{
 "cells": [
  {
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   "execution_count": 1,
   "metadata": {
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     "end_time": "2018-05-16T13:40:06.181056Z",
     "start_time": "2018-05-16T13:40:04.311156Z"
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   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/jan/anaconda3/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\n",
      "  from ._conv import register_converters as _register_converters\n"
     ]
    }
   ],
   "source": [
    "from pyiron import Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.224666Z",
     "start_time": "2018-05-16T13:40:06.185149Z"
    }
   },
   "outputs": [],
   "source": [
    "pr = Project('FeC')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.237269Z",
     "start_time": "2018-05-16T13:40:06.227203Z"
    }
   },
   "outputs": [],
   "source": [
    "pr.remove_jobs()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.275561Z",
     "start_time": "2018-05-16T13:40:06.243585Z"
    }
   },
   "outputs": [],
   "source": [
    "basis = pr.create_structure('Fe', 'bcc', 2.78)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.294010Z",
     "start_time": "2018-05-16T13:40:06.278517Z"
    }
   },
   "outputs": [],
   "source": [
    "basis[1] = 'C'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.306804Z",
     "start_time": "2018-05-16T13:40:06.297622Z"
    }
   },
   "outputs": [],
   "source": [
    "job = pr.create_job(pr.job_type.Lammps, 'lammpsFeC')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.318457Z",
     "start_time": "2018-05-16T13:40:06.313111Z"
    }
   },
   "outputs": [],
   "source": [
    "job.structure = basis "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.336867Z",
     "start_time": "2018-05-16T13:40:06.325240Z"
    }
   },
   "outputs": [],
   "source": [
    "job.potential = 'Fe_C_Hepburn_Ackland_eam'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.992900Z",
     "start_time": "2018-05-16T13:40:06.343563Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The job lammpsFeC was saved and received the ID: 10\n"
     ]
    }
   ],
   "source": [
    "job.run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.027750Z",
     "start_time": "2018-05-16T13:40:06.995987Z"
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([-7.47519366])"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
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  {
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     "end_time": "2018-05-16T13:40:07.063571Z",
     "start_time": "2018-05-16T13:40:07.033286Z"
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    {
     "data": {
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      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
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     "end_time": "2018-05-16T13:40:07.099836Z",
     "start_time": "2018-05-16T13:40:07.067199Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[[0.  , 0.  , 0.  ],\n",
       "        [1.39, 1.39, 1.39]]])"
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     "metadata": {},
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   "metadata": {
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     "end_time": "2018-05-16T13:40:07.138155Z",
     "start_time": "2018-05-16T13:40:07.106171Z"
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[[ 2.78000000e+00,  0.00000000e+00,  0.00000000e+00],\n",
       "        [-1.15608312e-32,  2.78000000e+00,  0.00000000e+00],\n",
       "        [-1.15608312e-32, -1.15608312e-32,  2.78000000e+00]]])"
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     "start_time": "2018-05-16T13:40:07.145512Z"
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     "end_time": "2018-05-16T13:40:07.237020Z",
     "start_time": "2018-05-16T13:40:07.206605Z"
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    {
     "data": {
      "text/plain": [
       "array([[[-2.22044605e-16, -9.02056208e-17,  2.08166817e-17],\n",
       "        [ 4.61694282e-49,  4.61694282e-49, -1.11022302e-16]]])"
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     "execution_count": 16,
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     "execution_count": 18,
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     "execution_count": 19,
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     "start_time": "2018-05-16T13:40:07.324075Z"
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     "data": {
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       "        [1.39, 1.39, 1.39]]])"
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