initial commit

README.md

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+# Periodic Boundary Exercise
+For this exercise we use [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/eisenforschung/periodic-boundary-exercise/master?filepath=periodic-boundary-exercise.ipynb). 

binder/environment.yml

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+channels:
+- conda-forge
+dependencies:
+- python
+- nglview
+- ase

binder/postBuild

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+# ngl view for jupyter
+jupyter nbextension install nglview --py --sys-prefix
+jupyter nbextension enable nglview --py --sys-prefix

periodic-boundary-exercise.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Task \n",
+    "Your task is to calculate the distance of two carbon atoms in an iron matrix, considering periodic boundaries. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Code"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Import required packages "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.806990Z",
+     "start_time": "2018-10-15T13:11:35.380379Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "from ase.build import bulk\n",
+    "import nglview\n",
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Function to display atoms"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.812039Z",
+     "start_time": "2018-10-15T13:11:35.809040Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "def display_atoms(atoms):\n",
+    "    view = nglview.show_ase(atoms)\n",
+    "    view.add_unitcell()\n",
+    "    view.add_spacefill()\n",
+    "    view.remove_ball_and_stick()\n",
+    "    return view"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create iron bluk matrix (without periodic boundaries)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.851979Z",
+     "start_time": "2018-10-15T13:11:35.813910Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "basis = bulk(name='Fe', cubic=True)\n",
+    "basis_repeated = basis.repeat([5,5,5])\n",
+    "display_atoms(basis_repeated)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Place carbon substitutionals in iron matrix"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.920721Z",
+     "start_time": "2018-10-15T13:11:35.853850Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "element_lst = basis_repeated.get_chemical_symbols()\n",
+    "element_lst[0] = 'C'\n",
+    "element_lst[-1] = 'C'\n",
+    "basis_repeated.set_chemical_symbols(element_lst)\n",
+    "display_atoms(basis_repeated)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Helpful properties"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.946702Z",
+     "start_time": "2018-10-15T13:11:35.922524Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "basis_repeated.positions"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.959564Z",
+     "start_time": "2018-10-15T13:11:35.948609Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "basis_repeated.cell"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.973154Z",
+     "start_time": "2018-10-15T13:11:35.961340Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "basis_repeated.get_chemical_symbols()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.982864Z",
+     "start_time": "2018-10-15T13:11:35.975066Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "elements_array = np.array(basis_repeated.get_chemical_symbols())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:35.992908Z",
+     "start_time": "2018-10-15T13:11:35.984732Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "selection_index = elements_array=='C'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2018-10-15T13:11:36.090524Z",
+     "start_time": "2018-10-15T13:11:35.994789Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "basis_repeated.positions[selection_index]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python [default]",
+   "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": "3.5.5"
+  },
+  "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": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": false
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}