{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "0",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T15:03:11.631193Z",
     "iopub.status.busy": "2026-04-14T15:03:11.630982Z",
     "iopub.status.idle": "2026-04-14T15:03:11.635518Z",
     "shell.execute_reply": "2026-04-14T15:03:11.634803Z"
    },
    "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==0.13.1"
   ]
  },
  {
   "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": "2026-04-14T15:03:11.637437Z",
     "iopub.status.busy": "2026-04-14T15:03:11.637238Z",
     "iopub.status.idle": "2026-04-14T15:03:14.271300Z",
     "shell.execute_reply": "2026-04-14T15:03:14.270360Z"
    }
   },
   "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": "2026-04-14T15:03:14.273275Z",
     "iopub.status.busy": "2026-04-14T15:03:14.272831Z",
     "iopub.status.idle": "2026-04-14T15:03:14.278065Z",
     "shell.execute_reply": "2026-04-14T15:03:14.277120Z"
    }
   },
   "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": "2026-04-14T15:03:14.279790Z",
     "iopub.status.busy": "2026-04-14T15:03:14.279607Z",
     "iopub.status.idle": "2026-04-14T15:03:14.283218Z",
     "shell.execute_reply": "2026-04-14T15:03:14.282456Z"
    }
   },
   "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": "2026-04-14T15:03:14.284931Z",
     "iopub.status.busy": "2026-04-14T15:03:14.284753Z",
     "iopub.status.idle": "2026-04-14T15:03:14.288003Z",
     "shell.execute_reply": "2026-04-14T15:03:14.287073Z"
    }
   },
   "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": "2026-04-14T15:03:14.289529Z",
     "iopub.status.busy": "2026-04-14T15:03:14.289370Z",
     "iopub.status.idle": "2026-04-14T15:03:14.296951Z",
     "shell.execute_reply": "2026-04-14T15:03:14.296091Z"
    },
    "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",
    "    wyckoff_letter='c',\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",
    "    wyckoff_letter='c',\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",
    "    wyckoff_letter='c',\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",
    "    wyckoff_letter='c',\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",
    "    wyckoff_letter='d',\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": "2026-04-14T15:03:14.298496Z",
     "iopub.status.busy": "2026-04-14T15:03:14.298333Z",
     "iopub.status.idle": "2026-04-14T15:03:14.539270Z",
     "shell.execute_reply": "2026-04-14T15:03:14.538412Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mGetting data\u001b[0m\u001b[1;34m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data #\u001b[1;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": "2026-04-14T15:03:14.540936Z",
     "iopub.status.busy": "2026-04-14T15:03:14.540755Z",
     "iopub.status.idle": "2026-04-14T15:03:14.713041Z",
     "shell.execute_reply": "2026-04-14T15:03:14.712179Z"
    }
   },
   "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": "2026-04-14T15:03:14.714934Z",
     "iopub.status.busy": "2026-04-14T15:03:14.714759Z",
     "iopub.status.idle": "2026-04-14T15:03:14.717978Z",
     "shell.execute_reply": "2026-04-14T15:03:14.717258Z"
    }
   },
   "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": "2026-04-14T15:03:14.719522Z",
     "iopub.status.busy": "2026-04-14T15:03:14.719361Z",
     "iopub.status.idle": "2026-04-14T15:03:14.722840Z",
     "shell.execute_reply": "2026-04-14T15:03:14.722007Z"
    }
   },
   "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": "2026-04-14T15:03:14.724647Z",
     "iopub.status.busy": "2026-04-14T15:03:14.724490Z",
     "iopub.status.idle": "2026-04-14T15:03:14.729901Z",
     "shell.execute_reply": "2026-04-14T15:03:14.729146Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mBackground type for experiment \u001b[0m\u001b[32m'npd'\u001b[0m\u001b[1;34m 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": "2026-04-14T15:03:14.731388Z",
     "iopub.status.busy": "2026-04-14T15:03:14.731226Z",
     "iopub.status.idle": "2026-04-14T15:03:14.736439Z",
     "shell.execute_reply": "2026-04-14T15:03:14.735651Z"
    }
   },
   "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": "2026-04-14T15:03:14.738291Z",
     "iopub.status.busy": "2026-04-14T15:03:14.738102Z",
     "iopub.status.idle": "2026-04-14T15:03:14.741274Z",
     "shell.execute_reply": "2026-04-14T15:03:14.740394Z"
    }
   },
   "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": "2026-04-14T15:03:14.742824Z",
     "iopub.status.busy": "2026-04-14T15:03:14.742633Z",
     "iopub.status.idle": "2026-04-14T15:03:14.916639Z",
     "shell.execute_reply": "2026-04-14T15:03:14.915652Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mGetting data\u001b[0m\u001b[1;34m...\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data #\u001b[1;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": "2026-04-14T15:03:14.918457Z",
     "iopub.status.busy": "2026-04-14T15:03:14.918227Z",
     "iopub.status.idle": "2026-04-14T15:03:15.199644Z",
     "shell.execute_reply": "2026-04-14T15:03:15.198789Z"
    }
   },
   "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": "2026-04-14T15:03:15.201470Z",
     "iopub.status.busy": "2026-04-14T15:03:15.201280Z",
     "iopub.status.idle": "2026-04-14T15:03:15.205091Z",
     "shell.execute_reply": "2026-04-14T15:03:15.203951Z"
    }
   },
   "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": "2026-04-14T15:03:15.206749Z",
     "iopub.status.busy": "2026-04-14T15:03:15.206557Z",
     "iopub.status.idle": "2026-04-14T15:03:15.211375Z",
     "shell.execute_reply": "2026-04-14T15:03:15.210084Z"
    }
   },
   "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": "2026-04-14T15:03:15.213478Z",
     "iopub.status.busy": "2026-04-14T15:03:15.213170Z",
     "iopub.status.idle": "2026-04-14T15:03:15.251445Z",
     "shell.execute_reply": "2026-04-14T15:03:15.248331Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mBackground type for experiment \u001b[0m\u001b[32m'xrd'\u001b[0m\u001b[1;34m 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": "2026-04-14T15:03:15.255912Z",
     "iopub.status.busy": "2026-04-14T15:03:15.255675Z",
     "iopub.status.idle": "2026-04-14T15:03:15.268185Z",
     "shell.execute_reply": "2026-04-14T15:03:15.264513Z"
    }
   },
   "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": "2026-04-14T15:03:15.270841Z",
     "iopub.status.busy": "2026-04-14T15:03:15.270543Z",
     "iopub.status.idle": "2026-04-14T15:03:15.280339Z",
     "shell.execute_reply": "2026-04-14T15:03:15.277448Z"
    }
   },
   "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": "2026-04-14T15:03:15.282438Z",
     "iopub.status.busy": "2026-04-14T15:03:15.282214Z",
     "iopub.status.idle": "2026-04-14T15:03:15.815147Z",
     "shell.execute_reply": "2026-04-14T15:03:15.814111Z"
    }
   },
   "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",
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       "                            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>"
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     },
     "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",
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   ],
   "source": [
    "project = Project()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "44",
   "metadata": {},
   "source": [
    "#### Add Structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "45",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T15:03:15.817201Z",
     "iopub.status.busy": "2026-04-14T15:03:15.816850Z",
     "iopub.status.idle": "2026-04-14T15:03:15.820403Z",
     "shell.execute_reply": "2026-04-14T15:03:15.819460Z"
    }
   },
   "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": "2026-04-14T15:03:15.821987Z",
     "iopub.status.busy": "2026-04-14T15:03:15.821825Z",
     "iopub.status.idle": "2026-04-14T15:03:15.824695Z",
     "shell.execute_reply": "2026-04-14T15:03:15.823896Z"
    }
   },
   "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": "2026-04-14T15:03:15.826361Z",
     "iopub.status.busy": "2026-04-14T15:03:15.826203Z",
     "iopub.status.idle": "2026-04-14T15:03:15.829751Z",
     "shell.execute_reply": "2026-04-14T15:03:15.828951Z"
    }
   },
   "outputs": [],
   "source": [
    "project.analysis.fit_mode.mode = 'joint'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "50",
   "metadata": {},
   "source": [
    "#### Set Minimizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "51",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T15:03:15.831568Z",
     "iopub.status.busy": "2026-04-14T15:03:15.831413Z",
     "iopub.status.idle": "2026-04-14T15:03:15.836782Z",
     "shell.execute_reply": "2026-04-14T15:03:15.835882Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[1;34mCurrent minimizer changed to\u001b[0m\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lmfit\n"
     ]
    }
   ],
   "source": [
    "project.analysis.current_minimizer = 'lmfit'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "52",
   "metadata": {},
   "source": [
    "#### Set Fitting Parameters\n",
    "\n",
    "Set structure parameters to be optimized."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "53",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T15:03:15.838346Z",
     "iopub.status.busy": "2026-04-14T15:03:15.838119Z",
     "iopub.status.idle": "2026-04-14T15:03:15.842074Z",
     "shell.execute_reply": "2026-04-14T15:03:15.841160Z"
    }
   },
   "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": "2026-04-14T15:03:15.843647Z",
     "iopub.status.busy": "2026-04-14T15:03:15.843490Z",
     "iopub.status.idle": "2026-04-14T15:03:15.846941Z",
     "shell.execute_reply": "2026-04-14T15:03:15.846240Z"
    }
   },
   "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": "2026-04-14T15:03:15.848764Z",
     "iopub.status.busy": "2026-04-14T15:03:15.848592Z",
     "iopub.status.idle": "2026-04-14T15:03:15.852772Z",
     "shell.execute_reply": "2026-04-14T15:03:15.851779Z"
    }
   },
   "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": [
    "#### Perform Fit"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "58",
   "metadata": {},
   "source": [
    "#### Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "59",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-04-14T15:03:15.854349Z",
     "iopub.status.busy": "2026-04-14T15:03:15.854169Z",
     "iopub.status.idle": "2026-04-14T15:03:16.098255Z",
     "shell.execute_reply": "2026-04-14T15:03:16.097419Z"
    }
   },
   "outputs": [
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