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

# ### A MINIMALIST, "get-started", demonstration for the reaction `A <-> B`,
# with 1st-order kinetics in both directions, taken to equilibrium.
# 
# **"No frills!"**  For advanced graphics, analysis, diagnostics, fine-tuning, etc, please see other experiments.

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LAST_REVISED = "July 24, 2024"
LIFE123_VERSION = "1.0.0.beta.37"      # 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

import life123


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life123.check_version(LIFE123_VERSION)


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# ## Initialize the System

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# Instantiate the simulator and specify the chemicals
dynamics = life123.UniformCompartment(names=["A", "B"])  

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

dynamics.describe_reactions()


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# Set the initial concentrations of all the chemicals
dynamics.set_conc({"A": 80., "B": 10.})


# ## Run the reaction

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dynamics.single_compartment_react(initial_step=0.1, target_end_time=1.)   # Using defaults for all other parameters


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dynamics.get_history()   # The system's history, saved during the run of single_compartment_react()


# ## Plots changes of concentration with time  
# Notice that adaptive variable time steps were automatically taken

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dynamics.plot_history(show_intervals=True)


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# Verify that the reaction has reached equilibrium
dynamics.is_in_equilibrium()


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