{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "a4d9978c-e611-429e-991c-8a550d9b123d",
   "metadata": {},
   "source": [
    "# Loading Molecular data\n",
    "\n",
    "The most common usecase for `FermionicOperator` is for representing molecules from Quantum Chemistry.  When using standard classical quantum chemistry software, molecules are often stored in FCIDump format, or as matrices representing one- and two-body integrals.  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "0228dcfd-f005-4065-a39e-fd52712c6f67",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pyscf\n",
    "import pyscf.mcscf\n",
    "\n",
    "import fulqrum as fq\n",
    "from fulqrum.convert import integrals_to_fq_fermionic_op"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e8b020a4-dc6a-417b-a352-9ffed161c212",
   "metadata": {},
   "source": [
    "## Loading an operator from an FCIDump file\n",
    "\n",
    "FCIDump is a common format for dealing with molecules with real-valued coefficients.  Fulqrum can directly load molecules in this format, evaluating only those terms that are unique: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "ac656bed-12f6-445a-b336-51676aa23ead",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Parsing ./data/fcidump_Fe4S4_MO.txt\n"
     ]
    }
   ],
   "source": [
    "fop = fq.FermionicOperator.from_fcidump(\"./data/fcidump_Fe4S4_MO.txt\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "532b117d-97e9-4a83-83dd-2790ce7640d3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2476008"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fop.size()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c2f5e982-22f3-49df-855a-913033ba30a1",
   "metadata": {},
   "source": [
    "Importantly, because only unique terms are present in the final operator, the Extended Jordan-Wigner transformation necessary to bring the operator into a `QubitOperator` is much faster."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cc8f5f0c-27cd-4ce2-b6cf-fd9949e71038",
   "metadata": {},
   "source": [
    "## Loading a molecule from integrals\n",
    "\n",
    "It is also possible to load molecules from the integrals generated by programs such as [PySCF]([https://pyscf.org/).  This is done using the `integrals_to_fq_fermionic_op` routine.  For example, generating the integrals from PySCF looks like:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "d2894305-a225-4f89-9caa-2a3e80146061",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "converged SCF energy = -108.835236570774\n"
     ]
    }
   ],
   "source": [
    "# Build N2 molecule\n",
    "mol = pyscf.gto.Mole()\n",
    "mol.build(\n",
    "    atom=[[\"N\", (0, 0, 0)], [\"N\", (1.0, 0, 0)]],\n",
    "    basis=\"6-31g\",\n",
    ")\n",
    "\n",
    "# Define active space\n",
    "n_frozen = 2\n",
    "active_space = range(n_frozen, mol.nao_nr())\n",
    "\n",
    "# Get molecular integrals\n",
    "scf = pyscf.scf.RHF(mol).run()\n",
    "num_orbitals = len(active_space)\n",
    "n_electrons = int(sum(scf.mo_occ[active_space]))\n",
    "num_elec_a = (n_electrons + mol.spin) // 2\n",
    "num_elec_b = (n_electrons - mol.spin) // 2\n",
    "cas = pyscf.mcscf.CASCI(scf, num_orbitals, (num_elec_a, num_elec_b))\n",
    "mo = cas.sort_mo(active_space, base=0)\n",
    "hcore, nuclear_repulsion_energy = cas.get_h1cas(mo)  # hcore: one-body integrals\n",
    "eri = pyscf.ao2mo.restore(1, cas.get_h2cas(mo), num_orbitals)  # eri: two-body integrals"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "92bcc248-c8e6-4abe-bd67-8511e1c15588",
   "metadata": {},
   "source": [
    "From which we can load an operator using the one- and two-body integrals, along with a constant term, if any"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "6354a211-d409-4097-89e0-18ecd089ec3b",
   "metadata": {},
   "outputs": [],
   "source": [
    "fop2 = integrals_to_fq_fermionic_op(one_body_integrals=hcore, two_body_integrals=eri)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "682a4250-9fd4-4723-b649-dee44cae1b75",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "21520"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fop2.size()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "88eeb56d-0af8-49f9-8a1f-26f5c1188276",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.14.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}