QCArchive_demo.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# QCArchive Demo\n",
    "## Molssi Software Summer School - day 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "\n",
    "client = ptl.FractalClient()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<h3>FractalClient</h3>\n",
       "<ul>\n",
       "  <li><b>Server:   &nbsp; </b>The MolSSI QCArchive Server</li>\n",
       "  <li><b>Address:  &nbsp; </b>https://api.qcarchive.molssi.org:443/</li>\n",
       "  <li><b>Username: &nbsp; </b>None</li>\n",
       "</ul>\n"
      ],
      "text/plain": [
       "FractalClient(server_name='The MolSSI QCArchive Server', address='https://api.qcarchive.molssi.org:443/', username='None')"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "client"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "butane = client.query_molecules(id=['61139','70659'])\n",
    "# different id means different conformations of butane"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Molecule(name='C4H10' formula='C4H10' hash='3bbc6db')>,\n",
       " <Molecule(name='C4H10' formula='C4H10' hash='bb665a3')>]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x1176304a8>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
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      "text/plain": [
       "<py3Dmol.view at 0x117630b38>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[1].show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Config',\n",
       " '__abstractmethods__',\n",
       " '__annotations__',\n",
       " '__class__',\n",
       " '__config__',\n",
       " '__delattr__',\n",
       " '__dict__',\n",
       " '__dir__',\n",
       " '__doc__',\n",
       " '__eq__',\n",
       " '__fields__',\n",
       " '__fields_set__',\n",
       " '__format__',\n",
       " '__ge__',\n",
       " '__get_validators__',\n",
       " '__getattr__',\n",
       " '__getattribute__',\n",
       " '__getstate__',\n",
       " '__gt__',\n",
       " '__hash__',\n",
       " '__init__',\n",
       " '__init_subclass__',\n",
       " '__iter__',\n",
       " '__le__',\n",
       " '__lt__',\n",
       " '__module__',\n",
       " '__ne__',\n",
       " '__new__',\n",
       " '__reduce__',\n",
       " '__reduce_ex__',\n",
       " '__repr__',\n",
       " '__setattr__',\n",
       " '__setstate__',\n",
       " '__sizeof__',\n",
       " '__slots__',\n",
       " '__str__',\n",
       " '__subclasshook__',\n",
       " '__validators__',\n",
       " '__values__',\n",
       " '__weakref__',\n",
       " '_abc_impl',\n",
       " '_calculate_keys',\n",
       " '_custom_root_type',\n",
       " '_decompose_class',\n",
       " '_get_key_factory',\n",
       " '_get_value',\n",
       " '_inertial_tensor',\n",
       " '_iter',\n",
       " '_json_encoder',\n",
       " '_orient_molecule_internal',\n",
       " '_repr_html_',\n",
       " '_schema_cache',\n",
       " 'align',\n",
       " 'atom_labels',\n",
       " 'atomic_numbers',\n",
       " 'comment',\n",
       " 'compare',\n",
       " 'connectivity',\n",
       " 'construct',\n",
       " 'copy',\n",
       " 'dict',\n",
       " 'extras',\n",
       " 'fields',\n",
       " 'fix_com',\n",
       " 'fix_orientation',\n",
       " 'fix_symmetry',\n",
       " 'fragment_charges',\n",
       " 'fragment_multiplicities',\n",
       " 'fragments',\n",
       " 'from_data',\n",
       " 'from_file',\n",
       " 'from_orm',\n",
       " 'geometry',\n",
       " 'get_fragment',\n",
       " 'get_hash',\n",
       " 'get_molecular_formula',\n",
       " 'hash_fields',\n",
       " 'id',\n",
       " 'identifiers',\n",
       " 'json',\n",
       " 'json_dict',\n",
       " 'mass_numbers',\n",
       " 'masses',\n",
       " 'measure',\n",
       " 'min_zero',\n",
       " 'molecular_charge',\n",
       " 'molecular_multiplicity',\n",
       " 'must_be_3n',\n",
       " 'must_be_n',\n",
       " 'must_be_n_frag',\n",
       " 'name',\n",
       " 'nelectrons',\n",
       " 'nuclear_repulsion_energy',\n",
       " 'orient_molecule',\n",
       " 'parse_file',\n",
       " 'parse_obj',\n",
       " 'parse_raw',\n",
       " 'populate_real',\n",
       " 'pretty_print',\n",
       " 'provenance',\n",
       " 'real',\n",
       " 'schema',\n",
       " 'schema_json',\n",
       " 'schema_name',\n",
       " 'schema_version',\n",
       " 'scramble',\n",
       " 'show',\n",
       " 'symbols',\n",
       " 'to_file',\n",
       " 'to_string',\n",
       " 'update_forward_refs',\n",
       " 'validate']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dir(butane[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].atomic_numbers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].symbols"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "14 14\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array([[ 0.60309252, -2.0666753 , -2.95631542],\n",
       "       [-0.54975128,  2.07257294,  2.96267825],\n",
       "       [ 0.17543623, -1.41965569, -0.1899598 ],\n",
       "       [-0.17535536,  1.41986451,  0.18990506],\n",
       "       [-0.98243014, -1.42706018, -4.12126516],\n",
       "       [ 2.32107194, -1.14665691, -3.64966894],\n",
       "       [ 0.81868895, -4.10783439, -3.21556669],\n",
       "       [ 1.07104045,  1.43010767,  4.07529687],\n",
       "       [-2.24715359,  1.16149057,  3.71618302],\n",
       "       [-0.73832413,  4.11600143,  3.22440978],\n",
       "       [ 1.79270627, -2.08396319,  0.92115557],\n",
       "       [-1.4961426 , -2.4339562 ,  0.49460988],\n",
       "       [-1.81551707,  2.07754179, -0.89074739],\n",
       "       [ 1.48034939,  2.43606453, -0.52991943]])"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(len(butane[0].geometry),len(butane[0].symbols))\n",
    "butane[0].geometry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "butane_geometries = [butane[0].geometry.copy(), butane[1].geometry.copy()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[ 0.60309252 -2.0666753  -2.95631542]\n",
      " [-0.54975128  2.07257294  2.96267825]\n",
      " [ 0.17543623 -1.41965569 -0.1899598 ]\n",
      " [-0.17535536  1.41986451  0.18990506]\n",
      " [-0.98243014 -1.42706018 -4.12126516]\n",
      " [ 2.32107194 -1.14665691 -3.64966894]\n",
      " [ 0.81868895 -4.10783439 -3.21556669]\n",
      " [ 1.07104045  1.43010767  4.07529687]\n",
      " [-2.24715359  1.16149057  3.71618302]\n",
      " [-0.73832413  4.11600143  3.22440978]\n",
      " [ 1.79270627 -2.08396319  0.92115557]\n",
      " [-1.4961426  -2.4339562   0.49460988]\n",
      " [-1.81551707  2.07754179 -0.89074739]\n",
      " [ 1.48034939  2.43606453 -0.52991943]] \n",
      "\n",
      "\n",
      " [[-0.69390481 -2.34149626 -1.69148799]\n",
      " [-1.52276705  2.12200941  1.41576994]\n",
      " [ 1.67240752 -1.04497304 -0.64735584]\n",
      " [ 1.23080507  1.33319296  1.00805961]\n",
      " [-1.91853592 -3.01948807 -0.12936141]\n",
      " [-1.76605429 -1.03734012 -2.93620015]\n",
      " [-0.12310659 -4.00556366 -2.83563025]\n",
      " [-2.59157782  0.60554767  2.39435231]\n",
      " [-2.43936476  2.58766899 -0.41251981]\n",
      " [-1.57944138  3.83705924  2.62381983]\n",
      " [ 2.89478004 -0.52016897 -2.27399626]\n",
      " [ 2.74546053 -2.46112357  0.47453866]\n",
      " [ 2.2490306   2.95672246  0.14611927]\n",
      " [ 2.09998041  1.01579454  2.89468766]]\n"
     ]
    }
   ],
   "source": [
    "print(butane_geometries[0],'\\n\\n\\n',butane_geometries[1])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "def calculate_distance(rA,rB):\n",
    "    \"\"\"calculate the distance between points A and B\"\"\"\n",
    "    dist_vec = (rA - rB)\n",
    "    distance = np.linalg.norm(dist_vec)\n",
    "    return distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[ 0.60309252 -2.0666753  -2.95631542]\n"
     ]
    }
   ],
   "source": [
    "atom1 = butane_geometries[0][0]   # coordinate of 1st atom in the 1st conformer\n",
    "print(atom1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[-0.54975128  2.07257294  2.96267825]\n"
     ]
    }
   ],
   "source": [
    "atom2 = butane_geometries[0][1]\n",
    "print(atom2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "7.314158248564329\n"
     ]
    }
   ],
   "source": [
    "measured_distance = calculate_distance(atom1,atom2)\n",
    "print(measured_distance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7.31415824856433"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].measure([0,1])   # measure atom0 and atom1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6.71634950813261\n",
      "6.71634950813261\n"
     ]
    }
   ],
   "source": [
    "# Use calculate_distance fct to measure the distance between atom3 and 10 in the 2nd butane molecule\n",
    "# Use the measure command to see if you get the same answer\n",
    "atom3 = butane_geometries[1][2]\n",
    "atom10 = butane_geometries[1][9]\n",
    "mea_dis = calculate_distance(atom3, atom10)\n",
    "print(mea_dis)\n",
    "print(butane[1].measure([2,9]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "def build_bond_list(coordinates, max_bond = 1.55, min_bond = 0):\n",
    "    num_atoms = len(coordinates)\n",
    "    bonds = {}\n",
    "    \n",
    "    for atom1 in range(num_atoms):\n",
    "        for atom2 in range(atom1, num_atoms):\n",
    "            distance = calculate_distance(coordinates[atom1],coordinates[atom2])\n",
    "            \n",
    "            if distance > min_bond and distance < max_bond:\n",
    "                bonds[(atom1,atom2)] = distance\n",
    "                \n",
    "    return bonds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(0, 2): 2.873020656801253,\n",
       " (0, 4): 2.068839651551603,\n",
       " (0, 5): 2.068484041315794,\n",
       " (0, 6): 2.068821759435787,\n",
       " (1, 3): 2.873059651780396,\n",
       " (1, 7): 2.068247482474781,\n",
       " (1, 8): 2.0685780442929644,\n",
       " (1, 9): 2.0687346633381822,\n",
       " (2, 3): 2.8862132661474598,\n",
       " (2, 10): 2.0715801221019885,\n",
       " (2, 11): 2.0716218178677623,\n",
       " (3, 12): 2.0713472807014583,\n",
       " (3, 13): 2.071754810836534}"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bond_list = build_bond_list(butane_geometries[0], max_bond = 2.93)\n",
    "bond_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(0, 2, 1.0),\n",
       " (0, 4, 1.0),\n",
       " (0, 5, 1.0),\n",
       " (0, 6, 1.0),\n",
       " (1, 3, 1.0),\n",
       " (1, 7, 1.0),\n",
       " (1, 8, 1.0),\n",
       " (1, 9, 1.0),\n",
       " (2, 3, 1.0),\n",
       " (2, 10, 1.0),\n",
       " (2, 11, 1.0),\n",
       " (3, 12, 1.0),\n",
       " (3, 13, 1.0)]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Use connectivity command to see the actual bond_list in the molecule\n",
    "# The 3rd column is the bond order\n",
    "butane[0].connectivity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.8897261254578281\n"
     ]
    }
   ],
   "source": [
    "import qcelemental\n",
    "angstrom_to_bohr = qcelemental.constants.conversion_factor(\"angstrom\",\"bohr\")\n",
    "print(angstrom_to_bohr)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<OptimizationRecord(id='2658710' status='COMPLETE')>]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Use qcportal to access a geometry optimization calculation\n",
    "# Use query_procedures\n",
    "# id = 2658710\n",
    "molecule = client.query_procedures(id = ['2658710'])\n",
    "molecule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "opt = molecule[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
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    2.586357829400     3.902336471225    -6.942502547464\\nH                     2.586357829400     3.902336471225     4.097455549610\\nH                     4.079591998090    -2.355354000793    -8.195632949853\\nH                     4.079591998090    -2.355354000793     5.350585951999\\nH                     4.079591998090     2.355354000793    -8.195632949853\\nH                     4.079591998090     2.355354000793     5.350585951999\\nH                     4.710707001441     0.000000000000    -8.195632949853\\nH                     4.710707001441     0.000000000000     5.350585951999\\n\",\"xyz\");\n",
       "\tviewer_1563894787649804.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
       "\tviewer_1563894787649804.zoomTo();\n",
       "viewer_1563894787649804.render();\n",
       "});\n",
       "</script>"
      ]
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     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x117630c50>"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "initial = opt.get_initial_molecule()\n",
    "initial.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
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       "        <p id=\"3dmolwarning_15638948315930822\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
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       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
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       "$3Dmolpromise.then(function() {\n",
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       "\tviewer_15638948315930822.addModel(\"72\\nC54H18\\nC                     1.219221001901    -4.550194001216    -2.133023000369\\nC                     1.219221001901    -4.550194001216    -0.712023002632\\nC                     1.219221001901     4.550194001216    -2.133023000369\\nC                     1.219221001901     4.550194001216    -0.712023002632\\nC                     2.355354000793    -4.079591998090    -4.266046000738\\nC                     2.355354000793    -4.079591998090    -2.845045997709\\nC                     2.355354000793    -4.079591998090     0.000000000000\\nC                     2.355354000793    -4.079591998090     1.420999997737\\nC                     2.355354000793     4.079591998090    -4.266046000738\\nC                     2.355354000793     4.079591998090    -2.845045997709\\nC                     2.355354000793     4.079591998090     0.000000000000\\nC                     2.355354000793     4.079591998090     1.420999997737\\nC                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       "\tviewer_15638948315930822.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
       "\tviewer_15638948315930822.zoomTo();\n",
       "viewer_15638948315930822.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x118520080>"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "final = opt.get_final_molecule()\n",
    "initial.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "initial.connectivity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "# max bond length is 2.93\n",
    "initial_coordinates = initial.geometry.copy()\n",
    "final_coordinate = final.geometry.copy()\n",
    "\n",
    "initial_bonds = build_bond_list(initial_coordinates, max_bond=2.93)\n",
    "final_bonds = build_bond_list(final_coordinate, max_bond=2.93)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "data": {
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       " (2, 9): 2.685300947458371,\n",
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       " (3, 10): 2.6853009524690883,\n",
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       " (4, 5): 2.685300829999999,\n",
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       " (4, 58): 2.0494834770587396,\n",
       " (5, 14): 2.6852998829666923,\n",
       " (6, 7): 2.68530082,\n",
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       " (7, 16): 2.6852998879774117,\n",
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       " (8, 9): 2.685300829999999,\n",
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       " (8, 60): 2.0494834770587396,\n",
       " (9, 20): 2.6852998829666923,\n",
       " (10, 11): 2.68530082,\n",
       " (10, 21): 2.6852998879774117,\n",
       " (11, 22): 2.6852998879774117,\n",
       " (11, 61): 2.0494834871062877,\n",
       " (12, 13): 2.685300829999999,\n",
       " (12, 24): 2.6852998829666923,\n",
       " (12, 62): 2.049483475383679,\n",
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       " (14, 15): 2.6853008199999997,\n",
       " (14, 26): 2.6852998829666923,\n",
       " (15, 27): 2.6852998879774117,\n",
       " (16, 17): 2.68530082,\n",
       " (16, 28): 2.6852998879774117,\n",
       " (17, 29): 2.6852998879774117,\n",
       " (17, 63): 2.049483480394398,\n",
       " (18, 19): 2.685300829999999,\n",
       " (18, 30): 2.6852998829666923,\n",
       " (18, 64): 2.049483475383679,\n",
       " (19, 31): 2.685300829993184,\n",
       " (20, 21): 2.6853008199999997,\n",
       " (20, 32): 2.6852998829666923,\n",
       " (21, 33): 2.6852998879774117,\n",
       " (22, 23): 2.68530082,\n",
       " (22, 34): 2.6852998879774117,\n",
       " (23, 35): 2.6852998879774117,\n",
       " (23, 65): 2.049483480394398,\n",
       " (24, 36): 2.685300947458371,\n",
       " (24, 66): 2.0494834799999992,\n",
       " (25, 26): 2.685300829999999,\n",
       " (25, 37): 2.6853018944844873,\n",
       " (26, 38): 2.685300947458371,\n",
       " (27, 28): 2.68530082,\n",
       " (27, 39): 2.6853009524690883,\n",
       " (28, 40): 2.6853009524690883,\n",
       " (29, 41): 2.6853009524690883,\n",
       " (29, 67): 2.049483480000001,\n",
       " (30, 42): 2.685300947458371,\n",
       " (30, 68): 2.0494834799999992,\n",
       " (31, 32): 2.685300829999999,\n",
       " (31, 43): 2.6853018944844873,\n",
       " (32, 44): 2.685300947458371,\n",
       " (33, 34): 2.68530082,\n",
       " (33, 45): 2.6853009524690883,\n",
       " (34, 46): 2.6853009524690883,\n",
       " (35, 47): 2.6853009524690883,\n",
       " (35, 69): 2.049483480000001,\n",
       " (36, 37): 2.685300829999999,\n",
       " (36, 48): 2.6853008398744698,\n",
       " (37, 49): 2.685301786900624,\n",
       " (38, 39): 2.6853008199999997,\n",
       " (38, 50): 2.6853008398744698,\n",
       " (39, 51): 2.6853008448851874,\n",
       " (40, 41): 2.68530082,\n",
       " (40, 52): 2.6853008448851874,\n",
       " (41, 53): 2.6853008448851874,\n",
       " (42, 43): 2.685300829999999,\n",
       " (42, 48): 2.6853008398744698,\n",
       " (43, 49): 2.685301786900624,\n",
       " (44, 45): 2.6853008199999997,\n",
       " (44, 50): 2.6853008398744698,\n",
       " (45, 51): 2.6853008448851874,\n",
       " (46, 47): 2.68530082,\n",
       " (46, 52): 2.6853008448851874,\n",
       " (47, 53): 2.6853008448851874,\n",
       " (48, 70): 2.0494834799999992,\n",
       " (49, 50): 2.685300829999999,\n",
       " (51, 52): 2.68530082,\n",
       " (53, 71): 2.049483480000001}"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "initial_bonds   "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(0, 1): 2.5640429800175255,\n",
       " (0, 5): 2.721830285918179,\n",
       " (0, 54): 2.050790758811911,\n",
       " (1, 6): 2.7218295881283754,\n",
       " (1, 55): 2.0507899790642936,\n",
       " (2, 3): 2.5640476200137154,\n",
       " (2, 9): 2.7218316161338745,\n",
       " (2, 56): 2.0507897182972523,\n",
       " (3, 10): 2.7218322358238627,\n",
       " (3, 57): 2.0507903323327072,\n",
       " (4, 5): 2.6362688969926538,\n",
       " (4, 13): 2.6362287673968563,\n",
       " (4, 58): 2.0526208230733363,\n",
       " (5, 14): 2.6960983036854445,\n",
       " (6, 7): 2.636270533714002,\n",
       " (6, 15): 2.6960997775436293,\n",
       " (7, 16): 2.6362286718268693,\n",
       " (7, 59): 2.052619784709002,\n",
       " (8, 9): 2.6362763589350253,\n",
       " (8, 19): 2.6362317513408633,\n",
       " (8, 60): 2.052618775995513,\n",
       " (9, 20): 2.696098946310403,\n",
       " (10, 11): 2.6362743770415618,\n",
       " (10, 21): 2.69609826814251,\n",
       " (11, 22): 2.636231235454784,\n",
       " (11, 61): 2.052619233623958,\n",
       " (12, 13): 2.72203531192571,\n",
       " (12, 24): 2.564169618543982,\n",
       " (12, 62): 2.0508445474196115,\n",
       " (13, 25): 2.696059263395006,\n",
       " (14, 15): 2.690631710020097,\n",
       " (14, 26): 2.682669276790726,\n",
       " (15, 27): 2.6826670389495995,\n",
       " (16, 17): 2.722037657492619,\n",
       " (16, 28): 2.6960582630681764,\n",
       " (17, 29): 2.5641705795606935,\n",
       " (17, 63): 2.050843862160726,\n",
       " (18, 19): 2.722041505034991,\n",
       " (18, 30): 2.5641788745730825,\n",
       " (18, 64): 2.050844447656416,\n",
       " (19, 31): 2.6960533339463475,\n",
       " (20, 21): 2.690642320026428,\n",
       " (20, 32): 2.6826726488841537,\n",
       " (21, 33): 2.682674602167853,\n",
       " (22, 23): 2.7220399755844102,\n",
       " (22, 34): 2.6960545100618356,\n",
       " (23, 35): 2.564176414497956,\n",
       " (23, 65): 2.0508448708356606,\n",
       " (24, 36): 2.7220230301094754,\n",
       " (24, 66): 2.0508044054115038,\n",
       " (25, 26): 2.6824863860456256,\n",
       " (25, 37): 2.6905465841620844,\n",
       " (26, 38): 2.680561957509339,\n",
       " (27, 28): 2.682489275183641,\n",
       " (27, 39): 2.6805642102547806,\n",
       " (28, 40): 2.6905484003099565,\n",
       " (29, 41): 2.722021376226541,\n",
       " (29, 67): 2.050805094682261,\n",
       " (30, 42): 2.7220185413147258,\n",
       " (30, 68): 2.0508036692319536,\n",
       " (31, 32): 2.6825010890496643,\n",
       " (31, 43): 2.6905580877221253,\n",
       " (32, 44): 2.6805640725487785,\n",
       " (33, 34): 2.6824977355443593,\n",
       " (33, 45): 2.680561091221982,\n",
       " (34, 46): 2.6905564118575427,\n",
       " (35, 47): 2.72201978044889,\n",
       " (35, 69): 2.0508039226853367,\n",
       " (36, 37): 2.696334759656457,\n",
       " (36, 48): 2.636532006559348,\n",
       " (37, 49): 2.682277014835587,\n",
       " (38, 39): 2.681397250048598,\n",
       " (38, 50): 2.6814386328151083,\n",
       " (39, 51): 2.6814346333317425,\n",
       " (40, 41): 2.696337004713522,\n",
       " (40, 52): 2.682275764899848,\n",
       " (41, 53): 2.6365345534604177,\n",
       " (42, 43): 2.696340442384856,\n",
       " (42, 48): 2.63654229620249,\n",
       " (43, 49): 2.682269911997115,\n",
       " (44, 45): 2.6814030000532503,\n",
       " (44, 50): 2.6814354394476605,\n",
       " (45, 51): 2.681438878673595,\n",
       " (46, 47): 2.6963381630025953,\n",
       " (46, 52): 2.6822704754077114,\n",
       " (47, 53): 2.636540300741533,\n",
       " (48, 70): 2.0526037064385148,\n",
       " (49, 50): 2.680171622154041,\n",
       " (51, 52): 2.6801721039324247,\n",
       " (53, 71): 2.0526024177470563}"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "final_bonds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "a\n",
      "b\n"
     ]
    }
   ],
   "source": [
    "a = {'a':2,'b':3}\n",
    "for i in a:\n",
    "    print(i)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(0, 1): -0.12125783998247419,\n",
       " (0, 5): 0.03652933845980799,\n",
       " (0, 54): 0.0013072821258468537,\n",
       " (1, 6): 0.0365286356592871,\n",
       " (1, 55): 0.0013065023782292684,\n",
       " (2, 3): -0.12125319998628425,\n",
       " (2, 9): 0.036530668675503364,\n",
       " (2, 56): 0.0013062416111879749,\n",
       " (3, 10): 0.0365312833547744,\n",
       " (3, 57): 0.0013068556466429015,\n",
       " (4, 5): -0.04903193300734543,\n",
       " (4, 13): -0.0490720625963279,\n",
       " (4, 58): 0.003137346014596698,\n",
       " (5, 14): 0.010798420718752144,\n",
       " (6, 7): -0.04903028628599815,\n",
       " (6, 15): 0.01079988956621758,\n",
       " (7, 16): -0.04907121615054244,\n",
       " (7, 59): 0.0031362976027144995,\n",
       " (8, 9): -0.049024471064973874,\n",
       " (8, 19): -0.04906907865232091,\n",
       " (8, 60): 0.003135298936773445,\n",
       " (9, 20): 0.010799063343710724,\n",
       " (10, 11): -0.04902644295843839,\n",
       " (10, 21): 0.010798380165098376,\n",
       " (11, 22): -0.0490686525226276,\n",
       " (11, 61): 0.003135746517670235,\n",
       " (12, 13): 0.03673448192571094,\n",
       " (12, 24): -0.12113026442271035,\n",
       " (12, 62): 0.001361072035932498,\n",
       " (13, 25): 0.010758433401821588,\n",
       " (14, 15): 0.005330890020097456,\n",
       " (14, 26): -0.0026306061759662214,\n",
       " (15, 27): -0.002632849027812245,\n",
       " (16, 17): 0.03673683749261869,\n",
       " (16, 28): 0.010758375090764716,\n",
       " (17, 29): -0.1211293084167182,\n",
       " (17, 63): 0.0013603817663279116,\n",
       " (18, 19): 0.0367406750349919,\n",
       " (18, 30): -0.12112100839360984,\n",
       " (18, 64): 0.0013609722727370155,\n",
       " (19, 31): 0.010752503953163295,\n",
       " (20, 21): 0.005341500026428303,\n",
       " (20, 32): -0.002627234082538621,\n",
       " (21, 33): -0.002625285809558786,\n",
       " (22, 23): 0.0367391555844101,\n",
       " (22, 34): 0.010754622084423904,\n",
       " (23, 35): -0.12112347347945551,\n",
       " (23, 65): 0.0013613904412626,\n",
       " (24, 36): 0.036722082651104326,\n",
       " (24, 66): 0.0013209254115045255,\n",
       " (25, 26): -0.00281444395437358,\n",
       " (25, 37): 0.005244689677597059,\n",
       " (26, 38): -0.004738989949032213,\n",
       " (27, 28): -0.002811544816359035,\n",
       " (27, 39): -0.004736742214307643,\n",
       " (28, 40): 0.005247447840868169,\n",
       " (29, 41): 0.03672042375745255,\n",
       " (29, 67): 0.0013216146822601083,\n",
       " (30, 42): 0.03671759385635465,\n",
       " (30, 68): 0.0013201892319543163,\n",
       " (31, 32): -0.0027997409503348614,\n",
       " (31, 43): 0.0052561932376380405,\n",
       " (32, 44): -0.0047368749095926255,\n",
       " (33, 34): -0.002803084455640814,\n",
       " (33, 45): -0.004739861247106347,\n",
       " (34, 46): 0.005255459388454398,\n",
       " (35, 47): 0.03671882797980164,\n",
       " (35, 69): 0.0013204426853357099,\n",
       " (36, 37): 0.011033929656457886,\n",
       " (36, 48): -0.04876883331512172,\n",
       " (37, 49): -0.0030247720650371512,\n",
       " (38, 39): -0.003903569951401842,\n",
       " (38, 50): -0.0038622070593614666,\n",
       " (39, 51): -0.0038662115534449093,\n",
       " (40, 41): 0.011036184713521635,\n",
       " (40, 52): -0.0030250799853392962,\n",
       " (41, 53): -0.04876629142476974,\n",
       " (42, 43): 0.011039612384856845,\n",
       " (42, 48): -0.04875854367197974,\n",
       " (43, 49): -0.003031874903509202,\n",
       " (44, 45): -0.0038978199467494257,\n",
       " (44, 50): -0.0038654004268092734,\n",
       " (45, 51): -0.0038619662115921827,\n",
       " (46, 47): 0.011037343002595179,\n",
       " (46, 52): -0.003030369477476036,\n",
       " (47, 53): -0.04876054414365427,\n",
       " (48, 70): 0.0031202264385155054,\n",
       " (49, 50): -0.005129207845958383,\n",
       " (51, 52): -0.005128716067575478,\n",
       " (53, 71): 0.003118937747055295}"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Compare the 2 dictionaries initial_bonds and final_bonds to find \n",
    "# the change in bond length for each bond\n",
    "def compute_bond_change(initial_bonds, final_bonds):\n",
    "    bonds_change = {}\n",
    "    for key in initial_bonds:\n",
    "        bonds_change[key] = final_bonds[key] - initial_bonds[key]\n",
    "    return bonds_change\n",
    "\n",
    "bonds_change = compute_bond_change(initial_bonds, final_bonds)\n",
    "bonds_change"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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