{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cb7ab0e6",
   "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: Si, NPD\n",
    "\n",
    "This example demonstrates a pair distribution function (PDF) analysis of Si,\n",
    "based on data collected from a time-of-flight neutron powder diffraction\n",
    "experiment at NOMAD at SNS."
   ]
  },
  {
   "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_max = 40"
   ]
  },
  {
   "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='si')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9",
   "metadata": {},
   "outputs": [],
   "source": [
    "sample_model = project.sample_models['si']\n",
    "sample_model.space_group.name_h_m.value = 'F d -3 m'\n",
    "sample_model.space_group.it_coordinate_system_code = '1'\n",
    "sample_model.cell.length_a = 5.43146\n",
    "sample_model.atom_sites.add(label='Si', type_symbol='Si', fract_x=0, fract_y=0, fract_z=0, wyckoff_letter='a', b_iso=0.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "10",
   "metadata": {},
   "source": [
    "## Add Experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "11",
   "metadata": {},
   "outputs": [],
   "source": [
    "ed.download_from_repository('NOM_9999_Si_640g_PAC_50_ff_ftfrgr_up-to-50.gr', destination='data')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "12",
   "metadata": {},
   "outputs": [],
   "source": [
    "project.experiments.add(\n",
    "    name='nomad',\n",
    "    sample_form='powder',\n",
    "    beam_mode='time-of-flight',\n",
    "    radiation_probe='neutron',\n",
    "    scattering_type='total',\n",
    "    data_path='data/NOM_9999_Si_640g_PAC_50_ff_ftfrgr_up-to-50.gr',\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "13",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment = project.experiments['nomad']\n",
    "experiment.linked_phases.add(id='si', scale=1.0)\n",
    "experiment.peak.damp_q = 0.02\n",
    "experiment.peak.broad_q = 0.03\n",
    "experiment.peak.cutoff_q = 35.0\n",
    "experiment.peak.sharp_delta_1 = 0.0\n",
    "experiment.peak.sharp_delta_2 = 4.0\n",
    "experiment.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['si'].cell.length_a.free = True\n",
    "project.sample_models['si'].atom_sites['Si'].b_iso.free = True\n",
    "experiment.linked_phases['si'].scale.free = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16",
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment.peak.damp_q.free = True\n",
    "experiment.peak.broad_q.free = True\n",
    "experiment.peak.sharp_delta_1.free = True\n",
    "experiment.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='nomad', show_residual=False)"
   ]
  }
 ],
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