From c29661899edc34bbf1298679dbdf447258042e61 Mon Sep 17 00:00:00 2001
From: M <35793078+PhysXu@users.noreply.github.com>
Date: Sun, 25 Aug 2024 14:34:52 +0800
Subject: [PATCH] Add files via upload

---
 writeXYZ for Prismatic.ipynb | 769 +++++++++++++++++++++++++++++++++++
 1 file changed, 769 insertions(+)
 create mode 100644 writeXYZ for Prismatic.ipynb

diff --git a/writeXYZ for Prismatic.ipynb b/writeXYZ for Prismatic.ipynb
new file mode 100644
index 0000000..5c12bc6
--- /dev/null
+++ b/writeXYZ for Prismatic.ipynb	
@@ -0,0 +1,769 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "1000b5d1-3e37-4712-95a4-4ede6d3a7b93",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "b3e5f906-5e09-4529-be1c-5107b3bf358c",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Element</th>\n",
+       "      <th>X</th>\n",
+       "      <th>Y</th>\n",
+       "      <th>Z</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>14.145616</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>0.000000</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>14.145616</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>14.214491</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1008</th>\n",
+       "      <td>O</td>\n",
+       "      <td>5.685796</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1009</th>\n",
+       "      <td>O</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1010</th>\n",
+       "      <td>O</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1011</th>\n",
+       "      <td>O</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1012</th>\n",
+       "      <td>O</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>1013 rows × 4 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "     Element          X          Y          Z\n",
+       "0         Li   0.000000   0.000000   0.000000\n",
+       "1         Li   0.000000   0.000000  14.145616\n",
+       "2         Li   0.000000  24.620222   0.000000\n",
+       "3         Li   0.000000  24.620222  14.145616\n",
+       "4         Li  14.214491   0.000000   0.000000\n",
+       "...      ...        ...        ...        ...\n",
+       "1008       O   5.685796  26.261570   8.104311\n",
+       "1009       O   8.528695  -1.641348   6.041305\n",
+       "1010       O   8.528695  26.261570   8.104311\n",
+       "1011       O  11.371593  -1.641348   6.041305\n",
+       "1012       O  11.371593  26.261570   8.104311\n",
+       "\n",
+       "[1013 rows x 4 columns]"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "column_names = ['Element', 'X', 'Y', 'Z']\n",
+    "coords  = pd.read_excel(r'C:\\Users\\STEM\\Desktop\\LiCoO2 initial.xlsx', header=None, names=column_names)\n",
+    "coords"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "110f4169-b74c-49eb-bd41-664b0358225b",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Element</th>\n",
+       "      <th>X</th>\n",
+       "      <th>Y</th>\n",
+       "      <th>Z</th>\n",
+       "      <th>occupancy</th>\n",
+       "      <th>isotropic thermal parameters</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>14.145616</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>14.145616</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>14.214491</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1008</th>\n",
+       "      <td>O</td>\n",
+       "      <td>5.685796</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1009</th>\n",
+       "      <td>O</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1010</th>\n",
+       "      <td>O</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1011</th>\n",
+       "      <td>O</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1012</th>\n",
+       "      <td>O</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>1013 rows × 6 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "     Element          X          Y          Z  occupancy  \\\n",
+       "0         Li   0.000000   0.000000   0.000000          1   \n",
+       "1         Li   0.000000   0.000000  14.145616          1   \n",
+       "2         Li   0.000000  24.620222   0.000000          1   \n",
+       "3         Li   0.000000  24.620222  14.145616          1   \n",
+       "4         Li  14.214491   0.000000   0.000000          1   \n",
+       "...      ...        ...        ...        ...        ...   \n",
+       "1008       O   5.685796  26.261570   8.104311          1   \n",
+       "1009       O   8.528695  -1.641348   6.041305          1   \n",
+       "1010       O   8.528695  26.261570   8.104311          1   \n",
+       "1011       O  11.371593  -1.641348   6.041305          1   \n",
+       "1012       O  11.371593  26.261570   8.104311          1   \n",
+       "\n",
+       "      isotropic thermal parameters  \n",
+       "0                             0.08  \n",
+       "1                             0.08  \n",
+       "2                             0.08  \n",
+       "3                             0.08  \n",
+       "4                             0.08  \n",
+       "...                            ...  \n",
+       "1008                          0.08  \n",
+       "1009                          0.08  \n",
+       "1010                          0.08  \n",
+       "1011                          0.08  \n",
+       "1012                          0.08  \n",
+       "\n",
+       "[1013 rows x 6 columns]"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Add the occupancy and isotropic thermal parameters\n",
+    "\n",
+    "coords['occupancy']=1\n",
+    "coords['isotropic thermal parameters']=0.08\n",
+    "coords"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "3ca4b865-37e7-4123-809d-e2b10dfecf19",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Element</th>\n",
+       "      <th>X</th>\n",
+       "      <th>Y</th>\n",
+       "      <th>Z</th>\n",
+       "      <th>occupancy</th>\n",
+       "      <th>isotropic thermal parameters</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>14.145616</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>14.145616</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Li</td>\n",
+       "      <td>14.214491</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1008</th>\n",
+       "      <td>O</td>\n",
+       "      <td>5.685796</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1009</th>\n",
+       "      <td>O</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1010</th>\n",
+       "      <td>O</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1011</th>\n",
+       "      <td>O</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1012</th>\n",
+       "      <td>O</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>1013 rows × 6 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "     Element          X          Y          Z  occupancy  \\\n",
+       "0         Li   0.000000   0.000000   0.000000          1   \n",
+       "1         Li   0.000000   0.000000  14.145616          1   \n",
+       "2         Li   0.000000  24.620222   0.000000          1   \n",
+       "3         Li   0.000000  24.620222  14.145616          1   \n",
+       "4         Li  14.214491   0.000000   0.000000          1   \n",
+       "...      ...        ...        ...        ...        ...   \n",
+       "1008       O   5.685796  26.261570   8.104311          1   \n",
+       "1009       O   8.528695  -1.641348   6.041305          1   \n",
+       "1010       O   8.528695  26.261570   8.104311          1   \n",
+       "1011       O  11.371593  -1.641348   6.041305          1   \n",
+       "1012       O  11.371593  26.261570   8.104311          1   \n",
+       "\n",
+       "      isotropic thermal parameters  \n",
+       "0                             0.06  \n",
+       "1                             0.06  \n",
+       "2                             0.06  \n",
+       "3                             0.06  \n",
+       "4                             0.06  \n",
+       "...                            ...  \n",
+       "1008                          0.08  \n",
+       "1009                          0.08  \n",
+       "1010                          0.08  \n",
+       "1011                          0.08  \n",
+       "1012                          0.08  \n",
+       "\n",
+       "[1013 rows x 6 columns]"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# If you want use different Uiso for different elements, run the Cell\n",
+    "\n",
+    "coords.loc[coords['Element'] == 'Li', 'isotropic thermal parameters'] = 0.06\n",
+    "coords"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "8df9ecc5-851d-47c5-8f42-3c57e0e8a78c",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "C:\\Users\\STEM\\AppData\\Local\\Temp\\ipykernel_1928\\469350156.py:1: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n",
+      "  coords['Element'] = coords['Element'].replace({'Li': 3, 'Co': 27, 'O': 8})\n"
+     ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Element</th>\n",
+       "      <th>X</th>\n",
+       "      <th>Y</th>\n",
+       "      <th>Z</th>\n",
+       "      <th>occupancy</th>\n",
+       "      <th>isotropic thermal parameters</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>3</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>3</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>14.145616</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>3</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>3</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>24.620222</td>\n",
+       "      <td>14.145616</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>3</td>\n",
+       "      <td>14.214491</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.06</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1008</th>\n",
+       "      <td>8</td>\n",
+       "      <td>5.685796</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1009</th>\n",
+       "      <td>8</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1010</th>\n",
+       "      <td>8</td>\n",
+       "      <td>8.528695</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1011</th>\n",
+       "      <td>8</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>-1.641348</td>\n",
+       "      <td>6.041305</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1012</th>\n",
+       "      <td>8</td>\n",
+       "      <td>11.371593</td>\n",
+       "      <td>26.261570</td>\n",
+       "      <td>8.104311</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.08</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>1013 rows × 6 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "      Element          X          Y          Z  occupancy  \\\n",
+       "0           3   0.000000   0.000000   0.000000          1   \n",
+       "1           3   0.000000   0.000000  14.145616          1   \n",
+       "2           3   0.000000  24.620222   0.000000          1   \n",
+       "3           3   0.000000  24.620222  14.145616          1   \n",
+       "4           3  14.214491   0.000000   0.000000          1   \n",
+       "...       ...        ...        ...        ...        ...   \n",
+       "1008        8   5.685796  26.261570   8.104311          1   \n",
+       "1009        8   8.528695  -1.641348   6.041305          1   \n",
+       "1010        8   8.528695  26.261570   8.104311          1   \n",
+       "1011        8  11.371593  -1.641348   6.041305          1   \n",
+       "1012        8  11.371593  26.261570   8.104311          1   \n",
+       "\n",
+       "      isotropic thermal parameters  \n",
+       "0                             0.06  \n",
+       "1                             0.06  \n",
+       "2                             0.06  \n",
+       "3                             0.06  \n",
+       "4                             0.06  \n",
+       "...                            ...  \n",
+       "1008                          0.08  \n",
+       "1009                          0.08  \n",
+       "1010                          0.08  \n",
+       "1011                          0.08  \n",
+       "1012                          0.08  \n",
+       "\n",
+       "[1013 rows x 6 columns]"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Chnage the Element to the element_No.\n",
+    "\n",
+    "coords['Element'] = coords['Element'].replace({'Li': 3, 'Co': 27, 'O': 8})\n",
+    "coords"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "3bee4319-3b82-4701-b9f3-4cc9e4f7e796",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fileName = r'C:\\Users\\STEM\\Desktop\\LiCoO2 final.xyz'\n",
+    "comment = 'LiCoO2'\n",
+    "cellDim = [14.214, 24.620, 14.146]   # the size of cell\n",
+    "\n",
+    "with open(fileName, 'w') as fid:\n",
+    "    # Write comment line (1st)\n",
+    "    fid.write(f\"{comment}\\n\")\n",
+    "\n",
+    "    # Write cell dimensions\n",
+    "    fid.write(f\"    {cellDim[0]} {cellDim[1]} {cellDim[2]}\\n\")\n",
+    "\n",
+    "    # Write atomic data\n",
+    "    dataAll = coords.values\n",
+    "    for row in dataAll:\n",
+    "        fid.write(f\"{int(row[0])}  {row[1]:.6f}  {row[2]:.6f}  {row[3]:.6f}  {int(row[4])}  {row[5]:.6f}\\n\")\n",
+    "\n",
+    "    # Write end of file, for compatibility\n",
+    "    fid.write(\"-1\\n\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "45732bd6-135b-4e1a-a7dc-7b4fe5b6af95",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}