user_guide.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pyscf\n",
    "from pyscf import gto, scf, dft\n",
    "import numpy\n",
    "import itertools\n",
    "import pandas\n",
    "pandas.set_option('display.max_columns', 500)\n",
    "\n",
    "\n",
    "def run(method, molecule, basis,\n",
    "        charge=0, ecp={}, spin=0, unit='Angstrom',\n",
    "        conv_tol=1e-12, conv_tol_grad=1e-8, direct_scf_tol=1e-13,\n",
    "        init_guess='minao', level_shift=0, max_cycle=100, max_memory=8000,\n",
    "        xc=None, nlc='', xc_grid=3, nlc_grid=1, small_rho_cutoff=1e-7,\n",
    "        atomic_radii='BRAGG', becke_scheme='BECKE', prune='NWCHEM',\n",
    "        radi_method='TREUTLER_AHLRICHS', radii_adjust='TREUTLER',\n",
    "        algo='DIIS', datapath='', getdict=False, lin_dep_thresh=1e-8,\n",
    "        prop=False, scf_type=None, stable=False, stable_cyc=3, verbose=0):\n",
    "\n",
    "    # modify inputs arguments that are strings\n",
    "    method = method.upper()\n",
    "    atomic_radii = atomic_radii.upper()\n",
    "    becke_scheme = becke_scheme.upper()\n",
    "    if isinstance(prune, str):\n",
    "        prune = prune.upper()\n",
    "    radi_method = radi_method.upper()\n",
    "    if isinstance(radii_adjust, str):\n",
    "        radii_adjust = radii_adjust.upper()\n",
    "    algo = algo.upper()\n",
    "\n",
    "    # create molecule object\n",
    "    mol = gto.Mole()\n",
    "\n",
    "    # set mol object attributes\n",
    "    try:\n",
    "        gto.Mole(atom=molecule, charge=charge, spin=spin).build()\n",
    "    except KeyError:\n",
    "        (mol.atom, charge, spin) = read_molecule(datapath + molecule)\n",
    "    else:\n",
    "        mol.atom = molecule\n",
    "    mol.basis = basis\n",
    "    mol.charge = charge\n",
    "    mol.ecp = ecp\n",
    "    mol.spin = spin\n",
    "    mol.unit = unit\n",
    "    mol.verbose = verbose\n",
    "    mol.build()\n",
    "\n",
    "    # check method for density functional\n",
    "    DFT = False\n",
    "    if method != 'HF':\n",
    "        try:\n",
    "            dft.libxc.parse_xc(method)\n",
    "        except KeyError:\n",
    "            pass\n",
    "        else:\n",
    "            xc = method\n",
    "            method = 'KS'\n",
    "\n",
    "    # determine restricted/unrestricted if unspecified\n",
    "    # automatically sets R if closed-shell and U if open-shell\n",
    "    if method in ['HF', 'KS', 'DFT'] and scf_type is None:\n",
    "        if spin == 0:\n",
    "            scf_type = 'R'\n",
    "        else:\n",
    "            scf_type = 'U'\n",
    "\n",
    "    # create HF/KS object\n",
    "    if method in ['RHF', 'ROHF'] or (method == 'HF' and scf_type in ['R', 'RO']):\n",
    "        mf = scf.RHF(mol)\n",
    "        scf_type = 'R'\n",
    "    elif method == 'UHF' or (method == 'HF' and scf_type == 'U'):\n",
    "        mf = scf.UHF(mol)\n",
    "        scf_type = 'U'\n",
    "    elif method in ['RKS', 'ROKS', 'RDFT', 'RODFT'] or (method in ['KS', 'DFT'] and scf_type in ['R', 'RO']):\n",
    "        mf = scf.RKS(mol)\n",
    "        scf_type = 'R'\n",
    "        DFT = True\n",
    "    elif method in ['UKS', 'UDFT'] or (method in ['KS', 'DFT'] and scf_type == 'U'):\n",
    "        mf = scf.UKS(mol)\n",
    "        scf_type = 'U'\n",
    "        DFT = True\n",
    "    else:\n",
    "        print \"CRASH 1\"\n",
    "\n",
    "    # set HF attributes\n",
    "    mf.conv_check = False\n",
    "    mf.conv_tol = conv_tol\n",
    "    mf.conv_tol_grad = conv_tol_grad\n",
    "    mf.direct_scf_tol = direct_scf_tol\n",
    "    mf.init_guess = init_guess\n",
    "    mf.level_shift = level_shift\n",
    "    mf.max_cycle = max_cycle\n",
    "    mf.max_memory = max_memory\n",
    "    mf.verbose = verbose\n",
    "\n",
    "    # set KS attributes\n",
    "    if DFT:\n",
    "\n",
    "        mf.xc = xc\n",
    "        if mf.xc is None:\n",
    "            print \"CRASH 2\"\n",
    "        mf.nlc = nlc\n",
    "\n",
    "        if isinstance(xc_grid, int):\n",
    "            mf.grids.level = xc_grid\n",
    "        elif isinstance(xc_grid, tuple) or isinstance(xc_grid, dict):\n",
    "            mf.grids.atom_grid = xc_grid\n",
    "        else:\n",
    "            print \"CRASH 3\"\n",
    "\n",
    "        if isinstance(nlc_grid, int):\n",
    "            mf.nlcgrids.level = nlc_grid\n",
    "        elif isinstance(nlc_grid, tuple) or isinstance(nlc_grid, dict):\n",
    "            mf.nlcgrids.atom_grid = nlc_grid\n",
    "        else:\n",
    "            print \"CRASH 4\"\n",
    "\n",
    "        if atomic_radii == 'BRAGG':\n",
    "            mf.grids.atomic_radii = dft.radi.BRAGG_RADII\n",
    "            mf.nlcgrids.atomic_radii = dft.radi.BRAGG_RADII\n",
    "        elif atomic_radii == 'COVALENT':\n",
    "            mf.grids.atomic_radii = dft.radi.COVALENT_RADII\n",
    "            mf.nlcgrids.atomic_radii = dft.radi.COVALENT_RADII\n",
    "        else:\n",
    "            print \"CRASH 5\"\n",
    "\n",
    "        if becke_scheme == 'BECKE':\n",
    "            mf.grids.becke_scheme = dft.gen_grid.original_becke\n",
    "            mf.nlcgrids.becke_scheme = dft.gen_grid.original_becke\n",
    "        elif becke_scheme == 'STRATMANN':\n",
    "            mf.grids.becke_scheme = dft.gen_grid.stratmann\n",
    "            mf.nlcgrids.becke_scheme = dft.gen_grid.stratmann\n",
    "        else:\n",
    "            print \"CRASH 6\"\n",
    "\n",
    "        if prune == 'NWCHEM':\n",
    "            mf.grids.prune = dft.gen_grid.nwchem_prune\n",
    "            mf.nlcgrids.prune = dft.gen_grid.nwchem_prune\n",
    "        elif prune == 'SG1':\n",
    "            mf.grids.prune = dft.gen_grid.sg1_prune\n",
    "            mf.nlcgrids.prune = dft.gen_grid.sg1_prune\n",
    "        elif prune == 'TREUTLER':\n",
    "            mf.grids.prune = dft.gen_grid.treutler_prune\n",
    "            mf.nlcgrids.prune = dft.gen_grid.treutler_prune\n",
    "        elif prune == 'NONE' or prune is None:\n",
    "            mf.grids.prune = None\n",
    "            mf.nlcgrids.prune = None\n",
    "        else:\n",
    "            print \"CRASH 7\"\n",
    "\n",
    "        if radi_method in ['TREUTLER_AHLRICHS', 'TREUTLER', 'AHLRICHS']:\n",
    "            mf.grids.radi_method = dft.radi.treutler_ahlrichs\n",
    "            mf.nlcgrids.radi_method = dft.radi.treutler_ahlrichs\n",
    "        elif radi_method == 'DELLEY':\n",
    "            mf.grids.radi_method = dft.radi.delley\n",
    "            mf.nlcgrids.radi_method = dft.radi.delley\n",
    "        elif radi_method in ['MURA_KNOWLES', 'MURA', 'KNOWLES']:\n",
    "            mf.grids.radi_method = dft.radi.mura_knowles\n",
    "            mf.nlcgrids.radi_method = dft.radi.mura_knowles\n",
    "        elif radi_method in ['GAUSS_CHEBYSHEV', 'GAUSS', 'CHEBYSHEV']:\n",
    "            mf.grids.radi_method = dft.radi.gauss_chebyshev\n",
    "            mf.nlcgrids.radi_method = dft.radi.gauss_chebyshev\n",
    "        else:\n",
    "            print \"CRASH 8\"\n",
    "\n",
    "        if radii_adjust == 'TREUTLER':\n",
    "            mf.grids.radii_adjust = dft.radi.treutler_atomic_radii_adjust\n",
    "            mf.nlcgrids.radii_adjust = dft.radi.treutler_atomic_radii_adjust\n",
    "        elif radii_adjust == 'BECKE':\n",
    "            mf.grids.radii_adjust = dft.radi.becke_atomic_radii_adjust\n",
    "            mf.nlcgrids.radii_adjust = dft.radi.becke_atomic_radii_adjust\n",
    "        elif radii_adjust == 'NONE' or radii_adjust is None:\n",
    "            mf.grids.radii_adjust = None\n",
    "            mf.nlcgrids.radii_adjust = None\n",
    "        else:\n",
    "            print \"CRASH 9\"\n",
    "\n",
    "        mf.small_rho_cutoff = small_rho_cutoff\n",
    "\n",
    "    # select optimizer\n",
    "    if algo == 'DIIS':\n",
    "        mf.diis = True\n",
    "    elif algo == 'ADIIS':\n",
    "        mf.diis = scf.diis.ADIIS()\n",
    "    elif algo == 'EDIIS':\n",
    "        mf.diis = scf.diis.EDIIS()\n",
    "    elif algo == 'NEWTON':\n",
    "        mf = mf.newton()\n",
    "    else:\n",
    "        print \"CRASH 10\"\n",
    "\n",
    "    # run SCF\n",
    "    mf.kernel()\n",
    "\n",
    "    # stability analysis (optional)\n",
    "    if stable:\n",
    "        print 'Initial SCF energy: ', mf.e_tot\n",
    "        print 'Performing Stability Analysis (up to ', stable_cyc, 'iterations)'\n",
    "        for i in range(stable_cyc):\n",
    "            new_mo_coeff = mf.stability(internal=True, external=False)[0]\n",
    "            if numpy.linalg.norm(numpy.array(new_mo_coeff) - numpy.array(mf.mo_coeff)) < 10**-14:\n",
    "                print \"Stable!\"\n",
    "                break\n",
    "            else:\n",
    "                print \"Unstable!\"\n",
    "                if scf_type == 'U':\n",
    "                    n_alpha = numpy.count_nonzero(mf.mo_occ[0])\n",
    "                    n_beta = numpy.count_nonzero(mf.mo_occ[1])\n",
    "                    P_alpha = numpy.dot(new_mo_coeff[0][:, :n_alpha], new_mo_coeff[0].T[:n_alpha])\n",
    "                    P_beta = numpy.dot(new_mo_coeff[1][:, :n_beta], new_mo_coeff[1].T[:n_beta])\n",
    "                    mf.kernel(dm0=(P_alpha, P_beta))\n",
    "                elif scf_type in ['R', 'RO']:\n",
    "                    n_alpha = numpy.count_nonzero(mf.mo_occ)\n",
    "                    P_alpha = 2*numpy.dot(new_mo_coeff[:, :n_alpha], new_mo_coeff.T[:n_alpha])\n",
    "                    mf.kernel(dm0=(P_alpha))\n",
    "                else:\n",
    "                    print \"CRASH 11\"\n",
    "                print 'Updated SCF energy: ', mf.e_tot\n",
    "\n",
    "    # properties\n",
    "    if prop:\n",
    "\n",
    "        # dipole moment\n",
    "        mf.dip_moment()\n",
    "\n",
    "        # S^2\n",
    "        if scf_type == 'U':\n",
    "            (ssq, mult) = mf.spin_square()\n",
    "            print '(S^2, 2S+1):', (ssq, mult)\n",
    "        elif scf_type in ['R', 'RO']:\n",
    "            S = float(mol.spin)/2.\n",
    "            (ssq, mult) = (S*(S+1.), 2.*S+1.)\n",
    "            print '(S^2, 2S+1):', (ssq, mult)\n",
    "        else:\n",
    "            print \"CRASH 12\"\n",
    "\n",
    "        # population analysis\n",
    "        print \"Mulliken population analysis\"\n",
    "        for ia in range(mol.natm):\n",
    "            symb = mol.atom_symbol(ia)\n",
    "            print symb, ':', mf.mulliken_meta(verbose=verbose)[1][ia]\n",
    "\n",
    "        print \"Mulliken population analysis, based on meta-Lowdin AOs\"\n",
    "        for ia in range(mol.natm):\n",
    "            symb = mol.atom_symbol(ia)\n",
    "            print symb, ':', mf.mulliken_pop(verbose=verbose)[1][ia]\n",
    "\n",
    "    # return either just an energy or (energy,dict)\n",
    "    if getdict:\n",
    "        mydict = dict()\n",
    "        mydict.update(mol.__dict__)\n",
    "        mydict.update(mf.__dict__)\n",
    "        if DFT:\n",
    "            mydict.update(mf.grids.__dict__)\n",
    "        return mf.e_tot, mydict\n",
    "    else:\n",
    "        return mf.e_tot\n",
    "\n",
    "\n",
    "def run_batch(method, molecule, basis, database=pandas.DataFrame(), **kwargs):\n",
    "    mand_args = ['method', 'molecule', 'basis']\n",
    "    num_mand_args = len(mand_args)\n",
    "    if not isinstance(method, list):\n",
    "        method = [method]\n",
    "    if not isinstance(molecule, list):\n",
    "        molecule = [molecule]\n",
    "    if not isinstance(basis, list):\n",
    "        basis = [basis]\n",
    "    for i in itertools.product(method, molecule, basis, list(parse_kwargs(**kwargs))):\n",
    "        mydict = dict()\n",
    "        mydict.update(i[num_mand_args:][0])\n",
    "        (en, rundict) = run(*i[:num_mand_args], getdict=True, **i[num_mand_args:][0])\n",
    "        mydict.update(rundict)\n",
    "        for num, val in enumerate(mand_args):\n",
    "            if val == 'molecule':\n",
    "                try:\n",
    "                    read_molecule(mydict['datapath'] + i[num])\n",
    "                except IOError:\n",
    "                    mydict.update({val: XYZtoMF(i[num])})\n",
    "                else:\n",
    "                    mydict.update({val: i[num]})\n",
    "            else:\n",
    "                mydict.update({val: i[num]})\n",
    "        database = database.append(mydict, ignore_index=True)\n",
    "\n",
    "    return database\n",
    "\n",
    "\n",
    "def parse_kwargs(**kwargs):\n",
    "    items = kwargs.items()\n",
    "    keys = [key for key, value in items]\n",
    "    sets = [value for key, value in items]\n",
    "    for index, item in enumerate(sets):\n",
    "        if not isinstance(item, list):\n",
    "            sets[index] = [sets[index]]\n",
    "    for values in itertools.product(*sets):\n",
    "        yield dict(zip(keys, values))\n",
    "\n",
    "\n",
    "def read_molecule(path):\n",
    "\n",
    "    charge = spin = 0\n",
    "    with open(path, 'r') as myfile:\n",
    "        output = myfile.read()\n",
    "        output = output.lstrip()\n",
    "        output = output.rstrip()\n",
    "        output = output.split('\\n')\n",
    "\n",
    "    try:\n",
    "        int(output[0])\n",
    "    except ValueError:\n",
    "        try:\n",
    "            charge = int(output[0].split(' ')[0])\n",
    "            spin = int(output[0].split(' ')[1]) - 1\n",
    "        except ValueError:\n",
    "            molecule = output\n",
    "        else:\n",
    "            molecule = '\\n'.join(output[1:])\n",
    "    else:\n",
    "        if int(output[0]) == len(output) - 2:\n",
    "            molecule = '\\n'.join(output[2:])\n",
    "            try:\n",
    "                charge = int(output[1].split(' ')[0])\n",
    "                spin = int(output[1].split(' ')[1])-1\n",
    "            except ValueError:\n",
    "                pass\n",
    "        else:\n",
    "            print \"THIS IS NOT A VALID XYZ FILE\"\n",
    "\n",
    "    return (molecule, charge, spin)\n",
    "\n",
    "\n",
    "def XYZtoMF(inp):\n",
    "\n",
    "    return filter(lambda x: x.isalpha(), inp)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Introduction: Welcome to the QuSim User Guide\n",
    "\n",
    "The QuSim user interface is the easiest way to perform computational chemistry calculations using PySCF. The `run` function accepts three mandatory, ordered inputs (as well as a variety of optional ones):\n",
    "\n",
    "* method\n",
    "* geometry\n",
    "* basis\n",
    "\n",
    "This guide will cover the basics of the QuSim user interface and demonstrate the computation of various types of chemical interactions such as atomization energies, bond dissociation energies, binding energies, etc. Furthermore, it will highlight the sensitivity of certain chemical interactions and methods to both the basis set as well as the integration grid (which pertains specifically to DFT).\n",
    "\n",
    "To begin, we will calculate the energy of H$_2$ with a bond length of 0.74 Å. First, it is necessary to define the geometry:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "h2=\"\"\"\n",
    "H 0.0 0.0 0.0\n",
    "H 0.0 0.0 0.74\"\"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For this specific example, we will use Hartree–Fock (HF) and the double-zeta cc-pVDZ basis set:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-1.1287000935564406"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "run('HF', h2, 'cc-pVDZ')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This should return an energy of -1.1287000935564406 Hartree.\n",
    "\n",
    "The `run` function has a variety of useful, optional features in addition to the three mandatory ones. For example, one can set the charge and spin of a molecule as follows:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-0.5652012007354672"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "run('HF', h2, 'cc-pVDZ', charge=1, spin=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The calculation above computes the energy of H$_2$$^+$, which has a single unpaired electron (hence `spin=1`, where spin is equal to 2S).\n",
    "\n",
    "By default, `run` will perform a restricted calculation if the molecule is closed-shell (no unpaired electrons or `spin=0`) and an unrestricted calculation if the molecule is open-shell (`spin>0`). This default can be overwritten in several ways. Either the method can be explicitly stated (i.e., `RHF`, `ROHF`, or `UHF`), or the `scf_type` input can be set explicitly (`R`, `RO`, or `U`).\n",
    "\n",
    "As an example, we will compute the energy of an open-shell molecule, namely, the hydroxyl radical, OH•."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "oh=\"\"\"\n",
    "O 0.0000000000 0.0000000000 0.0000000000\n",
    "H 0.0000000000 0.0000000000 0.9706601900\"\"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The following demonstrates the various ways of performing unrestricted vs. restricted calculations. The first three lines should produce identical results corresponding to an unrestricted calculation of OH•, while the last four lines should produce identical results corresponding to a restricted calculation of OH•."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "HF:  -75.3938226865\n",
      "UHF:  -75.3938226865\n",
      "HF/U:  -75.3938226865\n",
      "\n",
      "RHF:  -75.3899856282\n",
      "ROHF:  -75.3899856282\n",
      "HF/R:  -75.3899856282\n",
      "HF/RO:  -75.3899856282\n"
     ]
    }
   ],
   "source": [
    "# unrestricted\n",
    "print 'HF: ', run('HF', oh, 'cc-pVDZ', spin=1)\n",
    "print 'UHF: ', run('UHF', oh, 'cc-pVDZ', spin=1)\n",
    "print 'HF/U: ', run('HF', oh, 'cc-pVDZ', spin=1, scf_type='U')\n",
    "\n",
    "print ''\n",
    "\n",
    "# restricted\n",
    "print 'RHF: ', run('RHF', oh, 'cc-pVDZ', spin=1)\n",
    "print 'ROHF: ', run('ROHF', oh, 'cc-pVDZ', spin=1)\n",
    "print 'HF/R: ', run('HF', oh, 'cc-pVDZ', spin=1, scf_type='R')\n",
    "print 'HF/RO: ', run('HF', oh, 'cc-pVDZ', spin=1, scf_type='RO')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Naturally, the first three will all return the lower energy corresponding to a UHF calculation, while the rest will return a higher energy corresponding to an ROHF calculation.\n",
    "\n",
    "Another useful feature that can be turned on is `prop`. When `prop=True`, a variety of molecular properties (dipole moment, S$^2$ and 2S+1 values, as well as two different population analysis results) are computed after the SCF converges. For example:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dipole moment(X, Y, Z, A.U.):  0.00000,  0.00000,  1.80400\n",
      "(S^2, 2S+1): (0.75461173279801885, 2.0046064280032816)\n",
      "Mulliken population analysis\n",
      "O : -0.323214025599\n",
      "H : 0.323214025599\n",
      "Mulliken population analysis, based on meta-Lowdin AOs\n",
      "O : -0.184995587217\n",
      "H : 0.184995587217\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-75.393822686483375"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "run('UHF', oh, 'cc-pVDZ', spin=1, prop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "When dealing with radicals, multireference systems, or systems that can break spin symmetry, it is possible to land on an SCF solution that is unstable. For these notorious cases, the `stable=True` setting will attempt to resolve the instability 3 times (a setting that can be modified by `stable_cyc`). As an example, consider the singlet C$_2$ molecule. First, we will perform an RHF calculation without stability analysis:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "c2=\"\"\"\n",
    "C 0.0 0.0 0.0\n",
    "C 0.0 0.0 1.24\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-75.386817113966686"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "run('RHF', c2, 'cc-pVDZ')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This returns an energy of -75.386817113966686 Hartree. Running the same calculation with stability analysis confirms that the previous energy was a saddle point, and returns a lower restricted energy:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Initial SCF energy:  -75.386817114\n",
      "Performing Stability Analysis (up to  3 iterations)\n",
      "Unstable!\n",
      "Updated SCF energy:  -75.4159592748\n",
      "Stable!\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-75.41595927475602"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "run('RHF', c2, 'cc-pVDZ', stable=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The stable energy of -75.41595927475602 Hartree is lower than the unstable one by 18.29 kcal/mol! Thus, if one wanted to compute the bond dissociation energy of C$_2$ (C$_2$ - 2C), landing on the unstable solution would result in an error of nearly 20 kcal/mol.\n",
    "\n",
    "Since we are dealing with singlet C$_2$ in this example, one could expect an RHF calculation to be sufficient. However, the following UHF calculation demonstrates that C$_2$ can break spin symmetry:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Initial SCF energy:  -75.386817114\n",
      "Performing Stability Analysis (up to  3 iterations)\n",
      "Unstable!\n",
      "Updated SCF energy:  -75.5053140149\n",
      "Stable!\n",
      "Dipole moment(X, Y, Z, A.U.):  0.00000, -0.00000,  0.00000\n",
      "(S^2, 2S+1): (1.6577115386994441, 2.7623986234426372)\n",
      "Mulliken population analysis\n",
      "C : 1.15574838588e-09\n",
      "C : -1.15574483317e-09\n",
      "Mulliken population analysis, based on meta-Lowdin AOs\n",
      "C : 6.80303813283e-10\n",
      "C : -6.80300260569e-10\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-75.505314014915271"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "c2=\"\"\"\n",
    "C 0.0 0.0 0.0\n",
    "C 0.0 0.0 1.24\"\"\"\n",
    "\n",
    "run('UHF', c2, 'cc-pVDZ', stable=True, prop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Initially, the UHF calculation lands on the same unstable solution as RHF: -75.386817114 Hartree. However, once the instability has been resolved, the stable UHF energy of -75.5053140149 Hartree is 74.36 kcal/mol lower than the unstable solution, and 56.07 kcal/mol lower than the stable RHF solution. While the stable RHF solution has an S$^2$ value of 0, the stable UHF solution has an S$^2$ value of 1.66.\n",
    "\n",
    "Another useful feature is the ability to read molecule files from disk. The parser can automatically detect any of the three file formats contained in the geom folder (XYZ, MOL, QC). These formats are explained [here](#atom). It also takes an input variable called `datapath` which is the absolute or relative path to the directory where the files are contained. For example, the geom folder contains:\n",
    "\n",
    "* water_dimer.mol\n",
    "* water_dimer.qc\n",
    "* water_dimer.xyz\n",
    "\n",
    "The energies for the molecules contained in these three files can be computed very easily:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-152.06253625\n",
      "-152.06253625\n",
      "-152.06253625\n"
     ]
    }
   ],
   "source": [
    "print run('HF', 'water_dimer.mol', 'cc-pVDZ', datapath='geom/')\n",
    "print run('HF', 'water_dimer.qc', 'cc-pVDZ', datapath='geom/')\n",
    "print run('HF', 'water_dimer.xyz', 'cc-pVDZ', datapath='geom/')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This tutorial is also equipped with all of the molecules from the MGCDB84 database, found in this [DFT review paper](https://www.tandfonline.com/doi/full/10.1080/00268976.2017.1333644). These molecules can be found in the data folder. Running any of these molecules (ethyne for example) is also straightforward:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-76.8255572993\n"
     ]
    }
   ],
   "source": [
    "print run('HF', '126_c2h2_W4-11.xyz', 'cc-pVDZ', datapath='data/')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Because the QC file format contains the charge and multiplicity of the molecule, it is not necessary to specify the spin (for example) when reading in the hydroxyl radical file (222_oh_W4-11.xyz) from the data directory:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-75.3938226865\n"
     ]
    }
   ],
   "source": [
    "print run('HF', '222_oh_W4-11.xyz', 'cc-pVDZ', datapath='data/')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Another feature of the QuSim user interface is the ability to run batch jobs with the `run_batch` function. This function is essentially a wrapper for `run` and takes the same inputs. The first three inputs (method, molecule, basis) are mandatory, and can be lists. The optional arguments can also be lists."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "filenames=['11_Ar-Ar_dim_NC15.xyz', '11_Ar-Ar_monA_NC15.xyz', '11_Ar-Ar_monB_NC15.xyz']\n",
    "\n",
    "mydbase=run_batch(['UHF', 'RHF'], filenames, ['cc-pVDZ', 'def2-SVP'], datapath='data/')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This will return a pandas DataFrame that contains all of the data embedded in the molecule and mean-field objects. A truncated version of this DataFrame can be accessed via:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>molecule</th>\n",
       "      <th>method</th>\n",
       "      <th>basis</th>\n",
       "      <th>charge</th>\n",
       "      <th>spin</th>\n",
       "      <th>e_tot</th>\n",
       "      <th>converged</th>\n",
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       "    <tr>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1053.246842</td>\n",
       "      <td>1.0</td>\n",
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       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>11_Ar-Ar_monA_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>cc-pVDZ</td>\n",
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       "      <td>11_Ar-Ar_monB_NC15.xyz</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  molecule method     basis  charge  spin        e_tot  \\\n",
       "0    11_Ar-Ar_dim_NC15.xyz    UHF   cc-pVDZ     0.0   0.0 -1053.599476   \n",
       "1    11_Ar-Ar_dim_NC15.xyz    UHF  def2-SVP     0.0   0.0 -1053.246842   \n",
       "2   11_Ar-Ar_monA_NC15.xyz    UHF   cc-pVDZ     0.0   0.0  -526.799865   \n",
       "3   11_Ar-Ar_monA_NC15.xyz    UHF  def2-SVP     0.0   0.0  -526.623385   \n",
       "4   11_Ar-Ar_monB_NC15.xyz    UHF   cc-pVDZ     0.0   0.0  -526.799865   \n",
       "5   11_Ar-Ar_monB_NC15.xyz    UHF  def2-SVP     0.0   0.0  -526.623385   \n",
       "6    11_Ar-Ar_dim_NC15.xyz    RHF   cc-pVDZ     0.0   0.0 -1053.599476   \n",
       "7    11_Ar-Ar_dim_NC15.xyz    RHF  def2-SVP     0.0   0.0 -1053.246842   \n",
       "8   11_Ar-Ar_monA_NC15.xyz    RHF   cc-pVDZ     0.0   0.0  -526.799865   \n",
       "9   11_Ar-Ar_monA_NC15.xyz    RHF  def2-SVP     0.0   0.0  -526.623385   \n",
       "10  11_Ar-Ar_monB_NC15.xyz    RHF   cc-pVDZ     0.0   0.0  -526.799865   \n",
       "11  11_Ar-Ar_monB_NC15.xyz    RHF  def2-SVP     0.0   0.0  -526.623385   \n",
       "\n",
       "    converged  \n",
       "0         1.0  \n",
       "1         1.0  \n",
       "2         1.0  \n",
       "3         1.0  \n",
       "4         1.0  \n",
       "5         1.0  \n",
       "6         1.0  \n",
       "7         1.0  \n",
       "8         1.0  \n",
       "9         1.0  \n",
       "10        1.0  \n",
       "11        1.0  "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mydbase[['molecule', 'method', 'basis', 'charge', 'spin', 'e_tot', 'converged']]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can keep adding to the database if you specify the name of the database as an argument to run_batch:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "mydbase=run_batch(['UHF', 'RHF'], filenames, ['def2-SVPD', '6-31G'], database=mydbase, datapath='data/')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
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       "      <td>1.0</td>\n",
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       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>11_Ar-Ar_dim_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>def2-SVP</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1053.246842</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>11_Ar-Ar_monA_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>cc-pVDZ</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>1.0</td>\n",
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       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>11_Ar-Ar_monA_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>def2-SVP</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.623385</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>11_Ar-Ar_monB_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>cc-pVDZ</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.799865</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>11_Ar-Ar_monB_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>def2-SVP</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.623385</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>11_Ar-Ar_dim_NC15.xyz</td>\n",
       "      <td>UHF</td>\n",
       "      <td>def2-SVPD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1053.264582</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>11_Ar-Ar_dim_NC15.xyz</td>\n",
       "      <td>UHF</td>\n",
       "      <td>6-31G</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1053.543992</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>11_Ar-Ar_monA_NC15.xyz</td>\n",
       "      <td>UHF</td>\n",
       "      <td>def2-SVPD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.632397</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>11_Ar-Ar_monA_NC15.xyz</td>\n",
       "      <td>UHF</td>\n",
       "      <td>6-31G</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.772151</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>11_Ar-Ar_monB_NC15.xyz</td>\n",
       "      <td>UHF</td>\n",
       "      <td>def2-SVPD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.632397</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>11_Ar-Ar_monB_NC15.xyz</td>\n",
       "      <td>UHF</td>\n",
       "      <td>6-31G</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.772151</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>11_Ar-Ar_dim_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>def2-SVPD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1053.264582</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>11_Ar-Ar_dim_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>6-31G</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1053.543992</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>11_Ar-Ar_monA_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>def2-SVPD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.632397</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>11_Ar-Ar_monA_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>6-31G</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.772151</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>11_Ar-Ar_monB_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>def2-SVPD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.632397</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>11_Ar-Ar_monB_NC15.xyz</td>\n",
       "      <td>RHF</td>\n",
       "      <td>6-31G</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-526.772151</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  molecule method      basis  charge  spin        e_tot  \\\n",
       "0    11_Ar-Ar_dim_NC15.xyz    UHF    cc-pVDZ     0.0   0.0 -1053.599476   \n",
       "1    11_Ar-Ar_dim_NC15.xyz    UHF   def2-SVP     0.0   0.0 -1053.246842   \n",
       "2   11_Ar-Ar_monA_NC15.xyz    UHF    cc-pVDZ     0.0   0.0  -526.799865   \n",
       "3   11_Ar-Ar_monA_NC15.xyz    UHF   def2-SVP     0.0   0.0  -526.623385   \n",
       "4   11_Ar-Ar_monB_NC15.xyz    UHF    cc-pVDZ     0.0   0.0  -526.799865   \n",
       "5   11_Ar-Ar_monB_NC15.xyz    UHF   def2-SVP     0.0   0.0  -526.623385   \n",
       "6    11_Ar-Ar_dim_NC15.xyz    RHF    cc-pVDZ     0.0   0.0 -1053.599476   \n",
       "7    11_Ar-Ar_dim_NC15.xyz    RHF   def2-SVP     0.0   0.0 -1053.246842   \n",
       "8   11_Ar-Ar_monA_NC15.xyz    RHF    cc-pVDZ     0.0   0.0  -526.799865   \n",
       "9   11_Ar-Ar_monA_NC15.xyz    RHF   def2-SVP     0.0   0.0  -526.623385   \n",
       "10  11_Ar-Ar_monB_NC15.xyz    RHF    cc-pVDZ     0.0   0.0  -526.799865   \n",
       "11  11_Ar-Ar_monB_NC15.xyz    RHF   def2-SVP     0.0   0.0  -526.623385   \n",
       "12   11_Ar-Ar_dim_NC15.xyz    UHF  def2-SVPD     0.0   0.0 -1053.264582   \n",
       "13   11_Ar-Ar_dim_NC15.xyz    UHF      6-31G     0.0   0.0 -1053.543992   \n",
       "14  11_Ar-Ar_monA_NC15.xyz    UHF  def2-SVPD     0.0   0.0  -526.632397   \n",
       "15  11_Ar-Ar_monA_NC15.xyz    UHF      6-31G     0.0   0.0  -526.772151   \n",
       "16  11_Ar-Ar_monB_NC15.xyz    UHF  def2-SVPD     0.0   0.0  -526.632397   \n",
       "17  11_Ar-Ar_monB_NC15.xyz    UHF      6-31G     0.0   0.0  -526.772151   \n",
       "18   11_Ar-Ar_dim_NC15.xyz    RHF  def2-SVPD     0.0   0.0 -1053.264582   \n",
       "19   11_Ar-Ar_dim_NC15.xyz    RHF      6-31G     0.0   0.0 -1053.543992   \n",
       "20  11_Ar-Ar_monA_NC15.xyz    RHF  def2-SVPD     0.0   0.0  -526.632397   \n",
       "21  11_Ar-Ar_monA_NC15.xyz    RHF      6-31G     0.0   0.0  -526.772151   \n",
       "22  11_Ar-Ar_monB_NC15.xyz    RHF  def2-SVPD     0.0   0.0  -526.632397   \n",
       "23  11_Ar-Ar_monB_NC15.xyz    RHF      6-31G     0.0   0.0  -526.772151   \n",
       "\n",
       "    converged  \n",
       "0         1.0  \n",
       "1         1.0  \n",
       "2         1.0  \n",
       "3         1.0  \n",
       "4         1.0  \n",
       "5         1.0  \n",
       "6         1.0  \n",
       "7         1.0  \n",
       "8         1.0  \n",
       "9         1.0  \n",
       "10        1.0  \n",
       "11        1.0  \n",
       "12        1.0  \n",
       "13        1.0  \n",
       "14        1.0  \n",
       "15        1.0  \n",
       "16        1.0  \n",
       "17        1.0  \n",
       "18        1.0  \n",
       "19        1.0  \n",
       "20        1.0  \n",
       "21        1.0  \n",
       "22        1.0  \n",
       "23        1.0  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mydbase[['molecule', 'method', 'basis', 'charge', 'spin', 'e_tot', 'converged']]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The full pandas DataFrame contains a large amount of data:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>_atm</th>\n",
       "      <th>_atom</th>\n",
       "      <th>_bas</th>\n",
       "      <th>_basis</th>\n",
       "      <th>_built</th>\n",
       "      <th>_chkfile</th>\n",
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       "      <th>_eri</th>\n",
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       "      <th>basis</th>\n",
       "      <th>callback</th>\n",
       "      <th>cart</th>\n",
       "      <th>charge</th>\n",
       "      <th>chkfile</th>\n",
       "      <th>conv_check</th>\n",
       "      <th>conv_tol</th>\n",
       "      <th>conv_tol_grad</th>\n",
       "      <th>converged</th>\n",
       "      <th>datapath</th>\n",
       "      <th>diis</th>\n",
       "      <th>direct_scf_tol</th>\n",
       "      <th>e_tot</th>\n",
       "      <th>ecp</th>\n",
       "      <th>groupname</th>\n",
       "      <th>init_guess</th>\n",
       "      <th>irrep_id</th>\n",
       "      <th>irrep_name</th>\n",
       "      <th>level_shift</th>\n",
       "      <th>max_cycle</th>\n",
       "      <th>max_memory</th>\n",
       "      <th>method</th>\n",
       "      <th>mo_coeff</th>\n",
       "      <th>mo_energy</th>\n",
       "      <th>mo_occ</th>\n",
       "      <th>mol</th>\n",
       "      <th>molecule</th>\n",
       "      <th>nelec</th>\n",
       "      <th>nucmod</th>\n",
       "      <th>opt</th>\n",
       "      <th>output</th>\n",
       "      <th>spin</th>\n",
       "      <th>stdout</th>\n",
       "      <th>symm_orb</th>\n",
       "      <th>symmetry</th>\n",
       "      <th>symmetry_subgroup</th>\n",
       "      <th>topgroup</th>\n",
       "      <th>unit</th>\n",
       "      <th>verbose</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[[18, 20, 1, 23, 0, 0], [18, 24, 1, 27, 0, 0]]</td>\n",
       "      <td>[(Ar, [3.54323648356, 0.0, 0.0]), (Ar, [-3.543...</td>\n",
       "      <td>[[0, 0, 11, 3, 0, 28, 39, 0], [0, 0, 1, 1, 0, ...</td>\n",
       "      <td>{u'Ar': [[0, [145700.0, 0.0002367, -6.7491e-05...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>&lt;open file '&lt;fdopen&gt;', mode 'w+b' at 0x7f8d550...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[137.03599968, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0...</td>\n",
       "      <td>[10.9203114287, -1.31592562125, 0.263519480103...</td>\n",
       "      <td>{opt, direct_scf, verbose, stdout, level_shift...</td>\n",
       "      <td>None</td>\n",
       "      <td>5.191529</td>\n",
       "      <td>1.523914e+09</td>\n",
       "      <td>Ar 1.8750000000 0.0000000000 0.0000000000\\nAr ...</td>\n",
       "      <td>cc-pVDZ</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>/home/narbe/Tutorial_PySCF/tmpmYkCpq</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.000000e-12</td>\n",
       "      <td>1.000000e-08</td>\n",
       "      <td>1.0</td>\n",
       "      <td>data/</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.000000e-13</td>\n",
       "      <td>-1053.599476</td>\n",
       "      <td>{}</td>\n",
       "      <td>C1</td>\n",
       "      <td>minao</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>100.0</td>\n",
       "      <td>8000.0</td>\n",
       "      <td>UHF</td>\n",
       "      <td>([[0.707120975302, 0.707120352269, -5.71489765...</td>\n",
       "      <td>([-118.6061178, -118.606117699, -12.3176581742...</td>\n",
       "      <td>[[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,...</td>\n",
       "      <td>&lt;pyscf.gto.mole.Mole object at 0x7f8d52bdbd10&gt;</td>\n",
       "      <td>11_Ar-Ar_dim_NC15.xyz</td>\n",
       "      <td>None</td>\n",
       "      <td>{}</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>&lt;ipykernel.iostream.OutStream object at 0x7f8d...</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>None</td>\n",
       "      <td>C1</td>\n",
       "      <td>Angstrom</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[[18, 20, 1, 23, 0, 0], [18, 24, 1, 27, 0, 0]]</td>\n",
       "      <td>[(Ar, [3.54323648356, 0.0, 0.0]), (Ar, [-3.543...</td>\n",
       "      <td>[[0, 0, 5, 1, 0, 28, 33, 0], [0, 0, 3, 1, 0, 3...</td>\n",
       "      <td>{u'Ar': [[0, [11797.119765, 0.0020214479973], ...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>&lt;open file '&lt;fdopen&gt;', mode 'w+b' at 0x7f8d550...</td>\n",
       "      <td>[]</td>\n",
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       "      <td>[137.03599968, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0...</td>\n",
       "      <td>[11.0233591869, 2.02986621851, 0.460838722679,...</td>\n",
       "      <td>{opt, direct_scf, verbose, stdout, level_shift...</td>\n",
       "      <td>None</td>\n",
       "      <td>5.380022</td>\n",
       "      <td>1.523914e+09</td>\n",
       "      <td>Ar 1.8750000000 0.0000000000 0.0000000000\\nAr ...</td>\n",
       "      <td>def2-SVP</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>/home/narbe/Tutorial_PySCF/tmp8calp2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.000000e-12</td>\n",
       "      <td>1.000000e-08</td>\n",
       "      <td>1.0</td>\n",
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       "      <td>1.0</td>\n",
       "      <td>1.000000e-13</td>\n",
       "      <td>-1053.246842</td>\n",
       "      <td>{}</td>\n",
       "      <td>C1</td>\n",
       "      <td>minao</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>100.0</td>\n",
       "      <td>8000.0</td>\n",
       "      <td>UHF</td>\n",
       "      <td>([[0.702752480149, 0.702755043495, -0.22449745...</td>\n",
       "      <td>([-118.549384229, -118.549367281, -12.30248187...</td>\n",
       "      <td>[[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,...</td>\n",
       "      <td>&lt;pyscf.gto.mole.Mole object at 0x7f8d6ff9a7d0&gt;</td>\n",
       "      <td>11_Ar-Ar_dim_NC15.xyz</td>\n",
       "      <td>None</td>\n",
       "      <td>{}</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>&lt;ipykernel.iostream.OutStream object at 0x7f8d...</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>None</td>\n",
       "      <td>C1</td>\n",
       "      <td>Angstrom</td>\n",
       "      <td>0.0</td>\n",
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      ],
      "text/plain": [
       "                                             _atm  \\\n",
       "0  [[18, 20, 1, 23, 0, 0], [18, 24, 1, 27, 0, 0]]   \n",
       "1  [[18, 20, 1, 23, 0, 0], [18, 24, 1, 27, 0, 0]]   \n",
       "\n",
       "                                               _atom  \\\n",
       "0  [(Ar, [3.54323648356, 0.0, 0.0]), (Ar, [-3.543...   \n",
       "1  [(Ar, [3.54323648356, 0.0, 0.0]), (Ar, [-3.543...   \n",
       "\n",
       "                                                _bas  \\\n",
       "0  [[0, 0, 11, 3, 0, 28, 39, 0], [0, 0, 1, 1, 0, ...   \n",
       "1  [[0, 0, 5, 1, 0, 28, 33, 0], [0, 0, 3, 1, 0, 3...   \n",
       "\n",
       "                                              _basis  _built  \\\n",
       "0  {u'Ar': [[0, [145700.0, 0.0002367, -6.7491e-05...     1.0   \n",
       "1  {u'Ar': [[0, [11797.119765, 0.0020214479973], ...     1.0   \n",
       "\n",
       "                                            _chkfile _ecp _ecpbas  \\\n",
       "0  <open file '<fdopen>', mode 'w+b' at 0x7f8d550...   []      []   \n",
       "1  <open file '<fdopen>', mode 'w+b' at 0x7f8d550...   []      []   \n",
       "\n",
       "                                                _env  \\\n",
       "0  [137.03599968, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0...   \n",
       "1  [137.03599968, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0...   \n",
       "\n",
       "                                                _eri  \\\n",
       "0  [10.9203114287, -1.31592562125, 0.263519480103...   \n",
       "1  [11.0233591869, 2.02986621851, 0.460838722679,...   \n",
       "\n",
       "                                               _keys _nelectron       _t0  \\\n",
       "0  {opt, direct_scf, verbose, stdout, level_shift...       None  5.191529   \n",
       "1  {opt, direct_scf, verbose, stdout, level_shift...       None  5.380022   \n",
       "\n",
       "            _w0                                               atom     basis  \\\n",
       "0  1.523914e+09  Ar 1.8750000000 0.0000000000 0.0000000000\\nAr ...   cc-pVDZ   \n",
       "1  1.523914e+09  Ar 1.8750000000 0.0000000000 0.0000000000\\nAr ...  def2-SVP   \n",
       "\n",
       "  callback  cart  charge                               chkfile  conv_check  \\\n",
       "0     None   0.0     0.0  /home/narbe/Tutorial_PySCF/tmpmYkCpq         0.0   \n",
       "1     None   0.0     0.0  /home/narbe/Tutorial_PySCF/tmp8calp2         0.0   \n",
       "\n",
       "       conv_tol  conv_tol_grad  converged datapath  diis  direct_scf_tol  \\\n",
       "0  1.000000e-12   1.000000e-08        1.0    data/   1.0    1.000000e-13   \n",
       "1  1.000000e-12   1.000000e-08        1.0    data/   1.0    1.000000e-13   \n",
       "\n",
       "         e_tot ecp groupname init_guess irrep_id irrep_name  level_shift  \\\n",
       "0 -1053.599476  {}        C1      minao     None       None          0.0   \n",
       "1 -1053.246842  {}        C1      minao     None       None          0.0   \n",
       "\n",
       "   max_cycle  max_memory method  \\\n",
       "0      100.0      8000.0    UHF   \n",
       "1      100.0      8000.0    UHF   \n",
       "\n",
       "                                            mo_coeff  \\\n",
       "0  ([[0.707120975302, 0.707120352269, -5.71489765...   \n",
       "1  ([[0.702752480149, 0.702755043495, -0.22449745...   \n",
       "\n",
       "                                           mo_energy  \\\n",
       "0  ([-118.6061178, -118.606117699, -12.3176581742...   \n",
       "1  ([-118.549384229, -118.549367281, -12.30248187...   \n",
       "\n",
       "                                              mo_occ  \\\n",
       "0  [[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,...   \n",
       "1  [[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,...   \n",
       "\n",
       "                                              mol               molecule  \\\n",
       "0  <pyscf.gto.mole.Mole object at 0x7f8d52bdbd10>  11_Ar-Ar_dim_NC15.xyz   \n",
       "1  <pyscf.gto.mole.Mole object at 0x7f8d6ff9a7d0>  11_Ar-Ar_dim_NC15.xyz   \n",
       "\n",
       "  nelec nucmod   opt output  spin  \\\n",
       "0  None     {}  None   None   0.0   \n",
       "1  None     {}  None   None   0.0   \n",
       "\n",
       "                                              stdout symm_orb  symmetry  \\\n",
       "0  <ipykernel.iostream.OutStream object at 0x7f8d...     None       0.0   \n",
       "1  <ipykernel.iostream.OutStream object at 0x7f8d...     None       0.0   \n",
       "\n",
       "  symmetry_subgroup topgroup      unit  verbose  \n",
       "0              None       C1  Angstrom      0.0  \n",
       "1              None       C1  Angstrom      0.0  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mydbase.head(2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "ENDS HERE FOR NOW!\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6-31G : -30.3460907145\n",
      "cc-pVDZ : -37.7285547963\n",
      "cc-pVTZ : -37.9614307675\n",
      "cc-pVQZ : -37.4238020232\n",
      "cc-pV5Z : -37.0073200144\n"
     ]
    }
   ],
   "source": [
    "mol_list=['169_f2_W4-11.xyz',\"\"\"F\"\"\"]\n",
    "mol_int=[1,-2]\n",
    "spin_int=[0,1]\n",
    "basis_set_list=['6-31G','cc-pVDZ','cc-pVTZ','cc-pVQZ','cc-pV5Z']\n",
    "\n",
    "for j in range(len(basis_set_list)):\n",
    "    en=0.\n",
    "    for i in range(len(mol_list)):\n",
    "        en+=mol_int[i]*run('0.2*HF+0.08*LDA+0.72*B88,0.19*VWN_RPA+0.81*LYP',mol_list[i],basis_set_list[j],spin=spin_int[i],stable=False,datapath='/home/narbe/Tutorial_PySCF/data/',scf_type='U')\n",
    "    print basis_set_list[j], ':', en*627.5095"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "#mol.multiplicity=1 for closed shell\n",
    "#gaussian basis paerser in basis/parse_gaussian.py\n",
    "\n",
    "#TO-DO LIST\n",
    "\n",
    "#allow mol.atom to take something like @H or !H -- something to indicate Ghost easier (X-H updates)\n",
    "#mol.cart needs to be set based on the basis set (mostly for Pople -- do we care?)\n",
    "#be able to read mol.atom from any file, and the file can either be just XYZ/Zmat, coordinates, Q-Chem like, etc.\n",
    "\n",
    "#D3 has to be implemented, and VV10 sped up, and maybe D2 D3(BJ) D4 and all that new stuff\n",
    "\n",
    "#what about fragment monomoners?\n",
    "#be able to take input of Gaussian94 basis/ecp\n",
    "#be able to read basis from file on disk both formats\n",
    "#maybe for mol.cart instead of 0 and 1, do 'spherical' and 'Cartesian'\n",
    "\n",
    "#there should be a verbose level for Mole that doesn't print basis set coeffs and stuff\n",
    "#shouldn't the extra cycle for SCF (conv_check) only be initiated IF there is a level shift?\n",
    "#should we be using the norm of the orbital gradient for convergence or the rms\n",
    "#printing HOMO/LUMO on each cycle is unnecessary or at least we should be able to turn it off\n",
    "#we should print like orbital energies at end, split into occ and virt\n",
    "\n",
    "#what exactly is the minao guess? will it be expensive for large systems?\n",
    "#mp.frozen and cc.frozen should have a default!! like if true, it should just do something obvious\n",
    "#pt2 kernel should not return t2?!\n",
    "#cc kernel shouldt return t2?!\n",
    "#it's not clear what the default SCF conv_tol is? 1e-9 or 1e-10? it is 1e-9\n",
    "#nalpha and nbeta for UHF?\n",
    "\n",
    "#if atom_grid is specified, then don't print grids.level, that is confusing\n",
    "#some properties should be computed for free and by default -- atomic charges, S^2, multipole moments, mulliken population\n",
    "    #group all properties into def analyze and just make it default run in kernel\n",
    "#lin dep should be automatically removed!!!\n",
    "#stability_analysis easier\n",
    "#opitmizer options: diis, ediis, adiis, newton, gdm\n",
    "#breakdown of energy printed at end (nuclear rep./1e/2e/DFT/disp/PCM/EFP/total)\n",
    "#for DFT, it should allow 'M06-L' not 'M06_L,M06_L' need to hard-code the XC\n",
    "    #for DFT mf.xc=',' in addition to 'HF' maybe we should have 'SR-HF' and 'LR-HF'\n",
    "#allow setting of b and C for VV10\n",
    "#give RHF/ROHF a spin square function just to print it out so ppl dont have to compute in their head\n",
    "#spin per atom for UHF calc?\n",
    "\n",
    "#PSI4 output info:\n",
    "#rotational constants?\n",
    "#charge/mult/electron alph beta\n",
    "#dipole in different units, both nuclear/electron/full\n",
    "\n",
    "#NWChem - VWN1RPA\n",
    "#PySCF - VWN5\n",
    "#TURBOMOLE - VWN5\n",
    "#GAMESS - VWN5\n",
    "#MOLPRO - VWN5\n",
    "#ORCA - VWN5\n",
    "#PSI4 - VWN5\n",
    "#Q-Chem - VWN1RPA\n",
    "#Gaussian - VWN3\n",
    "\n",
    "#generate file that run function psueodcode\n",
    "#mf.RKS()\n",
    "#...\n",
    "#mf=mf.newton()\n",
    "\n",
    "#scf_guess read impement\n",
    "\n",
    "#        xc=None, nlc='', xc_grid=(99,590), nlc_grid=(50,194), small_rho_cutoff=1e-7,\n",
    "#        atomic_radii='BRAGG', becke_scheme='BECKE', prune=None, radi_method='GAUSS_CHEBYSHEV', radii_adjust=None,"
   ]
  }
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