bond_analyzer.ipynb

{
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  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "authorship_tag": "ABX9TyN071zWfr99ubgjfcy2trBk",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/YIF27/Dataset-of-Spinel/blob/main/bond_analyzer.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "id": "J43yz813v469",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 145
        },
        "outputId": "217bbd00-ad80-4ab0-9c63-4ff355a07a15"
      },
      "outputs": [
        {
          "output_type": "error",
          "ename": "IndentationError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-1-fa0881377191>\"\u001b[0;36m, line \u001b[0;32m3\u001b[0m\n\u001b[0;31m    def __init__(self, input_data):\u001b[0m\n\u001b[0m    ^\u001b[0m\n\u001b[0;31mIndentationError\u001b[0m\u001b[0;31m:\u001b[0m expected an indented block after class definition on line 2\n"
          ]
        }
      ],
      "source": [
        "from pymatgen.core import Structure\n",
        "class BondAnalyzer:\n",
        "def __init__(self, input_data):\n",
        "        if isinstance(input_data, Structure):\n",
        "            self.structure = input_data\n",
        "        elif isinstance(input_data, str):  # Assuming a file path is given as a string\n",
        "            self.structure = Structure.from_file(input_data)\n",
        "        else:\n",
        "            raise ValueError(\"Input must be a pymatgen Structure or a path to a POSCAR file.\")\n",
        "\n",
        "        def get_bonds_for_atom(self, atom_index):\n",
        "        \"\"\"\n",
        "        Get the bonds involving the atom with the specified index.\n",
        "\n",
        "        Args:\n",
        "            atom_index (int): Index of the atom in the pymatgen Structure.\n",
        "\n",
        "        Returns:\n",
        "            List[Tuple[int, str]]: List of bonds for the atom, represented as tuples containing the bonded atom's index and element type.\n",
        "        \"\"\"\n",
        "        cnn = CrystalNN()\n",
        "        neighbors = cnn.get_nn_info(self.structure, atom_index)\n",
        "        bonds = [(neighbor['site_index'], neighbor['site'].species_string) for neighbor in neighbors]\n",
        "\n",
        "        return bonds\n",
        "\n",
        "\n",
        "        @staticmethod\n",
        "        def generate_bond_info(self):\n",
        "          composition_values = list(self.structure.composition.as_dict().values())\n",
        "          metal1_number = int(composition_values[0])\n",
        "          metal2_number = int(composition_values[1])\n",
        "          oxygen_number = int(composition_values[2])\n",
        "          metal1_coords = self.structure.frac_coords[0: metal1_number]\n",
        "          metal2_coords = self.structure.frac_coords[metal1_number: metal2_number + metal1_number]\n",
        "          oxygen_coords = self.structure.frac_coords[metal2_number + metal1_number:]\n",
        "\n",
        "          R_metal1_oxygen = np.zeros((oxygen_number, metal1_number))\n",
        "          PBD_O_metal1_type = np.zeros((oxygen_number, metal1_number))\n",
        "          c_O_metal1 = np.zeros((oxygen_number * metal1_number, 3))\n",
        "          t = 0\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal1_number):\n",
        "                  r, d = compute_distances_and_displacements(oxygen_coords[i], metal1_coords[j])\n",
        "                  minimum_r = min(r)\n",
        "                  arg_minimum_r = int(np.argmin(r))\n",
        "                  R_metal1_oxygen[i, j] = minimum_r\n",
        "                  PBD_O_metal1_type[i, j] = arg_minimum_r\n",
        "                  c_O_metal1[t] = d[arg_minimum_r]\n",
        "                  t = t + 1\n",
        "\n",
        "          R_metal2_oxygen = np.zeros((oxygen_number, metal2_number))\n",
        "          PBD_O_metal2_type = np.zeros((oxygen_number, metal2_number))\n",
        "          c_O_metal2 = np.zeros((oxygen_number * metal2_number, 3))\n",
        "          t = 0\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal2_number):\n",
        "                  r, d = compute_distances_and_displacements(oxygen_coords[i], metal2_coords[j])\n",
        "                  minimum_r = min(r)\n",
        "                  arg_minimum_r = int(np.argmin(r))\n",
        "                  R_metal2_oxygen[i, j] = minimum_r\n",
        "                  PBD_O_metal2_type[i, j] = arg_minimum_r\n",
        "                  c_O_metal2[t] = d[arg_minimum_r]\n",
        "                  t = t + 1\n",
        "\n",
        "          metal1_oxygen_metal2_1 = []\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal1_number):\n",
        "                  for k in range(metal2_number):\n",
        "                      if R_metal1_oxygen[i][j] < 0.255 and R_metal2_oxygen[i][k] < 0.255:\n",
        "                          metal1_oxygen_metal2_1_tmp = [i, j, k]\n",
        "                          metal1_oxygen_metal2_1_tmp.append(R_metal1_oxygen[i][j])\n",
        "                          d1 = R_metal1_oxygen[i][j]\n",
        "                          metal1_oxygen_metal2_1_tmp.append(R_metal2_oxygen[i][k])\n",
        "                          d2 = R_metal2_oxygen[i][k]\n",
        "                          c1 = c_O_metal1[i * metal1_number + j][:]\n",
        "                          c2 = c_O_metal2[i * metal2_number + k][:]\n",
        "                          p = np.dot(c1, c2) / (d1 * d2)\n",
        "                          metal1_oxygen_metal2_1_tmp.append(np.degrees(np.arccos(p)))\n",
        "                          metal1_oxygen_metal2_1.append(metal1_oxygen_metal2_1_tmp)\n",
        "\n",
        "          metal1_oxygen_metal2_2 = []\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal1_number):\n",
        "                  for k in range(metal2_number):\n",
        "                      if R_metal1_oxygen[i][j] > 0.402:\n",
        "                          if R_metal1_oxygen[i][j] < 0.46:\n",
        "                              if R_metal2_oxygen[i][k] < 0.255:\n",
        "                                  metal1_oxygen_metal2_2_tmp = [i, j, k]\n",
        "                                  metal1_oxygen_metal2_2_tmp.append(R_metal1_oxygen[i][j])\n",
        "                                  d1 = R_metal1_oxygen[i][j]\n",
        "                                  metal1_oxygen_metal2_2_tmp.append(R_metal2_oxygen[i][k])\n",
        "                                  d2 = R_metal2_oxygen[i][k]\n",
        "                                  c1 = c_O_metal1[i * metal1_number + j][:]\n",
        "                                  c2 = c_O_metal2[i * metal2_number + k][:]\n",
        "                                  p = np.dot(c1, c2) / (d1 * d2)\n",
        "                                  if p < 0.2588:\n",
        "                                    metal1_oxygen_metal2_2_tmp.append(np.degrees(np.arccos(p)))\n",
        "                                    metal1_oxygen_metal2_2.append(metal1_oxygen_metal2_2_tmp)\n",
        "\n",
        "          metal1_oxygen_metal2_3 = []\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal1_number):\n",
        "                  for k in range(metal2_number):\n",
        "                      if R_metal1_oxygen[i][j] < 0.255:\n",
        "                          if R_metal2_oxygen[i][k] > 0.40:\n",
        "                              if R_metal2_oxygen[i][k] < 0.46:\n",
        "                                  metal1_oxygen_metal2_3_tmp = []\n",
        "                                  metal1_oxygen_metal2_3_tmp.append(i)\n",
        "                                  metal1_oxygen_metal2_3_tmp.append(j)\n",
        "                                  metal1_oxygen_metal2_3_tmp.append(k)\n",
        "                                  metal1_oxygen_metal2_3_tmp.append(R_metal1_oxygen[i][j])\n",
        "                                  d1 = R_metal1_oxygen[i][j]\n",
        "                                  metal1_oxygen_metal2_3_tmp.append(R_metal2_oxygen[i][k])\n",
        "                                  d2 = R_metal2_oxygen[i][k]\n",
        "                                  c1 = c_O_metal1[i * metal1_number + j][:]\n",
        "                                  c2 = c_O_metal2[i * metal2_number + k][:]\n",
        "                                  p = np.dot(c1, c2) / (d1 * d2)\n",
        "                                  if p < 0.2588:\n",
        "                                    metal1_oxygen_metal2_3_tmp.append(np.degrees(np.arccos(p)))\n",
        "                                    metal1_oxygen_metal2_3.append(metal1_oxygen_metal2_3_tmp)\n",
        "\n",
        "          metal2_oxygen_metal2_1 = []\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal2_number - 1):\n",
        "                  for k in range(j + 1, metal2_number):\n",
        "                      if R_metal2_oxygen[i][j] < 0.255:\n",
        "                          if R_metal2_oxygen[i][k] < 0.255:\n",
        "                              metal2_oxygen_metal2_1_tmp = []\n",
        "                              metal2_oxygen_metal2_1_tmp.append(i)\n",
        "                              metal2_oxygen_metal2_1_tmp.append(j)\n",
        "                              metal2_oxygen_metal2_1_tmp.append(k)\n",
        "                              metal2_oxygen_metal2_1_tmp.append(R_metal2_oxygen[i][j])\n",
        "                              d1 = R_metal2_oxygen[i][j]\n",
        "                              metal2_oxygen_metal2_1_tmp.append(R_metal2_oxygen[i][k])\n",
        "                              d2 = R_metal2_oxygen[i][k]\n",
        "                              c1 = c_O_metal2[i * metal2_number + j][:]\n",
        "                              c2 = c_O_metal2[i * metal2_number + k][:]\n",
        "                              p = np.dot(c1, c2) / (d1 * d2)\n",
        "                              metal2_oxygen_metal2_1_tmp.append(np.degrees(np.arccos(p)))\n",
        "                              metal2_oxygen_metal2_1.append(metal2_oxygen_metal2_1_tmp)\n",
        "\n",
        "          metal2_oxygen_metal2_2 = []\n",
        "          R_metal2_oxygen_1 = []\n",
        "          R_metal2_oxygen_2 = []\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal2_number - 1):\n",
        "                  for k in range(j + 1, metal2_number):\n",
        "                      if (R_metal2_oxygen[i][j] < 0.255 and 0.40 < R_metal2_oxygen[i][k] < 0.46) or (\n",
        "                              R_metal2_oxygen[i][k] < 0.255 and 0.40 < R_metal2_oxygen[i][j] < 0.46):\n",
        "                          metal2_oxygen_metal2_2_tmp = [i, j, k]\n",
        "                          metal2_oxygen_metal2_2_tmp.append(R_metal2_oxygen[i][j])\n",
        "                          d1 = R_metal2_oxygen[i][j]\n",
        "                          metal2_oxygen_metal2_2_tmp.append(R_metal2_oxygen[i][k])\n",
        "                          d2 = R_metal2_oxygen[i][k]\n",
        "                          c1 = c_O_metal2[i * metal2_number + j][:]\n",
        "                          c2 = c_O_metal2[i * metal2_number + k][:]\n",
        "                          p = np.dot(c1, c2) / (d1 * d2)\n",
        "                          if p < 0.2588:\n",
        "                              metal2_oxygen_metal2_2_tmp.append(np.degrees(np.arccos(p)))\n",
        "                              metal2_oxygen_metal2_2.append(metal2_oxygen_metal2_2_tmp)\n",
        "                              if d1 > d2:\n",
        "                                  R_metal2_oxygen_1.append(d2)\n",
        "                                  R_metal2_oxygen_2.append(d1)\n",
        "                              if d2 > d1:\n",
        "                                  R_metal2_oxygen_1.append(d1)\n",
        "                                  R_metal2_oxygen_2.append(d2)\n",
        "\n",
        "          metal1_oxygen_metal1_1 = []\n",
        "          R_metal1_oxygen_1 = []\n",
        "          R_metal1_oxygen_2 = []\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal1_number - 1):\n",
        "                  for k in range(j + 1, metal1_number):\n",
        "                      if (R_metal1_oxygen[i][j] < 0.255 and 0.40 < R_metal1_oxygen[i][k] < 0.46) or (\n",
        "                              R_metal1_oxygen[i][k] < 0.255 and 0.40 < R_metal1_oxygen[i][j] < 0.46):\n",
        "                          metal1_oxygen_metal1_1_tmp = [i,j,k]\n",
        "                          metal1_oxygen_metal1_1_tmp.append(R_metal1_oxygen[i][j])\n",
        "                          d1 = R_metal1_oxygen[i][j]\n",
        "                          metal1_oxygen_metal1_1_tmp.append(R_metal1_oxygen[i][k])\n",
        "                          d2 = R_metal1_oxygen[i][k]\n",
        "                          c1 = c_O_metal1[i * metal1_number + j][:]\n",
        "                          c2 = c_O_metal1[i * metal1_number + k][:]\n",
        "                          p = np.dot(c1, c2) / (d1 * d2)\n",
        "                          if p < 0.2588:\n",
        "                              metal1_oxygen_metal1_1_tmp.append(np.degrees(np.arccos(p)))\n",
        "                              metal1_oxygen_metal1_1.append(metal1_oxygen_metal1_1_tmp)\n",
        "                              if d1 > d2:\n",
        "                                  R_metal1_oxygen_1.append(d2)\n",
        "                                  R_metal1_oxygen_2.append(d1)\n",
        "                              if d2 > d1:\n",
        "                                  R_metal1_oxygen_1.append(d1)\n",
        "                                  R_metal1_oxygen_2.append(d2)\n",
        "\n",
        "          metal1_oxygen_metal1_2 = []\n",
        "          for i in range(oxygen_number):\n",
        "              for j in range(metal1_number - 1):\n",
        "                  for k in range(j + 1, metal1_number):\n",
        "                      if R_metal1_oxygen[i][j] < 0.255:\n",
        "                          if R_metal1_oxygen[i][k] < 0.255:\n",
        "                              d1 = R_metal1_oxygen[i][j]\n",
        "                              d2 = R_metal1_oxygen[i][k]\n",
        "                              c1 = c_O_metal1[i * metal1_number + j][:]\n",
        "                              c2 = c_O_metal1[i * metal1_number + k][:]\n",
        "                              p = np.dot(c1, c2) / (d1 * d2)\n",
        "                              angle = math.acos(p) * 180 / math.pi\n",
        "                              metal1_oxygen_metal1_2_tmp = [i, j, k, d1, d2, angle]\n",
        "                              metal1_oxygen_metal1_2.append(metal1_oxygen_metal1_2_tmp)\n",
        "\n",
        "          metal1_oxygen_metal2_1 = np.array(metal1_oxygen_metal2_1)\n",
        "          metal1_oxygen_metal2_1_new = metal1_oxygen_metal2_1[metal1_oxygen_metal2_1[:, 5].argsort()]\n",
        "\n",
        "          metal1_oxygen_metal2_2 = np.array(metal1_oxygen_metal2_2)\n",
        "          metal1_oxygen_metal2_2_new = metal1_oxygen_metal2_2[metal1_oxygen_metal2_2[:, 5].argsort()]\n",
        "\n",
        "          metal1_oxygen_metal2_3 = np.array(metal1_oxygen_metal2_3)\n",
        "          metal1_oxygen_metal2_3_new = metal1_oxygen_metal2_3[metal1_oxygen_metal2_3[:, 5].argsort()]\n",
        "\n",
        "          metal1_oxygen_metal1_1 = np.array(metal1_oxygen_metal1_1)\n",
        "          metal1_oxygen_metal1_1_new = metal1_oxygen_metal1_1[metal1_oxygen_metal1_1[:, 5].argsort()]\n",
        "\n",
        "          metal1_oxygen_metal1_2 = np.array(metal1_oxygen_metal1_2)\n",
        "          metal1_oxygen_metal1_2_new = metal1_oxygen_metal1_2[metal1_oxygen_metal1_2[:, 5].argsort()]\n",
        "\n",
        "          metal2_oxygen_metal2_1 = np.array(metal2_oxygen_metal2_1)\n",
        "          metal2_oxygen_metal2_1_new = metal2_oxygen_metal2_1[metal2_oxygen_metal2_1[:, 5].argsort()]\n",
        "\n",
        "          metal2_oxygen_metal2_2 = np.array(metal2_oxygen_metal2_2)\n",
        "          metal2_oxygen_metal2_2_new = metal2_oxygen_metal2_2[metal2_oxygen_metal2_2[:, 5].argsort()]\n",
        "\n",
        "          metal2_oxygen_metal2_79 = count_bond_number(metal2_oxygen_metal2_2_new, 76, 80)\n",
        "          metal2_oxygen_metal2_93 = count_bond_number(metal2_oxygen_metal2_1_new, 0, 94)\n",
        "          metal2_oxygen_metal2_123 = count_bond_number(metal2_oxygen_metal2_1_new, 120, 126)\n",
        "          metal2_oxygen_metal2_126 = count_bond_number(metal2_oxygen_metal2_2_new, 124, 127)\n",
        "          metal2_oxygen_metal2_158 = count_bond_number(metal2_oxygen_metal2_2_new, 157, 160)\n",
        "          metal2_oxygen_metal2_179 = count_bond_number(metal2_oxygen_metal2_2_new, 177, 180)\n",
        "          metal1_oxygen_metal2_79 = count_bond_number(metal1_oxygen_metal2_3_new, 0, 80)\n",
        "          metal1_oxygen_metal2_93 = count_bond_number(metal1_oxygen_metal2_1_new, 92, 94)\n",
        "          metal1_oxygen_metal2_123 = count_bond_number(metal1_oxygen_metal2_1_new, 120, 126)\n",
        "          metal1_oxygen_metal2_126 = count_bond_number(metal1_oxygen_metal2_3_new, 124, 127)\n",
        "          metal1_oxygen_metal2_158 = count_bond_number(metal1_oxygen_metal2_3_new, 157, 160)\n",
        "          metal1_oxygen_metal2_179 = count_bond_number(metal1_oxygen_metal2_3_new, 177, 180)\n",
        "          metal2_oxygen_metal1_79 = count_bond_number(metal1_oxygen_metal2_2_new, 77, 81)\n",
        "          metal2_oxygen_metal1_126 = count_bond_number(metal1_oxygen_metal2_2_new, 124, 127)\n",
        "          metal2_oxygen_metal1_158 = count_bond_number(metal1_oxygen_metal2_2_new, 157, 160)\n",
        "          metal2_oxygen_metal1_179 = count_bond_number(metal1_oxygen_metal2_2_new, 177, 180)\n",
        "          metal1_oxygen_metal1_79 = count_bond_number(metal1_oxygen_metal1_1_new, 77, 81)\n",
        "          metal1_oxygen_metal1_93 = count_bond_number(metal1_oxygen_metal1_2_new, 90, 95)\n",
        "          metal1_oxygen_metal1_123 = count_bond_number(metal1_oxygen_metal1_2_new, 120, 125)\n",
        "          metal1_oxygen_metal1_126 = count_bond_number(metal1_oxygen_metal1_1_new, 124, 127)\n",
        "          metal1_oxygen_metal1_158 = count_bond_number(metal1_oxygen_metal1_1_new, 157, 160)\n",
        "          metal1_oxygen_metal1_179 = count_bond_number(metal1_oxygen_metal1_1_new, 177, 180)\n",
        "          bond = [metal1_oxygen_metal2_123, metal2_oxygen_metal2_123, metal1_oxygen_metal1_123, metal2_oxygen_metal1_158,\n",
        "                  metal2_oxygen_metal2_158, metal1_oxygen_metal2_158, metal1_oxygen_metal1_158, metal1_oxygen_metal2_179,\n",
        "                  metal2_oxygen_metal2_179, metal2_oxygen_metal1_179, metal1_oxygen_metal1_179,\n",
        "                  metal1_oxygen_metal2_93, metal2_oxygen_metal2_93, metal1_oxygen_metal1_93, metal2_oxygen_metal1_126,\n",
        "                  metal1_oxygen_metal2_126, metal2_oxygen_metal2_126, metal1_oxygen_metal1_126, metal2_oxygen_metal2_79,\n",
        "                  metal2_oxygen_metal1_79, metal1_oxygen_metal2_79, metal1_oxygen_metal1_79]\n",
        "          return bond\n",
        "\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Usage in the same file:\n",
        "analyzer = BondAnalyzer()\n",
        "result = analyzer.generate_bond_info(\"H\", \"O\")\n",
        "\n",
        "# If you want to use this class in another file, you can import it.\n",
        "# Assuming you saved this class in a file named \"bond_analyzer.py\":\n",
        "# from bond_analyzer import BondAnalyzer"
      ],
      "metadata": {
        "id": "-tR3WEMY1Fnp"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}