{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d57a3c7e",
   "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: Ni, NPD\n",
    "\n",
    "This example demonstrates a pair distribution function (PDF) analysis of Ni,\n",
    "based on data collected from a constant wavelength neutron powder diffraction\n",
    "experiment.\n",
    "\n",
    "The dataset is taken from:\n",
    "https://github.com/diffpy/cmi_exchange/tree/main/cmi_scripts/fitNiPDF"
   ]
  },
  {
   "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'"
   ]
  },
  {
   "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='ni')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models['ni'].space_group.name_h_m = 'F m -3 m'\n",
    "project.sample_models['ni'].space_group.it_coordinate_system_code = '1'\n",
    "project.sample_models['ni'].cell.length_a = 3.52387\n",
    "project.sample_models['ni'].atom_sites.add(\n",
    "    label='Ni', type_symbol='Ni', fract_x=0.0, fract_y=0.0, fract_z=0.0, wyckoff_letter='a', b_iso=0.5\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('ni-q27r100-neutron_from-2.gr', destination='data')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "12",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments.add(\n",
    "    name='pdf',\n",
    "    sample_form='powder',\n",
    "    beam_mode='constant wavelength',\n",
    "    radiation_probe='neutron',\n",
    "    scattering_type='total',\n",
    "    data_path='data/ni-q27r100-neutron_from-2.gr',\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "13",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['pdf'].linked_phases.add(id='ni', scale=1.0)\n",
    "project.experiments['pdf'].peak.damp_q = 0\n",
    "project.experiments['pdf'].peak.broad_q = 0.03\n",
    "project.experiments['pdf'].peak.cutoff_q = 27.0\n",
    "project.experiments['pdf'].peak.sharp_delta_1 = 0.0\n",
    "project.experiments['pdf'].peak.sharp_delta_2 = 2.0\n",
    "project.experiments['pdf'].peak.damp_particle_diameter = 0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "14",
   "metadata": {},
   "source": [
    "## Select Fitting Parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "15",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.sample_models['ni'].cell.length_a.free = True\n",
    "project.sample_models['ni'].atom_sites['Ni'].b_iso.free = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments['pdf'].linked_phases['ni'].scale.free = True\n",
    "project.experiments['pdf'].peak.broad_q.free = True\n",
    "project.experiments['pdf'].peak.sharp_delta_2.free = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "17",
   "metadata": {},
   "source": [
    "## Run Fitting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "18",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.analysis.current_calculator = 'pdffit'\n",
    "project.analysis.fit()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "19",
   "metadata": {},
   "source": [
    "## Plot Measured vs Calculated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "20",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.plot_meas_vs_calc(expt_name='pdf', show_residual=True)"
   ]
  }
 ],
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  "jupytext": {
   "cell_metadata_filter": "-all",
   "main_language": "python",
   "notebook_metadata_filter": "-all"
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