{
"cells": [
{
"cell_type": "markdown",
"id": "8382e30e-2fac-41f1-ae50-baf0fc9f4f22",
"metadata": {},
"source": [
"# Exploring the change of delta_x (spatial resolution) in diffusion accuracy.\n",
"#### From the same initial setup, diffusion is carried out over a fixed time span,\n",
"#### at different spatial resolutions - and then the respective results are compared\n",
"\n",
"LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "b3ae84bc-72b9-4043-b5b9-70532eafdb44",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Added 'D:\\Docs\\- MY CODE\\BioSimulations\\life123-Win7' to sys.path\n"
]
}
],
"source": [
"import set_path # Importing this module will add the project's home directory to sys.path"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "52bd1bf4",
"metadata": {},
"outputs": [],
"source": [
"from experiments.get_notebook_info import get_notebook_basename\n",
"\n",
"from life123 import BioSim1D\n",
"from life123 import ChemData as chem\n",
"from life123 import Numerical as num\n",
"\n",
"import plotly.express as px\n",
"from life123 import HtmlLog as log\n",
"from life123 import GraphicLog"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "7a4dd331-d083-4929-b7f1-089f44776f85",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"-> Output will be LOGGED into the file 'spatial_resolution_1.log.htm'\n"
]
}
],
"source": [
"# Initialize the HTML logging\n",
"log_file = get_notebook_basename() + \".log.htm\" # Use the notebook base filename for the log file\n",
"\n",
"# Set up the use of some specified graphic (Vue) components\n",
"GraphicLog.config(filename=log_file,\n",
" components=[\"vue_heatmap_11\", \"vue_curves_3\"])"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "14b4a1c2-9854-41c6-b407-6008bb4738be",
"metadata": {},
"outputs": [],
"source": [
"# Set the heatmap parameters (for the log file)\n",
"heatmap_pars = {\"range\": [0, 150],\n",
" \"outer_width\": 850, \"outer_height\": 150,\n",
" \"margins\": {\"top\": 30, \"right\": 30, \"bottom\": 30, \"left\": 55}\n",
" }\n",
"\n",
"# Set the parameters of the line plots\n",
"lineplot_pars = {\"range\": [0, 150],\n",
" \"outer_width\": 850, \"outer_height\": 250,\n",
" \"margins\": {\"top\": 30, \"right\": 30, \"bottom\": 30, \"left\": 55}\n",
" }"
]
},
{
"cell_type": "markdown",
"id": "28c89c3d-a7f7-41d9-a99b-b0185620b5c1",
"metadata": {},
"source": [
"## Prepare the initial system"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "01b3a969-5122-4c25-900b-ad6fba315553",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"SYSTEM STATE at Time t = 0:\n",
"60 bins and 1 species:\n",
" Species 0 (A). Diff rate: 0.1. Conc: [ 10. 13. 17. 21. 25. 28. 30. 38. 42. 55. 65. 47. 35. 32.\n",
" 27. 23. 20. 17. 14. 8. 3. 10. 16. 18. 20. 25. 30. 35.\n",
" 40. 65. 85. 115. 150. 92. 73. 69. 65. 50. 42. 36. 20. 45.\n",
" 50. 55. 69. 82. 95. 77. 60. 43. 37. 31. 25. 22. 20. 18.\n",
" 15. 11. 9. 8.]\n"
]
}
],
"source": [
"chem_data = chem(names=[\"A\"], diffusion_rates=[0.1])\n",
"\n",
"conc_list=[10,13,17,21,25,28,30,38,42,55,65,47,35,32,27,23,20,17,14,8,3,10,16,18,\n",
" 20,25,30,35,40,65,85,115,150,92,73,69,65,50,42,36,20,45,50,55,69,82,95,\n",
" 77,60,43,37,31,25,22,20,18,15,11,9, 8]\n",
"\n",
"bio = BioSim1D(n_bins=len(conc_list), chem_data=chem_data)\n",
"\n",
"bio.set_species_conc(species_name=\"A\", conc_list=conc_list)\n",
"\n",
"bio.describe_state()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "1ae4f7f8-ad6f-4ff0-b484-c6e698164042",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
" \n",
" "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"hovertemplate": "Chemical=A
Bin number=%{x}
concentration=%{y}