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

# ### A minimalist 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.
# 
# LAST REVISED: Dec. 3, 2023

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import set_path      # Importing this module will add the project's home directory to sys.path


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from src.modules.reactions.reaction_dynamics import ReactionDynamics


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# ## Initialize the System

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# Instantiate the simulator and specify the chemicals
dynamics = ReactionDynamics(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, in their declared index order
dynamics.set_conc([80., 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(colors=['red', 'green'], show_intervals=True)


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


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