adjust sections in chemistry (#1037)

Co-authored-by: Paul Nation <nonhermitian@gmail.com>

Author: 1ucian0

tutorials/chemistry/1_programmatic_approach.ipynb

@@ -4,22 +4,18 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# _*Qiskit Chemistry, Programmatic Approach*_ \n",
-    "\n",
-    "The latest version of this notebook is available on https://github.com/Qiskit/qiskit-tutorial.\n",
-    "\n",
-    "***\n",
-    "## Contributors\n",
-    "Richard Chen<sup>[1]</sup>, Antonio Mezzacapo<sup>[1]</sup>, Marco Pistoia<sup>[1]</sup>, Stephen Wood<sup>[1]</sup>\n",
-    "### Affiliation\n",
-    "- <sup>[1]</sup>IBMQ"
+    "# _*Qiskit Chemistry, Programmatic Approach*_ \n"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
-    "### Introduction\n",
+    "## Introduction\n",
     "This notebook illustrates how to use Qiskit Chemistry's programmatic APIs.\n",
     "\n",
     "In this notebook, we decompose the computation of the ground state energy of a molecule into 4 steps:\n",
@@ -36,6 +32,9 @@
     "ExecuteTime": {
      "end_time": "2020-07-13T23:48:30.973884Z",
      "start_time": "2020-07-13T23:48:27.368639Z"
+    },
+    "pycharm": {
+     "name": "#%%\n"
     }
    },
    "outputs": [],
@@ -60,9 +59,13 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
-    "### Step 1: Define a molecule\n",
+    "## Step 1: Define a molecule\n",
     "Here, we use LiH in the sto3g basis with the PySCF driver as an example.\n",
     "The `molecule` object records the information from the PySCF driver."
    ]
@@ -74,6 +77,9 @@
     "ExecuteTime": {
      "end_time": "2020-07-13T23:48:31.129792Z",
      "start_time": "2020-07-13T23:48:30.975723Z"
+    },
+    "pycharm": {
+     "name": "#%%\n"
     }
    },
    "outputs": [],
@@ -87,9 +93,13 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
-    "### Step 2: Prepare qubit Hamiltonian\n",
+    "## Step 2: Prepare qubit Hamiltonian\n",
     "Here, we setup the **to-be-frozen** and **to-be-removed** orbitals to reduce the problem size when we map to the qubit Hamiltonian. Furthermore, we define the **mapping type** for the qubit Hamiltonian.\n",
     "For the particular `parity` mapping, we can further reduce the problem size."
    ]
@@ -138,6 +148,9 @@
     "ExecuteTime": {
      "end_time": "2020-07-13T23:48:31.599325Z",
      "start_time": "2020-07-13T23:48:31.163492Z"
+    },
+    "pycharm": {
+     "name": "#%%\n"
     }
    },
    "outputs": [
@@ -284,7 +297,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "We use the classical eigen decomposition to get the smallest eigenvalue as a reference."
    ]
@@ -296,6 +313,9 @@
     "ExecuteTime": {
      "end_time": "2020-07-13T23:48:31.684136Z",
      "start_time": "2020-07-13T23:48:31.601391Z"
+    },
+    "pycharm": {
+     "name": "#%%\n"
     }
    },
    "outputs": [
@@ -320,7 +340,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Step 3: Initiate and configure dynamically-loaded instances\n",
+    "## Step 3: Initiate and configure dynamically-loaded instances\n",
     "To run VQE with the UCCSD variational form, we require: \n",
     "\n",
     "- VQE algorithm\n",
@@ -331,9 +351,13 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
-    "### [Optional] Setup token to run the experiment on a real device\n",
+    "## [Optional] Setup token to run the experiment on a real device\n",
     "If you would like to run the experiment on a real device, you need to setup your account first.\n",
     "\n",
     "Note: If you did not store your token yet, use `IBMQ.save_account('MY_API_TOKEN')` to store it first."
@@ -376,7 +400,10 @@
      "end_time": "2020-07-13T23:48:31.837107Z",
      "start_time": "2020-07-13T23:48:31.696698Z"
     },
-    "scrolled": true
+    "scrolled": true,
+    "pycharm": {
+     "name": "#%%\n"
+    }
    },
    "outputs": [],
    "source": [
@@ -399,11 +426,23 @@
     "quantum_instance = QuantumInstance(backend=backend)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Step 4: Run algorithm and retrieve the results"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Step 4: Run algorithm and retrieve the results"
+    "results = vqe.run(quantum_instance)\n",
+    "print('The computed ground state energy is: {:.12f}'.format(results.eigenvalue.real))\n",
+    "print('The total ground state energy is: {:.12f}'.format(results.eigenvalue.real + energy_shift + nuclear_repulsion_energy))\n",
+    "print(\"Parameters: {}\".format(results.optimal_point))"
    ]
   },
   {
@@ -533,4 +572,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}