{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "909cd1e2",
   "metadata": {},
   "source": [
    "# Use mdapy efficiently"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bcaee006",
   "metadata": {},
   "source": [
    "## The key point is re-using the neighborlist information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "c12f2890",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[Taichi] version 1.7.1, llvm 15.0.1, commit 0f143b2f, win, python 3.10.14\n",
      "[Taichi] Starting on arch=x64\n"
     ]
    }
   ],
   "source": [
    "import mdapy as mp\n",
    "mp.init()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "fd819d69",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'0.11.1'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mp.__version__"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "22d00857",
   "metadata": {},
   "source": [
    "## Build a FCC lattice with 4,000,000 atoms."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "fc775eec",
   "metadata": {},
   "outputs": [],
   "source": [
    "FCC = mp.LatticeMaker(3.615, 'FCC', 100, 100, 100)\n",
    "FCC.compute()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "210f5d7d",
   "metadata": {},
   "source": [
    "## Generate a system class."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "538324d5",
   "metadata": {},
   "outputs": [],
   "source": [
    "system = mp.System(pos=FCC.pos, box=FCC.box, boundary=[1, 1, 1])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a7b67b89",
   "metadata": {},
   "source": [
    "## Check the system information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8ca9c22e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Filename: None\n",
       "Atom Number: 4000000\n",
       "Simulation Box:\n",
       "[[361.5   0.    0. ]\n",
       " [  0.  361.5   0. ]\n",
       " [  0.    0.  361.5]\n",
       " [  0.    0.    0. ]]\n",
       "TimeStep: 0\n",
       "Boundary: [1, 1, 1]\n",
       "Particle Information:\n",
       "shape: (4_000_000, 5)\n",
       "┌─────────┬──────┬──────────┬──────────┬──────────┐\n",
       "│ id      ┆ type ┆ x        ┆ y        ┆ z        │\n",
       "│ ---     ┆ ---  ┆ ---      ┆ ---      ┆ ---      │\n",
       "│ i32     ┆ i32  ┆ f64      ┆ f64      ┆ f64      │\n",
       "╞═════════╪══════╪══════════╪══════════╪══════════╡\n",
       "│ 1       ┆ 1    ┆ 0.0      ┆ 0.0      ┆ 0.0      │\n",
       "│ 2       ┆ 1    ┆ 1.8075   ┆ 1.8075   ┆ 0.0      │\n",
       "│ 3       ┆ 1    ┆ 1.8075   ┆ 0.0      ┆ 1.8075   │\n",
       "│ 4       ┆ 1    ┆ 0.0      ┆ 1.8075   ┆ 1.8075   │\n",
       "│ 5       ┆ 1    ┆ 0.0      ┆ 0.0      ┆ 3.615    │\n",
       "│ …       ┆ …    ┆ …        ┆ …        ┆ …        │\n",
       "│ 3999996 ┆ 1    ┆ 357.885  ┆ 359.6925 ┆ 356.0775 │\n",
       "│ 3999997 ┆ 1    ┆ 357.885  ┆ 357.885  ┆ 357.885  │\n",
       "│ 3999998 ┆ 1    ┆ 359.6925 ┆ 359.6925 ┆ 357.885  │\n",
       "│ 3999999 ┆ 1    ┆ 359.6925 ┆ 357.885  ┆ 359.6925 │\n",
       "│ 4000000 ┆ 1    ┆ 357.885  ┆ 359.6925 ┆ 359.6925 │\n",
       "└─────────┴──────┴──────────┴──────────┴──────────┘"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2d77a526",
   "metadata": {},
   "source": [
    "If we want to do a series of analysis, we can re-use the neighbor to save time."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fece836f",
   "metadata": {},
   "source": [
    "## Direct calculation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c07b1fa1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: total: 2min 15s\n",
      "Wall time: 10.3 s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "system.cal_centro_symmetry_parameter(12)\n",
    "system.cal_ackland_jones_analysis()\n",
    "system.cal_atomic_entropy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "5020e204",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       ".dataframe > thead > tr,\n",
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       "</style>\n",
       "<small>shape: (5, 8)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>id</th><th>type</th><th>x</th><th>y</th><th>z</th><th>csp</th><th>aja</th><th>atomic_entropy</th></tr><tr><td>i32</td><td>i32</td><td>f64</td><td>f64</td><td>f64</td><td>f64</td><td>i32</td><td>f64</td></tr></thead><tbody><tr><td>1</td><td>1</td><td>0.0</td><td>0.0</td><td>0.0</td><td>3.2952e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>2</td><td>1</td><td>1.8075</td><td>1.8075</td><td>0.0</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>3</td><td>1</td><td>1.8075</td><td>0.0</td><td>1.8075</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>4</td><td>1</td><td>0.0</td><td>1.8075</td><td>1.8075</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>5</td><td>1</td><td>0.0</td><td>0.0</td><td>3.615</td><td>2.1968e-26</td><td>1</td><td>-8.645166</td></tr></tbody></table></div>"
      ],
      "text/plain": [
       "shape: (5, 8)\n",
       "┌─────┬──────┬────────┬────────┬────────┬────────────┬─────┬────────────────┐\n",
       "│ id  ┆ type ┆ x      ┆ y      ┆ z      ┆ csp        ┆ aja ┆ atomic_entropy │\n",
       "│ --- ┆ ---  ┆ ---    ┆ ---    ┆ ---    ┆ ---        ┆ --- ┆ ---            │\n",
       "│ i32 ┆ i32  ┆ f64    ┆ f64    ┆ f64    ┆ f64        ┆ i32 ┆ f64            │\n",
       "╞═════╪══════╪════════╪════════╪════════╪════════════╪═════╪════════════════╡\n",
       "│ 1   ┆ 1    ┆ 0.0    ┆ 0.0    ┆ 0.0    ┆ 3.2952e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 2   ┆ 1    ┆ 1.8075 ┆ 1.8075 ┆ 0.0    ┆ 1.0984e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 3   ┆ 1    ┆ 1.8075 ┆ 0.0    ┆ 1.8075 ┆ 1.0984e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 4   ┆ 1    ┆ 0.0    ┆ 1.8075 ┆ 1.8075 ┆ 1.0984e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 5   ┆ 1    ┆ 0.0    ┆ 0.0    ┆ 3.615  ┆ 2.1968e-26 ┆ 1   ┆ -8.645166      │\n",
       "└─────┴──────┴────────┴────────┴────────┴────────────┴─────┴────────────────┘"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b90a344b",
   "metadata": {},
   "source": [
    "## Re-use neighborlist information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "7e7bdecf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: total: 1min 32s\n",
      "Wall time: 6.99 s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "system.build_neighbor(rc=5.0, max_neigh=50) # Obtain the neighbor first, the following calculation can use it.\n",
    "system.cal_atomic_entropy()\n",
    "system.cal_ackland_jones_analysis()\n",
    "system.cal_centro_symmetry_parameter(12)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "ecefac5e",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "}\n",
       "</style>\n",
       "<small>shape: (5, 8)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>id</th><th>type</th><th>x</th><th>y</th><th>z</th><th>csp</th><th>aja</th><th>atomic_entropy</th></tr><tr><td>i32</td><td>i32</td><td>f64</td><td>f64</td><td>f64</td><td>f64</td><td>i32</td><td>f64</td></tr></thead><tbody><tr><td>1</td><td>1</td><td>0.0</td><td>0.0</td><td>0.0</td><td>3.2952e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>2</td><td>1</td><td>1.8075</td><td>1.8075</td><td>0.0</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>3</td><td>1</td><td>1.8075</td><td>0.0</td><td>1.8075</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>4</td><td>1</td><td>0.0</td><td>1.8075</td><td>1.8075</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>5</td><td>1</td><td>0.0</td><td>0.0</td><td>3.615</td><td>2.1968e-26</td><td>1</td><td>-8.645166</td></tr></tbody></table></div>"
      ],
      "text/plain": [
       "shape: (5, 8)\n",
       "┌─────┬──────┬────────┬────────┬────────┬────────────┬─────┬────────────────┐\n",
       "│ id  ┆ type ┆ x      ┆ y      ┆ z      ┆ csp        ┆ aja ┆ atomic_entropy │\n",
       "│ --- ┆ ---  ┆ ---    ┆ ---    ┆ ---    ┆ ---        ┆ --- ┆ ---            │\n",
       "│ i32 ┆ i32  ┆ f64    ┆ f64    ┆ f64    ┆ f64        ┆ i32 ┆ f64            │\n",
       "╞═════╪══════╪════════╪════════╪════════╪════════════╪═════╪════════════════╡\n",
       "│ 1   ┆ 1    ┆ 0.0    ┆ 0.0    ┆ 0.0    ┆ 3.2952e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 2   ┆ 1    ┆ 1.8075 ┆ 1.8075 ┆ 0.0    ┆ 1.0984e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 3   ┆ 1    ┆ 1.8075 ┆ 0.0    ┆ 1.8075 ┆ 1.0984e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 4   ┆ 1    ┆ 0.0    ┆ 1.8075 ┆ 1.8075 ┆ 1.0984e-26 ┆ 1   ┆ -8.645166      │\n",
       "│ 5   ┆ 1    ┆ 0.0    ┆ 0.0    ┆ 3.615  ┆ 2.1968e-26 ┆ 1   ┆ -8.645166      │\n",
       "└─────┴──────┴────────┴────────┴────────┴────────────┴─────┴────────────────┘"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.data.head()"
   ]
  }
 ],
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