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Release v2.4.10
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public_models/3D-Cylinder.proj/3D_cylinder.wkgp/3D_cylinder.ipynb
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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# 3D Cylinder Demo\n", | ||
| "***\n", | ||
| "This is an example of a 3D reaction diffusion system.\n", | ||
| "\n", | ||
| "- The domain is a cylinder\n", | ||
| "- Species A is created at the right end of the cylinder\n", | ||
| "- Species B is created at the left end of the cylinder\n", | ||
| "- Diffusion occurs throughout the volume of the cylinder\n", | ||
| "- A and B are destroyed on contact\n", | ||
| "- Deterministic and Stochastic simulations are run\n", | ||
| "\n", | ||
| "This example allows us to check if reaction diffusion dynamics are accurate.\n", | ||
| "***\n", | ||
| "## Setup the Environment\n", | ||
| "***" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import spatialpy" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "***\n", | ||
| "## Create the 3D Cylinder Model\n", | ||
| "***" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "def create_3D_cylinder():\n", | ||
| " model = spatialpy.Model(\"3D_cylinder\")\n", | ||
| " \n", | ||
| " # Define Domain Type IDs as constants of the Model\n", | ||
| " model.MIDDLE = 'Middle'\n", | ||
| " model.EDGE1 = 'Edge1'\n", | ||
| " model.EDGE2 = 'Edge2'\n", | ||
| " \n", | ||
| " # Domain\n", | ||
| " domain = spatialpy.Domain.read_stochss_domain('3D_cylinder.smdl')\n", | ||
| " model.add_domain(domain)\n", | ||
| "\n", | ||
| " model.staticDomain = True\n", | ||
| "\n", | ||
| " # Variables\n", | ||
| " A = spatialpy.Species(name=\"A\", diffusion_coefficient=0.1, restrict_to=[model.MIDDLE, model.EDGE1])\n", | ||
| " B = spatialpy.Species(name=\"B\", diffusion_coefficient=0.1, restrict_to=[model.MIDDLE, model.EDGE2])\n", | ||
| " model.add_species([A, B])\n", | ||
| "\n", | ||
| " # Parameters\n", | ||
| " k_react = spatialpy.Parameter(name=\"k_react\", expression=\"1\")\n", | ||
| " k_creat1 = spatialpy.Parameter(name=\"k_creat1\", expression=\"100\")\n", | ||
| " k_creat2 = spatialpy.Parameter(name=\"k_creat2\", expression=\"100\")\n", | ||
| " left = spatialpy.Parameter(name=\"left\", expression=\"0.5092013833059308\")\n", | ||
| " right = spatialpy.Parameter(name=\"right\", expression=\"0.505804729089437\")\n", | ||
| " model.add_parameter([k_react, k_creat1, k_creat2, left, right])\n", | ||
| "\n", | ||
| " # Reactions\n", | ||
| " r1 = spatialpy.Reaction(\n", | ||
| " name=\"r1\", restrict_to=[model.EDGE1],\n", | ||
| " reactants={}, products={'A': 1},\n", | ||
| " propensity_function=\"k_creat1 / left * vol\",\n", | ||
| " ode_propensity_function=\"k_creat1\"\n", | ||
| " )\n", | ||
| " r2 = spatialpy.Reaction(\n", | ||
| " name=\"r2\", restrict_to=[model.EDGE2],\n", | ||
| " reactants={}, products={'B': 1},\n", | ||
| " propensity_function=\"k_creat2 / right * vol\",\n", | ||
| " ode_propensity_function=\"k_creat2\"\n", | ||
| " )\n", | ||
| " r3 = spatialpy.Reaction(\n", | ||
| " name=\"r3\", rate=\"k_react\",\n", | ||
| " reactants={'A': 1, 'B': 1}, products={}\n", | ||
| " )\n", | ||
| " model.add_reaction([r1, r2, r3])\n", | ||
| "\n", | ||
| " # Timespan\n", | ||
| "# tspan = spatialpy.TimeSpan.arange(1, t=500, timestep_size=1e-3)\n", | ||
| " tspan = spatialpy.TimeSpan.arange(1, t=500, timestep_size=1)\n", | ||
| " model.timespan(tspan)\n", | ||
| " return model" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### Instantiate the Model" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "model = create_3D_cylinder()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "***\n", | ||
| "## Simulation Parameters\n", | ||
| "***" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "def configure_simulation():\n", | ||
| " kwargs = {\n", | ||
| " # \"number_of_trajectories\":1,\n", | ||
| " # \"seed\":None,\n", | ||
| " }\n", | ||
| " return kwargs" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "***\n", | ||
| "## Run the Simulation\n", | ||
| "***" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "kwargs = configure_simulation()\n", | ||
| "results = model.run(**kwargs)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "***\n", | ||
| "## Visualization\n", | ||
| "***" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "results.plot_species('A', animated=True, width=None, height=None)" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.8.5" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 4 | ||
| } |
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public_models/3D-Cylinder.proj/3D_cylinder.wkgp/3D_cylinder.smdl
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