{
 "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": [
    {
     "data": {
      "text/plain": [
       "'1.0.5a2'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import mdapy as mp\n",
    "mp.__version__"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "22d00857",
   "metadata": {},
   "source": [
    "### Build a Copper system with 4,000,000 atoms."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "fc775eec",
   "metadata": {},
   "outputs": [],
   "source": [
    "system = mp.build_crystal('Cu', 'fcc', 3.615, nx=100, ny=100, nz=100)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a7b67b89",
   "metadata": {},
   "source": [
    "### Check the system information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "8ca9c22e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Atom Number: 4000000\n",
       "Box information:\n",
       "[[361.5   0.    0. ]\n",
       " [  0.  361.5   0. ]\n",
       " [  0.    0.  361.5]]\n",
       "Origin: [0. 0. 0.]\n",
       "Triclinic: False\n",
       "Boundary: [1 1 1]\n",
       "Particle Information:\n",
       "shape: (4_000_000, 4)\n",
       "┌──────────┬──────────┬──────────┬─────────┐\n",
       "│ x        ┆ y        ┆ z        ┆ element │\n",
       "│ ---      ┆ ---      ┆ ---      ┆ ---     │\n",
       "│ f64      ┆ f64      ┆ f64      ┆ str     │\n",
       "╞══════════╪══════════╪══════════╪═════════╡\n",
       "│ 0.0      ┆ 0.0      ┆ 0.0      ┆ Cu      │\n",
       "│ 1.8075   ┆ 1.8075   ┆ 0.0      ┆ Cu      │\n",
       "│ 0.0      ┆ 1.8075   ┆ 1.8075   ┆ Cu      │\n",
       "│ 1.8075   ┆ 0.0      ┆ 1.8075   ┆ Cu      │\n",
       "│ 0.0      ┆ 0.0      ┆ 3.615    ┆ Cu      │\n",
       "│ …        ┆ …        ┆ …        ┆ …       │\n",
       "│ 359.6925 ┆ 357.885  ┆ 356.0775 ┆ Cu      │\n",
       "│ 357.885  ┆ 357.885  ┆ 357.885  ┆ Cu      │\n",
       "│ 359.6925 ┆ 359.6925 ┆ 357.885  ┆ Cu      │\n",
       "│ 357.885  ┆ 359.6925 ┆ 359.6925 ┆ Cu      │\n",
       "│ 359.6925 ┆ 357.885  ┆ 359.6925 ┆ Cu      │\n",
       "└──────────┴──────────┴──────────┴─────────┘"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fece836f",
   "metadata": {},
   "source": [
    "### Direct calculation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "c07b1fa1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 1min 36s, sys: 9.58 s, total: 1min 45s\n",
      "Wall time: 8.72 s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "system.cal_centro_symmetry_parameter(12)\n",
    "system.cal_ackland_jones_analysis()\n",
    "system.cal_structure_entropy(rc=5.0, sigma=0.2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "5020e204",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div><style>\n",
       ".dataframe > thead > tr,\n",
       ".dataframe > tbody > tr {\n",
       "  text-align: right;\n",
       "  white-space: pre-wrap;\n",
       "}\n",
       "</style>\n",
       "<small>shape: (5, 7)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>x</th><th>y</th><th>z</th><th>element</th><th>csp</th><th>aja</th><th>entropy</th></tr><tr><td>f64</td><td>f64</td><td>f64</td><td>str</td><td>f64</td><td>i32</td><td>f64</td></tr></thead><tbody><tr><td>0.0</td><td>0.0</td><td>0.0</td><td>&quot;Cu&quot;</td><td>3.2952e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>1.8075</td><td>1.8075</td><td>0.0</td><td>&quot;Cu&quot;</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>0.0</td><td>1.8075</td><td>1.8075</td><td>&quot;Cu&quot;</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>1.8075</td><td>0.0</td><td>1.8075</td><td>&quot;Cu&quot;</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>0.0</td><td>0.0</td><td>3.615</td><td>&quot;Cu&quot;</td><td>2.1968e-26</td><td>1</td><td>-8.645166</td></tr></tbody></table></div>"
      ],
      "text/plain": [
       "shape: (5, 7)\n",
       "┌────────┬────────┬────────┬─────────┬────────────┬─────┬───────────┐\n",
       "│ x      ┆ y      ┆ z      ┆ element ┆ csp        ┆ aja ┆ entropy   │\n",
       "│ ---    ┆ ---    ┆ ---    ┆ ---     ┆ ---        ┆ --- ┆ ---       │\n",
       "│ f64    ┆ f64    ┆ f64    ┆ str     ┆ f64        ┆ i32 ┆ f64       │\n",
       "╞════════╪════════╪════════╪═════════╪════════════╪═════╪═══════════╡\n",
       "│ 0.0    ┆ 0.0    ┆ 0.0    ┆ Cu      ┆ 3.2952e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 1.8075 ┆ 1.8075 ┆ 0.0    ┆ Cu      ┆ 1.0984e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 0.0    ┆ 1.8075 ┆ 1.8075 ┆ Cu      ┆ 1.0984e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 1.8075 ┆ 0.0    ┆ 1.8075 ┆ Cu      ┆ 1.0984e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 0.0    ┆ 0.0    ┆ 3.615  ┆ Cu      ┆ 2.1968e-26 ┆ 1   ┆ -8.645166 │\n",
       "└────────┴────────┴────────┴─────────┴────────────┴─────┴───────────┘"
      ]
     },
     "execution_count": 5,
     "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": 6,
   "id": "7e7bdecf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 1min 17s, sys: 891 ms, total: 1min 18s\n",
      "Wall time: 6.39 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_structure_entropy(rc=5.0, sigma=0.2)\n",
    "system.cal_ackland_jones_analysis()\n",
    "system.cal_centro_symmetry_parameter(12)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "ecefac5e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div><style>\n",
       ".dataframe > thead > tr,\n",
       ".dataframe > tbody > tr {\n",
       "  text-align: right;\n",
       "  white-space: pre-wrap;\n",
       "}\n",
       "</style>\n",
       "<small>shape: (5, 7)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>x</th><th>y</th><th>z</th><th>element</th><th>csp</th><th>aja</th><th>entropy</th></tr><tr><td>f64</td><td>f64</td><td>f64</td><td>str</td><td>f64</td><td>i32</td><td>f64</td></tr></thead><tbody><tr><td>0.0</td><td>0.0</td><td>0.0</td><td>&quot;Cu&quot;</td><td>3.2952e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>1.8075</td><td>1.8075</td><td>0.0</td><td>&quot;Cu&quot;</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>0.0</td><td>1.8075</td><td>1.8075</td><td>&quot;Cu&quot;</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>1.8075</td><td>0.0</td><td>1.8075</td><td>&quot;Cu&quot;</td><td>1.0984e-26</td><td>1</td><td>-8.645166</td></tr><tr><td>0.0</td><td>0.0</td><td>3.615</td><td>&quot;Cu&quot;</td><td>2.1968e-26</td><td>1</td><td>-8.645166</td></tr></tbody></table></div>"
      ],
      "text/plain": [
       "shape: (5, 7)\n",
       "┌────────┬────────┬────────┬─────────┬────────────┬─────┬───────────┐\n",
       "│ x      ┆ y      ┆ z      ┆ element ┆ csp        ┆ aja ┆ entropy   │\n",
       "│ ---    ┆ ---    ┆ ---    ┆ ---     ┆ ---        ┆ --- ┆ ---       │\n",
       "│ f64    ┆ f64    ┆ f64    ┆ str     ┆ f64        ┆ i32 ┆ f64       │\n",
       "╞════════╪════════╪════════╪═════════╪════════════╪═════╪═══════════╡\n",
       "│ 0.0    ┆ 0.0    ┆ 0.0    ┆ Cu      ┆ 3.2952e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 1.8075 ┆ 1.8075 ┆ 0.0    ┆ Cu      ┆ 1.0984e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 0.0    ┆ 1.8075 ┆ 1.8075 ┆ Cu      ┆ 1.0984e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 1.8075 ┆ 0.0    ┆ 1.8075 ┆ Cu      ┆ 1.0984e-26 ┆ 1   ┆ -8.645166 │\n",
       "│ 0.0    ┆ 0.0    ┆ 3.615  ┆ Cu      ┆ 2.1968e-26 ┆ 1   ┆ -8.645166 │\n",
       "└────────┴────────┴────────┴─────────┴────────────┴─────┴───────────┘"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.data.head()"
   ]
  }
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