{
 "metadata": {
  "name": "",
  "signature": "sha256:e499dc236e18ffaa7e1f82d0ed379ae7c14212e0f8a89cd3fe9f7be8b49ef356"
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 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###1. Install required packages:\n",
      "\n",
      "- Install [Anaconda](https://www.continuum.io/downloads). For linux it is enought to install just [IPython](https://ipython.org/install.html) or [Jupyter Notebook](https://jupyter.readthedocs.io/en/latest/install.html)\n",
      "- Install [paramiko](http://www.paramiko.org/) package by running in command line *pip install paramiko*\n",
      "- Download siman package from https://github.com/dimonaks/siman/archive/v0.2.zip \n",
      "    and unpack into your folder, for example *'C:/programms/siman-0.2'*\n",
      "- Download SSHTools from http://zhugayevych.me/python/SSHTools/SSHTools.zip and unpack into *'C:/programms/SSHTools'*\n",
      "- open this file  (*siman-0.2/tutorials/working_with_database.ipynb*) in Notebook\n",
      "\n",
      "###2. Import packages:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import sys\n",
      "sys.path.extend(['/home/aksenov/Simulation_wrapper/siman', '/home/aksenov/Simulation_wrapper/SSHTools'])\n",
      "sys.path.extend(['C:/programms/siman-0.2', 'C:/programms/SSHTools']) #path to siman package and SSHtools\n",
      "from analysis import calc_redox\n",
      "from database import get_from_database\n",
      "from SSHTools import SSHTools"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###3. Initialize ssh:\n",
      "The database server address is '10.30.100.28'. Use your account data and private rsa key (created earlier and added to server)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ssh = SSHTools()\n",
      "# ssh.setup(user=\"Andriy.Zhugayevych\",host=\"cluster.skoltech.ru\",pkey=\"C:/Users/azh/Sys/Internet/SSH/skoltech/key2.ppk\")\n",
      "ssh.setup(user=\"aksenov\",host=\"10.30.100.28\",pkey=\"/home/aksenov/.ssh/id_rsa\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###4. Access to database\n",
      "The first two arguments are concentrations. The second argument is material. \n",
      "To clarify the inquiry use *inquiry_keys*. To switch off messages use *silent = 1*"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cl1, cl2 = get_from_database('x1', 'x0', 'LiTiS2', ssh_object = ssh)\n",
      "calc_redox(cl1, cl2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "Files for x1 :\n",
        "1 LiTiS2/bin/x1_PBEpaw400.pickle\n",
        "2 LiTiS2/bin/x1_UGGA-Upaw400.pickle\n",
        "3 LiTiS2/em/bin/x1_PBEpaw400_vs1.pickle\n",
        "4 LiTiS2/em/bin/x1_PBEpaw400_vs3.pickle\n",
        "5 LiTiS2/em/bin/x1_PBEpaw400_vs4.pickle\n",
        "6 LiTiS2/em/bin/x1_PBEpaw400_vs5.pickle\n",
        "7 LiTiS2/em/bin/x1_PBEpaw400_vs2.pickle\n",
        "8 LiTiS2/em/bin/x1_PBEpaw400_cg4.pickle\n",
        "9 LiTiS2/em/bin/x1_UGGA-Upaw400_vs3.pickle\n",
        "10 LiTiS2/em/bin/x1_UGGA-Upaw400_vs7.pickle\n",
        "11 LiTiS2/em/bin/x1_UGGA-Upaw400_vs5.pickle\n",
        "12 LiTiS2/em/bin/x1_UGGA-Upaw400_cg4.pickle\n",
        "13 LiTiS2/em/bin/x1_UGGA-Upaw400_vs4.pickle\n",
        "14 LiTiS2/em/bin/x1_UGGA-Upaw400_vs1.pickle\n",
        "15 LiTiS2/em/bin/x1_UGGA-Upaw400_vs6.pickle\n",
        "16 LiTiS2/em/bin/x1_UGGA-Upaw400_vs2.pickle\n",
        "17 LiTiS2/aks/bin/x1_UPBE-Upaw400_s10_su_4uis_100.pickle\n",
        "\n",
        "Files for x0 :\n",
        "1 LiTiS2/bin/x0_PBEpaw400.pickle\n",
        "2 LiTiS2/em/bin/x0_PBEpaw400_vs1.pickle\n",
        "3 LiTiS2/em/bin/x0_PBEpaw400_vs6.pickle\n",
        "4 LiTiS2/em/bin/x0_PBEpaw400_vs3.pickle\n",
        "5 LiTiS2/em/bin/x0_PBEpaw400_vs7.pickle\n",
        "6 LiTiS2/em/bin/x0_PBEpaw400_vs9.pickle\n",
        "7 LiTiS2/em/bin/x0_PBEpaw400_vs8.pickle\n",
        "8 LiTiS2/em/bin/x0_PBEpaw400_vs4.pickle\n",
        "9 LiTiS2/em/bin/x0_PBEpaw400_vs2.pickle\n",
        "10 LiTiS2/em/bin/x0_PBEpaw400_vs5.pickle\n",
        "11 LiTiS2/aks/bin/x0_UPBE-Upaw400_id_su_s10_su_4uis_100.pickle\n",
        "\n",
        "I choose first entries for both concentrations: LiTiS2/bin/x1_PBEpaw400.pickle and LiTiS2/bin/x0_PBEpaw400.pickle \n",
        "\n",
        "-- LiTiS2                         |       1.91 eV |       -2.7 % \n"
       ]
      },
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 3,
       "text": [
        "{}"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#clarifying with 'PBEpaw400' and 'vs2' tags\n",
      "cl1, cl2 = get_from_database('x1', 'x0', 'LiTiS2', inquiry_keys = ['PBEpaw400', 'vs2'], ssh_object = ssh)\n",
      "calc_redox(cl1, cl2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "Files for x1 :\n",
        "1 LiTiS2/em/bin/x1_PBEpaw400_vs2.pickle\n",
        "\n",
        "Files for x0 :\n",
        "1 LiTiS2/em/bin/x0_PBEpaw400_vs2.pickle\n",
        "\n",
        "I choose first entries for both concentrations: LiTiS2/em/bin/x1_PBEpaw400_vs2.pickle and LiTiS2/em/bin/x0_PBEpaw400_vs2.pickle \n",
        "\n",
        "-- LiTiS2                         |       1.91 eV |        3.6 % \n"
       ]
      },
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 4,
       "text": [
        "{}"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for mat in ['LiCoO2', 'LiMn2O4', 'LiFePO4', 'NaFePO4', 'NaMnAsO4', 'LiVPO4F',\n",
      "            'KVPO4F', 'Na2FePO4F', 'KFeSO4F', 'LiVP2O7', 'Na2FeVF7']:\n",
      "    cl1, cl2 = get_from_database('x1', 'x0', mat, inquiry_keys = ['UGGA'], silent = 1, ssh_object = ssh)\n",
      "    calc_redox(cl1, cl2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- LiCoO2                         |       3.93 eV |       -0.1 % \n",
        "-- LiMn2O4                        |       3.63 eV |        5.7 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- LiFePO4                        |       3.51 eV |        4.3 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- NaFePO4                        |       3.09 eV |       12.5 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- NaMnAsO4                       |       3.53 eV |       13.9 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- LiVPO4F                        |       3.93 eV |        7.3 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- KVPO4F                         |       4.03 eV |        8.7 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- Na2FePO4F                      |       4.11 eV |        3.9 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- KFeSO4F                        |       3.79 eV |       10.5 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- LiVP2O7                        |       3.93 eV |        3.5 % \n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "-- Na2FeVF7                       |       4.22 eV |        7.6 % \n"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cl1, cl2 = get_from_database('x1', 'x0', 'LiFePO4', inquiry_keys = ['aks'], silent = 0, ssh_object = ssh)\n",
      "calc_redox(cl1, cl2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "Files for x1 :\n",
        "1 LiFePO4/aks/bin/x1_UPBE-Upaw400_s10_su_4uis_100.pickle\n",
        "\n",
        "Files for x0 :\n",
        "1 LiFePO4/aks/bin/x0_UPBE-Upaw400_id_su_s10_su_4uis_100.pickle\n",
        "\n",
        "I choose first entries for both concentrations: LiFePO4/aks/bin/x1_UPBE-Upaw400_s10_su_4uis_100.pickle and LiFePO4/aks/bin/x0_UPBE-Upaw400_id_su_s10_su_4uis_100.pickle \n",
        "\n",
        "-- LiFePO4                        |       3.45 eV |        4.7 % \n"
       ]
      },
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 7,
       "text": [
        "{}"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Submitting new calculation"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "add_loop('YBaCo4O7_exp', '1uY', 1, input_geo_format = 'cee_database', cee_args = {'section':'Catalysts'},  it_folder = 'YBaCo4O7/P63MC', )"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}