{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/gaoxiang/pytorch-dev/pytorchdev/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",
      "WARNING:root:Unable to import NeuroChemAEV, please check your pyNeuroChem installation.\n"
     ]
    }
   ],
   "source": [
    "import h5py\n",
    "import torch\n",
    "from selected_system import mols, mol_file\n",
    "from ani_benchmark import ANIBenchmark\n",
    "import pandas\n",
    "import os\n",
    "import tqdm\n",
    "from IPython.display import display\n",
    "import itertools\n",
    "tqdm.monitor_interval = 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "torch.set_num_threads(1)\n",
    "fm = h5py.File(os.path.join('../',mol_file), \"r\")\n",
    "\n",
    "benchmarks = {\n",
    "    'C': ANIBenchmark(device=torch.device(\"cpu\")),\n",
    "}\n",
    "\n",
    "if torch.cuda.is_available():\n",
    "    benchmarks.update({\n",
    "        'G': ANIBenchmark(device=torch.device(\"cuda\")),\n",
    "    })"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of atoms: 20\n",
      "Running benchmark on molecule COC(=O)c1ccc([N+](=O)[O-])cc1\n"
     ]
    },
    {
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       "      <th>C,1</th>\n",
       "      <th>C,B</th>\n",
       "      <th>G,1</th>\n",
       "      <th>G,B</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>aev</th>\n",
       "      <td>0.700781</td>\n",
       "      <td>0.537888</td>\n",
       "      <td>1.095591</td>\n",
       "      <td>0.022238</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>energy</th>\n",
       "      <td>0.422604</td>\n",
       "      <td>0.183495</td>\n",
       "      <td>0.564654</td>\n",
       "      <td>0.002251</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>force</th>\n",
       "      <td>1.253797</td>\n",
       "      <td>0.561175</td>\n",
       "      <td>1.283622</td>\n",
       "      <td>0.010574</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>forward</th>\n",
       "      <td>1.123385</td>\n",
       "      <td>0.721383</td>\n",
       "      <td>1.660245</td>\n",
       "      <td>0.024489</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>total</th>\n",
       "      <td>2.377182</td>\n",
       "      <td>1.282558</td>\n",
       "      <td>2.943866</td>\n",
       "      <td>0.035064</td>\n",
       "    </tr>\n",
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       "</table>\n",
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      ],
      "text/plain": [
       "              C,1       C,B       G,1       G,B\n",
       "aev      0.700781  0.537888  1.095591  0.022238\n",
       "energy   0.422604  0.183495  0.564654  0.002251\n",
       "force    1.253797  0.561175  1.283622  0.010574\n",
       "forward  1.123385  0.721383  1.660245  0.024489\n",
       "total    2.377182  1.282558  2.943866  0.035064"
      ]
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of atoms: 50\n",
      "Running benchmark on molecule O=[N+]([O-])c1ccc(NN=Cc2ccc(C=NNc3ccc([N+](=O)[O-])cc3[N+](=O)[O-])cc2)c([N+](=O)[O-])c1\n"
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       "      <td>2.910254</td>\n",
       "      <td>1.120638</td>\n",
       "      <td>0.033106</td>\n",
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       "      <th>energy</th>\n",
       "      <td>0.546913</td>\n",
       "      <td>0.406957</td>\n",
       "      <td>0.474391</td>\n",
       "      <td>0.002537</td>\n",
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       "    <tr>\n",
       "      <th>force</th>\n",
       "      <td>3.637797</td>\n",
       "      <td>2.189924</td>\n",
       "      <td>1.495740</td>\n",
       "      <td>0.036373</td>\n",
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       "    <tr>\n",
       "      <th>forward</th>\n",
       "      <td>2.227671</td>\n",
       "      <td>3.317210</td>\n",
       "      <td>1.595029</td>\n",
       "      <td>0.035643</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>total</th>\n",
       "      <td>5.865469</td>\n",
       "      <td>5.507135</td>\n",
       "      <td>3.090769</td>\n",
       "      <td>0.072016</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "              C,1       C,B       G,1       G,B\n",
       "aev      1.680758  2.910254  1.120638  0.033106\n",
       "energy   0.546913  0.406957  0.474391  0.002537\n",
       "force    3.637797  2.189924  1.495740  0.036373\n",
       "forward  2.227671  3.317210  1.595029  0.035643\n",
       "total    5.865469  5.507135  3.090769  0.072016"
      ]
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of atoms: 10\n",
      "Running benchmark on molecule N#CCC(=O)N\n"
     ]
    },
    {
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       "      <td>1.081606</td>\n",
       "      <td>0.006245</td>\n",
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       "      <th>energy</th>\n",
       "      <td>0.288124</td>\n",
       "      <td>0.093577</td>\n",
       "      <td>0.446744</td>\n",
       "      <td>0.002521</td>\n",
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       "    <tr>\n",
       "      <th>force</th>\n",
       "      <td>0.755610</td>\n",
       "      <td>0.216397</td>\n",
       "      <td>1.218433</td>\n",
       "      <td>0.007300</td>\n",
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       "    <tr>\n",
       "      <th>forward</th>\n",
       "      <td>0.709054</td>\n",
       "      <td>0.243346</td>\n",
       "      <td>1.528349</td>\n",
       "      <td>0.008766</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>total</th>\n",
       "      <td>1.464663</td>\n",
       "      <td>0.459743</td>\n",
       "      <td>2.746782</td>\n",
       "      <td>0.016067</td>\n",
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      "text/plain": [
       "              C,1       C,B       G,1       G,B\n",
       "aev      0.420929  0.149769  1.081606  0.006245\n",
       "energy   0.288124  0.093577  0.446744  0.002521\n",
       "force    0.755610  0.216397  1.218433  0.007300\n",
       "forward  0.709054  0.243346  1.528349  0.008766\n",
       "total    1.464663  0.459743  2.746782  0.016067"
      ]
     },
     "metadata": {},
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of atoms: 4,5,6\n",
      "Running benchmark on molecule C\n"
     ]
    },
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       "      <td>0.017271</td>\n",
       "      <td>0.775032</td>\n",
       "      <td>0.004428</td>\n",
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       "      <th>energy</th>\n",
       "      <td>0.149350</td>\n",
       "      <td>0.048953</td>\n",
       "      <td>0.219576</td>\n",
       "      <td>0.001350</td>\n",
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       "    <tr>\n",
       "      <th>force</th>\n",
       "      <td>0.390866</td>\n",
       "      <td>0.121347</td>\n",
       "      <td>0.768956</td>\n",
       "      <td>0.005004</td>\n",
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       "    <tr>\n",
       "      <th>forward</th>\n",
       "      <td>0.356931</td>\n",
       "      <td>0.066225</td>\n",
       "      <td>0.994608</td>\n",
       "      <td>0.005778</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>total</th>\n",
       "      <td>0.747796</td>\n",
       "      <td>0.187572</td>\n",
       "      <td>1.763565</td>\n",
       "      <td>0.010781</td>\n",
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       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "              C,1       C,B       G,1       G,B\n",
       "aev      0.207580  0.017271  0.775032  0.004428\n",
       "energy   0.149350  0.048953  0.219576  0.001350\n",
       "force    0.390866  0.121347  0.768956  0.005004\n",
       "forward  0.356931  0.066225  0.994608  0.005778\n",
       "total    0.747796  0.187572  1.763565  0.010781"
      ]
     },
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of atoms: 100\n",
      "Running benchmark on molecule CC(C)C[C@@H](C(=O)O)NC(=O)C[C@@H]([C@H](CC1CCCCC1)NC(=O)CC[C@@H]([C@H](Cc2ccccc2)NC(=O)OC(C)(C)C)O)O\n"
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     "text": [
      "\n"
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       "      <th>energy</th>\n",
       "      <td>1.004400</td>\n",
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       "      <td>0.001794</td>\n",
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       "    <tr>\n",
       "      <th>force</th>\n",
       "      <td>8.206886</td>\n",
       "      <td>6.606211</td>\n",
       "      <td>1.827498</td>\n",
       "      <td>0.108411</td>\n",
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       "    <tr>\n",
       "      <th>forward</th>\n",
       "      <td>7.937472</td>\n",
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       "      <td>0.119997</td>\n",
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       "    <tr>\n",
       "      <th>total</th>\n",
       "      <td>16.144357</td>\n",
       "      <td>18.841565</td>\n",
       "      <td>3.571954</td>\n",
       "      <td>0.228409</td>\n",
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       "               C,1        C,B       G,1       G,B\n",
       "aev       6.933071  11.386394  1.226802  0.118203\n",
       "energy    1.004400   0.848959  0.517654  0.001794\n",
       "force     8.206886   6.606211  1.827498  0.108411\n",
       "forward   7.937472  12.235354  1.744456  0.119997\n",
       "total    16.144357  18.841565  3.571954  0.228409"
      ]
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of atoms: 305\n",
      "Running benchmark on molecule [H]/N=C(/N)\\NCCC[C@H](C(=O)N[C@H]([C@@H](C)O)C(=O)N[C@H](Cc1ccc(cc1)O)C(=O)NCCCC[C@@H](C(=O)NCCCC[C@@H](C(=O)NCC(=O)O)NC(=O)[C@H](CCCCNC(=O)[C@@H](Cc2ccc(cc2)O)NC(=O)[C@@H]([C@@H](C)O)NC(=O)[C@@H](CCCN/C(=N\\[H])/N)N)NC(=O)[C@@H](Cc3ccc(cc3)O)NC(=O)[C@@H]([C@@H](C)O)NC(=O)[C@@H](CCCN/C(=N\\[H])/N)N)NC(=O)[C@@H](Cc4ccc(cc4)O)NC(=O)[C@@H]([C@@H](C)O)NC(=O)[C@@H](CCCN/C(=N\\[H])/N)N)N\n"
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     "text": [
      "cuda runtime error (2) : out of memory at /home/gaoxiang/pytorch/aten/src/THC/generic/THCStorage.cu:58\n",
      "\n"
     ]
    },
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       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>C,1</th>\n",
       "      <th>C,B</th>\n",
       "      <th>G,1</th>\n",
       "      <th>G,B</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>aev</th>\n",
       "      <td>22.462832</td>\n",
       "      <td>38.629616</td>\n",
       "      <td>1.459434</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>energy</th>\n",
       "      <td>2.698251</td>\n",
       "      <td>2.419860</td>\n",
       "      <td>0.525845</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>force</th>\n",
       "      <td>21.112948</td>\n",
       "      <td>20.788418</td>\n",
       "      <td>3.065523</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>forward</th>\n",
       "      <td>25.161083</td>\n",
       "      <td>41.049476</td>\n",
       "      <td>1.985280</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>total</th>\n",
       "      <td>46.274031</td>\n",
       "      <td>61.837895</td>\n",
       "      <td>5.050802</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               C,1        C,B       G,1  G,B\n",
       "aev      22.462832  38.629616  1.459434  NaN\n",
       "energy    2.698251   2.419860  0.525845  NaN\n",
       "force    21.112948  20.788418  3.065523  NaN\n",
       "forward  25.161083  41.049476  1.985280  NaN\n",
       "total    46.274031  61.837895  5.050802  NaN"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "for i in mols:\n",
    "    print('number of atoms:', i)\n",
    "    smiles = mols[i]\n",
    "    for s in smiles:\n",
    "        print('Running benchmark on molecule', s)\n",
    "        key = s.replace('/', '_')\n",
    "        coordinates = torch.from_numpy(fm[key][()])\n",
    "        coordinates = coordinates[:200]\n",
    "        species = fm[key].attrs['species'].split()\n",
    "        results = {}\n",
    "        for b,m in tqdm.tqdm_notebook(list(itertools.product(benchmarks, ['1','B']))):\n",
    "            bench = benchmarks[b]\n",
    "            coordinates = coordinates.type(bench.aev_computer.dtype)\n",
    "            try:\n",
    "                if m == '1':\n",
    "                    result = bench.oneByOne(coordinates, species)\n",
    "                elif m == 'B':\n",
    "                    result = bench.inBatch(coordinates, species)\n",
    "                else:\n",
    "                    raise ValueError('BUG here')\n",
    "                result['forward'] = result['aev'] + result['energy']\n",
    "                result['total'] = result['forward'] + result['force']\n",
    "            except RuntimeError as e:\n",
    "                print(e)\n",
    "                result = {'aev': None, 'energy': None, 'force': None, 'total': None }\n",
    "            results[b + ',' + m] = result\n",
    "        df = pandas.DataFrame(results)\n",
    "        display(df)\n",
    "        break"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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