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" @@ -2,20 +2,12 @@ "cells": [ { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "id": "3200850a-b8fb-4f50-9815-16ae8da0f942", "metadata": { "tags": [] }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Selected GPU cuda:0 with 40240.80 MB free memory from 1 GPUs\n" - ] - } - ], + "outputs": [], "source": [ "import os\n", "from pathlib import Path\n", @@ -31,71 +23,47 @@ "\n", "from mlip_arena.models.utils import REGISTRY, MLIPEnum\n", "\n", - "model_name = \"ORB\"\n", + "# model_name = \"MACE-MP(M)\"\n", "\n", - "calc = MLIPEnum[model_name].value()" + "# calc = MLIPEnum[model_name].value()" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "id": "90887faa-1601-4c4c-9c44-d16731471d7f", "metadata": { "scrolled": true, "tags": [] }, "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "2a34049b06f74c64beb33d2e401fa32e", - "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 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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 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\"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": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "f26af1f9df7946ff86eef37f445660ad", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - " 0%| | 0/800 [00:00\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", 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namemethodREFS^2spearman-repulsionspearman-attractionspearman-descending-forcespearman-ascending-forcespearman-repulsion-energyspearman-attraction-energy
0HHORB[0.1549999999999998, 0.16504226000000033, 0.17...[-2.6258459091186523, -2.755453109741211, -1.8...[0.26894104, -0.0038066, 2.37577677, 7.8109564...[]NaNNaN-0.9080970.579246-0.8585280.504446
1HeHeORB[0.13999999999999968, 0.15003038000000046, 0.1...[-0.37155914306640625, -0.4051551818847656, 0....[0.02356668, -2.673e-05, 0.45423254, 1.2784304...[]NaNNaN-0.911505-0.046725-0.8666690.340055
2LiLiORB[0.6400000000000006, 0.6500202799999997, 0.660...[8.477561950683594, 8.438533782958984, 8.38090...[86.12041473, 84.16366577, 82.23960876, 80.216...[]NaNNaN-0.9959870.999664-0.9998580.948886
3BeBeORB[0.4800000000000004, 0.49003191999999984, 0.50...[7.427803039550781, 7.338706970214844, 7.19796...[116.66287994, 120.23416138, 123.43974304, 126...[]NaNNaN-0.9983460.972891-0.9588270.691532
4BBORB[0.41999999999999993, 0.4300200399999996, 0.44...[1.7283554077148438, 1.9046106338500977, 2.040...[118.15281677, 121.52095032, 124.86712646, 127...[]NaNNaN-0.9706580.922968-0.8087020.816218
.......................................
112NhNhORB[0.09999999999999964, 0.11001697999999926, 0.1...[-2.2965879440307617, -2.30364990234375, -2.30...[-0.01143722, -0.01140489, -0.01082459, 0.1164...[]NaNNaN-0.5880280.989775-0.2157460.963378
113FlFlORB[0.09999999999999964, 0.11001697999999926, 0.1...[-3.702641487121582, -3.683434009552002, -3.65...[-2.14600778, -2.05312586, -1.91521156, 0.2045...[]NaNNaNNaN-0.539312-0.4575060.870783
114McMcORB[0.09999999999999964, 0.11001697999999926, 0.1...[-1.6017036437988281, -1.5843744277954102, -1....[-0.02472172, 0.00170199, 0.0667266, 0.4929885...[]NaNNaN-0.7396830.998949-0.4346330.999944
115LvLvORB[0.09999999999999964, 0.11001697999999926, 0.1...[-8.688143730163574, -8.684117317199707, -8.66...[-2.57541442, -2.43290496, -2.19691253, 1.7867...[]NaNNaNNaN-0.762006-0.8641030.903459
116TsTsORB[0.09999999999999964, 0.11001697999999926, 0.1...[-0.1275949478149414, -0.09642791748046875, -0...[-1.2110672, -1.19077206, -1.1051929, 0.515652...[]NaNNaNNaN-0.868446-0.6205340.919588
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117 rows × 12 columns

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