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

# ## Exploring reaching equilibrium
# 
# The system starts out with a pulse in bins near the *left* and the *right* endpoints

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

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LAST_REVISED = "May 3, 2025"
LIFE123_VERSION = "1.0.0rc3"       # 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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# Initialize the system
chem_data = ChemData(names="A", diffusion_rates=0.1)
bio = BioSim1D(n_bins=9, chem_data=chem_data)

# Start out with a pulse in bins near the *left* and the *right* endpoints.  
# A total of 20 "units of concentration" is injected
bio.inject_conc_to_bin(chem_label="A", bin_address=2, delta_conc=10.)
bio.inject_conc_to_bin(chem_label="A", bin_address=6, delta_conc=10.)

bio.describe_state()


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bio.show_system_snapshot()


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# Visualize the system's initial state
bio.visualize_system(title_prefix="Diffusion")


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# Show as heatmap
bio.system_heatmaps(title_prefix="Diffusion")


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# # Start the simulation steps

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delta_time = 3.


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for i in range(15):
    status = bio.diffuse(total_duration=delta_time, time_step=0.1)

    print(f"\nAfter Delta time {delta_time}.  TOTAL TIME {bio.system_time}  ({status['steps']} steps taken):")
    bio.describe_state(concise=True)

    bio.visualize_system(title_prefix="Diffusion", show=True)
    
    bio.system_heatmaps(title_prefix="Diffusion", show=True)


# **All cells now have essentially uniform concentration**
# 
# The "20 units of concentration" are now uniformly spread across the 9 bins, leading to a near-constant concentration of 20/9 = **2.22**

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bio.check_mass_conservation(expected=20., chem_label="A")


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