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  {
   "cell_type": "markdown",
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   "source": [
    "Visualization with inquanto-nglview\n",
    "=============================================\n",
    "\n",
    "It is often useful to visualize certain molecular data.  For this purpose, InQuanto uses an extension to interface with the [NGLview](https://nglviewer.org/#nglview) nglview package.  The [inquanto-nglview](https://docs.quantinuum.com/inquanto/extensions/inquanto-nglview.html) extension is focused on providing some basic visualizing utilities to the user. The return types from the functions are widgets which can be viewed in a jupyter notebook. The functionality includes visualizing molecular structures, fragmentation patterns defined in the `Geometry` object and molecular orbitals.\n",
    "\n",
    "\n",
    "Visualizing Structures\n",
    "-----------------------\n",
    "VisualizerNGL is initialized by an InQuanto Geometry object specifying molecular, or unit cell, geometry. The molecule can then be visualized by calling the\n",
    "`.visualize_molecule()` in the last line of a notebook cell. See below for a short example.\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3328160f",
   "metadata": {},
   "outputs": [],
   "source": [
    "# pip install inquanto-nglview  --index https://...\n",
    "\n",
    "\n",
    "from inquanto.geometries import GeometryMolecular\n",
    "from inquanto.extensions.nglview import VisualizerNGL\n",
    "\n",
    "xyz = [\n",
    "    ['C', [ 0.0000000,  1.4113170, 0.0000000]],\n",
    "    ['C', [ 1.2222370,  0.7056590, 0.0000000]],\n",
    "    ['C', [ 1.2222370, -0.7056590, 0.0000000]],\n",
    "    ['C', [ 0.0000000, -1.4113170, 0.0000000]],\n",
    "    ['C', [-1.2222370, -0.7056590, 0.0000000]],\n",
    "    ['C', [-1.2222370,  0.7056590, 0.0000000]],\n",
    "    ['H', [ 0.0000000,  2.5070120, 0.0000000]],\n",
    "    ['H', [ 2.1711360,  1.2535060, 0.0000000]],\n",
    "    ['H', [ 2.1711360, -1.2535060, 0.0000000]],\n",
    "    ['H', [ 0.0000000, -2.5070120, 0.0000000]],\n",
    "    ['H', [-2.1711360, -1.2535060, 0.0000000]],\n",
    "    ['H', [-2.1711360,  1.2535060, 0.0000000]]\n",
    "]\n",
    "g = GeometryMolecular(xyz)\n",
    "visualizer = VisualizerNGL(g)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "69cf243b",
   "metadata": {},
   "outputs": [],
   "source": [
    "#visualizer.visualize_molecule(atom_labels=\"index\").display(gui=True)\n",
    "#markdown cell below is a presaved image "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "27020847",
   "metadata": {},
   "source": [
    "![1](_images/nglview_img1.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "852415de",
   "metadata": {},
   "source": [
    "Visualizing Fragments\n",
    "----------------------\n",
    "\n",
    "There are several [fragmentation methods](https://docs.quantinuum.com/inquanto/tutorials/tutorial_overview.html#fragmentation-tutorials) available in inquanto, to visualize a fragmentation defined in a `Geometry`\n",
    "object, call the `visualize_fragmentation()` method as illustrated in the code-snippet below.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "12fa4721",
   "metadata": {},
   "outputs": [],
   "source": [
    "g.set_groups(\n",
    "    \"fragments\",\n",
    "    {\n",
    "        \"ch1\": [0, 6],\n",
    "        \"ch2\": [5, 11],\n",
    "        \"ch3\": [4, 10],\n",
    "        \"ch4\": [3, 9],\n",
    "        \"ch5\": [2, 8],\n",
    "        \"ch6\": [1, 7]\n",
    "    }\n",
    ")\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b63ef40b",
   "metadata": {},
   "outputs": [],
   "source": [
    "#visualizer.visualize_fragmentation(\"fragments\", atom_labels=\"index\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b347f266",
   "metadata": {},
   "source": [
    "![2](_images/nglview_img2.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2149bf3f",
   "metadata": {},
   "source": [
    "Visualizing Orbitals\n",
    "---------------------\n",
    "\n",
    "To aid in active space selection, it is also possible to view the molecular orbitals of a system if the appropriate\n",
    "`.cube` strings are available.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6158f879",
   "metadata": {},
   "outputs": [],
   "source": [
    "from inquanto.extensions.pyscf import ChemistryDriverPySCFMolecularRHF\n",
    "\n",
    "driver = ChemistryDriverPySCFMolecularRHF(geometry=g.xyz, basis=\"sto3g\")\n",
    "\n",
    "# runs HF and returns orbitals\n",
    "cube_orbitals=driver.get_cube_orbitals()\n",
    "ngl_mos = [visualizer.visualize_orbitals(orb, atom_labels=\"index\") for i, orb in enumerate(cube_orbitals)]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d6c4b676",
   "metadata": {},
   "outputs": [],
   "source": [
    "#ngl_mos[16]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "da72575a",
   "metadata": {},
   "source": [
    "![3](_images/nglview_img3.png)"
   ]
  }
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