notebooks/structures.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Creating structures in pyiron"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This section gives a brief introduction about some of the tools available in pyiron to construct atomic structures. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For the sake of compatibility, our structure class is written to be compatible with the popular Atomistic Simulation Environment package ([ASE](https://wiki.fysik.dtu.dk/ase/)). This makes it possible to use routines from ASE to help set-up structures.\n",
    "\n",
    "Furthermore, pyiron uses the [NGLview](http://nglviewer.org/nglview/latest/api.html) package to visualize the structures and trajectories interactively in 3D using NGLview-widgets."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As preparation for the following discussion we import a few python libraries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:19.212727Z",
     "start_time": "2021-03-02T22:42:19.194770Z"
    }
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "%matplotlib inline\n",
    "import matplotlib.pylab as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "and create a pyiron project named 'structures':"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:23.454336Z",
     "start_time": "2021-03-02T22:42:19.221070Z"
    }
   },
   "outputs": [],
   "source": [
    "from pyiron_atomistics import Project\n",
    "pr = Project(path='structures')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Bulk crystals"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In this section we discuss various possibilities to create bulk crystal structures."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Using `create.structure.crystal`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The simplest way to generate simple crystal structures is using methods on the inbuilt `create.structure` attribute. Here we use the `crystal` method by specifying the element symbol, Bravais basis and the lattice constant(s).\n",
    "\n",
    "Note: The output gives a cubic cell rather than the smallest non-orthogonal unit cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:23.556680Z",
     "start_time": "2021-03-02T22:42:23.457872Z"
    }
   },
   "outputs": [],
   "source": [
    "structure = pr.create.structure.crystal(\n",
    "    'Al', \n",
    "    bravais_basis='fcc',\n",
    "    lattice_constant=4.05\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To plot the structure interactively in 3D simply use:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:23.820197Z",
     "start_time": "2021-03-02T22:42:23.559959Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9666c75ba3dd49c6931a53550fd6b1e4",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": []
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "366e3d0b1beb44bf85aad33553b8e5a5",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Using `create.structure.bulk`\n",
    "\n",
    "Another convenient way to set up structures is using the `create.structure.bulk` function which is built on top of the ASE build package for [bulk crystals](https://wiki.fysik.dtu.dk/ase/ase/build/build.html#ase.build.bulk). This function returns an object which is of the pyiron structure object type."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Example:** fcc bulk aluminum in a cubic cell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:24.316670Z",
     "start_time": "2021-03-02T22:42:23.824222Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d7a1684fa1894d9fb54efc9c9817a68c",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure = pr.create.structure.bulk('Al', cubic=True)\n",
    "structure.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Example:** wurtzite GaN in a 3x3x3 repeated orthorhombic cell.\n",
    "\n",
    "Note: \n",
    "- In contrast to new_structure = structure.repeat() which creates a new object, set_repeat() modifies the existing structure object.\n",
    "- Setting `spacefill=False` in the `plot3d()` method changes the atomic structure style to \"ball and stick\"."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:24.762809Z",
     "start_time": "2021-03-02T22:42:24.333106Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "380afc48864c4d57a393d541b692c241",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure = pr.create.structure.bulk(\n",
    "    'AlN', \n",
    "    crystalstructure='wurtzite', \n",
    "    a=3.5, orthorhombic=True\n",
    ")\n",
    "structure.set_repeat([3,3,3])\n",
    "structure.plot3d(spacefill=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating surfaces\n",
    "\n",
    "Surfaces can be created using the `create.structure.surface` function which is also built on top of the ASE build package for [surfaces](https://wiki.fysik.dtu.dk/ase/_modules/ase/build/surface.html)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Example:** Creating a 3x4 fcc Al(111) surface with 4 layers and a vacuum of 10 Ångström"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:25.116457Z",
     "start_time": "2021-03-02T22:42:24.768093Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c90c40d8e4254e66848e9d0140dfd458",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "Al_111 = pr.create.structure.surface(\n",
    "    \"Al\", \n",
    "    surface_type=\"fcc111\", \n",
    "    size=(3, 4, 4), \n",
    "    vacuum=10, \n",
    "    orthogonal=True\n",
    ")\n",
    "Al_111.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating structures without importing the project class\n",
    "\n",
    "In all the examples shown above, the structures are create from the pyiron `Project` object. We also offer legacy support for creating structures without importing/initializing this object. For this the appropriate imports must be made."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:25.145124Z",
     "start_time": "2021-03-02T22:42:25.137420Z"
    }
   },
   "outputs": [],
   "source": [
    "from pyiron_atomistics import create_ase_bulk, create_surface"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:25.500183Z",
     "start_time": "2021-03-02T22:42:25.162782Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c4e65d6e32be422799048621d2efdd19",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure = create_ase_bulk(\n",
    "    'AlN', \n",
    "    crystalstructure='wurtzite',\n",
    "    a=3.5, \n",
    "    orthorhombic=True\n",
    ")\n",
    "structure.set_repeat([3,3,3])\n",
    "structure.plot3d(spacefill=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:25.857485Z",
     "start_time": "2021-03-02T22:42:25.508428Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "726b084491b74e70b924b0f312362a5a",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "Al_111 = create_surface(\n",
    "    \"Al\", \n",
    "    surface_type=\"fcc111\", \n",
    "    size=(3, 4, 4), \n",
    "    vacuum=10, \n",
    "    orthogonal=True\n",
    ")\n",
    "Al_111.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Using ase bindings\n",
    "\n",
    "We also have some direct bindings to ASE methods, which will always maintain *exactly* the same signature and behaviour as the corresponding ASE methods, except that the final result is wrapped as our `Atoms` class where needed.\n",
    "\n",
    "Below is an example binding to `ase.spacegroup.crystal`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.334753Z",
     "start_time": "2021-03-02T22:42:25.864114Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c08c3ff68fa34982b4e7268eca0999d3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "skutterudite = pr.create.structure.ase.crystal(('Co', 'Sb'),\n",
    "                       basis=[(0.25, 0.25, 0.25), (0.0, 0.335, 0.158)],\n",
    "                       spacegroup=204,\n",
    "                       cellpar=[9.04, 9.04, 9.04, 90, 90, 90])\n",
    "skutterudite.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Accessing the properties of the structure object"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Using the bulk aluminum fcc example from before the structure object can be created by"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.416995Z",
     "start_time": "2021-03-02T22:42:26.344577Z"
    }
   },
   "outputs": [],
   "source": [
    "structure = pr.create.structure.bulk('Al', cubic=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A summary of the information about the structure is given by using"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.428866Z",
     "start_time": "2021-03-02T22:42:26.421645Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Al: [0. 0. 0.]\n",
      "Al: [0.    2.025 2.025]\n",
      "Al: [2.025 0.    2.025]\n",
      "Al: [2.025 2.025 0.   ]\n",
      "pbc: [ True  True  True]\n",
      "cell: \n",
      "Cell([4.05, 4.05, 4.05])\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(structure)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The cell vectors of the structure object can be accessed and edited through"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.450054Z",
     "start_time": "2021-03-02T22:42:26.437640Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Cell([4.05, 4.05, 4.05])"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structure.cell"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The positions of the atoms in the structure object can be accessed and edited through"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.472167Z",
     "start_time": "2021-03-02T22:42:26.458727Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[0.   , 0.   , 0.   ],\n",
       "       [0.   , 2.025, 2.025],\n",
       "       [2.025, 0.   , 2.025],\n",
       "       [2.025, 2.025, 0.   ]])"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structure.positions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Point defects"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Creating a single vacancy"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We start by setting up a 4x4x4 supercell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.613807Z",
     "start_time": "2021-03-02T22:42:26.480390Z"
    }
   },
   "outputs": [],
   "source": [
    "structure = pr.create.structure.bulk('Al', cubic=True)\n",
    "structure.set_repeat([4,4,4])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To create the vacancy at position index \"0\" simply use:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.680274Z",
     "start_time": "2021-03-02T22:42:26.625909Z"
    }
   },
   "outputs": [],
   "source": [
    "del structure[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To plot the structure that now contains a vacancy run:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.854895Z",
     "start_time": "2021-03-02T22:42:26.683126Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "134c2f7a56a54c78a6dae560bf56e373",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Creating multiple vacancies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.912470Z",
     "start_time": "2021-03-02T22:42:26.859486Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of atoms in the repeat unit: 256\n"
     ]
    }
   ],
   "source": [
    "# First create a 4x4x4 supercell\n",
    "structure = pr.create.structure.bulk('Al', cubic=True)\n",
    "structure.set_repeat([4,4,4])\n",
    "print(f'Number of atoms in the repeat unit: {len(structure)}')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The `del` command works for passing a list of indices to the structure object. For example, a random set of n$_{\\text{vac}}$ vacancies can be created by using"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:26.934366Z",
     "start_time": "2021-03-02T22:42:26.916922Z"
    }
   },
   "outputs": [],
   "source": [
    "# Generate a list of indices for the vacancies\n",
    "n_vac = 24\n",
    "vac_ind_lst = np.random.permutation(len(structure))[:n_vac]\n",
    "\n",
    "# Remove atoms according to the \"vac_ind_lst\"\n",
    "del structure[vac_ind_lst]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:27.413950Z",
     "start_time": "2021-03-02T22:42:26.942489Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of atoms in the repeat unit: 232\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9ce0c034066d4cdeb21d4cd3422065fb",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Visualize the structure\n",
    "print(f'Number of atoms in the repeat unit: {len(structure)}')\n",
    "structure.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Random substitutial alloys"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:27.503293Z",
     "start_time": "2021-03-02T22:42:27.418168Z"
    }
   },
   "outputs": [],
   "source": [
    "# Create a 4x4x4 supercell\n",
    "structure = pr.create.structure.bulk('Al', cubic=True)\n",
    "structure.set_repeat([4,4,4])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Substitutional atoms can be defined by changing the atomic species accessed through its position index.\n",
    "\n",
    "Here, we set $n_{\\text{sub}}$ magnesium substitutional atoms at random positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:27.606443Z",
     "start_time": "2021-03-02T22:42:27.536954Z"
    }
   },
   "outputs": [],
   "source": [
    "n_sub = 24\n",
    "structure[np.random.permutation(len(structure))[:n_sub]] = 'Mg'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:27.788133Z",
     "start_time": "2021-03-02T22:42:27.618461Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of atoms in the repeat unit: 256\n",
      "Chemical formula: Al232Mg24\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "ad8b5ee55943448f83949d59aae393fb",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Visualize the structure and print some additional information about the structure\n",
    "print(f'Number of atoms in the repeat unit: {len(structure)}')\n",
    "print(f'Chemical formula: {structure.get_chemical_formula()}')\n",
    "structure.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Explicit definition of the structure\n",
    "\n",
    "You can also set-up structures through the explicit input of the cell parameters and positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:28.125950Z",
     "start_time": "2021-03-02T22:42:27.794921Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "44787375f77945868b330c94174cc757",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "cell = 10.0 * np.eye(3) # Specifying the cell dimensions\n",
    "positions = [[0.25, 0.25, 0.25], [0.75, 0.75, 0.75]]\n",
    "elements = ['O', 'O']\n",
    "\n",
    "# Now use the Atoms class to create the instance.\n",
    "O_dimer = pr.create_atoms(elements=elements, scaled_positions=positions, cell=cell)\n",
    "\n",
    "O_dimer.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Importing from cif/other file formats\n",
    "\n",
    "Parsers from ASE can be used to import structures from other formats. In this example, we will download and import a Nepheline structure from the [Crystallography Open Database (COD)](http://www.crystallography.net/cod/index.php)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:28.157226Z",
     "start_time": "2021-03-02T22:42:28.142033Z"
    }
   },
   "outputs": [],
   "source": [
    "# The COD structures can be accessed through their unique COD identifier\n",
    "cod = 1008753\n",
    "filename = '{}.cif'.format(cod)\n",
    "url = 'http://www.crystallography.net/cod/{}'.format(filename)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:28.211191Z",
     "start_time": "2021-03-02T22:42:28.172934Z"
    }
   },
   "outputs": [],
   "source": [
    "cif_structure = \"\"\"\\\n",
    "#------------------------------------------------------------------------------\n",
    "#$Date: 2015-01-27 21:58:39 +0200 (Tue, 27 Jan 2015) $\n",
    "#$Revision: 130149 $\n",
    "#$URL: svn://www.crystallography.net/cod/cif/1/00/87/1008753.cif $\n",
    "#------------------------------------------------------------------------------\n",
    "#\n",
    "# This file is available in the Crystallography Open Database (COD),\n",
    "# http://www.crystallography.net/\n",
    "#\n",
    "# All data on this site have been placed in the public domain by the\n",
    "# contributors.\n",
    "#\n",
    "data_1008753\n",
    "loop_\n",
    "_publ_author_name\n",
    "'Buerger, M J'\n",
    "'Klein, G E'\n",
    "'Donnay, G'\n",
    "_publ_section_title\n",
    ";\n",
    "Determination of the crystal structure of nepheline\n",
    ";\n",
    "_journal_coden_ASTM              AMMIAY\n",
    "_journal_name_full               'American Mineralogist'\n",
    "_journal_page_first              805\n",
    "_journal_page_last               818\n",
    "_journal_volume                  39\n",
    "_journal_year                    1954\n",
    "_chemical_formula_structural     'K Na3 Al4 Si4 O16'\n",
    "_chemical_formula_sum            'Al4 K Na3 O16 Si4'\n",
    "_chemical_name_mineral           Nepheline\n",
    "_chemical_name_systematic        'Potassium trisodium tetraaluminium silicate'\n",
    "_space_group_IT_number           173\n",
    "_symmetry_cell_setting           hexagonal\n",
    "_symmetry_Int_Tables_number      173\n",
    "_symmetry_space_group_name_Hall  'P 6c'\n",
    "_symmetry_space_group_name_H-M   'P 63'\n",
    "_cell_angle_alpha                90\n",
    "_cell_angle_beta                 90\n",
    "_cell_angle_gamma                120\n",
    "_cell_formula_units_Z            2\n",
    "_cell_length_a                   10.01\n",
    "_cell_length_b                   10.01\n",
    "_cell_length_c                   8.405\n",
    "_cell_volume                     729.4\n",
    "_cod_database_code               1008753\n",
    "loop_\n",
    "_symmetry_equiv_pos_as_xyz\n",
    "x,y,z\n",
    "-y,x-y,z\n",
    "y-x,-x,z\n",
    "-x,-y,1/2+z\n",
    "y,y-x,1/2+z\n",
    "x-y,x,1/2+z\n",
    "loop_\n",
    "_atom_site_label\n",
    "_atom_site_type_symbol\n",
    "_atom_site_symmetry_multiplicity\n",
    "_atom_site_Wyckoff_symbol\n",
    "_atom_site_fract_x\n",
    "_atom_site_fract_y\n",
    "_atom_site_fract_z\n",
    "_atom_site_occupancy\n",
    "_atom_site_attached_hydrogens\n",
    "_atom_site_calc_flag\n",
    "K1 K1+ 2 a 0. 0. 0. 1. 0 d\n",
    "Al1 Al3+ 2 b 0.3333 0.6667 0.18 1. 0 d\n",
    "Si1 Si4+ 2 b 0.3333 0.6667 0.82 1. 0 d\n",
    "O1 O2- 2 b 0.3333 0.6667 0. 1. 0 d\n",
    "Na1 Na1+ 6 c 0.008 0.432 0. 1. 0 d\n",
    "Al2 Al3+ 6 c 0.092 0.33 0.67 1. 0 d\n",
    "Si2 Si4+ 6 c 0.092 0.33 0.33 1. 0 d\n",
    "O2 O2- 6 c 0.02 0.33 0.5 1. 0 d\n",
    "O3 O2- 6 c 0.18 0.5 0.75 1. 0 d\n",
    "O4 O2- 6 c 0.17 0.53 0.25 1. 0 d\n",
    "O5 O2- 6 c 0.23 0.28 0.25 1. 0 d\n",
    "O6 O2- 6 c 0.23 0.28 0.75 1. 0 d\n",
    "loop_\n",
    "_atom_type_symbol\n",
    "_atom_type_oxidation_number\n",
    "K1+ 1.000\n",
    "Al3+ 3.000\n",
    "Si4+ 4.000\n",
    "O2- -2.000\n",
    "Na1+ 1.000\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:28.240290Z",
     "start_time": "2021-03-02T22:42:28.229545Z"
    }
   },
   "outputs": [],
   "source": [
    "# Download and save the structure file locally\n",
    "# import urllib\n",
    "# urllib.request.urlretrieve(url=url, filename='strucs.'+filename);\n",
    "with open('strucs.'+filename, \"w\") as f:\n",
    "    f.writelines(cif_structure)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:28.695547Z",
     "start_time": "2021-03-02T22:42:28.245384Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/huber/anaconda3/envs/pyiron_38/lib/python3.8/site-packages/ase/io/cif.py:377: UserWarning: crystal system 'hexagonal' is not interpreted for space group Spacegroup(173, setting=1). This may result in wrong setting!\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "# Read the structure from file\n",
    "structure = pr.create.structure.read(filename='strucs.'+filename, format='cif')\n",
    "structure.info[\"cod\"] = cod"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:28.958810Z",
     "start_time": "2021-03-02T22:42:28.704019Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "da78c130db4b40d09854ccec8807ac50",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "structure.plot3d()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Structures can be stored indepently from jobs in HDF5 by using the special `StructureContainer` job.  To save to disk, call `run()`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:30.693243Z",
     "start_time": "2021-03-02T22:42:28.966960Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-03-02 23:42:30,330 - pyiron_log - WARNING - The job nepheline is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
     ]
    }
   ],
   "source": [
    "container = pr.create.job.StructureContainer(\"nepheline\")\n",
    "container.structure = structure\n",
    "container.run()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "It's also possible to store multiple structures in one container and to store directly from a job.  Let's use this here to store the equilibrated structures at finite temperatures."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:34.661735Z",
     "start_time": "2021-03-02T22:42:30.706767Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-03-02 23:42:31,369 - pyiron_log - WARNING - The job T_400 is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n",
      "2021-03-02 23:42:32,540 - pyiron_log - WARNING - The job T_600 is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n",
      "2021-03-02 23:42:33,590 - pyiron_log - WARNING - The job T_800 is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The job al_temp was saved and received the ID: 319\n"
     ]
    }
   ],
   "source": [
    "al_container = pr.create.job.StructureContainer(\"al_temp\", delete_existing_job=True)\n",
    "for T in (400, 600, 800):\n",
    "    j = pr.create.job.Lammps(\"T_{}\".format(T))\n",
    "    j.structure = pr.create.structure.bulk(\"Al\", cubic = True)\n",
    "    j.potential = j.list_potentials()[0]\n",
    "    j.calc_md(temperature=T, n_ionic_steps=1000, pressure=0)\n",
    "    j.run()\n",
    "    structure = j.get_structure()\n",
    "    structure.info[\"T\"] = T\n",
    "    structure.info[\"P\"] = 0\n",
    "    al_container.append(structure)\n",
    "    \n",
    "al_container.run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:34.703519Z",
     "start_time": "2021-03-02T22:42:34.692435Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'T': 400, 'P': 0}"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "al_container.structure_lst[0].info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-03-02T22:42:34.733351Z",
     "start_time": "2021-03-02T22:42:34.712347Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/json": [
       "Al: [3.93424437 0.07221925 0.08417997]\nAl: [0.10301795 1.89092377 2.04275429]\nAl: [2.09340832 0.10564475 2.11581609]\nAl: [2.04830801 2.02070157 3.93622831]\npbc: [ True  True  True]\ncell: \nCell([[4.089489326903685, 2.504090007169931e-16, 2.504090007169931e-16], [0.0, 4.089489326903685, 2.504090007169931e-16], [0.0, 0.0, 4.089489326903685]])\n",
       "Al: [4.01844916 4.0801717  0.23352673]\nAl: [0.08294026 1.90936605 1.88581354]\nAl: [2.20693355 0.01487369 2.13065821]\nAl: [1.9653831  2.26929463 4.02370759]\npbc: [ True  True  True]\ncell: \nCell([[4.136853033317934, 2.533091912897913e-16, 2.533091912897913e-16], [0.0, 4.136853033317934, 2.533091912897913e-16], [0.0, 0.0, 4.136853033317934]])\n",
       "Al: [0.20220842 0.35216229 3.99649156]\nAl: [4.00547338 2.01546242 1.92571135]\nAl: [2.29072766 4.03095336 2.19600819]\nAl: [1.84631556 1.94614695 0.22651391]\npbc: [ True  True  True]\ncell: \nCell([[4.17236250917528, 2.554835195871963e-16, 2.554835195871963e-16], [0.0, 4.17236250917528, 2.554835195871963e-16], [0.0, 0.0, 4.17236250917528]])\n"
      ],
      "text/plain": [
       "InputList([Al: [3.93424437 0.07221925 0.08417997]\n",
       "Al: [0.10301795 1.89092377 2.04275429]\n",
       "Al: [2.09340832 0.10564475 2.11581609]\n",
       "Al: [2.04830801 2.02070157 3.93622831]\n",
       "pbc: [ True  True  True]\n",
       "cell: \n",
       "Cell([[4.089489326903685, 2.504090007169931e-16, 2.504090007169931e-16], [0.0, 4.089489326903685, 2.504090007169931e-16], [0.0, 0.0, 4.089489326903685]])\n",
       ", Al: [4.01844916 4.0801717  0.23352673]\n",
       "Al: [0.08294026 1.90936605 1.88581354]\n",
       "Al: [2.20693355 0.01487369 2.13065821]\n",
       "Al: [1.9653831  2.26929463 4.02370759]\n",
       "pbc: [ True  True  True]\n",
       "cell: \n",
       "Cell([[4.136853033317934, 2.533091912897913e-16, 2.533091912897913e-16], [0.0, 4.136853033317934, 2.533091912897913e-16], [0.0, 0.0, 4.136853033317934]])\n",
       ", Al: [0.20220842 0.35216229 3.99649156]\n",
       "Al: [4.00547338 2.01546242 1.92571135]\n",
       "Al: [2.29072766 4.03095336 2.19600819]\n",
       "Al: [1.84631556 1.94614695 0.22651391]\n",
       "pbc: [ True  True  True]\n",
       "cell: \n",
       "Cell([[4.17236250917528, 2.554835195871963e-16, 2.554835195871963e-16], [0.0, 4.17236250917528, 2.554835195871963e-16], [0.0, 0.0, 4.17236250917528]])\n",
       "])"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "al_container.structure_lst"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "anaconda-cloud": {},
  "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": "3.8.6"
  },
  "latex_envs": {
   "LaTeX_envs_menu_present": true,
   "autocomplete": true,
   "bibliofile": "biblio.bib",
   "cite_by": "apalike",
   "current_citInitial": 1,
   "eqLabelWithNumbers": true,
   "eqNumInitial": 1,
   "hotkeys": {
    "equation": "Ctrl-E",
    "itemize": "Ctrl-I"
   },
   "labels_anchors": false,
   "latex_user_defs": false,
   "report_style_numbering": false,
   "user_envs_cfg": false
  },
  "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": "block",
   "toc_window_display": false
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}