examples/threedgraph/threedgraph.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Trained model and optimal hyperparameters\n",
    "\n",
    "We have provided trained model and hyperparameters of SphereNet on QM9 and MD17 [here](https://github.com/divelab/DIG_storage/tree/main/3dgraph)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Example of 3D Graph\n",
    "\n",
    "Here we provide the example code for SphereNet on QM93D and MD17 datasets. You can easily replace SphereNet with SchNet, DimeNetPP, and ComENet by changing model name and model parameters."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import torch\n",
    "from dig.threedgraph.dataset import QM93D\n",
    "from dig.threedgraph.dataset import MD17\n",
    "from dig.threedgraph.method import SphereNet #SchNet, DimeNetPP, ComENet\n",
    "from dig.threedgraph.method import run\n",
    "from dig.threedgraph.evaluation import ThreeDEvaluator"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "device(type='cuda', index=0)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "device = torch.device('cuda:0') if torch.cuda.is_available() else torch.device(\"cpu\")\n",
    "device"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. QM9\n",
    "\n",
    "**QM9 dataset includes geometric, energetic, electronic, and thermodynamic properties for 134k stable small organic molecules.**\n",
    "\n",
    "There are 12 properties. Here are the units for each property.\n",
    "\n",
    "|                          | mu     | alpha  | homo | lumo | gap  | r2    | zpve | U0   | U    | H    | G    | Cv     | std. MAE |\n",
    "| ------------------------ | ------ | ------ | ---- | ---- | ---- | ----- | ---- | ---- | ---- | ---- | ---- | ------ | -------- |\n",
    "| Unit in the dataset      | D      | a_0^3  | eV   | eV   | eV   | a_0^2 | eV   | eV   | eV   | eV   | eV   | cal / mol K  |    |\n",
    "| Unit of the reported MAE | D      | a_0^3  | meV  | meV  | meV  | a_0^2 | meV  | meV  | meV  | meV  | meV  | cal / mol K  | %  |\n",
    "\n",
    "**We trained a separate model for each target** except for _gap_, which was predicted by taking _lumo-homo_.\n",
    "\n",
    "**The default hyperparameters for QM9 are:** \n",
    "    &ensp; energy_and_force=False, cutoff=5.0, num_layers=4, hidden_channels=128, out_channels=1, int_emb_size=64,  \n",
    "    &ensp; basis_emb_size_dist=8, basis_emb_size_angle=8, basis_emb_size_torsion=8, out_emb_channels=256,  \n",
    "    &ensp; num_spherical=3, num_radial=6, envelope_exponent=5,  \n",
    "    &ensp; num_before_skip=1, num_after_skip=2, num_output_layers=3,  \n",
    "    &ensp; epochs=1000, batch_size=32, vt_batch_size=32, lr=0.0005, lr_decay_factor=0.5, lr_decay_step_size=100.\n",
    "\n",
    "\n"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Trained model\n",
    "\n",
    "We provide trained models to obtain optimal results.\n",
    "The models are in https://github.com/divelab/DIG_storage/tree/main/3dgraph/qm9.\n",
    "\n",
    "The results using the trained models are listed in the table. \n",
    "\n",
    "|            | mu     | alpha  | homo | lumo | gap  | r2    | zpve | U0   | U    | H    | G    | Cv     | std. MAE |\n",
    "| ---------- | ------ | ------ | ---- | ---- | ---- | ----- | ---- | ---- | ---- | ---- | ---- | ------ | -------- |\n",
    "| MAE | 0.0245 | 0.0449 | 22.8 | 19.6 | 31.1 | 0.268 | 1.26 | 6.31 | 6.36 | 6.33 | 7.78 | 0.024  | 0.92     |"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Loading dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "train, validaion, test: 110000 10000 10831\n"
     ]
    }
   ],
   "source": [
    "dataset = QM93D(root='dataset/')\n",
    "target = 'U0' # choose from: mu, alpha, homo, lumo, r2, zpve, U0, U, H, G, Cv\n",
    "dataset.data.y = dataset.data[target]\n",
    "\n",
    "split_idx = dataset.get_idx_split(len(dataset.data.y), train_size=110000, valid_size=10000, seed=42)\n",
    "\n",
    "train_dataset, valid_dataset, test_dataset = dataset[split_idx['train']], dataset[split_idx['valid']], dataset[split_idx['test']]\n",
    "print('train, validaion, test:', len(train_dataset), len(valid_dataset), len(test_dataset))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Loading model, loss and evaluation function\n",
    "\n",
    "The evaluation metric is mean absolute error (MAE)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "model = SphereNet(energy_and_force=False, cutoff=5.0, num_layers=4, \n",
    "        hidden_channels=128, out_channels=1, int_emb_size=64, \n",
    "        basis_emb_size_dist=8, basis_emb_size_angle=8, basis_emb_size_torsion=8, out_emb_channels=256, \n",
    "        num_spherical=3, num_radial=6, envelope_exponent=5, \n",
    "        num_before_skip=1, num_after_skip=2, num_output_layers=3, use_node_features=True\n",
    "        )\n",
    "loss_func = torch.nn.L1Loss()\n",
    "evaluation = ThreeDEvaluator()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Training"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#Params: 1890118\n",
      "\n",
      "=====Epoch 1\n",
      "\n",
      "Training...\n"
     ]
    },
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     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
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    {
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     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
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    {
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     "text": [
      "\n",
      "{'Train': 0.8305539944409076, 'Validation': 0.7885677814483643, 'Test': 0.7943109273910522}\n",
      "\n",
      "=====Epoch 2\n",
      "\n",
      "Training...\n"
     ]
    },
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     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
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      "\n",
      "\n",
      "Testing...\n"
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      "\n",
      "{'Train': 0.3417653005923415, 'Validation': 0.16290859878063202, 'Test': 0.16250823438167572}\n",
      "\n",
      "=====Epoch 3\n",
      "\n",
      "Training...\n"
     ]
    },
    {
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      "\n",
      "\n",
      "Evaluating...\n"
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     "text": [
      "\n",
      "\n",
      "Testing...\n"
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      "\n",
      "{'Train': 0.2626579807482881, 'Validation': 0.10924234241247177, 'Test': 0.1091669574379921}\n",
      "\n",
      "=====Epoch 4\n",
      "\n",
      "Training...\n"
     ]
    },
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      "\n",
      "\n",
      "Evaluating...\n"
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      "\n",
      "\n",
      "Testing...\n"
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      "\n",
      "{'Train': 0.2185871605092249, 'Validation': 0.1412947177886963, 'Test': 0.14113298058509827}\n",
      "\n",
      "=====Epoch 5\n",
      "\n",
      "Training...\n"
     ]
    },
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      "\n",
      "\n",
      "Evaluating...\n"
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      "\n",
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      "Testing...\n"
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      "\n",
      "{'Train': 0.18415136586759867, 'Validation': 0.08948442339897156, 'Test': 0.08791808038949966}\n",
      "\n",
      "=====Epoch 6\n",
      "\n",
      "Training...\n"
     ]
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      "Evaluating...\n"
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      "Testing...\n"
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      "\n",
      "{'Train': 0.17059671088246983, 'Validation': 0.10857655853033066, 'Test': 0.1086759939789772}\n",
      "\n",
      "=====Epoch 7\n",
      "\n",
      "Training...\n"
     ]
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      "\n",
      "{'Train': 0.15622219235277093, 'Validation': 0.08192159235477448, 'Test': 0.08170071989297867}\n",
      "\n",
      "=====Epoch 8\n",
      "\n",
      "Training...\n"
     ]
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      "\n",
      "{'Train': 0.1442768630192958, 'Validation': 0.08120342344045639, 'Test': 0.08138693124055862}\n",
      "\n",
      "=====Epoch 9\n",
      "\n",
      "Training...\n"
     ]
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      "\n",
      "{'Train': 0.13906806218478485, 'Validation': 0.07339970022439957, 'Test': 0.0732196718454361}\n",
      "\n",
      "=====Epoch 10\n",
      "\n",
      "Training...\n"
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      "\n",
      "{'Train': 0.12617339688792625, 'Validation': 0.11456501483917236, 'Test': 0.11438193917274475}\n",
      "\n",
      "=====Epoch 11\n",
      "\n",
      "Training...\n"
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      "\n",
      "{'Train': 0.12321726725571651, 'Validation': 0.0715189278125763, 'Test': 0.07092428207397461}\n",
      "\n",
      "=====Epoch 12\n",
      "\n",
      "Training...\n"
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      "\n",
      "{'Train': 0.11304465457233598, 'Validation': 0.1164650246500969, 'Test': 0.11696784943342209}\n",
      "\n",
      "=====Epoch 13\n",
      "\n",
      "Training...\n"
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:10<00:00, 28.54it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:11<00:00, 29.32it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.11311055924429181, 'Validation': 0.1142609491944313, 'Test': 0.11372711509466171}\n",
      "\n",
      "=====Epoch 14\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3438/3438 [04:25<00:00, 12.97it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:10<00:00, 29.43it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:12<00:00, 27.68it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.1103381712277869, 'Validation': 0.05894898623228073, 'Test': 0.05792950466275215}\n",
      "\n",
      "=====Epoch 15\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3438/3438 [04:30<00:00, 12.69it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:10<00:00, 29.26it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:11<00:00, 28.55it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.09813584842398945, 'Validation': 0.13913576304912567, 'Test': 0.1383834183216095}\n",
      "\n",
      "=====Epoch 16\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3438/3438 [04:26<00:00, 12.89it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:10<00:00, 29.29it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:11<00:00, 28.72it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.05428033658000465, 'Validation': 0.06030373275279999, 'Test': 0.059175316244363785}\n",
      "\n",
      "=====Epoch 17\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3438/3438 [04:28<00:00, 12.80it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:11<00:00, 27.83it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:12<00:00, 27.47it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.054203004988561614, 'Validation': 0.03810606151819229, 'Test': 0.03703922778367996}\n",
      "\n",
      "=====Epoch 18\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3438/3438 [04:29<00:00, 12.77it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:11<00:00, 28.11it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:12<00:00, 26.31it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.0530719623151666, 'Validation': 0.04359658062458038, 'Test': 0.043418560177087784}\n",
      "\n",
      "=====Epoch 19\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3438/3438 [04:26<00:00, 12.89it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:10<00:00, 28.87it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:12<00:00, 28.13it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.05202796294149651, 'Validation': 0.04247582331299782, 'Test': 0.04204947501420975}\n",
      "\n",
      "=====Epoch 20\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3438/3438 [04:31<00:00, 12.64it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 313/313 [00:10<00:00, 29.59it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 339/339 [00:11<00:00, 29.71it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "{'Train': 0.04962607438894397, 'Validation': 0.04090351238846779, 'Test': 0.040894996374845505}\n",
      "Best validation MAE so far: 0.03810606151819229\n",
      "Test MAE when got best validation result: 0.03703922778367996\n"
     ]
    }
   ],
   "source": [
    "run3d = run()\n",
    "run3d.run(device, train_dataset, valid_dataset, test_dataset, model, loss_func, evaluation, epochs=20, batch_size=32, vt_batch_size=32, lr=0.0005, lr_decay_factor=0.5, lr_decay_step_size=15)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. MD17\n",
    "\n",
    "**MD17 is a collection of eight molecular dynamics simulations for small organic molecules.**\n",
    "\n",
    "**The units for energy and force are kcal / mol and kcal / mol A.**\n",
    "\n",
    "**We trained a separate model for each molecule.** \n",
    "\n",
    "**The default hyperparameters for MD17 are:** \n",
    "    &ensp; energy_and_force=True, cutoff=5.0, num_layers=4, hidden_channels=128, out_channels=1, int_emb_size=64,  \n",
    "    &ensp; basis_emb_size_dist=8, basis_emb_size_angle=8, basis_emb_size_torsion=8, out_emb_channels=256,  \n",
    "    &ensp; num_spherical=3, num_radial=6, envelope_exponent=5,  \n",
    "    &ensp; num_before_skip=1, num_after_skip=2, num_output_layers=3,  \n",
    "    &ensp; epochs=1000, batch_size=1, vt_batch_size=32, lr=0.0005, lr_decay_factor=0.5, lr_decay_step_size=200."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Trained model\n",
    "\n",
    "We provide trained models to obtain optimal results.\n",
    "The models are in https://github.com/divelab/DIG_storage/tree/main/3dgraph/md17.\n",
    "\n",
    "The results using the trained models are listed in the table. \n",
    "\n",
    "|         | aspirin | benzene2017 | ethanol | malonaldehyde | naphthalene | salicylic | toluene | uracil |\n",
    "| ---------------- | ------- | ----------- | ------- | ------------- | ----------- | --------- | ------- | ------ |\n",
    "| force MAE    |0.375|0.181|0.187|0.273|0.139|0.284|0.142|0.245|"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Loading dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "train, validaion, test: 1000 1000 209762\n"
     ]
    }
   ],
   "source": [
    "dataset_md17 = MD17(root='dataset/', name='aspirin')\n",
    "\n",
    "split_idx_md17 = dataset_md17.get_idx_split(len(dataset_md17.data.y), train_size=1000, valid_size=1000, seed=42)\n",
    "\n",
    "train_dataset_md17, valid_dataset_md17, test_dataset_md17 = dataset_md17[split_idx_md17['train']], dataset_md17[split_idx_md17['valid']], dataset_md17[split_idx_md17['test']]\n",
    "print('train, validaion, test:', len(train_dataset_md17), len(valid_dataset_md17), len(test_dataset_md17))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Loading model, loss and evaluation function\n",
    "\n",
    "We predict energy and take the negative of the derivative of the energy with respect to the atomic positions as predicted forces.\n",
    "\n",
    "The evaluation metric is mean absolute error (MAE)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "model_md17 = SphereNet(energy_and_force=True, cutoff=5.0, num_layers=4, \n",
    "        hidden_channels=128, out_channels=1, int_emb_size=64, \n",
    "        basis_emb_size_dist=8, basis_emb_size_angle=8, basis_emb_size_torsion=8, out_emb_channels=256, \n",
    "        num_spherical=3, num_radial=6, envelope_exponent=5, \n",
    "        num_before_skip=1, num_after_skip=2, num_output_layers=3 \n",
    "        )\n",
    "loss_func_md17 = torch.nn.L1Loss()\n",
    "evaluation_md17 = ThreeDEvaluator()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Training"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#Params: 1890118\n",
      "\n",
      "=====Epoch 1\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/data1/limei/anaconda3/envs/graph/lib/python3.8/site-packages/torch_geometric/deprecation.py:13: UserWarning: 'data.DataLoader' is deprecated, use 'loader.DataLoader' instead\n",
      "  warnings.warn(out)\n",
      "100%|██████████| 1000/1000 [03:20<00:00,  4.99it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 16/16 [00:03<00:00,  5.06it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 21076.162109375, 'Force MAE': 88.1651611328125}\n",
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3278/3278 [10:49<00:00,  5.05it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 21079.103515625, 'Force MAE': 87.94914245605469}\n",
      "\n",
      "{'Train': 62999.26555371094, 'Validation': 29892.67822265625, 'Test': 29874.01776123047}\n",
      "\n",
      "=====Epoch 2\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 1000/1000 [03:35<00:00,  4.65it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 16/16 [00:03<00:00,  5.09it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 11752.1220703125, 'Force MAE': 41.66204833984375}\n",
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3278/3278 [10:27<00:00,  5.23it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 11752.3837890625, 'Force MAE': 41.8145866394043}\n",
      "\n",
      "{'Train': 21397.7178671875, 'Validation': 15918.326904296875, 'Test': 15933.84245300293}\n",
      "\n",
      "=====Epoch 3\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 1000/1000 [03:44<00:00,  4.46it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 16/16 [00:03<00:00,  5.15it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 12009.2421875, 'Force MAE': 70.98027038574219}\n",
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3278/3278 [10:42<00:00,  5.10it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 12010.466796875, 'Force MAE': 71.2234115600586}\n",
      "\n",
      "{'Train': 14609.853533203124, 'Validation': 19107.26922607422, 'Test': 19132.80795288086}\n",
      "\n",
      "=====Epoch 4\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 1000/1000 [03:46<00:00,  4.42it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 16/16 [00:03<00:00,  5.11it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 14571.55078125, 'Force MAE': 49.371952056884766}\n",
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3278/3278 [10:43<00:00,  5.09it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 14570.435546875, 'Force MAE': 49.68278121948242}\n",
      "\n",
      "{'Train': 13809.444167358399, 'Validation': 19508.745986938477, 'Test': 19538.713668823242}\n",
      "\n",
      "=====Epoch 5\n",
      "\n",
      "Training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 1000/1000 [03:43<00:00,  4.47it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Evaluating...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 16/16 [00:03<00:00,  5.20it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 19717.771484375, 'Force MAE': 30.181947708129883}\n",
      "\n",
      "\n",
      "Testing...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████| 3278/3278 [10:41<00:00,  5.11it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Energy MAE': 19717.19140625, 'Force MAE': 30.4222354888916}\n",
      "\n",
      "{'Train': 12309.488090698242, 'Validation': 22735.96625518799, 'Test': 22759.41495513916}\n",
      "Best validation MAE so far: 15918.326904296875\n",
      "Test MAE when got best validation result: 15933.84245300293\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    }
   ],
   "source": [
    "run3d_md17 = run()\n",
    "run3d_md17.run(device, train_dataset_md17, valid_dataset_md17, test_dataset_md17, model_md17, loss_func_md17, evaluation_md17, epochs=5, batch_size=1, vt_batch_size=64, lr=0.0005, lr_decay_factor=0.5, lr_decay_step_size=200, energy_and_force=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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