{
"cells": [
{
"cell_type": "markdown",
"id": "e6111b3f",
"metadata": {},
"source": [
"# Basic\n",
"\n",
"We will define a simple model of\n",
"water creation from hydrogen and oxygen.\n",
"\n",
"First,\n",
"we need to import `EmptyCompartment` and `Species`,\n",
"a `Synthesis` reaction,\n",
"and a `Simulator` to integrate the equations."
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "26e276c6",
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"\n",
"from simbio.components import EmptyCompartment, Species\n",
"from simbio.reactions.single import Synthesis\n",
"from simbio.simulator import Simulator"
]
},
{
"cell_type": "markdown",
"id": "3bd0c330",
"metadata": {},
"source": [
"To define the model,\n",
"we create 3 species,\n",
"corresponding to\n",
"hydrogen $H₂$, oxygen $O₂$, and water $H₂O$,\n",
"with initial conditions of `1`, `1` and `0`,\n",
"respectively.\n",
"And we add a `create_water` reaction,\n",
"corresponding to $2 H₂ + O₂ → 2 H₂ O$,\n",
"with a rate of `1`."
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "6828da32",
"metadata": {},
"outputs": [],
"source": [
"class Model(EmptyCompartment):\n",
" H2: Species = 1\n",
" O2: Species = 1\n",
" H2O: Species = 0\n",
"\n",
" create_water = Synthesis(A=2 * H2, B=O2, AB=2 * H2O, rate=1)"
]
},
{
"cell_type": "markdown",
"id": "504be334",
"metadata": {},
"source": [
"To simulate it,\n",
"we feed the model named `Model` into `Simulator`,\n",
"and use the `.run()` method.\n",
"It will compile and integrate an `ODE`-based simulation,\n",
"returning a `pandas.DataFrame` with the result:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "d0566f41",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" H2 | \n",
" O2 | \n",
" H2O | \n",
"
\n",
" \n",
" | time | \n",
" | \n",
" | \n",
" | \n",
"
\n",
" \n",
" \n",
" \n",
" | 0.00000 | \n",
" 1.000000 | \n",
" 1.000000 | \n",
" 0.000000 | \n",
"
\n",
" \n",
" | 0.10101 | \n",
" 0.838051 | \n",
" 0.919025 | \n",
" 0.161949 | \n",
"
\n",
" \n",
" | 0.20202 | \n",
" 0.728306 | \n",
" 0.864153 | \n",
" 0.271694 | \n",
"
\n",
" \n",
" | 0.30303 | \n",
" 0.647931 | \n",
" 0.823965 | \n",
" 0.352069 | \n",
"
\n",
" \n",
" | 0.40404 | \n",
" 0.585968 | \n",
" 0.792984 | \n",
" 0.414032 | \n",
"
\n",
" \n",
"
\n",
"