psi4_students.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# A simple DFT calculation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "import psi4\n",
    "import numpy as np\n",
    "\n",
    "psi4.set_memory(int(2e9))\n",
    "psi4.core.set_output_file('output.dat', False)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-76.02663646061744"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "psi4.set_memory('500 MB')\n",
    "\n",
    "h2o = psi4.geometry(\"\"\"\n",
    "O\n",
    "H 1 0.96\n",
    "H 1 0.96 2 104.1\n",
    "\"\"\")\n",
    "\n",
    "psi4.energy('scf/cc-pvdz')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Optimizer: Optimization complete!\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-76.02703268911131"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "psi4.set_options({'reference': 'rhf'})\n",
    "psi4.optimize('scf/cc-pvdz', molecule=h2o)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "scf_e, scf_wfn = psi4.frequency('scf/cc-pvdz', molecule=h2o, return_wfn=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Water has a Energy of -47707.68 kcal/mol\n"
     ]
    }
   ],
   "source": [
    "e = scf_e * psi4.constants.hartree2kcalmol\n",
    "print(\"Water has a Energy of {:.2f} kcal/mol\".format(e))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "9\n",
      "\n",
      "C      0.947210   -0.032539    0.006768\n",
      "C     -0.513540   -0.274228   -0.226357\n",
      "O     -1.173341    0.948982    0.011803\n",
      "H      1.402735   -0.752157    0.727744\n",
      "H      1.162151    1.005239    0.378556\n",
      "H      1.457267   -0.114186   -0.976477\n",
      "H     -0.738303   -0.617200   -1.266553\n",
      "H     -0.938713   -1.062133    0.443102\n",
      "H     -1.605466    0.898222    0.901415\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 100x100 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": "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",
      "text/plain": [
       "<Figure size 100x100 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem import AllChem\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "myMoleculeSMILES = 'CCO'\n",
    "myMolecule = Chem.MolFromSmiles(myMoleculeSMILES)\n",
    "Draw.MolToMPL(myMolecule, size=(100, 100))\n",
    "myMolecule = Chem.AddHs(myMolecule)  # Add implicit hydrogens\n",
    "AllChem.EmbedMolecule(myMolecule) # Embed molecule in 3D space\n",
    "print(Chem.MolToXYZBlock(myMolecule)) # Print coordinates\n",
    "\n",
    "Draw.MolToMPL(myMolecule, size=(100, 100))\n",
    "\n",
    "mol = psi4.geometry(Chem.MolToXYZBlock(myMolecule))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\tPrevious geometry is closer to target in internal coordinates, so using that one.\n",
      "\n",
      "\tBest geometry has RMS(Delta(q)) = 1.19e-05\n",
      "\n",
      "\tChange in internal coordinate of 5.16e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 2.\n",
      "\tChange in internal coordinate of 5.23e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 1.\n",
      "\tChange in internal coordinate of 6.56e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 3.\n",
      "\tChange in internal coordinate of 8.58e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 2.\n",
      "\tChange in internal coordinate of 8.65e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 1.\n",
      "\tChange in internal coordinate of 8.04e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 3.\n",
      "\tChange in internal coordinate of 1.01e+00 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 2.\n",
      "\tChange in internal coordinate of 1.01e+00 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 1.\n",
      "\tChange in internal coordinate of 6.71e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 4.\n",
      "\tChange in internal coordinate of 8.13e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 3.\n",
      "\tChange in internal coordinate of 1.01e+00 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 2.\n",
      "\tChange in internal coordinate of 1.02e+00 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 1.\n",
      "\tChange in internal coordinate of 6.13e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 5.\n",
      "\tChange in internal coordinate of 7.93e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 4.\n",
      "\tChange in internal coordinate of 8.75e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 3.\n",
      "\tChange in internal coordinate of 9.19e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 2.\n",
      "\tChange in internal coordinate of 9.88e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 1.\n",
      "\tChange in internal coordinate of 6.64e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 5.\n",
      "\tChange in internal coordinate of 8.64e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 4.\n",
      "\tChange in internal coordinate of 9.71e-01 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 3.\n",
      "\tChange in internal coordinate of 1.02e+00 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 2.\n",
      "\tChange in internal coordinate of 1.08e+00 exceeds limit of 5.00e-01.\n",
      "\tSkipping Hessian update for step 1.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Optimizer: Optimization complete!\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-154.09263149307012"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "psi4.optimize('scf/cc-pvdz', molecule=mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Warning: used thermodynamics relations inappropriate for low-frequency modes: ['273.4527' '314.6375' '444.6219']\n"
     ]
    }
   ],
   "source": [
    "scf_e, scf_wfn = psi4.frequency('scf/cc-pvdz', molecule=mol, return_wfn=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-154.09268840053312"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "scf_e"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# A Toy example\n",
    "\n",
    "Is it possibile to dertermine if a reaction is upfill or downhill?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Optimizer: Optimization complete!\n",
      "Optimizer: Optimization complete!\n",
      "Optimizer: Optimization complete!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "\tThe following linear bends should be present:\n",
      "  L(2,1,3), already present.\n",
      "\t l(2,1,3), already present.\n",
      "\n",
      "AlgError: Exception created. Mesg: New linear angles\n",
      "AlgError: New bends detected.\n",
      "\n",
      " Caught AlgError exception\n",
      "\n",
      " Erasing history.\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Optimizer: Optimization complete!\n"
     ]
    }
   ],
   "source": [
    "O2 = \"[O][O]\"\n",
    "H2O =\"O\"\n",
    "CH4 =\"C\"\n",
    "CO2 =\"C(=O)=O\""
   ]
  }
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