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    "## Visualizing QM/MM systems\n",
    "\n",
    "Once the method object has been initialized with the corresponding potential file, which describes the surroundings, the geometry of the full system can be visualized by using the ``show_pe`` function. Note that all visualizations requires installation of the ``py3dmol`` package."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import penguin\n",
    "import veloxchem as vlx\n",
    "\n",
    "molecule = penguin.get_molecule(\"\"\"\n",
    "    C  0.997930 -0.087600 -0.014220\n",
    "    O  2.222560 -0.087600 -0.014220\n",
    "    H  0.410270 -0.803000  0.582940\n",
    "    H  0.410270 0.6278000 -0.611380\"\"\"\n",
    ")\n",
    "\n",
    "basis = penguin.get_molecular_basis(molecule, \"cc-pVDZ\")\n",
    "\n",
    "scf_drv = vlx.ScfRestrictedDriver()\n",
    "\n",
    "pe_dict = {'potfile': '../../data/potfiles/50water.pot'}\n",
    "scf_drv.update_settings({},method_dict=pe_dict)\n",
    "scf_drv.ostream.mute()\n",
    "\n",
    "scf_results = scf_drv.compute(molecule, basis)\n",
    "\n",
    "ref_state = penguin.create_reference_state(molecule, basis, scf_drv)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
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   "source": [
    "ccsd_drv = penguin.CCSD()\n",
    "settings_dict = {\n",
    "    'reference_state': ref_state,\n",
    "}\n",
    "ccsd_drv.update_settings(settings_dict,pe_dict=pe_dict)\n",
    "\n",
    "ccsd_drv.show_pe()"
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