{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7c151045",
   "metadata": {
    "tags": [
     "hide-in-docs"
    ]
   },
   "outputs": [],
   "source": [
    "# Check if the easydiffraction library is installed.\n",
    "# If not, install it including the 'visualization' extras.\n",
    "# This is needed, e.g., when running this as a notebook via Google Colab or\n",
    "# Jupyter Notebook in an environment where the library is not pre-installed.\n",
    "import builtins\n",
    "import importlib.util\n",
    "\n",
    "if hasattr(builtins, '__IPYTHON__'):\n",
    "    if importlib.util.find_spec('easydiffraction') is None:\n",
    "        !pip install 'easydiffraction[visualization]'\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0",
   "metadata": {},
   "source": [
    "# Structure Refinement: Si, SEPD\n",
    "\n",
    "This example demonstrates a Rietveld refinement of Si crystal structure using\n",
    "time-of-flight neutron powder diffraction data from SEPD at Argonne."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1",
   "metadata": {},
   "source": [
    "## Import Library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2",
   "metadata": {},
   "outputs": [],
   "source": [
    "from easydiffraction import Experiment\n",
    "from easydiffraction import Project\n",
    "from easydiffraction import SampleModel\n",
    "from easydiffraction import download_from_repository"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3",
   "metadata": {},
   "source": [
    "## Define Sample Model\n",
    "\n",
    "This section shows how to add sample models and modify their parameters.\n",
    "\n",
    "#### Create Sample Model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4",
   "metadata": {},
   "outputs": [],
   "source": [
    "model = SampleModel('si')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5",
   "metadata": {},
   "source": [
    "#### Set Space Group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6",
   "metadata": {},
   "outputs": [],
   "source": [
    "model.space_group.name_h_m = 'F d -3 m'\n",
    "model.space_group.it_coordinate_system_code = '2'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7",
   "metadata": {},
   "source": [
    "#### Set Unit Cell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8",
   "metadata": {},
   "outputs": [],
   "source": [
    "model.cell.length_a = 5.431"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9",
   "metadata": {},
   "source": [
    "#### Set Atom Sites"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "10",
   "metadata": {},
   "outputs": [],
   "source": [
    "model.atom_sites.add('Si', 'Si', 0.125, 0.125, 0.125, b_iso=0.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "11",
   "metadata": {},
   "source": [
    "## Define Experiment\n",
    "\n",
    "This section shows how to add experiments, configure their parameters, and\n",
    "link the sample models defined in the previous step.\n",
    "\n",
    "#### Download Measured Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "12",
   "metadata": {},
   "outputs": [],
   "source": [
    "download_from_repository('sepd_si.xye', destination='data')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "13",
   "metadata": {},
   "source": [
    "#### Create Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "14",
   "metadata": {},
   "outputs": [],
   "source": [
    "expt = Experiment('sepd', beam_mode='time-of-flight', data_path='data/sepd_si.xye')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "15",
   "metadata": {},
   "source": [
    "#### Set Instrument"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16",
   "metadata": {},
   "outputs": [],
   "source": [
    "expt.instrument.setup_twotheta_bank = 144.845\n",
    "expt.instrument.calib_d_to_tof_offset = 0.0\n",
    "expt.instrument.calib_d_to_tof_linear = 7476.91\n",
    "expt.instrument.calib_d_to_tof_quad = -1.54"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "17",
   "metadata": {},
   "source": [
    "#### Set Peak Profile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "18",
   "metadata": {},
   "outputs": [],
   "source": [
    "expt.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'\n",
    "expt.peak.broad_gauss_sigma_0 = 3.0\n",
    "expt.peak.broad_gauss_sigma_1 = 40.0\n",
    "expt.peak.broad_gauss_sigma_2 = 2.0\n",
    "expt.peak.broad_mix_beta_0 = 0.04221\n",
    "expt.peak.broad_mix_beta_1 = 0.00946"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "19",
   "metadata": {},
   "source": [
    "#### Set Peak Asymmetry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "20",
   "metadata": {},
   "outputs": [],
   "source": [
    "expt.peak.asym_alpha_0 = 0.0\n",
    "expt.peak.asym_alpha_1 = 0.5971"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "21",
   "metadata": {},
   "source": [
    "#### Set Background"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "22",
   "metadata": {},
   "outputs": [],
   "source": [
    "expt.background_type = 'line-segment'\n",
    "for x in range(0, 35000, 5000):\n",
    "    expt.background.add(x=x, y=200)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "23",
   "metadata": {},
   "source": [
    "#### Set Linked Phases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "24",
   "metadata": {},
   "outputs": [],
   "source": [
    "expt.linked_phases.add('si', scale=10.0)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "25",
   "metadata": {},
   "source": [
    "## Define Project\n",
    "\n",
    "The project object is used to manage the sample model, experiment, and\n",
    "analysis.\n",
    "\n",
    "#### Create Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "26",
   "metadata": {},
   "outputs": [],
   "source": [
    "project = Project()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "27",
   "metadata": {},
   "source": [
    "#### Set Plotting Engine"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "28",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plotter.engine = 'plotly'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "29",
   "metadata": {},
   "source": [
    "#### Add Sample Model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "30",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models.add(model)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "31",
   "metadata": {},
   "source": [
    "#### Add Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "32",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments.add(expt)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "33",
   "metadata": {},
   "source": [
    "## Perform Analysis\n",
    "\n",
    "This section shows the analysis process, including how to set up\n",
    "calculation and fitting engines.\n",
    "\n",
    "#### Set Calculator"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "34",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.current_calculator = 'cryspy'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "35",
   "metadata": {},
   "source": [
    "#### Set Minimizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "36",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.current_minimizer = 'lmfit (leastsq)'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "37",
   "metadata": {},
   "source": [
    "#### Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "38",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', show_residual=True)\n",
    "project.plot_meas_vs_calc(expt_name='sepd', x_min=23200, x_max=23700, show_residual=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "39",
   "metadata": {},
   "source": [
    "### Perform Fit 1/5\n",
    "\n",
    "Set parameters to be refined."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "40",
   "metadata": {},
   "outputs": [],
   "source": [
    "model.cell.length_a.free = True\n",
    "\n",
    "expt.linked_phases['si'].scale.free = True\n",
    "expt.instrument.calib_d_to_tof_offset.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "41",
   "metadata": {},
   "source": [
    "Show free parameters after selection."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "42",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.show_free_params()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "43",
   "metadata": {},
   "source": [
    "#### Run Fitting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "44",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "45",
   "metadata": {},
   "source": [
    "#### Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "46",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', show_residual=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "47",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', x_min=23200, x_max=23700, show_residual=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "48",
   "metadata": {},
   "source": [
    "### Perform Fit 2/5\n",
    "\n",
    "Set more parameters to be refined."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "49",
   "metadata": {},
   "outputs": [],
   "source": [
    "for point in expt.background:\n",
    "    point.y.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "50",
   "metadata": {},
   "source": [
    "Show free parameters after selection."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "51",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.show_free_params()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "52",
   "metadata": {},
   "source": [
    "#### Run Fitting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "53",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "54",
   "metadata": {},
   "source": [
    "#### Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "55",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', show_residual=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "56",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', x_min=23200, x_max=23700, show_residual=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "57",
   "metadata": {},
   "source": [
    "### Perform Fit 3/5\n",
    "\n",
    "Fix background points."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "58",
   "metadata": {},
   "outputs": [],
   "source": [
    "for point in expt.background:\n",
    "    point.y.free = False"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "59",
   "metadata": {},
   "source": [
    "Set more parameters to be refined."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "60",
   "metadata": {},
   "outputs": [],
   "source": [
    "expt.peak.broad_gauss_sigma_0.free = True\n",
    "expt.peak.broad_gauss_sigma_1.free = True\n",
    "expt.peak.broad_gauss_sigma_2.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "61",
   "metadata": {},
   "source": [
    "Show free parameters after selection."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "62",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.show_free_params()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "63",
   "metadata": {},
   "source": [
    "#### Run Fitting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "64",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "65",
   "metadata": {},
   "source": [
    "#### Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "66",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', show_residual=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "67",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', x_min=23200, x_max=23700, show_residual=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "68",
   "metadata": {},
   "source": [
    "### Perform Fit 4/5\n",
    "\n",
    "Set more parameters to be refined."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "69",
   "metadata": {},
   "outputs": [],
   "source": [
    "model.atom_sites['Si'].b_iso.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "70",
   "metadata": {},
   "source": [
    "Show free parameters after selection."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "71",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.show_free_params()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "72",
   "metadata": {},
   "source": [
    "#### Run Fitting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "73",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "74",
   "metadata": {},
   "source": [
    "#### Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "75",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', show_residual=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "76",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='sepd', x_min=23200, x_max=23700, show_residual=True)"
   ]
  }
 ],
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