notebooks/lammps-fe-c-example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:06.181056Z",
     "start_time": "2018-05-16T13:40:04.311156Z"
    }
   },
   "outputs": [],
   "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": 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 = '2008--Hepburn-D-J--Fe-C--LAMMPS--ipr1'"
   ]
  },
  {
   "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: 3\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"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([-7.47519366])"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.energy_tot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.063571Z",
     "start_time": "2018-05-16T13:40:07.033286Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([-7.47519366])"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.energy_pot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "ExecuteTime": {
     "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]]])"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.138155Z",
     "start_time": "2018-05-16T13:40:07.106171Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[[2.78000000e+00, 1.15608312e-32, 1.15608312e-32],\n",
       "        [0.00000000e+00, 2.78000000e+00, 1.15608312e-32],\n",
       "        [0.00000000e+00, 0.00000000e+00, 2.78000000e+00]]])"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.173932Z",
     "start_time": "2018-05-16T13:40:07.145512Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[[ 3.53781395e+01, -1.09310765e-15, -1.09310765e-15],\n",
       "        [-1.09310765e-15,  3.53781395e+01, -1.35829945e-15],\n",
       "        [-1.09310765e-15, -1.35829945e-15,  3.53781395e+01]]])"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.pressures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.202983Z",
     "start_time": "2018-05-16T13:40:07.177425Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([0])"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.temperature"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.237020Z",
     "start_time": "2018-05-16T13:40:07.206605Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[[-2.22044605e-16, -9.02056208e-17,  2.08166817e-17],\n",
       "        [ 0.00000000e+00,  0.00000000e+00, -1.11022302e-16]]])"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.forces"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.264895Z",
     "start_time": "2018-05-16T13:40:07.239790Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([0])"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.steps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.291500Z",
     "start_time": "2018-05-16T13:40:07.267149Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([], dtype=float64)"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.time"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.319872Z",
     "start_time": "2018-05-16T13:40:07.295010Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([21.484952])"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.volume"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-05-16T13:40:07.351623Z",
     "start_time": "2018-05-16T13:40:07.324075Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[[0.  , 0.  , 0.  ],\n",
       "        [1.39, 1.39, 1.39]]])"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "job.output.unwrapped_positions"
   ]
  },
  {
   "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": "3.7.6"
  },
  "toc": {
   "nav_menu": {},
   "number_sections": true,
   "sideBar": true,
   "skip_h1_title": false,
   "toc_cell": false,
   "toc_position": {},
   "toc_section_display": "block",
   "toc_window_display": false
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}