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

# ### One-bin `A <-> 3B` reaction, with 1st-order kinetics in both directions,
# ### taken to equilibrium
# 
# Diffusion not applicable (just 1 bin)
# 
# LAST REVISED: May 6, 2024
# 
# * [First Step](#reaction_2_sec_2_first_step)
# * [Numerous more steps](#reaction_2_sec_2)
# * [Equilibrium](#reaction_2_sec_2_equilibrium)

# In[1]:


import set_path      # Importing this module will add the project's home directory to sys.path


# In[2]:


from experiments.get_notebook_info import get_notebook_basename

from src.modules.chemicals.chem_data import ChemData as chem
from src.life_1D.bio_sim_1d import BioSim1D

import plotly.express as px
from src.modules.visualization.graphic_log import GraphicLog


# In[3]:


# Initialize the HTML logging
log_file = get_notebook_basename() + ".log.htm"    # Use the notebook base filename for the log file

# Set up the use of some specified graphic (Vue) components
GraphicLog.config(filename=log_file,
                  components=["vue_cytoscape_2"],
                  extra_js="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.21.2/cytoscape.umd.js")


# In[4]:


# Initialize the system
chem_data = chem(names=["A", "B"])     # NOTE: Diffusion not applicable (just 1 bin)

# Reaction A <-> 3B , with 1st-order kinetics in both directions
chem_data.add_reaction(reactants=["A"], products=[(3,"B",1)], forward_rate=5., reverse_rate=2.)

bio = BioSim1D(n_bins=1, chem_data=chem_data)

bio.set_uniform_concentration(species_index=0, conc=10.)
bio.set_uniform_concentration(species_index=1, conc=50.)

bio.describe_state()


# In[5]:


chem_data.describe_reactions()


# In[6]:


# Save the state of the concentrations of all species at bin 0
bio.add_snapshot(bio.bin_snapshot(bin_address = 0), caption="Initial state")
bio.get_history()


# In[7]:


# Send the plot to the HTML log file
chem_data.plot_reaction_network("vue_cytoscape_2")


# ### <a name="reaction_2_sec_2_first_step"></a>First step

# In[8]:


# First step
bio.react(time_step=0.1, n_steps=1, snapshots={"sample_bin": 0})
bio.describe_state()


# _Early in the reaction :_  
# [A] = 15.   [B] = 35.

# In[9]:


bio.get_history()


# ### <a name="reaction_2_sec_2"></a>Numerous more steps

# In[10]:


# Numerous more steps
bio.react(time_step=0.1, n_steps=10, snapshots={"sample_bin": 0})

bio.describe_state()


# ### <a name="reaction_2_sec_2_equilibrium"></a>Equilibrium

# Consistent with the 5/2 ratio of forward/reverse rates (and the 1st order reactions),
# the systems settles in the equilibrium:   [A] = 14.54545455 , [B] = 36.36363636

# In[11]:


# Verify that the reaction has reached equilibrium
bio.reaction_dynamics.is_in_equilibrium(conc=bio.bin_snapshot(bin_address = 0))


# In[12]:


bio.get_history()


# Note how the simulation initially **OVERSHOT** the equilibrium values; the first step was too large!

# # Plots of changes of concentration with time

# In[13]:


fig = px.line(data_frame=bio.get_history(), x="SYSTEM TIME", y=["A", "B"], 
              title="Changes in concentrations with time",
              color_discrete_sequence = ['navy', 'darkorange'],
              labels={"value":"concentration", "variable":"Chemical"})
fig.show()


# In[14]:


# Same plot, but with smooth line
fig = px.line(data_frame=bio.get_history(), x="SYSTEM TIME", y=["A", "B"], 
              title="Changes in concentrations with time (smoothed)",
              color_discrete_sequence = ['navy', 'darkorange'],
              labels={"value":"concentration", "variable":"Chemical"},
              line_shape="spline")
fig.show()


# The early **OVERSHOOTING** of the equilibrium values shows prominently in the last plot!

# In[ ]: