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

# # Membranes, with selective permeability, separate 2 previously fully-mixed chemicals
# 
# #### The membranes are permeable to one of the chemicals, and impermeable to the other one.  
# 
# See also experiment `diffusion_3`, where a transient separation is achieved WITHOUT membranes

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

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LAST_REVISED = "May 31, 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, os
#os.getcwd()
#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, PlotlyHelper, check_version


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check_version(LIFE123_VERSION)


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# ## Prepare the initial system
# with two chemicals `A` and `B`

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chem_data = ChemData(diffusion_rates=[2., 2.], plot_colors=["turquoise", "green"])   # Names "A", "B" automatically assigned

bio = BioSim1D(n_bins=9, chem_data=chem_data)


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bio.set_bin_conc(bin_address=4, chem_label="A", conc=10.)
bio.set_bin_conc(bin_address=4, chem_label="B", conc=10.)

bio.set_membranes(membranes=[ (4,5) ])    # By default impermeable
bio.change_permeability("B", 1.)          # Permeable to `B` (and only to `B`)

bio.describe_state()


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bio.system_snapshot()


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bio.system_heatmaps()


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# ## Request history-keeping for some bins

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# Request to save the concentration history at the bin with the initial concentration injection, 
# and at a couple of other bins
bio.enable_history(bins=[0, 2, 4], frequency=3, take_snapshot=True)    


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# ## Now, let's start the diffusion

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bio.diffuse(time_step=0.02, n_steps=1)


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bio.system_snapshot()


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bio.system_heatmaps()


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bio.visualize_system()   # Line curve view


# ### The concentrations of `A` and `B` start to differ
# The membranes are impermeable to `A` but permeable to `B`
# 

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# ### Let's advance the diffusion

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bio.diffuse(time_step=0.02, n_steps=4)


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bio.system_heatmaps()


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bio.visualize_system()   # Line curve view


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bio.diffuse(time_step=0.02, n_steps=15)


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bio.system_heatmaps()


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bio.visualize_system()   # Line curve view


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# ## Finally, let's advance the diffusion to equilibrium

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bio.diffuse(time_step=0.02, n_steps=600)


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bio.system_heatmaps()


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bio.visualize_system()   # Line curve view


# # The membranes, with their selective permeability, have managed to separate the previously fully-mixed `A` and `B`|

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# #### Verify that the total amount of each chemicals hasn't changed; in the case of `B`, it has simply shifted across bins

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# Let's verify mass conservation
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 in time, like in the previous diagrams, let's now look at the time evolution of the concentrations of `A` and `B` at selected bins (bins whose history-keeping we requested prior to running the simulation)

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bio.plot_history_single_bin(bin_address=4, title_prefix="`A` and `B` get separated")


# ## The transient separation of `A` and `B` is best seen by plotting the difference of their concentrations, as a function of time

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bin4_hist = bio.conc_history.bin_history(bin_address=4)   # The bin where the initial concentration of `A` and `B` was applied
bin4_hist


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PlotlyHelper.plot_curves(x=bin4_hist['SYSTEM TIME'], y = bin4_hist['A'] - bin4_hist['B'], 
                         x_label="SYSTEM TIME", y_label="[A] - [B]", 
                         colors="purple", title="The separation of `A` and `B`, as seen in central bin 4")


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# ## The separation of `A` and `B` is also seen in other bins...

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bio.plot_history_single_bin(bin_address=0, title_prefix="The separation of `A` and `B` happens at other bins, too...")


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bio.plot_history_single_bin(bin_address=2, title_prefix="The separation of `A` and `B` happens at other bins, too...")


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