{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "0",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:11.629913Z",
     "iopub.status.busy": "2026-06-04T16:27:11.629756Z",
     "iopub.status.idle": "2026-06-04T16:27:11.633587Z",
     "shell.execute_reply": "2026-06-04T16:27:11.632777Z"
    },
    "tags": [
     "hide-in-docs"
    ]
   },
   "outputs": [],
   "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==0.18.0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1",
   "metadata": {},
   "source": [
    "# Structure Refinement: PbSO4, NPD + XRD\n",
    "\n",
    "This example demonstrates a more advanced use of the EasyDiffraction\n",
    "library by explicitly creating and configuring structures and\n",
    "experiments before adding them to a project. It could be more suitable\n",
    "for users who are interested in creating custom workflows. This\n",
    "tutorial provides minimal explanation and is intended for users\n",
    "already familiar with EasyDiffraction.\n",
    "\n",
    "The tutorial covers a Rietveld refinement of PbSO4 crystal structure\n",
    "based on the joint fit of both X-ray and neutron diffraction data."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2",
   "metadata": {},
   "source": [
    "## 🛠️ Import Library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:11.635276Z",
     "iopub.status.busy": "2026-06-04T16:27:11.635076Z",
     "iopub.status.idle": "2026-06-04T16:27:14.358933Z",
     "shell.execute_reply": "2026-06-04T16:27:14.358014Z"
    }
   },
   "outputs": [],
   "source": [
    "from easydiffraction import ExperimentFactory\n",
    "from easydiffraction import Project\n",
    "from easydiffraction import StructureFactory\n",
    "from easydiffraction import download_data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4",
   "metadata": {},
   "source": [
    "## 🧩 Define Structure\n",
    "\n",
    "This section shows how to add structures and modify their\n",
    "parameters.\n",
    "\n",
    "### Create Structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "5",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.360712Z",
     "iopub.status.busy": "2026-06-04T16:27:14.360421Z",
     "iopub.status.idle": "2026-06-04T16:27:14.365190Z",
     "shell.execute_reply": "2026-06-04T16:27:14.364340Z"
    }
   },
   "outputs": [],
   "source": [
    "structure = StructureFactory.from_scratch(name='pbso4')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6",
   "metadata": {},
   "source": [
    "### Set Space Group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "7",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.366764Z",
     "iopub.status.busy": "2026-06-04T16:27:14.366610Z",
     "iopub.status.idle": "2026-06-04T16:27:14.369369Z",
     "shell.execute_reply": "2026-06-04T16:27:14.368768Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.space_group.name_h_m = 'P n m a'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8",
   "metadata": {},
   "source": [
    "### Set Unit Cell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "9",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.371105Z",
     "iopub.status.busy": "2026-06-04T16:27:14.370955Z",
     "iopub.status.idle": "2026-06-04T16:27:14.374090Z",
     "shell.execute_reply": "2026-06-04T16:27:14.373244Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.cell.length_a = 8.47\n",
    "structure.cell.length_b = 5.39\n",
    "structure.cell.length_c = 6.95"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "10",
   "metadata": {},
   "source": [
    "### Set Atom Sites"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "11",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.375543Z",
     "iopub.status.busy": "2026-06-04T16:27:14.375380Z",
     "iopub.status.idle": "2026-06-04T16:27:14.382664Z",
     "shell.execute_reply": "2026-06-04T16:27:14.381629Z"
    },
    "lines_to_next_cell": 2
   },
   "outputs": [],
   "source": [
    "structure.atom_sites.create(\n",
    "    label='Pb',\n",
    "    type_symbol='Pb',\n",
    "    fract_x=0.1876,\n",
    "    fract_y=0.25,\n",
    "    fract_z=0.167,\n",
    "    adp_iso=1.37,\n",
    ")\n",
    "structure.atom_sites.create(\n",
    "    label='S',\n",
    "    type_symbol='S',\n",
    "    fract_x=0.0654,\n",
    "    fract_y=0.25,\n",
    "    fract_z=0.684,\n",
    "    adp_iso=0.3777,\n",
    ")\n",
    "structure.atom_sites.create(\n",
    "    label='O1',\n",
    "    type_symbol='O',\n",
    "    fract_x=0.9082,\n",
    "    fract_y=0.25,\n",
    "    fract_z=0.5954,\n",
    "    adp_iso=1.9764,\n",
    ")\n",
    "structure.atom_sites.create(\n",
    "    label='O2',\n",
    "    type_symbol='O',\n",
    "    fract_x=0.1935,\n",
    "    fract_y=0.25,\n",
    "    fract_z=0.5432,\n",
    "    adp_iso=1.4456,\n",
    ")\n",
    "structure.atom_sites.create(\n",
    "    label='O3',\n",
    "    type_symbol='O',\n",
    "    fract_x=0.0811,\n",
    "    fract_y=0.0272,\n",
    "    fract_z=0.8086,\n",
    "    adp_iso=1.2822,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "12",
   "metadata": {},
   "source": [
    "## 🔬 Define Experiments\n",
    "\n",
    "This section shows how to add experiments, configure their parameters,\n",
    "and link the structures defined in the previous step.\n",
    "\n",
    "### Experiment 1: npd\n",
    "\n",
    "#### Download Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "13",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.384291Z",
     "iopub.status.busy": "2026-06-04T16:27:14.384123Z",
     "iopub.status.idle": "2026-06-04T16:27:14.560343Z",
     "shell.execute_reply": "2026-06-04T16:27:14.559744Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;36mGetting data\u001b[0m\u001b[1;36m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data #\u001b[1;36m13\u001b[0m: PbSO4, D1A \u001b[1m(\u001b[0mILL\u001b[1m)\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ Data #\u001b[1;36m13\u001b[0m downloaded to \u001b[32m'../../../data/ed-13.dat'\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "data_path1 = download_data(id=13, destination='data')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "14",
   "metadata": {},
   "source": [
    "#### Create Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "15",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.562406Z",
     "iopub.status.busy": "2026-06-04T16:27:14.562239Z",
     "iopub.status.idle": "2026-06-04T16:27:14.788731Z",
     "shell.execute_reply": "2026-06-04T16:27:14.787833Z"
    }
   },
   "outputs": [],
   "source": [
    "expt1 = ExperimentFactory.from_data_path(\n",
    "    name='npd',\n",
    "    data_path=data_path1,\n",
    "    radiation_probe='neutron',\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "16",
   "metadata": {},
   "source": [
    "#### Set Instrument"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "17",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.790484Z",
     "iopub.status.busy": "2026-06-04T16:27:14.790261Z",
     "iopub.status.idle": "2026-06-04T16:27:14.793725Z",
     "shell.execute_reply": "2026-06-04T16:27:14.792950Z"
    }
   },
   "outputs": [],
   "source": [
    "expt1.instrument.setup_wavelength = 1.91\n",
    "expt1.instrument.calib_twotheta_offset = -0.1406"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "18",
   "metadata": {},
   "source": [
    "#### Set Peak Profile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "19",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.795419Z",
     "iopub.status.busy": "2026-06-04T16:27:14.795258Z",
     "iopub.status.idle": "2026-06-04T16:27:14.799196Z",
     "shell.execute_reply": "2026-06-04T16:27:14.798424Z"
    }
   },
   "outputs": [],
   "source": [
    "expt1.peak.broad_gauss_u = 0.139\n",
    "expt1.peak.broad_gauss_v = -0.412\n",
    "expt1.peak.broad_gauss_w = 0.386\n",
    "expt1.peak.broad_lorentz_x = 0\n",
    "expt1.peak.broad_lorentz_y = 0.088"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "20",
   "metadata": {},
   "source": [
    "#### Set Background"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "21",
   "metadata": {},
   "source": [
    "Select the background type."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "22",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.801091Z",
     "iopub.status.busy": "2026-06-04T16:27:14.800854Z",
     "iopub.status.idle": "2026-06-04T16:27:14.806274Z",
     "shell.execute_reply": "2026-06-04T16:27:14.805363Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;36mBackground type for experiment \u001b[0m\u001b[32m'npd'\u001b[0m\u001b[1;36m already set to\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "line-segment\n"
     ]
    }
   ],
   "source": [
    "expt1.background.type = 'line-segment'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "23",
   "metadata": {},
   "source": [
    "Add background points."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "24",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.808437Z",
     "iopub.status.busy": "2026-06-04T16:27:14.808258Z",
     "iopub.status.idle": "2026-06-04T16:27:14.814093Z",
     "shell.execute_reply": "2026-06-04T16:27:14.813322Z"
    }
   },
   "outputs": [],
   "source": [
    "for id, x, y in [\n",
    "    ('1', 11.0, 206.1624),\n",
    "    ('2', 15.0, 194.75),\n",
    "    ('3', 20.0, 194.505),\n",
    "    ('4', 30.0, 188.4375),\n",
    "    ('5', 50.0, 207.7633),\n",
    "    ('6', 70.0, 201.7002),\n",
    "    ('7', 120.0, 244.4525),\n",
    "    ('8', 153.0, 226.0595),\n",
    "]:\n",
    "    expt1.background.create(id=id, x=x, y=y)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "25",
   "metadata": {},
   "source": [
    "#### Set Linked Phases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "26",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.815507Z",
     "iopub.status.busy": "2026-06-04T16:27:14.815334Z",
     "iopub.status.idle": "2026-06-04T16:27:14.818338Z",
     "shell.execute_reply": "2026-06-04T16:27:14.817643Z"
    }
   },
   "outputs": [],
   "source": [
    "expt1.linked_phases.create(id='pbso4', scale=1.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "27",
   "metadata": {},
   "source": [
    "### Experiment 2: xrd\n",
    "\n",
    "#### Download Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "28",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.819832Z",
     "iopub.status.busy": "2026-06-04T16:27:14.819687Z",
     "iopub.status.idle": "2026-06-04T16:27:14.919678Z",
     "shell.execute_reply": "2026-06-04T16:27:14.918917Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;36mGetting data\u001b[0m\u001b[1;36m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data #\u001b[1;36m16\u001b[0m: PbSO4, laboratory X-ray\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✅ Data #\u001b[1;36m16\u001b[0m downloaded to \u001b[32m'../../../data/ed-16.dat'\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "data_path2 = download_data(id=16, destination='data')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "29",
   "metadata": {},
   "source": [
    "#### Create Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "30",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:14.921513Z",
     "iopub.status.busy": "2026-06-04T16:27:14.921347Z",
     "iopub.status.idle": "2026-06-04T16:27:15.358546Z",
     "shell.execute_reply": "2026-06-04T16:27:15.357842Z"
    }
   },
   "outputs": [],
   "source": [
    "expt2 = ExperimentFactory.from_data_path(\n",
    "    name='xrd',\n",
    "    data_path=data_path2,\n",
    "    radiation_probe='xray',\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "31",
   "metadata": {},
   "source": [
    "#### Set Instrument"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "32",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.360901Z",
     "iopub.status.busy": "2026-06-04T16:27:15.360726Z",
     "iopub.status.idle": "2026-06-04T16:27:15.363776Z",
     "shell.execute_reply": "2026-06-04T16:27:15.362958Z"
    }
   },
   "outputs": [],
   "source": [
    "expt2.instrument.setup_wavelength = 1.540567\n",
    "expt2.instrument.calib_twotheta_offset = -0.05181"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "33",
   "metadata": {},
   "source": [
    "#### Set Peak Profile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "34",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.365218Z",
     "iopub.status.busy": "2026-06-04T16:27:15.365051Z",
     "iopub.status.idle": "2026-06-04T16:27:15.368287Z",
     "shell.execute_reply": "2026-06-04T16:27:15.367528Z"
    }
   },
   "outputs": [],
   "source": [
    "expt2.peak.broad_gauss_u = 0.304138\n",
    "expt2.peak.broad_gauss_v = -0.112622\n",
    "expt2.peak.broad_gauss_w = 0.021272\n",
    "expt2.peak.broad_lorentz_x = 0\n",
    "expt2.peak.broad_lorentz_y = 0.057691"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "35",
   "metadata": {},
   "source": [
    "#### Set Background"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "36",
   "metadata": {},
   "source": [
    "Select background type."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "37",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.369856Z",
     "iopub.status.busy": "2026-06-04T16:27:15.369652Z",
     "iopub.status.idle": "2026-06-04T16:27:15.374587Z",
     "shell.execute_reply": "2026-06-04T16:27:15.373859Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;36mBackground type for experiment \u001b[0m\u001b[32m'xrd'\u001b[0m\u001b[1;36m changed to\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "chebyshev\n"
     ]
    }
   ],
   "source": [
    "expt2.background.type = 'chebyshev'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "38",
   "metadata": {},
   "source": [
    "Add background points."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "39",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.376009Z",
     "iopub.status.busy": "2026-06-04T16:27:15.375848Z",
     "iopub.status.idle": "2026-06-04T16:27:15.380109Z",
     "shell.execute_reply": "2026-06-04T16:27:15.379380Z"
    }
   },
   "outputs": [],
   "source": [
    "for id, x, y in [\n",
    "    ('1', 0, 119.195),\n",
    "    ('2', 1, 6.221),\n",
    "    ('3', 2, -45.725),\n",
    "    ('4', 3, 8.119),\n",
    "    ('5', 4, 54.552),\n",
    "    ('6', 5, -20.661),\n",
    "]:\n",
    "    expt2.background.create(id=id, order=x, coef=y)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "40",
   "metadata": {},
   "source": [
    "#### Set Linked Phases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "41",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.381842Z",
     "iopub.status.busy": "2026-06-04T16:27:15.381642Z",
     "iopub.status.idle": "2026-06-04T16:27:15.385071Z",
     "shell.execute_reply": "2026-06-04T16:27:15.384228Z"
    }
   },
   "outputs": [],
   "source": [
    "expt2.linked_phases.create(id='pbso4', scale=0.001)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "42",
   "metadata": {},
   "source": [
    "## 📦 Define Project\n",
    "\n",
    "The project object is used to manage structures, experiments, and\n",
    "analysis.\n",
    "\n",
    "### Create Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "43",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.386553Z",
     "iopub.status.busy": "2026-06-04T16:27:15.386405Z",
     "iopub.status.idle": "2026-06-04T16:27:15.870344Z",
     "shell.execute_reply": "2026-06-04T16:27:15.869493Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "                })();\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",
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     "metadata": {},
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   ],
   "source": [
    "project = Project(name='pbso4_joint')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "44",
   "metadata": {},
   "source": [
    "### Add Structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "45",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.872078Z",
     "iopub.status.busy": "2026-06-04T16:27:15.871908Z",
     "iopub.status.idle": "2026-06-04T16:27:15.874845Z",
     "shell.execute_reply": "2026-06-04T16:27:15.874036Z"
    }
   },
   "outputs": [],
   "source": [
    "project.structures.add(structure)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "46",
   "metadata": {},
   "source": [
    "### Add Experiments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "47",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.876336Z",
     "iopub.status.busy": "2026-06-04T16:27:15.876169Z",
     "iopub.status.idle": "2026-06-04T16:27:15.879173Z",
     "shell.execute_reply": "2026-06-04T16:27:15.878403Z"
    }
   },
   "outputs": [],
   "source": [
    "project.experiments.add(expt1)\n",
    "project.experiments.add(expt2)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "48",
   "metadata": {},
   "source": [
    "## 🚀 Perform Analysis\n",
    "\n",
    "This section outlines the analysis process, including how to configure\n",
    "calculation and fitting engines.\n",
    "\n",
    "### Set Fit Mode"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "49",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.880787Z",
     "iopub.status.busy": "2026-06-04T16:27:15.880626Z",
     "iopub.status.idle": "2026-06-04T16:27:15.885221Z",
     "shell.execute_reply": "2026-06-04T16:27:15.884464Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;36mFitting mode changed to\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "joint\n"
     ]
    }
   ],
   "source": [
    "project.analysis.fitting_mode.type = 'joint'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "50",
   "metadata": {},
   "source": [
    "### Set Minimizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "51",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.886762Z",
     "iopub.status.busy": "2026-06-04T16:27:15.886603Z",
     "iopub.status.idle": "2026-06-04T16:27:15.891632Z",
     "shell.execute_reply": "2026-06-04T16:27:15.890546Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;36mCurrent minimizer changed to\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lmfit\n"
     ]
    }
   ],
   "source": [
    "project.analysis.minimizer.type = 'lmfit'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "52",
   "metadata": {},
   "source": [
    "### Set Free Parameters\n",
    "\n",
    "Set structure parameters to be optimized."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "53",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.893063Z",
     "iopub.status.busy": "2026-06-04T16:27:15.892920Z",
     "iopub.status.idle": "2026-06-04T16:27:15.896834Z",
     "shell.execute_reply": "2026-06-04T16:27:15.895770Z"
    }
   },
   "outputs": [],
   "source": [
    "structure.cell.length_a.free = True\n",
    "structure.cell.length_b.free = True\n",
    "structure.cell.length_c.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "54",
   "metadata": {},
   "source": [
    "Set experiment parameters to be optimized."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "55",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.898242Z",
     "iopub.status.busy": "2026-06-04T16:27:15.898103Z",
     "iopub.status.idle": "2026-06-04T16:27:15.901301Z",
     "shell.execute_reply": "2026-06-04T16:27:15.900596Z"
    }
   },
   "outputs": [],
   "source": [
    "expt1.linked_phases['pbso4'].scale.free = True\n",
    "\n",
    "expt1.instrument.calib_twotheta_offset.free = True\n",
    "\n",
    "expt1.peak.broad_gauss_u.free = True\n",
    "expt1.peak.broad_gauss_v.free = True\n",
    "expt1.peak.broad_gauss_w.free = True\n",
    "expt1.peak.broad_lorentz_y.free = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "56",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.902985Z",
     "iopub.status.busy": "2026-06-04T16:27:15.902837Z",
     "iopub.status.idle": "2026-06-04T16:27:15.906467Z",
     "shell.execute_reply": "2026-06-04T16:27:15.905719Z"
    }
   },
   "outputs": [],
   "source": [
    "expt2.linked_phases['pbso4'].scale.free = True\n",
    "\n",
    "expt2.instrument.calib_twotheta_offset.free = True\n",
    "\n",
    "expt2.peak.broad_gauss_u.free = True\n",
    "expt2.peak.broad_gauss_v.free = True\n",
    "expt2.peak.broad_gauss_w.free = True\n",
    "expt2.peak.broad_lorentz_y.free = True\n",
    "\n",
    "for term in expt2.background:\n",
    "    term.coef.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "57",
   "metadata": {},
   "source": [
    "### Run Fitting"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "58",
   "metadata": {},
   "source": [
    "### Display Structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "59",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:15.907911Z",
     "iopub.status.busy": "2026-06-04T16:27:15.907765Z",
     "iopub.status.idle": "2026-06-04T16:27:16.224131Z",
     "shell.execute_reply": "2026-06-04T16:27:16.223322Z"
    }
   },
   "outputs": [
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       "                    var themeAttr = document.body.getAttribute('data-jp-theme-name');\n",
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       "                        isDark = true;\n",
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       "                    // Check computed background color\n",
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      "\u001b[1;36mStructure 🧩 \u001b[0m\u001b[32m'pbso4'\u001b[0m\u001b[1;36m \u001b[0m\u001b[1;36m(\u001b[0m\u001b[1;36mAtom view type: \u001b[0m\u001b[32m'covalent'\u001b[0m\u001b[1;36m)\u001b[0m\n"
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       "    color: var(--cv-panel-fg); background: var(--cv-panel-bg);\n",
       "    border: 1px solid var(--cv-panel-border); padding: 5px 9px; border-radius: 0;\n",
       "    line-height: 1.5; text-align: left; box-shadow: var(--cv-panel-shadow);\n",
       "  }\n",
       "  #crysview-88a30112b48044bfb1f88fc11171a38f .cv-tooltip {\n",
       "    position: absolute; z-index: 4; pointer-events: none; display: none;\n",
       "    background: rgba(33, 42, 62, 0.92); color: #fff; padding: 3px 8px;\n",
       "    border-radius: 0; font-size: 12px; white-space: nowrap;\n",
       "  }\n",
       "  #crysview-88a30112b48044bfb1f88fc11171a38f .cv-atom-label {\n",
       "    font-size: 11px; font-weight: 600; color: var(--cv-scene-fg);\n",
       "    text-shadow: 0 0 3px var(--cv-label-shadow-bg), 0 0 3px var(--cv-label-shadow-bg), 0 0 3px var(--cv-label-shadow-bg);\n",
       "    pointer-events: none; white-space: nowrap;\n",
       "  }\n",
       "</style>\n",
       "\n",
       "<script type=\"module\">\n",
       "import * as THREE from 'three';\n",
       "import { OrbitControls } from 'three/addons/controls/OrbitControls.js';\n",
       "import { CSS2DRenderer, CSS2DObject } from 'three/addons/renderers/CSS2DRenderer.js';\n",
       "\n",
       "const SCENE = {\"atoms\": [{\"centre\": [1.588972, 1.3475, 1.1606500000000002], \"radius\": 0.3624913792078372, \"colour\": [87, 89, 97], \"label\": \"Pb\", \"asymmetric\": true}, {\"centre\": [5.823972, 1.3475000000000001, 2.3143499999999997], \"radius\": 0.3624913792078372, \"colour\": [87, 89, 97], \"label\": \"Pb\", \"asymmetric\": false}, {\"centre\": [6.881028000000001, 4.0424999999999995, 5.78935], \"radius\": 0.3624913792078372, \"colour\": [87, 89, 97], \"label\": \"Pb\", \"asymmetric\": false}, {\"centre\": [2.646028000000001, 4.0424999999999995, 4.63565], \"radius\": 0.3624913792078372, \"colour\": [87, 89, 97], \"label\": \"Pb\", \"asymmetric\": false}, {\"centre\": [0.5539380000000005, 1.3475000000000001, 4.753800000000001], \"radius\": 0.30740852297878796, \"colour\": [255, 255, 48], \"label\": \"S\", \"asymmetric\": true}, {\"centre\": [4.788938000000001, 1.3475000000000004, 5.6712], \"radius\": 0.30740852297878796, \"colour\": [255, 255, 48], \"label\": \"S\", \"asymmetric\": false}, {\"centre\": [7.916062000000001, 4.0424999999999995, 2.1961999999999997], \"radius\": 0.30740852297878796, \"colour\": [255, 255, 48], \"label\": \"S\", \"asymmetric\": false}, {\"centre\": [3.6810620000000003, 4.0424999999999995, 1.2788000000000013], \"radius\": 0.30740852297878796, \"colour\": [255, 255, 48], \"label\": \"S\", \"asymmetric\": false}, {\"centre\": [7.692454000000001, 1.3475000000000001, 4.1380300000000005], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O1\", \"asymmetric\": true}, {\"centre\": [3.457454, 1.3475000000000004, 6.28697], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O1\", \"asymmetric\": false}, {\"centre\": [0.7775460000000005, 4.0424999999999995, 2.8119699999999996], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O1\", \"asymmetric\": false}, {\"centre\": [5.012546, 4.0424999999999995, 0.6630300000000011], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O1\", \"asymmetric\": false}, {\"centre\": [1.6389450000000005, 1.3475000000000001, 3.77524], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O2\", \"asymmetric\": true}, {\"centre\": [5.873945000000001, 1.3475000000000004, 6.64976], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O2\", \"asymmetric\": false}, {\"centre\": [6.831055000000001, 4.0424999999999995, 3.17476], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O2\", \"asymmetric\": false}, {\"centre\": [2.5960550000000002, 4.0424999999999995, 0.3002400000000009], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O2\", \"asymmetric\": false}, {\"centre\": [0.6869170000000004, 0.14660800000000032, 5.61977], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": true}, {\"centre\": [4.9219170000000005, 2.548392, 4.80523], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": false}, {\"centre\": [7.783083000000001, 2.841608, 1.3302300000000002], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": false}, {\"centre\": [3.5480830000000005, 5.243392, 2.14477], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": false}, {\"centre\": [7.783083000000001, 5.243392, 1.3302300000000002], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": false}, {\"centre\": [3.5480830000000005, 2.841608, 2.14477], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": false}, {\"centre\": [0.6869170000000006, 2.548392, 5.61977], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": false}, {\"centre\": [4.921917, 0.1466080000000003, 4.80523], \"radius\": 0.2437211521390788, \"colour\": [255, 13, 13], \"label\": \"O3\", \"asymmetric\": false}], \"wedgeSpheres\": [], \"ellipsoids\": [], \"bonds\": [{\"start\": [0.5539380000000005, 1.3475000000000001, 4.753800000000001], \"end\": [1.6389450000000005, 1.3475000000000001, 3.77524], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [0.5539380000000005, 1.3475000000000001, 4.753800000000001], \"end\": [0.6869170000000004, 0.14660800000000032, 5.61977], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [0.5539380000000005, 1.3475000000000001, 4.753800000000001], \"end\": [0.6869170000000006, 2.548392, 5.61977], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [4.788938000000001, 1.3475000000000004, 5.6712], \"end\": [3.457454, 1.3475000000000004, 6.28697], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [4.788938000000001, 1.3475000000000004, 5.6712], \"end\": [5.873945000000001, 1.3475000000000004, 6.64976], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [4.788938000000001, 1.3475000000000004, 5.6712], \"end\": [4.9219170000000005, 2.548392, 4.80523], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [4.788938000000001, 1.3475000000000004, 5.6712], \"end\": [4.921917, 0.1466080000000003, 4.80523], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [7.916062000000001, 4.0424999999999995, 2.1961999999999997], \"end\": [6.831055000000001, 4.0424999999999995, 3.17476], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [7.916062000000001, 4.0424999999999995, 2.1961999999999997], \"end\": [7.783083000000001, 2.841608, 1.3302300000000002], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [7.916062000000001, 4.0424999999999995, 2.1961999999999997], \"end\": [7.783083000000001, 5.243392, 1.3302300000000002], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [3.6810620000000003, 4.0424999999999995, 1.2788000000000013], \"end\": [5.012546, 4.0424999999999995, 0.6630300000000011], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [3.6810620000000003, 4.0424999999999995, 1.2788000000000013], \"end\": [2.5960550000000002, 4.0424999999999995, 0.3002400000000009], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [3.6810620000000003, 4.0424999999999995, 1.2788000000000013], \"end\": [3.5480830000000005, 5.243392, 2.14477], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}, {\"start\": [3.6810620000000003, 4.0424999999999995, 1.2788000000000013], \"end\": [3.5480830000000005, 2.841608, 2.14477], \"startColour\": [255, 255, 48], \"endColour\": [255, 13, 13], \"startElement\": \"S\", \"endElement\": \"O\"}], \"cellEdges\": [{\"start\": [0.0, 0.0, 0.0], \"end\": [8.47, 0.0, 0.0]}, {\"start\": [0.0, 0.0, 0.0], \"end\": [3.300423123702117e-16, 5.39, 0.0]}, {\"start\": [0.0, 0.0, 0.0], \"end\": [4.2556476270370527e-16, 4.2556476270370527e-16, 6.95]}, {\"start\": [4.2556476270370527e-16, 4.2556476270370527e-16, 6.95], \"end\": [8.47, 4.2556476270370527e-16, 6.95]}, {\"start\": [4.2556476270370527e-16, 4.2556476270370527e-16, 6.95], \"end\": [7.55607075073917e-16, 5.39, 6.95]}, {\"start\": [3.300423123702117e-16, 5.39, 0.0], \"end\": [8.47, 5.39, 0.0]}, {\"start\": [3.300423123702117e-16, 5.39, 0.0], \"end\": [7.55607075073917e-16, 5.39, 6.95]}, {\"start\": [7.55607075073917e-16, 5.39, 6.95], \"end\": [8.47, 5.39, 6.95]}, {\"start\": [8.47, 0.0, 0.0], \"end\": [8.47, 5.39, 0.0]}, {\"start\": [8.47, 0.0, 0.0], \"end\": [8.47, 4.2556476270370527e-16, 6.95]}, {\"start\": [8.47, 4.2556476270370527e-16, 6.95], \"end\": [8.47, 5.39, 6.95]}, {\"start\": [8.47, 5.39, 0.0], \"end\": [8.47, 5.39, 6.95]}], \"axes\": {\"origin\": [0.0, 0.0, 0.0], \"arrows\": [{\"vector\": [11.011000000000001, 0.0, 0.0], \"colour\": [220, 40, 40], \"letter\": \"a\"}, {\"vector\": [4.856336882018829e-16, 7.930999999999999, 0.0], \"colour\": [40, 180, 40], \"letter\": \"b\"}, {\"vector\": [5.811561385353765e-16, 5.811561385353765e-16, 9.491], \"colour\": [40, 80, 220], \"letter\": \"c\"}]}, \"labels\": [{\"anchor\": [1.588972, 1.3475, 1.1606500000000002], \"text\": \"Pb\"}, {\"anchor\": [5.823972, 1.3475000000000001, 2.3143499999999997], \"text\": \"Pb\"}, {\"anchor\": [6.881028000000001, 4.0424999999999995, 5.78935], \"text\": \"Pb\"}, {\"anchor\": [2.646028000000001, 4.0424999999999995, 4.63565], \"text\": \"Pb\"}, {\"anchor\": [0.5539380000000005, 1.3475000000000001, 4.753800000000001], \"text\": \"S\"}, {\"anchor\": [4.788938000000001, 1.3475000000000004, 5.6712], \"text\": \"S\"}, {\"anchor\": [7.916062000000001, 4.0424999999999995, 2.1961999999999997], \"text\": \"S\"}, {\"anchor\": [3.6810620000000003, 4.0424999999999995, 1.2788000000000013], \"text\": \"S\"}, {\"anchor\": [7.692454000000001, 1.3475000000000001, 4.1380300000000005], \"text\": \"O1\"}, {\"anchor\": [3.457454, 1.3475000000000004, 6.28697], \"text\": \"O1\"}, {\"anchor\": [0.7775460000000005, 4.0424999999999995, 2.8119699999999996], \"text\": \"O1\"}, {\"anchor\": [5.012546, 4.0424999999999995, 0.6630300000000011], \"text\": \"O1\"}, {\"anchor\": [1.6389450000000005, 1.3475000000000001, 3.77524], \"text\": \"O2\"}, {\"anchor\": [5.873945000000001, 1.3475000000000004, 6.64976], \"text\": \"O2\"}, {\"anchor\": [6.831055000000001, 4.0424999999999995, 3.17476], \"text\": \"O2\"}, {\"anchor\": [2.5960550000000002, 4.0424999999999995, 0.3002400000000009], \"text\": \"O2\"}, {\"anchor\": [0.6869170000000004, 0.14660800000000032, 5.61977], \"text\": \"O3\"}, {\"anchor\": [4.9219170000000005, 2.548392, 4.80523], \"text\": \"O3\"}, {\"anchor\": [7.783083000000001, 2.841608, 1.3302300000000002], \"text\": \"O3\"}, {\"anchor\": [3.5480830000000005, 5.243392, 2.14477], \"text\": \"O3\"}, {\"anchor\": [7.783083000000001, 5.243392, 1.3302300000000002], \"text\": \"O3\"}, {\"anchor\": [3.5480830000000005, 2.841608, 2.14477], \"text\": \"O3\"}, {\"anchor\": [0.6869170000000006, 2.548392, 5.61977], \"text\": \"O3\"}, {\"anchor\": [4.921917, 0.1466080000000003, 4.80523], \"text\": \"O3\"}], \"legend\": [{\"symbol\": \"Pb\", \"colour\": [87, 89, 97]}, {\"symbol\": \"S\", \"colour\": [255, 255, 48]}, {\"symbol\": \"O\", \"colour\": [255, 13, 13]}], \"palettes\": {\"jmol\": {\"Pb\": [87, 89, 97], \"S\": [255, 255, 48], \"O\": [255, 13, 13]}, \"vesta\": {\"Pb\": [87, 89, 97], \"S\": [255, 250, 0], \"O\": [254, 3, 0]}}};\n",
       "const FEATURES = [\"atoms\", \"axes\", \"bonds\", \"cell\"];\n",
       "const INITIAL_THEME = 'light';\n",
       "\n",
       "const ICONS = {\n",
       "  perspective: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.7\" stroke-linecap=\"round\" stroke-linejoin=\"round\"><rect x=\"3.5\" y=\"4.5\" width=\"17\" height=\"15\" rx=\"1.5\"/><path d=\"M9 4.5 11 19.5M15 4.5 13 19.5\"/></svg>',\n",
       "  orthographic: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.7\" stroke-linecap=\"round\" stroke-linejoin=\"round\"><rect x=\"3.5\" y=\"4.5\" width=\"17\" height=\"15\" rx=\"1.5\"/><path d=\"M9.5 4.5V19.5M14.5 4.5V19.5\"/></svg>',\n",
       "  home: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.8\" stroke-linecap=\"round\" stroke-linejoin=\"round\"><path d=\"M3 11 12 3l9 8\"/><path d=\"M5 9.5V20h5v-6h4v6h5V9.5\"/></svg>',\n",
       "  cell: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.7\" stroke-linejoin=\"round\" stroke-linecap=\"round\"><path d=\"M12 2.5 20 7v9l-8 4.5L4 16V7Z\"/><path d=\"M4 7l8 4.5L20 7M12 11.5v9\"/></svg>',\n",
       "  axes: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.7\" stroke-linecap=\"round\" stroke-linejoin=\"round\"><path d=\"M5 19V6M5 19h13M5 19l7-7\"/><path d=\"M5 6 3.3 8.2M5 6l1.7 2.2M18 19l-2.2-1.4M18 19l-2.2 1.4\"/></svg>',\n",
       "  atoms: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.7\" stroke-linecap=\"round\"><path d=\"M11.8 12.2 14 10M12.9 16.1l1.8.4\"/><circle cx=\"9\" cy=\"15\" r=\"4.2\" fill=\"currentColor\" stroke=\"none\"/><circle cx=\"16\" cy=\"8\" r=\"3\" fill=\"currentColor\" stroke=\"none\"/><circle cx=\"17\" cy=\"17\" r=\"2.6\" fill=\"currentColor\" stroke=\"none\"/></svg>',\n",
       "  bonds: '<svg viewBox=\"0 0 24 24\"><line x1=\"8\" y1=\"16\" x2=\"16\" y2=\"8\" stroke=\"currentColor\" stroke-width=\"2.4\" stroke-linecap=\"round\"/><circle cx=\"6.7\" cy=\"17.3\" r=\"3.1\" fill=\"currentColor\"/><circle cx=\"17.3\" cy=\"6.7\" r=\"3.1\" fill=\"currentColor\"/></svg>',\n",
       "  asymmetricUnit: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.7\" stroke-linecap=\"round\"><circle cx=\"9\" cy=\"15\" r=\"4.2\" fill=\"currentColor\" stroke=\"none\"/><circle cx=\"16\" cy=\"8\" r=\"3\" opacity=\".48\"/><circle cx=\"17\" cy=\"17\" r=\"2.6\" opacity=\".34\"/><path d=\"M11.8 12.2 14 10M12.9 16.1l1.8.4\" opacity=\".34\"/></svg>',\n",
       "  atomsOff: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.7\" stroke-linecap=\"round\"><path d=\"M11.8 12.2 14 10M12.9 16.1l1.8.4\"/><circle cx=\"9\" cy=\"15\" r=\"4.2\"/><circle cx=\"16\" cy=\"8\" r=\"3\"/><circle cx=\"17\" cy=\"17\" r=\"2.6\"/></svg>',\n",
       "  moments: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.9\" stroke-linecap=\"round\" stroke-linejoin=\"round\"><path d=\"M12 20V5\"/><path d=\"M7 10l5-6 5 6\"/></svg>',\n",
       "  labels: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.6\" stroke-linejoin=\"round\" stroke-linecap=\"round\"><rect x=\"3.5\" y=\"5\" width=\"17\" height=\"14\" rx=\"2\"/><path d=\"M9 15.5 12 8.5l3 7M10.1 13.2h3.8\"/></svg>',\n",
       "  camera: '<svg viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.6\" stroke-linecap=\"round\" stroke-linejoin=\"round\"><path d=\"M4 8h3l1.5-2h7L17 8h3a1 1 0 0 1 1 1v9a1 1 0 0 1-1 1H4a1 1 0 0 1-1-1V9a1 1 0 0 1 1-1Z\"/><circle cx=\"12\" cy=\"13\" r=\"3.4\"/></svg>',\n",
       "};\n",
       "\n",
       "const root = document.getElementById('crysview-88a30112b48044bfb1f88fc11171a38f');\n",
       "const host = root.querySelector('.cv-canvas');\n",
       "const modebar = root.querySelector('.cv-modebar');\n",
       "const downloadHost = root.querySelector('.cv-download');\n",
       "const legend = root.querySelector('.cv-legend');\n",
       "const tooltip = root.querySelector('.cv-tooltip');\n",
       "\n",
       "// Element palettes are authored in sRGB; tag the colour space so Three.js\n",
       "// converts to linear for lighting instead of treating it as already-linear\n",
       "// (which washes out and desaturates the atoms).\n",
       "const col = (rgb) => new THREE.Color().setRGB(rgb[0] / 255, rgb[1] / 255, rgb[2] / 255, THREE.SRGBColorSpace);\n",
       "const vec = (xyz) => new THREE.Vector3(xyz[0], xyz[1], xyz[2]);\n",
       "const rgbCss = (rgb) => `rgb(${rgb[0]},${rgb[1]},${rgb[2]})`;\n",
       "const cssVar = (name, fallback) => getComputedStyle(root).getPropertyValue(name).trim() || fallback;\n",
       "const elementOf = (label) => (label.match(/[A-Z][a-z]?/) || [label])[0];\n",
       "const PALETTES = SCENE.palettes || {};\n",
       "\n",
       "// Phong material with a small, subtle highlight (mirrors the raster figure:\n",
       "// bright saturated atoms, tight specular spot, small dark region).\n",
       "const SPECULAR = new THREE.Color(0.2, 0.2, 0.2);\n",
       "const solidMat = (c, doubleSide) => new THREE.MeshPhongMaterial({\n",
       "  color: c, shininess: 90, specular: SPECULAR,\n",
       "  side: doubleSide ? THREE.DoubleSide : THREE.FrontSide,\n",
       "});\n",
       "\n",
       "let width = host.clientWidth || 640;\n",
       "let height = host.clientHeight || 480;\n",
       "\n",
       "const scene = new THREE.Scene();\n",
       "const renderer = new THREE.WebGLRenderer({ antialias: true, alpha: true, preserveDrawingBuffer: true });\n",
       "renderer.setPixelRatio(window.devicePixelRatio);\n",
       "renderer.setSize(width, height);\n",
       "host.appendChild(renderer.domElement);\n",
       "\n",
       "const labelRenderer = new CSS2DRenderer();\n",
       "labelRenderer.setSize(width, height);\n",
       "labelRenderer.domElement.style.position = 'absolute';\n",
       "labelRenderer.domElement.style.top = '0';\n",
       "labelRenderer.domElement.style.pointerEvents = 'none';\n",
       "host.appendChild(labelRenderer.domElement);\n",
       "\n",
       "// Camera-relative key + fill (headlights) so atoms stay bright and saturated\n",
       "// from any angle, with a small dark region — matching the raster figure.\n",
       "scene.add(new THREE.AmbientLight(0xffffff, 0.68));\n",
       "const key = new THREE.DirectionalLight(0xffffff, 1.25);\n",
       "const fill = new THREE.DirectionalLight(0xffffff, 0.34);\n",
       "scene.add(key, key.target, fill, fill.target);\n",
       "\n",
       "const groups = {};\n",
       "for (const name of ['cell', 'axes', 'atoms', 'bonds', 'moments', 'labels']) {\n",
       "  groups[name] = new THREE.Group();\n",
       "  groups[name].visible = FEATURES.includes(name);\n",
       "  scene.add(groups[name]);\n",
       "}\n",
       "\n",
       "const unitSphere = new THREE.SphereGeometry(1, 24, 16);\n",
       "\n",
       "for (const a of SCENE.atoms) {\n",
       "  const mesh = new THREE.Mesh(unitSphere, solidMat(col(a.colour)));\n",
       "  mesh.position.copy(vec(a.centre));\n",
       "  mesh.scale.setScalar(a.radius);\n",
       "  mesh.userData.label = a.label;\n",
       "  mesh.userData.element = elementOf(a.label);\n",
       "  mesh.userData.asymmetric = a.asymmetric;\n",
       "  groups.atoms.add(mesh);\n",
       "}\n",
       "\n",
       "// Occupancy-wedge spheres: carve longitude wedges (proportional phi spans) and\n",
       "// orient them toward the camera below, once the view basis is known.\n",
       "const wedgeMeshes = [];\n",
       "for (const s of SCENE.wedgeSpheres) {\n",
       "  let phi = 0;\n",
       "  const parts = s.label.split('/');\n",
       "  s.wedges.forEach((w, i) => {\n",
       "    const span = w.fraction * Math.PI * 2;\n",
       "    const geo = new THREE.SphereGeometry(s.radius, Math.max(6, Math.round(48 * w.fraction)), 16, phi, span);\n",
       "    const mesh = new THREE.Mesh(geo, solidMat(col(w.colour), true));\n",
       "    mesh.position.copy(vec(s.centre));\n",
       "    mesh.userData.label = s.label;\n",
       "    mesh.userData.element = parts[i] || null;   // null for the vacancy wedge\n",
       "    mesh.userData.asymmetric = s.asymmetric;\n",
       "    groups.atoms.add(mesh);\n",
       "    wedgeMeshes.push(mesh);\n",
       "    phi += span;\n",
       "  });\n",
       "}\n",
       "\n",
       "for (const e of SCENE.ellipsoids) {\n",
       "  const basis = new THREE.Matrix4().makeBasis(vec(e.orientation[0]), vec(e.orientation[1]), vec(e.orientation[2]));\n",
       "  const quat = new THREE.Quaternion().setFromRotationMatrix(basis);\n",
       "  const split = e.wedges && e.wedges.length;\n",
       "  const wedges = split ? e.wedges : [{ fraction: 1, colour: e.colour }];\n",
       "  const parts = e.label.split('/');\n",
       "  let phi = 0;\n",
       "  wedges.forEach((w, i) => {\n",
       "    const span = w.fraction * Math.PI * 2;\n",
       "    const geo = new THREE.SphereGeometry(1, Math.max(6, Math.round(48 * w.fraction)), 16, phi, span);\n",
       "    const mesh = new THREE.Mesh(geo, solidMat(col(w.colour), true));\n",
       "    mesh.position.copy(vec(e.centre));\n",
       "    mesh.scale.set(e.semiAxes[0], e.semiAxes[1], e.semiAxes[2]);\n",
       "    mesh.quaternion.copy(quat);\n",
       "    mesh.userData.label = e.label;\n",
       "    mesh.userData.element = split ? (parts[i] || null) : elementOf(e.label);\n",
       "    mesh.userData.asymmetric = e.asymmetric;\n",
       "    groups.atoms.add(mesh);\n",
       "    phi += span;\n",
       "  });\n",
       "}\n",
       "\n",
       "const addHalfBond = (p0, p1, colour, element) => {\n",
       "  const direction = p1.clone().sub(p0);\n",
       "  const length = direction.length();\n",
       "  if (length < 1e-6) return;\n",
       "  const geo = new THREE.CylinderGeometry(0.06, 0.06, length, 12);\n",
       "  const mesh = new THREE.Mesh(geo, solidMat(col(colour)));\n",
       "  mesh.position.copy(p0.clone().add(p1).multiplyScalar(0.5));\n",
       "  mesh.quaternion.setFromUnitVectors(new THREE.Vector3(0, 1, 0), direction.normalize());\n",
       "  mesh.userData.element = element || null;\n",
       "  groups.bonds.add(mesh);\n",
       "};\n",
       "for (const b of SCENE.bonds) {\n",
       "  const start = vec(b.start);\n",
       "  const end = vec(b.end);\n",
       "  const mid = start.clone().add(end).multiplyScalar(0.5);\n",
       "  addHalfBond(start, mid, b.startColour, b.startElement);\n",
       "  addHalfBond(mid, end, b.endColour, b.endElement);\n",
       "}\n",
       "\n",
       "const cellMaterial = new THREE.LineBasicMaterial({\n",
       "  color: new THREE.Color(cssVar('--cv-scene-fg', 'rgb(34, 34, 34)')),\n",
       "});\n",
       "for (const edge of SCENE.cellEdges) {\n",
       "  const geo = new THREE.BufferGeometry().setFromPoints([vec(edge.start), vec(edge.end)]);\n",
       "  groups.cell.add(new THREE.Line(geo, cellMaterial));\n",
       "}\n",
       "\n",
       "// Axis arrows are built after the camera fit (below), so their thickness, head,\n",
       "// and overhang can be sized from the on-screen zoom and look identical in\n",
       "// every cell regardless of size or proportions.\n",
       "\n",
       "for (const label of SCENE.labels) {\n",
       "  const div = document.createElement('div');\n",
       "  div.className = 'cv-atom-label';\n",
       "  div.textContent = label.text;\n",
       "  const obj = new CSS2DObject(div);\n",
       "  obj.visible = groups.labels.visible;\n",
       "  obj.position.copy(vec(label.anchor));\n",
       "  groups.labels.add(obj);\n",
       "}\n",
       "\n",
       "const box = new THREE.Box3();\n",
       "scene.traverse((obj) => {\n",
       "  if (obj.isMesh || obj.isLine) box.expandByObject(obj);\n",
       "});\n",
       "if (box.isEmpty()) box.set(new THREE.Vector3(-1, -1, -1), new THREE.Vector3(1, 1, 1));\n",
       "const target = box.getBoundingSphere(new THREE.Sphere()).center;\n",
       "const aspect = width / height;\n",
       "const cellBasis = SCENE.axes ? SCENE.axes.arrows.map((a) => vec(a.vector)) : [];\n",
       "\n",
       "// Real content points the framing must enclose — atom centres, cell vertices,\n",
       "// and the cell origin. (AABB corners are wrong here: they stick out into empty\n",
       "// space and over-zoom-out the view.) Axis arrows are sized from the zoom and\n",
       "// reserved via `margin` below, not enclosed point-by-point. fitPad grows the\n",
       "// extent by the largest atom radius so boundary spheres are not clipped.\n",
       "const fitPoints = [];\n",
       "let fitPad = 0;\n",
       "for (const a of SCENE.atoms) { fitPoints.push(vec(a.centre)); fitPad = Math.max(fitPad, a.radius); }\n",
       "for (const s of SCENE.wedgeSpheres || []) { fitPoints.push(vec(s.centre)); fitPad = Math.max(fitPad, s.radius); }\n",
       "for (const e of SCENE.ellipsoids || []) { fitPoints.push(vec(e.centre)); fitPad = Math.max(fitPad, Math.max(...e.semiAxes)); }\n",
       "for (const edge of SCENE.cellEdges || []) { fitPoints.push(vec(edge.start), vec(edge.end)); }\n",
       "if (SCENE.axes) fitPoints.push(vec(SCENE.axes.origin));\n",
       "if (!fitPoints.length) fitPoints.push(box.min.clone(), box.max.clone());\n",
       "\n",
       "// Default orientation: longest cell axis horizontal, 2nd-longest vertical, the\n",
       "// shortest axis into depth, then a small azimuth + elevation for a trimetric\n",
       "// 3D read. Falls back to a fixed angle when the cell axes are absent.\n",
       "let viewUp;\n",
       "let viewDir;\n",
       "if (SCENE.axes && SCENE.axes.arrows.length === 3) {\n",
       "  // Default view (by axis length): longest axis horizontal, 2nd-longest up,\n",
       "  // shortest into depth, viewed along 0.37·longest + 0.24·middle + 0.90·shortest.\n",
       "  const sorted = SCENE.axes.arrows.map((a) => vec(a.vector)).sort((p, q) => q.length() - p.length());\n",
       "  const longest = sorted[0].clone().normalize();\n",
       "  const middle = sorted[1].clone().normalize();\n",
       "  const shortest = sorted[2].clone().normalize();\n",
       "  viewUp = middle.clone();\n",
       "  viewDir = longest.clone().multiplyScalar(0.37)\n",
       "    .add(middle.clone().multiplyScalar(0.24))\n",
       "    .add(shortest.clone().multiplyScalar(0.90))\n",
       "    .normalize();\n",
       "} else {\n",
       "  viewUp = new THREE.Vector3(0, 1, 0);\n",
       "  viewDir = new THREE.Vector3(1.0, 0.8, 1.5).normalize();\n",
       "}\n",
       "\n",
       "// Screen-space fit: project the fit points onto the camera right/up axes and\n",
       "// frame their 2D bounding box. Recentering the target on that box keeps the\n",
       "// content centred even though arrows/labels extend it asymmetrically, and the\n",
       "// extent-based zoom is independent of cell size, axis ratios, and aspect.\n",
       "const look = viewDir.clone().negate();\n",
       "const camRight = new THREE.Vector3().crossVectors(look, viewUp).normalize();\n",
       "const camUp = new THREE.Vector3().crossVectors(camRight, look).normalize();\n",
       "// Orient occupancy-wedge spheres so their carve pole (+Y) points at the camera\n",
       "// (azimuthal spans then project as a proportional pie) and the wedge seam plane\n",
       "// is vertical (its normal is camRight), so a two-way split reads as a left/right\n",
       "// vertical seam matching the raster figure.\n",
       "const wedgeQuat = new THREE.Quaternion().setFromRotationMatrix(\n",
       "  new THREE.Matrix4().makeBasis(\n",
       "    new THREE.Vector3().crossVectors(viewDir, camRight), viewDir, camRight));\n",
       "for (const m of wedgeMeshes) m.quaternion.copy(wedgeQuat);\n",
       "let minU = Infinity, maxU = -Infinity, minV = Infinity, maxV = -Infinity;\n",
       "for (const p of fitPoints) {\n",
       "  const d = p.clone().sub(target);\n",
       "  const u = d.dot(camRight), v = d.dot(camUp);\n",
       "  minU = Math.min(minU, u); maxU = Math.max(maxU, u);\n",
       "  minV = Math.min(minV, v); maxV = Math.max(maxV, v);\n",
       "}\n",
       "target.addScaledVector(camRight, (minU + maxU) / 2).addScaledVector(camUp, (minV + maxV) / 2);\n",
       "// Reserve extra extent for the axis arrows (drawn beyond the cell, sized from\n",
       "// the zoom below) and their letters, so they stay inside the frame.\n",
       "const margin = SCENE.axes ? 1.24 : 1.06;\n",
       "const halfW = Math.max((maxU - minU) / 2 + fitPad, 0.5) * margin;\n",
       "const halfH = Math.max((maxV - minV) / 2 + fitPad, 0.5) * margin;\n",
       "const radius = Math.max(halfW, halfH);\n",
       "const far = radius * 100;\n",
       "const PERSPECTIVE_FOV_DEG = 30;\n",
       "const tanV = Math.tan((PERSPECTIVE_FOV_DEG * Math.PI) / 360);\n",
       "const distance = Math.max(halfH / tanV, halfW / (tanV * aspect)) * 1.05;\n",
       "const home = target.clone().add(viewDir.clone().multiplyScalar(distance));\n",
       "\n",
       "const perspective = new THREE.PerspectiveCamera(PERSPECTIVE_FOV_DEG, aspect, Math.max(distance * 0.01, 0.01), far);\n",
       "// Ortho frustum sized to the projected extent; reserve a top band for the\n",
       "// modebar/legend so the cell sits a little lower and clears them.\n",
       "const orthoHalfH = Math.max(halfH, halfW / aspect);\n",
       "const topBandPx = 84;\n",
       "// Reserve a band at the top for the modebar by growing the vertical extent and\n",
       "// shifting the centre up, keeping width/height === aspect so spheres stay round.\n",
       "// (Adding the band only to `top` skews the frustum and distorts the scene.)\n",
       "const band = (2 * orthoHalfH / height) * topBandPx;\n",
       "const halfV = orthoHalfH + band * 0.5;\n",
       "const ortho = new THREE.OrthographicCamera(\n",
       "  -halfV * aspect, halfV * aspect, halfV + band * 0.5, -halfV + band * 0.5, -far, far);\n",
       "perspective.up.copy(viewUp);\n",
       "ortho.up.copy(viewUp);\n",
       "perspective.position.copy(home);\n",
       "ortho.position.copy(home);\n",
       "let camera = ortho;\n",
       "let projection = 'orthographic';\n",
       "\n",
       "// Build the axis arrows now (after the fit) so every dimension is a fixed\n",
       "// fraction of the on-screen zoom (orthoHalfH): identical thickness, head\n",
       "// length, and overhang past the cell corner in every cell, regardless of size\n",
       "// or proportions. The cell-edge length is recovered per axis so the shaft still\n",
       "// reaches the cell corner before overhanging.\n",
       "if (SCENE.axes && SCENE.axes.arrows.length === 3) {\n",
       "  const Y_AXIS = new THREE.Vector3(0, 1, 0);\n",
       "  const origin = vec(SCENE.axes.origin);\n",
       "  const arrowVecs = SCENE.axes.arrows.map((a) => vec(a.vector));\n",
       "  const maxAxis = Math.max(...arrowVecs.map((v) => v.length()), 1e-3) / 1.3;\n",
       "  const shaftR = orthoHalfH * 0.009;\n",
       "  const headR = orthoHalfH * 0.028;\n",
       "  const headLen = orthoHalfH * 0.085;\n",
       "  // Overhang past the cell corner: at least clear the largest atom (corner\n",
       "  // atoms otherwise hide the head) plus the head length and a small gap, so the\n",
       "  // cap is always fully visible beyond any corner atom.\n",
       "  const overhang = Math.max(orthoHalfH * 0.09, fitPad + headLen + orthoHalfH * 0.04);\n",
       "  SCENE.axes.arrows.forEach((arrow, i) => {\n",
       "    const v = arrowVecs[i];\n",
       "    const dir = v.clone().normalize();\n",
       "    const axisLen = Math.max(v.length() - 0.3 * maxAxis, 1e-3);\n",
       "    const total = axisLen + overhang;\n",
       "    const shaftLen = Math.max(total - headLen, 1e-3);\n",
       "    const material = solidMat(col(arrow.colour));\n",
       "    const group = new THREE.Group();\n",
       "    const shaft = new THREE.Mesh(new THREE.CylinderGeometry(shaftR, shaftR, shaftLen, 16), material);\n",
       "    shaft.position.y = shaftLen / 2;\n",
       "    const head = new THREE.Mesh(new THREE.ConeGeometry(headR, headLen, 20), material);\n",
       "    head.position.y = shaftLen + headLen / 2;\n",
       "    group.add(shaft, head);\n",
       "    group.quaternion.setFromUnitVectors(Y_AXIS, dir);\n",
       "    group.position.copy(origin);\n",
       "    groups.axes.add(group);\n",
       "    const div = document.createElement('div');\n",
       "    div.className = 'cv-axis-letter';\n",
       "    div.textContent = arrow.letter;\n",
       "    div.style.color = rgbCss(arrow.colour);\n",
       "    const tag = new CSS2DObject(div);\n",
       "    tag.position.copy(origin).addScaledVector(dir, total + orthoHalfH * 0.05);\n",
       "    groups.axes.add(tag);\n",
       "  });\n",
       "}\n",
       "\n",
       "const controls = new OrbitControls(camera, renderer.domElement);\n",
       "controls.enableDamping = true;\n",
       "controls.dampingFactor = 0.08;\n",
       "controls.zoomSpeed = 20.0;   // larger wheel/touchpad zoom steps (tune to taste)\n",
       "controls.target.copy(target);\n",
       "controls.update();\n",
       "\n",
       "const setCamera = (next) => {\n",
       "  next.position.copy(camera.position);\n",
       "  next.up.copy(camera.up);\n",
       "  controls.object = next;\n",
       "  camera = next;\n",
       "  controls.update();\n",
       "};\n",
       "const viewAlong = (axisVector, upVector) => {\n",
       "  camera.up.copy(upVector);\n",
       "  camera.position.copy(target.clone().add(axisVector.clone().normalize().multiplyScalar(distance)));\n",
       "  controls.update();\n",
       "};\n",
       "const projectedOnViewPlane = (vector, normal) => (\n",
       "  vector.clone().addScaledVector(normal, -vector.dot(normal))\n",
       ");\n",
       "const viewAlongAxis = (axisIndex) => {\n",
       "  const viewAxis = cellBasis[axisIndex].clone().normalize();\n",
       "  const remaining = cellBasis\n",
       "    .map((axis, index) => ({ axis, index }))\n",
       "    .filter(({ index }) => index !== axisIndex)\n",
       "    .sort((left, right) => right.axis.length() - left.axis.length());\n",
       "  let horizontalSource = remaining[0];\n",
       "  let secondarySource = remaining[1];\n",
       "  let horizontal = projectedOnViewPlane(horizontalSource.axis.clone().normalize(), viewAxis);\n",
       "  if (horizontal.lengthSq() < 1e-8) {\n",
       "    [horizontalSource, secondarySource] = [secondarySource, horizontalSource];\n",
       "    horizontal = projectedOnViewPlane(horizontalSource.axis.clone().normalize(), viewAxis);\n",
       "  }\n",
       "  horizontal.normalize();\n",
       "  const secondary = projectedOnViewPlane(secondarySource.axis.clone().normalize(), viewAxis).normalize();\n",
       "  const cameraAxis = viewAxis.clone();\n",
       "  const look = cameraAxis.clone().negate();\n",
       "  const up = new THREE.Vector3().crossVectors(horizontal, look).normalize();\n",
       "  if (secondary.dot(up) < 0) {\n",
       "    cameraAxis.negate();\n",
       "    up.negate();\n",
       "  }\n",
       "  viewAlong(cameraAxis, up);\n",
       "};\n",
       "\n",
       "const iconButton = (parent, html, title, cls) => {\n",
       "  const el = document.createElement('button');\n",
       "  el.className = 'mb' + (cls ? ' ' + cls : '');\n",
       "  el.innerHTML = html;\n",
       "  el.title = title;\n",
       "  parent.appendChild(el);\n",
       "  return el;\n",
       "};\n",
       "\n",
       "const cameraGroup = document.createElement('div');\n",
       "cameraGroup.className = 'mb-grp';\n",
       "modebar.appendChild(cameraGroup);\n",
       "\n",
       "const projButton = iconButton(cameraGroup, ICONS.orthographic, 'Parallel (orthographic) view');\n",
       "projButton.addEventListener('click', () => {\n",
       "  projection = projection === 'orthographic' ? 'perspective' : 'orthographic';\n",
       "  setCamera(projection === 'orthographic' ? ortho : perspective);\n",
       "  projButton.innerHTML = ICONS[projection];\n",
       "  projButton.title = projection === 'orthographic' ? 'Parallel (orthographic) view' : 'Perspective view';\n",
       "});\n",
       "\n",
       "if (SCENE.axes) {\n",
       "  SCENE.axes.arrows.forEach((arrow, i) => {\n",
       "    const button = iconButton(cameraGroup, arrow.letter, `View along ${arrow.letter}`, 'lt');\n",
       "    button.style.color = rgbCss(arrow.colour);\n",
       "    button.addEventListener('click', () => viewAlongAxis(i));\n",
       "  });\n",
       "}\n",
       "\n",
       "const homeButton = iconButton(cameraGroup, ICONS.home, 'Reset view');\n",
       "homeButton.addEventListener('click', () => {\n",
       "  perspective.zoom = 1;\n",
       "  perspective.updateProjectionMatrix();\n",
       "  ortho.zoom = 1;\n",
       "  ortho.updateProjectionMatrix();\n",
       "  camera.up.copy(viewUp);\n",
       "  camera.position.copy(home);\n",
       "  controls.target.copy(target);\n",
       "  controls.update();\n",
       "});\n",
       "\n",
       "const featureGroup = document.createElement('div');\n",
       "featureGroup.className = 'mb-grp';\n",
       "let hasFeatureToggle = false;\n",
       "// Atoms control: one button cycling all atoms -> asymmetric unit only -> no\n",
       "// atoms. The asymmetric-unit step is offered only when the scene actually\n",
       "// contains symmetry-equivalent copies to hide; otherwise it is a plain\n",
       "// show/hide toggle.\n",
       "const hasNonAU = SCENE.atoms.some((a) => !a.asymmetric)\n",
       "  || SCENE.wedgeSpheres.some((s) => !s.asymmetric)\n",
       "  || SCENE.ellipsoids.some((e) => !e.asymmetric);\n",
       "const ATOM_STATES = hasNonAU\n",
       "  ? [\n",
       "      { key: 'all', icon: ICONS.atoms, on: true },\n",
       "      { key: 'asym', icon: ICONS.asymmetricUnit, on: true },\n",
       "      { key: 'none', icon: ICONS.atomsOff, on: false },\n",
       "    ]\n",
       "  : [\n",
       "      { key: 'all', icon: ICONS.atoms, on: true },\n",
       "      { key: 'none', icon: ICONS.atomsOff, on: false },\n",
       "    ];\n",
       "const ATOMS_TOOLTIP = hasNonAU\n",
       "  ? 'Atoms: all / asymmetric unit / none'\n",
       "  : 'Atoms: show / hide';\n",
       "const addAtomsControl = (parent) => {\n",
       "  let index = groups.atoms.visible ? 0 : ATOM_STATES.length - 1;\n",
       "  const start = ATOM_STATES[index];\n",
       "  const button = iconButton(parent, start.icon, ATOMS_TOOLTIP, 'tog' + (start.on ? ' on' : ''));\n",
       "  button.addEventListener('click', () => {\n",
       "    index = (index + 1) % ATOM_STATES.length;\n",
       "    const state = ATOM_STATES[index];\n",
       "    groups.atoms.visible = state.key !== 'none';\n",
       "    groups.atoms.children.forEach((m) => {\n",
       "      m.visible = state.key !== 'asym' || !!m.userData.asymmetric;\n",
       "    });\n",
       "    // CSS2D atom labels ignore ancestor visibility, so match them to the group.\n",
       "    groups.atoms.traverse((o) => { if (o.isCSS2DObject) o.visible = groups.atoms.visible; });\n",
       "    button.innerHTML = state.icon;\n",
       "    button.classList.toggle('on', state.on);\n",
       "  });\n",
       "};\n",
       "for (const name of ['atoms', 'labels', 'bonds', 'cell', 'axes', 'moments']) {\n",
       "  if (!groups[name] || groups[name].children.length === 0) continue;\n",
       "  hasFeatureToggle = true;\n",
       "  if (name === 'atoms') {\n",
       "    addAtomsControl(featureGroup);\n",
       "    continue;\n",
       "  }\n",
       "  const visible = groups[name].visible;\n",
       "  const button = iconButton(featureGroup, ICONS[name], name.charAt(0).toUpperCase() + name.slice(1), 'tog' + (visible ? ' on' : ''));\n",
       "  button.addEventListener('click', () => {\n",
       "    const next = !groups[name].visible;\n",
       "    groups[name].visible = next;\n",
       "    // CSS2D labels (a/b/c, atom labels) ignore ancestor visibility in the\n",
       "    // CSS2DRenderer, so toggle them explicitly to match the meshes.\n",
       "    groups[name].traverse((o) => { if (o.isCSS2DObject) o.visible = next; });\n",
       "    button.classList.toggle('on', next);\n",
       "  });\n",
       "}\n",
       "if (hasFeatureToggle) {\n",
       "  modebar.appendChild(featureGroup);\n",
       "}\n",
       "\n",
       "const legendSwatches = [];\n",
       "const addLegendItem = (background, text, symbol) => {\n",
       "  const item = document.createElement('div');\n",
       "  const swatch = document.createElement('span');\n",
       "  swatch.className = 'sw';\n",
       "  swatch.style.background = background;\n",
       "  item.appendChild(swatch);\n",
       "  item.appendChild(document.createTextNode(text));\n",
       "  legend.appendChild(item);\n",
       "  if (symbol) legendSwatches.push({ symbol, el: swatch });\n",
       "};\n",
       "\n",
       "// One solid swatch per distinct element, mirroring the PDF report legend.\n",
       "for (const entry of SCENE.legend) addLegendItem(rgbCss(entry.colour), entry.symbol, entry.symbol);\n",
       "\n",
       "if (!legend.children.length) legend.style.display = 'none';\n",
       "\n",
       "// Colour-scheme selector: recolours atoms and legend swatches live. The\n",
       "// crystallography stays in Python; the JS only picks a pre-computed palette.\n",
       "const schemeNames = Object.keys(PALETTES);\n",
       "if (schemeNames.length > 1 && SCENE.legend.length) {\n",
       "  const matches = (a, b) => a && b && a[0] === b[0] && a[1] === b[1] && a[2] === b[2];\n",
       "  const first = SCENE.legend[0];\n",
       "  let current = schemeNames.find((name) => matches(PALETTES[name][first.symbol], first.colour))\n",
       "    || schemeNames[0];\n",
       "  const applyScheme = (name) => {\n",
       "    const palette = PALETTES[name] || {};\n",
       "    const recolor = (obj) => {\n",
       "      if (obj.isMesh && palette[obj.userData.element]) {\n",
       "        obj.material.color.copy(col(palette[obj.userData.element]));\n",
       "      }\n",
       "    };\n",
       "    groups.atoms.traverse(recolor);\n",
       "    groups.bonds.traverse(recolor);\n",
       "    for (const { symbol, el } of legendSwatches) {\n",
       "      if (palette[symbol]) el.style.background = rgbCss(palette[symbol]);\n",
       "    }\n",
       "  };\n",
       "  const select = document.createElement('select');\n",
       "  select.className = 'mb-select';\n",
       "  select.title = 'Colour scheme';\n",
       "  for (const name of schemeNames) {\n",
       "    const opt = document.createElement('option');\n",
       "    opt.value = name;\n",
       "    opt.textContent = name;\n",
       "    opt.selected = name === current;\n",
       "    select.appendChild(opt);\n",
       "  }\n",
       "  select.addEventListener('change', () => applyScheme(select.value));\n",
       "  const schemeGroup = document.createElement('div');\n",
       "  schemeGroup.className = 'mb-grp';\n",
       "  schemeGroup.appendChild(select);\n",
       "  modebar.appendChild(schemeGroup);\n",
       "}\n",
       "\n",
       "const downloadButton = iconButton(downloadHost, ICONS.camera, 'Download PNG');\n",
       "downloadButton.addEventListener('click', () => {\n",
       "  renderer.render(scene, camera);\n",
       "  const link = document.createElement('a');\n",
       "  link.download = 'structure.png';\n",
       "  link.href = renderer.domElement.toDataURL('image/png');\n",
       "  link.click();\n",
       "});\n",
       "\n",
       "const raycaster = new THREE.Raycaster();\n",
       "const pointer = new THREE.Vector2();\n",
       "renderer.domElement.addEventListener('pointermove', (event) => {\n",
       "  const rect = renderer.domElement.getBoundingClientRect();\n",
       "  pointer.x = ((event.clientX - rect.left) / rect.width) * 2 - 1;\n",
       "  pointer.y = -((event.clientY - rect.top) / rect.height) * 2 + 1;\n",
       "  raycaster.setFromCamera(pointer, camera);\n",
       "  const hits = raycaster.intersectObjects(groups.atoms.children, false);\n",
       "  const labelled = hits.find((hit) => hit.object.userData.label);\n",
       "  if (labelled) {\n",
       "    tooltip.textContent = labelled.object.userData.label;\n",
       "    tooltip.style.left = `${event.clientX - rect.left + 8}px`;\n",
       "    tooltip.style.top = `${event.clientY - rect.top + 8}px`;\n",
       "    tooltip.style.display = 'block';\n",
       "  } else {\n",
       "    tooltip.style.display = 'none';\n",
       "  }\n",
       "});\n",
       "\n",
       "const resize = () => {\n",
       "  width = host.clientWidth || width;\n",
       "  height = host.clientHeight || height;\n",
       "  const ratio = width / height;\n",
       "  perspective.aspect = ratio;\n",
       "  perspective.updateProjectionMatrix();\n",
       "  // Recompute the ortho frustum for the new aspect exactly as on setup, so\n",
       "  // width/height === ratio (spheres stay round) and the modebar band is kept.\n",
       "  const oh = Math.max(halfH, halfW / ratio);\n",
       "  const reserve = (2 * oh / height) * topBandPx;\n",
       "  const hv = oh + reserve * 0.5;\n",
       "  ortho.left = -hv * ratio;\n",
       "  ortho.right = hv * ratio;\n",
       "  ortho.top = hv + reserve * 0.5;\n",
       "  ortho.bottom = -hv + reserve * 0.5;\n",
       "  ortho.updateProjectionMatrix();\n",
       "  renderer.setSize(width, height);\n",
       "  labelRenderer.setSize(width, height);\n",
       "};\n",
       "if (window.ResizeObserver) new ResizeObserver(resize).observe(host);\n",
       "\n",
       "const hostTheme = () => {\n",
       "  const scheme = (document.body && document.body.getAttribute('data-md-color-scheme'))\n",
       "    || (document.documentElement && document.documentElement.getAttribute('data-md-color-scheme'));\n",
       "  if (scheme === 'slate') return 'dark';\n",
       "  if (scheme === 'default') return 'light';\n",
       "  const jpLight = (document.body && document.body.getAttribute('data-jp-theme-light'))\n",
       "    || (document.documentElement && document.documentElement.getAttribute('data-jp-theme-light'));\n",
       "  if (jpLight === 'true') return 'light';\n",
       "  if (jpLight === 'false') return 'dark';\n",
       "  return INITIAL_THEME;\n",
       "};\n",
       "\n",
       "const applyTheme = (name) => {\n",
       "  const themeName = name === 'dark' ? 'dark' : 'light';\n",
       "  root.classList.toggle('cv-theme-dark', themeName === 'dark');\n",
       "  root.classList.toggle('cv-theme-light', themeName !== 'dark');\n",
       "  cellMaterial.color.setStyle(cssVar('--cv-scene-fg', 'rgb(34, 34, 34)'));\n",
       "  // Paint the scene background via the renderer clear color so it always\n",
       "  // matches the Plotly axes-rectangle background, independent of any\n",
       "  // host-page CSS that might otherwise leave the canvas transparent.\n",
       "  const sceneBg = themeName === 'dark' ? 'rgb(33, 33, 33)' : 'rgb(255, 255, 255)';\n",
       "  renderer.setClearColor(new THREE.Color().setStyle(sceneBg), 1);\n",
       "};\n",
       "\n",
       "root.__crysviewApplyTheme = applyTheme;\n",
       "applyTheme(hostTheme());\n",
       "if (window.MutationObserver) {\n",
       "  const themeObserver = new MutationObserver(() => applyTheme(hostTheme()));\n",
       "  themeObserver.observe(document.documentElement, {\n",
       "    attributes: true,\n",
       "    attributeFilter: ['data-md-color-scheme', 'data-jp-theme-light', 'data-jp-theme-name'],\n",
       "  });\n",
       "  if (document.body) {\n",
       "    themeObserver.observe(document.body, {\n",
       "      attributes: true,\n",
       "      attributeFilter: ['data-md-color-scheme', 'data-jp-theme-light', 'data-jp-theme-name'],\n",
       "    });\n",
       "  }\n",
       "}\n",
       "\n",
       "// Camera-relative light directions (right, up, toward-camera), matching the\n",
       "// raster figure's _LIGHT / _FILL so both engines shade atoms identically.\n",
       "const KEY_LOCAL = [0.3, 0.45, 0.85];\n",
       "const FILL_LOCAL = [-0.4, -0.2, -0.45];\n",
       "const keyDir = new THREE.Vector3();\n",
       "const fillDir = new THREE.Vector3();\n",
       "const placeLight = (light, local, dir) => {\n",
       "  const m = camera.matrixWorld.elements;\n",
       "  dir.set(\n",
       "    local[0] * m[0] + local[1] * m[4] + local[2] * m[8],\n",
       "    local[0] * m[1] + local[1] * m[5] + local[2] * m[9],\n",
       "    local[0] * m[2] + local[1] * m[6] + local[2] * m[10],\n",
       "  ).normalize();\n",
       "  light.position.copy(target).addScaledVector(dir, radius * 5);\n",
       "  light.target.position.copy(target);\n",
       "};\n",
       "\n",
       "const animate = () => {\n",
       "  requestAnimationFrame(animate);\n",
       "  controls.update();\n",
       "  placeLight(key, KEY_LOCAL, keyDir);\n",
       "  placeLight(fill, FILL_LOCAL, fillDir);\n",
       "  renderer.render(scene, camera);\n",
       "  labelRenderer.render(scene, camera);\n",
       "};\n",
       "animate();\n",
       "const cvLoading = root.querySelector('.cv-loading');\n",
       "if (cvLoading) cvLoading.remove();\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "project.display.structure(struct_name='pbso4')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "60",
   "metadata": {},
   "source": [
    "### Display Pattern"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "61",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:16.226001Z",
     "iopub.status.busy": "2026-06-04T16:27:16.225827Z",
     "iopub.status.idle": "2026-06-04T16:27:17.311991Z",
     "shell.execute_reply": "2026-06-04T16:27:17.311219Z"
    }
   },
   "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",
       "                     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",
       "            }\n",
       "        "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "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",
       "                     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",
       "            }\n",
       "        "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "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",
       "                     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",
       "            }\n",
       "        "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "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",
       "                     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",
       "            }\n",
       "        "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
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   ],
   "source": [
    "project.display.pattern(expt_name='xrd', x_min=29.0, x_max=30.4)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "63",
   "metadata": {},
   "source": [
    "## 💾 Save Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "64",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-06-04T16:27:18.764722Z",
     "iopub.status.busy": "2026-06-04T16:27:18.764493Z",
     "iopub.status.idle": "2026-06-04T16:27:20.486241Z",
     "shell.execute_reply": "2026-06-04T16:27:20.485475Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;36mSaving project 📦 \u001b[0m\u001b[32m'pbso4_joint'\u001b[0m\u001b[1;36m to \u001b[0m\u001b[32m'../../../projects/ed_4_pbso4_joint'\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "├── 📄 project.cif\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "├── 📁 structures/\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "│   └── 📄 pbso4.cif\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "├── 📁 experiments/\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "│   └── 📄 npd.cif\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "│   └── 📄 xrd.cif\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "├── 📁 analysis/\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "│   └── 📄 analysis.cif\n"
     ]
    },
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       "            }\n",
       "        "
      ],
      "text/plain": [
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     "metadata": {},
     "output_type": "display_data"
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    {
     "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",
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       "\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",
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       "                            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",
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       "                })();\n",
       "            "
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      "text/plain": [
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       "                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",
       "            }\n",
       "        "
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      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "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": {
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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",
       "            }\n",
       "        "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
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     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "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",
       "                     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",
       "            }\n",
       "        "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "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",
       "                     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",
       "            }\n",
       "        "
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "└── 📁 reports/\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    └── 📄 pbso4_joint.html\n"
     ]
    }
   ],
   "source": [
    "project.save_as(dir_path='projects/ed_4_pbso4_joint')"
   ]
  }
 ],
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