{
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   "id": "3200850a-b8fb-4f50-9815-16ae8da0f942",
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    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:root:Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.\n",
      "WARNING:root:Skipping scheduler setup. No training set found.\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "from pathlib import Path\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "from ase import Atom, Atoms\n",
    "from ase.data import chemical_symbols, covalent_radii, vdw_alvarez\n",
    "from ase.io import read, write\n",
    "from pymatgen.core import Element\n",
    "from scipy import stats\n",
    "from tqdm.auto import tqdm\n",
    "\n",
    "from mlip_arena.models.utils import REGISTRY, MLIPEnum\n",
    "\n",
    "model_name = \"EquiformerV2(OC20)\"\n",
    "\n",
    "calc = MLIPEnum[model_name].value()"
   ]
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      "Atoms(symbols='H2', pbc=True, cell=[7.4399999999999995, 7.441, 7.441999999999999], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='Er2', pbc=True, cell=[17.546, 17.547, 17.548], calculator=SinglePointCalculator(...))\n"
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      "Atoms(symbols='Lu2', pbc=True, cell=[16.988000000000003, 16.989000000000004, 16.990000000000002], calculator=SinglePointCalculator(...))\n"
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      "Atoms(symbols='Hf2', pbc=True, cell=[16.306, 16.307000000000002, 16.308], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='Ta2', pbc=True, cell=[15.686, 15.687, 15.688], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='W2', pbc=True, cell=[15.934, 15.934999999999999, 15.936], calculator=SinglePointCalculator(...))\n"
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      "Atoms(symbols='Re2', pbc=True, cell=[15.438000000000002, 15.439000000000002, 15.440000000000003], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='Os2', pbc=True, cell=[15.376, 15.376999999999999, 15.378], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='Ir2', pbc=True, cell=[14.942000000000002, 14.943000000000001, 14.944000000000003], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='Pt2', pbc=True, cell=[14.198, 14.199, 14.200000000000001], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='Au2', pbc=True, cell=[14.383999999999999, 14.384999999999998, 14.386], calculator=SinglePointCalculator(...))\n"
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     "text": [
      "Atoms(symbols='Hg2', pbc=True, cell=[15.190000000000001, 15.191, 15.192000000000002], calculator=SinglePointCalculator(...))\n"
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='Tl2', pbc=True, cell=[15.314000000000002, 15.315000000000001, 15.316000000000003], calculator=SinglePointCalculator(...))\n"
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='Pb2', pbc=True, cell=[16.12, 16.121000000000002, 16.122], calculator=SinglePointCalculator(...))\n"
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='Bi2', pbc=True, cell=[15.748000000000001, 15.749, 15.750000000000002], calculator=SinglePointCalculator(...))\n"
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     "metadata": {},
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    {
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='Po2', pbc=True, cell=[12.0, 12.001, 12.002], calculator=SinglePointCalculator(...))\n"
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='At2', pbc=True, cell=[12.0, 12.001, 12.002], calculator=SinglePointCalculator(...))\n"
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='Rn2', pbc=True, cell=[12.0, 12.001, 12.002], calculator=SinglePointCalculator(...))\n"
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     "metadata": {},
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    {
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='Fr2', pbc=True, cell=[12.0, 12.001, 12.002], calculator=SinglePointCalculator(...))\n"
     ]
    },
    {
     "data": {
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     "metadata": {},
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    {
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     "output_type": "stream",
     "text": [
      "Atoms(symbols='Ra2', pbc=True, cell=[12.0, 12.001, 12.002], calculator=SinglePointCalculator(...))\n"
     ]
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    {
     "data": {
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     "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Atoms(symbols='Ac2', pbc=True, cell=[17.36, 17.361, 17.362], calculator=SinglePointCalculator(...))\n"
     ]
    },
    {
     "data": {
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     "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Atoms(symbols='Th2', pbc=True, cell=[18.166, 18.167, 18.168])\n"
     ]
    },
    {
     "data": {
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     "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Pa2', pbc=True, cell=[17.855999999999998, 17.857, 17.857999999999997])\n"
     ]
    },
    {
     "data": {
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       "model_id": "ab7d607c7217458eb53eaa7b7accf6b7",
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     "metadata": {},
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='U2', pbc=True, cell=[16.802, 16.803, 16.804])\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "../aten/src/ATen/native/cuda/Indexing.cu:1237: indexSelectSmallIndex: block: [0,0,0], thread: [64,0,0] Assertion `srcIndex < srcSelectDimSize` failed.\n",
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     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "ca1f8486169847478d779ce93faa155c",
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     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Np2', pbc=True, cell=[17.483999999999998, 17.485, 17.485999999999997])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "55494155d4cb4c8d9ba701f95a005999",
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     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Pu2', pbc=True, cell=[17.422, 17.423000000000002, 17.424])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9e8141fdafc24ab4943e51129c13c0fd",
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     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Am2', pbc=True, cell=[17.546, 17.547, 17.548])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f8021cbe5a42488798642d455ac5bf4d",
       "version_major": 2,
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     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Cm2', pbc=True, cell=[18.91, 18.911, 18.912])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9c86275b258549d482b9718465820cb3",
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     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Bk2', pbc=True, cell=[21.08, 21.081, 21.081999999999997])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b236798ee57d4100a904c7d163ca41a8",
       "version_major": 2,
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     "metadata": {},
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    },
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     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Cf2', pbc=True, cell=[18.91, 18.911, 18.912])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "eb0068e5944c48729646c6577ed60e08",
       "version_major": 2,
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     "metadata": {},
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Es2', pbc=True, cell=[16.740000000000002, 16.741000000000003, 16.742])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "07fd96a912874a83a8bae27cc0a569f0",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/827 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Fm2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "34f8d1058783470aa891409656ed75d2",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Md2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9f8f687c8bab45869b749aa3e668c890",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='No2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "bd017f1152934ce79927791ec7374f4b",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Lr2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "96349229e8964cb1a9f8696060668b62",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Rf2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9b67bbbd67bd4b87834f93f665ff09a4",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Db2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "39b4c6459b854896b884307ea152c9e9",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Sg2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "10cf6e57435a4d85a7a49c3e2c28a9ae",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Bh2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "76ca1aa2e3404667987c12e22682db0b",
       "version_major": 2,
       "version_minor": 0
      },
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Hs2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "fb00cd19567e436b8db802bcabf71398",
       "version_major": 2,
       "version_minor": 0
      },
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Mt2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "0dbce3e07cb148ad94681b70caa30ffc",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Ds2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
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       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Rg2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "7e45470145cc420a9e2ec8c742ae531d",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Cn2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "ee9036f26458472786c7e0ac9d08e746",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Nh2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "7a708943975a40678d2202c43c3ef691",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Fl2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "afb2a3a6e58b4b6595b90170e74eabe2",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Mc2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "056fc56c2899412cbe291513d1f82dbe",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Lv2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "967172d7e9d1410d9a4efc015f039dbe",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Ts2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "8035c83802ee4e19a4ce004470b50ea4",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n",
      "Atoms(symbols='Og2', pbc=True, cell=[12.0, 12.001, 12.002])\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "195236ad3f85477598ed2c118f2939d1",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/590 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CUDA error: device-side assert triggered\n",
      "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
      "For debugging consider passing CUDA_LAUNCH_BLOCKING=1.\n",
      "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "for symbol in tqdm(chemical_symbols[1:]):\n",
    "\n",
    "    s = set([symbol])\n",
    "\n",
    "    if \"X\" in s:\n",
    "        continue\n",
    "\n",
    "    try:\n",
    "        atom = Atom(symbol)\n",
    "        rmin = min(covalent_radii[atom.number] * 0.5, 1.0)\n",
    "        rvdw = vdw_alvarez.vdw_radii[atom.number] if atom.number < len(vdw_alvarez.vdw_radii) else np.nan\n",
    "        rmax = 3.1 * rvdw if not np.isnan(rvdw) else 6\n",
    "        rstep = 0.01 #if rmin < 1 else 0.4\n",
    "\n",
    "        a = 2 * rmax\n",
    "\n",
    "        npts = int((rmax - rmin)/rstep)\n",
    "\n",
    "        rs = np.linspace(rmin, rmax, npts)\n",
    "        e = np.zeros_like(rs)\n",
    "\n",
    "        da = symbol + symbol\n",
    "\n",
    "        out_dir = Path(REGISTRY[model_name][\"family\"]) / str(da)\n",
    "\n",
    "        os.makedirs(out_dir, exist_ok=True)\n",
    "\n",
    "        skip = 0\n",
    "\n",
    "        element = Element(symbol)\n",
    "\n",
    "        try:\n",
    "            m = element.valence[1]\n",
    "            if element.valence == (0, 2):\n",
    "                m = 0\n",
    "        except:\n",
    "            m = 0\n",
    "\n",
    "\n",
    "        r = rs[0]\n",
    "\n",
    "        positions = [\n",
    "            [a/2-r/2, a/2, a/2],\n",
    "            [a/2+r/2, a/2, a/2],\n",
    "        ]\n",
    "\n",
    "        traj_fpath = out_dir / f\"{model_name}.extxyz\"\n",
    "\n",
    "        if traj_fpath.exists():\n",
    "            traj = read(traj_fpath, index=\":\")\n",
    "            skip = len(traj)\n",
    "            atoms = traj[-1]\n",
    "        else:\n",
    "            # Create the unit cell with two atoms\n",
    "            atoms = Atoms(\n",
    "                da,\n",
    "                positions=positions,\n",
    "                # magmoms=magmoms,\n",
    "                cell=[a, a+0.001, a+0.002],\n",
    "                pbc=True\n",
    "            )\n",
    "\n",
    "        print(atoms)\n",
    "\n",
    "        calc = calc\n",
    "\n",
    "        atoms.calc = calc\n",
    "\n",
    "        for i, r in enumerate(tqdm(rs)):\n",
    "\n",
    "            if i < skip:\n",
    "                continue\n",
    "\n",
    "            positions = [\n",
    "                [a/2-r/2, a/2, a/2],\n",
    "                [a/2+r/2, a/2, a/2],\n",
    "            ]\n",
    "\n",
    "            # atoms.set_initial_magnetic_moments(magmoms)\n",
    "\n",
    "            atoms.set_positions(positions)\n",
    "\n",
    "            e[i] = atoms.get_potential_energy()\n",
    "\n",
    "            write(traj_fpath, atoms, append=\"a\")\n",
    "    except Exception as e:\n",
    "        print(e)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "a0ac2c09-370b-4fdd-bf74-ea5c4ade0215",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d47aae6dd71642049e2784e703609b0a",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/118 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "\n",
    "\n",
    "df = pd.DataFrame(columns=[\"name\", \"method\", \"R\", \"E\", \"F\", \"S^2\", \"spearman-repulsion\", \"spearman-attraction\"])\n",
    "\n",
    "for symbol in tqdm(chemical_symbols[1:]):\n",
    "\n",
    "    da = symbol + symbol\n",
    "\n",
    "    out_dir = Path(REGISTRY[model_name][\"family\"]) / da\n",
    "\n",
    "    traj_fpath = out_dir / f\"{model_name}.extxyz\"\n",
    "\n",
    "\n",
    "    if traj_fpath.exists():\n",
    "        traj = read(traj_fpath, index=\":\")\n",
    "    else:\n",
    "        continue\n",
    "\n",
    "    Rs, Es, Fs, S2s = [], [], [], []\n",
    "    for atoms in traj:\n",
    "\n",
    "        vec = atoms.positions[1] - atoms.positions[0]\n",
    "        r = np.linalg.norm(vec)\n",
    "        e = atoms.get_potential_energy()\n",
    "        f = np.inner(vec/r, atoms.get_forces()[1])\n",
    "        # s2 = np.mean(np.power(atoms.get_magnetic_moments(), 2))\n",
    "\n",
    "        Rs.append(r)\n",
    "        Es.append(e)\n",
    "        Fs.append(f)\n",
    "        # S2s.append(s2)\n",
    "\n",
    "    rs = np.array(Rs)\n",
    "    es = np.array(Es)\n",
    "    fs = np.array(Fs)\n",
    "\n",
    "    indices = np.argsort(rs)[::-1]\n",
    "    rs = rs[indices]\n",
    "    es = es[indices]\n",
    "    fs = fs[indices]\n",
    "\n",
    "    iminf = np.argmin(fs)\n",
    "    imine = np.argmin(es)\n",
    "\n",
    "    data = {\n",
    "        \"name\": da,\n",
    "        \"method\": model_name,\n",
    "        \"R\": Rs,\n",
    "        \"E\": Es,\n",
    "        \"F\": Fs,\n",
    "        \"S^2\": S2s,\n",
    "        \"spearman-descending-force\": stats.spearmanr(rs[iminf:], fs[iminf:]).statistic,\n",
    "        \"spearman-ascending-force\": stats.spearmanr(rs[:iminf], fs[:iminf]).statistic,\n",
    "        \"spearman-repulsion-energy\": stats.spearmanr(rs[imine:], es[imine:]).statistic,\n",
    "        \"spearman-attraction-energy\": stats.spearmanr(rs[:imine], es[:imine]).statistic,\n",
    "    }\n",
    "\n",
    "    df = pd.concat([df, pd.DataFrame([data])], ignore_index=True)\n",
    "\n",
    "\n",
    "json_fpath = Path(REGISTRY[model_name][\"family\"]) / \"homonuclear-diatomics.json\"\n",
    "\n",
    "if json_fpath.exists():\n",
    "    df0 = pd.read_json(json_fpath)\n",
    "    df = pd.concat([df0, df], ignore_index=True)\n",
    "    df.drop_duplicates(inplace=True, subset=[\"name\", \"method\"])\n",
    "\n",
    "df.to_json(json_fpath, orient=\"records\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e0dd4367-3dca-440f-a7a9-7fdd84183f2c",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4e6ae884-89f3-43f2-8fd9-19bf00c91566",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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