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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# UUID and Lineage Tracking in ASSYST\n",
    "\n",
    "This notebook demonstrates how ASSYST tracks the derivation history of structures using UUIDs."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from assyst.crystals import pyxtal\n",
    "from assyst.perturbations import Rattle, Stretch, Series\n",
    "from assyst.relax import Relax\n",
    "from assyst.calculators import Morse\n",
    "import ase"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Initial Structure Generation\n",
    "\n",
    "When we generate a structure with `pyxtal`, it automatically receives a UUID and a seed."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "atoms = pyxtal(225, species=['Cu'], num_ions=[4])\n",
    "print(f\"Current UUID: {atoms.info['uuid']}\")\n",
    "print(f\"Seed UUID:    {atoms.info['seed']}\")\n",
    "print(f\"Lineage:      {atoms.info.get('lineage', [])}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. Relaxation\n",
    "\n",
    "Relaxation creates a new structure with a new UUID and updates the lineage."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "calc = Morse()\n",
    "relax = Relax(max_steps=5)\n",
    "\n",
    "atoms.calc = calc.get_calculator()\n",
    "relaxed = relax.relax(atoms)\n",
    "\n",
    "print(f\"Current UUID: {relaxed.info['uuid']}\")\n",
    "print(f\"Seed UUID:    {relaxed.info['seed']}\")\n",
    "print(f\"Lineage:      {relaxed.info['lineage']}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. Applying Perturbations\n",
    "\n",
    "Perturbations further extend the lineage."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "rattle = Rattle(sigma=0.05)\n",
    "perturbed = rattle(relaxed.copy())\n",
    "\n",
    "print(f\"Current UUID: {perturbed.info['uuid']}\")\n",
    "print(f\"Seed UUID:    {perturbed.info['seed']}\")\n",
    "print(f\"Lineage:      {perturbed.info['lineage']}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 4. Multiple Steps\n",
    "\n",
    "Lineage accumulates as we apply more modifications."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "stretch = Stretch(hydro=0.05, shear=0.05)\n",
    "final = stretch(perturbed.copy())\n",
    "\n",
    "print(f\"Current UUID: {final.info['uuid']}\")\n",
    "print(f\"Seed UUID:    {final.info['seed']}\")\n",
    "print(f\"Lineage:      {final.info['lineage']}\")"
   ]
  }
 ],
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