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

# ## One-bin reaction `2A + 5B <-> 4C + 3D`, with 1st-order kinetics for each species, taken to equilibrium
# 
# Diffusion not applicable (just 1 bin)

# ### TAGS :  "reactions 1D", "under-the-hood"

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LAST_REVISED = "June 6, 2025"
LIFE123_VERSION = "1.0.0rc6"        # Library version this experiment is based on


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


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#import sys
#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 BioSim1D, ChemData, check_version

from life123 import HtmlLog as log
from life123 import GraphicLog


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check_version(LIFE123_VERSION)


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# 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")


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# Initialize the system; NOTE: Diffusion not applicable (just 1 bin)
chem_data = ChemData(names=["A", "B", "C", "D"], plot_colors=['navy', 'cyan', 'red', 'orange'])    

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

bio.set_all_uniform_concentrations( [4., 7., 5., 2.] )

bio.describe_state()


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# Specify the reaction
reactions = bio.get_reactions()

# Reaction 2A + 5B <-> 4C + 3D , with 1st-order kinetics for each species
reactions.add_reaction(reactants=[(2,"A",1) , (5,"B",1)], products=[(4,"C",1) , (3,"D",1)],
                       forward_rate=5., reverse_rate=2.)

reactions.describe_reactions()


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# Send a header and a plot to the HTML log file
log.write("Reaction 2 A + 5 B <-> 4 C + 3 D",
          style=log.h2)
reactions.plot_reaction_network("vue_cytoscape_2")


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


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bio.get_bin_history(bin_address=0)


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# ### First step

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bio.get_reaction_handler().enable_diagnostics()   # To save diagnostic information for the simulation run, below


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# First step
bio.react(time_step=0.001, n_steps=1)
bio.describe_state()


# _Early in the reaction :_
# [A] = 3.76 ,  [B] = 6.4 ,  [C] = 5.48 ,  [D] = 2.36

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bio.get_bin_history(bin_address=0)


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# ### <a name="sec_2"></a>Numerous more steps

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# Numerous more steps
bio.react(time_step=0.001, n_steps=40)

bio.describe_state()


# ### <a name="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 following equilibrium:  
# [A] = 2.80284552 , [B] = 4.00711381 , [C] = 7.39430896 , [D] = 3.79573172

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


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df = bio.get_bin_history(bin_address=0)
df


# A and B get depleted, while C and D get produced.
# 
# **2A + 5B <-> 4C + 3D**

# #### Let's verify that the stoichiometry is being respected

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# We'll check the first two arrays of concentrations, from the run's history
arr0 = bio.get_reaction_handler().get_historical_concentrations(row=0, df=df)
arr1 = bio.get_reaction_handler().get_historical_concentrations(row=1, df=df)
arr0, arr1


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# Check that the changes in the first reaction step conform to the stoichiometry
bio.get_reaction_handler().get_diagnostics().stoichiometry_checker(rxn_index=0, 
                                                                   conc_arr_before = arr0, 
                                                                   conc_arr_after = arr1)


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arr1 - arr0


# Indeed, the change in [A] is -2 x 0.12, and the change in [B] is -5 X 0.12,  
#   while the change in [C] is  4 x 0.12, and the change in [D] is  3 X 0.12

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(arr1 - arr0) / 0.12    # 0.12 is the "moles of reactions" change


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# # Plots of changes of concentration with time

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bio.plot_history_single_bin(bin_address=0, 
                            title_prefix="Reaction `2A + 5B <-> 4C + 3D`")


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