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  {
   "cell_type": "markdown",
   "id": "a559242a",
   "metadata": {},
   "source": [
    "# Atomization energy\n",
    "\n",
    "## Introduction\n",
    "The atomization energy, $\\Delta E$, of a molecule can be expressed as:\n",
    "\n",
    "$$\n",
    "\\Delta E = n_{\\text{atom}} \\times E_{\\text{atom}} - E_{\\text{molecule}}\n",
    "$$\n",
    "\n",
    "Where:\n",
    "\n",
    "- $\\Delta E$ is the atomization energy of the molecule.\n",
    "- $n_{\\text{atom}}$ is the number of atoms.\n",
    "- $E_{\\text{atom}}$ is the energy of an isolated atom.\n",
    "- $E_{\\text{molecule}}$ is the energy of the molecule.\n",
    "\n",
    "## Visualizing the WorkGraph Builder\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "138f6157",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"100%\"\n",
       "            height=\"600px\"\n",
       "            src=\"html/atomization_energy0.html\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "            \n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7bf78d1d2ed0>"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from workgraph_collections.ase.emt.atomization_energy import atomization_energy\n",
    "\n",
    "task = atomization_energy.TaskCls()\n",
    "task.to_html()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9e6360d8",
   "metadata": {},
   "source": [
    "## Visualizing the WorkGraph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "01bedd69",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"100%\"\n",
       "            height=\"600px\"\n",
       "            src=\"html/Atomization energy.html\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "            \n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7bf78d1f8a50>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from workgraph_collections.ase.emt.atomization_energy import atomization_energy\n",
    "\n",
    "wg = atomization_energy()\n",
    "wg.to_html()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "efa095d0",
   "metadata": {},
   "source": [
    "## Example: Atomization energy of a molecule N2\n",
    "\n",
    "### Prepare the inputs and submit the workflow\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "8ee799d2-0b5b-4609-957f-6b3f2cd451f0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WorkGraph process created, PK: 16423\n",
      "Atomization energy:                  9.651 eV\n"
     ]
    }
   ],
   "source": [
    "from ase.build import molecule\n",
    "from ase import Atoms\n",
    "from workgraph_collections.ase.emt.atomization_energy import atomization_energy\n",
    "from aiida import load_profile\n",
    "\n",
    "load_profile()\n",
    "\n",
    "# create input structure\n",
    "n_atom = Atoms(\"N\", pbc=True)\n",
    "n_atom.center(vacuum=5.0)\n",
    "n2_molecule = molecule(\"N2\", pbc=True)\n",
    "n2_molecule.center(vacuum=5.0)\n",
    "\n",
    "metadata = {\n",
    "    \"options\": {\n",
    "        \"prepend_text\": \"\"\"\n",
    "eval \"$(conda shell.posix hook)\"\n",
    "conda activate aiida\n",
    "export OMP_NUM_THREADS=1\n",
    "        \"\"\",\n",
    "    }\n",
    "}\n",
    "# ------------------------- Set the inputs -------------------------\n",
    "wg = atomization_energy()\n",
    "wg.tasks[\"scf_atom\"].set(\n",
    "    {\"atoms\": n_atom, \"computer\": \"localhost\", \"metadata\": metadata}\n",
    ")\n",
    "wg.tasks[\"scf_mol\"].set(\n",
    "    {\"atoms\": n2_molecule, \"computer\": \"localhost\", \"metadata\": metadata}\n",
    ")\n",
    "wg.tasks[\"calc_atomization_energy\"].set({\"molecule\": n2_molecule, \"computer\": \"localhost\"})\n",
    "# ------------------------- Submit the calculation -------------------\n",
    "wg.submit(wait=True, timeout=200)\n",
    "# ------------------------- Print the output -------------------------\n",
    "print(\n",
    "    \"Atomization energy:                  {:0.3f} eV\".format(\n",
    "        wg.tasks[\"calc_atomization_energy\"].outputs[\"result\"].value.value\n",
    "    )\n",
    ")\n"
   ]
  }
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