#!/usr/bin/env python
# coding: utf-8

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import sympy as sm
import matplotlib.pyplot as plt
import numpy as np
from chempy import ReactionSystem
from chempy.units import to_unitless, SI_base_registry as si, default_units as u, default_constants as const
from chempy.kinetics.ode import get_odesys
from chempy.kinetics.integrated import binary_rev
sm.init_printing()
get_ipython().run_line_magic('matplotlib', 'inline')


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R = 8.314472
T_K = 273.15 + 20  # 20 degree celsius
kB = 1.3806504e-23
h = 6.62606896e-34

dHf = 74e3
dSf = R*np.log(h/kB/T_K*1e16)

dHb = 79e3
dSb = dSf - 23

rsys1 = ReactionSystem.from_string("""
Fe+3 + SCN- -> FeSCN+2; EyringParam(dH={dHf}*J/mol, dS={dSf}*J/K/mol)
FeSCN+2 -> Fe+3 + SCN-; EyringParam(dH={dHb}*J/mol, dS={dSb}*J/K/mol)
""".format(dHf=dHf, dSf=dSf, dHb=dHb, dSb=dSb))
kf_ref = 20836643994.118652*T_K*np.exp(-(dHf - T_K*dSf)/(R*T_K))
kb_ref = 20836643994.118652*T_K*np.exp(-(dHb - T_K*dSb)/(R*T_K))
kf_ref, kb_ref


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Fe0 = 6e-3
SCN0 = 2e-3
init_cond = {
    'Fe+3': Fe0*u.M,
    'SCN-': SCN0*u.M,
    'FeSCN+2': 0*u.M
}
t = 3*u.second


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def integrate_and_plot(rsys, params):
    odes, extra = get_odesys(rsys, include_params=False, unit_registry=si, constants=const)
    fig, all_axes = plt.subplots(2, 3, figsize=(14, 6))
    for axes, odesys in zip(all_axes, [odes, odes.as_autonomous()]):
        res = odesys.integrate(t, init_cond, params, integrator='cvode')
        t_sec = to_unitless(res.xout, u.second)
        FeSCN_ref = binary_rev(t_sec, kf_ref, kb_ref, 0, Fe0, SCN0)
        cmp = to_unitless(res.yout, u.M)
        ref = np.empty_like(cmp)
        ref[:, odesys.names.index('FeSCN+2')] = FeSCN_ref
        ref[:, odesys.names.index('Fe+3')] = Fe0 - FeSCN_ref
        ref[:, odesys.names.index('SCN-')] = SCN0 - FeSCN_ref
        axes[0].plot(t_sec, cmp)
        axes[1].plot(t_sec, cmp - ref)
        res.plot_invariant_violations(ax=axes[2])
        assert np.allclose(cmp, ref)
        print({k: v for k, v in res.info.items() if not k.startswith('internal')})    


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integrate_and_plot(rsys1, {'temperature': T_K*u.K})


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rsys2 = ReactionSystem.from_string("""
Fe+3 + SCN- -> FeSCN+2; MassAction(EyringHS([{dHf}*J/mol, {dSf}*J/K/mol]))
FeSCN+2 -> Fe+3 + SCN-; MassAction(EyringHS([{dHb}*J/mol, {dSb}*J/K/mol]))
""".format(dHf=dHf, dSf=dSf, dHb=dHb, dSb=dSb))


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integrate_and_plot(rsys2, {'temperature': T_K*u.K})


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rsys3 = ReactionSystem.from_string("""
Fe+3 + SCN- -> FeSCN+2; MassAction(EyringHS.fk('dHf', 'dSf'))
FeSCN+2 -> Fe+3 + SCN-; MassAction(EyringHS.fk('dHb', 'dSb'))
""")


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integrate_and_plot(rsys3, dict(temperature=T_K*u.K,
                               dHf=dHf*u.J/u.mol, dSf=dSf*u.J/u.mol/u.K,
                               dHb=dHb*u.J/u.mol, dSb=dSb*u.J/u.mol/u.K))