Feat/tutorials2

docs/source/index.rst

@@ -58,7 +58,7 @@ Contents
    :maxdepth: 2
 
    installation
-   tutorials/tutorials
+   tutorials/index
    whitepaper
    SOAP
    representation/representations

docs/source/tutorials/Advanced_SOAP.ipynb

@@ -0,0 +1,122 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "toc": true
+   },
+   "source": [
+    "<h1>Table of Contents<span class=\"tocSkip\"></span></h1>\n",
+    "<div class=\"toc\"><ul class=\"toc-item\"><li><span><a href=\"#Advanced-SOAP-Representations\" data-toc-modified-id=\"Advanced-SOAP-Representations-1\"><span class=\"toc-item-num\">1&nbsp;&nbsp;</span>Advanced SOAP Representations</a></span><ul class=\"toc-item\"><li><span><a href=\"#$\\lambda$-SOAP\" data-toc-modified-id=\"$\\lambda$-SOAP-1.1\"><span class=\"toc-item-num\">1.1&nbsp;&nbsp;</span>$\\lambda$-SOAP</a></span></li><li><span><a href=\"#Bispectrum\" data-toc-modified-id=\"Bispectrum-1.2\"><span class=\"toc-item-num\">1.2&nbsp;&nbsp;</span>Bispectrum</a></span></li><li><span><a href=\"#DVR\" data-toc-modified-id=\"DVR-1.3\"><span class=\"toc-item-num\">1.3&nbsp;&nbsp;</span>DVR</a></span></li></ul></li></ul></div>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Advanced SOAP Representations\n",
+    "\n",
+    "This notebook is intended showcase some more advanced examples of SOAP representations.\n",
+    "For more information on the variable conventions, derivation, and utility of atomic descriptors, please refer to (among others): \n",
+    "<ul>\n",
+    "  <li> <a href=\"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.87.184115\">On representing chemical environments (Bartók 2013)</a></li>\n",
+    "  <li><a href=\"https://onlinelibrary.wiley.com/doi/full/10.1002/qua.24927\">Gaussian approximation potentials: A brief tutorial introduction (Bartók 2015)</li>\n",
+    "  <li><a href=\"https://pubs.rsc.org/en/content/articlepdf/2016/cp/c6cp00415f\">Comparing molecules and solids across structural and alchemical space (De 2016)</li>\n",
+    "    <li><a href=\"https://link.springer.com/content/pdf/10.1007%2F978-3-319-42913-7_68-1.pdf\">Machine Learning of Atomic-Scale Properties Based on Physical Principles (Ceriotti 2018)</li>\n",
+    "</ul>\n",
+    "\n",
+    "Beyond libRascal, the packages used in this tutorial are:  [json](https://docs.python.org/2/library/json.html), [numpy](https://numpy.org/), [ipywidgets](https://ipywidgets.readthedocs.io/en/latest/), [matplotlib](https://matplotlib.org/), and [ase](https://wiki.fysik.dtu.dk/ase/index.html)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "\n",
+    "# may omit in final version\n",
+    "%reload_ext autoreload\n",
+    "%autoreload 2 \n",
+    "\n",
+    "import os\n",
+    "import time\n",
+    "import sys\n",
+    "\n",
+    "import numpy as np\n",
+    "import ase\n",
+    "from ase.io import read\n",
+    "from matplotlib import pyplot as plt\n",
+    "import json\n",
+    "\n",
+    "wd=!(pwd)\n",
+    "sys.path.append(f'{wd[0]}/utilities')\n",
+    "from general_utils import *\n",
+    "from rascal.representations import SphericalInvariants as SOAP"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## $\\lambda$-SOAP"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Bispectrum"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## DVR"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.3"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": true,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": true
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/source/tutorials/Benefits_Performance.ipynb

@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "toc": true
+   },
+   "source": [
+    "<h1>Table of Contents<span class=\"tocSkip\"></span></h1>\n",
+    "<div class=\"toc\"><ul class=\"toc-item\"><li><span><a href=\"#What-can-libRascal-do?\" data-toc-modified-id=\"What-can-libRascal-do?-1\"><span class=\"toc-item-num\">1&nbsp;&nbsp;</span>What can libRascal do?</a></span></li></ul></div>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# What can libRascal do?\n",
+    "\n",
+    "This notebook is intended to _purpose of tutorial_.\n",
+    "For more information on _nuances of tutorial_, please refer to (among others): \n",
+    "- [Title (Surname Year)](url) \n",
+    "- [Title (Surname Year)](url)\n",
+    "\n",
+    "Beyond libRascal, the packages used in this tutorial are:  [pkg](url), [pkg](url), and [pkg](url)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "\n",
+    "# may omit in final version\n",
+    "%reload_ext autoreload\n",
+    "%autoreload 2 \n",
+    "\n",
+    "import os\n",
+    "import time\n",
+    "import sys\n",
+    "\n",
+    "import numpy as np\n",
+    "import ase\n",
+    "from ase.io import read\n",
+    "from matplotlib import pyplot as plt\n",
+    "import json\n",
+    "\n",
+    "wd=!(pwd)\n",
+    "sys.path.append(f'{wd[0]}/utilities')\n",
+    "from general_utils import *\n",
+    "from rascal.representations import SphericalInvariants as SOAP"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.3"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": true,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": true
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}