{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit WARNING: [21:49:30] Enabling RDKit 2019.09.3 jupyter extensions\n"
     ]
    }
   ],
   "source": [
    "from psikit import Psikit"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from orbkit import options\n",
    "from orbkit import main\n",
    "from orbkit import read, grid, extras, output, display"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "pk = Psikit()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "pk.read_from_smiles('c1ccncc1C#N')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "pk.rdkit_optimize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Optimizer: Optimization complete!\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-338.4355393893239"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pk.optimize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "fchk_writer = pk.psi4.core.FCHKWriter(pk.wfn)\n",
    "fchk_writer.write('output.fchk')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "options.filename = \"output.fchk\"\n",
    "options.outputname = 'vis/mol'\n",
    "options.otype = ['vmd','mayavi']\n",
    "#options.otype = ['vmd']\n",
    "options.adjust_grid = [5,0.1]\n",
    "options.calc_mo = 'homo-1:lumo+2'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is ORBKIT.\n",
      "  Copyright (C) 2017 Gunter Hermann, Vincent Pohl, Lukas Eugen Marsoner Steinkasserer, Axel Schild, and Jean Christophe Tremblay\n",
      "  This program comes with ABSOLUTELY NO WARRANTY.\n",
      "  This is free software, and you are welcome to redistribute it\n",
      "  under certain conditions. Type '-l' for details.\n",
      "\n",
      "Writing log to vis/mol.oklog\n",
      "\n",
      "Checking orbkit.options...\n",
      "\n",
      "Loading data from fchk type file output.fchk\n",
      "\n",
      "\n",
      "Setting up the grid...\n",
      "\tx[0] = -10.76 x[-1] = 10.64 Nx = 215 dx = 0.100\n",
      "\ty[0] = -8.66 y[-1] = 9.14 Ny = 179 dy = 0.100\n",
      "\tz[0] = -5.88 z[-1] = 5.92 Nz = 119 dz = 0.100\n",
      "\n",
      "\n",
      "Processing molecular orbital list...\n",
      "\tLine 1: homo-1:lumo+2\n",
      "\n",
      "\n",
      "The following orbitals will be considered...\n",
      "\tLine 1: [25 26 27 28]\n",
      "\n",
      "Converting the regular grid to a vector grid containing 4.58e+06 grid points...\n",
      "\n",
      "Starting the calculation of the molecular orbitals...\n",
      "The grid has been separated into 458 slices each having 1.00e+04 grid points.\n",
      "The calculation will be carried out using only one process.\n",
      "\n",
      "\tThe number of subprocesses can be changed with -p\n",
      "\n",
      "\n",
      "There are 140 contracted Cartesian AOs and 4 MOs to be calculated.\n",
      "\tFinished 10 % (47 slices in 1.747 s)\n",
      "\tFinished 20 % (46 slices in 1.861 s)\n",
      "\tFinished 30 % (46 slices in 1.684 s)\n",
      "\tFinished 40 % (46 slices in 1.717 s)\n",
      "\tFinished 50 % (45 slices in 1.647 s)\n",
      "\tFinished 60 % (46 slices in 1.681 s)\n",
      "\tFinished 70 % (46 slices in 1.704 s)\n",
      "\tFinished 80 % (46 slices in 1.708 s)\n",
      "\tFinished 90 % (46 slices in 1.697 s)\n",
      "Converting the output from a vector grid to a regular grid...\n",
      "\n",
      "Norm of the MOs:\n",
      "\t0.999994\tMO 26.1 (Occ = 2.00, E = -0.4081 E_h)\n",
      "\t0.999988\tMO 27.1 (Occ = 2.00, E = -0.3688 E_h)\n",
      "\t0.999978\tMO 28.1 (Occ = 0.00, E = +0.0775 E_h)\n",
      "\t0.999987\tMO 29.1 (Occ = 0.00, E = +0.1024 E_h)\n",
      "\n",
      "Saving to cube file...\n",
      "\tvis/mol_MO_0.cube\n",
      "\n",
      "Saving to cube file...\n",
      "\tvis/mol_MO_1.cube\n",
      "\n",
      "Saving to cube file...\n",
      "\tvis/mol_MO_2.cube\n",
      "\n",
      "Saving to cube file...\n",
      "\tvis/mol_MO_3.cube\n",
      "\n",
      "Creating VMD network file...\n",
      "\tvis/mol_MO.vmd\n",
      "\n",
      "Depicting the results with MayaVi...\n",
      "\t\n"
     ]
    }
   ],
   "source": [
    "m = main.run_orbkit()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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