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

# # Diffusion of 2 chemicals in 1D
# 
# ## Two symmetric initial concentration pulses (near the opposite edges of the system) diffusing out towards equilibrium, with identical diffusion rates
# 
# Symmetry is observed throughout

# ### TAGS :  "diffusion 1D", "basic"

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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 life123 import BioSim1D, ChemData, check_version


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check_version(LIFE123_VERSION)


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# ## Prepare the initial system
# with a non-zero bin concentration of the chemical `A`, near the left edge of the system,   
# and an identical bin concentration of the chemical `B`, near the left edge

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chem_data = ChemData(names=["A", "B"], diffusion_rates=[0.1, 0.1], plot_colors=["turquoise", "green"])

bio = BioSim1D(n_bins=10, chem_data=chem_data)


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bio.inject_conc_to_bin(bin_address=2, chem_label="A", delta_conc=10.)
bio.inject_conc_to_bin(bin_address=7, chem_label="B", delta_conc=10.)

bio.describe_state()


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bio.system_snapshot()


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bio.visualize_system(title_prefix="Diffusion")   # Line curve view


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bio.system_heatmaps(title_prefix="Diffusion")


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# ## Request history-keeping for some bins

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# Request to save the concentration history at the bins with the initial concentration injection, 
# and the bins at the ends of the system
bio.enable_history(bins=[0, 2, 7, 9], frequency=3, take_snapshot=True)    


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# # Initial Diffusion Step

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# Advancing to time t=10, with time steps of 0.1 ...
delta_time = 10.

status = bio.diffuse(total_duration=delta_time, time_step=0.1)
print(status)

bio.describe_state(concise=True)


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bio.visualize_system(title_prefix="Diffusion")   # Line curve view


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bio.system_heatmaps(title_prefix="Diffusion")


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# ## This is still an early stage in the diffusion process; let's advance it more...  
# (Visualization from results shown at selected times)

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for i in range(50):
    status = bio.diffuse(total_duration=delta_time, time_step=0.1)

    if i<2 or i==6 or i>=49:
        bio.describe_state(concise=True)
    
        # Line curve view
        fig = bio.visualize_system(title_prefix="Diffusion")   # Line curve view
        fig.show()
        
        # Heatmap view
        fig = bio.system_heatmaps()
        fig.show()


# ## All bins now have essentially uniform concentration
# 
# **Mass conservations**: The initial "10 units of concentration" are now uniformly spread across the 10 bins, leading to a near-constant concentration of 10/10 = **1.0**

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# Mass conservation can also be verified as follows:
bio.check_mass_conservation(chem_label="A", expected=10.)


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bio.check_mass_conservation(chem_label="B", expected=10.)


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# ## Visualization of time changes at particular bins

# #### Instead of visualizing the entire system at a moment of time, like in the previous heatmaps, let's now look at the time evolution of the (only) chemical `A` at either of the bins whose history we requested prior to running the simulation

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bio.conc_history.bin_history(bin_address=2)   # The bin where the initial concentration of `A` was applied


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bio.plot_history_single_bin(bin_address=2)


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bio.plot_history_single_bin(bin_address=7)  # The bin where the initial concentration of `B` was applied


# Notice the symmetery between bins 2 and 7 (if you switch `A` and `B`)

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bio.plot_history_single_bin(bin_address=0)   # Left "edge" of the 1D system


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bio.plot_history_single_bin(bin_address=9)   # Right "edge" of the 1D system


# Notice the symmetery between bins 0 and 9 (if you switch `A` and `B`)

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