OQMD_v1_2_dataset_for_CGNN.ipynb

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  "cells": [
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      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/Tony-Y/oqmd-v1.2-dataset-for-cgnn/blob/main/OQMD_v1_2_dataset_for_CGNN.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "The OQMD is a database of DFT calculated thermodynamic and structural properties of one million materials, created in Chris Wolverton's group at Northwestern University.\n",
        "\n",
        "The OQMD v1.2 dataset for CGNN is downloadable from [this link](https://drive.google.com/file/d/1I6nS4l15SeX5S4VcU3jKG5Iqvomj7eXB/view?usp=sharing), which contains 561,888 materials. Its format is described in [here](https://github.com/Tony-Y/cgnn#dataset-files). The original data is available at [the OQMD website](https://oqmd.org/)."
      ],
      "metadata": {
        "id": "lJlWVvPyUmfe"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# The OQMD v1.2 Dataset"
      ],
      "metadata": {
        "id": "O84cHhZNqS1k"
      }
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "id": "5A-uU_jDODlR"
      },
      "outputs": [],
      "source": [
        "!wget -q \"https://drive.google.com/uc?export=download&id=1I6nS4l15SeX5S4VcU3jKG5Iqvomj7eXB\" -O oqmd.7z\n",
        "!7z x -bsp0 -bso0 oqmd.7z"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!ls oqmd_dataset"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "-QEA0xAfPFoH",
        "outputId": "41f03cbe-d03d-44d5-9d16-02e5c27441de"
      },
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "config.json\tLicense\t\t       split.json   targets.csv\n",
            "graph_data.npz\toqmd_dataset_utils.py  summary.txt\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!fmt oqmd_dataset/License"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "6fA1wC0QPHGB",
        "outputId": "fd4cfdaa-21bf-4dab-93e5-efa942c3f2da"
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "This work, \"OQMD v1.2 for CGNN\", is a derivative of \"OQMD\"\n",
            "(https://oqmd.org) by Chris Wolverton's group at Northwestern University,\n",
            "used under CC BY 4.0. \"OQMD v1.2 for CGNN\" © 2019 by Takenori Yamamoto\n",
            "is licensed under CC BY 4.0. To view a copy of this license, visit\n",
            "http://creativecommons.org/licenses/by/4.0/\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!fmt oqmd_dataset/summary.txt"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ADVDpH4IUfdU",
        "outputId": "d3c1099d-05d3-448f-ea7d-07d27d571ec5"
      },
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\n",
            "oqmd_data.py 562/562 [3:16:30<00:00, 19.71s/it]\n",
            "\n",
            "mp_graph.py [Parallel(n_jobs=-1)]: Done 562 out of 562 | elapsed:\n",
            "186.1min finished\n",
            "\n",
            "oqmd.py Total Data: 561888 unique_z: 89 min z: 1 max z: 94 [ 1  2  3  4\n",
            "5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24\n",
            " 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47\n",
            " 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70\n",
            " 71 72 73 74 75 76 77 78 79 80 81 82 83 89 90 91 92 93 94]\n",
            "Unary formulas: 89 Multi formulas: 338047 Train formulas: 270528 Val\n",
            "formulas: 33804 Test formulas: 33804 Train: 449867 Val: 56289 Test: 55732\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Data Loading"
      ],
      "metadata": {
        "id": "fgW617WTqxyH"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import pandas as pd\n",
        "\n",
        "dataset_path = \"oqmd_dataset/targets.csv\"\n",
        "dataset = pd.read_csv(dataset_path, keep_default_na=False, na_values=['_'])\n",
        "dataset.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 353
        },
        "id": "cCsZVDRKVVJf",
        "outputId": "fd91e556-bad5-434b-8d99-9e64ee743442"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "          name   formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "0  oqmd-823191  ZrZnNiMo         216          4       4        -6.399036   \n",
              "1  oqmd-362450   DySc2Ir         225          3       4        -6.795189   \n",
              "2  oqmd-758369       YZr          59          2      16        -7.445319   \n",
              "3  oqmd-516941   CrMoAu2         225          3       4        -6.218335   \n",
              "4  oqmd-344596      Ge3O         221          2       4        -4.382844   \n",
              "\n",
              "   formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "0                   0.157939       0.0        16.014199   \n",
              "1                  -0.266899       0.0        19.931045   \n",
              "2                   0.060478       0.0        27.308156   \n",
              "3                   0.504200       0.0        15.436073   \n",
              "4                   0.215750       0.0        15.868661   \n",
              "\n",
              "   magnetization_per_atom  atomic_volume_per_atom  volume_deviation  \n",
              "0                0.452473               22.799641         -0.423714  \n",
              "1                0.212367               31.566053         -0.583763  \n",
              "2                0.002801               38.264481         -0.401211  \n",
              "3                0.715628               23.006243         -0.490421  \n",
              "4                0.000000                6.251735          0.606033  "
            ],
            "text/html": [
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              "  <div id=\"df-5fe767eb-624b-43c3-b6ea-1a15c0520b61\">\n",
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              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>name</th>\n",
              "      <th>formula</th>\n",
              "      <th>spacegroup</th>\n",
              "      <th>nelements</th>\n",
              "      <th>nsites</th>\n",
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              "      <th>volume_deviation</th>\n",
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              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>oqmd-823191</td>\n",
              "      <td>ZrZnNiMo</td>\n",
              "      <td>216</td>\n",
              "      <td>4</td>\n",
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              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>oqmd-362450</td>\n",
              "      <td>DySc2Ir</td>\n",
              "      <td>225</td>\n",
              "      <td>3</td>\n",
              "      <td>4</td>\n",
              "      <td>-6.795189</td>\n",
              "      <td>-0.266899</td>\n",
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              "      <td>0.212367</td>\n",
              "      <td>31.566053</td>\n",
              "      <td>-0.583763</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>oqmd-758369</td>\n",
              "      <td>YZr</td>\n",
              "      <td>59</td>\n",
              "      <td>2</td>\n",
              "      <td>16</td>\n",
              "      <td>-7.445319</td>\n",
              "      <td>0.060478</td>\n",
              "      <td>0.0</td>\n",
              "      <td>27.308156</td>\n",
              "      <td>0.002801</td>\n",
              "      <td>38.264481</td>\n",
              "      <td>-0.401211</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>oqmd-516941</td>\n",
              "      <td>CrMoAu2</td>\n",
              "      <td>225</td>\n",
              "      <td>3</td>\n",
              "      <td>4</td>\n",
              "      <td>-6.218335</td>\n",
              "      <td>0.504200</td>\n",
              "      <td>0.0</td>\n",
              "      <td>15.436073</td>\n",
              "      <td>0.715628</td>\n",
              "      <td>23.006243</td>\n",
              "      <td>-0.490421</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>oqmd-344596</td>\n",
              "      <td>Ge3O</td>\n",
              "      <td>221</td>\n",
              "      <td>2</td>\n",
              "      <td>4</td>\n",
              "      <td>-4.382844</td>\n",
              "      <td>0.215750</td>\n",
              "      <td>0.0</td>\n",
              "      <td>15.868661</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>6.251735</td>\n",
              "      <td>0.606033</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
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              "              style=\"display:none;\">\n",
              "        \n",
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              "       width=\"24px\">\n",
              "    <path d=\"M0 0h24v24H0V0z\" fill=\"none\"/>\n",
              "    <path d=\"M18.56 5.44l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94zm-11 1L8.5 8.5l.94-2.06 2.06-.94-2.06-.94L8.5 2.5l-.94 2.06-2.06.94zm10 10l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94z\"/><path d=\"M17.41 7.96l-1.37-1.37c-.4-.4-.92-.59-1.43-.59-.52 0-1.04.2-1.43.59L10.3 9.45l-7.72 7.72c-.78.78-.78 2.05 0 2.83L4 21.41c.39.39.9.59 1.41.59.51 0 1.02-.2 1.41-.59l7.78-7.78 2.81-2.81c.8-.78.8-2.07 0-2.86zM5.41 20L4 18.59l7.72-7.72 1.47 1.35L5.41 20z\"/>\n",
              "  </svg>\n",
              "      </button>\n",
              "      \n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-5fe767eb-624b-43c3-b6ea-1a15c0520b61 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-5fe767eb-624b-43c3-b6ea-1a15c0520b61');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "dataset.hist(column=\"formation_energy_per_atom\", bins=200)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 315
        },
        "id": "6KbZvkmJXY4U",
        "outputId": "9e05c381-9407-4d18-f79e-d9b8a812cf98"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "array([[<matplotlib.axes._subplots.AxesSubplot object at 0x7f79f78f2250>]],\n",
              "      dtype=object)"
            ]
          },
          "metadata": {},
          "execution_count": 6
        },
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "<Figure size 432x288 with 1 Axes>"
            ],
            "image/png": "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\n"
          },
          "metadata": {
            "needs_background": "light"
          }
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import json\n",
        "config_path=\"oqmd_dataset/config.json\"\n",
        "with open(config_path) as f:\n",
        "  config = json.load(f)"
      ],
      "metadata": {
        "id": "9Zze8q-bXu97"
      },
      "execution_count": 7,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "config.keys()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "cle9DKTkZ0Xu",
        "outputId": "fe23a1da-3e9b-491c-d297-c2c6bd97393f"
      },
      "execution_count": 8,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "dict_keys(['node_vectors', 'atomic_numbers'])"
            ]
          },
          "metadata": {},
          "execution_count": 8
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "for element_id in range(5):\n",
        "  z = config[\"atomic_numbers\"][element_id]\n",
        "  v = config[\"node_vectors\"][element_id]\n",
        "  print(f'{z:2d} {v[:10]}')\n",
        "print('')\n",
        "for element_id in range(84,89):\n",
        "  z = config[\"atomic_numbers\"][element_id]\n",
        "  v = config[\"node_vectors\"][element_id]\n",
        "  print(f'{z:2d} {v[79:]}')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "1ooGHONNZ_nC",
        "outputId": "28d998c3-2aef-4597-d503-c07675044e38"
      },
      "execution_count": 9,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            " 1 [1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]\n",
            " 2 [0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]\n",
            " 3 [0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]\n",
            " 4 [0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]\n",
            " 5 [0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0]\n",
            "\n",
            "90 [0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0]\n",
            "91 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0]\n",
            "92 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0]\n",
            "93 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0]\n",
            "94 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Here is a graph loader for this dataset."
      ],
      "metadata": {
        "id": "R5tDLVBgJnH4"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!cat oqmd_dataset/oqmd_dataset_utils.py"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "7u0Zhm34XgwY",
        "outputId": "b9e558f6-c46f-420b-ae6b-03ccea26a4af"
      },
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "import numpy as np\n",
            "\n",
            "def load_graph_data(graph_data_path):\n",
            "  \"\"\"\n",
            "  This function loads graph data from the specified file.\n",
            "\n",
            "  Example:\n",
            "    >>> graphs = load_graph_data(\"oqmd_dataset/graph_data.npz\")\n",
            "    >>> oqmd_id = \"oqmd-758369\"\n",
            "    >>> nodes, neighbors = graphs[oqmd_id]\n",
            "    >>> nodes\n",
            "    [38, 38, 38, 38, 38, 38, 38, 38, 39, 39, 39, 39, 39, 39, 39, 39]\n",
            "    >>> neighbors\n",
            "    [[1, 6, 6, 7, 7, 13, 13],\n",
            "     [0, 0, 2, 7, 7, 11, 11, 13, 13, 14, 14],\n",
            "     [1, 3, 3, 4, 4, 11, 11, 14, 14, 15, 15],\n",
            "    ...\n",
            "  \"\"\"\n",
            "  graphs = np.load(graph_data_path, allow_pickle=True, encoding='latin1')['graph_dict'].item()\n",
            "  graphs = { k.decode() : v for k, v in graphs.items() }\n",
            "  return graphs\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Let's load all of the graph data in this dataset."
      ],
      "metadata": {
        "id": "jyOZbhDuJ0Jr"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import sys\n",
        "\n",
        "sys.path.append(\"oqmd_dataset\")\n",
        "\n",
        "from oqmd_dataset_utils import load_graph_data\n",
        "\n",
        "graphs = load_graph_data(\"oqmd_dataset/graph_data.npz\")"
      ],
      "metadata": {
        "id": "WvF7U3gdXyxa"
      },
      "execution_count": 11,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Visualization of Crystal Graphs\n",
        "\n",
        "Let's get a graph of the stablest structure of ZrO<sub>2</sub> in this dataset and draw it by using [Graphviz](https://graphviz.readthedocs.io/en/stable/)."
      ],
      "metadata": {
        "id": "f6Xq813RI4cx"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "formula0 = \"ZrO2\"\n",
        "\n",
        "def get_subset(formula):\n",
        "  return dataset[dataset[\"formula\"] == formula].sort_values(\"formation_energy_per_atom\")\n",
        "\n",
        "oqmd_id = get_subset(formula=formula0)[\"name\"].tolist()[0]\n",
        "nodes, neighbors = graphs[oqmd_id]"
      ],
      "metadata": {
        "id": "bbCP_9v8b-VH"
      },
      "execution_count": 12,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "oqmd_id"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 37
        },
        "id": "yphv4gzoecTn",
        "outputId": "f7c29848-a5bc-4aea-dd0e-f3449a0fb966"
      },
      "execution_count": 13,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "'oqmd-3278'"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            }
          },
          "metadata": {},
          "execution_count": 13
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "nodes"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "yV2PIatheua_",
        "outputId": "7a532a6e-b29b-4949-8031-d763c46ba356"
      },
      "execution_count": 14,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[7, 7, 7, 7, 7, 7, 7, 7, 39, 39, 39, 39]"
            ]
          },
          "metadata": {},
          "execution_count": 14
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "neighbors"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "W6ZoLtKZewmm",
        "outputId": "fae99e8b-f832-42af-b51a-de9b12513862"
      },
      "execution_count": 15,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[[8, 9],\n",
              " [8, 9],\n",
              " [8, 9],\n",
              " [8, 9],\n",
              " [10, 11],\n",
              " [10, 11],\n",
              " [10, 11],\n",
              " [10, 11],\n",
              " [0, 1, 2, 3, 6, 9, 9, 10, 10, 11, 11],\n",
              " [0, 1, 2, 3, 5, 8, 8, 10, 10, 11, 11],\n",
              " [2, 4, 5, 6, 7, 8, 8, 9, 9, 11, 11],\n",
              " [1, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10]]"
            ]
          },
          "metadata": {},
          "execution_count": 15
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "dataset[dataset[\"name\"] == oqmd_id]"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 161
        },
        "id": "O-HaTjxLLTyA",
        "outputId": "66daac60-ba39-4fae-9b32-567ba7130059"
      },
      "execution_count": 16,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "             name formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "183001  oqmd-3278    ZrO2          14          2      12         -9.49757   \n",
              "\n",
              "        formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "183001                  -3.632982     3.843        11.965782   \n",
              "\n",
              "        magnetization_per_atom  atomic_volume_per_atom  volume_deviation  \n",
              "183001                0.000015               12.514709         -0.045875  "
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-27e29e62-afa7-4468-ae97-c5844212e8d4\">\n",
              "    <div class=\"colab-df-container\">\n",
              "      <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>name</th>\n",
              "      <th>formula</th>\n",
              "      <th>spacegroup</th>\n",
              "      <th>nelements</th>\n",
              "      <th>nsites</th>\n",
              "      <th>energy_per_atom</th>\n",
              "      <th>formation_energy_per_atom</th>\n",
              "      <th>band_gap</th>\n",
              "      <th>volume_per_atom</th>\n",
              "      <th>magnetization_per_atom</th>\n",
              "      <th>atomic_volume_per_atom</th>\n",
              "      <th>volume_deviation</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>183001</th>\n",
              "      <td>oqmd-3278</td>\n",
              "      <td>ZrO2</td>\n",
              "      <td>14</td>\n",
              "      <td>2</td>\n",
              "      <td>12</td>\n",
              "      <td>-9.49757</td>\n",
              "      <td>-3.632982</td>\n",
              "      <td>3.843</td>\n",
              "      <td>11.965782</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>12.514709</td>\n",
              "      <td>-0.045875</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
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              "  </svg>\n",
              "      </button>\n",
              "      \n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
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              "      gap: 12px;\n",
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              "\n",
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              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
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              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
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              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-27e29e62-afa7-4468-ae97-c5844212e8d4 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-27e29e62-afa7-4468-ae97-c5844212e8d4');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
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              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 16
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "We extract element information from [mendeleev](https://github.com/lmmentel/mendeleev) because its installation fails in Colab notebooks."
      ],
      "metadata": {
        "id": "GykkVaSr4e30"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!wget -q https://github.com/lmmentel/mendeleev/blob/master/mendeleev/elements.db?raw=true -O elements.db"
      ],
      "metadata": {
        "id": "xwS2T9891FS-"
      },
      "execution_count": 17,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "from dataclasses import dataclass\n",
        "\n",
        "@dataclass\n",
        "class Element:\n",
        "    symbol: float\n",
        "    jmol_color: float"
      ],
      "metadata": {
        "id": "5Apnhd3Y3jXp"
      },
      "execution_count": 18,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "import sqlite3\n",
        "dbname = 'elements.db'\n",
        "conn = sqlite3.connect(dbname)\n",
        "cur = conn.cursor()\n",
        "cur.execute('SELECT atomic_number, symbol, jmol_color FROM elements')\n",
        "element = dict()\n",
        "for row in cur:\n",
        "    element[row[0]] = Element(symbol=row[1], jmol_color=row[2])\n",
        "conn.close()"
      ],
      "metadata": {
        "id": "iggl5Jx31IqX"
      },
      "execution_count": 19,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "import graphviz"
      ],
      "metadata": {
        "id": "zn9ntLN_Tu08"
      },
      "execution_count": 20,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "dot = graphviz.Digraph(f'{oqmd_id}', comment=f'{formula0} in OQMD ({oqmd_id})', engine='neato')\n",
        "dot.attr(overlap='false', size='6,6')\n",
        "\n",
        "dot.attr('node', shape='circle', style='filled')\n",
        "for i, element_id in enumerate(nodes):\n",
        "  z = config[\"atomic_numbers\"][element_id]\n",
        "  e = element[z]\n",
        "  dot.node(f'{i}', f'{e.symbol}@{i}', color=e.jmol_color)\n",
        "\n",
        "dot.attr('edge', constraint='false', penwidth='2')\n",
        "for i, element_id in enumerate(nodes):\n",
        "  z = config[\"atomic_numbers\"][element_id]\n",
        "  e = element[z]\n",
        "  for j in neighbors[i]:\n",
        "    dot.edge(f'{i}', f'{j}', color=e.jmol_color)\n"
      ],
      "metadata": {
        "id": "TRD8D7c4lnOX"
      },
      "execution_count": 21,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# print(dot.source)"
      ],
      "metadata": {
        "id": "fxJ5Jj7AoOPj"
      },
      "execution_count": 22,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "dot"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 418
        },
        "id": "NTVGx5eToQz7",
        "outputId": "47e44226-5893-46aa-a9e2-1ce956a46c59"
      },
      "execution_count": 23,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "<graphviz.dot.Digraph at 0x7f79aafe9f90>"
            ],
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          },
          "metadata": {},
          "execution_count": 23
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Original Data and Structures\n",
        "\n",
        "We can obtain the original data from the online database by using the OQMD API."
      ],
      "metadata": {
        "id": "yIENaPPnMQgq"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import json, requests\n",
        "\n",
        "def get_oqmd_entry(entry_id):\n",
        "  base_url = 'http://oqmd.org/oqmdapi/entry'\n",
        "  url = f'{base_url}/{entry_id}'\n",
        "\n",
        "  response = requests.get(url)\n",
        "  if response.status_code != 200:\n",
        "    print('Status code:', response.status_code)\n",
        "    print('You can see its meaning at https://developer.mozilla.org/en-US/docs/Web/HTTP/Status')\n",
        "  else:\n",
        "    response = json.loads(response.text)\n",
        "    return response"
      ],
      "metadata": {
        "id": "JEEG59Babtrx"
      },
      "execution_count": 24,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "entry_id = int(oqmd_id.split('-')[1])\n",
        "get_oqmd_entry(entry_id)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ijcsX7IdcQ0q",
        "outputId": "36df3829-14d9-450d-966e-1b6e9ce58348"
      },
      "execution_count": 25,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'band_gap': 3.843,\n",
              " 'calculations': [{'id': 37919,\n",
              "   'label': 'standard',\n",
              "   'path': '/home/oqmd/libraries/icsd/15983/standard'},\n",
              "  {'id': 801995,\n",
              "   'label': 'static',\n",
              "   'path': '/home/oqmd/libraries/icsd/15983/static'},\n",
              "  {'id': 1988392,\n",
              "   'label': 'relaxation_lda',\n",
              "   'path': '/home/oqmd/libraries/icsd/15983/relaxation_lda'},\n",
              "  {'id': 1997902,\n",
              "   'label': 'static_lda',\n",
              "   'path': '/home/oqmd/libraries/icsd/15983/static_lda'}],\n",
              " 'composition': 'O2 Zr1',\n",
              " 'composition_generic': 'AB2',\n",
              " 'energy_per_atom': -9.49757019,\n",
              " 'formation_energy': -3.63298243058584,\n",
              " 'holds': [],\n",
              " 'icsd_id': '15983',\n",
              " 'id': 3278,\n",
              " 'keywords': ['icsd'],\n",
              " 'name': 'ZrO2',\n",
              " 'natoms': 12,\n",
              " 'ntypes': 2,\n",
              " 'path': '/home/oqmd/libraries/icsd/15983',\n",
              " 'prototype': 'ZrO2(mP)',\n",
              " 'sites': None,\n",
              " 'spacegroup': None,\n",
              " 'stability': -0.4717609644791705,\n",
              " 'unit_cell': None,\n",
              " 'volume': None}"
            ]
          },
          "metadata": {},
          "execution_count": 25
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "We could not get the crystal structure of ZrO<sub>2</sub> from the online database, but an entry of Ge<sub>3</sub>O appears with the structure as the following:"
      ],
      "metadata": {
        "id": "_u1Je2I4XwvA"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "get_oqmd_entry(entry_id=344596)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "yYVLXPsxduKp",
        "outputId": "09478508-6307-4061-8fc4-40dcdad0970a"
      },
      "execution_count": 26,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'band_gap': 0.0,\n",
              " 'calculations': [{'id': 352471,\n",
              "   'label': 'initialize',\n",
              "   'path': '/home/oqmd/libraries/prototypes/binaries/L1_2/O_Ge/initialize'},\n",
              "  {'id': 352472,\n",
              "   'label': 'coarse_relax',\n",
              "   'path': '/home/oqmd/libraries/prototypes/binaries/L1_2/O_Ge/coarse_relax'},\n",
              "  {'id': 352473,\n",
              "   'label': 'fine_relax',\n",
              "   'path': '/home/oqmd/libraries/prototypes/binaries/L1_2/O_Ge/fine_relax'},\n",
              "  {'id': 352474,\n",
              "   'label': 'standard',\n",
              "   'path': '/home/oqmd/libraries/prototypes/binaries/L1_2/O_Ge/standard'},\n",
              "  {'id': 1253775,\n",
              "   'label': 'static',\n",
              "   'path': '/home/oqmd/libraries/prototypes/binaries/L1_2/O_Ge/static'},\n",
              "  {'id': 1253776,\n",
              "   'label': 'relaxation',\n",
              "   'path': '/home/oqmd/libraries/prototypes/binaries/L1_2/O_Ge/relaxation'}],\n",
              " 'composition': 'Ge3 O1',\n",
              " 'composition_generic': 'AB3',\n",
              " 'energy_per_atom': -4.382843515,\n",
              " 'formation_energy': 0.21574978978031,\n",
              " 'holds': [],\n",
              " 'icsd_id': None,\n",
              " 'id': 344596,\n",
              " 'keywords': ['prototype', 'L1_2'],\n",
              " 'name': 'Ge3O',\n",
              " 'natoms': 4,\n",
              " 'ntypes': 2,\n",
              " 'path': '/home/oqmd/libraries/prototypes/binaries/L1_2/O_Ge',\n",
              " 'prototype': 'L1_2_Cu3Au',\n",
              " 'sites': ['Ge @ 0 0.5 0.5', 'Ge @ 0.5 0 0.5', 'Ge @ 0.5 0.5 0', 'O @ 0 0 0'],\n",
              " 'spacegroup': 'Pm-3m',\n",
              " 'stability': 0.9247098084374985,\n",
              " 'unit_cell': [[4.32815, 0.0, 0.0], [0.0, 4.32815, 0.0], [0.0, 0.0, 4.32815]],\n",
              " 'volume': 81.0787}"
            ]
          },
          "metadata": {},
          "execution_count": 26
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Alternatively, we can use another structure database to get the structure of ZrO<sub>2</sub> as the following:"
      ],
      "metadata": {
        "id": "m-H3PxdljCjA"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import json, requests\n",
        "\n",
        "base_url = 'http://oqmd.org/optimade/structures'\n",
        "url = f'{base_url}?filter=chemical_formula_descriptive=\"{formula0}\"'\n",
        "# If you want to know details of \"chemical_formula_descriptive\", see the link below:\n",
        "# https://github.com/Materials-Consortia/OPTIMADE/blob/v1.0/optimade.rst#id65\n",
        "\n",
        "response = requests.get(url)\n",
        "if response.status_code != 200:\n",
        "  print('Status code:', response.status_code)\n",
        "  print('You can see its meaning at https://developer.mozilla.org/en-US/docs/Web/HTTP/Status')\n",
        "else:\n",
        "  response = json.loads(response.text)\n",
        "  if 'detail' in response.keys():\n",
        "    print(response['detail'])\n",
        "  else:\n",
        "    print('Meta data:')\n",
        "    display(response['meta'])"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 272
        },
        "id": "VbP9tv9HY5AK",
        "outputId": "6c620959-ec9d-4cd7-8fac-a4407d7bc199"
      },
      "execution_count": 27,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Meta data:\n"
          ]
        },
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "{'_oqmd_data_in_response': 35,\n",
              " 'api_version': '1.0.0',\n",
              " 'data_available': 1022603,\n",
              " 'data_returned': 35,\n",
              " 'more_data_available': False,\n",
              " 'provider': {'description': 'The Open Quantum Materials Database',\n",
              "  'homepage': 'http://oqmd.org',\n",
              "  'name': 'OQMD',\n",
              "  'prefix': 'oqmd'},\n",
              " 'query': {'_oqmd_final_query': \"( composition__formula__in=['O2 Zr1'] )\",\n",
              "  'representation': 'http://oqmd.org/optimade/structures?filter=chemical_formula_descriptive=%22ZrO2%22'},\n",
              " 'response_message': 'OK',\n",
              " 'time_stamp': '2022-03-25 21:36:30',\n",
              " 'warnings': []}"
            ]
          },
          "metadata": {}
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "response['data'][0].keys()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "OzhR1vKvfhxH",
        "outputId": "4ff203ae-e501-4751-ed97-6466937511b2"
      },
      "execution_count": 28,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "dict_keys(['id', 'type', 'attributes'])"
            ]
          },
          "metadata": {},
          "execution_count": 28
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "We retrieve the structure with the wanted entry id from the database response. "
      ],
      "metadata": {
        "id": "EpfVTAZBmQxq"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "entry_structure = None\n",
        "for x in response['data']:\n",
        "  x = x['attributes']\n",
        "  if x['_oqmd_entry_id'] == entry_id:\n",
        "    entry_structure = x\n",
        "    break\n",
        "\n",
        "if entry_structure == None:\n",
        "  print(f'No structure for the entry {entry_id}')"
      ],
      "metadata": {
        "id": "ZnqhcmOCcRLP"
      },
      "execution_count": 29,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "entry_structure"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "tvvugb4okwjz",
        "outputId": "dd011963-aaad-4047-8aba-f0932679ae90"
      },
      "execution_count": 30,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'_oqmd_band_gap': 3.843,\n",
              " '_oqmd_calculation_id': 801995,\n",
              " '_oqmd_delta_e': -3.633,\n",
              " '_oqmd_entry_id': 3278,\n",
              " '_oqmd_icsd_id': 15983,\n",
              " '_oqmd_prototype': 'ZrO2(mP)',\n",
              " '_oqmd_spacegroup': 'P21/c',\n",
              " '_oqmd_stability': 0.0,\n",
              " '_oqmd_volume': 143.589,\n",
              " 'cartesian_site_positions': [[2.36194, 1.27627, 0.13447],\n",
              "  [0.42102, 3.5834, 0.73934],\n",
              "  [5.20898, 0.97766, 1.92667],\n",
              "  [3.26807, 3.88201, 2.53154],\n",
              "  [2.80732, 1.32948, 2.79231],\n",
              "  [0.8664, 4.23383, 3.39718],\n",
              "  [5.65436, 1.62809, 4.58451],\n",
              "  [3.71345, 3.93522, 5.18937],\n",
              "  [3.94249, 2.38202, 1.13006],\n",
              "  [1.68751, 4.98776, 1.53595],\n",
              "  [4.38787, 0.22372, 3.7879],\n",
              "  [2.13289, 2.82946, 4.19379]],\n",
              " 'chemical_formula_anonymous': 'A2B',\n",
              " 'chemical_formula_descriptive': 'O2Zr',\n",
              " 'chemical_formula_reduced': 'O2Zr',\n",
              " 'elements': ['O', 'Zr'],\n",
              " 'last_modified': None,\n",
              " 'lattice_vectors': [[5.18462, 0.0, 0.008175],\n",
              "  [0.0, 5.211486, 0.0],\n",
              "  [0.890761, 0.0, 5.315677]],\n",
              " 'nelements': 2,\n",
              " 'nperiodic_dimensions': 3,\n",
              " 'nsites': 12,\n",
              " 'species_at_sites': ['O',\n",
              "  'O',\n",
              "  'O',\n",
              "  'O',\n",
              "  'O',\n",
              "  'O',\n",
              "  'O',\n",
              "  'O',\n",
              "  'Zr',\n",
              "  'Zr',\n",
              "  'Zr',\n",
              "  'Zr'],\n",
              " 'structure_features': []}"
            ]
          },
          "metadata": {},
          "execution_count": 30
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "There are many visualization softwares for chemical structrues in 3D: [Jmol](http://jmol.sourceforge.net), [VESTA](http://jp-minerals.org/vesta/en/), etc.\n",
        "You can visualize the crystal structure of ZrO2 by using this information, that is, cartesian_site_positions, lattice_vectors, and species_at_sites."
      ],
      "metadata": {
        "id": "GmkhZ6gumrMO"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "n = entry_structure['nsites']\n",
        "print(n)\n",
        "print(f'{formula0} {oqmd_id} in XYZ format')\n",
        "for i in range(n):\n",
        "  s = entry_structure['species_at_sites'][i]\n",
        "  x, y, z = entry_structure['cartesian_site_positions'][i]\n",
        "  print(f'{s:2s} {x:10.6f} {y:10.6f} {z:10.6f}')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "v7muO371kenS",
        "outputId": "37884c6b-c572-41d5-bebc-fa6b4715ee52"
      },
      "execution_count": 31,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "12\n",
            "ZrO2 oqmd-3278 in XYZ format\n",
            "O    2.361940   1.276270   0.134470\n",
            "O    0.421020   3.583400   0.739340\n",
            "O    5.208980   0.977660   1.926670\n",
            "O    3.268070   3.882010   2.531540\n",
            "O    2.807320   1.329480   2.792310\n",
            "O    0.866400   4.233830   3.397180\n",
            "O    5.654360   1.628090   4.584510\n",
            "O    3.713450   3.935220   5.189370\n",
            "Zr   3.942490   2.382020   1.130060\n",
            "Zr   1.687510   4.987760   1.535950\n",
            "Zr   4.387870   0.223720   3.787900\n",
            "Zr   2.132890   2.829460   4.193790\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "for i in range(3):\n",
        "  x, y, z = entry_structure['lattice_vectors'][i]\n",
        "  print(f'{x:10.6f} {y:10.6f} {z:10.6f}')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "UyfwKwO5qi-D",
        "outputId": "8d4abdd1-c937-4a5a-f34c-21663149077a"
      },
      "execution_count": 32,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "  5.184620   0.000000   0.008175\n",
            "  0.000000   5.211486   0.000000\n",
            "  0.890761   0.000000   5.315677\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Gallery"
      ],
      "metadata": {
        "id": "4hRWtYsdtqDY"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "We first define some useful functions for drawing graphs."
      ],
      "metadata": {
        "id": "7npeYN_zOq6A"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import cv2\n",
        "import numpy as np\n",
        "\n",
        "def square_image(data):\n",
        "  img_buf= np.frombuffer(data, dtype=np.uint8)\n",
        "  img = cv2.imdecode(img_buf, cv2.IMREAD_UNCHANGED)\n",
        "  bgc = img[0,0,:]\n",
        "  height, width, _ = img.shape\n",
        "  if height > width:\n",
        "    new_img = np.full(shape=(height, height, len(bgc)), fill_value=bgc, dtype=np.uint8)\n",
        "    shift = int(float(height-width)/2)\n",
        "    new_img[:,shift:shift+width,:] = img\n",
        "  else:\n",
        "    new_img = np.full(shape=(width, width, len(bgc)), fill_value=bgc, dtype=np.uint8)\n",
        "    shift = int(float(width-height)/2)\n",
        "    new_img[shift:shift+height,:,:] = img\n",
        "  return cv2.imencode('.png', new_img)[1].tobytes()"
      ],
      "metadata": {
        "id": "M4h5eRt1xt4U"
      },
      "execution_count": 33,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "def gen_graph_image(oqmd_id, size=4, bgcolor='white'):\n",
        "  nodes, neighbors = graphs[oqmd_id]\n",
        "\n",
        "  dot = graphviz.Digraph(f'{oqmd_id}', comment=f'{oqmd_id}', engine='neato')\n",
        "  dot.attr(overlap='false', size=f'{size}', bgcolor=bgcolor)\n",
        "\n",
        "  dot.attr('node', shape='circle', style='filled')\n",
        "  for i, element_id in enumerate(nodes):\n",
        "    z = config[\"atomic_numbers\"][element_id]\n",
        "    e = element[z]\n",
        "    dot.node(f'{i}', f'{e.symbol}', color=e.jmol_color)\n",
        "\n",
        "  dot.attr('edge', constraint='false', penwidth='2')\n",
        "  for i, element_id in enumerate(nodes):\n",
        "    z = config[\"atomic_numbers\"][element_id]\n",
        "    e = element[z]\n",
        "    for j in neighbors[i]:\n",
        "      dot.edge(f'{i}', f'{j}', color=e.jmol_color)\n",
        "\n",
        "  return square_image(dot.pipe(format='png'))"
      ],
      "metadata": {
        "id": "zUdWW6gJw2nX"
      },
      "execution_count": 34,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "from ipywidgets import HBox, VBox, Image, HTML\n",
        "\n",
        "def gen_boxes(formula, length=100, max_num_boxes=5, bgcolor='white'):\n",
        "  oqmd_ids = get_subset(formula=formula)[\"name\"].tolist()\n",
        "\n",
        "  boxes = []\n",
        "  for x in oqmd_ids[:max_num_boxes]:\n",
        "    image = gen_graph_image(oqmd_id=x, size=4*length/100, bgcolor=bgcolor)\n",
        "    box = Image(\n",
        "      value=image,\n",
        "      format='png',\n",
        "      width=length,\n",
        "      height=length,\n",
        "    )\n",
        "    h = HTML(value=x)\n",
        "    vb = VBox([h, box])\n",
        "    vb.layout.align_items = 'center'\n",
        "    vb.layout.border = '1px solid gray'\n",
        "    boxes.append(vb)\n",
        "  return boxes"
      ],
      "metadata": {
        "id": "PJhobwGa118r"
      },
      "execution_count": 35,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "def show_table_and_graphs(formula):\n",
        "  display(get_subset(formula))\n",
        "  hb = HBox(gen_boxes(formula, length=300))\n",
        "  display(hb)"
      ],
      "metadata": {
        "id": "nPtvoN7IuLn7"
      },
      "execution_count": 36,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Jadeite\n",
        "\n",
        "https://en.wikipedia.org/wiki/Jadeite"
      ],
      "metadata": {
        "id": "l7rk36eODilI"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='NaAl(SiO3)2') # Jadeite"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 499,
          "referenced_widgets": [
            "ffe8f8b049914f06b5f99016033d342e",
            "3e625a365d994574a69f4ba8c30ee3e3",
            "65bbbeca47b545b49ad37d40c8f2ddf1",
            "237c4d7166fa4d6788a10886b8f7994c",
            "742c9c7e8869447ab8f21fdd96ea17cc",
            "c9e985624ac94edfa6a8e32bf88a318c",
            "001cf03138c240f6a44ef54e96151c43",
            "9844bab4e0394239be76f84bbef2cccd",
            "32333637db8a488f9e45249ad8cc8771"
          ]
        },
        "id": "R6rFB0VqBog4",
        "outputId": "4cb260ad-dfd3-4e58-db1b-3dc08dde8fe4"
      },
      "execution_count": 37,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "             name      formula  spacegroup  nelements  nsites  \\\n",
              "445264  oqmd-2688  NaAl(SiO3)2          15          4      20   \n",
              "\n",
              "        energy_per_atom  formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "445264         -7.30066                   -3.00721     5.633        10.024731   \n",
              "\n",
              "        magnetization_per_atom  atomic_volume_per_atom  volume_deviation  \n",
              "445264                     0.0                4.985015          0.502728  "
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-2e5f2b83-9528-4445-aba8-fb9995549864\">\n",
              "    <div class=\"colab-df-container\">\n",
              "      <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>name</th>\n",
              "      <th>formula</th>\n",
              "      <th>spacegroup</th>\n",
              "      <th>nelements</th>\n",
              "      <th>nsites</th>\n",
              "      <th>energy_per_atom</th>\n",
              "      <th>formation_energy_per_atom</th>\n",
              "      <th>band_gap</th>\n",
              "      <th>volume_per_atom</th>\n",
              "      <th>magnetization_per_atom</th>\n",
              "      <th>atomic_volume_per_atom</th>\n",
              "      <th>volume_deviation</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>445264</th>\n",
              "      <td>oqmd-2688</td>\n",
              "      <td>NaAl(SiO3)2</td>\n",
              "      <td>15</td>\n",
              "      <td>4</td>\n",
              "      <td>20</td>\n",
              "      <td>-7.30066</td>\n",
              "      <td>-3.00721</td>\n",
              "      <td>5.633</td>\n",
              "      <td>10.024731</td>\n",
              "      <td>0.0</td>\n",
              "      <td>4.985015</td>\n",
              "      <td>0.502728</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "      <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-2e5f2b83-9528-4445-aba8-fb9995549864')\"\n",
              "              title=\"Convert this dataframe to an interactive table.\"\n",
              "              style=\"display:none;\">\n",
              "        \n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
              "    <path d=\"M0 0h24v24H0V0z\" fill=\"none\"/>\n",
              "    <path d=\"M18.56 5.44l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94zm-11 1L8.5 8.5l.94-2.06 2.06-.94-2.06-.94L8.5 2.5l-.94 2.06-2.06.94zm10 10l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94z\"/><path d=\"M17.41 7.96l-1.37-1.37c-.4-.4-.92-.59-1.43-.59-.52 0-1.04.2-1.43.59L10.3 9.45l-7.72 7.72c-.78.78-.78 2.05 0 2.83L4 21.41c.39.39.9.59 1.41.59.51 0 1.02-.2 1.41-.59l7.78-7.78 2.81-2.81c.8-.78.8-2.07 0-2.86zM5.41 20L4 18.59l7.72-7.72 1.47 1.35L5.41 20z\"/>\n",
              "  </svg>\n",
              "      </button>\n",
              "      \n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-2e5f2b83-9528-4445-aba8-fb9995549864 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-2e5f2b83-9528-4445-aba8-fb9995549864');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {}
        },
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "HBox(children=(VBox(children=(HTML(value='oqmd-2688'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x00\\x00\\rIHDR\\x00\\x…"
            ],
            "application/vnd.jupyter.widget-view+json": {
              "version_major": 2,
              "version_minor": 0,
              "model_id": "ffe8f8b049914f06b5f99016033d342e"
            }
          },
          "metadata": {}
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Benitoite\n",
        "\n",
        "https://en.wikipedia.org/wiki/Benitoite"
      ],
      "metadata": {
        "id": "PPESaWcVF8bj"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='BaTi(SiO3)3') # Benitoite"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 499,
          "referenced_widgets": [
            "68e2309a4a044fe78fe536551eca6470",
            "4672fbd779c34a8a829034048b896c41",
            "513bb60f79be40e48829a5b75900e0a0",
            "76ff750a23b24d13854cc7f3cab1e85d",
            "14ffcd48b85f4093ae4605b0488c8716",
            "e17cca0758234faca98d1f02cd6fa3e6",
            "24d4587e82084c23a5fa3783b6136362",
            "a675acb1124a4a7bb026864e7e5540e7",
            "4a0a8f78a99b4e26bc6f78792083cd38"
          ]
        },
        "id": "mKbLKzxCFttH",
        "outputId": "1ede0d8e-105d-469c-ad2f-6bb82863c39c"
      },
      "execution_count": 38,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "             name      formula  spacegroup  nelements  nsites  \\\n",
              "527844  oqmd-3694  BaTi(SiO3)3         188          4      28   \n",
              "\n",
              "        energy_per_atom  formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "527844        -7.946506                   -3.18894     3.113        13.336027   \n",
              "\n",
              "        magnetization_per_atom  atomic_volume_per_atom  volume_deviation  \n",
              "527844                0.000125                8.001868          0.399981  "
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              "      <th>volume_deviation</th>\n",
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              "      <th>527844</th>\n",
              "      <td>oqmd-3694</td>\n",
              "      <td>BaTi(SiO3)3</td>\n",
              "      <td>188</td>\n",
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              "      <td>8.001868</td>\n",
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              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
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              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
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              "\n",
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              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
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              "          element.appendChild(docLink);\n",
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              "    </div>\n",
              "  </div>\n",
              "  "
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          "output_type": "display_data",
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              "HBox(children=(VBox(children=(HTML(value='oqmd-3694'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x00\\x00\\rIHDR\\x00\\x…"
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    },
    {
      "cell_type": "markdown",
      "source": [
        "## Taaffeite\n",
        "\n",
        "https://en.wikipedia.org/wiki/Taaffeite"
      ],
      "metadata": {
        "id": "-UvfWMFxB36t"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='MgBeAl4O8') # Taaffeite"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 499,
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            "adcff1a886ec4a88a1339a1e8a080254"
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        },
        "id": "Rlk390ll9E-e",
        "outputId": "ab23f966-1109-45ad-978a-bf389a1e7220"
      },
      "execution_count": 39,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "              name    formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "363421  oqmd-44418  MgBeAl4O8         186          4      56        -7.206451   \n",
              "\n",
              "        formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "363421                   -3.17309     5.873         8.875545   \n",
              "\n",
              "        magnetization_per_atom  atomic_volume_per_atom  volume_deviation  \n",
              "363421                     0.0                3.563588          0.598494  "
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              "      display:flex;\n",
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              "      gap: 12px;\n",
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              "\n",
              "    .colab-df-convert {\n",
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              "      border-radius: 50%;\n",
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              "      height: 32px;\n",
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              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-0438b6e8-8586-4e2d-9640-77b0781995a1 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-0438b6e8-8586-4e2d-9640-77b0781995a1');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {}
        },
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "HBox(children=(VBox(children=(HTML(value='oqmd-44418'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x00\\x00\\rIHDR\\x00\\…"
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          "metadata": {}
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      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Kettnerite\n",
        "\n",
        "https://www.mindat.org/min-2190.html"
      ],
      "metadata": {
        "id": "3kyWl71xjeJi"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='CaBiCO4F')"
      ],
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        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 547,
          "referenced_widgets": [
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        "id": "BlObv9mpjGHD",
        "outputId": "72ed751e-c31a-4936-9f00-cde5f54d68b5"
      },
      "execution_count": 40,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "              name   formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "340755  oqmd-20108  CaBiCO4F          54          5      32        -6.729267   \n",
              "270761  oqmd-15534  CaBiCO4F          59          5      16        -6.562982   \n",
              "\n",
              "        formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "340755                  -2.381276     2.925        11.995659   \n",
              "270761                  -2.214990     0.949        12.249077   \n",
              "\n",
              "        magnetization_per_atom  atomic_volume_per_atom  volume_deviation  \n",
              "340755                     0.0                5.782002          0.517992  \n",
              "270761                     0.0                5.782002          0.527964  "
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              "              title=\"Convert this dataframe to an interactive table.\"\n",
              "              style=\"display:none;\">\n",
              "        \n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
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              "HBox(children=(VBox(children=(HTML(value='oqmd-20108'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x00\\x00\\rIHDR\\x00\\…"
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    },
    {
      "cell_type": "markdown",
      "source": [
        "## Li-Na-K carbonates"
      ],
      "metadata": {
        "id": "0EWSfyPvB_C6"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "### Lithium carbonate\n",
        "\n",
        "https://en.wikipedia.org/wiki/Lithium_carbonate"
      ],
      "metadata": {
        "id": "jAgoQyrwnkBm"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='Li2CO3') # Lithium carbonate"
      ],
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      "execution_count": 41,
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              "              name formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "397777   oqmd-3549  Li2CO3          15          3      12        -6.540866   \n",
              "269017  oqmd-16579  Li2CO3         193          3      12        -6.464600   \n",
              "\n",
              "        formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
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    {
      "cell_type": "markdown",
      "source": [
        "### Sodium carbonate\n",
        "\n",
        "https://en.wikipedia.org/wiki/Sodium_carbonate"
      ],
      "metadata": {
        "id": "wihM8JmdnpoG"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='Na2CO3') # Sodium carbonate"
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      "execution_count": 42,
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        {
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              "               name formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "16488   oqmd-644611  Na2CO3          12          3      12        -6.171835   \n",
              "170605   oqmd-14595  Na2CO3         194          3      12        -6.158762   \n",
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    {
      "cell_type": "markdown",
      "source": [
        "### Potassium carbonate\n",
        "\n",
        "https://en.wikipedia.org/wiki/Potassium_carbonate"
      ],
      "metadata": {
        "id": "5ENdq0C5nsxb"
      }
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      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='K2CO3') # Potassium carbonate"
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              "               name formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "337133    oqmd-1755   K2CO3          15          3      12        -6.144577   \n",
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    },
    {
      "cell_type": "markdown",
      "source": [
        "### Lithium sodium carbonate"
      ],
      "metadata": {
        "id": "DQSrxcOJppx8"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='NaLiCO3') # Lithium sodium carbonate"
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              "              name  formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "42195   oqmd-70795  NaLiCO3         174          4      54        -6.365491   \n",
              "537483  oqmd-15829  NaLiCO3         174          4      18        -6.347711   \n",
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              "76365   oqmd-44504  NaLiCO3          38          4      18        -4.885046   \n",
              "\n",
              "        formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "42195                   -2.051695     4.913        10.655306   \n",
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    {
      "cell_type": "markdown",
      "source": [
        "### Lithium potassium carbonate"
      ],
      "metadata": {
        "id": "QQf9b9xvpu2L"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "show_table_and_graphs(formula='KLiCO3') # Lithium potassium carbonate"
      ],
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        "id": "OozLKYRYoAPM",
        "outputId": "423a1e0b-bc7f-4805-fc44-12357b3d0144"
      },
      "execution_count": 45,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "              name formula  spacegroup  nelements  nsites  energy_per_atom  \\\n",
              "506199  oqmd-12216  KLiCO3          14          4      24        -6.350897   \n",
              "\n",
              "        formation_energy_per_atom  band_gap  volume_per_atom  \\\n",
              "506199                  -2.054186     5.369        12.409933   \n",
              "\n",
              "        magnetization_per_atom  atomic_volume_per_atom  volume_deviation  \n",
              "506199                     0.0               13.710545         -0.104804  "
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              "      <th>volume_per_atom</th>\n",
              "      <th>magnetization_per_atom</th>\n",
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              "      <th>506199</th>\n",
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              "      <td>KLiCO3</td>\n",
              "      <td>14</td>\n",
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          },
          "metadata": {}
        },
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "HBox(children=(VBox(children=(HTML(value='oqmd-12216'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x00\\x00\\rIHDR\\x00\\…"
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    },
    {
      "cell_type": "markdown",
      "source": [
        "## Oxides of Carbon Group Elements\n",
        "\n",
        "https://en.wikipedia.org/wiki/Carbon_group"
      ],
      "metadata": {
        "id": "rSVVHZyIDzKZ"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "def graph_tiling(formulas):\n",
        "  vb = []\n",
        "  for formula in formulas:\n",
        "    hb = gen_boxes(formula)\n",
        "    vb.append(HBox(hb))\n",
        "\n",
        "  display(VBox(vb))"
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      "metadata": {
        "id": "nVGw9freEDst"
      },
      "execution_count": 46,
      "outputs": []
    },
    {
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        "graph_tiling(formulas=[\"SiO2\", \"GeO2\", \"SnO2\", \"PbO2\"])"
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        },
        "id": "hqpIA1rIExH_",
        "outputId": "87559b34-d64e-427c-936c-a0579ef96134"
      },
      "execution_count": 47,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "VBox(children=(HBox(children=(VBox(children=(HTML(value='oqmd-104526'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x0…"
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        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Oxides of Boron Group Elements\n",
        "\n",
        "https://en.wikipedia.org/wiki/Boron_group"
      ],
      "metadata": {
        "id": "-5tNdQYgHj7w"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "graph_tiling(formulas=[\"B2O3\", \"Al2O3\", \"Ga2O3\", \"In2O3\", \"Tl2O3\"])"
      ],
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        },
        "id": "u3uoVAB7GWSW",
        "outputId": "403019df-eaa8-4832-f4e9-88a3871b996e"
      },
      "execution_count": 48,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "VBox(children=(HBox(children=(VBox(children=(HTML(value='oqmd-9107'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x00\\…"
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        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Be Careful of Hydrogen"
      ],
      "metadata": {
        "id": "m35qdLbtGjos"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "Since the Jmol color of hydrogen is white, the background color should be another one than white if the formula contains hydrogen. You can use [the SVG color scheme](https://graphviz.org/doc/info/colors.html#svg)."
      ],
      "metadata": {
        "id": "lqREC17u_AMx"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "boxes =  gen_boxes('LaSiHO4', length=150, max_num_boxes=12, bgcolor='cornflowerblue')\n",
        "n = 4\n",
        "VBox(\n",
        "    [HBox(boxes[i:i + n]) for i in range(0, len(boxes), n)]\n",
        ")"
      ],
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        },
        "id": "FjUV4BU94ZC3",
        "outputId": "dec7d4af-c50a-4928-abeb-272b359e937b"
      },
      "execution_count": 49,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "VBox(children=(HBox(children=(VBox(children=(HTML(value='oqmd-1101037'), Image(value=b'\\x89PNG\\r\\n\\x1a\\n\\x00\\x…"
            ],
            "application/vnd.jupyter.widget-view+json": {
              "version_major": 2,
              "version_minor": 0,
              "model_id": "f059708d9715470a97c38654a6f0aced"
            }
          },
          "metadata": {}
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Now, you can append graphs of your faverite formulas to the gallery using the code above. "
      ],
      "metadata": {
        "id": "xKkBSA0CBEyK"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Appendix"
      ],
      "metadata": {
        "id": "eDv76fv-K-qB"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "Let's search chemical formulas containing Hydrogen in this dataset."
      ],
      "metadata": {
        "id": "LqX4IyEyE4_F"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "def search_formulas(element_set, limit=100):\n",
        "  url = f'http://oqmd.org/oqmdapi/formationenergy?fields=entry_id&limit={limit}&noduplicate=True&filter=element_set={element_set}'\n",
        "  response = requests.get(url)\n",
        "  if response.status_code != 200:\n",
        "    print('Status code:', response.status_code)\n",
        "    print('You can see its meaning at https://developer.mozilla.org/en-US/docs/Web/HTTP/Status')\n",
        "  else:\n",
        "    response = json.loads(response.text)\n",
        "    dataset_oqmd_ids = set(dataset['name'].tolist())\n",
        "    \n",
        "    entry_ids = [t['entry_id'] for t in response['data'] if f'oqmd-{t[\"entry_id\"]}' in dataset_oqmd_ids]\n",
        "    formulas = set([dataset[dataset['name'] == f'oqmd-{x}']['formula'].values[0] for x in entry_ids])\n",
        "    return formulas"
      ],
      "metadata": {
        "id": "Zx_KLymmFWtL"
      },
      "execution_count": 50,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "search_formulas(element_set='H,La,O')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "T6ErPfyWOx6f",
        "outputId": "1f4f63c3-4bc2-4a2b-d228-a97ce0707683"
      },
      "execution_count": 51,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'K2LaH4N5O17',\n",
              " 'La(HO)3',\n",
              " 'LaCrHO5',\n",
              " 'LaGe(HO2)2',\n",
              " 'LaGeHO4',\n",
              " 'LaH3(CO2)3',\n",
              " 'LaH3(SeO4)3',\n",
              " 'LaH4S2NO8',\n",
              " 'LaH6(ClO3)3',\n",
              " 'LaHO',\n",
              " 'LaHO2',\n",
              " 'LaP3(HO)6',\n",
              " 'LaP3(HO2)6',\n",
              " 'LaP3H8O7',\n",
              " 'LaSi(HO2)2',\n",
              " 'LaSiHO4',\n",
              " 'LiLa2HO3'}"
            ]
          },
          "metadata": {},
          "execution_count": 51
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "search_formulas(element_set='H,Ta,O')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "rEWcaPJOKFVK",
        "outputId": "f0985232-55fe-4f6c-c297-e010b1df5f94"
      },
      "execution_count": 52,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'Cs2Ta2H2O7', 'Cs2TaHO4', 'CsTa(HO2)2', 'SrLiTa2HO7', 'Ta2Tl2P7HO24'}"
            ]
          },
          "metadata": {},
          "execution_count": 52
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Tanzanite\n",
        "# (Ca2Al3(SiO4)(Si2O7)O(OH)) + (Cr,Sr)\n",
        "search_formulas(element_set='Ca,Al,Si,O,H')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "xuZhcLnBKIC4",
        "outputId": "efa4ea30-1c4d-473c-a51b-4935b1fbff30"
      },
      "execution_count": 53,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'Ca2Al2FeSi4BHO16',\n",
              " 'CaAl2Si(HO2)4',\n",
              " 'CaAl2Si2(H2O5)2',\n",
              " 'CaAl2Si3H6O13',\n",
              " 'CaAl4Si2(HO6)2',\n",
              " 'CaAlSiHO5'}"
            ]
          },
          "metadata": {},
          "execution_count": 53
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "[Tanzanite](https://en.wikipedia.org/wiki/Tanzanite) is not included in this dataset based on \"OQMD v1.2\", but you can absolutely find it at the online database (OQMD v1.5): [link](https://oqmd.org/materials/entry/33759)"
      ],
      "metadata": {
        "id": "PQ1dPKF4K96H"
      }
    }
  ]
}