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  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
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   "source": [
    "import warnings\n",
    "from pylj import md, sample\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "warnings.filterwarnings('ignore')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "source": [
    "def md_simulation(number_of_particles, temperature, box_length, number_of_steps, sample_frequency):\n",
    "    # Creates the visualisation environment\n",
    "    %matplotlib notebook\n",
    "    # Initialise the system\n",
    "    system = md.initialise(number_of_particles, temperature, box_length, 'square')\n",
    "    # This sets the sampling class\n",
    "    sample_system = sample.MaxBolt(system)\n",
    "    # Start at time 0\n",
    "    system.time = 0\n",
    "    # Begin the molecular dynamics loop\n",
    "    for i in range(0, number_of_steps):\n",
    "        # Run the equations of motion integrator algorithm, this \n",
    "        # includes the force calculation\n",
    "        system.integrate(md.velocity_verlet)\n",
    "        # Sample the thermodynamic and structural parameters of the system\n",
    "        system.md_sample()\n",
    "        # Allow the system to interact with a heat bath\n",
    "        system.heat_bath(temperature)\n",
    "        # Iterate the time\n",
    "        system.time += system.timestep_length\n",
    "        system.step += 1\n",
    "        # At a given frequency sample the positions and plot the RDF\n",
    "        if system.step % sample_frequency == 0:\n",
    "            sample_system.update(system)\n",
    "    return system"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The `md_simulation` function takes five variables:\n",
    "- The number of particles\n",
    "- The simulation temperature\n",
    "- The simulation cell vector\n",
    "- The number of steps\n",
    "- The sampling frequency (how often the image is updated)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "md_simulation(20, 1000, 100, 50000, 100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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