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import math
from collections import defaultdict
import matplotlib.pyplot as plt
from chempy import ReactionSystem
from chempy.kinetics.ode import get_odesys
from chempy.kinetics.rates import SinTemp
%matplotlib inline


    

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rsys = ReactionSystem.from_string("""
2 HNO2 -> H2O + NO + NO2; MassAction(EyringHS.fk('dH1', 'dS1'))
2 NO2 -> N2O4; MassAction(EyringHS.fk('dH2', 'dS2'))
""")  # fictitious thermodynamic parameters


    

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st = SinTemp(unique_keys='Tbase Tamp Tangvel Tphase'.split())


    

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class Constants:
    Planck_constant = 6.63e-34
    Boltzmann_constant = 1.38e-23
    molar_gas_constant = 8.314

odesys, extra = get_odesys(rsys, include_params=False, substitutions={'temperature': st}, constants=Constants())


    

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init_conc = defaultdict(lambda: 0, HNO2=1, H2O=55)
params = dict(
    Tbase=300,
    Tamp=10,
    Tangvel=2*math.pi/10,
    Tphase=-math.pi/2,
    dH1=85e3,
    dS1=10,
    dH2=70e3,
    dS2=20
)
duration = 60


    

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def integrate_and_plot(system):
    result = system.integrate(duration, init_conc, params, integrator='cvode', nsteps=2000)
    fig, axes = plt.subplots(1, 2, figsize=(14, 4))
    result.plot(names='NO HNO2 N2O4'.split(), ax=axes[0])
    result.plot(names='NO2'.split(), ax=axes[1])
    print({k: v for k, v in sorted(result.info.items()) if not k.startswith('internal')})


    

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integrate_and_plot(odesys)


    

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odesys.param_names


    

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len(odesys.exprs)


    

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asys = odesys.as_autonomous()
len(asys.exprs)


    

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[a - o for a, o in zip(asys.exprs[:-1],odesys.exprs)]


    

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asys.exprs[-1]


    

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asys.get_jac()[:-1,:-1] - odesys.get_jac()


    

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import sympy as sym
sym.init_printing()
args = _x, _y, _p = asys.pre_process(*asys.to_arrays(1, init_conc, params))
args


    

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asys.f_cb(*args)


    

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asys.j_cb(*args)


    

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argsode = odesys.pre_process(*odesys.to_arrays(1, init_conc, params))
argsode


    

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argsode[0] - args[0], argsode[1] - args[1][:-1], argsode[2] - args[2]


    

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odesys.f_cb(*argsode)


    

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odesys.j_cb(*argsode)


    

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integrate_and_plot(asys)


    

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odesys.ny, asys.ny


    

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asys.pre_process(1, [0,1,2,3,4], [5,6,7,8])


    

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