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

# ## One-bin reaction `2A <-> B`  
# ### COMPARING 1st-order and 2nd-order kinetics in *forward* direction; reverse direction always 1-st order
# 
# Diffusion not applicable (just 1 bin)
# 
# See also the experiment _"reactions_single_compartment/react_4"_ 

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

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LAST_REVISED = "June 5, 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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# # INITIALLY, with 1st-order kinetics in both directions

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

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

bio.set_all_uniform_concentrations( [3., 5.] )

bio.describe_state()


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# Specify the reaction
reactions = bio.get_reactions()

# Reaction  2A <-> B , FOR NOW with 1st-order kinetics in both directions
reactions.add_reaction(reactants=[(2, "A", 1)], products="B", 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 2A <-> B is 1st order in all species:",
          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=0.02, n_steps=1)
bio.describe_state()


# Small conc. changes so far:  [A] = 2.8 , [B] = 5.1

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bio.get_bin_history(bin_address=0)


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# Numerous more steps, to equilibrium
bio.react(time_step=0.02, n_steps=20)

bio.describe_state()


# Consistent with the 5/2 ratio of forward/reverse rates (and the *1st order* reactions),
# the systems settles in the following equilibrium:  
# [A] = 2.16928427 , [B] = 5.41535786

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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


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bio.plot_history_single_bin(bin_address=0, 
                            title_prefix="Reaction `2A <-> B`")


# A gets depleted, while B gets produced.

# #### 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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bio.get_reaction_handler().get_diagnostics().stoichiometry_checker(rxn_index=0, 
                               conc_arr_before = arr0, 
                               conc_arr_after = arr1)


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# # STARTING OVER, this time with 2nd-order kinetics in the forward reaction

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reactions = bio.get_reactions()


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reactions.clear_reactions_data()


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# Reaction  2A <-> B , NOW WITH 2nd-order kinetics in the forward direction
reactions.add_reaction(reactants=[(2, "A", 2)], products="B", forward_rate=5., reverse_rate=2.)


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reactions.describe_reactions()


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# RESET the concentrations to their original values
bio.set_all_uniform_concentrations( [3., 5.] )

bio.describe_state()


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# Save this manual concentration change into the ongoing history
bio.capture_snapshot(caption="RESET all concentrations to initial values")
bio.get_bin_history(bin_address=0)


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# Send a header and a plot to the HTML log file
log.write("Reaction 2A <-> B is 2nd order in A, and 1st order in B:",
          style=log.h2)
reactions.plot_reaction_network("vue_cytoscape_2")


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# First step
bio.react(time_step=0.02, n_steps=1)
bio.describe_state()


# [A] = 1.6 , [B] = 5.7
# _(Contrast with the counterpart in the 1st order kinetics:  [A] = 2.8 , [B] = 5.1)_

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bio.get_bin_history(bin_address=0)


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# Numerous more steps
bio.react(time_step=0.02, n_steps=20)

bio.describe_state()


# The systems settles in the following equilibrium:  [A] = 1.51554944 , [B] = 5.74222528

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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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bio.plot_history_single_bin(bin_address=0, 
                            title_prefix="Reaction `2A <-> B` (the jump at 0.42 is the concentration reset)",
                            vertical_lines_to_add=[0.42])


# In[32]:


df2 = bio.get_bin_history(bin_address=0)
df2


# **Compared to first-order kinetics in A**, the (2nd order in A) reaction now takes place much more quickly, and proceeds to almost complete depletion of A

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

# In[33]:


# We'll check the first two arrays of concentrations, from the run's history
arr0 = bio.get_reaction_handler().get_historical_concentrations(row=22, df=df2)  # Row 22 is the conc. reset
arr1 = bio.get_reaction_handler().get_historical_concentrations(row=23, df=df2)
arr0, arr1


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bio.get_reaction_handler().get_diagnostics().stoichiometry_checker(rxn_index=0, 
                                                       conc_arr_before = arr0, 
                                                       conc_arr_after = arr1)


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