducts)
else:
raise NotImplementedError('Not able to set cantera kinetics for {0}'.format(self.kinetics))
# Set reversibility, duplicate, and ID attributes
if isinstance(ctReaction,list):
for rxn in ctReaction:
rxn.reversible = self.reversible
# Set the duplicate flag to true since this reaction comes from multiarrhenius or multipdeparrhenius
rxn.duplicate = True
# Set the ID flag to the original rmg index
rxn.ID = str(self.index)
else:
ctReaction.reversible = self.reversible
ctReaction.duplicate = self.duplicate
ctReaction.ID = str(self.index)
self.kinetics.setCanteraKinetics(ctReaction, speciesList)
return ctReaction
else:
raise Exception('Cantera reaction cannot be created because there was no kinetics.')
