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Microfluidics Flow past a Yeast Cell #201

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Microfluidics Flow past a Yeast Cell #201

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227 changes: 227 additions & 0 deletions examples/Microfluidics Flow/Microfluidics Flow.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "cd233b01",
"metadata": {},
"source": [
"# Microfluidics flow past Yeast Cell with SpatialPy"
]
},
{
"cell_type": "markdown",
"id": "ed346aba",
"metadata": {},
"source": [
"## Definition of the model"
]
},
{
"cell_type": "markdown",
"id": "110aa888",
"metadata": {},
"source": [
"### Imports and definitions"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "3724e038",
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import sys\n",
"import math\n",
"sys.path.insert(1, \"../../\")\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"\n",
"import spatialpy"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "21e18b70",
"metadata": {},
"outputs": [],
"source": [
"class Fluid(spatialpy.Geometry):\n",
" def __init__(self, external_radius):\n",
" self.ers = external_radius**2\n",
" \n",
" def create_particles(self, domain, xmin, xmax, ymin, ymax, zmin, zmax, delta):\n",
" Np = 0\n",
" for x in np.arange(xmin, xmax+delta, delta):\n",
" for y in np.arange(ymin, ymax+delta, delta):\n",
" for z in np.arange(zmin, zmax+delta, delta):\n",
" if self.inside((x, y, z), False):\n",
" domain.add_point([x, y, z], type=0, vol=1, mass=1, nu=0, fixed=False)\n",
" Np += 1\n",
" return Np\n",
" \n",
" def inside(self, x, on_boundary):\n",
" return x[0]**2 + x[1]**2 + x[2]**2 > self.ers"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "90b0634a",
"metadata": {},
"outputs": [],
"source": [
"class CellWall(spatialpy.Geometry):\n",
" def __init__(self, external_radius, internal_radius):\n",
" self.ers = external_radius**2\n",
" self.irs = internal_radius**2\n",
" \n",
" def create_particles(self, domain, external_radius, delta):\n",
" Np = 0\n",
" for x in np.arange(-external_radius, external_radius+delta, delta):\n",
" for y in np.arange(-external_radius, external_radius+delta, delta):\n",
" for z in np.arange(-external_radius, external_radius+delta, delta):\n",
" if self.inside((x, y, z), False):\n",
" domain.add_point([x, y, z], type=0, vol=1, mass=1, nu=0, fixed=False)\n",
" Np += 1\n",
" return Np\n",
" \n",
" def inside(self, x, on_boundary):\n",
" radius = x[0]**2 + x[1]**2 + x[2]**2\n",
" return radius < self.ers and radius > self.irs"
]
},
{
"cell_type": "markdown",
"id": "6f7417b4",
"metadata": {},
"source": [
"### Model"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "2b454eb2",
"metadata": {},
"outputs": [],
"source": [
"class MicrofluidicsFlow(spatialpy.Model):\n",
" FLUID = 1\n",
" \n",
" def __init__(self, model_name=\"Microfluidics Flow past Yeast Cell\"):\n",
" spatialpy.Model.__init__(self, model_name)\n",
" \n",
" # System Constants\n",
" Lxint = 80e-6\n",
" Lyint = 40e-6\n",
" Lzint = 20e-6\n",
" radius_external = 2.5e-6\n",
" radius_internal = 2.4e-6\n",
" rhof = rhoc = 1000\n",
" \n",
" # Species\n",
" \n",
" # Discretization\n",
" Npx = 40\n",
" \n",
" # Compute domain bounds (including the boundary)\n",
" deltaf = Lxint/Npx\n",
" deltac = deltaf/3\n",
" xmin = -Lxint/2\n",
" xmax = Lxint/2\n",
" ymin = -Lyint/2\n",
" ymax = Lyint/2\n",
" zmin = -Lzint/2\n",
" zmax = Lzint/2\n",
" \n",
" # Domain\n",
" domain = spatialpy.Domain(\n",
" 0, xlim=(xmin, xmax), ylim=(ymin, ymax), zlim=(zmin, zmax), gravity=[0, -1, 0]\n",
" )\n",
" # Fluid Region\n",
" fluid_region = Fluid(radius_external)\n",
" Nfp = fluid_region.create_particles(domain, xmin, xmax, ymin, ymax, zmin, zmax, deltaf)\n",
" # Cell Wall Region\n",
" cell_region = CellWall(radius_external, radius_internal)\n",
" Ncp = cell_region.create_particles(domain, radius_external, deltac)\n",
" \n",
" self.add_domain(domain)\n",
" \n",
" # Compute volume and mass per particle\n",
" vol = Lxint*Lyint*Lzint\n",
" vol_cell_int = 4/3*math.pi*math.pow(radius_internal, 3)\n",
" vol_cell_ext = 4/3*math.pi*math.pow(radius_external, 3)\n",
" vol_cell_wall = vol_cell_ext-vol_cell_int\n",
" vol_fluid = vol-vol_cell_ext\n",
" mfluid = vol_fluid*rhof/Nfp\n",
" mcell = vol_cell_wall*rhoc/Ncp\n",
" \n",
" # Types\n",
" \n",
" # Static Domain\n",
" \n",
" # Initial Conditions\n",
" \n",
" # Boundary Conditions\n",
" \n",
" # Timespan\n",
" dt = 1e-6\n",
" nt = 10000000\n",
" freq_results = 100\n",
" self.timespan(np.arange(0, (nt + 1) * dt, freq_results * dt), timestep_size=dt)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5fd22cfc",
"metadata": {},
"outputs": [],
"source": [
"model = MicrofluidicsFlow()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "cb8b3513",
"metadata": {},
"outputs": [],
"source": [
"model.domain"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ff946d58",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.9.7"
}
},
"nbformat": 4,
"nbformat_minor": 5
}