{
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   "id": "0",
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    "execution": {
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     "shell.execute_reply": "2026-04-14T14:55:36.126293Z"
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    "tags": [
     "hide-in-docs"
    ]
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   "source": [
    "# Check whether easydiffraction is installed; install it if needed.\n",
    "# Required for remote environments such as Google Colab.\n",
    "import importlib.util\n",
    "\n",
    "if importlib.util.find_spec('easydiffraction') is None:\n",
    "    %pip install easydiffraction==0.13.1"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1",
   "metadata": {},
   "source": [
    "# Structure Refinement: Tb2TiO7, HEiDi\n",
    "\n",
    "Crystal structure refinement of Tb2TiO7 using single crystal neutron\n",
    "diffraction data from HEiDi at FRM II."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2",
   "metadata": {},
   "source": [
    "## Import Library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:36.128782Z",
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     "shell.execute_reply": "2026-04-14T14:55:38.677807Z"
    }
   },
   "outputs": [],
   "source": [
    "import easydiffraction as ed"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4",
   "metadata": {},
   "source": [
    "## Step 1: Define Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "5",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2026-04-14T14:55:39.174256Z"
    }
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   "outputs": [
    {
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       "\n",
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   "source": [
    "# Create minimal project without name and description\n",
    "project = ed.Project()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6",
   "metadata": {},
   "source": [
    "## Step 2: Define Structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "7",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2026-04-14T14:55:39.480813Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mGetting data\u001b[0m\u001b[1;34m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data #\u001b[1;36m20\u001b[0m: Tb2Ti2O7 \u001b[1m(\u001b[0mcrystal structure\u001b[1m)\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ Data #\u001b[1;36m20\u001b[0m downloaded to \u001b[32m'data/ed-20.cif'\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "# Download CIF file from repository\n",
    "structure_path = ed.download_data(id=20, destination='data')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2026-04-14T14:55:39.490782Z"
    }
   },
   "outputs": [],
   "source": [
    "project.structures.add_from_cif_path(structure_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2026-04-14T14:55:39.497313Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mDefined structures 🧩\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1m[\u001b[0m\u001b[32m'tbti'\u001b[0m\u001b[1m]\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "project.structures.show_names()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "10",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.499652Z",
     "iopub.status.busy": "2026-04-14T14:55:39.499467Z",
     "iopub.status.idle": "2026-04-14T14:55:39.502788Z",
     "shell.execute_reply": "2026-04-14T14:55:39.502024Z"
    }
   },
   "outputs": [],
   "source": [
    "structure = project.structures['tbti']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "11",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.504332Z",
     "iopub.status.busy": "2026-04-14T14:55:39.504116Z",
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     "shell.execute_reply": "2026-04-14T14:55:39.763696Z"
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mStructure 🧩 \u001b[0m\u001b[32m'tbti'\u001b[0m\u001b[1;34m as cif\u001b[0m\n"
     ]
    },
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       "#T_e3ba2 tbody tr:nth-child(odd) {\n",
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       "#T_e3ba2_row0_col0, #T_e3ba2_row1_col0, #T_e3ba2_row2_col0, #T_e3ba2_row3_col0, #T_e3ba2_row4_col0, #T_e3ba2_row5_col0, #T_e3ba2_row6_col0, #T_e3ba2_row7_col0, #T_e3ba2_row8_col0, #T_e3ba2_row9_col0, #T_e3ba2_row10_col0, #T_e3ba2_row11_col0, #T_e3ba2_row12_col0, #T_e3ba2_row13_col0, #T_e3ba2_row14_col0, #T_e3ba2_row15_col0, #T_e3ba2_row16_col0, #T_e3ba2_row17_col0, #T_e3ba2_row18_col0, #T_e3ba2_row19_col0, #T_e3ba2_row20_col0, #T_e3ba2_row21_col0, #T_e3ba2_row22_col0, #T_e3ba2_row23_col0, #T_e3ba2_row24_col0, #T_e3ba2_row25_col0, #T_e3ba2_row26_col0 {\n",
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       "    <tr>\n",
       "      <th class=\"blank level0\" >&nbsp;</th>\n",
       "      <th id=\"T_e3ba2_level0_col0\" class=\"col_heading level0 col0\" >CIF</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row0\" class=\"row_heading level0 row0\" >1</th>\n",
       "      <td id=\"T_e3ba2_row0_col0\" class=\"data row0 col0\" >data_tbti</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row1\" class=\"row_heading level0 row1\" >2</th>\n",
       "      <td id=\"T_e3ba2_row1_col0\" class=\"data row1 col0\" ></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row2\" class=\"row_heading level0 row2\" >3</th>\n",
       "      <td id=\"T_e3ba2_row2_col0\" class=\"data row2 col0\" >_cell.length_a 10.13000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row3\" class=\"row_heading level0 row3\" >4</th>\n",
       "      <td id=\"T_e3ba2_row3_col0\" class=\"data row3 col0\" >_cell.length_b 10.13000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row4\" class=\"row_heading level0 row4\" >5</th>\n",
       "      <td id=\"T_e3ba2_row4_col0\" class=\"data row4 col0\" >_cell.length_c 10.13000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row5\" class=\"row_heading level0 row5\" >6</th>\n",
       "      <td id=\"T_e3ba2_row5_col0\" class=\"data row5 col0\" >_cell.angle_alpha 90.00000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row6\" class=\"row_heading level0 row6\" >7</th>\n",
       "      <td id=\"T_e3ba2_row6_col0\" class=\"data row6 col0\" >_cell.angle_beta 90.00000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row7\" class=\"row_heading level0 row7\" >8</th>\n",
       "      <td id=\"T_e3ba2_row7_col0\" class=\"data row7 col0\" >_cell.angle_gamma 90.00000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row8\" class=\"row_heading level0 row8\" >9</th>\n",
       "      <td id=\"T_e3ba2_row8_col0\" class=\"data row8 col0\" ></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row9\" class=\"row_heading level0 row9\" >10</th>\n",
       "      <td id=\"T_e3ba2_row9_col0\" class=\"data row9 col0\" >_space_group.name_H-M_alt \"F d -3 m\"</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row10\" class=\"row_heading level0 row10\" >11</th>\n",
       "      <td id=\"T_e3ba2_row10_col0\" class=\"data row10 col0\" >_space_group.IT_coordinate_system_code 2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row11\" class=\"row_heading level0 row11\" >12</th>\n",
       "      <td id=\"T_e3ba2_row11_col0\" class=\"data row11 col0\" ></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row12\" class=\"row_heading level0 row12\" >13</th>\n",
       "      <td id=\"T_e3ba2_row12_col0\" class=\"data row12 col0\" >loop_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row13\" class=\"row_heading level0 row13\" >14</th>\n",
       "      <td id=\"T_e3ba2_row13_col0\" class=\"data row13 col0\" >_atom_site.label</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row14\" class=\"row_heading level0 row14\" >15</th>\n",
       "      <td id=\"T_e3ba2_row14_col0\" class=\"data row14 col0\" >_atom_site.type_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row15\" class=\"row_heading level0 row15\" >16</th>\n",
       "      <td id=\"T_e3ba2_row15_col0\" class=\"data row15 col0\" >_atom_site.fract_x</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row16\" class=\"row_heading level0 row16\" >17</th>\n",
       "      <td id=\"T_e3ba2_row16_col0\" class=\"data row16 col0\" >_atom_site.fract_y</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row17\" class=\"row_heading level0 row17\" >18</th>\n",
       "      <td id=\"T_e3ba2_row17_col0\" class=\"data row17 col0\" >_atom_site.fract_z</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row18\" class=\"row_heading level0 row18\" >19</th>\n",
       "      <td id=\"T_e3ba2_row18_col0\" class=\"data row18 col0\" >_atom_site.Wyckoff_letter</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row19\" class=\"row_heading level0 row19\" >20</th>\n",
       "      <td id=\"T_e3ba2_row19_col0\" class=\"data row19 col0\" >_atom_site.occupancy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row20\" class=\"row_heading level0 row20\" >21</th>\n",
       "      <td id=\"T_e3ba2_row20_col0\" class=\"data row20 col0\" >_atom_site.B_iso_or_equiv</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row21\" class=\"row_heading level0 row21\" >22</th>\n",
       "      <td id=\"T_e3ba2_row21_col0\" class=\"data row21 col0\" >_atom_site.adp_type</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row22\" class=\"row_heading level0 row22\" >23</th>\n",
       "      <td id=\"T_e3ba2_row22_col0\" class=\"data row22 col0\" >Tb Tb 0.50000000 0.50000000 0.50000000 d 1.00000000 0.53000000(2000000) Biso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row23\" class=\"row_heading level0 row23\" >24</th>\n",
       "      <td id=\"T_e3ba2_row23_col0\" class=\"data row23 col0\" >Ti Ti 0.00000000 0.00000000 0.00000000 c 1.00000000 0.48000000(3000000) Biso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row24\" class=\"row_heading level0 row24\" >25</th>\n",
       "      <td id=\"T_e3ba2_row24_col0\" class=\"data row24 col0\" >O1 O 0.32804000(9000) 0.12500000 0.12500000 f 1.00000000(1000000) 0.45000000(2000000) Biso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row25\" class=\"row_heading level0 row25\" >26</th>\n",
       "      <td id=\"T_e3ba2_row25_col0\" class=\"data row25 col0\" >O2 O 0.37500000 0.37500000 0.37500000 b 0.97000000(2000000) 0.23000000(4000000) Biso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e3ba2_level0_row26\" class=\"row_heading level0 row26\" >27</th>\n",
       "      <td id=\"T_e3ba2_row26_col0\" class=\"data row26 col0\" ></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f44921ff4d0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure.show_as_cif()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "12",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.766273Z",
     "iopub.status.busy": "2026-04-14T14:55:39.766068Z",
     "iopub.status.idle": "2026-04-14T14:55:39.770283Z",
     "shell.execute_reply": "2026-04-14T14:55:39.769466Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.atom_sites['Tb'].adp_type = 'Uiso'\n",
    "structure.atom_sites['Ti'].adp_type = 'Uiso'\n",
    "structure.atom_sites['O1'].adp_type = 'Uiso'\n",
    "structure.atom_sites['O2'].adp_type = 'Uiso'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "13",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.771872Z",
     "iopub.status.busy": "2026-04-14T14:55:39.771675Z",
     "iopub.status.idle": "2026-04-14T14:55:39.775227Z",
     "shell.execute_reply": "2026-04-14T14:55:39.774383Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loop_\n",
      "_atom_site.label\n",
      "_atom_site.type_symbol\n",
      "_atom_site.fract_x\n",
      "_atom_site.fract_y\n",
      "_atom_site.fract_z\n",
      "_atom_site.Wyckoff_letter\n",
      "_atom_site.occupancy\n",
      "_atom_site.U_iso_or_equiv\n",
      "_atom_site.adp_type\n",
      "Tb Tb 0.50000000 0.50000000 0.50000000 d 1.00000000 0.00671253(2000000) Uiso\n",
      "Ti Ti 0.00000000 0.00000000 0.00000000 c 1.00000000 0.00607927(3000000) Uiso\n",
      "O1 O 0.32804000(9000) 0.12500000 0.12500000 f 1.00000000(1000000) 0.00569932(2000000) Uiso\n",
      "O2 O 0.37500000 0.37500000 0.37500000 b 0.97000000(2000000) 0.00291298(4000000) Uiso\n"
     ]
    }
   ],
   "source": [
    "print(structure.atom_sites.as_cif)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "14",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.776775Z",
     "iopub.status.busy": "2026-04-14T14:55:39.776584Z",
     "iopub.status.idle": "2026-04-14T14:55:39.780509Z",
     "shell.execute_reply": "2026-04-14T14:55:39.779854Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.atom_sites['Tb'].adp_iso = 0.0\n",
    "structure.atom_sites['Ti'].adp_iso = 0.0\n",
    "structure.atom_sites['O1'].adp_iso = 0.0\n",
    "structure.atom_sites['O2'].adp_iso = 0.0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "15",
   "metadata": {},
   "source": [
    "## Step 3: Define Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "16",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.781989Z",
     "iopub.status.busy": "2026-04-14T14:55:39.781834Z",
     "iopub.status.idle": "2026-04-14T14:55:39.958908Z",
     "shell.execute_reply": "2026-04-14T14:55:39.957936Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mGetting data\u001b[0m\u001b[1;34m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data #\u001b[1;36m19\u001b[0m: Tb2Ti2O7, HEiDi \u001b[1m(\u001b[0mMLZ\u001b[1m)\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ Data #\u001b[1;36m19\u001b[0m downloaded to \u001b[32m'data/ed-19.xye'\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "# Download data file from repository\n",
    "data_path = ed.download_data(id=19, destination='data')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "17",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.960527Z",
     "iopub.status.busy": "2026-04-14T14:55:39.960351Z",
     "iopub.status.idle": "2026-04-14T14:55:39.984921Z",
     "shell.execute_reply": "2026-04-14T14:55:39.983999Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mData loaded successfully\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Experiment 🔬 \u001b[32m'heidi'\u001b[0m. Number of data points: \u001b[1;36m220\u001b[0m.\n"
     ]
    }
   ],
   "source": [
    "project.experiments.add_from_data_path(\n",
    "    name='heidi',\n",
    "    data_path=data_path,\n",
    "    sample_form='single crystal',\n",
    "    beam_mode='constant wavelength',\n",
    "    radiation_probe='neutron',\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "18",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.986493Z",
     "iopub.status.busy": "2026-04-14T14:55:39.986323Z",
     "iopub.status.idle": "2026-04-14T14:55:39.989149Z",
     "shell.execute_reply": "2026-04-14T14:55:39.988314Z"
    }
   },
   "outputs": [],
   "source": [
    "experiment = project.experiments['heidi']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "19",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.990642Z",
     "iopub.status.busy": "2026-04-14T14:55:39.990486Z",
     "iopub.status.idle": "2026-04-14T14:55:39.993593Z",
     "shell.execute_reply": "2026-04-14T14:55:39.992797Z"
    }
   },
   "outputs": [],
   "source": [
    "experiment.linked_crystal.id = 'tbti'\n",
    "experiment.linked_crystal.scale = 1.0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "20",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.995043Z",
     "iopub.status.busy": "2026-04-14T14:55:39.994888Z",
     "iopub.status.idle": "2026-04-14T14:55:39.997937Z",
     "shell.execute_reply": "2026-04-14T14:55:39.996900Z"
    }
   },
   "outputs": [],
   "source": [
    "experiment.instrument.setup_wavelength = 0.793"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "21",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:39.999406Z",
     "iopub.status.busy": "2026-04-14T14:55:39.999233Z",
     "iopub.status.idle": "2026-04-14T14:55:40.002172Z",
     "shell.execute_reply": "2026-04-14T14:55:40.001431Z"
    }
   },
   "outputs": [],
   "source": [
    "experiment.extinction.mosaicity = 35000\n",
    "experiment.extinction.radius = 10"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "22",
   "metadata": {},
   "source": [
    "## Step 4: Perform Analysis I (ADP iso)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "23",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:40.003705Z",
     "iopub.status.busy": "2026-04-14T14:55:40.003544Z",
     "iopub.status.idle": "2026-04-14T14:55:40.480079Z",
     "shell.execute_reply": "2026-04-14T14:55:40.478931Z"
    }
   },
   "outputs": [
    {
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   "source": [
    "project.plotter.plot_meas_vs_calc(expt_name='heidi')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "24",
   "metadata": {
    "execution": {
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     "iopub.status.busy": "2026-04-14T14:55:40.482031Z",
     "iopub.status.idle": "2026-04-14T14:55:40.487231Z",
     "shell.execute_reply": "2026-04-14T14:55:40.486260Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.atom_sites['O1'].fract_x.free = True\n",
    "\n",
    "structure.atom_sites['Ti'].occupancy.free = True\n",
    "structure.atom_sites['O1'].occupancy.free = True\n",
    "structure.atom_sites['O2'].occupancy.free = True\n",
    "\n",
    "structure.atom_sites['Tb'].adp_iso.free = True\n",
    "structure.atom_sites['Ti'].adp_iso.free = True\n",
    "structure.atom_sites['O1'].adp_iso.free = True\n",
    "structure.atom_sites['O2'].adp_iso.free = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "25",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:40.489377Z",
     "iopub.status.busy": "2026-04-14T14:55:40.488568Z",
     "iopub.status.idle": "2026-04-14T14:55:40.492735Z",
     "shell.execute_reply": "2026-04-14T14:55:40.491704Z"
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   "outputs": [],
   "source": [
    "experiment.linked_crystal.scale.free = True\n",
    "experiment.extinction.radius.free = True"
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  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "26",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:40.494220Z",
     "iopub.status.busy": "2026-04-14T14:55:40.494013Z",
     "iopub.status.idle": "2026-04-14T14:55:42.968033Z",
     "shell.execute_reply": "2026-04-14T14:55:42.967072Z"
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mStandard fitting\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📋 Using experiment 🔬 \u001b[32m'heidi'\u001b[0m for \u001b[32m'single'\u001b[0m fitting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "🚀 Starting fit process with \u001b[32m'lmfit \u001b[0m\u001b[32m(\u001b[0m\u001b[32mleastsq\u001b[0m\u001b[32m)\u001b[0m\u001b[32m'\u001b[0m\u001b[33m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📈 Goodness-of-fit \u001b[1m(\u001b[0mreduced χ²\u001b[1m)\u001b[0m change:\n"
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    },
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       "                IPython.notebook.kernel.execute(\"_jupyter_dark_detect_result = \" + \n",
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     "text": [
      "🏆 Best goodness-of-fit \u001b[1m(\u001b[0mreduced χ²\u001b[1m)\u001b[0m is \u001b[1;36m12.75\u001b[0m at iteration \u001b[1;36m80\u001b[0m\n"
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     "text": [
      "✅ Fitting complete.\n"
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    "# Start refinement. All parameters, which have standard uncertainties\n",
    "# in the input CIF files, are refined by default.\n",
    "project.analysis.fit()"
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   "id": "27",
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     "text": [
      "\u001b[1;34mFit results\u001b[0m\n"
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     "name": "stdout",
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     "text": [
      "✅ Success: \u001b[3;92mTrue\u001b[0m\n"
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     "text": [
      "⏱️ Fitting time: \u001b[1;36m2.03\u001b[0m seconds\n"
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📏 Goodness-of-fit \u001b[1m(\u001b[0mreduced χ²\u001b[1m)\u001b[0m: \u001b[1;36m12.75\u001b[0m\n"
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     "text": [
      "📏 R-factor \u001b[1m(\u001b[0mRf\u001b[1m)\u001b[0m: \u001b[1;36m7.65\u001b[0m%\n"
     ]
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     "output_type": "stream",
     "text": [
      "📏 R-factor squared \u001b[1m(\u001b[0mRf²\u001b[1m)\u001b[0m: \u001b[1;36m8.10\u001b[0m%\n"
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     "text": [
      "📏 Weighted R-factor \u001b[1m(\u001b[0mwR\u001b[1m)\u001b[0m: \u001b[1;36m8.59\u001b[0m%\n"
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    },
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     "text": [
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       "#T_a6d0c th.col5 {\n",
       "  text-align: right;\n",
       "}\n",
       "#T_a6d0c th.col6 {\n",
       "  text-align: right;\n",
       "}\n",
       "#T_a6d0c th.col7 {\n",
       "  text-align: left;\n",
       "}\n",
       "#T_a6d0c th.col8 {\n",
       "  text-align: right;\n",
       "}\n",
       "#T_a6d0c_row0_col0, #T_a6d0c_row0_col1, #T_a6d0c_row0_col2, #T_a6d0c_row0_col3, #T_a6d0c_row0_col7, #T_a6d0c_row1_col0, #T_a6d0c_row1_col1, #T_a6d0c_row1_col2, #T_a6d0c_row1_col3, #T_a6d0c_row1_col7, #T_a6d0c_row2_col0, #T_a6d0c_row2_col1, #T_a6d0c_row2_col2, #T_a6d0c_row2_col3, #T_a6d0c_row2_col7, #T_a6d0c_row3_col0, #T_a6d0c_row3_col1, #T_a6d0c_row3_col2, #T_a6d0c_row3_col3, #T_a6d0c_row3_col7, #T_a6d0c_row4_col0, #T_a6d0c_row4_col1, #T_a6d0c_row4_col2, #T_a6d0c_row4_col3, #T_a6d0c_row4_col7, #T_a6d0c_row5_col0, #T_a6d0c_row5_col1, #T_a6d0c_row5_col2, #T_a6d0c_row5_col3, #T_a6d0c_row5_col7, #T_a6d0c_row6_col0, #T_a6d0c_row6_col1, #T_a6d0c_row6_col2, #T_a6d0c_row6_col3, #T_a6d0c_row6_col7, #T_a6d0c_row7_col0, #T_a6d0c_row7_col1, #T_a6d0c_row7_col2, #T_a6d0c_row7_col3, #T_a6d0c_row7_col7, #T_a6d0c_row8_col0, #T_a6d0c_row8_col1, #T_a6d0c_row8_col2, #T_a6d0c_row8_col3, #T_a6d0c_row8_col7, #T_a6d0c_row9_col0, #T_a6d0c_row9_col1, #T_a6d0c_row9_col2, #T_a6d0c_row9_col3, #T_a6d0c_row9_col7 {\n",
       "  text-align: left;\n",
       "}\n",
       "#T_a6d0c_row0_col4, #T_a6d0c_row0_col5, #T_a6d0c_row0_col6, #T_a6d0c_row0_col8, #T_a6d0c_row1_col4, #T_a6d0c_row1_col5, #T_a6d0c_row1_col6, #T_a6d0c_row1_col8, #T_a6d0c_row2_col4, #T_a6d0c_row2_col5, #T_a6d0c_row2_col6, #T_a6d0c_row2_col8, #T_a6d0c_row3_col4, #T_a6d0c_row3_col5, #T_a6d0c_row3_col6, #T_a6d0c_row3_col8, #T_a6d0c_row4_col4, #T_a6d0c_row4_col5, #T_a6d0c_row4_col6, #T_a6d0c_row4_col8, #T_a6d0c_row5_col4, #T_a6d0c_row5_col5, #T_a6d0c_row5_col6, #T_a6d0c_row5_col8, #T_a6d0c_row6_col4, #T_a6d0c_row6_col5, #T_a6d0c_row6_col6, #T_a6d0c_row6_col8, #T_a6d0c_row7_col4, #T_a6d0c_row7_col5, #T_a6d0c_row7_col6, #T_a6d0c_row7_col8, #T_a6d0c_row8_col4, #T_a6d0c_row8_col5, #T_a6d0c_row8_col6, #T_a6d0c_row8_col8, #T_a6d0c_row9_col4, #T_a6d0c_row9_col5, #T_a6d0c_row9_col6, #T_a6d0c_row9_col8 {\n",
       "  text-align: right;\n",
       "}\n",
       "</style>\n",
       "<table id=\"T_a6d0c\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr>\n",
       "      <th class=\"blank level0\" >&nbsp;</th>\n",
       "      <th id=\"T_a6d0c_level0_col0\" class=\"col_heading level0 col0\" >datablock</th>\n",
       "      <th id=\"T_a6d0c_level0_col1\" class=\"col_heading level0 col1\" >category</th>\n",
       "      <th id=\"T_a6d0c_level0_col2\" class=\"col_heading level0 col2\" >entry</th>\n",
       "      <th id=\"T_a6d0c_level0_col3\" class=\"col_heading level0 col3\" >parameter</th>\n",
       "      <th id=\"T_a6d0c_level0_col4\" class=\"col_heading level0 col4\" >start</th>\n",
       "      <th id=\"T_a6d0c_level0_col5\" class=\"col_heading level0 col5\" >fitted</th>\n",
       "      <th id=\"T_a6d0c_level0_col6\" class=\"col_heading level0 col6\" >uncertainty</th>\n",
       "      <th id=\"T_a6d0c_level0_col7\" class=\"col_heading level0 col7\" >units</th>\n",
       "      <th id=\"T_a6d0c_level0_col8\" class=\"col_heading level0 col8\" >change</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row0\" class=\"row_heading level0 row0\" >1</th>\n",
       "      <td id=\"T_a6d0c_row0_col0\" class=\"data row0 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row0_col1\" class=\"data row0 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row0_col2\" class=\"data row0 col2\" >Tb</td>\n",
       "      <td id=\"T_a6d0c_row0_col3\" class=\"data row0 col3\" >adp_iso</td>\n",
       "      <td id=\"T_a6d0c_row0_col4\" class=\"data row0 col4\" >0.0000</td>\n",
       "      <td id=\"T_a6d0c_row0_col5\" class=\"data row0 col5\" >0.0068</td>\n",
       "      <td id=\"T_a6d0c_row0_col6\" class=\"data row0 col6\" >0.0003</td>\n",
       "      <td id=\"T_a6d0c_row0_col7\" class=\"data row0 col7\" >Ų</td>\n",
       "      <td id=\"T_a6d0c_row0_col8\" class=\"data row0 col8\" >N/A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row1\" class=\"row_heading level0 row1\" >2</th>\n",
       "      <td id=\"T_a6d0c_row1_col0\" class=\"data row1 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row1_col1\" class=\"data row1 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row1_col2\" class=\"data row1 col2\" >Ti</td>\n",
       "      <td id=\"T_a6d0c_row1_col3\" class=\"data row1 col3\" >occupancy</td>\n",
       "      <td id=\"T_a6d0c_row1_col4\" class=\"data row1 col4\" >1.0000</td>\n",
       "      <td id=\"T_a6d0c_row1_col5\" class=\"data row1 col5\" >0.9730</td>\n",
       "      <td id=\"T_a6d0c_row1_col6\" class=\"data row1 col6\" >0.0178</td>\n",
       "      <td id=\"T_a6d0c_row1_col7\" class=\"data row1 col7\" ></td>\n",
       "      <td id=\"T_a6d0c_row1_col8\" class=\"data row1 col8\" >2.70 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row2\" class=\"row_heading level0 row2\" >3</th>\n",
       "      <td id=\"T_a6d0c_row2_col0\" class=\"data row2 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row2_col1\" class=\"data row2 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row2_col2\" class=\"data row2 col2\" >Ti</td>\n",
       "      <td id=\"T_a6d0c_row2_col3\" class=\"data row2 col3\" >adp_iso</td>\n",
       "      <td id=\"T_a6d0c_row2_col4\" class=\"data row2 col4\" >0.0000</td>\n",
       "      <td id=\"T_a6d0c_row2_col5\" class=\"data row2 col5\" >0.0054</td>\n",
       "      <td id=\"T_a6d0c_row2_col6\" class=\"data row2 col6\" >0.0006</td>\n",
       "      <td id=\"T_a6d0c_row2_col7\" class=\"data row2 col7\" >Ų</td>\n",
       "      <td id=\"T_a6d0c_row2_col8\" class=\"data row2 col8\" >N/A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row3\" class=\"row_heading level0 row3\" >4</th>\n",
       "      <td id=\"T_a6d0c_row3_col0\" class=\"data row3 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row3_col1\" class=\"data row3 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row3_col2\" class=\"data row3 col2\" >O1</td>\n",
       "      <td id=\"T_a6d0c_row3_col3\" class=\"data row3 col3\" >fract_x</td>\n",
       "      <td id=\"T_a6d0c_row3_col4\" class=\"data row3 col4\" >0.3280</td>\n",
       "      <td id=\"T_a6d0c_row3_col5\" class=\"data row3 col5\" >0.3280</td>\n",
       "      <td id=\"T_a6d0c_row3_col6\" class=\"data row3 col6\" >0.0001</td>\n",
       "      <td id=\"T_a6d0c_row3_col7\" class=\"data row3 col7\" ></td>\n",
       "      <td id=\"T_a6d0c_row3_col8\" class=\"data row3 col8\" >0.00 % ↑</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row4\" class=\"row_heading level0 row4\" >5</th>\n",
       "      <td id=\"T_a6d0c_row4_col0\" class=\"data row4 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row4_col1\" class=\"data row4 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row4_col2\" class=\"data row4 col2\" >O1</td>\n",
       "      <td id=\"T_a6d0c_row4_col3\" class=\"data row4 col3\" >occupancy</td>\n",
       "      <td id=\"T_a6d0c_row4_col4\" class=\"data row4 col4\" >1.0000</td>\n",
       "      <td id=\"T_a6d0c_row4_col5\" class=\"data row4 col5\" >0.9989</td>\n",
       "      <td id=\"T_a6d0c_row4_col6\" class=\"data row4 col6\" >0.0104</td>\n",
       "      <td id=\"T_a6d0c_row4_col7\" class=\"data row4 col7\" ></td>\n",
       "      <td id=\"T_a6d0c_row4_col8\" class=\"data row4 col8\" >0.11 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row5\" class=\"row_heading level0 row5\" >6</th>\n",
       "      <td id=\"T_a6d0c_row5_col0\" class=\"data row5 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row5_col1\" class=\"data row5 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row5_col2\" class=\"data row5 col2\" >O1</td>\n",
       "      <td id=\"T_a6d0c_row5_col3\" class=\"data row5 col3\" >adp_iso</td>\n",
       "      <td id=\"T_a6d0c_row5_col4\" class=\"data row5 col4\" >0.0000</td>\n",
       "      <td id=\"T_a6d0c_row5_col5\" class=\"data row5 col5\" >0.0057</td>\n",
       "      <td id=\"T_a6d0c_row5_col6\" class=\"data row5 col6\" >0.0002</td>\n",
       "      <td id=\"T_a6d0c_row5_col7\" class=\"data row5 col7\" >Ų</td>\n",
       "      <td id=\"T_a6d0c_row5_col8\" class=\"data row5 col8\" >N/A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row6\" class=\"row_heading level0 row6\" >7</th>\n",
       "      <td id=\"T_a6d0c_row6_col0\" class=\"data row6 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row6_col1\" class=\"data row6 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row6_col2\" class=\"data row6 col2\" >O2</td>\n",
       "      <td id=\"T_a6d0c_row6_col3\" class=\"data row6 col3\" >occupancy</td>\n",
       "      <td id=\"T_a6d0c_row6_col4\" class=\"data row6 col4\" >0.9700</td>\n",
       "      <td id=\"T_a6d0c_row6_col5\" class=\"data row6 col5\" >0.9688</td>\n",
       "      <td id=\"T_a6d0c_row6_col6\" class=\"data row6 col6\" >0.0183</td>\n",
       "      <td id=\"T_a6d0c_row6_col7\" class=\"data row6 col7\" ></td>\n",
       "      <td id=\"T_a6d0c_row6_col8\" class=\"data row6 col8\" >0.12 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row7\" class=\"row_heading level0 row7\" >8</th>\n",
       "      <td id=\"T_a6d0c_row7_col0\" class=\"data row7 col0\" >tbti</td>\n",
       "      <td id=\"T_a6d0c_row7_col1\" class=\"data row7 col1\" >atom_site</td>\n",
       "      <td id=\"T_a6d0c_row7_col2\" class=\"data row7 col2\" >O2</td>\n",
       "      <td id=\"T_a6d0c_row7_col3\" class=\"data row7 col3\" >adp_iso</td>\n",
       "      <td id=\"T_a6d0c_row7_col4\" class=\"data row7 col4\" >0.0000</td>\n",
       "      <td id=\"T_a6d0c_row7_col5\" class=\"data row7 col5\" >0.0030</td>\n",
       "      <td id=\"T_a6d0c_row7_col6\" class=\"data row7 col6\" >0.0005</td>\n",
       "      <td id=\"T_a6d0c_row7_col7\" class=\"data row7 col7\" >Ų</td>\n",
       "      <td id=\"T_a6d0c_row7_col8\" class=\"data row7 col8\" >N/A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row8\" class=\"row_heading level0 row8\" >9</th>\n",
       "      <td id=\"T_a6d0c_row8_col0\" class=\"data row8 col0\" >heidi</td>\n",
       "      <td id=\"T_a6d0c_row8_col1\" class=\"data row8 col1\" >extinction</td>\n",
       "      <td id=\"T_a6d0c_row8_col2\" class=\"data row8 col2\" ></td>\n",
       "      <td id=\"T_a6d0c_row8_col3\" class=\"data row8 col3\" >radius</td>\n",
       "      <td id=\"T_a6d0c_row8_col4\" class=\"data row8 col4\" >10.0000</td>\n",
       "      <td id=\"T_a6d0c_row8_col5\" class=\"data row8 col5\" >26.4348</td>\n",
       "      <td id=\"T_a6d0c_row8_col6\" class=\"data row8 col6\" >1.0122</td>\n",
       "      <td id=\"T_a6d0c_row8_col7\" class=\"data row8 col7\" >μm</td>\n",
       "      <td id=\"T_a6d0c_row8_col8\" class=\"data row8 col8\" >164.35 % ↑</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_a6d0c_level0_row9\" class=\"row_heading level0 row9\" >10</th>\n",
       "      <td id=\"T_a6d0c_row9_col0\" class=\"data row9 col0\" >heidi</td>\n",
       "      <td id=\"T_a6d0c_row9_col1\" class=\"data row9 col1\" >linked_crystal</td>\n",
       "      <td id=\"T_a6d0c_row9_col2\" class=\"data row9 col2\" ></td>\n",
       "      <td id=\"T_a6d0c_row9_col3\" class=\"data row9 col3\" >scale</td>\n",
       "      <td id=\"T_a6d0c_row9_col4\" class=\"data row9 col4\" >1.0000</td>\n",
       "      <td id=\"T_a6d0c_row9_col5\" class=\"data row9 col5\" >2.9329</td>\n",
       "      <td id=\"T_a6d0c_row9_col6\" class=\"data row9 col6\" >0.0586</td>\n",
       "      <td id=\"T_a6d0c_row9_col7\" class=\"data row9 col7\" ></td>\n",
       "      <td id=\"T_a6d0c_row9_col8\" class=\"data row9 col8\" >193.29 % ↑</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f446b53fd90>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Show fit results summary\n",
    "project.analysis.display.fit_results()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "28",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:43.523711Z",
     "iopub.status.busy": "2026-04-14T14:55:43.523491Z",
     "iopub.status.idle": "2026-04-14T14:55:43.738793Z",
     "shell.execute_reply": "2026-04-14T14:55:43.737754Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mStructure 🧩 \u001b[0m\u001b[32m'tbti'\u001b[0m\u001b[1;34m as cif\u001b[0m\n"
     ]
    },
    {
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       "\n",
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       "                    var notebookEl = document.querySelector('.jp-Notebook') || \n",
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       "\n",
       "                    // Store result\n",
       "                    if (typeof IPython !== 'undefined' && IPython.notebook && IPython.notebook.kernel) {\n",
       "                        IPython.notebook.kernel.execute('_jupyter_dark_detect_result = ' + isDark);\n",
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     "metadata": {},
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    {
     "data": {
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       "\n",
       "            if (typeof IPython !== 'undefined' && IPython.notebook) {\n",
       "                IPython.notebook.kernel.execute(\"_jupyter_dark_detect_result = \" + \n",
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       "                     document.body.classList.contains('jp-mod-dark') ||\n",
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       "#T_735f5_row0_col0, #T_735f5_row1_col0, #T_735f5_row2_col0, #T_735f5_row3_col0, #T_735f5_row4_col0, #T_735f5_row5_col0, #T_735f5_row6_col0, #T_735f5_row7_col0, #T_735f5_row8_col0, #T_735f5_row9_col0, #T_735f5_row10_col0, #T_735f5_row11_col0, #T_735f5_row12_col0, #T_735f5_row13_col0, #T_735f5_row14_col0, #T_735f5_row15_col0, #T_735f5_row16_col0, #T_735f5_row17_col0, #T_735f5_row18_col0, #T_735f5_row19_col0, #T_735f5_row20_col0, #T_735f5_row21_col0, #T_735f5_row22_col0, #T_735f5_row23_col0, #T_735f5_row24_col0, #T_735f5_row25_col0, #T_735f5_row26_col0 {\n",
       "  text-align: left;\n",
       "}\n",
       "</style>\n",
       "<table id=\"T_735f5\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr>\n",
       "      <th class=\"blank level0\" >&nbsp;</th>\n",
       "      <th id=\"T_735f5_level0_col0\" class=\"col_heading level0 col0\" >CIF</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row0\" class=\"row_heading level0 row0\" >1</th>\n",
       "      <td id=\"T_735f5_row0_col0\" class=\"data row0 col0\" >data_tbti</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row1\" class=\"row_heading level0 row1\" >2</th>\n",
       "      <td id=\"T_735f5_row1_col0\" class=\"data row1 col0\" ></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row2\" class=\"row_heading level0 row2\" >3</th>\n",
       "      <td id=\"T_735f5_row2_col0\" class=\"data row2 col0\" >_cell.length_a 10.13000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row3\" class=\"row_heading level0 row3\" >4</th>\n",
       "      <td id=\"T_735f5_row3_col0\" class=\"data row3 col0\" >_cell.length_b 10.13000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row4\" class=\"row_heading level0 row4\" >5</th>\n",
       "      <td id=\"T_735f5_row4_col0\" class=\"data row4 col0\" >_cell.length_c 10.13000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row5\" class=\"row_heading level0 row5\" >6</th>\n",
       "      <td id=\"T_735f5_row5_col0\" class=\"data row5 col0\" >_cell.angle_alpha 90.00000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row6\" class=\"row_heading level0 row6\" >7</th>\n",
       "      <td id=\"T_735f5_row6_col0\" class=\"data row6 col0\" >_cell.angle_beta 90.00000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row7\" class=\"row_heading level0 row7\" >8</th>\n",
       "      <td id=\"T_735f5_row7_col0\" class=\"data row7 col0\" >_cell.angle_gamma 90.00000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row8\" class=\"row_heading level0 row8\" >9</th>\n",
       "      <td id=\"T_735f5_row8_col0\" class=\"data row8 col0\" ></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row9\" class=\"row_heading level0 row9\" >10</th>\n",
       "      <td id=\"T_735f5_row9_col0\" class=\"data row9 col0\" >_space_group.name_H-M_alt \"F d -3 m\"</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row10\" class=\"row_heading level0 row10\" >11</th>\n",
       "      <td id=\"T_735f5_row10_col0\" class=\"data row10 col0\" >_space_group.IT_coordinate_system_code 2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row11\" class=\"row_heading level0 row11\" >12</th>\n",
       "      <td id=\"T_735f5_row11_col0\" class=\"data row11 col0\" ></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row12\" class=\"row_heading level0 row12\" >13</th>\n",
       "      <td id=\"T_735f5_row12_col0\" class=\"data row12 col0\" >loop_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row13\" class=\"row_heading level0 row13\" >14</th>\n",
       "      <td id=\"T_735f5_row13_col0\" class=\"data row13 col0\" >_atom_site.label</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row14\" class=\"row_heading level0 row14\" >15</th>\n",
       "      <td id=\"T_735f5_row14_col0\" class=\"data row14 col0\" >_atom_site.type_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row15\" class=\"row_heading level0 row15\" >16</th>\n",
       "      <td id=\"T_735f5_row15_col0\" class=\"data row15 col0\" >_atom_site.fract_x</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row16\" class=\"row_heading level0 row16\" >17</th>\n",
       "      <td id=\"T_735f5_row16_col0\" class=\"data row16 col0\" >_atom_site.fract_y</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row17\" class=\"row_heading level0 row17\" >18</th>\n",
       "      <td id=\"T_735f5_row17_col0\" class=\"data row17 col0\" >_atom_site.fract_z</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row18\" class=\"row_heading level0 row18\" >19</th>\n",
       "      <td id=\"T_735f5_row18_col0\" class=\"data row18 col0\" >_atom_site.Wyckoff_letter</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row19\" class=\"row_heading level0 row19\" >20</th>\n",
       "      <td id=\"T_735f5_row19_col0\" class=\"data row19 col0\" >_atom_site.occupancy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row20\" class=\"row_heading level0 row20\" >21</th>\n",
       "      <td id=\"T_735f5_row20_col0\" class=\"data row20 col0\" >_atom_site.U_iso_or_equiv</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row21\" class=\"row_heading level0 row21\" >22</th>\n",
       "      <td id=\"T_735f5_row21_col0\" class=\"data row21 col0\" >_atom_site.adp_type</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row22\" class=\"row_heading level0 row22\" >23</th>\n",
       "      <td id=\"T_735f5_row22_col0\" class=\"data row22 col0\" >Tb Tb 0.50000000 0.50000000 0.50000000 d 1.00000000 0.00681683(28758) Uiso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row23\" class=\"row_heading level0 row23\" >24</th>\n",
       "      <td id=\"T_735f5_row23_col0\" class=\"data row23 col0\" >Ti Ti 0.00000000 0.00000000 0.00000000 c 0.97299648(1780992) 0.00539742(59789) Uiso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row24\" class=\"row_heading level0 row24\" >25</th>\n",
       "      <td id=\"T_735f5_row24_col0\" class=\"data row24 col0\" >O1 O 0.32804378(9395) 0.12500000 0.12500000 f 0.99893142(1039031) 0.00572628(24749) Uiso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row25\" class=\"row_heading level0 row25\" >26</th>\n",
       "      <td id=\"T_735f5_row25_col0\" class=\"data row25 col0\" >O2 O 0.37500000 0.37500000 0.37500000 b 0.96880340(1827132) 0.00302999(48336) Uiso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_735f5_level0_row26\" class=\"row_heading level0 row26\" >27</th>\n",
       "      <td id=\"T_735f5_row26_col0\" class=\"data row26 col0\" ></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f446b53fd90>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure.show_as_cif()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "29",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:43.740449Z",
     "iopub.status.busy": "2026-04-14T14:55:43.740253Z",
     "iopub.status.idle": "2026-04-14T14:55:43.745933Z",
     "shell.execute_reply": "2026-04-14T14:55:43.744579Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mDefined experiments 🔬\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1m[\u001b[0m\u001b[32m'heidi'\u001b[0m\u001b[1m]\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "project.experiments.show_names()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "30",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:43.747435Z",
     "iopub.status.busy": "2026-04-14T14:55:43.747264Z",
     "iopub.status.idle": "2026-04-14T14:55:43.770106Z",
     "shell.execute_reply": "2026-04-14T14:55:43.769260Z"
    }
   },
   "outputs": [
    {
     "data": {
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   ],
   "source": [
    "project.plotter.plot_meas_vs_calc(expt_name='heidi')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "31",
   "metadata": {},
   "source": [
    "## Step 5: Perform Analysis (ADP aniso)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "32",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:43.771808Z",
     "iopub.status.busy": "2026-04-14T14:55:43.771609Z",
     "iopub.status.idle": "2026-04-14T14:55:43.776710Z",
     "shell.execute_reply": "2026-04-14T14:55:43.775903Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.atom_sites['Tb'].adp_type = 'Uani'\n",
    "structure.atom_sites['Ti'].adp_type = 'Uani'\n",
    "structure.atom_sites['O1'].adp_type = 'Uani'\n",
    "# structure.atom_sites['O2'].adp_type = 'Uani'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "33",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:43.778221Z",
     "iopub.status.busy": "2026-04-14T14:55:43.778012Z",
     "iopub.status.idle": "2026-04-14T14:55:43.781454Z",
     "shell.execute_reply": "2026-04-14T14:55:43.780647Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loop_\n",
      "_atom_site_aniso.label\n",
      "_atom_site_aniso.U_11\n",
      "_atom_site_aniso.U_22\n",
      "_atom_site_aniso.U_33\n",
      "_atom_site_aniso.U_12\n",
      "_atom_site_aniso.U_13\n",
      "_atom_site_aniso.U_23\n",
      "Tb 0.00681683 0.00681683 0.00681683 0.00000000 0.00000000 0.00000000\n",
      "Ti 0.00539742 0.00539742 0.00539742 0.00000000 0.00000000 0.00000000\n",
      "O1 0.00572628 0.00572628 0.00572628 0.00000000 0.00000000 0.00000000\n",
      "O2 ? ? ? ? ? ?\n"
     ]
    }
   ],
   "source": [
    "print(structure.atom_site_aniso.as_cif)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "34",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:43.782938Z",
     "iopub.status.busy": "2026-04-14T14:55:43.782778Z",
     "iopub.status.idle": "2026-04-14T14:55:43.786296Z",
     "shell.execute_reply": "2026-04-14T14:55:43.785478Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.atom_site_aniso['Tb'].adp_11.free = True\n",
    "structure.atom_site_aniso['Tb'].adp_12.free = True\n",
    "structure.atom_site_aniso['Ti'].adp_11.free = True\n",
    "structure.atom_site_aniso['Ti'].adp_12.free = True\n",
    "structure.atom_site_aniso['O1'].adp_11.free = True\n",
    "structure.atom_site_aniso['O1'].adp_22.free = True\n",
    "structure.atom_site_aniso['O1'].adp_23.free = True\n",
    "# structure.atom_site_aniso['O2'].adp_11.free = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "35",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:43.787759Z",
     "iopub.status.busy": "2026-04-14T14:55:43.787604Z",
     "iopub.status.idle": "2026-04-14T14:55:46.803882Z",
     "shell.execute_reply": "2026-04-14T14:55:46.803179Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mStandard fitting\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📋 Using experiment 🔬 \u001b[32m'heidi'\u001b[0m for \u001b[32m'single'\u001b[0m fitting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "🚀 Starting fit process with \u001b[32m'lmfit \u001b[0m\u001b[32m(\u001b[0m\u001b[32mleastsq\u001b[0m\u001b[32m)\u001b[0m\u001b[32m'\u001b[0m\u001b[33m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📈 Goodness-of-fit \u001b[1m(\u001b[0mreduced χ²\u001b[1m)\u001b[0m change:\n"
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       "                    // Check JupyterLab theme\n",
       "                    if (document.body.classList.contains('jp-mod-dark') || \n",
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       "\n",
       "                    // Check theme attribute\n",
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       "\n",
       "                    // Check computed background color\n",
       "                    var notebookEl = document.querySelector('.jp-Notebook') || \n",
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       "                    }\n",
       "\n",
       "                    // Store result\n",
       "                    if (typeof IPython !== 'undefined' && IPython.notebook && IPython.notebook.kernel) {\n",
       "                        IPython.notebook.kernel.execute('_jupyter_dark_detect_result = ' + isDark);\n",
       "                    }\n",
       "                })();\n",
       "            "
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    {
     "data": {
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       "\n",
       "            if (typeof IPython !== 'undefined' && IPython.notebook) {\n",
       "                IPython.notebook.kernel.execute(\"_jupyter_dark_detect_result = \" + \n",
       "                    (document.body.classList.contains('theme-dark') || \n",
       "                     document.body.classList.contains('jp-mod-dark') ||\n",
       "                     (document.body.getAttribute('data-jp-theme-name') && \n",
       "                      document.body.getAttribute('data-jp-theme-name').includes('dark'))));\n",
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     "name": "stdout",
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     "text": [
      "🏆 Best goodness-of-fit \u001b[1m(\u001b[0mreduced χ²\u001b[1m)\u001b[0m is \u001b[1;36m2.94\u001b[0m at iteration \u001b[1;36m78\u001b[0m\n"
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ Fitting complete.\n"
     ]
    }
   ],
   "source": [
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "36",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:46.805473Z",
     "iopub.status.busy": "2026-04-14T14:55:46.805308Z",
     "iopub.status.idle": "2026-04-14T14:55:47.365988Z",
     "shell.execute_reply": "2026-04-14T14:55:47.365122Z"
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mFit results\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ Success: \u001b[3;92mTrue\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "⏱️ Fitting time: \u001b[1;36m2.57\u001b[0m seconds\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📏 Goodness-of-fit \u001b[1m(\u001b[0mreduced χ²\u001b[1m)\u001b[0m: \u001b[1;36m2.94\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📏 R-factor \u001b[1m(\u001b[0mRf\u001b[1m)\u001b[0m: \u001b[1;36m4.21\u001b[0m%\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📏 R-factor squared \u001b[1m(\u001b[0mRf²\u001b[1m)\u001b[0m: \u001b[1;36m6.61\u001b[0m%\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📏 Weighted R-factor \u001b[1m(\u001b[0mwR\u001b[1m)\u001b[0m: \u001b[1;36m13.29\u001b[0m%\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "📈 Fitted parameters:\n"
     ]
    },
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       "  text-align: left;\n",
       "}\n",
       "#T_4b60e_row0_col4, #T_4b60e_row0_col5, #T_4b60e_row0_col6, #T_4b60e_row0_col8, #T_4b60e_row1_col4, #T_4b60e_row1_col5, #T_4b60e_row1_col6, #T_4b60e_row1_col8, #T_4b60e_row2_col4, #T_4b60e_row2_col5, #T_4b60e_row2_col6, #T_4b60e_row2_col8, #T_4b60e_row3_col4, #T_4b60e_row3_col5, #T_4b60e_row3_col6, #T_4b60e_row3_col8, #T_4b60e_row4_col4, #T_4b60e_row4_col5, #T_4b60e_row4_col6, #T_4b60e_row4_col8, #T_4b60e_row5_col4, #T_4b60e_row5_col5, #T_4b60e_row5_col6, #T_4b60e_row5_col8, #T_4b60e_row6_col4, #T_4b60e_row6_col5, #T_4b60e_row6_col6, #T_4b60e_row6_col8, #T_4b60e_row7_col4, #T_4b60e_row7_col5, #T_4b60e_row7_col6, #T_4b60e_row7_col8, #T_4b60e_row8_col4, #T_4b60e_row8_col5, #T_4b60e_row8_col6, #T_4b60e_row8_col8, #T_4b60e_row9_col4, #T_4b60e_row9_col5, #T_4b60e_row9_col6, #T_4b60e_row9_col8, #T_4b60e_row10_col4, #T_4b60e_row10_col5, #T_4b60e_row10_col6, #T_4b60e_row10_col8, #T_4b60e_row11_col4, #T_4b60e_row11_col5, #T_4b60e_row11_col6, #T_4b60e_row11_col8, #T_4b60e_row12_col4, #T_4b60e_row12_col5, #T_4b60e_row12_col6, #T_4b60e_row12_col8, #T_4b60e_row13_col4, #T_4b60e_row13_col5, #T_4b60e_row13_col6, #T_4b60e_row13_col8 {\n",
       "  text-align: right;\n",
       "}\n",
       "</style>\n",
       "<table id=\"T_4b60e\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr>\n",
       "      <th class=\"blank level0\" >&nbsp;</th>\n",
       "      <th id=\"T_4b60e_level0_col0\" class=\"col_heading level0 col0\" >datablock</th>\n",
       "      <th id=\"T_4b60e_level0_col1\" class=\"col_heading level0 col1\" >category</th>\n",
       "      <th id=\"T_4b60e_level0_col2\" class=\"col_heading level0 col2\" >entry</th>\n",
       "      <th id=\"T_4b60e_level0_col3\" class=\"col_heading level0 col3\" >parameter</th>\n",
       "      <th id=\"T_4b60e_level0_col4\" class=\"col_heading level0 col4\" >start</th>\n",
       "      <th id=\"T_4b60e_level0_col5\" class=\"col_heading level0 col5\" >fitted</th>\n",
       "      <th id=\"T_4b60e_level0_col6\" class=\"col_heading level0 col6\" >uncertainty</th>\n",
       "      <th id=\"T_4b60e_level0_col7\" class=\"col_heading level0 col7\" >units</th>\n",
       "      <th id=\"T_4b60e_level0_col8\" class=\"col_heading level0 col8\" >change</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row0\" class=\"row_heading level0 row0\" >1</th>\n",
       "      <td id=\"T_4b60e_row0_col0\" class=\"data row0 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row0_col1\" class=\"data row0 col1\" >atom_site</td>\n",
       "      <td id=\"T_4b60e_row0_col2\" class=\"data row0 col2\" >Ti</td>\n",
       "      <td id=\"T_4b60e_row0_col3\" class=\"data row0 col3\" >occupancy</td>\n",
       "      <td id=\"T_4b60e_row0_col4\" class=\"data row0 col4\" >0.9730</td>\n",
       "      <td id=\"T_4b60e_row0_col5\" class=\"data row0 col5\" >0.9661</td>\n",
       "      <td id=\"T_4b60e_row0_col6\" class=\"data row0 col6\" >0.0085</td>\n",
       "      <td id=\"T_4b60e_row0_col7\" class=\"data row0 col7\" ></td>\n",
       "      <td id=\"T_4b60e_row0_col8\" class=\"data row0 col8\" >0.71 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row1\" class=\"row_heading level0 row1\" >2</th>\n",
       "      <td id=\"T_4b60e_row1_col0\" class=\"data row1 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row1_col1\" class=\"data row1 col1\" >atom_site</td>\n",
       "      <td id=\"T_4b60e_row1_col2\" class=\"data row1 col2\" >O1</td>\n",
       "      <td id=\"T_4b60e_row1_col3\" class=\"data row1 col3\" >fract_x</td>\n",
       "      <td id=\"T_4b60e_row1_col4\" class=\"data row1 col4\" >0.3280</td>\n",
       "      <td id=\"T_4b60e_row1_col5\" class=\"data row1 col5\" >0.3280</td>\n",
       "      <td id=\"T_4b60e_row1_col6\" class=\"data row1 col6\" >0.0000</td>\n",
       "      <td id=\"T_4b60e_row1_col7\" class=\"data row1 col7\" ></td>\n",
       "      <td id=\"T_4b60e_row1_col8\" class=\"data row1 col8\" >0.01 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row2\" class=\"row_heading level0 row2\" >3</th>\n",
       "      <td id=\"T_4b60e_row2_col0\" class=\"data row2 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row2_col1\" class=\"data row2 col1\" >atom_site</td>\n",
       "      <td id=\"T_4b60e_row2_col2\" class=\"data row2 col2\" >O1</td>\n",
       "      <td id=\"T_4b60e_row2_col3\" class=\"data row2 col3\" >occupancy</td>\n",
       "      <td id=\"T_4b60e_row2_col4\" class=\"data row2 col4\" >0.9989</td>\n",
       "      <td id=\"T_4b60e_row2_col5\" class=\"data row2 col5\" >0.9940</td>\n",
       "      <td id=\"T_4b60e_row2_col6\" class=\"data row2 col6\" >0.0050</td>\n",
       "      <td id=\"T_4b60e_row2_col7\" class=\"data row2 col7\" ></td>\n",
       "      <td id=\"T_4b60e_row2_col8\" class=\"data row2 col8\" >0.50 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row3\" class=\"row_heading level0 row3\" >4</th>\n",
       "      <td id=\"T_4b60e_row3_col0\" class=\"data row3 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row3_col1\" class=\"data row3 col1\" >atom_site</td>\n",
       "      <td id=\"T_4b60e_row3_col2\" class=\"data row3 col2\" >O2</td>\n",
       "      <td id=\"T_4b60e_row3_col3\" class=\"data row3 col3\" >occupancy</td>\n",
       "      <td id=\"T_4b60e_row3_col4\" class=\"data row3 col4\" >0.9688</td>\n",
       "      <td id=\"T_4b60e_row3_col5\" class=\"data row3 col5\" >0.9718</td>\n",
       "      <td id=\"T_4b60e_row3_col6\" class=\"data row3 col6\" >0.0088</td>\n",
       "      <td id=\"T_4b60e_row3_col7\" class=\"data row3 col7\" ></td>\n",
       "      <td id=\"T_4b60e_row3_col8\" class=\"data row3 col8\" >0.31 % ↑</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row4\" class=\"row_heading level0 row4\" >5</th>\n",
       "      <td id=\"T_4b60e_row4_col0\" class=\"data row4 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row4_col1\" class=\"data row4 col1\" >atom_site</td>\n",
       "      <td id=\"T_4b60e_row4_col2\" class=\"data row4 col2\" >O2</td>\n",
       "      <td id=\"T_4b60e_row4_col3\" class=\"data row4 col3\" >adp_iso</td>\n",
       "      <td id=\"T_4b60e_row4_col4\" class=\"data row4 col4\" >0.0030</td>\n",
       "      <td id=\"T_4b60e_row4_col5\" class=\"data row4 col5\" >0.0033</td>\n",
       "      <td id=\"T_4b60e_row4_col6\" class=\"data row4 col6\" >0.0002</td>\n",
       "      <td id=\"T_4b60e_row4_col7\" class=\"data row4 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row4_col8\" class=\"data row4 col8\" >7.87 % ↑</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row5\" class=\"row_heading level0 row5\" >6</th>\n",
       "      <td id=\"T_4b60e_row5_col0\" class=\"data row5 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row5_col1\" class=\"data row5 col1\" >atom_site_aniso</td>\n",
       "      <td id=\"T_4b60e_row5_col2\" class=\"data row5 col2\" >Tb</td>\n",
       "      <td id=\"T_4b60e_row5_col3\" class=\"data row5 col3\" >adp_11</td>\n",
       "      <td id=\"T_4b60e_row5_col4\" class=\"data row5 col4\" >0.0068</td>\n",
       "      <td id=\"T_4b60e_row5_col5\" class=\"data row5 col5\" >0.0066</td>\n",
       "      <td id=\"T_4b60e_row5_col6\" class=\"data row5 col6\" >0.0001</td>\n",
       "      <td id=\"T_4b60e_row5_col7\" class=\"data row5 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row5_col8\" class=\"data row5 col8\" >3.45 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row6\" class=\"row_heading level0 row6\" >7</th>\n",
       "      <td id=\"T_4b60e_row6_col0\" class=\"data row6 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row6_col1\" class=\"data row6 col1\" >atom_site_aniso</td>\n",
       "      <td id=\"T_4b60e_row6_col2\" class=\"data row6 col2\" >Tb</td>\n",
       "      <td id=\"T_4b60e_row6_col3\" class=\"data row6 col3\" >adp_12</td>\n",
       "      <td id=\"T_4b60e_row6_col4\" class=\"data row6 col4\" >0.0000</td>\n",
       "      <td id=\"T_4b60e_row6_col5\" class=\"data row6 col5\" >-0.0023</td>\n",
       "      <td id=\"T_4b60e_row6_col6\" class=\"data row6 col6\" >0.0001</td>\n",
       "      <td id=\"T_4b60e_row6_col7\" class=\"data row6 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row6_col8\" class=\"data row6 col8\" >N/A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row7\" class=\"row_heading level0 row7\" >8</th>\n",
       "      <td id=\"T_4b60e_row7_col0\" class=\"data row7 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row7_col1\" class=\"data row7 col1\" >atom_site_aniso</td>\n",
       "      <td id=\"T_4b60e_row7_col2\" class=\"data row7 col2\" >Ti</td>\n",
       "      <td id=\"T_4b60e_row7_col3\" class=\"data row7 col3\" >adp_11</td>\n",
       "      <td id=\"T_4b60e_row7_col4\" class=\"data row7 col4\" >0.0054</td>\n",
       "      <td id=\"T_4b60e_row7_col5\" class=\"data row7 col5\" >0.0049</td>\n",
       "      <td id=\"T_4b60e_row7_col6\" class=\"data row7 col6\" >0.0003</td>\n",
       "      <td id=\"T_4b60e_row7_col7\" class=\"data row7 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row7_col8\" class=\"data row7 col8\" >9.56 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row8\" class=\"row_heading level0 row8\" >9</th>\n",
       "      <td id=\"T_4b60e_row8_col0\" class=\"data row8 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row8_col1\" class=\"data row8 col1\" >atom_site_aniso</td>\n",
       "      <td id=\"T_4b60e_row8_col2\" class=\"data row8 col2\" >Ti</td>\n",
       "      <td id=\"T_4b60e_row8_col3\" class=\"data row8 col3\" >adp_12</td>\n",
       "      <td id=\"T_4b60e_row8_col4\" class=\"data row8 col4\" >0.0000</td>\n",
       "      <td id=\"T_4b60e_row8_col5\" class=\"data row8 col5\" >-0.0005</td>\n",
       "      <td id=\"T_4b60e_row8_col6\" class=\"data row8 col6\" >0.0002</td>\n",
       "      <td id=\"T_4b60e_row8_col7\" class=\"data row8 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row8_col8\" class=\"data row8 col8\" >N/A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row9\" class=\"row_heading level0 row9\" >10</th>\n",
       "      <td id=\"T_4b60e_row9_col0\" class=\"data row9 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row9_col1\" class=\"data row9 col1\" >atom_site_aniso</td>\n",
       "      <td id=\"T_4b60e_row9_col2\" class=\"data row9 col2\" >O1</td>\n",
       "      <td id=\"T_4b60e_row9_col3\" class=\"data row9 col3\" >adp_11</td>\n",
       "      <td id=\"T_4b60e_row9_col4\" class=\"data row9 col4\" >0.0057</td>\n",
       "      <td id=\"T_4b60e_row9_col5\" class=\"data row9 col5\" >0.0067</td>\n",
       "      <td id=\"T_4b60e_row9_col6\" class=\"data row9 col6\" >0.0002</td>\n",
       "      <td id=\"T_4b60e_row9_col7\" class=\"data row9 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row9_col8\" class=\"data row9 col8\" >17.67 % ↑</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row10\" class=\"row_heading level0 row10\" >11</th>\n",
       "      <td id=\"T_4b60e_row10_col0\" class=\"data row10 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row10_col1\" class=\"data row10 col1\" >atom_site_aniso</td>\n",
       "      <td id=\"T_4b60e_row10_col2\" class=\"data row10 col2\" >O1</td>\n",
       "      <td id=\"T_4b60e_row10_col3\" class=\"data row10 col3\" >adp_22</td>\n",
       "      <td id=\"T_4b60e_row10_col4\" class=\"data row10 col4\" >0.0057</td>\n",
       "      <td id=\"T_4b60e_row10_col5\" class=\"data row10 col5\" >0.0049</td>\n",
       "      <td id=\"T_4b60e_row10_col6\" class=\"data row10 col6\" >0.0001</td>\n",
       "      <td id=\"T_4b60e_row10_col7\" class=\"data row10 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row10_col8\" class=\"data row10 col8\" >14.61 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row11\" class=\"row_heading level0 row11\" >12</th>\n",
       "      <td id=\"T_4b60e_row11_col0\" class=\"data row11 col0\" >tbti</td>\n",
       "      <td id=\"T_4b60e_row11_col1\" class=\"data row11 col1\" >atom_site_aniso</td>\n",
       "      <td id=\"T_4b60e_row11_col2\" class=\"data row11 col2\" >O1</td>\n",
       "      <td id=\"T_4b60e_row11_col3\" class=\"data row11 col3\" >adp_23</td>\n",
       "      <td id=\"T_4b60e_row11_col4\" class=\"data row11 col4\" >0.0000</td>\n",
       "      <td id=\"T_4b60e_row11_col5\" class=\"data row11 col5\" >0.0019</td>\n",
       "      <td id=\"T_4b60e_row11_col6\" class=\"data row11 col6\" >0.0001</td>\n",
       "      <td id=\"T_4b60e_row11_col7\" class=\"data row11 col7\" >Ų</td>\n",
       "      <td id=\"T_4b60e_row11_col8\" class=\"data row11 col8\" >N/A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row12\" class=\"row_heading level0 row12\" >13</th>\n",
       "      <td id=\"T_4b60e_row12_col0\" class=\"data row12 col0\" >heidi</td>\n",
       "      <td id=\"T_4b60e_row12_col1\" class=\"data row12 col1\" >extinction</td>\n",
       "      <td id=\"T_4b60e_row12_col2\" class=\"data row12 col2\" ></td>\n",
       "      <td id=\"T_4b60e_row12_col3\" class=\"data row12 col3\" >radius</td>\n",
       "      <td id=\"T_4b60e_row12_col4\" class=\"data row12 col4\" >26.4348</td>\n",
       "      <td id=\"T_4b60e_row12_col5\" class=\"data row12 col5\" >24.8317</td>\n",
       "      <td id=\"T_4b60e_row12_col6\" class=\"data row12 col6\" >0.4931</td>\n",
       "      <td id=\"T_4b60e_row12_col7\" class=\"data row12 col7\" >μm</td>\n",
       "      <td id=\"T_4b60e_row12_col8\" class=\"data row12 col8\" >6.06 % ↓</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_4b60e_level0_row13\" class=\"row_heading level0 row13\" >14</th>\n",
       "      <td id=\"T_4b60e_row13_col0\" class=\"data row13 col0\" >heidi</td>\n",
       "      <td id=\"T_4b60e_row13_col1\" class=\"data row13 col1\" >linked_crystal</td>\n",
       "      <td id=\"T_4b60e_row13_col2\" class=\"data row13 col2\" ></td>\n",
       "      <td id=\"T_4b60e_row13_col3\" class=\"data row13 col3\" >scale</td>\n",
       "      <td id=\"T_4b60e_row13_col4\" class=\"data row13 col4\" >2.9329</td>\n",
       "      <td id=\"T_4b60e_row13_col5\" class=\"data row13 col5\" >2.8744</td>\n",
       "      <td id=\"T_4b60e_row13_col6\" class=\"data row13 col6\" >0.0274</td>\n",
       "      <td id=\"T_4b60e_row13_col7\" class=\"data row13 col7\" ></td>\n",
       "      <td id=\"T_4b60e_row13_col8\" class=\"data row13 col8\" >1.99 % ↓</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f446b53d810>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "project.analysis.display.fit_results()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "37",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T14:55:47.367821Z",
     "iopub.status.busy": "2026-04-14T14:55:47.367622Z",
     "iopub.status.idle": "2026-04-14T14:55:47.813399Z",
     "shell.execute_reply": "2026-04-14T14:55:47.812632Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "\n",
       "                (function() {\n",
       "                    var isDark = false;\n",
       "\n",
       "                    // Check JupyterLab theme\n",
       "                    if (document.body.classList.contains('jp-mod-dark') || \n",
       "                        document.body.classList.contains('theme-dark') ||\n",
       "                        document.body.classList.contains('vscode-dark')) {\n",
       "                        isDark = true;\n",
       "                    }\n",
       "\n",
       "                    // Check theme attribute\n",
       "                    var themeAttr = document.body.getAttribute('data-jp-theme-name');\n",
       "                    if (themeAttr && themeAttr.includes('dark')) {\n",
       "                        isDark = true;\n",
       "                    }\n",
       "\n",
       "                    // Check computed background color\n",
       "                    var notebookEl = document.querySelector('.jp-Notebook') || \n",
       "                                   document.querySelector('.notebook_app') ||\n",
       "                                   document.body;\n",
       "                    if (notebookEl) {\n",
       "                        var bgColor = window.getComputedStyle(notebookEl).backgroundColor;\n",
       "                        var rgb = bgColor.match(/\\d+/g);\n",
       "                        if (rgb && rgb.length >= 3) {\n",
       "                            var brightness = (parseInt(rgb[0]) + parseInt(rgb[1]) + parseInt(rgb[2])) / 3;\n",
       "                            if (brightness < 128) {\n",
       "                                isDark = true;\n",
       "                            }\n",
       "                        }\n",
       "                    }\n",
       "\n",
       "                    // Store result\n",
       "                    if (typeof IPython !== 'undefined' && IPython.notebook && IPython.notebook.kernel) {\n",
       "                        IPython.notebook.kernel.execute('_jupyter_dark_detect_result = ' + isDark);\n",
       "                    }\n",
       "                })();\n",
       "            "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "\n",
       "            if (typeof IPython !== 'undefined' && IPython.notebook) {\n",
       "                IPython.notebook.kernel.execute(\"_jupyter_dark_detect_result = \" + \n",
       "                    (document.body.classList.contains('theme-dark') || \n",
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       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row19\" class=\"row_heading level0 row19\" >20</th>\n",
       "      <td id=\"T_e7ca4_row19_col0\" class=\"data row19 col0\" >_atom_site.occupancy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row20\" class=\"row_heading level0 row20\" >21</th>\n",
       "      <td id=\"T_e7ca4_row20_col0\" class=\"data row20 col0\" >_atom_site.U_iso_or_equiv</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row21\" class=\"row_heading level0 row21\" >22</th>\n",
       "      <td id=\"T_e7ca4_row21_col0\" class=\"data row21 col0\" >_atom_site.adp_type</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row22\" class=\"row_heading level0 row22\" >23</th>\n",
       "      <td id=\"T_e7ca4_row22_col0\" class=\"data row22 col0\" >Tb Tb 0.50000000 0.50000000 0.50000000 d 1.00000000 0.00658189 Uani</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row23\" class=\"row_heading level0 row23\" >24</th>\n",
       "      <td id=\"T_e7ca4_row23_col0\" class=\"data row23 col0\" >Ti Ti 0.00000000 0.00000000 0.00000000 c 0.96606424(850635) 0.00488144 Uani</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row24\" class=\"row_heading level0 row24\" >25</th>\n",
       "      <td id=\"T_e7ca4_row24_col0\" class=\"data row24 col0\" >O1 O 0.32799582(4713) 0.12500000 0.12500000 f 0.99395914(497554) 0.00550586 Uani</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row25\" class=\"row_heading level0 row25\" >26</th>\n",
       "      <td id=\"T_e7ca4_row25_col0\" class=\"data row25 col0\" >O2 O 0.37500000 0.37500000 0.37500000 b 0.97182102(883817) 0.00326851(23641) Uiso</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row26\" class=\"row_heading level0 row26\" >27</th>\n",
       "      <td id=\"T_e7ca4_row26_col0\" class=\"data row26 col0\" ></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row27\" class=\"row_heading level0 row27\" >28</th>\n",
       "      <td id=\"T_e7ca4_row27_col0\" class=\"data row27 col0\" >loop_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row28\" class=\"row_heading level0 row28\" >29</th>\n",
       "      <td id=\"T_e7ca4_row28_col0\" class=\"data row28 col0\" >_atom_site_aniso.label</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row29\" class=\"row_heading level0 row29\" >30</th>\n",
       "      <td id=\"T_e7ca4_row29_col0\" class=\"data row29 col0\" >_atom_site_aniso.U_11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row30\" class=\"row_heading level0 row30\" >31</th>\n",
       "      <td id=\"T_e7ca4_row30_col0\" class=\"data row30 col0\" >_atom_site_aniso.U_22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row31\" class=\"row_heading level0 row31\" >32</th>\n",
       "      <td id=\"T_e7ca4_row31_col0\" class=\"data row31 col0\" >_atom_site_aniso.U_33</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row32\" class=\"row_heading level0 row32\" >33</th>\n",
       "      <td id=\"T_e7ca4_row32_col0\" class=\"data row32 col0\" >_atom_site_aniso.U_12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row33\" class=\"row_heading level0 row33\" >34</th>\n",
       "      <td id=\"T_e7ca4_row33_col0\" class=\"data row33 col0\" >_atom_site_aniso.U_13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row34\" class=\"row_heading level0 row34\" >35</th>\n",
       "      <td id=\"T_e7ca4_row34_col0\" class=\"data row34 col0\" >_atom_site_aniso.U_23</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row35\" class=\"row_heading level0 row35\" >36</th>\n",
       "      <td id=\"T_e7ca4_row35_col0\" class=\"data row35 col0\" >Tb 0.00658189(13905) 0.00658189 0.00658189 -0.00228459(11215) -0.00228459 -0.00228459</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row36\" class=\"row_heading level0 row36\" >37</th>\n",
       "      <td id=\"T_e7ca4_row36_col0\" class=\"data row36 col0\" >Ti 0.00488144(28692) 0.00488144 0.00488144 -0.00048176(24537) -0.00048176 -0.00048176</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row37\" class=\"row_heading level0 row37\" >38</th>\n",
       "      <td id=\"T_e7ca4_row37_col0\" class=\"data row37 col0\" >O1 0.00673797(18380) 0.00488980(13460) 0.00488980 0.00000000 0.00000000 0.00188994(12724)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th id=\"T_e7ca4_level0_row38\" class=\"row_heading level0 row38\" >39</th>\n",
       "      <td id=\"T_e7ca4_row38_col0\" class=\"data row38 col0\" >O2 ? ? ? ? ? ?</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f446b5f4a50>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure.show_as_cif()"
   ]
  }
 ],
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