diff --git "a/mlip_arena/tasks/diatomics/run.ipynb" "b/mlip_arena/tasks/diatomics/run.ipynb" --- "a/mlip_arena/tasks/diatomics/run.ipynb" +++ "b/mlip_arena/tasks/diatomics/run.ipynb" @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "id": "3200850a-b8fb-4f50-9815-16ae8da0f942", "metadata": { "tags": [] @@ -30,7 +30,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "90887faa-1601-4c4c-9c44-d16731471d7f", "metadata": { "scrolled": true, @@ -41,24 +41,15 @@ "name": "stdout", "output_type": "stream", "text": [ - "========== EquiformerV2(OC20) ==========\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING:root:Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.\n", - "WARNING:root:Couldn't modify the submission pickle with error: [Errno 2] No such file or directory: '/checkpoint/abhshkdz/open-catalyst-project/logs/equiformer_v2/8307793/30669435_submitted.pkl'\n", - "WARNING:root:Skipping scheduler setup. No training set found.\n", - "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).\n", - " \"mean\": torch.tensor(state_dict[\"mean\"]),\n" + "========== MACE-OFF(M) ==========\n", + "Selected GPU cuda:0 with 40338.06 MB free memory from 4 GPUs\n", + "Default dtype float32 does not match model dtype float64, converting models to float32.\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "fb3a1b082e65432392452cd49c970a73", + "model_id": "60f14aee9df9484997239ace3de2e101", "version_major": 2, "version_minor": 0 }, @@ -79,7 +70,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "ae877fcff60b488b9bf999c8e60ede7b", + "model_id": "01f85ac837a44f64950df4fbe5f108f1", "version_major": 2, "version_minor": 0 }, @@ -100,7 +91,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "3129493feb1341f8a481440ca48c3022", + "model_id": "ab613d7a045e45bd939214bfc6ff0b3f", "version_major": 2, "version_minor": 0 }, @@ -115,13 +106,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "2 is not in list\n", "Atoms(symbols='Li2', pbc=True, cell=[13.144000000000002, 13.145000000000001, 13.146000000000003])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "740fe86bac484a61b83a384823b1645b", + "model_id": "a44cf4d8d9af41ea98901956c5b2e800", "version_major": 2, "version_minor": 0 }, @@ -136,13 +128,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "3 is not in list\n", "Atoms(symbols='Be2', pbc=True, cell=[12.276, 12.277, 12.278])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "f2649afe32f7486398ffd71c098b5481", + "model_id": "e3a16426d1cb4f9785fcfc1fd83dd8cd", "version_major": 2, "version_minor": 0 }, @@ -157,13 +150,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "4 is not in list\n", "Atoms(symbols='B2', pbc=True, cell=[11.842, 11.843, 11.844000000000001])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c7bbc608a47f413496fd445fb83dd747", + "model_id": "0b96202a2c594947b6093ecab0d89a25", "version_major": 2, "version_minor": 0 }, @@ -178,13 +172,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "5 is not in list\n", "Atoms(symbols='C2', pbc=True, cell=[10.974, 10.975, 10.976])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d73537663862482798c4512e13763b16", + "model_id": "55e1867137bb450f8c31b378ddcf5f2b", "version_major": 2, "version_minor": 0 }, @@ -205,7 +200,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d26f8600f65f41a2a754ba489bd1fe64", + "model_id": "0c71c7705dbc428d81308cdc16942921", "version_major": 2, "version_minor": 0 }, @@ -226,7 +221,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2445be9f8d824f8a960a2380a50ed5ad", + "model_id": "52a86764001b45cab2fef7af36f4d16a", "version_major": 2, "version_minor": 0 }, @@ -247,7 +242,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "87d7c2beadb94a98a85736521676a92f", + "model_id": "34a2485e76cd4acc8c5d4caa724037ae", "version_major": 2, "version_minor": 0 }, @@ -268,7 +263,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c0b5603b4b7a4f798d28003cb8017e24", + "model_id": "da6bf461ce4849ef8b723a140aee5e46", "version_major": 2, "version_minor": 0 }, @@ -283,13 +278,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "10 is not in list\n", "Atoms(symbols='Na2', pbc=True, cell=[15.5, 15.501, 15.502])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "717e21591149423f98c6ec8a57e2c007", + "model_id": "07b8b95e8418423193b3eb48a1c3197a", "version_major": 2, "version_minor": 0 }, @@ -304,13 +300,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "11 is not in list\n", "Atoms(symbols='Mg2', pbc=True, cell=[15.562, 15.562999999999999, 15.564])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c48f33f121084bc2a47c96a26bb24d40", + "model_id": "1032c8118d4e4da6b9ea753d152490b2", "version_major": 2, "version_minor": 0 }, @@ -325,13 +322,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "12 is not in list\n", "Atoms(symbols='Al2', pbc=True, cell=[13.950000000000001, 13.951, 13.952000000000002])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c49da4c1a00f4ef89ab53a8a58d8494c", + "model_id": "a907fe3e32644eaa884b9c11b80e503e", "version_major": 2, "version_minor": 0 }, @@ -346,13 +344,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "13 is not in list\n", "Atoms(symbols='Si2', pbc=True, cell=[13.578, 13.578999999999999, 13.58])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "8062fddb9b7c4d5fbf7342785acc73bc", + "model_id": "fd88635852dc4d2ca1c3cd298a760a2e", "version_major": 2, "version_minor": 0 }, @@ -367,13 +366,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "14 is not in list\n", "Atoms(symbols='P2', pbc=True, cell=[11.78, 11.780999999999999, 11.782])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "7d320bd7c5484dfab71ace8529b70d1d", + "model_id": "12bf703b946a4f038142fb8531dbdd44", "version_major": 2, "version_minor": 0 }, @@ -394,7 +394,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "6324d2c298a542828c07291c18c221cb", + "model_id": "84232451800944dd931a9cc1a3f7c76a", "version_major": 2, "version_minor": 0 }, @@ -415,7 +415,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "54c5575c22574894b4818ffdf81a76d5", + "model_id": "49a6bc3910244f04b9a74e8d2e8c4142", "version_major": 2, "version_minor": 0 }, @@ -436,7 +436,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "16ee4481621d4b2ab2814a926ec66961", + "model_id": "ebb843c27f634344bd10a526081ca13c", "version_major": 2, "version_minor": 0 }, @@ -451,13 +451,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "18 is not in list\n", "Atoms(symbols='K2', pbc=True, cell=[16.926000000000002, 16.927000000000003, 16.928])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "40c58d9009e14342b5d63daffa92e500", + "model_id": "c3cee6fcc4894e5085ce78549feb9177", "version_major": 2, "version_minor": 0 }, @@ -472,13 +473,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "19 is not in list\n", "Atoms(symbols='Ca2', pbc=True, cell=[16.244, 16.245, 16.246])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "6c26cc1757ea4f1c92a4260d2eebaca9", + "model_id": "df8ca2be9bfd496ca5cabda54ab5c6fc", "version_major": 2, "version_minor": 0 }, @@ -493,13 +495,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "20 is not in list\n", "Atoms(symbols='Sc2', pbc=True, cell=[15.996, 15.997, 15.998000000000001])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "1a8a3149ff4f4c7797b366cab2419e19", + "model_id": "4861cf3841bf4bce95c6f28db390c90c", "version_major": 2, "version_minor": 0 }, @@ -514,13 +517,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "21 is not in list\n", "Atoms(symbols='Ti2', pbc=True, cell=[15.252, 15.253, 15.254000000000001])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "e17caa1e90444469a529c782f74c6f44", + "model_id": "b8de0654f19c406da7709f59f4d5ab46", "version_major": 2, "version_minor": 0 }, @@ -535,13 +539,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "22 is not in list\n", "Atoms(symbols='V2', pbc=True, cell=[15.004, 15.004999999999999, 15.006])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "80181fe3673a4f9c81237113fb09241a", + "model_id": "436311045ab541f3b42f9e3082c888c4", "version_major": 2, "version_minor": 0 }, @@ -556,13 +561,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "23 is not in list\n", "Atoms(symbols='Cr2', pbc=True, cell=[15.190000000000001, 15.191, 15.192000000000002])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "cec3efec611048898f3c253919e77c9c", + "model_id": "790a63d1478f4313b967ca5ac646b60e", "version_major": 2, "version_minor": 0 }, @@ -577,13 +583,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "24 is not in list\n", "Atoms(symbols='Mn2', pbc=True, cell=[15.190000000000001, 15.191, 15.192000000000002])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "0cbe0177d37145a09368da269439e9d3", + "model_id": "842404aaf77046fb95be4886c3c6b204", "version_major": 2, "version_minor": 0 }, @@ -598,13 +605,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "25 is not in list\n", "Atoms(symbols='Fe2', pbc=True, cell=[15.128, 15.129, 15.13])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "0224bdbfba704f7d8e7bbab53038785d", + "model_id": "421357cb56af4b589fdeafc354559700", "version_major": 2, "version_minor": 0 }, @@ -619,13 +627,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "26 is not in list\n", "Atoms(symbols='Co2', pbc=True, cell=[14.879999999999999, 14.880999999999998, 14.882])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c9e09cee05b749e3b4be596a46d11584", + "model_id": "c0a0dc53185143dc99d99695bc93ffbc", "version_major": 2, "version_minor": 0 }, @@ -640,13 +649,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "27 is not in list\n", "Atoms(symbols='Ni2', pbc=True, cell=[14.879999999999999, 14.880999999999998, 14.882])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "857608f7605140ecb55488b3ffbc0dc7", + "model_id": "686f870641b645e19ab34b492285d65b", "version_major": 2, "version_minor": 0 }, @@ -661,13 +671,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "28 is not in list\n", "Atoms(symbols='Cu2', pbc=True, cell=[14.756, 14.757, 14.758000000000001])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "1d5ed5324d4c401ca9479f06587a593b", + "model_id": "af3aa8ccc84a4e9c90cf7be3058f8974", "version_major": 2, "version_minor": 0 }, @@ -682,13 +693,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "29 is not in list\n", "Atoms(symbols='Zn2', pbc=True, cell=[14.818000000000001, 14.819, 14.820000000000002])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d89a24804f30470994a9777666d7a055", + "model_id": "1663ce2f57b94ba58726f1807ace289f", "version_major": 2, "version_minor": 0 }, @@ -703,13 +715,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "30 is not in list\n", "Atoms(symbols='Ga2', pbc=True, cell=[14.383999999999999, 14.384999999999998, 14.386])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "9b88430fbc464a5fa1114cb251948b94", + "model_id": "b4101abb835e446ba361c5f4b8347f75", "version_major": 2, "version_minor": 0 }, @@ -724,13 +737,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "31 is not in list\n", "Atoms(symbols='Ge2', pbc=True, cell=[14.198, 14.199, 14.200000000000001])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "169860b84069488380ae557fb7cf5ed1", + "model_id": "3f974765427c4cb5ac7eea72a57cfa58", "version_major": 2, "version_minor": 0 }, @@ -745,13 +759,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "32 is not in list\n", "Atoms(symbols='As2', pbc=True, cell=[11.655999999999999, 11.656999999999998, 11.658])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "0a76df7eccb14dea84019b81b0fd0b3e", + "model_id": "a8e033dbae494467a5028eab97e28bbe", "version_major": 2, "version_minor": 0 }, @@ -766,13 +781,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "33 is not in list\n", "Atoms(symbols='Se2', pbc=True, cell=[11.284, 11.285, 11.286000000000001])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "a7187637bd0449baa9ba01567467692f", + "model_id": "c430c0fe2a6a4f45a6b15cf6a6266c70", "version_major": 2, "version_minor": 0 }, @@ -787,13 +803,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "34 is not in list\n", "Atoms(symbols='Br2', pbc=True, cell=[11.532000000000002, 11.533000000000001, 11.534000000000002])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "08eecc5ce1da4e4a852a5439bc2d7845", + "model_id": "adc60afc577747f4ab184e8bc4ec889e", "version_major": 2, "version_minor": 0 }, @@ -814,7 +831,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "bd3e4d3b58e14a9783ee394a15e1aca1", + "model_id": "a7c29ad28c4148e8899542b0dbf542a4", "version_major": 2, "version_minor": 0 }, @@ -829,13 +846,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "36 is not in list\n", "Atoms(symbols='Rb2', pbc=True, cell=[19.902, 19.903000000000002, 19.904])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d304b8fb931645d8b7f0ff5e31fcb21f", + "model_id": "54d89e170cca451c8c3f04f7c921c1c4", "version_major": 2, "version_minor": 0 }, @@ -850,13 +868,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "37 is not in list\n", "Atoms(symbols='Sr2', pbc=True, cell=[17.608, 17.609, 17.61])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "48b5a4ab0c6c46eea0623f3b419935ed", + "model_id": "3108baf3f8ae40069fb5c5d282eb45f0", "version_major": 2, "version_minor": 0 }, @@ -871,13 +890,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "38 is not in list\n", "Atoms(symbols='Y2', pbc=True, cell=[17.05, 17.051000000000002, 17.052])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "5e95b61650f6494fbd300072e7f8ad60", + "model_id": "f83629d595504b658a703122591784a1", "version_major": 2, "version_minor": 0 }, @@ -892,13 +912,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "39 is not in list\n", "Atoms(symbols='Zr2', pbc=True, cell=[15.624, 15.625, 15.626000000000001])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "1abe8f3089954547af62d929e97d55fa", + "model_id": "31f0e507a3414cde8f21821b16eae5ca", "version_major": 2, "version_minor": 0 }, @@ -913,13 +934,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "40 is not in list\n", "Atoms(symbols='Nb2', pbc=True, cell=[15.872000000000002, 15.873000000000001, 15.874000000000002])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "94f02034d0cd465181de8b39084dad42", + "model_id": "25d1d0e58c5948b7af0bf6435f32a5af", "version_major": 2, "version_minor": 0 }, @@ -934,13 +956,14 @@ "name": "stdout", "output_type": "stream", "text": [ + "41 is not in list\n", "Atoms(symbols='Mo2', pbc=True, cell=[15.190000000000001, 15.191, 15.192000000000002])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2210fd8038384aa6888b45285c474e47", + "model_id": "f0fa99be9cb04af081dcb4ce3d7728f2", "version_major": 2, "version_minor": 0 }, @@ -950,321 +973,265 @@ }, "metadata": {}, "output_type": "display_data" - } - ], - "source": [ - "for model in MLIPEnum:\n", - " \n", - " model_name = model.name\n", - " \n", - " if model_name == 'EquiformerV2(OC22)':\n", - " continue\n", - " \n", - " json_fpath = Path(REGISTRY[model_name][\"family\"]) / \"homonuclear-diatomics.json\"\n", - " \n", - " if json_fpath.exists():\n", - " continue\n", - " \n", - " print(f\"========== {model_name} ==========\")\n", - "\n", - " calc = MLIPEnum[model_name].value()\n", - "\n", - " 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 = 0.9 * covalent_radii[atom.number]\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\n", - "\n", - " a = 2 * rmax\n", - "\n", - " npts = int((rmax - rmin)/rstep)\n", - "\n", - " rs = np.linspace(rmin, rmax, npts)\n", - " es = np.zeros_like(rs)\n", - "\n", - " da = symbol + symbol\n", - "\n", - " out_dir = Path(REGISTRY[model_name][\"family\"]) / str(da)\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", - " 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", - " es[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": 3, - "id": "a0ac2c09-370b-4fdd-bf74-ea5c4ade0215", - "metadata": { - "tags": [] - }, - "outputs": [ + }, { "name": "stdout", "output_type": "stream", "text": [ - "========== MACE-MP(M) ==========\n" + "42 is not in list\n", + "Atoms(symbols='Tc2', pbc=True, cell=[15.128, 15.129, 15.13])\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "597310b16837405fa6674583f7ea6892", + "model_id": "937365c9a05a4cabb90e4f56bf63ad51", "version_major": 2, "version_minor": 0 }, "text/plain": [ - " 0%| | 0/118 [00:00 117\u001b[0m \u001b[43mdf\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_json\u001b[49m\u001b[43m(\u001b[49m\u001b[43mjson_fpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43morient\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mrecords\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/pandas/util/_decorators.py:333\u001b[0m, in \u001b[0;36mdeprecate_nonkeyword_arguments..decorate..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 327\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(args) \u001b[38;5;241m>\u001b[39m num_allow_args:\n\u001b[1;32m 328\u001b[0m warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m 329\u001b[0m msg\u001b[38;5;241m.\u001b[39mformat(arguments\u001b[38;5;241m=\u001b[39m_format_argument_list(allow_args)),\n\u001b[1;32m 330\u001b[0m \u001b[38;5;167;01mFutureWarning\u001b[39;00m,\n\u001b[1;32m 331\u001b[0m stacklevel\u001b[38;5;241m=\u001b[39mfind_stack_level(),\n\u001b[1;32m 332\u001b[0m )\n\u001b[0;32m--> 333\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/pandas/core/generic.py:2702\u001b[0m, in \u001b[0;36mNDFrame.to_json\u001b[0;34m(self, path_or_buf, orient, date_format, double_precision, force_ascii, date_unit, default_handler, lines, compression, index, indent, storage_options, mode)\u001b[0m\n\u001b[1;32m 2699\u001b[0m config\u001b[38;5;241m.\u001b[39mis_nonnegative_int(indent)\n\u001b[1;32m 2700\u001b[0m indent \u001b[38;5;241m=\u001b[39m indent \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m-> 2702\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mjson\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_json\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2703\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_or_buf\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpath_or_buf\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2704\u001b[0m \u001b[43m \u001b[49m\u001b[43mobj\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2705\u001b[0m \u001b[43m \u001b[49m\u001b[43morient\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43morient\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2706\u001b[0m \u001b[43m \u001b[49m\u001b[43mdate_format\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdate_format\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2707\u001b[0m \u001b[43m \u001b[49m\u001b[43mdouble_precision\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdouble_precision\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2708\u001b[0m \u001b[43m \u001b[49m\u001b[43mforce_ascii\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mforce_ascii\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2709\u001b[0m \u001b[43m \u001b[49m\u001b[43mdate_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdate_unit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2710\u001b[0m \u001b[43m \u001b[49m\u001b[43mdefault_handler\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdefault_handler\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2711\u001b[0m \u001b[43m \u001b[49m\u001b[43mlines\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlines\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2712\u001b[0m \u001b[43m \u001b[49m\u001b[43mcompression\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompression\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2713\u001b[0m \u001b[43m \u001b[49m\u001b[43mindex\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mindex\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2714\u001b[0m \u001b[43m \u001b[49m\u001b[43mindent\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mindent\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2715\u001b[0m \u001b[43m \u001b[49m\u001b[43mstorage_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstorage_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2716\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2717\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/pandas/io/json/_json.py:217\u001b[0m, in \u001b[0;36mto_json\u001b[0;34m(path_or_buf, obj, orient, date_format, double_precision, force_ascii, date_unit, default_handler, lines, compression, index, indent, storage_options, mode)\u001b[0m\n\u001b[1;32m 213\u001b[0m s \u001b[38;5;241m=\u001b[39m convert_to_line_delimits(s)\n\u001b[1;32m 215\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m path_or_buf \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 216\u001b[0m \u001b[38;5;66;03m# apply compression and byte/text conversion\u001b[39;00m\n\u001b[0;32m--> 217\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[43mget_handle\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 218\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_or_buf\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcompression\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompression\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstorage_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstorage_options\u001b[49m\n\u001b[1;32m 219\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m handles:\n\u001b[1;32m 220\u001b[0m handles\u001b[38;5;241m.\u001b[39mhandle\u001b[38;5;241m.\u001b[39mwrite(s)\n\u001b[1;32m 221\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", - "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/pandas/io/common.py:749\u001b[0m, in \u001b[0;36mget_handle\u001b[0;34m(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)\u001b[0m\n\u001b[1;32m 747\u001b[0m \u001b[38;5;66;03m# Only for write methods\u001b[39;00m\n\u001b[1;32m 748\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m mode \u001b[38;5;129;01mand\u001b[39;00m is_path:\n\u001b[0;32m--> 749\u001b[0m \u001b[43mcheck_parent_directory\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mhandle\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 751\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression:\n\u001b[1;32m 752\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mzstd\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 753\u001b[0m \u001b[38;5;66;03m# compression libraries do not like an explicit text-mode\u001b[39;00m\n", - "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/pandas/io/common.py:616\u001b[0m, in \u001b[0;36mcheck_parent_directory\u001b[0;34m(path)\u001b[0m\n\u001b[1;32m 614\u001b[0m parent \u001b[38;5;241m=\u001b[39m Path(path)\u001b[38;5;241m.\u001b[39mparent\n\u001b[1;32m 615\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m parent\u001b[38;5;241m.\u001b[39mis_dir():\n\u001b[0;32m--> 616\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124mrf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCannot save file into a non-existent directory: \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mparent\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "\u001b[0;31mOSError\u001b[0m: Cannot save file into a non-existent directory: 'alignn'" + "name": "stdout", + "output_type": "stream", + "text": [ + "58 is not in list\n", + "Atoms(symbols='Pr2', pbc=True, cell=[18.104, 18.105, 18.105999999999998])\n" ] - } - ], - "source": [ - "\n", - "\n", - "for model in MLIPEnum:\n", - " \n", - " model_name = model.name\n", - " \n", - " print(f\"========== {model_name} ==========\")\n", - " \n", - " df = pd.DataFrame(columns=[\n", - " \"name\", \n", - " \"method\", \n", - " \"R\", \"E\", \"F\", \"S^2\", \n", - " \"force-flip-times\",\n", - " \"force-total-variation\",\n", - " \"energy-diff-flip-times\",\n", - " \"energy-grad-norm-max\",\n", - " \"energy-jump\",\n", - " \"energy-total-variation\",\n", - " \"conservation-deviation\",\n", - " \"spearman-descending-force\",\n", - " \"spearman-ascending-force\",\n", - " \"spearman-repulsion-energy\",\n", - " \"spearman-attraction-energy\"\n", - " ])\n", - " \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", - " de_dr = np.gradient(es, rs)\n", - " d2e_dr2 = np.gradient(de_dr, rs)\n", - "\n", - " rounded_fs = np.copy(fs)\n", - " rounded_fs[np.abs(rounded_fs) < 1e-2] = 0\n", - " fs_sign = np.sign(rounded_fs)\n", - " fs_sign = fs_sign[fs_sign != 0]\n", - "\n", - " # rounded_ediff = np.diff(es)\n", - " # rounded_ediff[np.abs(rounded_ediff) < zero_threshold] = 0\n", - " ediff = np.diff(es)\n", - " ediff[np.abs(ediff) < 1e-3] = 0\n", - " ediff_sign = np.sign(ediff)\n", - " mask = ediff_sign != 0\n", - " ediff = ediff[mask]\n", - " ediff_sign = ediff_sign[mask]\n", - " ediff_flip = np.diff(ediff_sign) != 0\n", - " ejump = np.abs(ediff[:-1][ediff_flip]).sum() + np.abs(ediff[1:][ediff_flip]).sum()\n", - "\n", - " conservation_deviation = np.mean(np.abs(fs + de_dr))\n", - "\n", - " data = {\n", - " \"name\": da,\n", - " \"method\": model_name,\n", - " \"R\": rs,\n", - " \"E\": es,\n", - " \"F\": fs,\n", - " \"S^2\": S2s,\n", - " \"force-flip-times\": np.sum(np.diff(fs_sign)!=0),\n", - " \"force-total-variation\": np.sum(np.abs(np.diff(fs))),\n", - " \"energy-diff-flip-times\": np.sum(ediff_flip),\n", - " \"energy-grad-norm-max\": np.max(np.abs(de_dr)),\n", - " \"energy-jump\": ejump,\n", - " # \"energy-grad-norm-mean\": np.mean(de_dr_abs),\n", - " \"energy-total-variation\": np.sum(np.abs(np.diff(es))),\n", - " \"conservation-deviation\": conservation_deviation,\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\"], keep='last')\n", - "\n", - " df.to_json(json_fpath, orient=\"records\")" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "id": "e0dd4367-3dca-440f-a7a9-7fdd84183f2c", - "metadata": { - "tags": [] - }, - "outputs": [ + }, { "data": { - "text/html": [ - "
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namemethodREFS^2force-flip-timesforce-total-variationenergy-diff-flip-timesenergy-grad-norm-maxenergy-jumpenergy-total-variationconservation-deviationspearman-descending-forcespearman-ascending-forcespearman-repulsion-energyspearman-attraction-energy
89HHMACE-MP(M)[3.7199999999999998, 3.70996794, 3.69993586, 3...[-2.348365306854248, -2.3483591079711914, -2.3...[1.7e-07, 0.00035892, 0.00068535, 0.00112034, ...[]380.309463265.8752680.00983515.8163390.043480-0.9994210.840215-1.0000000.794565
90HeHeMACE-MP(M)[4.433, 4.4229736200000005, 4.41294724, 4.4029...[0.022882699966430664, 0.022882461547851562, 0...[0.0, -0.00010788, -0.00021458, -0.00032269, -...[]21.48521000.8212360.0000000.3447550.001872-0.9044330.077295-1.0000000.093575
91LiLiMACE-MP(M)[6.572000000000001, 6.561981520000001, 6.55196...[-1.8418288230895996, -1.8418288230895996, -1....[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]18.58357218.1223110.0022245.3322800.013703-0.9998580.993021-0.9999960.995153
92BeBeMACE-MP(M)[6.138000000000001, 6.12797338, 6.117946759999...[-0.6769685745239258, -0.6769685745239258, -0....[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]229.133944210.3461940.0162836.2392250.022079NaN-0.044580-0.9986910.999892
93BBMACE-MP(M)[5.921000000000001, 5.91097088, 5.900941739999...[-1.404820442199707, -1.404820442199707, -1.40...[-6e-08, -0.00011319, -0.00023184, -0.0003534,...[]2330.0786662123.5816180.54375540.0394580.138081NaN0.201590-0.9999210.999947
......................................................
173ThThMACE-MP(M)[9.082999999999998, 9.07297364, 9.062947300000...[-4.095590591430664, -4.095590591430664, -4.09...[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]216.22665726.4135360.0068233.3922940.024297NaN0.026348-0.9971690.918191
174PaPaMACE-MP(M)[8.927999999999999, 8.91797468, 8.90794936, 8....[-8.707170486450195, -8.707170486450195, -8.70...[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]26.40740322.5366450.0068782.3494560.018977-0.6272560.460505NaN0.950999
175UUMACE-MP(M)[8.401, 8.390974320000002, 8.38094864, 8.37092...[-11.437246322631836, -11.437246322631836, -11...[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]134.878494125.8245100.00496711.7349950.025810-0.9741650.939272-1.0000000.966465
176NpNpMACE-MP(M)[8.741999999999999, 8.7319829, 8.72196582, 8.7...[-18.34619903564453, -18.34619903564453, -18.3...[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]314.38634538.6324030.0101392.8240850.015532-1.0000000.189479-1.0000000.439673
177PuPuMACE-MP(M)[8.710999999999999, 8.70097432, 8.690948639999...[-23.70560073852539, -23.70560073852539, -23.7...[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]210.91642126.8153840.0058143.2957530.012909-1.0000000.115110NaN0.260405
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89 rows × 17 columns

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" - ], + "application/vnd.jupyter.widget-view+json": { + "model_id": "896a935ef0df4527a8b386c63d407889", + "version_major": 2, + "version_minor": 0 + }, "text/plain": [ - " name method R \\\n", - "89 HH MACE-MP(M) [3.7199999999999998, 3.70996794, 3.69993586, 3... \n", - "90 HeHe MACE-MP(M) [4.433, 4.4229736200000005, 4.41294724, 4.4029... \n", - "91 LiLi MACE-MP(M) [6.572000000000001, 6.561981520000001, 6.55196... \n", - "92 BeBe MACE-MP(M) [6.138000000000001, 6.12797338, 6.117946759999... \n", - "93 BB MACE-MP(M) [5.921000000000001, 5.91097088, 5.900941739999... \n", - ".. ... ... ... \n", - "173 ThTh MACE-MP(M) [9.082999999999998, 9.07297364, 9.062947300000... \n", - "174 PaPa MACE-MP(M) [8.927999999999999, 8.91797468, 8.90794936, 8.... \n", - "175 UU MACE-MP(M) [8.401, 8.390974320000002, 8.38094864, 8.37092... \n", - "176 NpNp MACE-MP(M) [8.741999999999999, 8.7319829, 8.72196582, 8.7... \n", - "177 PuPu MACE-MP(M) [8.710999999999999, 8.70097432, 8.690948639999... \n", - "\n", - " E \\\n", - "89 [-2.348365306854248, -2.3483591079711914, -2.3... \n", - "90 [0.022882699966430664, 0.022882461547851562, 0... \n", - "91 [-1.8418288230895996, -1.8418288230895996, -1.... \n", - "92 [-0.6769685745239258, -0.6769685745239258, -0.... \n", - "93 [-1.404820442199707, -1.404820442199707, -1.40... \n", - ".. ... \n", - "173 [-4.095590591430664, -4.095590591430664, -4.09... \n", - "174 [-8.707170486450195, -8.707170486450195, -8.70... \n", - "175 [-11.437246322631836, -11.437246322631836, -11... \n", - "176 [-18.34619903564453, -18.34619903564453, -18.3... \n", - "177 [-23.70560073852539, -23.70560073852539, -23.7... \n", - "\n", - " F S^2 force-flip-times \\\n", - "89 [1.7e-07, 0.00035892, 0.00068535, 0.00112034, ... [] 3 \n", - "90 [0.0, -0.00010788, -0.00021458, -0.00032269, -... [] 2 \n", - "91 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... [] 1 \n", - "92 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... [] 2 \n", - "93 [-6e-08, -0.00011319, -0.00023184, -0.0003534,... [] 2 \n", - ".. ... .. ... \n", - "173 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... [] 2 \n", - "174 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... [] 2 \n", - "175 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... [] 1 \n", - "176 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... [] 3 \n", - "177 [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... [] 2 \n", - "\n", - " force-total-variation energy-diff-flip-times energy-grad-norm-max \\\n", - "89 80.309463 2 65.875268 \n", - "90 1.485210 0 0.821236 \n", - "91 8.583572 1 8.122311 \n", - "92 29.133944 2 10.346194 \n", - "93 330.078666 2 123.581618 \n", - ".. ... ... ... \n", - "173 16.226657 2 6.413536 \n", - "174 6.407403 2 2.536645 \n", - "175 34.878494 1 25.824510 \n", - "176 14.386345 3 8.632403 \n", - "177 10.916421 2 6.815384 \n", - "\n", - " energy-jump energy-total-variation conservation-deviation \\\n", - "89 0.009835 15.816339 0.043480 \n", - "90 0.000000 0.344755 0.001872 \n", - "91 0.002224 5.332280 0.013703 \n", - "92 0.016283 6.239225 0.022079 \n", - "93 0.543755 40.039458 0.138081 \n", - ".. ... ... ... \n", - "173 0.006823 3.392294 0.024297 \n", - "174 0.006878 2.349456 0.018977 \n", - "175 0.004967 11.734995 0.025810 \n", - "176 0.010139 2.824085 0.015532 \n", - "177 0.005814 3.295753 0.012909 \n", - "\n", - " spearman-descending-force spearman-ascending-force \\\n", - "89 -0.999421 0.840215 \n", - "90 -0.904433 0.077295 \n", - "91 -0.999858 0.993021 \n", - "92 NaN -0.044580 \n", - "93 NaN 0.201590 \n", - ".. ... ... \n", - "173 NaN 0.026348 \n", - "174 -0.627256 0.460505 \n", - "175 -0.974165 0.939272 \n", - "176 -1.000000 0.189479 \n", - "177 -1.000000 0.115110 \n", - "\n", - " spearman-repulsion-energy spearman-attraction-energy \n", - "89 -1.000000 0.794565 \n", - "90 -1.000000 0.093575 \n", - "91 -0.999996 0.995153 \n", - "92 -0.998691 0.999892 \n", - "93 -0.999921 0.999947 \n", - ".. ... ... \n", - "173 -0.997169 0.918191 \n", - "174 NaN 0.950999 \n", - "175 -1.000000 0.966465 \n", - "176 -1.000000 0.439673 \n", - "177 NaN 0.260405 \n", - "\n", - "[89 rows x 17 columns]" + " 0%| | 0/722 [00:00\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
namemethodREFS^2force-flip-timesforce-total-variationenergy-diff-flip-timesenergy-grad-norm-maxenergy-jumpenergy-total-variationconservation-deviationspearman-descending-forcespearman-ascending-forcespearman-repulsion-energyspearman-attraction-energytortuosity
118HHALIGNN[3.7199999999999998, 3.70996794, 3.69993586, 3...[-1.2249419689178467, -1.2238645553588867, -1....[1.91e-06, 0.00826454, 0.00533009, -0.00355052...[]29443.6142553040.6565014.07424813.6760802.022960-0.200684-0.119952-0.9865720.8447861.797762
119HeHeALIGNN[4.433, 4.4229736200000005, 4.41294724, 4.4029...[2.4748411178588867, 2.4748411178588867, 2.474...[0.0, -1e-08, 0.0, 0.0, 1e-08, 0.0, 0.0, 0.0, ...[]441448.97943643160.17554413.83107232.5447414.849522-0.021494-0.195001-0.7202180.6095193.921846
120LiLiALIGNN[6.572000000000001, 6.561981520000001, 6.55196...[-0.21738338470458984, -0.21738338470458984, -...[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...[]221127.74959120281.6591362.06720320.0534662.469147-0.714286-0.444127-0.991010-0.6547151.386696
121BeBeALIGNN[6.138000000000001, 6.12797338, 6.117946759999...[2.665587902069092, 2.665587902069092, 2.66558...[0.0, 0.0, 0.0, 0.0, 1e-08, 0.0, 0.0, 0.0, 0.0...[]251645.96035721145.0404629.42209451.6479555.0765230.544090-0.158055-0.9899620.3424761.715953
122BBALIGNN[5.921000000000001, 5.91097088, 5.900941739999...[0.6220548152923584, 0.6220548152923584, 0.622...[0.0, 0.0, 1e-08, 0.0, 0.0, 1e-08, -1e-08, -1e...[]351811.41373236131.34079113.08836852.6918565.5517870.052632-0.171460-0.9850240.7578801.617372
.........................................................
231FlFlALIGNN[6.0, 5.989982779999999, 5.979965579999999, 5....[-10.127323150634766, -10.127323150634766, -10...[0.0, 0.0, -9.5e-07, 0.0, 0.0, 0.0, 0.0, 9.5e-...[]393329.77083144181.33814212.29284484.2394348.151059-0.249255-0.316556-0.9467700.1595762.694147
232McMcALIGNN[6.0, 5.989982779999999, 5.979965579999999, 5....[-10.127323150634766, -10.127323150634766, -10...[0.0, 0.0, -9.5e-07, 0.0, 0.0, 0.0, 0.0, 9.5e-...[]393329.77083144181.33814212.29284484.2394348.151059-0.249255-0.316556-0.9467700.1595762.694147
233LvLvALIGNN[6.0, 5.989982779999999, 5.979965579999999, 5....[-10.127323150634766, -10.127323150634766, -10...[0.0, 0.0, -9.5e-07, 0.0, 0.0, 0.0, 0.0, 9.5e-...[]393329.77083144181.33814212.29284484.2394348.151059-0.249255-0.316556-0.9467700.1595762.694147
234TsTsALIGNN[6.0, 5.989982779999999, 5.979965579999999, 5....[-10.127323150634766, -10.127323150634766, -10...[0.0, 0.0, -9.5e-07, 0.0, 0.0, 0.0, 0.0, 9.5e-...[]393329.77083144181.33814212.29284484.2394348.151059-0.249255-0.316556-0.9467700.1595762.694147
235OgOgALIGNN[6.0, 5.989982779999999, 5.979965579999999, 5....[-10.127323150634766, -10.127323150634766, -10...[0.0, 0.0, -9.5e-07, 0.0, 0.0, 0.0, 0.0, 9.5e-...[]393329.77083144181.33814212.29284484.2394348.151059-0.249255-0.316556-0.9467700.1595762.694147
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118 rows × 18 columns

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