{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#  Cell Division\n",
    "<hr style=\"border-top-width: 4px; border-top-color: #34609b;\">\n",
    "\n",
    "\n",
    "This model creates a grid of 4x4x4 cells. Each cell grows untill a specific\n",
    "volume, after which it proliferates (i.e. divides)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%jsroot on\n",
    "gROOT->LoadMacro(\"${BDMSYS}/etc/binder_rootlogon.C\");"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create a new simulation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "Simulation simulation(\"cell_division\");"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's define the number of cells we wish to create along each dimension,\n",
    " the spacing between the cells, and each cell's diameter."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "size_t cells_per_dim = 4;\n",
    "size_t spacing = 20;\n",
    "size_t diameter = 10;"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To define how are cells will look like we will create a construct in the\n",
    " form of a C++ lambda as follows."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "auto construct = [&](const Double3& position) {\n",
    "  Cell* cell = new Cell(position);\n",
    "  cell->SetDiameter(diameter);\n",
    "  // Add the \"grow and divide\" behavior to each cell\n",
    "  cell->AddBiologyModule(new GrowDivide());\n",
    "  return cell;\n",
    "};\n",
    "ModelInitializer::Grid3D(cells_per_dim, spacing, construct);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Run simulation for one timestep"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "simulation.Simulate(1);\n",
    "\n",
    "std::cout << \"Simulation completed successfully!\" << std::endl;"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " Let's visualize the output!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "VisualizeInNotebook();"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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   "codemirror_mode": "text/x-c++src",
   "file_extension": ".C",
   "mimetype": " text/x-c++src",
   "name": "c++"
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