classify_list_of_formulas.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import math\n",
    "from PredictPerovskites import PredictABX3, PredictAABBXX6"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "81 candidate formulas\n",
      "9 single perovskite candidates: ['LiTiO3', 'LiMnO3', 'LiAlO3', 'SrTiO3', 'SrMnO3', 'SrAlO3', 'LaTiO3', 'LaMnO3', 'LaAlO3']\n",
      "18 A2BB'X6 candidates: ['Li2TiMnO6', 'Li2TiAlO6', 'Li2MnTiO6', 'Li2MnAlO6', 'Li2AlTiO6', 'Li2AlMnO6', 'Sr2TiMnO6', 'Sr2TiAlO6', 'Sr2MnTiO6', 'Sr2MnAlO6', 'Sr2AlTiO6', 'Sr2AlMnO6', 'La2TiMnO6', 'La2TiAlO6', 'La2MnTiO6', 'La2MnAlO6', 'La2AlTiO6', 'La2AlMnO6']\n"
     ]
    }
   ],
   "source": [
    "# generate some potential single and double perovskites\n",
    "\n",
    "A_cations = ['Li', 'Sr', 'La']\n",
    "B_cations = ['Ti', 'Mn', 'Al']\n",
    "X_anions = ['O']\n",
    "\n",
    "count = 0\n",
    "candidates = {}\n",
    "X1 = X_anions[0]\n",
    "for A1 in A_cations:\n",
    "    for A2 in A_cations:\n",
    "        for B1 in B_cations:\n",
    "            for B2 in B_cations:\n",
    "                if (A1 != A2) and (B1 != B2):\n",
    "                    candidate = ''.join([A1, A2, B1, B2, X1, '6'])\n",
    "                    tag = 'double_AB'\n",
    "                elif (A1 != A2):\n",
    "                    candidate = ''.join([A1, A2, B1, '2', X1, '6'])\n",
    "                    tag = 'double_A'\n",
    "                elif (B1 != B2):\n",
    "                    candidate = ''.join([A1, '2', B1, B2, X1, '6'])\n",
    "                    tag = 'double_B'\n",
    "                else:\n",
    "                    candidate = ''.join([A1, B1, X1, '3'])\n",
    "                    tag = 'single'\n",
    "                tmp_dict = {}\n",
    "                tmp_dict['A1'] = A1\n",
    "                tmp_dict['A2'] = A2\n",
    "                tmp_dict['B1'] = B1\n",
    "                tmp_dict['B2'] = B2\n",
    "                tmp_dict['X1'] = X1\n",
    "                tmp_dict['X2'] = X1\n",
    "                tmp_dict['tag'] = tag\n",
    "                tmp_dict['formula'] = candidate\n",
    "                candidates[candidate] = tmp_dict\n",
    "                count += 1\n",
    "\n",
    "print('%i candidate formulas' % count)\n",
    "CCX3s = [k for k in candidates if candidates[k]['tag'] == 'single']\n",
    "A2BBX6s = [k for k in candidates if candidates[k]['tag'] == 'double_B']\n",
    "print('%i single perovskite candidates: %s' % (len(CCX3s), CCX3s))\n",
    "print(\"%i A2BB'X6 candidates: %s\" % (len(A2BBX6s), A2BBX6s))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LiTiO3 could not be charge-balanced...\n",
      "Li2TiMnO6 classified as nonperovskite (tau = 5.07; P = 0.19)\n",
      "Li2TiAlO6 could not be charge-balanced...\n",
      "Li2MnTiO6 classified as nonperovskite (tau = 5.07; P = 0.19)\n",
      "LiMnO3 classified as nonperovskite (tau = 5.96; P = 0.06)\n",
      "Li2MnAlO6 classified as nonperovskite (tau = 4.82; P = 0.26)\n",
      "Li2AlTiO6 could not be charge-balanced...\n",
      "Li2AlMnO6 classified as nonperovskite (tau = 4.82; P = 0.26)\n",
      "LiAlO3 could not be charge-balanced...\n",
      "LiSrTi2O6 could not be charge-balanced...\n",
      "LiSrTiMnO6 classified as nonperovskite (tau = 4.83; P = 0.26)\n",
      "LiSrTiAlO6 could not be charge-balanced...\n",
      "LiSrMnTiO6 classified as nonperovskite (tau = 4.83; P = 0.26)\n",
      "LiSrMn2O6 could not be charge-balanced...\n",
      "LiSrMnAlO6 classified as nonperovskite (tau = 5.39; P = 0.12)\n",
      "LiSrAlTiO6 could not be charge-balanced...\n",
      "LiSrAlMnO6 classified as nonperovskite (tau = 5.39; P = 0.12)\n",
      "LiSrAl2O6 could not be charge-balanced...\n",
      "LiLaTi2O6 classified as nonperovskite (tau = 4.26; P = 0.49)\n",
      "LiLaTiMnO6 classified as nonperovskite (tau = 4.23; P = 0.51)\n",
      "LiLaTiAlO6 could not be charge-balanced...\n",
      "LiLaMnTiO6 classified as nonperovskite (tau = 4.23; P = 0.51)\n",
      "LiLaMn2O6 classified as nonperovskite (tau = 4.26; P = 0.50)\n",
      "LiLaMnAlO6 classified as nonperovskite (tau = 4.68; P = 0.31)\n",
      "LiLaAlTiO6 could not be charge-balanced...\n",
      "LiLaAlMnO6 classified as nonperovskite (tau = 4.68; P = 0.31)\n",
      "LiLaAl2O6 could not be charge-balanced...\n",
      "SrLiTi2O6 could not be charge-balanced...\n",
      "SrLiTiMnO6 classified as nonperovskite (tau = 4.83; P = 0.26)\n",
      "SrLiTiAlO6 could not be charge-balanced...\n",
      "SrLiMnTiO6 classified as nonperovskite (tau = 4.83; P = 0.26)\n",
      "SrLiMn2O6 could not be charge-balanced...\n",
      "SrLiMnAlO6 classified as nonperovskite (tau = 5.39; P = 0.12)\n",
      "SrLiAlTiO6 could not be charge-balanced...\n",
      "SrLiAlMnO6 classified as nonperovskite (tau = 5.39; P = 0.12)\n",
      "SrLiAl2O6 could not be charge-balanced...\n",
      "SrTiO3 classified as perovskite (tau = 3.80; P = 0.70)\n",
      "Sr2TiMnO6 classified as perovskite (tau = 3.92; P = 0.66)\n",
      "Sr2TiAlO6 could not be charge-balanced...\n",
      "Sr2MnTiO6 classified as perovskite (tau = 3.92; P = 0.66)\n",
      "SrMnO3 classified as perovskite (tau = 4.08; P = 0.58)\n",
      "Sr2MnAlO6 classified as nonperovskite (tau = 4.77; P = 0.28)\n",
      "Sr2AlTiO6 could not be charge-balanced...\n",
      "Sr2AlMnO6 classified as nonperovskite (tau = 4.77; P = 0.28)\n",
      "SrAlO3 could not be charge-balanced...\n",
      "SrLaTi2O6 could not be charge-balanced...\n",
      "SrLaTiMnO6 classified as perovskite (tau = 2.93; P = 0.92)\n",
      "SrLaTiAlO6 classified as perovskite (tau = 3.04; P = 0.91)\n",
      "SrLaMnTiO6 classified as perovskite (tau = 2.93; P = 0.92)\n",
      "SrLaMn2O6 could not be charge-balanced...\n",
      "SrLaMnAlO6 classified as perovskite (tau = 3.18; P = 0.88)\n",
      "SrLaAlTiO6 classified as perovskite (tau = 3.04; P = 0.91)\n",
      "SrLaAlMnO6 classified as perovskite (tau = 3.18; P = 0.88)\n",
      "SrLaAl2O6 could not be charge-balanced...\n",
      "LaLiTi2O6 classified as nonperovskite (tau = 4.26; P = 0.49)\n",
      "LaLiTiMnO6 classified as nonperovskite (tau = 4.23; P = 0.51)\n",
      "LaLiTiAlO6 could not be charge-balanced...\n",
      "LaLiMnTiO6 classified as nonperovskite (tau = 4.23; P = 0.51)\n",
      "LaLiMn2O6 classified as nonperovskite (tau = 4.26; P = 0.50)\n",
      "LaLiMnAlO6 classified as nonperovskite (tau = 4.68; P = 0.31)\n",
      "LaLiAlTiO6 could not be charge-balanced...\n",
      "LaLiAlMnO6 classified as nonperovskite (tau = 4.68; P = 0.31)\n",
      "LaLiAl2O6 could not be charge-balanced...\n",
      "LaSrTi2O6 could not be charge-balanced...\n",
      "LaSrTiMnO6 classified as perovskite (tau = 2.93; P = 0.92)\n",
      "LaSrTiAlO6 classified as perovskite (tau = 3.04; P = 0.91)\n",
      "LaSrMnTiO6 classified as perovskite (tau = 2.93; P = 0.92)\n",
      "LaSrMn2O6 could not be charge-balanced...\n",
      "LaSrMnAlO6 classified as perovskite (tau = 3.18; P = 0.88)\n",
      "LaSrAlTiO6 classified as perovskite (tau = 3.04; P = 0.91)\n",
      "LaSrAlMnO6 classified as perovskite (tau = 3.18; P = 0.88)\n",
      "LaSrAl2O6 could not be charge-balanced...\n",
      "LaTiO3 classified as perovskite (tau = 1.69; P = 0.99)\n",
      "La2TiMnO6 classified as perovskite (tau = 1.67; P = 0.99)\n",
      "La2TiAlO6 classified as perovskite (tau = 1.64; P = 0.99)\n",
      "La2MnTiO6 classified as perovskite (tau = 1.67; P = 0.99)\n",
      "LaMnO3 classified as perovskite (tau = 1.65; P = 0.99)\n",
      "La2MnAlO6 classified as perovskite (tau = 1.65; P = 0.99)\n",
      "La2AlTiO6 classified as perovskite (tau = 1.64; P = 0.99)\n",
      "La2AlMnO6 classified as perovskite (tau = 1.65; P = 0.99)\n",
      "LaAlO3 classified as perovskite (tau = 1.79; P = 0.99)\n"
     ]
    }
   ],
   "source": [
    "# if single, assign A/B and classify; if double, use given A/B and classify\n",
    "\n",
    "properties = ['A', 'B',\n",
    "              'nA', 'nB', 'nX',\n",
    "              'rA', 'rB', 'rX',\n",
    "              't', 't_pred',\n",
    "              'tau', 'tau_pred']\n",
    "\n",
    "results = {}\n",
    "clf = PredictABX3('').calibrate_tau\n",
    "for candidate in candidates:\n",
    "    tmp_dict = candidates[candidate]\n",
    "    A1 = tmp_dict['A1']\n",
    "    A2 = tmp_dict['A2']\n",
    "    B1 = tmp_dict['B1']\n",
    "    B2 = tmp_dict['B2']\n",
    "    X1 = tmp_dict['X1']\n",
    "    X2 = tmp_dict['X2']\n",
    "    classifier = PredictAABBXX6(A1, A2, B1, B2, X1, X2)\n",
    "    for prop in properties:\n",
    "        tmp_dict[prop] = getattr(classifier, prop)\n",
    "    tmp_dict['tau_prob'] = classifier.tau_prob(clf)\n",
    "    results[candidate] = tmp_dict        \n",
    "    if not math.isnan(tmp_dict['tau']):\n",
    "        print('%s classified as %s (tau = %.2f; P = %.2f)' % (candidate, ['perovskite' if tmp_dict['tau_pred'] == 1 else 'nonperovskite'][0],\n",
    "                                                  tmp_dict['tau'], tmp_dict['tau_prob']))\n",
    "    else:\n",
    "        print('%s could not be charge-balanced...' % candidate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# write results to file\n",
    "\n",
    "with open('classified_formulas.csv', 'w') as f:\n",
    "    f.write('formula,tag,tau,tau_pred,tau_prob,t,t_pred,A,B,A1,A2,B1,B2,X1,X2,nA,nB,nX,rA,rB,rX\\n')\n",
    "    for r in results:\n",
    "        d = results[r]\n",
    "        seq = [d['formula'], d['tag'],\n",
    "               d['tau'], d['tau_pred'], d['tau_prob'],\n",
    "               d['t'], d['t_pred'],\n",
    "               d['A'], d['B'],\n",
    "               d['A1'], d['A2'], d['B1'], d['B2'], d['X1'], d['X2'],\n",
    "               d['nA'], d['nB'], d['nX'],\n",
    "               d['rA'], d['rB'], d['rX']\n",
    "               ]\n",
    "        seq = [str(val) for val in seq]\n",
    "        seq = [val if val != 'nan' else '' for val in seq]\n",
    "        f.write(','.join(seq)+'\\n')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>formula</th>\n",
       "      <th>tag</th>\n",
       "      <th>tau</th>\n",
       "      <th>tau_pred</th>\n",
       "      <th>tau_prob</th>\n",
       "      <th>t</th>\n",
       "      <th>t_pred</th>\n",
       "      <th>A</th>\n",
       "      <th>B</th>\n",
       "      <th>A1</th>\n",
       "      <th>...</th>\n",
       "      <th>B1</th>\n",
       "      <th>B2</th>\n",
       "      <th>X1</th>\n",
       "      <th>X2</th>\n",
       "      <th>nA</th>\n",
       "      <th>nB</th>\n",
       "      <th>nX</th>\n",
       "      <th>rA</th>\n",
       "      <th>rB</th>\n",
       "      <th>rX</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>LiTiO3</td>\n",
       "      <td>single</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Li</td>\n",
       "      <td>Ti</td>\n",
       "      <td>Li</td>\n",
       "      <td>...</td>\n",
       "      <td>Ti</td>\n",
       "      <td>Ti</td>\n",
       "      <td>O</td>\n",
       "      <td>O</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Li2TiMnO6</td>\n",
       "      <td>double_B</td>\n",
       "      <td>5.068813</td>\n",
       "      <td>-1.0</td>\n",
       "      <td>0.187661</td>\n",
       "      <td>0.896441</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Li</td>\n",
       "      <td>...</td>\n",
       "      <td>Ti</td>\n",
       "      <td>Mn</td>\n",
       "      <td>O</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>-2.0</td>\n",
       "      <td>0.92</td>\n",
       "      <td>0.43</td>\n",
       "      <td>1.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Li2TiAlO6</td>\n",
       "      <td>double_B</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Li</td>\n",
       "      <td>...</td>\n",
       "      <td>Ti</td>\n",
       "      <td>Al</td>\n",
       "      <td>O</td>\n",
       "      <td>O</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Li2MnTiO6</td>\n",
       "      <td>double_B</td>\n",
       "      <td>5.068813</td>\n",
       "      <td>-1.0</td>\n",
       "      <td>0.187661</td>\n",
       "      <td>0.896441</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Li</td>\n",
       "      <td>...</td>\n",
       "      <td>Mn</td>\n",
       "      <td>Ti</td>\n",
       "      <td>O</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>-2.0</td>\n",
       "      <td>0.92</td>\n",
       "      <td>0.43</td>\n",
       "      <td>1.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>LiMnO3</td>\n",
       "      <td>single</td>\n",
       "      <td>5.961561</td>\n",
       "      <td>-1.0</td>\n",
       "      <td>0.055315</td>\n",
       "      <td>0.948259</td>\n",
       "      <td>1.0</td>\n",
       "      <td>Li</td>\n",
       "      <td>Mn</td>\n",
       "      <td>Li</td>\n",
       "      <td>...</td>\n",
       "      <td>Mn</td>\n",
       "      <td>Mn</td>\n",
       "      <td>O</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>-2.0</td>\n",
       "      <td>0.92</td>\n",
       "      <td>0.33</td>\n",
       "      <td>1.4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 21 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     formula       tag       tau  tau_pred  tau_prob         t  t_pred    A  \\\n",
       "0     LiTiO3    single       NaN       NaN       NaN       NaN     NaN   Li   \n",
       "1  Li2TiMnO6  double_B  5.068813      -1.0  0.187661  0.896441     1.0  NaN   \n",
       "2  Li2TiAlO6  double_B       NaN       NaN       NaN       NaN     NaN  NaN   \n",
       "3  Li2MnTiO6  double_B  5.068813      -1.0  0.187661  0.896441     1.0  NaN   \n",
       "4     LiMnO3    single  5.961561      -1.0  0.055315  0.948259     1.0   Li   \n",
       "\n",
       "     B  A1 ...   B1  B2 X1 X2   nA   nB   nX    rA    rB   rX  \n",
       "0   Ti  Li ...   Ti  Ti  O  O  NaN  NaN  NaN   NaN   NaN  1.4  \n",
       "1  NaN  Li ...   Ti  Mn  O  O  1.0  5.0 -2.0  0.92  0.43  1.4  \n",
       "2  NaN  Li ...   Ti  Al  O  O  NaN  NaN  NaN   NaN   NaN  NaN  \n",
       "3  NaN  Li ...   Mn  Ti  O  O  1.0  5.0 -2.0  0.92  0.43  1.4  \n",
       "4   Mn  Li ...   Mn  Mn  O  O  1.0  5.0 -2.0  0.92  0.33  1.4  \n",
       "\n",
       "[5 rows x 21 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# read file into pandas DataFrame\n",
    "# NOTE: tau_prob can be > 0.5 with tau_pred == -1 because of the cross-validation used during Platt's scaling\n",
    "\n",
    "df = pd.read_csv('classified_formulas.csv')\n",
    "\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The rA of LiMnO3 = 0.92\n"
     ]
    }
   ],
   "source": [
    "# retrieve data for a given compound\n",
    "\n",
    "compound = 'LiMnO3'\n",
    "prop = 'rA'\n",
    "\n",
    "print('The %s of %s = %.2f' % (prop, compound, df[prop].get((df.formula == compound)).tolist()[0]))"
   ]
  }
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