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[Python] Enable creation of Kinetics objects from Reaction objects

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This commit is contained in:
Ray Speth 2015-04-28 00:20:02 -04:00
parent 23642ded3c
commit 25c2d6c781
4 changed files with 105 additions and 6 deletions
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5
interfaces/cython/cantera/_cantera.pxd
View file

@ -300,6 +300,11 @@ cdef extern from "cantera/kinetics/Kinetics.h" namespace "Cantera":
CxxThermoPhase& thermo(int)
void addPhase(CxxThermoPhase&) except +
void init() except +
void addReaction(shared_ptr[CxxReaction]) except +
void finalize() except +
shared_ptr[CxxReaction] reaction(size_t) except +
cbool isReversible(int) except +
int reactionType(int) except +

23
interfaces/cython/cantera/base.pyx
View file

@ -1,6 +1,7 @@
cdef class _SolutionBase:
def __cinit__(self, infile='', phaseid='', phases=(), origin=None,
source=None, thermo=None, species=(), **kwargs):
source=None, thermo=None, species=(), kinetics=None,
reactions=(), **kwargs):
# Shallow copy of an existing Solution (for slicing support)
cdef _SolutionBase other
if origin is not None:
@ -21,7 +22,7 @@ cdef class _SolutionBase:
if infile or source:
self._init_cti_xml(infile, phaseid, phases, source)
elif thermo and species:
self._init_parts(thermo, species)
self._init_parts(thermo, species, kinetics, phases, reactions)
else:
raise ValueError("Arguments are insufficient to define a phase")
@ -72,7 +73,7 @@ cdef class _SolutionBase:
else:
self.kinetics = NULL
def _init_parts(self, thermo, species):
def _init_parts(self, thermo, species, kinetics, phases, reactions):
"""
Instantiate a set of new Cantera C++ objects based on a string defining
the model type and a list of Species objects.
@ -84,9 +85,21 @@ cdef class _SolutionBase:
self.thermo.addSpecies(S._species)
self.thermo.initThermo()
if not kinetics:
kinetics = "none"
cdef ThermoPhase phase
cdef Reaction reaction
if isinstance(self, Kinetics):
# Not yet implemented
self.kinetics = CxxNewKinetics(stringify("none"))
self.kinetics = CxxNewKinetics(stringify(kinetics))
self.kinetics.addPhase(deref(self.thermo))
for phase in phases:
self.kinetics.addPhase(deref(phase.thermo))
self.kinetics.init()
for reaction in reactions:
self.kinetics.addReaction(reaction._reaction)
self.kinetics.finalize()
def __getitem__(self, selection):
copy = self.__class__(origin=self)

2
interfaces/cython/cantera/kinetics.pyx
View file

@ -313,7 +313,7 @@ cdef class InterfaceKinetics(Kinetics):
A kinetics manager for heterogeneous reaction mechanisms. The
reactions are assumed to occur at an interface between bulk phases.
"""
def __init__(self, infile, phaseid='', phases=(), *args, **kwargs):
def __init__(self, infile='', phaseid='', phases=(), *args, **kwargs):
super().__init__(infile, phaseid, phases, *args, **kwargs)
if self.kinetics.type() not in (kinetics_type_interface,
kinetics_type_edge):

81
interfaces/cython/cantera/test/test_kinetics.py
View file

@ -1,6 +1,7 @@
import unittest
import numpy as np
import re
import itertools
import cantera as ct
from . import utilities
@ -143,6 +144,86 @@ class TestKinetics(utilities.CanteraTest):
self.phase.delta_standard_gibbs)
class KineticsFromReactions(utilities.CanteraTest):
"""
Test for Kinetics objects which are constructed directly from Reaction
objects instead of from CTI/XML files.
"""
def test_idealgas(self):
gas1 = ct.Solution('h2o2.xml')
S = ct.Species.listFromFile('h2o2.xml')
R = ct.Reaction.listFromFile('h2o2.xml')
gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
species=S, reactions=R)
self.assertEqual(gas1.n_reactions, gas2.n_reactions)
gas1.TPY = 800, 2*ct.one_atm, 'H2:0.3, O2:0.7, OH:2e-4, O:1e-3, H:5e-5'
gas2.TPY = gas1.TPY
self.assertTrue((gas1.reactant_stoich_coeffs() ==
gas2.reactant_stoich_coeffs()).all())
self.assertTrue((gas1.product_stoich_coeffs() ==
gas2.product_stoich_coeffs()).all())
self.assertArrayNear(gas1.delta_gibbs,
gas2.delta_gibbs)
self.assertArrayNear(gas1.reverse_rate_constants,
gas2.reverse_rate_constants)
self.assertArrayNear(gas1.net_production_rates,
gas2.net_production_rates)
def test_surface(self):
gas_species = ct.Species.listFromFile('gri30.xml')
surf_species = ct.Species.listFromFile('ptcombust.xml')
reactions = ct.Reaction.listFromFile('ptcombust.xml')
gas = ct.Solution('ptcombust.xml', 'gas')
surf1 = ct.Interface('ptcombust.xml', 'Pt_surf', [gas])
surf2 = ct.Interface(thermo='Surface', kinetics='interface',
species=surf_species, reactions=reactions,
phases=[gas])
surf1.site_density = surf2.site_density = 5e-9
gas.TP = surf2.TP = surf1.TP = 900, 2*ct.one_atm
surf2.concentrations = surf1.concentrations
self.assertEqual(surf1.n_reactions, surf2.n_reactions)
for k,i in itertools.product(['PT(S)','H2','OH','OH(S)'],
range(surf1.n_species)):
self.assertEqual(surf1.reactant_stoich_coeff(k,i),
surf2.reactant_stoich_coeff(k,i))
self.assertEqual(surf1.product_stoich_coeff(k,i),
surf2.product_stoich_coeff(k,i))
for i in range(surf1.n_reactions):
r1 = surf1.reaction(i)
r2 = surf2.reaction(i)
self.assertEqual(r1.reactants, r2.reactants)
self.assertEqual(r1.products, r2.products)
self.assertEqual(r1.rate.preexponential_factor,
r2.rate.preexponential_factor)
self.assertEqual(r1.rate.temperature_exponent,
r2.rate.temperature_exponent)
self.assertEqual(r1.rate.activation_energy,
r2.rate.activation_energy)
self.assertArrayNear(surf1.delta_enthalpy,
surf2.delta_enthalpy)
self.assertArrayNear(surf1.forward_rate_constants,
surf2.forward_rate_constants)
self.assertArrayNear(surf1.reverse_rate_constants,
surf2.reverse_rate_constants)
rop1 = surf1.net_production_rates
rop2 = surf2.net_production_rates
for k in gas.species_names + surf1.species_names:
k1 = surf1.kinetics_species_index(k)
k2 = surf2.kinetics_species_index(k)
self.assertNear(rop1[k1], rop2[k2])
class KineticsRepeatability(utilities.CanteraTest):
"""
Tests to make sure that lazily evaluated of terms in the rate expression