{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "70451e70",
   "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": [
    "# Pair Distribution Function: NaCl, XRD\n",
    "\n",
    "This example demonstrates a pair distribution function (PDF) analysis of\n",
    "NaCl, based on data collected from an X-ray powder diffraction experiment.\n",
    "\n",
    "The dataset is taken from:\n",
    "https://github.com/diffpy/add2019-diffpy-cmi/tree/master"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1",
   "metadata": {},
   "source": [
    "## Import Library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2",
   "metadata": {},
   "outputs": [],
   "source": [
    "import easydiffraction as ed"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3",
   "metadata": {},
   "source": [
    "## Create Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4",
   "metadata": {},
   "outputs": [],
   "source": [
    "project = ed.Project()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5",
   "metadata": {},
   "source": [
    "## Set Plotting Engine"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plotter.engine = 'plotly'\n",
    "project.plotter.x_min = 2.0\n",
    "project.plotter.x_max = 30.0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7",
   "metadata": {},
   "source": [
    "## Add Sample Model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models.add(name='nacl')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models['nacl'].space_group.name_h_m = 'F m -3 m'\n",
    "project.sample_models['nacl'].space_group.it_coordinate_system_code = '1'\n",
    "project.sample_models['nacl'].cell.length_a = 5.62\n",
    "project.sample_models['nacl'].atom_sites.add(\n",
    "    label='Na', type_symbol='Na', fract_x=0, fract_y=0, fract_z=0, wyckoff_letter='a', b_iso=1.0\n",
    ")\n",
    "project.sample_models['nacl'].atom_sites.add(\n",
    "    label='Cl', type_symbol='Cl', fract_x=0.5, fract_y=0.5, fract_z=0.5, wyckoff_letter='b', b_iso=1.0\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "10",
   "metadata": {},
   "source": [
    "## Add Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "11",
   "metadata": {},
   "outputs": [],
   "source": [
    "ed.download_from_repository('NaCl.gr', destination='data')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "12",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments.add(\n",
    "    name='xray_pdf',\n",
    "    sample_form='powder',\n",
    "    beam_mode='constant wavelength',\n",
    "    radiation_probe='xray',\n",
    "    scattering_type='total',\n",
    "    data_path='data/NaCl.gr',\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "13",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['xray_pdf'].show_supported_peak_profile_types()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "14",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['xray_pdf'].show_current_peak_profile_type()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "15",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['xray_pdf'].peak_profile_type = 'gaussian-damped-sinc'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['xray_pdf'].peak.damp_q = 0.03\n",
    "project.experiments['xray_pdf'].peak.broad_q = 0\n",
    "project.experiments['xray_pdf'].peak.cutoff_q = 21\n",
    "project.experiments['xray_pdf'].peak.sharp_delta_1 = 0\n",
    "project.experiments['xray_pdf'].peak.sharp_delta_2 = 5\n",
    "project.experiments['xray_pdf'].peak.damp_particle_diameter = 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "17",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['xray_pdf'].linked_phases.add(id='nacl', scale=0.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "18",
   "metadata": {},
   "source": [
    "## Select Fitting Parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "19",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models['nacl'].cell.length_a.free = True\n",
    "project.sample_models['nacl'].atom_sites['Na'].b_iso.free = True\n",
    "project.sample_models['nacl'].atom_sites['Cl'].b_iso.free = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "20",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['xray_pdf'].linked_phases['nacl'].scale.free = True\n",
    "project.experiments['xray_pdf'].peak.damp_q.free = True\n",
    "project.experiments['xray_pdf'].peak.sharp_delta_2.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "21",
   "metadata": {},
   "source": [
    "## Run Fitting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "22",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.current_calculator = 'pdffit'\n",
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "23",
   "metadata": {},
   "source": [
    "## Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "24",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='xray_pdf')"
   ]
  }
 ],
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  "jupytext": {
   "cell_metadata_filter": "-all",
   "main_language": "python",
   "notebook_metadata_filter": "-all"
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 "nbformat_minor": 5
}