{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "edccddaa",
   "metadata": {},
   "source": [
    "# Crystallography\n",
    "Notebook to explore crystallography functions in Anri."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ce75e4d1",
   "metadata": {},
   "outputs": [],
   "source": [
    "import anri\n",
    "\n",
    "import urllib.request"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5a1b2102",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc = anri.crystal.Structure.from_cif(\"../../../tests/data/cif/Fe.cif\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c7bc2ecc",
   "metadata": {},
   "source": [
    "Now let's generate some HKLs up to a d-star limit (with a given wavelength): "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e9c36779",
   "metadata": {},
   "outputs": [],
   "source": [
    "dsmax = 0.75\n",
    "wavelength = 0.18\n",
    "struc.make_hkls(dsmax=dsmax, wavelength=wavelength)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d92d7bfb",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.allhkls"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a2c18e11",
   "metadata": {},
   "source": [
    "Because we have a structure with atoms, we can simulate intensities. Calling `rings_table` will get the intensities for each hkl, and filter out the ones with very low intensity:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e328e70d",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.rings_table"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f1271279",
   "metadata": {},
   "source": [
    "We can also get a dictionary grouped by ring ID:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0d033119",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.rings_dict"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "51d66016",
   "metadata": {},
   "source": [
    "Each entry in the dict is an individual ring, grouped by $d^*$. This is useful for further indexing procedures etc.  \n",
    "There are some other helpful methods:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3f42b354",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.ringhkls  # dict, grouped by d-star"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "acd3e0df",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.ringhkls_arr # just a single array of all hkls with meaningful intensities"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0462b0d3",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.ringtth  # the unique two-theta values of the rings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "68ba350d",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.ringds  # the unique d* values of the rings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5d152c8c",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.ringmult  # the multiplicities of the rings"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2c494bb0",
   "metadata": {},
   "source": [
    "We can confirm against ImageD11 too:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ff00f455",
   "metadata": {},
   "outputs": [],
   "source": [
    "from ImageD11.unitcell import unitcell\n",
    "uc = unitcell(struc.lattice_parameters, struc.sgno)\n",
    "uc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cfb80944",
   "metadata": {},
   "outputs": [],
   "source": [
    "uc.makerings(dsmax, tol=0.0001)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ae9ccbb6",
   "metadata": {},
   "outputs": [],
   "source": [
    "import jax.numpy as jnp\n",
    "jnp.array(uc.ringds)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5188082f",
   "metadata": {},
   "outputs": [],
   "source": [
    "(struc.ringds - jnp.array(uc.ringds)).sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c29b8dce",
   "metadata": {},
   "outputs": [],
   "source": [
    "uc.ringhkls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c22867d3",
   "metadata": {},
   "outputs": [],
   "source": [
    "struc.ringhkls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2df9b0c3",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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