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

# ## A strong, localized transient concentration becomes irrelevant with distance
# 
# Diffusion of a narrow, bell-shaped, initial concentration of a single chemical.   
# With increasing distance from the initial location of the transient signal, hardly any change with time is detected as the system goes to equilibrium

# ### TAGS :  "diffusion 1D"

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LAST_REVISED = "Aug. 10, 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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# Initialize the system
chem_data = ChemData(diffusion_rates=10.)    # Name "A" automatically assigned to only chemical

bio = BioSim1D(n_bins=500, chem_data=chem_data)


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# Set up the initial bell-shape concentration, with the very narrow peak close to one end of the system,
# centered at 1/10 of the width of the system, i.e. at bin 50
bio.inject_bell_curve(chem_label="A", center=0.1, sd=0.005, amplitude=0.1, bias=10.)


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df = bio.describe_state()
df


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df[df.columns[38:62:2]]  # Zoom in where the action is


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# Visualize the system state so far
bio.visualize_system(title_prefix="Initial strong, localized transient")


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# Show as heatmap
bio.system_heatmaps(title_prefix="Initial strong, localized transient")


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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, or near, both ends of the system
bio.enable_history(bins=[0, 25, 48, 50, 100, 200, 400], frequency=25, take_snapshot=True)    


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# ## Start the diffusion

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bio.diffuse(total_duration=5, time_step=0.01)


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bio.visualize_system()


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bio.system_heatmaps()


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# ### Scrutinize the changes with time, at bins increasingly further away from the transient peak of bin 50

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bio.plot_history_single_bin(title_prefix="Bin with the concentration injection.", bin_address=50)


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bio.plot_history_single_bin(title_prefix="Bin very close to the location of the concentration injection.", bin_address=48)


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bio.plot_history_single_bin(title_prefix="Bin relatively far from the location of the concentration injection.", bin_address=25)


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# ### Continue the diffusion, to equilibrium

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# Do several rounds of diffusion, over relatively small time steps
for _ in range(5):
    bio.diffuse(total_duration=25, time_step=0.02)
    bio.visualize_system(show=True)


# #### Notice how the wave of diffusion hits the left edge of the system

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# Do more rounds of diffusion, over larger time steps
for _ in range(5):
    bio.diffuse(total_duration=400, time_step=0.025)
    bio.visualize_system(show=True)


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bio.system_heatmaps()


# #### We're now close to equilibrium

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# ### Scrutinize the changes with time, at bins increasingly further away from the transient peak of bin 50

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bio.plot_history_single_bin(title_prefix="Bin with the concentration injection.", bin_address=50)


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bio.plot_history_single_bin(title_prefix="Bin very close to the location of the concentration injection.", bin_address=48)


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bio.plot_history_single_bin(title_prefix="Bin relatively far from the location of the concentration injection.", bin_address=25)


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bio.plot_history_single_bin(title_prefix="Bin also relatively far from the location of the concentration injection (but on opposite side).", 
                            bin_address=0)


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bio.plot_history_single_bin(title_prefix="Bin quite far from the location of the concentration injection.", bin_address=100)


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bio.plot_history_single_bin(title_prefix="Bin very far from the location of the concentration injection.", bin_address=200)


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bio.plot_history_single_bin(title_prefix="Bin hugely far from the location of the concentration injection.", bin_address=400)


# # Notice how faraway locations (such as bin 400) barely register that the distant transient ever happened!

# #### **VARIATION:**   
# Transients that never make it far from their origin, because of _chemical reactions consuming them_, are explored in the experiment `1D/reaction_diffusion/transient_getting_mopped_up`

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