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

# ## `A <-> B` reaction, with 1st-order kinetics in both directions,
# ### taken to equilibrium
# 
# Diffusion NOT done

# ### TAGS :  "reactions 2D"

# In[1]:


LAST_REVISED = "Dec. 16, 2024"
LIFE123_VERSION = "1.0-rc.1"        # 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
#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 UniformCompartment, BioSim2D, GraphicLog


# In[4]:


# 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[5]:


# Initialize the system.  NOTE: Diffusion not done
uc = UniformCompartment(names=["A", "B"])

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

uc.describe_reactions()


# In[6]:


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


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bio = BioSim2D(n_bins=(3,4), reaction_handler=uc)

bio.set_bin_conc_all_species(bin_x=0, bin_y=0, conc_list=[10.,50.])
bio.set_bin_conc_all_species(bin_x=0, bin_y=1, conc_list=[20.,35.])
bio.set_bin_conc_all_species(bin_x=2, bin_y=3, conc_list=[5.,100.])

bio.describe_state()


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# ## First step

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# First step (NOTE: here we're using a lower-level function that doesn't update the system state;
#                   it only computes the delta_reactions array)
bio.reaction_step(delta_time=0.1)
print("bio.delta_reactions:\n", bio.delta_reactions)


# In[9]:


bio.system += bio.delta_reactions       # Matrix operation to update all the concentrations
bio.system_time += 0.1

bio.describe_state()


# ## Second step

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# NOTE: now, we're using a highel-level function that also updates the system state
bio.react(time_step=0.1, n_steps=1)
bio.describe_state()


# ## Many more steps, to equilibrium

# In[11]:


bio.react(time_step=0.1, n_steps=8)
bio.describe_state()


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bio.react(time_step=0.1, n_steps=10)
bio.describe_state()


# ### The system has now reached equilibrium
# ### in individual bins, which remain separate because we're NOT doing diffusion in this experiment

# Verify the equilibrium in each of the active bins

# In[13]:


bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={"A": 23.99998665, "B": 36.00001335})


# In[14]:


bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={"A": 21.99999809, "B": 33.00000191})


# In[15]:


bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={"A": 41.99996471, "B": 63.00003529}, explain=False)


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