#!/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)
# 
# * [First Step](#reaction_2_sec_2_first_step)
# * [Numerous more steps](#reaction_2_sec_2)
# * [Equilibrium](#reaction_2_sec_2_equilibrium)

# ### TAGS :  "reactions 1D"

# In[1]:


LAST_REVISED = "May 4, 2025"
LIFE123_VERSION = "1.0.0rc3"        # Library version this experiment is based on


# In[2]:


#import set_path                    # Using MyBinder?  Uncomment this before running the next cell!


# In[3]:


#import sys, os
#os.getcwd()
#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path

from experiments.get_notebook_info import get_notebook_basename

from life123 import ChemData, BioSim1D, check_version

from life123 import GraphicLog


# In[4]:


check_version(LIFE123_VERSION)


# In[ ]:





# In[5]:


# 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[6]:


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

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

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

bio.describe_state()


# In[7]:


# Specify the reaction
reactions = bio.get_reactions()

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

reactions.describe_reactions()


# In[8]:


# Send the plot of the reaction network to the HTML log file
reactions.plot_reaction_network("vue_cytoscape_2")


# In[ ]:





# In[9]:


# Let's enable history - by default for all chemicals and all bins
bio.enable_history(take_snapshot=True, caption="Initial state")


# In[10]:


bio.get_bin_history(bin_address=0)


# In[ ]:





# In[ ]:





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

# In[11]:


# First step
bio.react(time_step=0.1, n_steps=1)
bio.describe_state()


# In[12]:


bio.get_bin_history(bin_address=0)


# In[ ]:





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

# In[13]:


# Numerous more steps
bio.react(time_step=0.1, n_steps=10)

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[14]:


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


# In[15]:


bio.get_bin_history(bin_address=0)


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

# # Plots of changes of concentration with time

# In[16]:


bio.plot_history_single_bin(bin_address=0, 
                            title="Reaction  A <-> B . Concentrations at bin 0")


# In[17]:


# Same plot, but with smooth line
bio.plot_history_single_bin(bin_address=0, 
                            title="Reaction  A <-> B . Concentrations at bin 0",
                            smoothed=True)


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

# In[ ]: