{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Classification of atoms as solid or liquid"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "pyscal can also be used to distinguish solid and liquid atoms. The\n",
    "classification is based on [Steinhardt\\'s\n",
    "parameters](https://pyscal.readthedocs.io/en/latest/steinhardtparameters.html),\n",
    "specifically $q_6$. The method defines two neighboring atoms $i$ and $j$\n",
    "as having solid bonds if a parameter $s_{ij}$ {cite}`Auer2005`,\n",
    "\n",
    "> $$s_{ij} = \\sum_{m=-6}^6 q_{6m}(i) q_{6m}^*(j) \\geq \\mathrm{threshold}$$\n",
    "\n",
    "Additionally, a second order parameter is used to improve the\n",
    "distinction in solid-liquid boundaries {cite}`Bokeloh2014`. This is defined by the\n",
    "criteria,\n",
    "\n",
    "> $$\\langle s_{ij} \\rangle > \\mathrm{avgthreshold}$$\n",
    "\n",
    "If a particle has $n$ number of bonds with\n",
    "$s_{ij} \\geq \\mathrm{threshold}$ and the above condition is also\n",
    "satisfied, it is considered as a solid. The solid atoms can be clustered\n",
    "to find the largest solid cluster of atoms. \n",
    "\n",
    "Finding solid atoms in liquid start with reading in a file and\n",
    "calculation of neighbors.\n",
    "\n",
    "``` python\n",
    "import pyscal.core as pc\n",
    "sys = pc.System()\n",
    "sys.read_inputfile('conf.dump')\n",
    "sys.find_neighbors(method='cutoff', cutoff=4)\n",
    "```\n",
    "\n",
    "Once again, there are various methods for finding neighbors. Please\n",
    "check\n",
    "[here](../part2/intro.md)\n",
    "for details on neighbor calculation methods. Once the neighbors are\n",
    "calculated, solid atoms can be found directly by,\n",
    "\n",
    "``` python\n",
    "sys.find_solids(bonds=6, threshold=0.5, avgthreshold=0.6, cluster=True)\n",
    "```\n",
    "\n",
    "`bonds` set the number of minimum bonds a particle should have (as\n",
    "defined above), `threshold` and `avgthreshold` are the same quantities\n",
    "that appear in the equations above. Setting the keyword `cluster` to\n",
    "True returns the size of the largest solid cluster. It is also possible\n",
    "to check if each atom is solid or not.\n",
    "\n",
    "``` python\n",
    "atoms = sys.atom\n",
    "solids = [atom.solid for atom in atoms]\n",
    "```\n",
    "\n",
    "## References\n",
    "\n",
    "```{bibliography} ../references.bib\n",
    ":filter: docname in docnames\n",
    ":style: unsrt\n",
    "```"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "py3",
   "language": "python",
   "name": "py3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}