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

# In[ ]:


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
get_ipython().run_line_magic('matplotlib', 'inline')


# In[ ]:


R = 8.314472
T_K = 300
dH=80e3
dS=10
rsys1 = ReactionSystem.from_string("""
NOBr -> NO + Br; EyringParam(dH={dH}*J/mol, dS={dS}*J/K/mol)
""".format(dH=dH, dS=dS))
kref = 20836643994.118652*T_K*np.exp(-(dH - T_K*dS)/(R*T_K))
kref


# In[ ]:


NOBr0_M = 0.7
init_cond = dict(
    NOBr=NOBr0_M*u.M,
    NO=0*u.M,
    Br=0*u.M
)
t = 5*u.second
params = dict(
    temperature=T_K*u.K
)


# In[ ]:


def integrate_and_plot(rsys):
    odesys, extra = get_odesys(rsys, unit_registry=si, constants=const)
    fig, axes = plt.subplots(1, 3, figsize=(14, 6))
    res = odesys.integrate(t, init_cond, params, integrator='cvode')
    t_sec = to_unitless(res.xout, u.second)
    NOBr_ref = NOBr0_M*np.exp(-kref*t_sec)
    cmp = to_unitless(res.yout, u.M)
    ref = np.empty_like(cmp)
    ref[:, odesys.names.index('NOBr')] = NOBr_ref
    ref[:, odesys.names.index('Br')] = NOBr0_M - NOBr_ref
    ref[:, odesys.names.index('NO')] = NOBr0_M - NOBr_ref
    assert np.allclose(cmp, ref)
    axes[0].plot(t_sec, cmp)
    axes[1].plot(t_sec, cmp - ref)
    res.plot_invariant_violations(ax=axes[2])


# In[ ]:


integrate_and_plot(rsys1)


# In[ ]:


rsys2 = ReactionSystem.from_string("""
NOBr -> NO + Br; MassAction(EyringHS([{dH}*J/mol, {dS}*J/K/mol]))
""".format(dH=dH, dS=dS))


# In[ ]:


integrate_and_plot(rsys2)