{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "287e0e45",
   "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: LBCO+Si, McStas\n",
    "\n",
    "This example demonstrates a Rietveld refinement of La0.5Ba0.5CoO3 crystal\n",
    "structure with a small amount of Si phase using time-of-flight neutron powder\n",
    "diffraction data simulated with McStas."
   ]
  },
  {
   "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 Models\n",
    "\n",
    "This section shows how to add sample models and modify their parameters.\n",
    "\n",
    "### Create Sample Model 1: LBCO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_1 = SampleModel('lbco')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5",
   "metadata": {},
   "source": [
    "#### Set Space Group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_1.space_group.name_h_m = 'P m -3 m'\n",
    "model_1.space_group.it_coordinate_system_code = '1'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7",
   "metadata": {},
   "source": [
    "#### Set Unit Cell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_1.cell.length_a = 3.8909"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9",
   "metadata": {},
   "source": [
    "#### Set Atom Sites"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "10",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_1.atom_sites.add(\n",
    "    'La',\n",
    "    'La',\n",
    "    0,\n",
    "    0,\n",
    "    0,\n",
    "    wyckoff_letter='a',\n",
    "    b_iso=0.2,\n",
    "    occupancy=0.5,\n",
    ")\n",
    "model_1.atom_sites.add(\n",
    "    'Ba',\n",
    "    'Ba',\n",
    "    0,\n",
    "    0,\n",
    "    0,\n",
    "    wyckoff_letter='a',\n",
    "    b_iso=0.2,\n",
    "    occupancy=0.5,\n",
    ")\n",
    "model_1.atom_sites.add(\n",
    "    'Co',\n",
    "    'Co',\n",
    "    0.5,\n",
    "    0.5,\n",
    "    0.5,\n",
    "    wyckoff_letter='b',\n",
    "    b_iso=0.2567,\n",
    ")\n",
    "model_1.atom_sites.add(\n",
    "    'O',\n",
    "    'O',\n",
    "    0,\n",
    "    0.5,\n",
    "    0.5,\n",
    "    wyckoff_letter='c',\n",
    "    b_iso=1.4041,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "11",
   "metadata": {},
   "source": [
    "### Create Sample Model 2: Si"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "12",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_2 = SampleModel('si')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "13",
   "metadata": {},
   "source": [
    "#### Set Space Group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "14",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_2.space_group.name_h_m = 'F d -3 m'\n",
    "model_2.space_group.it_coordinate_system_code = '2'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "15",
   "metadata": {},
   "source": [
    "#### Set Unit Cell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_2.cell.length_a = 5.43146"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "17",
   "metadata": {},
   "source": [
    "#### Set Atom Sites"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "18",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_2.atom_sites.add(\n",
    "    'Si',\n",
    "    'Si',\n",
    "    0.0,\n",
    "    0.0,\n",
    "    0.0,\n",
    "    wyckoff_letter='a',\n",
    "    b_iso=0.0,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "19",
   "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 Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "20",
   "metadata": {},
   "outputs": [],
   "source": [
    "download_from_repository('mcstas_lbco-si.xye', destination='data')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "21",
   "metadata": {},
   "source": [
    "#### Create Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "22",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment = Experiment(\n",
    "    'mcstas',\n",
    "    sample_form='powder',\n",
    "    beam_mode='time-of-flight',\n",
    "    radiation_probe='neutron',\n",
    "    scattering_type='bragg',\n",
    "    data_path='data/mcstas_lbco-si.xye',\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "23",
   "metadata": {},
   "source": [
    "#### Set Instrument"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "24",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.instrument.setup_twotheta_bank = 94.90931761529106\n",
    "experiment.instrument.calib_d_to_tof_offset = 0.0\n",
    "experiment.instrument.calib_d_to_tof_linear = 58724.76869981215\n",
    "experiment.instrument.calib_d_to_tof_quad = -0.00001"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "25",
   "metadata": {},
   "source": [
    "#### Set Peak Profile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "26",
   "metadata": {},
   "outputs": [],
   "source": [
    "# experiment.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'\n",
    "experiment.peak.broad_gauss_sigma_0 = 45137\n",
    "experiment.peak.broad_gauss_sigma_1 = -52394\n",
    "experiment.peak.broad_gauss_sigma_2 = 22998\n",
    "experiment.peak.broad_mix_beta_0 = 0.0055\n",
    "experiment.peak.broad_mix_beta_1 = 0.0041\n",
    "experiment.peak.asym_alpha_0 = 0\n",
    "experiment.peak.asym_alpha_1 = 0.0097"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "27",
   "metadata": {},
   "source": [
    "#### Set Background"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "28",
   "metadata": {},
   "source": [
    "Select the background type."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "29",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.background_type = 'line-segment'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "30",
   "metadata": {},
   "source": [
    "Add background points."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "31",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.background.add(x=45000, y=0.2)\n",
    "experiment.background.add(x=50000, y=0.2)\n",
    "experiment.background.add(x=55000, y=0.2)\n",
    "experiment.background.add(x=65000, y=0.2)\n",
    "experiment.background.add(x=70000, y=0.2)\n",
    "experiment.background.add(x=75000, y=0.2)\n",
    "experiment.background.add(x=80000, y=0.2)\n",
    "experiment.background.add(x=85000, y=0.2)\n",
    "experiment.background.add(x=90000, y=0.2)\n",
    "experiment.background.add(x=95000, y=0.2)\n",
    "experiment.background.add(x=100000, y=0.2)\n",
    "experiment.background.add(x=105000, y=0.2)\n",
    "experiment.background.add(x=110000, y=0.2)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "32",
   "metadata": {},
   "source": [
    "#### Set Linked Phases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "33",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.linked_phases.add('lbco', scale=4.0)\n",
    "experiment.linked_phases.add('si', scale=0.2)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "34",
   "metadata": {},
   "source": [
    "## Define Project\n",
    "\n",
    "The project object is used to manage sample models, experiments, and analysis.\n",
    "\n",
    "#### Create Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "35",
   "metadata": {},
   "outputs": [],
   "source": [
    "project = Project()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "36",
   "metadata": {},
   "source": [
    "#### Set Plotting Engine"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "37",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plotter.engine = 'plotly'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "38",
   "metadata": {},
   "source": [
    "#### Add Sample Models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "39",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models.add(model_1)\n",
    "project.sample_models.add(model_2)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "40",
   "metadata": {},
   "source": [
    "#### Show Sample Models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "41",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models.show_names()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "42",
   "metadata": {},
   "source": [
    "#### Add Experiments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "43",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments.add(experiment)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "44",
   "metadata": {},
   "source": [
    "#### Set Excluded Regions\n",
    "\n",
    "Show measured data as loaded from the file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "45",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas(expt_name='mcstas')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "46",
   "metadata": {},
   "source": [
    "Add excluded regions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "47",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.excluded_regions.add(minimum=0, maximum=40000)\n",
    "experiment.excluded_regions.add(minimum=108000, maximum=200000)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "48",
   "metadata": {},
   "source": [
    "Show excluded regions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "49",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.excluded_regions.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "50",
   "metadata": {},
   "source": [
    "Show measured data after adding excluded regions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "51",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas(expt_name='mcstas')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "52",
   "metadata": {},
   "source": [
    "Show experiment as CIF."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "53",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['mcstas'].show_as_cif()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "54",
   "metadata": {},
   "source": [
    "## Perform Analysis\n",
    "\n",
    "This section outlines the analysis process, including how to configure\n",
    "calculation and fitting engines.\n",
    "\n",
    "#### Set Calculator"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "55",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.current_calculator = 'cryspy'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "56",
   "metadata": {},
   "source": [
    "#### Set Minimizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "57",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.current_minimizer = 'lmfit (leastsq)'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "58",
   "metadata": {},
   "source": [
    "#### Set Fitting Parameters\n",
    "\n",
    "Set sample model parameters to be optimized."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "59",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_1.cell.length_a.free = True\n",
    "model_1.atom_sites['Co'].b_iso.free = True\n",
    "model_1.atom_sites['O'].b_iso.free = True\n",
    "\n",
    "model_2.cell.length_a.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "60",
   "metadata": {},
   "source": [
    "Set experiment parameters to be optimized."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "61",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.linked_phases['lbco'].scale.free = True\n",
    "experiment.linked_phases['si'].scale.free = True\n",
    "\n",
    "experiment.peak.broad_gauss_sigma_0.free = True\n",
    "experiment.peak.broad_gauss_sigma_1.free = True\n",
    "experiment.peak.broad_gauss_sigma_2.free = True\n",
    "\n",
    "experiment.peak.asym_alpha_1.free = True\n",
    "experiment.peak.broad_mix_beta_0.free = True\n",
    "experiment.peak.broad_mix_beta_1.free = True\n",
    "\n",
    "for point in experiment.background:\n",
    "    point.y.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "62",
   "metadata": {},
   "source": [
    "#### Perform Fit"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "63",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "64",
   "metadata": {},
   "source": [
    "#### Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "65",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='mcstas')"
   ]
  }
 ],
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