#!/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
# 
# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)

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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 experiments.get_notebook_info import get_notebook_basename

from life123 import BioSim1D

import plotly.express as px

from life123 import ChemData as chem
from life123 import HtmlLog as log
from life123 import GraphicLog


# In[3]:


# Initialize the HTML logging
log_file = get_notebook_basename() + ".log.htm"    # Use the notebook base filename for the log file
GraphicLog.config(filename=log_file,
                  components=["vue_heatmap_11", "vue_curves_3"])


# In[4]:


# Set the heatmap parameters
heatmap_pars = {"range": [0, 2.5],
                "outer_width": 850, "outer_height": 150,
                "margins": {"top": 30, "right": 30, "bottom": 30, "left": 55}
                }

# Set the parameters of the line plots
lineplot_pars = {"range": [0, 10],
                "outer_width": 850, "outer_height": 250,
                "margins": {"top": 30, "right": 30, "bottom": 30, "left": 55}
                }


# In[5]:


# Initialize the system
chem_data = chem(names=["A"], diffusion_rates=[0.1])
bio = BioSim1D(n_bins=9, chem_data=chem_data)

bio.set_uniform_concentration(species_index=0, conc=0.)

# 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(species_index=0, bin_address=2, delta_conc=10.)
bio.inject_conc_to_bin(species_index=0, bin_address=6, delta_conc=10.)

bio.describe_state()


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bio.show_system_snapshot()


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fig = px.line(data_frame=bio.system_snapshot(), y=["A"], 
              title= f"Diffusion. System snapshot at time t={bio.system_time}",
              color_discrete_sequence = ['red'],
              labels={"value":"concentration", "variable":"Chemical", "index":"Bin number"})
fig.show()


# In[8]:


# Output to the log file
log.write("1-D diffusion to equilibrium of a single species, with Diffusion rate 0.1. Time steps of 0.1",
          style=log.h2)

log.write(f"System state at time t={bio.system_time}:", blanks_before=2, style=log.bold)

# Output a heatmap to the log file
bio.single_species_heatmap(species_index=0, heatmap_pars=heatmap_pars, header=f"Time {bio.system_time} :\n", graphic_component="vue_heatmap_11")
# Output a line plot the log file
bio.single_species_line_plot(species_index=0, plot_pars=lineplot_pars, graphic_component="vue_curves_3")


# # 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)

    fig = px.line(data_frame=bio.system_snapshot(), y=["A"], 
              title= f"Diffusion. System snapshot at time t={bio.system_time}",
              color_discrete_sequence = ['red'],
              labels={"value":"concentration", "variable":"Chemical", "index":"Bin number"})
    fig.show()

    #if i<2 or i==6 or i>=14:
    bio.single_species_heatmap(species_index=0, heatmap_pars=heatmap_pars, header=f"Time {bio.system_time}\n", graphic_component="vue_heatmap_11")
    # Output a line plot the log file
    bio.single_species_line_plot(species_index=0, plot_pars=lineplot_pars, graphic_component="vue_curves_3")


# **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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